From mike.thon at gmail.com Tue Sep 4 03:59:06 2012 From: mike.thon at gmail.com (Michael Thon) Date: Tue, 4 Sep 2012 10:59:06 +0200 Subject: [maker-devel] model_gff not in output Message-ID: <1A01E0C5-E60A-42AA-BD7B-A6429F435645@gmail.com> I'm using maker to update a legacy annotation. As input I'm using RNA-Seq aligned with cufflinks, ESTs, provided in fasta format, and proteins downloaded from UniProt.SwissProt. I have done two runs of maker so far. The first one using the legacy annotations in both the model_gff and pred_gff parameters. In the second run I used the legacy annotations in model_gff and in pred_gff I included gene models created with GeneMark-ES. In both runs 1 and 2 I have found two genes (so far) that exist in the legacy annotations but are not in the final gene models output by maker. Both genes have overlapping cufflinks annotations, in addition to having annotations in model_gff. I thought maker was supposed to keep all the annotations in model_gff, only replacing ones in which it could find an alternative model with better support. Is there any case in which is will remove a model? Another discrepency I found in run1 is a gene that maker 'moved' upstream approx. 150 bases. The gene locus annotated by maker covers the original annotation, but the CDS does not. The site of the original CDS is covered by an annotation in model_gff, pred_gff, two ESTs and a cufflinks annotation. Maker still seems to have moved is is upstream where it only has an overlapping cufflinks annotation. the three-prime utr annotated by cufflinks still covers the legacy annotation though. Here's a link to download the maker gff file I'm looking at: https://dl.dropbox.com/u/320712/supercont1%252E1.gff.zip The genes that are in the legacy annotation but missing in the maker annotation are: GLRG_00074 and GLRG_00092 the 'moved' gene model I described is model GLRG_00081. they all within the first 350 K of sequence. mike From chrisi.hahni at gmail.com Wed Sep 5 06:59:48 2012 From: chrisi.hahni at gmail.com (Christoph Hahn) Date: Wed, 05 Sep 2012 13:59:48 +0200 Subject: [maker-devel] keep_preds option? In-Reply-To: References: Message-ID: <50473EB4.7070501@gmail.com> Hello Barry and Carson, Thank you very much for the extensive replies!! Very helpful!! > > 2. I tried to use EST data of an alternative organism in altest= > (#EST/cDNA sequence file in fasta format from an alternate organism). > The organism is quite distantly related, but its the closest I have so > I thought I d give it a shot. I ran maker twice with identical settigs > expect in altest and est2genome=0/1. The number of genes predicted is > identical with both approaches, so I am not sure whether or not the > EST data was actually used or its just to distantly related. Any easy > way to assess this? > Typically EST evidence from another organism with alt_est will add little in the way of additional support (compared to just using protein evidence from say Swiss-prot) and this would be especially true if your alt_est is > distantly related. I'm not sure I really understand you alt_est/est2genome combo's to comment in more detail. I could see four possible combinations there: which two gave identical results? What I meant was that I ran maker once without any alt_est evidence and est2genome=0 and a second time with alt_est=some.fasta and est2genome=1. The result was the same. Sorry, for not making myself clear enough. I thought that the est2genome=1 switch is is just enabling physical est evidence to be used. Therefore, I thought neither alt_est=some.fasta, est2genome=0 nor alt_est=nothing, est2genome=1 would make any sense. I had misunderstood this. Will follow Carsons advice and will try to use more protein evidence from related species (in addition to uniprot). Running right now - Let s see where that leaves me. The IPRScan approach suggested by Barry to assess gene models without physical evidence sounds very interesting. I will definitely look into that. A question concerning an issue I just discovered: Ran maker twice with the same physical evidence. First time using SNAP and Genemark, second time using SNAP, Genemark and AUGUSTUS (set to the closest related species available - same phylum, different class). Second run gives less gene models. IN another context I found that the second pass of Maker using SNAP and Genemark (after training SNAP on the predictions of the first Pass) and the same physical evidence yields less gene annotations. How can that be given the same physical evidence? Thanks again for your help! It is much appreciated! cheers, Christoph Am 31.08.2012 21:03, schrieb Carson Holt: > I concur with everything Barry said. Also let me add that alt-ESTs do > not get polished around splice sites (exonerate won't handle them). > However ESTs and proteins do. This means that the utility of > alt-ESTs in adding UTR, and splice information is zero. They just > function as an anchor to maintain gene models that might have > otherwise been rejected. This also means alt_est=some.fasta together > with est2genome=1 will produce virtually no additional results because > est2genome requires that the splice site makes sense. You are better > off using proteins with protein2genome=1 if you don't have ESTs and > want partial models for training. Once you have a trained ab initio > gene predictor, turn the est2genome and protein2genome options off. > Otherwise they will give weird partial models that decrease the > quality of your final annotations. (partial models are ok for training > but that's about it). > > If you are getting too low a gene count with keep_preds=0, then you > probably need to add more evidence. Try adding all proteins from a > couple of related species (the protein= option accepts comma separated > lists of files). If your genome is a fungi, oomycete, or a prokaryote, > then setting keep_preds=1 is usually safe. Theses are genomes with > high gene density and simple gene structure, so ab initio predictors > do really well and don't need as much help from the evidence. For > other organisms, leave it set to 0 or you will get a lot of false > positives (false positives on some genomes with complex gene structure > can outnumber the genes by 10 to 1 if you turn this on). > > Thanks, > Carson > > > > > From: Barry Moore > > Date: Friday, 31 August, 2012 12:52 PM > To: Christoph Hahn > > Cc: > > Subject: Re: [maker-devel] keep_preds option? > > Hi Christopher, > > Comments below: > > On Aug 31, 2012, at 6:43 AM, Christoph Hahn wrote: > >> Hello maker users and developers, >> >> I am new to gene prediction and I am trying to use maker 2.25 on a >> newly assembled non-model organisms draft genome. Within maker I use >> genemark, SNAP and Augustus. I have a few questions: >> > > Welcome! > >> 1. I was wondering what the keep_preds option means exactly. >> >> I found two slightly different explanations on the option >> #Add unsupported gene prediction to final annotation set (maker2.25) >> #Add non-overlapping ab-inito gene prediction to final annotation set >> (found on the net - probably older maker version) >> > > It means to keep ab initio gene predictions for which there is no > physical evidence. There are two pieces of information that are > required for every MAKER annotation (by default). MAKER runs the ab > initio gene predictors and aligns transcript (EST/cDNA/mRNASeq > transcripts) and protein sequences to the genome. For each locus > where one or more gene predictions exist MAKER checks to see if there > is any physical evidence for gene expression at that locus > (RNA/protein sequence alignments) and if there is (splice EST or > protein alignments) evidence overlapping the predictions, MAKER > decides which prediction best matches the evidence and promotes that > prediction to an annotation. If there is no evidence overlapping any > of the predictions then those predictions are not included in the > output annotation file (although they are saved). If you set > keep_preds=1 then for each locus where prediction(s) exist maker keeps > one and promotes it to an annotation even though there is no physical > evidence. The description of 'non-overlapping ab-initio' means that > MAKER has clustered all ab-initio predictions at one locus and chose > one representative transcript to output. > >> As far as I understood keep_preds=0 only retains gene models for >> which the ab initio predictions agree. But how many, all three? two >> of three? >> keep_preds=1 instead keeps all gene models regardless if the >> different programs agree, right? >> > > MAKER does not take the presence of multiple ab initio predictions as > evidence and thus in the absence of aligned physical evidence MAKER > will not output an annotation even if all three ab initio tools > predict a gene at that locus. > >> In my case I get substantial differences in the number of gene models >> found between the two settings, while with =1 I get a number that is >> close to what we would expect. How would you interpret that? What >> would you recommend me to do? Obiously =0 is the saver option. > > If you think that the number of genes you are getting from a MAKER run > is too few, you could run MAKER with keep_preds=1. After the run is > finished, use a tool like IPRScan to search all MAKER predictions for > protein domain content and push that IPRScan output back into the > MAKER GFF file with the ipr_update_gff script. Then as a final step > you can run over the GFF file and remove any gene model that doesn't > have either physical evidence (AED < 1) or protein domain content > (Dbxref=PFAM:XXX etc...) sorry there's not a script prepackaged with > MAKER for that yet. > >> >> 2. I tried to use EST data of an alternative organism in altest= >> (#EST/cDNA sequence file in fasta format from an alternate organism). >> The organism is quite distantly related, but its the closest I have >> so I thought I d give it a shot. I ran maker twice with identical >> settigs expect in altest and est2genome=0/1. The number of genes >> predicted is identical with both approaches, so I am not sure whether >> or not the EST data was actually used or its just to distantly >> related. Any easy way to assess this? > > Typically EST evidence from another organism with alt_est will add > little in the way of additional support (compared to just using > protein evidence from say Swiss-prot) and this would be especially > true if your alt_est is distantly related. I'm not sure I really > understand you alt_est/est2genome combo's to comment in more detail. > I could see four possible combinations there: which two gave > identical results? > >> >> 3. I am running maker in several passes and after each pass I am >> training SNAP using the result of the previous pass. Then for every >> pass I run maker from scratch. Would you recommend to supply the gff >> of the previous pass in "#-----Re-annotation Using MAKER Derived GFF3 >> maker_gff= #re-annotate genome based on this gff3 file", instead? >> > > No, 'Re-annotation using MAKER Derived GFF3' is used for re-annotation > of a genome when you want certain parts of the previous run to be > passed through unchanged, but with retraining SNAP you want MAKER to > re-evaluate each annotation in light of the new predictions made by > the retrained SNAP. MAKER should run really fast in all of the runs > after the first one because as long as you haven't changed the > evidence files it won't have to redo any of the alignments. > > > B > >> Thanks in advance for any thoughts/advice on these things! I >> appreciate your help! >> >> much obliged, >> Christoph >> >> _______________________________________________ >> maker-devel mailing list >> maker-devel at box290.bluehost.com >> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org > > Barry Moore > Research Scientist > Dept. of Human Genetics > University of Utah > Salt Lake City, UT 84112 > -------------------------------------------- > (801) 585-3543 > > > > > _______________________________________________ maker-devel mailing > list maker-devel at box290.bluehost.com > > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org -------------- next part -------------- An HTML attachment was scrubbed... URL: From muntjaczhou at gmail.com Wed Sep 5 21:26:38 2012 From: muntjaczhou at gmail.com (Zhou Qi) Date: Wed, 5 Sep 2012 19:26:38 -0700 Subject: [maker-devel] gene duplicates and track the query protein Message-ID: Dear maker users and developers: I'm new to maker and trying to use it to annotate a Drosophila genome given protein sequences of its closely related species. I have two questions: 1. How maker decide which one to keep if one query protein has two similarly best hits in the target genome, e.g., gene duplication? 2. Is there any way to track the maker gene to its corresponding query proteins through setting up some parameters in maker? Or is it possible to directly let maker name the gene model based on its query protein? I looked through the previous threads, one possible way seems to use model_gff and map_forward option combined. I guess people more experienced than me using maker might know other ways? Many thanks! Qi From barry.moore at genetics.utah.edu Thu Sep 6 11:35:02 2012 From: barry.moore at genetics.utah.edu (Barry Moore) Date: Thu, 6 Sep 2012 10:35:02 -0600 Subject: [maker-devel] gene duplicates and track the query protein In-Reply-To: References: Message-ID: On Sep 5, 2012, at 8:26 PM, Zhou Qi wrote: > Dear maker users and developers: > > I'm new to maker and trying to use it to annotate a Drosophila genome given protein sequences of its closely related species. I have two questions: > > 1. How maker decide which one to keep if one query protein has two similarly best hits in the target genome, e.g., gene duplication? MAKER uses the aligned proteins as evidence to support gene predictions (i.e. from SNAP). If the supporting protein can align within the specified parameters (as defined in maker_bopts.ctl) then all of the valid alignments could be used as evidence for gene predictions at those loci. > > 2. Is there any way to track the maker gene to its corresponding query proteins through setting up some parameters in maker? Or is it possible to directly let maker name the gene model based on its query protein? > I don't know of a way to do this by setting parameters in the MAKER control file - maybe Carson has some idea for you here? B > I looked through the previous threads, one possible way seems to use model_gff and map_forward option combined. I guess people more experienced than me using maker might know other ways? > > Many thanks! > > Qi > _______________________________________________ > maker-devel mailing list > maker-devel at box290.bluehost.com > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org Barry Moore Research Scientist Dept. of Human Genetics University of Utah Salt Lake City, UT 84112 -------------------------------------------- (801) 585-3543 -------------- next part -------------- An HTML attachment was scrubbed... URL: From david.powell at monash.edu Thu Sep 6 19:23:57 2012 From: david.powell at monash.edu (David Powell) Date: Fri, 7 Sep 2012 10:23:57 +1000 Subject: [maker-devel] Problem with cegma2zff Message-ID: Greetings, I am using CEGMA to train SNAP for use with maker. However, I had a problem with the cegma2zff script that comes with maker. This script converts the gff file from CEGMA into a zff file for SNAP. The problem is that it was producing a zff file with every multi-exon gene as being "invalid" from SNAPs point of view. My fix was to modify cegma2zff to ignore any feature with the tag "Exon" - as these are always duplicated by cegma as another feature (one of First, Internal, Terminal, Single). Just wanted to post this here in case this fix is useful to anyone else. Cheers, -- David Powell diff --git a/cegma2zff b/cegma2zff index c795da8..a3bbb77 100755 --- a/cegma2zff +++ b/cegma2zff @@ -39,6 +39,8 @@ while(my $line = ){ my @F = split("\t", $line); ($F[3], $F[4]) = ($F[4], $F[3]) if($F[6] eq '-'); + next if $F[2] =~ /Exon/; + $F[2] =~ s/First/Einit/; $F[2] =~ s/Terminal/Eterm/; $F[2] =~ s/Internal/Exon/; -------------- next part -------------- An HTML attachment was scrubbed... URL: From guoyunfei1989 at gmail.com Fri Sep 7 12:54:12 2012 From: guoyunfei1989 at gmail.com (Yunfei Guo) Date: Fri, 7 Sep 2012 10:54:12 -0700 Subject: [maker-devel] maker annotate two species, same evidence, same settings Message-ID: Hi Carson, I have a quick question about maker annotations. I want to annotate two sets of assemblies from two related species using the same sets of evidence and settings except that the est assemblies would be specified as 'est' for one species (along with 'altest' evidence from other species) and as 'altest' (combined with est evidence from other species) for the other, would the annotation reflect the real difference between these two species? Or there might be some variations within the annotations themselves which might make the real difference more or less significant? Thank you! Yunfei From carsonhh at gmail.com Fri Sep 7 13:35:50 2012 From: carsonhh at gmail.com (Carson Holt) Date: Fri, 07 Sep 2012 14:35:50 -0400 Subject: [maker-devel] maker annotate two species, same evidence, same settings In-Reply-To: Message-ID: Let me explain how ESTs and alt-ESTs are use and maybe that will answer your question. ESTs will be polished around splice sites to give information on intron boundaries and UTR location. The polished ESTs can override ab initio gene predictor structure and be used to extend gene models by what is basically an exon cut and paste operation. The alt-ESTs are not polished (exoneerate can't handle them). So the splice site boundaries will be off. Maker will only try and infer UTR and intron boundaries from these if the alignment produces canonical splice sites (almost never happens). So they are relegated to the same status as the unpolished protein alignment (lower scoring hints to the gene predictor as to exon boundaries). They will also contribute to AED score with a little less accuracy than ESTs. When possible use protein models rather than alt-ESTs, primarily because they are computationally less intense than a tblastx type alignment that occurs with alt-ESTs. Exonerate will also polish protein alignments. Thanks, Carson On 12-09-07 1:54 PM, "Yunfei Guo" wrote: >Hi Carson, > >I have a quick question about maker annotations. I want to annotate >two sets of assemblies from two related species using the same sets of >evidence and settings except that the est assemblies would be >specified as 'est' for one species (along with 'altest' evidence from >other species) and as 'altest' (combined with est evidence from other >species) for the other, would the annotation reflect the real >difference between these two species? Or there might be some >variations within the annotations themselves which might make the real >difference more or less significant? > >Thank you! > >Yunfei > >_______________________________________________ >maker-devel mailing list >maker-devel at box290.bluehost.com >http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org From carsonhh at gmail.com Fri Sep 7 21:33:49 2012 From: carsonhh at gmail.com (Carson Holt) Date: Fri, 07 Sep 2012 22:33:49 -0400 Subject: [maker-devel] Problem with cegma2zff In-Reply-To: Message-ID: Yes. There was an update for CEGMA that causes features to be duplicated in it's output. Thanks for the post and the fix. --Carson From: David Powell Date: Thursday, 6 September, 2012 8:23 PM To: Subject: [maker-devel] Problem with cegma2zff Greetings, I am using CEGMA to train SNAP for use with maker. However, I had a problem with the cegma2zff script that comes with maker. This script converts the gff file from CEGMA into a zff file for SNAP. The problem is that it was producing a zff file with every multi-exon gene as being "invalid" from SNAPs point of view. My fix was to modify cegma2zff to ignore any feature with the tag "Exon" - as these are always duplicated by cegma as another feature (one of First, Internal, Terminal, Single). Just wanted to post this here in case this fix is useful to anyone else. Cheers, -- David Powell diff --git a/cegma2zff b/cegma2zff index c795da8..a3bbb77 100755 --- a/cegma2zff +++ b/cegma2zff @@ -39,6 +39,8 @@ while(my $line = ){ my @F = split("\t", $line); ($F[3], $F[4]) = ($F[4], $F[3]) if($F[6] eq '-'); + next if $F[2] =~ /Exon/; + $F[2] =~ s/First/Einit/; $F[2] =~ s/Terminal/Eterm/; $F[2] =~ s/Internal/Exon/; _______________________________________________ maker-devel mailing list maker-devel at box290.bluehost.com http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org -------------- next part -------------- An HTML attachment was scrubbed... URL: From jeremy.semeiks at utsw.edu Sun Sep 9 14:49:36 2012 From: jeremy.semeiks at utsw.edu (Jeremy Semeiks) Date: Sun, 9 Sep 2012 14:49:36 -0500 Subject: [maker-devel] How to preserve human-friendly IDs when reannotating Message-ID: Hi all, I have sequenced some novel fungal genomes, and I am annotating them with maker-2.26-beta. The entire project is pretty iterative, in the sense that I first get some seemingly-sane annotation sets, then analyze and compare the proteomes biologically, then reannotate when new data comes in or as I learn more about how maker works. Because I have already attached biological meaning to some of my proteins, I would like to retain the same human-friendly IDs across annotations. Eg, if maker suddenly finds 1,000 new proteins on a reannotation run because I turned on keep_preds, then I don't want the transcript formerly known as mymold_09652T0 to become mymold_10698T0 when I run maker_map_ids; I want to keep it named mymold_09652T0. So, is there any built-in way to preserve human-friendly IDs, or do I need to write my own script for this? I have tried setting map_forward=1 and maker_gff=, but setting these seems to preserve neither the human-friendly IDs nor even the original IDs. (Eg, protein "genemark-scaffold353-processed-gene-0.9-mRNA-1" changed its name to "genemark-scaffold353-processed-gene-0.6-mRNA-1" when reannotated.) I haven't turned on any of the *_pass options, eg protein_pass; would this be relevant? Extra credit question: I am making some mate-pair libraries for these fungi; when I re-assemble, that will completely change my scaffold names. Is there any easy way to preserve human-friendly transcript names in this case? As with the above simpler case, I think it would be pretty easy to transfer 90% of the names just by doing an all-vs-all blastp between two annotation sets and fishing out the best hits, but the remaining 10% might be a headache. Thanks, Jeremy Grad student, Grishin lab UT Southwestern, Dallas TX 510.385.8959 -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Mon Sep 10 06:01:46 2012 From: carsonhh at gmail.com (Carson Holt) Date: Mon, 10 Sep 2012 07:01:46 -0400 Subject: [maker-devel] How to preserve human-friendly IDs when reannotating In-Reply-To: Message-ID: The map_forward option requires that the pass option for the gene models be turned on. Otherwise you will have to do some spacial overlap test outside of MAKER. If you have a new assembly, you can try mapping the old models onto the new assembly using the old transcripts as input to the est= and setting est2genome=1 (nothing else set, i.e no repeat masking etc.). Then there is an undocumented option that is still a little buggy (hence why it is still undocumented). Add the line est_forward=1 to your control files. This tells MAKER to copy names from the ESTs, build the models directly from their alignment, and to do other things to try and make a 1 to 1 match across the genome. You will have to manually check that it is 1 to 1 in the end (as I said still a little buggy and hence undocumented). Use the resulting file as input to the model_gff option on a separate run with map_forward=1 for additional reannotation wil more evidence, etc. where you want to still be able to map names forward. From: Jeremy Semeiks Date: Sunday, 9 September, 2012 3:49 PM To: Subject: [maker-devel] How to preserve human-friendly IDs when reannotating Hi all, I have sequenced some novel fungal genomes, and I am annotating them with maker-2.26-beta. The entire project is pretty iterative, in the sense that I first get some seemingly-sane annotation sets, then analyze and compare the proteomes biologically, then reannotate when new data comes in or as I learn more about how maker works. Because I have already attached biological meaning to some of my proteins, I would like to retain the same human-friendly IDs across annotations. Eg, if maker suddenly finds 1,000 new proteins on a reannotation run because I turned on keep_preds, then I don't want the transcript formerly known as mymold_09652T0 to become mymold_10698T0 when I run maker_map_ids; I want to keep it named mymold_09652T0. So, is there any built-in way to preserve human-friendly IDs, or do I need to write my own script for this? I have tried setting map_forward=1 and maker_gff=, but setting these seems to preserve neither the human-friendly IDs nor even the original IDs. (Eg, protein "genemark-scaffold353-processed-gene-0.9-mRNA-1" changed its name to "genemark-scaffold353-processed-gene-0.6-mRNA-1" when reannotated.) I haven't turned on any of the *_pass options, eg protein_pass; would this be relevant? Extra credit question: I am making some mate-pair libraries for these fungi; when I re-assemble, that will completely change my scaffold names. Is there any easy way to preserve human-friendly transcript names in this case? As with the above simpler case, I think it would be pretty easy to transfer 90% of the names just by doing an all-vs-all blastp between two annotation sets and fishing out the best hits, but the remaining 10% might be a headache. Thanks, Jeremy Grad student, Grishin lab UT Southwestern, Dallas TX 510.385.8959 _______________________________________________ maker-devel mailing list maker-devel at box290.bluehost.com http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Mon Sep 10 06:10:33 2012 From: carsonhh at gmail.com (Carson Holt) Date: Mon, 10 Sep 2012 07:10:33 -0400 Subject: [maker-devel] keep_preds option? In-Reply-To: <50473EB4.7070501@gmail.com> Message-ID: The final annotations are really produced by GeneMark, SNAP, Augustus etc. MAKER basically takes the physical evidence, turns it into 'hints' for these programs (I.e. Exon and CDS scoring bonuses), and then lets them run again. If you retrain them they will behave different. If you add a new one you may also get a model from the third algorithm that seems to match the evidence better. Sometimes one algorithm will call one gene where another thinks it should be two genes while the third thinks it is really a larger gene merged with exons from a neighboring gene. MAKER will add hints to try and improve the ab initio predictors performance and choose the model that seems to be make sense given the evidence. The source of a gene model is eventually inherent from the name MAKER gives it. If snap is in the name, then the model was derived from snap. If maker and snap are in the name, then it is a model derived from snap with MAKER hints (otherwise it was derived completely from SNAP's training with no MAKER input). Thanks, Carson From: Christoph Hahn Date: Wednesday, 5 September, 2012 7:59 AM To: Carson Holt , Barry Moore Cc: Subject: Re: [maker-devel] keep_preds option? Hello Barry and Carson, Thank you very much for the extensive replies!! Very helpful!! > > > 2. I tried to use EST data of an alternative organism in altest= (#EST/cDNA > sequence file in fasta format from an alternate organism). The organism is > quite distantly related, but its the closest I have so I thought I d give it a > shot. I ran maker twice with identical settigs expect in altest and > est2genome=0/1. The number of genes predicted is identical with both > approaches, so I am not sure whether or not the EST data was actually used or > its just to distantly related. Any easy way to assess this? > > > Typically EST evidence from another organism with alt_est will add little in the way of additional support (compared to just using protein evidence from say Swiss-prot) and this would be especially true if your alt_est is > distantly related. I'm not sure I really understand you alt_est/est2genome combo's to comment in more detail. I could see four possible combinations there: which two gave identical results? What I meant was that I ran maker once without any alt_est evidence and est2genome=0 and a second time with alt_est=some.fasta and est2genome=1. The result was the same. Sorry, for not making myself clear enough. I thought that the est2genome=1 switch is is just enabling physical est evidence to be used. Therefore, I thought neither alt_est=some.fasta, est2genome=0 nor alt_est=nothing, est2genome=1 would make any sense. I had misunderstood this. Will follow Carsons advice and will try to use more protein evidence from related species (in addition to uniprot). Running right now - Let s see where that leaves me. The IPRScan approach suggested by Barry to assess gene models without physical evidence sounds very interesting. I will definitely look into that. A question concerning an issue I just discovered: Ran maker twice with the same physical evidence. First time using SNAP and Genemark, second time using SNAP, Genemark and AUGUSTUS (set to the closest related species available - same phylum, different class). Second run gives less gene models. IN another context I found that the second pass of Maker using SNAP and Genemark (after training SNAP on the predictions of the first Pass) and the same physical evidence yields less gene annotations. How can that be given the same physical evidence? Thanks again for your help! It is much appreciated! cheers, Christoph Am 31.08.2012 21:03, schrieb Carson Holt: > > I concur with everything Barry said. Also let me add that alt-ESTs do not get > polished around splice sites (exonerate won't handle them). However ESTs and > proteins do. This means that the utility of alt-ESTs in adding UTR, and > splice information is zero. They just function as an anchor to maintain gene > models that might have otherwise been rejected. This also means > alt_est=some.fasta together with est2genome=1 will produce virtually no > additional results because est2genome requires that the splice site makes > sense. You are better off using proteins with protein2genome=1 if you don?t > have ESTs and want partial models for training. Once you have a trained ab > initio gene predictor, turn the est2genome and protein2genome options off. > Otherwise they will give weird partial models that decrease the quality of > your final annotations. (partial models are ok for training but that's about > it). > > > > > If you are getting too low a gene count with keep_preds=0, then you probably > need to add more evidence. Try adding all proteins from a couple of related > species (the protein= option accepts comma separated lists of files). If your > genome is a fungi, oomycete, or a prokaryote, then setting keep_preds=1 is > usually safe. Theses are genomes with high gene density and simple gene > structure, so ab initio predictors do really well and don't need as much help > from the evidence. For other organisms, leave it set to 0 or you will get a > lot of false positives (false positives on some genomes with complex gene > structure can outnumber the genes by 10 to 1 if you turn this on). > > > > > Thanks, > > Carson > > > > > > > > > > > > > > From: Barry Moore > Date: Friday, 31 August, 2012 12:52 PM > To: Christoph Hahn > Cc: > Subject: Re: [maker-devel] keep_preds option? > > > > > > > Hi Christopher, > > > > Comments below: > > > > > On Aug 31, 2012, at 6:43 AM, Christoph Hahn wrote: > > >> >> Hello maker users and developers, >> >> I am new to gene prediction and I am trying to use maker 2.25 on a newly >> assembled non-model organisms draft genome. Within maker I use genemark, SNAP >> and Augustus. I have a few questions: >> >> >> > > > > > Welcome! > > >> >> 1. I was wondering what the keep_preds option means exactly. >> >> I found two slightly different explanations on the option >> #Add unsupported gene prediction to final annotation set (maker2.25) >> #Add non-overlapping ab-inito gene prediction to final annotation set (found >> on the net - probably older maker version) >> >> >> > > > > > It means to keep ab initio gene predictions for which there is no physical > evidence. There are two pieces of information that are required for every > MAKER annotation (by default). MAKER runs the ab initio gene predictors and > aligns transcript (EST/cDNA/mRNASeq transcripts) and protein sequences to the > genome. For each locus where one or more gene predictions exist MAKER checks > to see if there is any physical evidence for gene expression at that locus > (RNA/protein sequence alignments) and if there is (splice EST or protein > alignments) evidence overlapping the predictions, MAKER decides which > prediction best matches the evidence and promotes that prediction to an > annotation. If there is no evidence overlapping any of the predictions then > those predictions are not included in the output annotation file (although > they are saved). If you set keep_preds=1 then for each locus where > prediction(s) exist maker keeps one and promotes it to an annotation even > though there is no physical evidence. The description of 'non-overlapping > ab-initio' means that MAKER has clustered all ab-initio predictions at one > locus and chose one representative transcript to output. > > >> >> As far as I understood keep_preds=0 only retains gene models for which the ab >> initio predictions agree. But how many, all three? two of three? >> keep_preds=1 instead keeps all gene models regardless if the different >> programs agree, right? >> >> >> > > > > > MAKER does not take the presence of multiple ab initio predictions as evidence > and thus in the absence of aligned physical evidence MAKER will not output an > annotation even if all three ab initio tools predict a gene at that locus. > > >> >> In my case I get substantial differences in the number of gene models found >> between the two settings, while with =1 I get a number that is close to what >> we would expect. How would you interpret that? What would you recommend me to >> do? Obiously =0 is the saver option. >> >> > > > > > If you think that the number of genes you are getting from a MAKER run is too > few, you could run MAKER with keep_preds=1. After the run is finished, use a > tool like IPRScan to search all MAKER predictions for protein domain content > and push that IPRScan output back into the MAKER GFF file with the > ipr_update_gff script. Then as a final step you can run over the GFF file and > remove any gene model that doesn't have either physical evidence (AED < 1) or > protein domain content (Dbxref=PFAM:XXX etc?) sorry there's not a script > prepackaged with MAKER for that yet. > > > > >> >> >> 2. I tried to use EST data of an alternative organism in altest= (#EST/cDNA >> sequence file in fasta format from an alternate organism). The organism is >> quite distantly related, but its the closest I have so I thought I d give it >> a shot. I ran maker twice with identical settigs expect in altest and >> est2genome=0/1. The number of genes predicted is identical with both >> approaches, so I am not sure whether or not the EST data was actually used or >> its just to distantly related. Any easy way to assess this? >> >> > > > > > Typically EST evidence from another organism with alt_est will add little in > the way of additional support (compared to just using protein evidence from > say Swiss-prot) and this would be especially true if your alt_est is distantly > related. I'm not sure I really understand you alt_est/est2genome combo's to > comment in more detail. I could see four possible combinations there: which > two gave identical results? > > >> >> >> 3. I am running maker in several passes and after each pass I am training >> SNAP using the result of the previous pass. Then for every pass I run maker >> from scratch. Would you recommend to supply the gff of the previous pass in >> "#-----Re-annotation Using MAKER Derived GFF3 >> maker_gff= #re-annotate genome based on this gff3 file", instead? >> >> >> > > > > > No, 'Re-annotation using MAKER Derived GFF3' is used for re-annotation of a > genome when you want certain parts of the previous run to be passed through > unchanged, but with retraining SNAP you want MAKER to re-evaluate each > annotation in light of the new predictions made by the retrained SNAP. MAKER > should run really fast in all of the runs after the first one because as long > as you haven't changed the evidence files it won't have to redo any of the > alignments. > > > > > > > B > > > >> >> Thanks in advance for any thoughts/advice on these things! I appreciate your >> help! >> >> much obliged, >> Christoph >> >> _______________________________________________ >> maker-devel mailing list >> maker-devel at box290.bluehost.com >> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org >> >> > > > > > > Barry Moore > > Research Scientist > > Dept. of Human Genetics > > University of Utah > > Salt Lake City, UT 84112 > > -------------------------------------------- > > (801) 585-3543 > > > > > > > > > > > > > > _______________________________________________ maker-devel mailing list > maker-devel at box290.bluehost.com > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Mon Sep 10 06:17:26 2012 From: carsonhh at gmail.com (Carson Holt) Date: Mon, 10 Sep 2012 07:17:26 -0400 Subject: [maker-devel] model_gff not in output In-Reply-To: <1A01E0C5-E60A-42AA-BD7B-A6429F435645@gmail.com> Message-ID: The only way MAKER should ignore a legacy annotation (only what's in model_gff is considered legacy by MAKER) is if, you also set one of the ab iniio predictors to run simultaneously or provide a pred_gff file and one of those models scores higher and would overlap the legacy model. Then MAKER chooses that model instead. Also if you have two overlapping legacy models MAKER will only keep one or the other under these same conditions. MAKER will only keep all legacy models regardless of overlap if you only supply model_gff with no other predictors turned on. Once you turn a predictor on, MAKER takes this as a cue that you are letting it make changes. Legacy models should always be kept under all circumstances if there is nothing overlapping them with a higher score. Are the missing models partially overlapped by anything in the resulting MAKER annotations? Thanks, Carson On 12-09-04 4:59 AM, "Michael Thon" wrote: >I'm using maker to update a legacy annotation. As input I'm using >RNA-Seq aligned with cufflinks, ESTs, provided in fasta format, and >proteins downloaded from UniProt.SwissProt. I have done two runs of >maker so far. The first one using the legacy annotations in both the >model_gff and pred_gff parameters. In the second run I used the legacy >annotations in model_gff and in pred_gff I included gene models created >with GeneMark-ES. > >In both runs 1 and 2 I have found two genes (so far) that exist in the >legacy annotations but are not in the final gene models output by maker. >Both genes have overlapping cufflinks annotations, in addition to having >annotations in model_gff. I thought maker was supposed to keep all the >annotations in model_gff, only replacing ones in which it could find an >alternative model with better support. Is there any case in which is >will remove a model? > > >Another discrepency I found in run1 is a gene that maker 'moved' upstream >approx. 150 bases. The gene locus annotated by maker covers the original >annotation, but the CDS does not. The site of the original CDS is covered >by an annotation in model_gff, pred_gff, two ESTs and a cufflinks >annotation. Maker still seems to have moved is is upstream where it only >has an overlapping cufflinks annotation. the three-prime utr annotated >by cufflinks still covers the legacy annotation though. > >Here's a link to download the maker gff file I'm looking at: > >https://dl.dropbox.com/u/320712/supercont1%252E1.gff.zip > >The genes that are in the legacy annotation but missing in the maker >annotation are: >GLRG_00074 and GLRG_00092 > >the 'moved' gene model I described is model GLRG_00081. they all within >the first 350 K of sequence. >mike > > > > > >_______________________________________________ >maker-devel mailing list >maker-devel at box290.bluehost.com >http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org From carsonhh at gmail.com Mon Sep 10 06:18:34 2012 From: carsonhh at gmail.com (Carson Holt) Date: Mon, 10 Sep 2012 07:18:34 -0400 Subject: [maker-devel] Maker Re-tries In-Reply-To: <1E417039-68CF-4EFE-90BF-964DC86B1864@uchicago.edu> Message-ID: Killing a job yourself should not increase the failure count for a contig. Thanks, Carson From: Kipp Johnson Date: Tuesday, 21 August, 2012 5:25 PM To: Carson Holt Cc: Kipp Johnson , Subject: Re: Maker Re-tries Hi Carson, Simple question: If I start maker and then kill the job before a thread finishes processing a contig, does this failure to complete the contig count in the number of tries maker will try to complete the contig before skipping to another? Basically, does the "tries=2 #number of times to try a contig if there is a failure for some reason" parameter take into account failures resulting from me killing the job? Best, Kipp Johnson kippjohnson at uchicago.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: From Carson.Holt at oicr.on.ca Mon Sep 10 05:50:09 2012 From: Carson.Holt at oicr.on.ca (Carson Holt) Date: Mon, 10 Sep 2012 10:50:09 +0000 Subject: [maker-devel] gene duplicates and track the query protein In-Reply-To: Message-ID: 2. Is there any way to track the maker gene to its corresponding query proteins through setting up some parameters in maker? Or is it possible to directly let maker name the gene model based on its query protein? Not directly. Proteins can align to multiple locations, so you will get more than one protein overlapping a gene. A reciprocal BLAST would probably be the best thing to do here. If the MAKER derived annotation, and a gene are both each others best hit in separate blast jobs, then you could usually safely call them the same gene. You would have to do that outside of MAKER. Thanks, Carson From: Barry Moore > Date: Thursday, 6 September, 2012 12:35 PM To: Zhou Qi > Cc: > Subject: Re: [maker-devel] gene duplicates and track the query protein On Sep 5, 2012, at 8:26 PM, Zhou Qi wrote: Dear maker users and developers: I'm new to maker and trying to use it to annotate a Drosophila genome given protein sequences of its closely related species. I have two questions: 1. How maker decide which one to keep if one query protein has two similarly best hits in the target genome, e.g., gene duplication? MAKER uses the aligned proteins as evidence to support gene predictions (i.e. from SNAP). If the supporting protein can align within the specified parameters (as defined in maker_bopts.ctl) then all of the valid alignments could be used as evidence for gene predictions at those loci. 2. Is there any way to track the maker gene to its corresponding query proteins through setting up some parameters in maker? Or is it possible to directly let maker name the gene model based on its query protein? I don't know of a way to do this by setting parameters in the MAKER control file - maybe Carson has some idea for you here? B I looked through the previous threads, one possible way seems to use model_gff and map_forward option combined. I guess people more experienced than me using maker might know other ways? Many thanks! Qi _______________________________________________ maker-devel mailing list maker-devel at box290.bluehost.com http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org Barry Moore Research Scientist Dept. of Human Genetics University of Utah Salt Lake City, UT 84112 -------------------------------------------- (801) 585-3543 _______________________________________________ maker-devel mailing list maker-devel at box290.bluehost.com http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org -------------- next part -------------- An HTML attachment was scrubbed... URL: From jeremy.semeiks at utsw.edu Mon Sep 10 10:02:25 2012 From: jeremy.semeiks at utsw.edu (Jeremy Semeiks) Date: Mon, 10 Sep 2012 10:02:25 -0500 Subject: [maker-devel] How to preserve human-friendly IDs when reannotating In-Reply-To: References: Message-ID: OK, thanks. So if I understand correctly, to preserve human-friendly IDs requires setting just three options: map_forward=1, maker_gff=, and model_pass=1. (Or instead of the last two I could equivalently just set model_gff to a GFF containing only models.) A couple new issues came up when I tried to run with these options. I started maker like this: /usr/bin/time mpiexec -n 10 maker -q < /dev/null > maker.oe 2>&1 1. I get a bunch of messages as follows, but with variable line number: DBD::SQLite::db do failed: database is locked at /home/jrs/maker-2.26-beta/bin/../lib/GFFDB.pm line 186. I saw that this came up in another thread < https://groups.google.com/forum/?fromgroups=#!topic/maker-devel/TscBgbQfBX4>, but I'm not sure it was ever resolved, nor whether it will affect my reannotation results (as I'm not sure what "your GFF3 results will not be integrated" means). This error did not come up the last time I ran maker for reannotation with similar options in a different directory. And both my current directory and my tmp directory are locally mounted, ie not NFS. 2. Both in this run and in previous runs, I get a lot of lines like this, seemingly at random: Warning: unable to close filehandle DF properly. On Mon, Sep 10, 2012 at 6:01 AM, Carson Holt wrote: > The map_forward option requires that the pass option for the gene models > be turned on. Otherwise you will have to do some spacial overlap test > outside of MAKER. > > If you have a new assembly, you can try mapping the old models onto the > new assembly using the old transcripts as input to the est= and setting > est2genome=1 (nothing else set, i.e no repeat masking etc.). Then there is > an undocumented option that is still a little buggy (hence why it is still > undocumented). Add the line est_forward=1 to your control files. This > tells MAKER to copy names from the ESTs, build the models directly from > their alignment, and to do other things to try and make a 1 to 1 match > across the genome. You will have to manually check that it is 1 to 1 in > the end (as I said still a little buggy and hence undocumented). Use the > resulting file as input to the model_gff option on a separate run with > map_forward=1 for additional reannotation wil more evidence, etc. where you > want to still be able to map names forward. > > From: Jeremy Semeiks > Date: Sunday, 9 September, 2012 3:49 PM > To: > Subject: [maker-devel] How to preserve human-friendly IDs when > reannotating > > Hi all, > > I have sequenced some novel fungal genomes, and I am annotating them with > maker-2.26-beta. The entire project is pretty iterative, in the sense that > I first get some seemingly-sane annotation sets, then analyze and compare > the proteomes biologically, then reannotate when new data comes in or as I > learn more about how maker works. Because I have already attached > biological meaning to some of my proteins, I would like to retain the same > human-friendly IDs across annotations. Eg, if maker suddenly finds 1,000 > new proteins on a reannotation run because I turned on keep_preds, then I > don't want the transcript formerly known as mymold_09652T0 to become > mymold_10698T0 when I run maker_map_ids; I want to keep it named > mymold_09652T0. > > So, is there any built-in way to preserve human-friendly IDs, or do I need > to write my own script for this? I have tried setting map_forward=1 and > maker_gff=, but > setting these seems to preserve neither the human-friendly IDs nor even the > original IDs. (Eg, protein "genemark-scaffold353-processed-gene-0.9-mRNA-1" > changed its name to "genemark-scaffold353-processed-gene-0.6-mRNA-1" when > reannotated.) I haven't turned on any of the *_pass options, eg > protein_pass; would this be relevant? > > Extra credit question: I am making some mate-pair libraries for these > fungi; when I re-assemble, that will completely change my scaffold names. > Is there any easy way to preserve human-friendly transcript names in this > case? As with the above simpler case, I think it would be pretty easy to > transfer 90% of the names just by doing an all-vs-all blastp between two > annotation sets and fishing out the best hits, but the remaining 10% might > be a headache. > > Thanks, > Jeremy > Grad student, Grishin lab > UT Southwestern, Dallas TX > 510.385.8959 > _______________________________________________ maker-devel mailing list > maker-devel at box290.bluehost.com > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org > -------------- next part -------------- An HTML attachment was scrubbed... URL: From carson.holt at genetics.utah.edu Mon Sep 10 12:21:05 2012 From: carson.holt at genetics.utah.edu (Carson Holt) Date: Mon, 10 Sep 2012 17:21:05 +0000 Subject: [maker-devel] MWAS: User Feedback In-Reply-To: Message-ID: MAKER won't really annotate those. Transcriptome annotation is a very different problem from genome annotation. I'm CC'ing this to the MAKER mailing list to see if anyone has good suggestion for transcriptome annotation. I would recommend using Repeatmasker to remove transposons from your transcriptome set, and then InterProScan for domain identification and maybe blast2go for GO term association. --Carson On 12-09-10 1:10 PM, "grind001 at umn.edu" wrote: >I have assembled RNAseq transcripts. There's no genome assembly for our >species right now, so I was trying to do an organized assembly pipeline >and >use your system. > >On Sep 10 2012, Carson Holt wrote: > >>Tell me a little more about your project. Based on your brief >>description >>I think you might need a different tool. MAKER doesn't assemble or >>annotate transcriptomes (i.e. RNA only). It works with de novo genome >>assemblies to identify the genes from them (I.e entire chromosomes or >>large fragments of chromosomes). It can use RNA-seq result to help >>annotate the genome but still requires a genome assembly. >> >>The online server will annotate maximum of 5 Mb at a time and it's slow >>(mostly built for small jobs). You will get 10-20 faster performance >>locally. >> >>Thanks, >>Carson >> >> >> >>On 12-09-10 12:17 PM, "grind001 at umn.edu" wrote: >> >>>Maker Web Annotation Service - User Feedback: >>>--------------------------------------------- >>>Hi, >>> >>>I'm working on getting your software installed on my systems, and have >>>done a test run on your web page with a portion of my data. >>>I have 150,000 contigs from a de novo assembly of our transcriptome. Do >>>you have room on your server for a large run? or is this just a sample >>>space to test the software? I'm under some time constraints and an just >>>checking and hoping to push this forward a bit faster. >>> >>> >>> >>>Best, >>>Suzanne >>>University of MN >>> >>> >>>--------------------------------------------- >>>User: 1440 >>>First: Suzanne >>>Last: Grindle >>>Institution: University of Minnesota >>>E-mail: grind001 at umn.edu >>> >> >> From felix.bemm at uni-wuerzburg.de Mon Sep 10 14:15:22 2012 From: felix.bemm at uni-wuerzburg.de (Felix Bemm) Date: Mon, 10 Sep 2012 21:15:22 +0200 Subject: [maker-devel] MWAS: User Feedback In-Reply-To: References: Message-ID: <504E3C4A.2040401@uni-wuerzburg.de> hi suzanne, the trinity assembler mailing list has some good ideas for that. You could think about using an "intelligent" orf finder like transdecoder (transdecoder.sourceforge.net). the predicted orfs can than be used for an interpro and blast2go run. merge the interpro and the b2g run with the built-in tool of blast2go. simply put the interpro xml's for each orf of a given transcript into one file for that and use the built-in import function of blast2go. this might help you to improve the GO annotation. it also works with the b2g pipeline tool (which is much faster). In addition, you could try to use interproscan standalone 5 (http://code.google.com/p/interproscan/) since it has an improved support for nucleic acid sequences. cheers felix Am 10.09.2012 19:21, schrieb Carson Holt: > MAKER won't really annotate those. Transcriptome annotation is a very > different problem from genome annotation. I'm CC'ing this to the MAKER > mailing list to see if anyone has good suggestion for transcriptome > annotation. > > I would recommend using Repeatmasker to remove transposons from your > transcriptome set, and then InterProScan for domain identification and > maybe blast2go for GO term association. > > --Carson > > > > > On 12-09-10 1:10 PM, "grind001 at umn.edu" wrote: > >> I have assembled RNAseq transcripts. There's no genome assembly for our >> species right now, so I was trying to do an organized assembly pipeline >> and >> use your system. >> >> On Sep 10 2012, Carson Holt wrote: >> >>> Tell me a little more about your project. Based on your brief >>> description >>> I think you might need a different tool. MAKER doesn't assemble or >>> annotate transcriptomes (i.e. RNA only). It works with de novo genome >>> assemblies to identify the genes from them (I.e entire chromosomes or >>> large fragments of chromosomes). It can use RNA-seq result to help >>> annotate the genome but still requires a genome assembly. >>> >>> The online server will annotate maximum of 5 Mb at a time and it's slow >>> (mostly built for small jobs). You will get 10-20 faster performance >>> locally. >>> >>> Thanks, >>> Carson >>> >>> >>> >>> On 12-09-10 12:17 PM, "grind001 at umn.edu" wrote: >>> >>>> Maker Web Annotation Service - User Feedback: >>>> --------------------------------------------- >>>> Hi, >>>> >>>> I'm working on getting your software installed on my systems, and have >>>> done a test run on your web page with a portion of my data. >>>> I have 150,000 contigs from a de novo assembly of our transcriptome. Do >>>> you have room on your server for a large run? or is this just a sample >>>> space to test the software? I'm under some time constraints and an just >>>> checking and hoping to push this forward a bit faster. >>>> >>>> >>>> >>>> Best, >>>> Suzanne >>>> University of MN >>>> >>>> >>>> --------------------------------------------- >>>> User: 1440 >>>> First: Suzanne >>>> Last: Grindle >>>> Institution: University of Minnesota >>>> E-mail: grind001 at umn.edu >>>> >>> >>> > > > _______________________________________________ > maker-devel mailing list > maker-devel at box290.bluehost.com > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org > -- Felix Bemm Department of Bioinformatics University of W?rzburg, Germany Tel: +49 931 - 31 83696 Fax: +49 931 - 31 84552 felix.bemm at uni-wuerzburg.de From ranjani at uga.edu Tue Sep 11 10:38:33 2012 From: ranjani at uga.edu (Sivaranjani Namasivayam) Date: Tue, 11 Sep 2012 15:38:33 +0000 Subject: [maker-devel] MAKER training Message-ID: Hi, I am using MAKER to annotate a newly sequenced genome. I have trained and retrained with datasets but I would like some advice on assessing the output and how this is affected by the input provided. - I have transcriptome data from 454 and Illumina platforms. Illumina is from a single time point and 454 from multiple time point. 454 was assembled using Newbler(dataset 1) and Illumina using Tophat-Cufflinks (dataset 2) and the denovo Trinity pipeline (dataset 3). I now have3 assemblies - 454 and Illumina will have some redunant transcripts (because of one overlapping time point); TopHat-Cufflinks and Trinity will have highly redundant transcripts (because they use same raw reads). Is it OK to provide all 3 datasets as EST evidence, how does it affect the quality of annotation. (For now I have used dataset 1 and dataset 2 as EST evidence) - I used the above model to retrain, I passed through everything except the abinitio gene predictions. I also provided a set a manually annotated genes , many of which have EST evidence. Is this OK to do? [ For proteins evidence, I gave a set from related organisms, same as above] - In my third retraining, I used the above retrained model, but this time I only provided the genome_gff but did not pass through any other data. However I did provide the manually annotated genes as EST evidence and related proteins as protein_evidence. Can you please give me some advice on which of these could give me the best prediction, or if I can alter something to get a better prediction. - A quick question about Augustus - I used a Augustus model (trained for a closely related organism) for ab-initio prediction. Does MAKER adjust this model based on the evidence provided, or use the model as such for a prediction. Greatly appreciate your help! Thanks! Ranjani -------------- next part -------------- An HTML attachment was scrubbed... URL: From dence at genetics.utah.edu Tue Sep 11 10:46:04 2012 From: dence at genetics.utah.edu (Daniel Ence) Date: Tue, 11 Sep 2012 15:46:04 +0000 Subject: [maker-devel] MAKER training In-Reply-To: References: Message-ID: Hi Ranjani, It is fine to include all three of those transcriptome datatsets. The more (relevant) evidence the better. I'm not certain what you mean when you say "you used the above model to retrain". Did you train an abinitio gene predictor using the results from your first maker run? Daniel Ence Graduate Student Eccles Institute of Human Genetics University of Utah 15 North 2030 East, Room 2100 Salt Lake City, UT 84112-5330 ________________________________ From: maker-devel-bounces at yandell-lab.org [maker-devel-bounces at yandell-lab.org] on behalf of Sivaranjani Namasivayam [ranjani at uga.edu] Sent: Tuesday, September 11, 2012 9:38 AM To: maker-devel at yandell-lab.org Subject: [maker-devel] MAKER training Hi, I am using MAKER to annotate a newly sequenced genome. I have trained and retrained with datasets but I would like some advice on assessing the output and how this is affected by the input provided. - I have transcriptome data from 454 and Illumina platforms. Illumina is from a single time point and 454 from multiple time point. 454 was assembled using Newbler(dataset 1) and Illumina using Tophat-Cufflinks (dataset 2) and the denovo Trinity pipeline (dataset 3). I now have3 assemblies - 454 and Illumina will have some redunant transcripts (because of one overlapping time point); TopHat-Cufflinks and Trinity will have highly redundant transcripts (because they use same raw reads). Is it OK to provide all 3 datasets as EST evidence, how does it affect the quality of annotation. (For now I have used dataset 1 and dataset 2 as EST evidence) - I used the above model to retrain, I passed through everything except the abinitio gene predictions. I also provided a set a manually annotated genes , many of which have EST evidence. Is this OK to do? [ For proteins evidence, I gave a set from related organisms, same as above] - In my third retraining, I used the above retrained model, but this time I only provided the genome_gff but did not pass through any other data. However I did provide the manually annotated genes as EST evidence and related proteins as protein_evidence. Can you please give me some advice on which of these could give me the best prediction, or if I can alter something to get a better prediction. - A quick question about Augustus - I used a Augustus model (trained for a closely related organism) for ab-initio prediction. Does MAKER adjust this model based on the evidence provided, or use the model as such for a prediction. Greatly appreciate your help! Thanks! Ranjani -------------- next part -------------- An HTML attachment was scrubbed... URL: From ranjani at uga.edu Tue Sep 11 10:57:31 2012 From: ranjani at uga.edu (Sivaranjani Namasivayam) Date: Tue, 11 Sep 2012 15:57:31 +0000 Subject: [maker-devel] MAKER training In-Reply-To: References: , Message-ID: Hey, I used the MAKER model to retrain MAKER itself. I read somewhere it improves MAKER's predictions. I did train abinitio gene predictors using MAKERs output, but I wanted to identify the best prediction before using it to train other gene predictors. Thanks, Ranjani ________________________________ From: Daniel Ence [dence at genetics.utah.edu] Sent: Tuesday, September 11, 2012 11:46 AM To: Sivaranjani Namasivayam; maker-devel at yandell-lab.org Subject: RE: MAKER training Hi Ranjani, It is fine to include all three of those transcriptome datatsets. The more (relevant) evidence the better. I'm not certain what you mean when you say "you used the above model to retrain". Did you train an abinitio gene predictor using the results from your first maker run? Daniel Ence Graduate Student Eccles Institute of Human Genetics University of Utah 15 North 2030 East, Room 2100 Salt Lake City, UT 84112-5330 ________________________________ From: maker-devel-bounces at yandell-lab.org [maker-devel-bounces at yandell-lab.org] on behalf of Sivaranjani Namasivayam [ranjani at uga.edu] Sent: Tuesday, September 11, 2012 9:38 AM To: maker-devel at yandell-lab.org Subject: [maker-devel] MAKER training Hi, I am using MAKER to annotate a newly sequenced genome. I have trained and retrained with datasets but I would like some advice on assessing the output and how this is affected by the input provided. - I have transcriptome data from 454 and Illumina platforms. Illumina is from a single time point and 454 from multiple time point. 454 was assembled using Newbler(dataset 1) and Illumina using Tophat-Cufflinks (dataset 2) and the denovo Trinity pipeline (dataset 3). I now have3 assemblies - 454 and Illumina will have some redunant transcripts (because of one overlapping time point); TopHat-Cufflinks and Trinity will have highly redundant transcripts (because they use same raw reads). Is it OK to provide all 3 datasets as EST evidence, how does it affect the quality of annotation. (For now I have used dataset 1 and dataset 2 as EST evidence) - I used the above model to retrain, I passed through everything except the abinitio gene predictions. I also provided a set a manually annotated genes , many of which have EST evidence. Is this OK to do? [ For proteins evidence, I gave a set from related organisms, same as above] - In my third retraining, I used the above retrained model, but this time I only provided the genome_gff but did not pass through any other data. However I did provide the manually annotated genes as EST evidence and related proteins as protein_evidence. Can you please give me some advice on which of these could give me the best prediction, or if I can alter something to get a better prediction. - A quick question about Augustus - I used a Augustus model (trained for a closely related organism) for ab-initio prediction. Does MAKER adjust this model based on the evidence provided, or use the model as such for a prediction. Greatly appreciate your help! Thanks! Ranjani -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Tue Sep 11 11:04:53 2012 From: carsonhh at gmail.com (Carson Holt) Date: Tue, 11 Sep 2012 12:04:53 -0400 Subject: [maker-devel] MAKER training In-Reply-To: Message-ID: > - I have transcriptome data from 454 and Illumina platforms. Illumina is from > a single time point and 454 from multiple time point. 454 was assembled using > Newbler(dataset 1) and Illumina using Tophat-Cufflinks (dataset 2) and the > denovo Trinity pipeline (dataset 3). I now have3 assemblies - 454 and > Illumina will have some redunant transcripts (because of one overlapping time > point); TopHat-Cufflinks and Trinity will have highly redundant transcripts > (because they use same raw reads). Is it OK to provide all 3 datasets as EST > evidence, how does it affect the quality of annotation. (For now I have used > dataset 1 and dataset 2 as EST evidence) This is fine. You can give them as a comma separated list est=file1,file2,file3 > - I used the above model to retrain, I passed through everything except the > abinitio gene predictions. I also provided a set a manually annotated genes , > many of which have EST evidence. Is this OK to do? [ For proteins evidence, I > gave a set from related organisms, same as above] > > - In my third retraining, I used the above retrained model, but this time I > only provided the genome_gff but did not pass through any other data. However > I did provide the manually annotated genes as EST evidence and related > proteins as protein_evidence. > > Can you please give me some advice on which of these could give me the best > prediction, or if I can alter something to get a better prediction. > Everything you've done sounds reasonable. Better training comes from having the most correct models to train with, so providing the manual annotations as training works, or you can also select MAKER models with the lowest AED score (i.e. models that most closely match evidence). The goal is to try and make the process as unbias as possible, so a consistent usually automated selection method is often the easiest to justify justifiable. > > - A quick question about Augustus - I used a Augustus model (trained for a > closely related organism) for ab-initio prediction. Does MAKER adjust this > model based on the evidence provided, or use the model as such for a > prediction. MAKER will provide hints to Augustus during the run to make it perform better. MAKER will report the raw unaided augustus results in the GFF3 file as a reference, but will use evidence to improve performance where it can. The gene name will let you know if it is a hint based or ab initio model prediction. When 'maker', is part of the gene name it is hint based. Thanks, Carson -------------- next part -------------- An HTML attachment was scrubbed... URL: From dence at genetics.utah.edu Tue Sep 11 11:29:21 2012 From: dence at genetics.utah.edu (Daniel Ence) Date: Tue, 11 Sep 2012 16:29:21 +0000 Subject: [maker-devel] MAKER training In-Reply-To: References: , , Message-ID: So, MAKER itself isn't probabilistic. If you give it the same data and the same options, it will give you the same outputs. The iterative approach for MAKER is to get gene models on the first round using the est2genome option and the Augustus model that you mentioned. After that first round, you train the ab-initio predictors and tell maker to use those newly trained gene predictors in the second round. Regarding the set of manually annotated genes, I think you should put those in the model_gff option. Thanks, Daniel Daniel Ence Graduate Student Eccles Institute of Human Genetics University of Utah 15 North 2030 East, Room 2100 Salt Lake City, UT 84112-5330 ________________________________ From: Sivaranjani Namasivayam [ranjani at uga.edu] Sent: Tuesday, September 11, 2012 9:57 AM To: Daniel Ence; maker-devel at yandell-lab.org Subject: RE: MAKER training Hey, I used the MAKER model to retrain MAKER itself. I read somewhere it improves MAKER's predictions. I did train abinitio gene predictors using MAKERs output, but I wanted to identify the best prediction before using it to train other gene predictors. Thanks, Ranjani ________________________________ From: Daniel Ence [dence at genetics.utah.edu] Sent: Tuesday, September 11, 2012 11:46 AM To: Sivaranjani Namasivayam; maker-devel at yandell-lab.org Subject: RE: MAKER training Hi Ranjani, It is fine to include all three of those transcriptome datatsets. The more (relevant) evidence the better. I'm not certain what you mean when you say "you used the above model to retrain". Did you train an abinitio gene predictor using the results from your first maker run? Daniel Ence Graduate Student Eccles Institute of Human Genetics University of Utah 15 North 2030 East, Room 2100 Salt Lake City, UT 84112-5330 ________________________________ From: maker-devel-bounces at yandell-lab.org [maker-devel-bounces at yandell-lab.org] on behalf of Sivaranjani Namasivayam [ranjani at uga.edu] Sent: Tuesday, September 11, 2012 9:38 AM To: maker-devel at yandell-lab.org Subject: [maker-devel] MAKER training Hi, I am using MAKER to annotate a newly sequenced genome. I have trained and retrained with datasets but I would like some advice on assessing the output and how this is affected by the input provided. - I have transcriptome data from 454 and Illumina platforms. Illumina is from a single time point and 454 from multiple time point. 454 was assembled using Newbler(dataset 1) and Illumina using Tophat-Cufflinks (dataset 2) and the denovo Trinity pipeline (dataset 3). I now have3 assemblies - 454 and Illumina will have some redunant transcripts (because of one overlapping time point); TopHat-Cufflinks and Trinity will have highly redundant transcripts (because they use same raw reads). Is it OK to provide all 3 datasets as EST evidence, how does it affect the quality of annotation. (For now I have used dataset 1 and dataset 2 as EST evidence) - I used the above model to retrain, I passed through everything except the abinitio gene predictions. I also provided a set a manually annotated genes , many of which have EST evidence. Is this OK to do? [ For proteins evidence, I gave a set from related organisms, same as above] - In my third retraining, I used the above retrained model, but this time I only provided the genome_gff but did not pass through any other data. However I did provide the manually annotated genes as EST evidence and related proteins as protein_evidence. Can you please give me some advice on which of these could give me the best prediction, or if I can alter something to get a better prediction. - A quick question about Augustus - I used a Augustus model (trained for a closely related organism) for ab-initio prediction. Does MAKER adjust this model based on the evidence provided, or use the model as such for a prediction. Greatly appreciate your help! Thanks! Ranjani -------------- next part -------------- An HTML attachment was scrubbed... URL: From ranjani at uga.edu Tue Sep 11 11:45:42 2012 From: ranjani at uga.edu (Sivaranjani Namasivayam) Date: Tue, 11 Sep 2012 16:45:42 +0000 Subject: [maker-devel] MAKER training In-Reply-To: References: , , , Message-ID: I will try the model_gff option. For the retraining I noticed the count of the annotated genes vary, I haven't examined if the gene structure varies. I will use the models to train ab-initio predictions and providing that as input. But I did notice the number of genes output by MAKER is fairly lower when compared to the transcriptome. I understand this is because MAKER annotations are based on good evidence but can this improve/increase with ab-initio gene models input. Thanks, Ranjani ________________________________ From: Daniel Ence [dence at genetics.utah.edu] Sent: Tuesday, September 11, 2012 12:29 PM To: Sivaranjani Namasivayam; maker-devel at yandell-lab.org Subject: RE: MAKER training So, MAKER itself isn't probabilistic. If you give it the same data and the same options, it will give you the same outputs. The iterative approach for MAKER is to get gene models on the first round using the est2genome option and the Augustus model that you mentioned. After that first round, you train the ab-initio predictors and tell maker to use those newly trained gene predictors in the second round. Regarding the set of manually annotated genes, I think you should put those in the model_gff option. Thanks, Daniel Daniel Ence Graduate Student Eccles Institute of Human Genetics University of Utah 15 North 2030 East, Room 2100 Salt Lake City, UT 84112-5330 ________________________________ From: Sivaranjani Namasivayam [ranjani at uga.edu] Sent: Tuesday, September 11, 2012 9:57 AM To: Daniel Ence; maker-devel at yandell-lab.org Subject: RE: MAKER training Hey, I used the MAKER model to retrain MAKER itself. I read somewhere it improves MAKER's predictions. I did train abinitio gene predictors using MAKERs output, but I wanted to identify the best prediction before using it to train other gene predictors. Thanks, Ranjani ________________________________ From: Daniel Ence [dence at genetics.utah.edu] Sent: Tuesday, September 11, 2012 11:46 AM To: Sivaranjani Namasivayam; maker-devel at yandell-lab.org Subject: RE: MAKER training Hi Ranjani, It is fine to include all three of those transcriptome datatsets. The more (relevant) evidence the better. I'm not certain what you mean when you say "you used the above model to retrain". Did you train an abinitio gene predictor using the results from your first maker run? Daniel Ence Graduate Student Eccles Institute of Human Genetics University of Utah 15 North 2030 East, Room 2100 Salt Lake City, UT 84112-5330 ________________________________ From: maker-devel-bounces at yandell-lab.org [maker-devel-bounces at yandell-lab.org] on behalf of Sivaranjani Namasivayam [ranjani at uga.edu] Sent: Tuesday, September 11, 2012 9:38 AM To: maker-devel at yandell-lab.org Subject: [maker-devel] MAKER training Hi, I am using MAKER to annotate a newly sequenced genome. I have trained and retrained with datasets but I would like some advice on assessing the output and how this is affected by the input provided. - I have transcriptome data from 454 and Illumina platforms. Illumina is from a single time point and 454 from multiple time point. 454 was assembled using Newbler(dataset 1) and Illumina using Tophat-Cufflinks (dataset 2) and the denovo Trinity pipeline (dataset 3). I now have3 assemblies - 454 and Illumina will have some redunant transcripts (because of one overlapping time point); TopHat-Cufflinks and Trinity will have highly redundant transcripts (because they use same raw reads). Is it OK to provide all 3 datasets as EST evidence, how does it affect the quality of annotation. (For now I have used dataset 1 and dataset 2 as EST evidence) - I used the above model to retrain, I passed through everything except the abinitio gene predictions. I also provided a set a manually annotated genes , many of which have EST evidence. Is this OK to do? [ For proteins evidence, I gave a set from related organisms, same as above] - In my third retraining, I used the above retrained model, but this time I only provided the genome_gff but did not pass through any other data. However I did provide the manually annotated genes as EST evidence and related proteins as protein_evidence. Can you please give me some advice on which of these could give me the best prediction, or if I can alter something to get a better prediction. - A quick question about Augustus - I used a Augustus model (trained for a closely related organism) for ab-initio prediction. Does MAKER adjust this model based on the evidence provided, or use the model as such for a prediction. Greatly appreciate your help! Thanks! Ranjani -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Tue Sep 11 15:33:11 2012 From: carsonhh at gmail.com (Carson Holt) Date: Tue, 11 Sep 2012 16:33:11 -0400 Subject: [maker-devel] How to preserve human-friendly IDs when reannotating In-Reply-To: Message-ID: Which version of MAKER are you running (maker --version)? --Carson From: Jeremy Semeiks Date: Monday, 10 September, 2012 11:02 AM To: Carson Holt Cc: Subject: Re: [maker-devel] How to preserve human-friendly IDs when reannotating OK, thanks. So if I understand correctly, to preserve human-friendly IDs requires setting just three options: map_forward=1, maker_gff=, and model_pass=1. (Or instead of the last two I could equivalently just set model_gff to a GFF containing only models.) A couple new issues came up when I tried to run with these options. I started maker like this: /usr/bin/time mpiexec -n 10 maker -q < /dev/null > maker.oe 2>&1 1. I get a bunch of messages as follows, but with variable line number: DBD::SQLite::db do failed: database is locked at /home/jrs/maker-2.26-beta/bin/../lib/GFFDB.pm line 186. I saw that this came up in another thread , but I'm not sure it was ever resolved, nor whether it will affect my reannotation results (as I'm not sure what "your GFF3 results will not be integrated" means). This error did not come up the last time I ran maker for reannotation with similar options in a different directory. And both my current directory and my tmp directory are locally mounted, ie not NFS. 2. Both in this run and in previous runs, I get a lot of lines like this, seemingly at random: Warning: unable to close filehandle DF properly. On Mon, Sep 10, 2012 at 6:01 AM, Carson Holt wrote: > The map_forward option requires that the pass option for the gene models be > turned on. Otherwise you will have to do some spacial overlap test outside of > MAKER. > > If you have a new assembly, you can try mapping the old models onto the new > assembly using the old transcripts as input to the est= and setting > est2genome=1 (nothing else set, i.e no repeat masking etc.). Then there is an > undocumented option that is still a little buggy (hence why it is still > undocumented). Add the line est_forward=1 to your control files. This tells > MAKER to copy names from the ESTs, build the models directly from their > alignment, and to do other things to try and make a 1 to 1 match across the > genome. You will have to manually check that it is 1 to 1 in the end (as I > said still a little buggy and hence undocumented). Use the resulting file as > input to the model_gff option on a separate run with map_forward=1 for > additional reannotation wil more evidence, etc. where you want to still be > able to map names forward. > > From: Jeremy Semeiks > Date: Sunday, 9 September, 2012 3:49 PM > To: > Subject: [maker-devel] How to preserve human-friendly IDs when reannotating > > Hi all, > > I have sequenced some novel fungal genomes, and I am annotating them with > maker-2.26-beta. The entire project is pretty iterative, in the sense that I > first get some seemingly-sane annotation sets, then analyze and compare the > proteomes biologically, then reannotate when new data comes in or as I learn > more about how maker works. Because I have already attached biological meaning > to some of my proteins, I would like to retain the same human-friendly IDs > across annotations. Eg, if maker suddenly finds 1,000 new proteins on a > reannotation run because I turned on keep_preds, then I don't want the > transcript formerly known as mymold_09652T0 to become mymold_10698T0 when I > run maker_map_ids; I want to keep it named mymold_09652T0. > > So, is there any built-in way to preserve human-friendly IDs, or do I need to > write my own script for this? I have tried setting map_forward=1 and > maker_gff=, but > setting these seems to preserve neither the human-friendly IDs nor even the > original IDs. (Eg, protein "genemark-scaffold353-processed-gene-0.9-mRNA-1" > changed its name to "genemark-scaffold353-processed-gene-0.6-mRNA-1" when > reannotated.) I haven't turned on any of the *_pass options, eg protein_pass; > would this be relevant? > > Extra credit question: I am making some mate-pair libraries for these fungi; > when I re-assemble, that will completely change my scaffold names. Is there > any easy way to preserve human-friendly transcript names in this case? As with > the above simpler case, I think it would be pretty easy to transfer 90% of the > names just by doing an all-vs-all blastp between two annotation sets and > fishing out the best hits, but the remaining 10% might be a headache. > > Thanks, > Jeremy > Grad student, Grishin lab > UT Southwestern, Dallas TX > 510.385.8959 > _______________________________________________ maker-devel mailing list > maker-devel at box290.bluehost.comhttp://box290.bluehost.com/mailman/listinfo/mak > er-devel_yandell-lab.org -------------- next part -------------- An HTML attachment was scrubbed... URL: From jeremy.semeiks at utsw.edu Tue Sep 11 18:56:23 2012 From: jeremy.semeiks at utsw.edu (Jeremy Semeiks) Date: Tue, 11 Sep 2012 18:56:23 -0500 Subject: [maker-devel] How to preserve human-friendly IDs when reannotating In-Reply-To: References: Message-ID: maker 2.26. And I have verified for myself that the three options I mentioned below suffice to preserve human-friendly IDs when reannotating. Thanks, J On Tue, Sep 11, 2012 at 3:33 PM, Carson Holt wrote: > Which version of MAKER are you running (maker --version)? > > --Carson > > > > From: Jeremy Semeiks > Date: Monday, 10 September, 2012 11:02 AM > To: Carson Holt > Cc: > Subject: Re: [maker-devel] How to preserve human-friendly IDs when > reannotating > > OK, thanks. So if I understand correctly, to preserve human-friendly IDs > requires setting just three options: map_forward=1, > maker_gff=, and model_pass=1. (Or instead of the > last two I could equivalently just set model_gff to a GFF containing only > models.) > > A couple new issues came up when I tried to run with these options. I > started maker like this: > > /usr/bin/time mpiexec -n 10 maker -q < /dev/null > maker.oe 2>&1 > > 1. I get a bunch of messages as follows, but with variable line number: > > DBD::SQLite::db do failed: database is locked at > /home/jrs/maker-2.26-beta/bin/../lib/GFFDB.pm line 186. > > I saw that this came up in another thread < > https://groups.google.com/forum/?fromgroups=#!topic/maker-devel/TscBgbQfBX4>, > but I'm not sure it was ever resolved, nor whether it will affect my > reannotation results (as I'm not sure what "your GFF3 results will not be > integrated" means). This error did not come up the last time I ran maker > for reannotation with similar options in a different directory. And both my > current directory and my tmp directory are locally mounted, ie not NFS. > > 2. Both in this run and in previous runs, I get a lot of lines like this, > seemingly at random: > > Warning: unable to close filehandle DF properly. > > > On Mon, Sep 10, 2012 at 6:01 AM, Carson Holt wrote: > >> The map_forward option requires that the pass option for the gene models >> be turned on. Otherwise you will have to do some spacial overlap test >> outside of MAKER. >> >> If you have a new assembly, you can try mapping the old models onto the >> new assembly using the old transcripts as input to the est= and setting >> est2genome=1 (nothing else set, i.e no repeat masking etc.). Then there is >> an undocumented option that is still a little buggy (hence why it is still >> undocumented). Add the line est_forward=1 to your control files. This >> tells MAKER to copy names from the ESTs, build the models directly from >> their alignment, and to do other things to try and make a 1 to 1 match >> across the genome. You will have to manually check that it is 1 to 1 in >> the end (as I said still a little buggy and hence undocumented). Use the >> resulting file as input to the model_gff option on a separate run with >> map_forward=1 for additional reannotation wil more evidence, etc. where you >> want to still be able to map names forward. >> >> From: Jeremy Semeiks >> Date: Sunday, 9 September, 2012 3:49 PM >> To: >> Subject: [maker-devel] How to preserve human-friendly IDs when >> reannotating >> >> Hi all, >> >> I have sequenced some novel fungal genomes, and I am annotating them with >> maker-2.26-beta. The entire project is pretty iterative, in the sense that >> I first get some seemingly-sane annotation sets, then analyze and compare >> the proteomes biologically, then reannotate when new data comes in or as I >> learn more about how maker works. Because I have already attached >> biological meaning to some of my proteins, I would like to retain the same >> human-friendly IDs across annotations. Eg, if maker suddenly finds 1,000 >> new proteins on a reannotation run because I turned on keep_preds, then I >> don't want the transcript formerly known as mymold_09652T0 to become >> mymold_10698T0 when I run maker_map_ids; I want to keep it named >> mymold_09652T0. >> >> So, is there any built-in way to preserve human-friendly IDs, or do I >> need to write my own script for this? I have tried setting map_forward=1 >> and maker_gff=, >> but setting these seems to preserve neither the human-friendly IDs nor even >> the original IDs. (Eg, protein >> "genemark-scaffold353-processed-gene-0.9-mRNA-1" changed its name to >> "genemark-scaffold353-processed-gene-0.6-mRNA-1" when reannotated.) I >> haven't turned on any of the *_pass options, eg protein_pass; would this be >> relevant? >> >> Extra credit question: I am making some mate-pair libraries for these >> fungi; when I re-assemble, that will completely change my scaffold names. >> Is there any easy way to preserve human-friendly transcript names in this >> case? As with the above simpler case, I think it would be pretty easy to >> transfer 90% of the names just by doing an all-vs-all blastp between two >> annotation sets and fishing out the best hits, but the remaining 10% might >> be a headache. >> >> Thanks, >> Jeremy >> Grad student, Grishin lab >> UT Southwestern, Dallas TX >> 510.385.8959 >> _______________________________________________ maker-devel mailing list >> maker-devel at box290.bluehost.com >> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org >> > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From ranjani at uga.edu Wed Sep 12 12:53:37 2012 From: ranjani at uga.edu (Sivaranjani Namasivayam) Date: Wed, 12 Sep 2012 17:53:37 +0000 Subject: [maker-devel] MAKER training In-Reply-To: References: , Message-ID: I have a few questions based on your comment about augustus/MAKER naming convention. I have been sorting the data using the second column of the GFF file, I wanted to be sure I have it right - Doesn't 'maker' in the second column signify MAKER's final annotations based on all evidence (EST, protein and abinitio prediction) ? I noticed two types of gene IDs, example 1. augustus_masked-scaffold00030-abinit-gene-3.2 2. maker-scaffold00030-augustus-gene-3.7 Is the first one, a direct augustus prediction without a hints file and the second based on a hints file (made from the EST and protein evidence)? If this is the case, could 2 be a better annotation than 1? - In case of augustus_masked in the 2nd column, I believe all are predictions are without a hints file. Thanks, Ranjani ________________________________ From: Carson Holt [carsonhh at gmail.com] Sent: Tuesday, September 11, 2012 12:04 PM To: Sivaranjani Namasivayam; maker-devel at yandell-lab.org Subject: Re: [maker-devel] MAKER training - I have transcriptome data from 454 and Illumina platforms. Illumina is from a single time point and 454 from multiple time point. 454 was assembled using Newbler(dataset 1) and Illumina using Tophat-Cufflinks (dataset 2) and the denovo Trinity pipeline (dataset 3). I now have3 assemblies - 454 and Illumina will have some redunant transcripts (because of one overlapping time point); TopHat-Cufflinks and Trinity will have highly redundant transcripts (because they use same raw reads). Is it OK to provide all 3 datasets as EST evidence, how does it affect the quality of annotation. (For now I have used dataset 1 and dataset 2 as EST evidence) This is fine. You can give them as a comma separated list est=file1,file2,file3 - I used the above model to retrain, I passed through everything except the abinitio gene predictions. I also provided a set a manually annotated genes , many of which have EST evidence. Is this OK to do? [ For proteins evidence, I gave a set from related organisms, same as above] - In my third retraining, I used the above retrained model, but this time I only provided the genome_gff but did not pass through any other data. However I did provide the manually annotated genes as EST evidence and related proteins as protein_evidence. Can you please give me some advice on which of these could give me the best prediction, or if I can alter something to get a better prediction. Everything you've done sounds reasonable. Better training comes from having the most correct models to train with, so providing the manual annotations as training works, or you can also select MAKER models with the lowest AED score (i.e. models that most closely match evidence). The goal is to try and make the process as unbias as possible, so a consistent usually automated selection method is often the easiest to justify justifiable. - A quick question about Augustus - I used a Augustus model (trained for a closely related organism) for ab-initio prediction. Does MAKER adjust this model based on the evidence provided, or use the model as such for a prediction. MAKER will provide hints to Augustus during the run to make it perform better. MAKER will report the raw unaided augustus results in the GFF3 file as a reference, but will use evidence to improve performance where it can. The gene name will let you know if it is a hint based or ab initio model prediction. When 'maker', is part of the gene name it is hint based. Thanks, Carson -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Thu Sep 13 08:11:27 2012 From: carsonhh at gmail.com (Carson Holt) Date: Thu, 13 Sep 2012 09:11:27 -0400 Subject: [maker-devel] How to preserve human-friendly IDs when reannotating In-Reply-To: Message-ID: The error --> DBD::SQLite::db do failed: database is locked at /home/jrs/maker-2.26-beta/bin/../lib/GFFDB.pm line 186. The location of the specific error you are getting is probably benign. It is a failure to alter the default cache size for the database. The database should already be populated. I'm planning removing the SQLlite database entirely in the future. Perhaps in favor of something like tabix based indexing of the GFF3 file. Thanks, Carson From: Jeremy Semeiks Date: Tuesday, 11 September, 2012 7:56 PM To: Carson Holt Cc: Subject: Re: [maker-devel] How to preserve human-friendly IDs when reannotating maker 2.26. And I have verified for myself that the three options I mentioned below suffice to preserve human-friendly IDs when reannotating. Thanks, J On Tue, Sep 11, 2012 at 3:33 PM, Carson Holt wrote: > Which version of MAKER are you running (maker --version)? > > --Carson > > > > From: Jeremy Semeiks > Date: Monday, 10 September, 2012 11:02 AM > To: Carson Holt > Cc: > Subject: Re: [maker-devel] How to preserve human-friendly IDs when > reannotating > > OK, thanks. So if I understand correctly, to preserve human-friendly IDs > requires setting just three options: map_forward=1, > maker_gff=, and model_pass=1. (Or instead of the last > two I could equivalently just set model_gff to a GFF containing only models.) > > A couple new issues came up when I tried to run with these options. I started > maker like this: > > /usr/bin/time mpiexec -n 10 maker -q < /dev/null > maker.oe 2>&1 > > 1. I get a bunch of messages as follows, but with variable line number: > > DBD::SQLite::db do failed: database is locked at > /home/jrs/maker-2.26-beta/bin/../lib/GFFDB.pm line 186. > > I saw that this came up in another thread > , > but I'm not sure it was ever resolved, nor whether it will affect my > reannotation results (as I'm not sure what "your GFF3 results will not be > integrated" means). This error did not come up the last time I ran maker for > reannotation with similar options in a different directory. And both my > current directory and my tmp directory are locally mounted, ie not NFS. > > 2. Both in this run and in previous runs, I get a lot of lines like this, > seemingly at random: > > Warning: unable to close filehandle DF properly. > > > On Mon, Sep 10, 2012 at 6:01 AM, Carson Holt wrote: >> The map_forward option requires that the pass option for the gene models be >> turned on. Otherwise you will have to do some spacial overlap test outside >> of MAKER. >> >> If you have a new assembly, you can try mapping the old models onto the new >> assembly using the old transcripts as input to the est= and setting >> est2genome=1 (nothing else set, i.e no repeat masking etc.). Then there is >> an undocumented option that is still a little buggy (hence why it is still >> undocumented). Add the line est_forward=1 to your control files. This tells >> MAKER to copy names from the ESTs, build the models directly from their >> alignment, and to do other things to try and make a 1 to 1 match across the >> genome. You will have to manually check that it is 1 to 1 in the end (as I >> said still a little buggy and hence undocumented). Use the resulting file as >> input to the model_gff option on a separate run with map_forward=1 for >> additional reannotation wil more evidence, etc. where you want to still be >> able to map names forward. >> >> From: Jeremy Semeiks >> Date: Sunday, 9 September, 2012 3:49 PM >> To: >> Subject: [maker-devel] How to preserve human-friendly IDs when reannotating >> >> Hi all, >> >> I have sequenced some novel fungal genomes, and I am annotating them with >> maker-2.26-beta. The entire project is pretty iterative, in the sense that I >> first get some seemingly-sane annotation sets, then analyze and compare the >> proteomes biologically, then reannotate when new data comes in or as I learn >> more about how maker works. Because I have already attached biological >> meaning to some of my proteins, I would like to retain the same >> human-friendly IDs across annotations. Eg, if maker suddenly finds 1,000 new >> proteins on a reannotation run because I turned on keep_preds, then I don't >> want the transcript formerly known as mymold_09652T0 to become mymold_10698T0 >> when I run maker_map_ids; I want to keep it named mymold_09652T0. >> >> So, is there any built-in way to preserve human-friendly IDs, or do I need to >> write my own script for this? I have tried setting map_forward=1 and >> maker_gff=, but >> setting these seems to preserve neither the human-friendly IDs nor even the >> original IDs. (Eg, protein "genemark-scaffold353-processed-gene-0.9-mRNA-1" >> changed its name to "genemark-scaffold353-processed-gene-0.6-mRNA-1" when >> reannotated.) I haven't turned on any of the *_pass options, eg protein_pass; >> would this be relevant? >> >> Extra credit question: I am making some mate-pair libraries for these fungi; >> when I re-assemble, that will completely change my scaffold names. Is there >> any easy way to preserve human-friendly transcript names in this case? As >> with the above simpler case, I think it would be pretty easy to transfer 90% >> of the names just by doing an all-vs-all blastp between two annotation sets >> and fishing out the best hits, but the remaining 10% might be a headache. >> >> Thanks, >> Jeremy >> Grad student, Grishin lab >> UT Southwestern, Dallas TX >> 510.385.8959 >> _______________________________________________ maker-devel mailing list >> maker-devel at box290.bluehost.comhttp://box290.bluehost.com/mailman/listinfo/ma >> ker-devel_yandell-lab.org > -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Thu Sep 13 08:30:22 2012 From: carsonhh at gmail.com (Carson Holt) Date: Thu, 13 Sep 2012 09:30:22 -0400 Subject: [maker-devel] MAKER training In-Reply-To: Message-ID: Yes, those are the final annotations, and yes one is derived from the ab initio model and one from hint based models. The selection between hint based models and ab initio models is based on evidence overlap, so either can be better than the other or vice versa. The bets models will have lower AED scores. So if for a given locus I have both hint based and ab initio based models, I keep the one that best matches the evidence (lowest AED score). augustus_masked means the genome was masked for repeats before running augustus. Anything with augustus_masked in the second column will be ab initio models kept for reference purposes. Every ab initio model produced by augustus will have an entry there. Thanks, Carson From: Sivaranjani Namasivayam Date: Wednesday, 12 September, 2012 1:53 PM To: Carson Holt , "maker-devel at yandell-lab.org" Subject: RE: [maker-devel] MAKER training I have a few questions based on your comment about augustus/MAKER naming convention. I have been sorting the data using the second column of the GFF file, I wanted to be sure I have it right - Doesn't 'maker' in the second column signify MAKER's final annotations based on all evidence (EST, protein and abinitio prediction) ? I noticed two types of gene IDs, example 1. augustus_masked-scaffold00030-abinit-gene-3.2 2. maker-scaffold00030-augustus-gene-3.7 Is the first one, a direct augustus prediction without a hints file and the second based on a hints file (made from the EST and protein evidence)? If this is the case, could 2 be a better annotation than 1? - In case of augustus_masked in the 2nd column, I believe all are predictions are without a hints file. Thanks, Ranjani From: Carson Holt [carsonhh at gmail.com] Sent: Tuesday, September 11, 2012 12:04 PM To: Sivaranjani Namasivayam; maker-devel at yandell-lab.org Subject: Re: [maker-devel] MAKER training > - I have transcriptome data from 454 and Illumina platforms. Illumina is from > a single time point and 454 from multiple time point. 454 was assembled using > Newbler(dataset 1) and Illumina using Tophat-Cufflinks (dataset 2) and the > denovo Trinity pipeline (dataset 3). I now have3 assemblies - 454 and > Illumina will have some redunant transcripts (because of one overlapping time > point); TopHat-Cufflinks and Trinity will have highly redundant transcripts > (because they use same raw reads). Is it OK to provide all 3 datasets as EST > evidence, how does it affect the quality of annotation. (For now I have used > dataset 1 and dataset 2 as EST evidence) This is fine. You can give them as a comma separated list est=file1,file2,file3 > - I used the above model to retrain, I passed through everything except the > abinitio gene predictions. I also provided a set a manually annotated genes , > many of which have EST evidence. Is this OK to do? [ For proteins evidence, I > gave a set from related organisms, same as above] > > - In my third retraining, I used the above retrained model, but this time I > only provided the genome_gff but did not pass through any other data. However > I did provide the manually annotated genes as EST evidence and related > proteins as protein_evidence. > > Can you please give me some advice on which of these could give me the best > prediction, or if I can alter something to get a better prediction. > Everything you've done sounds reasonable. Better training comes from having the most correct models to train with, so providing the manual annotations as training works, or you can also select MAKER models with the lowest AED score (i.e. models that most closely match evidence). The goal is to try and make the process as unbias as possible, so a consistent usually automated selection method is often the easiest to justify justifiable. > > - A quick question about Augustus - I used a Augustus model (trained for a > closely related organism) for ab-initio prediction. Does MAKER adjust this > model based on the evidence provided, or use the model as such for a > prediction. MAKER will provide hints to Augustus during the run to make it perform better. MAKER will report the raw unaided augustus results in the GFF3 file as a reference, but will use evidence to improve performance where it can. The gene name will let you know if it is a hint based or ab initio model prediction. When 'maker', is part of the gene name it is hint based. Thanks, Carson -------------- next part -------------- An HTML attachment was scrubbed... URL: From guoyunfei1989 at gmail.com Wed Sep 19 11:41:40 2012 From: guoyunfei1989 at gmail.com (Yunfei Guo) Date: Wed, 19 Sep 2012 09:41:40 -0700 Subject: [maker-devel] open3: fork failed: Cannot allocate memory Message-ID: Hi Carson, Sorry to bother you again because I really can't find a solution to it. Have you seen this error before? I simply started multiple jobs in the same directory and got the following msg after hours of running. >From Admin: "Your batch job 2511011 encountered the following error: open3: fork failed: Cannot allocate memory ERROR: Failed while polishig ESTs ERROR: Chunk failed at level:2, tier_type:2 FAILED CONTIG:scaffold740 It continued generating errors in a loop until the /var filesystem filled. I will cancel the job. You may find it useful within your job script to check for errors and exit if present." And this is not because of lack of memory since this job has exclusive access to the node. Let me know if you want the entire stderr file. Thanks. From carsonhh at gmail.com Fri Sep 21 08:28:34 2012 From: carsonhh at gmail.com (Carson Holt) Date: Fri, 21 Sep 2012 09:28:34 -0400 Subject: [maker-devel] open3: fork failed: Cannot allocate memory In-Reply-To: Message-ID: Exclusive access doesn't necessarily mean that memory is not full, especially if you are running via MPI. Under MPI each MAKER instance will have a separate memory footprint (the sum of which may be too high for your system). You can lower the memory footprint per instance by setting all the blast_depth options in the maker_bopt.ctl file. Set them to 30 for example. Also in you have set max_dna_len to a value greater than 100000, bring it back down. A value of 200000 for example will cause MAEKR to use twice as much memory as 100000. The primary cause of high memory is too much evidence aligning in a region. Setting the depth parameter to 30 will cause MAKER to sort the alignments as they come in and drop all but the best 30 alignments. Each instance of MAKER will usually take up 500Mb to 1Gb of RAM when max_dna_len is set to 100,000. It will take up twice that when max_dna_len is set to 200,000. Alternatively, if you are also using MPI, you can set the job up to launch fewer instances of MAKER, but allow each instance to use more CPUs. You do this by halving the value of the -n option given to mpiexec and then setting cpus=2 in the maker_opts file. The result in that BLAST analyses will run on 2 cpus each but MAKER will only keep the results for 6 jobs in memory at a time rather than 12 jobs (I.e. Lower memory footprint). When using this technique, make sure the hostfile used by mpiexec is set to follow a round robin distribution or all instances will start on half your nodes while the other half of your nodes will be left idle. Example - this is correct: host1 host2 host3 host1 host2 host3 host1 host2 host3 This is incorrect: host1 host1 host1 host2 host2 host2 host3 host3 host3 FYI when using MPI the -n parameter given to mpiexec and the -cpus parameter given to MAKER have a multiplicative affect on CPU usage. Example: mpiexec -n 12 maker -cpus 1 (will launch 12 maker instances and use a total of 12 cpus) mpiexec -n 12 maker -cpus 2 (will launch 12 maker instances but use a total of 24 cpus) mpiexec -n 6 maker -cpus 4 (will launch 6 maker instances but use a total of 24 cpus) Why is this? It's because CPUs affects how many processors to use to solve a single 100,000 bp chunk (per instance). But mpiexec -n sets how many simultaneous instances and as a result how many chunks to run together. So mpiexec -n will cause memory usage to increase in a way that -cpus doesn't. But mpiexec also scales across machines for parallelization where -cpus can't (it's use applies to a single machine). Thanks, Carson On 12-09-19 12:41 PM, "Yunfei Guo" wrote: >Hi Carson, > >Sorry to bother you again because I really can't find a solution to >it. Have you seen this error before? I simply started multiple jobs in >the same directory and got the following msg after hours of running. > >From Admin: >"Your batch job 2511011 encountered the following error: > open3: fork failed: Cannot allocate memory > ERROR: Failed while polishig ESTs > ERROR: Chunk failed at level:2, tier_type:2 > FAILED CONTIG:scaffold740 >It continued generating errors in a loop until the /var filesystem filled. >I will cancel the job. You may find it useful within your job script to >check for errors and exit if present." > >And this is not because of lack of memory since this job has exclusive >access to the node. Let me know if you want the entire stderr file. >Thanks. > >_______________________________________________ >maker-devel mailing list >maker-devel at box290.bluehost.com >http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org From fourie.joubert at up.ac.za Fri Sep 21 08:58:26 2012 From: fourie.joubert at up.ac.za (Fourie Joubert) Date: Fri, 21 Sep 2012 15:58:26 +0200 Subject: [maker-devel] Problems parsing iprscan results with iprscan2gff3 Message-ID: <505C7282.3090107@up.ac.za> Hi Folks I am running into some problems parsing iprscan results. I run iprscan as follows: > iprscan -cli -i bot.all.maker.proteins.fasta -o bot.all.maker.proteins.raw -format raw -goterms -iprlookup and obtain the iprscan output (the iprscan output file is at http://www.bi.up.ac.za/~fourie/bot.all.maker.proteins.raw if anyone is interested in the detailed output, and the initial maker gff3 file is at http://www.bi.up.ac.za/~fourie/bot.all.gff). I then try to run the conversion to gff3, but I get very long list of errors: > iprscan2gff3 bot.all.maker.proteins.raw bot.all.gff > domains.gff ERROR: In maker-NODE_4797_length_138874_cov_96.632576-augustus-gene-0.113 Use of uninitialized value $seqid in concatenation (.) or string at /usr/local/maker/bin/iprscan2gff3 line 255. Use of uninitialized value $start in concatenation (.) or string at /usr/local/maker/bin/iprscan2gff3 line 255. Use of uninitialized value $end in concatenation (.) or string at /usr/local/maker/bin/iprscan2gff3 line 255. Use of uninitialized value $strand in concatenation (.) or string at /usr/local/maker/bin/iprscan2gff3 line 255. Use of uninitialized value $off in subtraction (-) at /usr/local/maker/bin/iprscan2gff3 line 267. Use of uninitialized value $pB in subtraction (-) at /usr/local/maker/bin/iprscan2gff3 line 267. Use of uninitialized value $off in subtraction (-) at /usr/local/maker/bin/iprscan2gff3 line 267. Use of uninitialized value $pE in subtraction (-) at /usr/local/maker/bin/iprscan2gff3 line 267. Use of uninitialized value $seqid in concatenation (.) or string at /usr/local/maker/bin/iprscan2gff3 line 269. Use of uninitialized value $start in concatenation (.) or string at /usr/local/maker/bin/iprscan2gff3 line 269. Use of uninitialized value $end in concatenation (.) or string at /usr/local/maker/bin/iprscan2gff3 line 269. Use of uninitialized value $strand in concatenation (.) or string at /usr/local/maker/bin/iprscan2gff3 line 269. ....... ....... ....... for most of the entries. Any advice or help would be sincerely appreciated! Best regards! Fourie -- -------------- Prof Fourie Joubert Bioinformatics and Computational Biology Unit Department of Biochemistry University of Pretoria fourie.joubert at up.ac.za http://www.bi.up.ac.za Tel. +27-12-420-5825 Fax. +27-12-420-5800 ------------------------------------------------------------------------- This message and attachments are subject to a disclaimer. Please refer to www.it.up.ac.za/documentation/governance/disclaimer/ for full details. -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Fri Sep 21 09:10:21 2012 From: carsonhh at gmail.com (Carson Holt) Date: Fri, 21 Sep 2012 10:10:21 -0400 Subject: [maker-devel] Problems parsing iprscan results with iprscan2gff3 In-Reply-To: <505C7282.3090107@up.ac.za> Message-ID: Some of your iprscan results contain truncated names Example: maker-NODE_5172_length_118591_cov_102.277115-snap-gene-0.100-mR This seems to be the case for almost all HMMPanther and HMMSmart results. Try just removing those two groups of results from your file for now. Then use the iprscan_wrap script that comes with maker to just re-run just those two application within iprscan it will fix the truncation issue (it creates temporary short names and then converts back to the longer names when it parses the results). Thanks, Carson From: Fourie Joubert Date: Friday, 21 September, 2012 9:58 AM To: "maker-devel at yandell-lab.org" Subject: [maker-devel] Problems parsing iprscan results with iprscan2gff3 Hi Folks I am running into some problems parsing iprscan results. I run iprscan as follows: > iprscan -cli -i bot.all.maker.proteins.fasta -o bot.all.maker.proteins.raw -format raw -goterms -iprlookup and obtain the iprscan output (the iprscan output file is at http://www.bi.up.ac.za/~fourie/bot.all.maker.proteins.raw if anyone is interested in the detailed output, and the initial maker gff3 file is at http://www.bi.up.ac.za/~fourie/bot.all.gff). I then try to run the conversion to gff3, but I get very long list of errors: > iprscan2gff3 bot.all.maker.proteins.raw bot.all.gff > domains.gff ERROR: In maker-NODE_4797_length_138874_cov_96.632576-augustus-gene-0.113 Use of uninitialized value $seqid in concatenation (.) or string at /usr/local/maker/bin/iprscan2gff3 line 255. Use of uninitialized value $start in concatenation (.) or string at /usr/local/maker/bin/iprscan2gff3 line 255. Use of uninitialized value $end in concatenation (.) or string at /usr/local/maker/bin/iprscan2gff3 line 255. Use of uninitialized value $strand in concatenation (.) or string at /usr/local/maker/bin/iprscan2gff3 line 255. Use of uninitialized value $off in subtraction (-) at /usr/local/maker/bin/iprscan2gff3 line 267. Use of uninitialized value $pB in subtraction (-) at /usr/local/maker/bin/iprscan2gff3 line 267. Use of uninitialized value $off in subtraction (-) at /usr/local/maker/bin/iprscan2gff3 line 267. Use of uninitialized value $pE in subtraction (-) at /usr/local/maker/bin/iprscan2gff3 line 267. Use of uninitialized value $seqid in concatenation (.) or string at /usr/local/maker/bin/iprscan2gff3 line 269. Use of uninitialized value $start in concatenation (.) or string at /usr/local/maker/bin/iprscan2gff3 line 269. Use of uninitialized value $end in concatenation (.) or string at /usr/local/maker/bin/iprscan2gff3 line 269. Use of uninitialized value $strand in concatenation (.) or string at /usr/local/maker/bin/iprscan2gff3 line 269. ....... ....... ....... for most of the entries. Any advice or help would be sincerely appreciated! Best regards! Fourie -- -------------- Prof Fourie Joubert Bioinformatics and Computational Biology Unit Department of Biochemistry University of Pretoria fourie.joubert at up.ac.zahttp://www.bi.up.ac.za Tel. +27-12-420-5825 Fax. +27-12-420-5800 ------------------------------------------------------------------------- This message and attachments are subject to a disclaimer. Please refer to www.it.up.ac.za/documentation/governance/disclaimer/ for full details. _______________________________________________ maker-devel mailing list maker-devel at box290.bluehost.com http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org -------------- next part -------------- An HTML attachment was scrubbed... URL: From jeremy.semeiks at utsw.edu Fri Sep 21 10:39:15 2012 From: jeremy.semeiks at utsw.edu (Jeremy Semeiks) Date: Fri, 21 Sep 2012 10:39:15 -0500 Subject: [maker-devel] How to preserve human-friendly IDs when reannotating In-Reply-To: References: Message-ID: For the record: After analyzing these runs, I have confirmed that neither error I described (ie, "DBD::SQLite::db do failed" and "Warning: unable to close filehandle DF properly") affects maker's protein output in any way I can detect. Thanks, J On Thu, Sep 13, 2012 at 8:11 AM, Carson Holt wrote: > The error --> DBD::SQLite::db do failed: database is locked at > /home/jrs/maker-2.26-beta/bin/../lib/GFFDB.pm line 186. > > The location of the specific error you are getting is probably benign. It > is a failure to alter the default cache size for the database. The > database should already be populated. I'm planning removing the SQLlite > database entirely in the future. Perhaps in favor of something like tabix > based indexing of the GFF3 file. > > Thanks, > Carson > > > > From: Jeremy Semeiks > Date: Tuesday, 11 September, 2012 7:56 PM > > To: Carson Holt > Cc: > Subject: Re: [maker-devel] How to preserve human-friendly IDs when > reannotating > > maker 2.26. > > And I have verified for myself that the three options I mentioned below > suffice to preserve human-friendly IDs when reannotating. > > Thanks, > J > > On Tue, Sep 11, 2012 at 3:33 PM, Carson Holt wrote: > >> Which version of MAKER are you running (maker --version)? >> >> --Carson >> >> >> >> From: Jeremy Semeiks >> Date: Monday, 10 September, 2012 11:02 AM >> To: Carson Holt >> Cc: >> Subject: Re: [maker-devel] How to preserve human-friendly IDs when >> reannotating >> >> OK, thanks. So if I understand correctly, to preserve human-friendly IDs >> requires setting just three options: map_forward=1, >> maker_gff=, and model_pass=1. (Or instead of the >> last two I could equivalently just set model_gff to a GFF containing only >> models.) >> >> A couple new issues came up when I tried to run with these options. I >> started maker like this: >> >> /usr/bin/time mpiexec -n 10 maker -q < /dev/null > maker.oe 2>&1 >> >> 1. I get a bunch of messages as follows, but with variable line number: >> >> DBD::SQLite::db do failed: database is locked at >> /home/jrs/maker-2.26-beta/bin/../lib/GFFDB.pm line 186. >> >> I saw that this came up in another thread < >> https://groups.google.com/forum/?fromgroups=#!topic/maker-devel/TscBgbQfBX4>, >> but I'm not sure it was ever resolved, nor whether it will affect my >> reannotation results (as I'm not sure what "your GFF3 results will not be >> integrated" means). This error did not come up the last time I ran maker >> for reannotation with similar options in a different directory. And both my >> current directory and my tmp directory are locally mounted, ie not NFS. >> >> 2. Both in this run and in previous runs, I get a lot of lines like this, >> seemingly at random: >> >> Warning: unable to close filehandle DF properly. >> >> >> On Mon, Sep 10, 2012 at 6:01 AM, Carson Holt wrote: >> >>> The map_forward option requires that the pass option for the gene models >>> be turned on. Otherwise you will have to do some spacial overlap test >>> outside of MAKER. >>> >>> If you have a new assembly, you can try mapping the old models onto the >>> new assembly using the old transcripts as input to the est= and setting >>> est2genome=1 (nothing else set, i.e no repeat masking etc.). Then there is >>> an undocumented option that is still a little buggy (hence why it is still >>> undocumented). Add the line est_forward=1 to your control files. This >>> tells MAKER to copy names from the ESTs, build the models directly from >>> their alignment, and to do other things to try and make a 1 to 1 match >>> across the genome. You will have to manually check that it is 1 to 1 in >>> the end (as I said still a little buggy and hence undocumented). Use the >>> resulting file as input to the model_gff option on a separate run with >>> map_forward=1 for additional reannotation wil more evidence, etc. where you >>> want to still be able to map names forward. >>> >>> From: Jeremy Semeiks >>> Date: Sunday, 9 September, 2012 3:49 PM >>> To: >>> Subject: [maker-devel] How to preserve human-friendly IDs when >>> reannotating >>> >>> Hi all, >>> >>> I have sequenced some novel fungal genomes, and I am annotating them >>> with maker-2.26-beta. The entire project is pretty iterative, in the sense >>> that I first get some seemingly-sane annotation sets, then analyze and >>> compare the proteomes biologically, then reannotate when new data comes in >>> or as I learn more about how maker works. Because I have already attached >>> biological meaning to some of my proteins, I would like to retain the same >>> human-friendly IDs across annotations. Eg, if maker suddenly finds 1,000 >>> new proteins on a reannotation run because I turned on keep_preds, then I >>> don't want the transcript formerly known as mymold_09652T0 to become >>> mymold_10698T0 when I run maker_map_ids; I want to keep it named >>> mymold_09652T0. >>> >>> So, is there any built-in way to preserve human-friendly IDs, or do I >>> need to write my own script for this? I have tried setting map_forward=1 >>> and maker_gff=, >>> but setting these seems to preserve neither the human-friendly IDs nor even >>> the original IDs. (Eg, protein >>> "genemark-scaffold353-processed-gene-0.9-mRNA-1" changed its name to >>> "genemark-scaffold353-processed-gene-0.6-mRNA-1" when reannotated.) I >>> haven't turned on any of the *_pass options, eg protein_pass; would this be >>> relevant? >>> >>> Extra credit question: I am making some mate-pair libraries for these >>> fungi; when I re-assemble, that will completely change my scaffold names. >>> Is there any easy way to preserve human-friendly transcript names in this >>> case? As with the above simpler case, I think it would be pretty easy to >>> transfer 90% of the names just by doing an all-vs-all blastp between two >>> annotation sets and fishing out the best hits, but the remaining 10% might >>> be a headache. >>> >>> Thanks, >>> Jeremy >>> Grad student, Grishin lab >>> UT Southwestern, Dallas TX >>> 510.385.8959 >>> _______________________________________________ maker-devel mailing list >>> maker-devel at box290.bluehost.com >>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org >>> >> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Fri Sep 21 10:42:46 2012 From: carsonhh at gmail.com (Carson Holt) Date: Fri, 21 Sep 2012 11:42:46 -0400 Subject: [maker-devel] How to preserve human-friendly IDs when reannotating In-Reply-To: Message-ID: That's good to know :-) --Carson From: Jeremy Semeiks Date: Friday, 21 September, 2012 11:39 AM To: Carson Holt Cc: Subject: Re: [maker-devel] How to preserve human-friendly IDs when reannotating For the record: After analyzing these runs, I have confirmed that neither error I described (ie, "DBD::SQLite::db do failed" and "Warning: unable to close filehandle DF properly") affects maker's protein output in any way I can detect. Thanks, J On Thu, Sep 13, 2012 at 8:11 AM, Carson Holt wrote: > The error --> DBD::SQLite::db do failed: database is locked at > /home/jrs/maker-2.26-beta/bin/../lib/GFFDB.pm line 186. > > The location of the specific error you are getting is probably benign. It is > a failure to alter the default cache size for the database. The database > should already be populated. I'm planning removing the SQLlite database > entirely in the future. Perhaps in favor of something like tabix based > indexing of the GFF3 file. > > Thanks, > Carson > > > > From: Jeremy Semeiks > Date: Tuesday, 11 September, 2012 7:56 PM > > To: Carson Holt > Cc: > Subject: Re: [maker-devel] How to preserve human-friendly IDs when > reannotating > > maker 2.26. > > And I have verified for myself that the three options I mentioned below > suffice to preserve human-friendly IDs when reannotating. > > Thanks, > J > > On Tue, Sep 11, 2012 at 3:33 PM, Carson Holt wrote: >> Which version of MAKER are you running (maker --version)? >> >> --Carson >> >> >> >> From: Jeremy Semeiks >> Date: Monday, 10 September, 2012 11:02 AM >> To: Carson Holt >> Cc: >> Subject: Re: [maker-devel] How to preserve human-friendly IDs when >> reannotating >> >> OK, thanks. So if I understand correctly, to preserve human-friendly IDs >> requires setting just three options: map_forward=1, >> maker_gff=, and model_pass=1. (Or instead of the last >> two I could equivalently just set model_gff to a GFF containing only models.) >> >> A couple new issues came up when I tried to run with these options. I started >> maker like this: >> >> /usr/bin/time mpiexec -n 10 maker -q < /dev/null > maker.oe 2>&1 >> >> 1. I get a bunch of messages as follows, but with variable line number: >> >> DBD::SQLite::db do failed: database is locked at >> /home/jrs/maker-2.26-beta/bin/../lib/GFFDB.pm line 186. >> >> I saw that this came up in another thread >> >> , but I'm not sure it was ever resolved, nor whether it will affect my >> reannotation results (as I'm not sure what "your GFF3 results will not be >> integrated" means). This error did not come up the last time I ran maker for >> reannotation with similar options in a different directory. And both my >> current directory and my tmp directory are locally mounted, ie not NFS. >> >> 2. Both in this run and in previous runs, I get a lot of lines like this, >> seemingly at random: >> >> Warning: unable to close filehandle DF properly. >> >> >> On Mon, Sep 10, 2012 at 6:01 AM, Carson Holt wrote: >>> The map_forward option requires that the pass option for the gene models be >>> turned on. Otherwise you will have to do some spacial overlap test outside >>> of MAKER. >>> >>> If you have a new assembly, you can try mapping the old models onto the new >>> assembly using the old transcripts as input to the est= and setting >>> est2genome=1 (nothing else set, i.e no repeat masking etc.). Then there is >>> an undocumented option that is still a little buggy (hence why it is still >>> undocumented). Add the line est_forward=1 to your control files. This >>> tells MAKER to copy names from the ESTs, build the models directly from >>> their alignment, and to do other things to try and make a 1 to 1 match >>> across the genome. You will have to manually check that it is 1 to 1 in the >>> end (as I said still a little buggy and hence undocumented). Use the >>> resulting file as input to the model_gff option on a separate run with >>> map_forward=1 for additional reannotation wil more evidence, etc. where you >>> want to still be able to map names forward. >>> >>> From: Jeremy Semeiks >>> Date: Sunday, 9 September, 2012 3:49 PM >>> To: >>> Subject: [maker-devel] How to preserve human-friendly IDs when reannotating >>> >>> Hi all, >>> >>> I have sequenced some novel fungal genomes, and I am annotating them with >>> maker-2.26-beta. The entire project is pretty iterative, in the sense that I >>> first get some seemingly-sane annotation sets, then analyze and compare the >>> proteomes biologically, then reannotate when new data comes in or as I learn >>> more about how maker works. Because I have already attached biological >>> meaning to some of my proteins, I would like to retain the same >>> human-friendly IDs across annotations. Eg, if maker suddenly finds 1,000 new >>> proteins on a reannotation run because I turned on keep_preds, then I don't >>> want the transcript formerly known as mymold_09652T0 to become >>> mymold_10698T0 when I run maker_map_ids; I want to keep it named >>> mymold_09652T0. >>> >>> So, is there any built-in way to preserve human-friendly IDs, or do I need >>> to write my own script for this? I have tried setting map_forward=1 and >>> maker_gff=, but >>> setting these seems to preserve neither the human-friendly IDs nor even the >>> original IDs. (Eg, protein "genemark-scaffold353-processed-gene-0.9-mRNA-1" >>> changed its name to "genemark-scaffold353-processed-gene-0.6-mRNA-1" when >>> reannotated.) I haven't turned on any of the *_pass options, eg >>> protein_pass; would this be relevant? >>> >>> Extra credit question: I am making some mate-pair libraries for these fungi; >>> when I re-assemble, that will completely change my scaffold names. Is there >>> any easy way to preserve human-friendly transcript names in this case? As >>> with the above simpler case, I think it would be pretty easy to transfer 90% >>> of the names just by doing an all-vs-all blastp between two annotation sets >>> and fishing out the best hits, but the remaining 10% might be a headache. >>> >>> Thanks, >>> Jeremy >>> Grad student, Grishin lab >>> UT Southwestern, Dallas TX >>> 510.385.8959 >>> _______________________________________________ maker-devel mailing list >>> maker-devel at box290.bluehost.comhttp://box290.bluehost.com/mailman/listinfo/m >>> aker-devel_yandell-lab.org >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From ianmisner17 at aim.com Tue Sep 25 07:27:04 2012 From: ianmisner17 at aim.com (Ian Misner) Date: Tue, 25 Sep 2012 08:27:04 -0400 Subject: [maker-devel] problem with maker_map_ids Message-ID: Hello, I'm trying to create human friendly ids and I'm getting an error when I use the -sort_file option. Without the sort file it runs fine just not numbered from the first contig. I have had some programers at our cluster look at the script and they attempted a fix but it did not work. They mentioned the script was "buggy" so this might be part of the problem. I've attached the error as well as the sort file. I can send more files if necessary. Thanks for you time. Cheers Ian $ maker_map_ids --prefix THRCLA_ --justify 5 --sort_order 34112_sort.txt 34112_3June11Ass.gff > 34112_3June11Ass_named.txt Can't use string ("34112_sort.txt") as a HASH ref while "strict refs" in use at /gpfs/runtime/opt/maker/2.10/maker/bin/maker_map_ids line 311, <$IN> line 499186. -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: 34112_sort.txt URL: From ianmisner at my.uri.edu Tue Sep 25 07:31:23 2012 From: ianmisner at my.uri.edu (Ian Misner) Date: Tue, 25 Sep 2012 08:31:23 -0400 Subject: [maker-devel] Problem with maker_map_ids Message-ID: <0FCB8ACD-35A0-4ED8-BAE2-02C2621E3F65@my.uri.edu> Hello, I'm trying to create human friendly ids and I'm getting an error when I use the -sort_file option. Without the sort file it runs fine just not numbered from the first contig. I have had some programers at our cluster look at the script and they attempted a fix but it did not work. They mentioned the script was "buggy" so this might be part of the problem. I've attached the error as well as the sort file. I can send more files if necessary. Thanks for you time. Cheers Ian $ maker_map_ids --prefix THRCLA_ --justify 5 --sort_order 34112_sort.txt 34112_3June11Ass.gff > 34112_3June11Ass_named.txt Can't use string ("34112_sort.txt") as a HASH ref while "strict refs" in use at /gpfs/runtime/opt/maker/2.10/maker/bin/maker_map_ids line 311, <$IN> line 499186. -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: 34112_sort.txt URL: From carsonhh at gmail.com Tue Sep 25 07:44:02 2012 From: carsonhh at gmail.com (Carson Holt) Date: Tue, 25 Sep 2012 08:44:02 -0400 Subject: [maker-devel] Problem with maker_map_ids In-Reply-To: <0FCB8ACD-35A0-4ED8-BAE2-02C2621E3F65@my.uri.edu> Message-ID: Could you also provide 34112_3June11Ass.gff? Thanks, Carson On 12-09-25 8:31 AM, "Ian Misner" wrote: >Hello, > >I'm trying to create human friendly ids and I'm getting an error when I >use the -sort_file option. Without the sort file it runs fine just not >numbered from the first contig. I have had some programers at our cluster >look at the script and they attempted a fix but it did not work. They >mentioned the script was "buggy" so this might be part of the problem. >I've attached the error as well as the sort file. I can send more files >if necessary. Thanks for you time. > >Cheers >Ian > >$ maker_map_ids --prefix THRCLA_ --justify 5 --sort_order 34112_sort.txt >34112_3June11Ass.gff > 34112_3June11Ass_named.txt >Can't use string ("34112_sort.txt") as a HASH ref while "strict refs" in >use at /gpfs/runtime/opt/maker/2.10/maker/bin/maker_map_ids line 311, ><$IN> line 499186._______________________________________________ >maker-devel mailing list >maker-devel at box290.bluehost.com >http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org From carsonhh at gmail.com Tue Sep 25 08:01:31 2012 From: carsonhh at gmail.com (Carson Holt) Date: Tue, 25 Sep 2012 09:01:31 -0400 Subject: [maker-devel] Problem with maker_map_ids In-Reply-To: Message-ID: While you are sending me the GFF3 file also try the sort order file attached. I found a number of illegal meta character contaminating the file. Sometimes those can be introduced by text editors or sometimes e-mail clients. In case it wasn't the e-mail client I'm sending you this fixed version. Also I see you are using maker_map_ids from version 2.10. Try the 2.26 version. They are different. Thanks, Carson On 12-09-25 8:44 AM, "Carson Holt" wrote: >Could you also provide 34112_3June11Ass.gff? > >Thanks, >Carson > > >On 12-09-25 8:31 AM, "Ian Misner" wrote: > >>Hello, >> >>I'm trying to create human friendly ids and I'm getting an error when I >>use the -sort_file option. Without the sort file it runs fine just not >>numbered from the first contig. I have had some programers at our >>cluster >>look at the script and they attempted a fix but it did not work. They >>mentioned the script was "buggy" so this might be part of the problem. >>I've attached the error as well as the sort file. I can send more files >>if necessary. Thanks for you time. >> >>Cheers >>Ian >> >>$ maker_map_ids --prefix THRCLA_ --justify 5 --sort_order 34112_sort.txt >>34112_3June11Ass.gff > 34112_3June11Ass_named.txt >>Can't use string ("34112_sort.txt") as a HASH ref while "strict refs" in >>use at /gpfs/runtime/opt/maker/2.10/maker/bin/maker_map_ids line 311, >><$IN> line 499186._______________________________________________ >>maker-devel mailing list >>maker-devel at box290.bluehost.com >>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org -------------- next part -------------- A non-text attachment was scrubbed... Name: 34112_sort.txt.gz Type: application/x-gzip Size: 27598 bytes Desc: not available URL: From carsonhh at gmail.com Tue Sep 25 08:13:54 2012 From: carsonhh at gmail.com (Carson Holt) Date: Tue, 25 Sep 2012 09:13:54 -0400 Subject: [maker-devel] Problem with maker_map_ids In-Reply-To: Message-ID: Thanks for the GFF3 file. The meta character came across in the GFF3 as well, so I think it's safe to assume they are being introduced by the e-mail client used to add the attachment (so ignore the last file I sent). I've attached the fixed maker_map_ids. Thanks, Carson On 12-09-25 9:01 AM, "Carson Holt" wrote: >While you are sending me the GFF3 file also try the sort order file >attached. I found a number of illegal meta character contaminating the >file. Sometimes those can be introduced by text editors or sometimes >e-mail clients. In case it wasn't the e-mail client I'm sending you this >fixed version. > >Also I see you are using maker_map_ids from version 2.10. Try the 2.26 >version. They are different. > >Thanks, >Carson > > >On 12-09-25 8:44 AM, "Carson Holt" wrote: > >>Could you also provide 34112_3June11Ass.gff? >> >>Thanks, >>Carson >> >> >>On 12-09-25 8:31 AM, "Ian Misner" wrote: >> >>>Hello, >>> >>>I'm trying to create human friendly ids and I'm getting an error when I >>>use the -sort_file option. Without the sort file it runs fine just not >>>numbered from the first contig. I have had some programers at our >>>cluster >>>look at the script and they attempted a fix but it did not work. They >>>mentioned the script was "buggy" so this might be part of the problem. >>>I've attached the error as well as the sort file. I can send more files >>>if necessary. Thanks for you time. >>> >>>Cheers >>>Ian >>> >>>$ maker_map_ids --prefix THRCLA_ --justify 5 --sort_order >>>34112_sort.txt >>>34112_3June11Ass.gff > 34112_3June11Ass_named.txt >>>Can't use string ("34112_sort.txt") as a HASH ref while "strict refs" >>>in >>>use at /gpfs/runtime/opt/maker/2.10/maker/bin/maker_map_ids line 311, >>><$IN> line 499186._______________________________________________ >>>maker-devel mailing list >>>maker-devel at box290.bluehost.com >>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org -------------- next part -------------- A non-text attachment was scrubbed... Name: maker_map_ids.gz Type: application/x-gzip Size: 3216 bytes Desc: not available URL: From fourie.joubert at up.ac.za Thu Sep 27 09:37:53 2012 From: fourie.joubert at up.ac.za (Fourie Joubert) Date: Thu, 27 Sep 2012 16:37:53 +0200 Subject: [maker-devel] Problem with maker2chado Message-ID: <506464C1.40103@up.ac.za> Hi I am trying to load a maker gff file into chado using maker2chado, but I am seeing the following type of error: Can't locate object method "value" via package "NODE_1002_length_51300_cov_98.972473" (perhaps you forgot to load "NODE_1002_length_51300_cov_98.972473"?) at /usr/local/bin/gmod_bulk_load_gff3.pl line 722, line 2. Any advice would be sincerely appreciated! Best regards! Fourie -- -------------- Prof Fourie Joubert Bioinformatics and Computational Biology Unit Department of Biochemistry University of Pretoria fourie.joubert at up.ac.za http://www.bi.up.ac.za Tel. +27-12-420-5825 Fax. +27-12-420-5800 ------------------------------------------------------------------------- This message and attachments are subject to a disclaimer. Please refer to www.it.up.ac.za/documentation/governance/disclaimer/ for full details. From carsonhh at gmail.com Thu Sep 27 11:27:14 2012 From: carsonhh at gmail.com (Carson Holt) Date: Thu, 27 Sep 2012 12:27:14 -0400 Subject: [maker-devel] Problem with maker2chado In-Reply-To: <506464C1.40103@up.ac.za> Message-ID: The error is being thrown by /usr/local/bin/gmod_bulk_load_gff3.pl It is called by MAKER and is part of the chado install. Try getting the latest version of chado from the SVN repository and then reinstalling it. Command to use --> svn co https://gmod.svn.sourceforge.net/svnroot/gmod/schema/trunk chado --Carson On 12-09-27 10:37 AM, "Fourie Joubert" wrote: >Hi > >I am trying to load a maker gff file into chado using maker2chado, but I >am seeing the following type of error: > >Can't locate object method "value" via package >"NODE_1002_length_51300_cov_98.972473" (perhaps you forgot to load >"NODE_1002_length_51300_cov_98.972473"?) at >/usr/local/bin/gmod_bulk_load_gff3.pl line 722, line 2. > >Any advice would be sincerely appreciated! > >Best regards! > >Fourie > >-- >-------------- >Prof Fourie Joubert >Bioinformatics and Computational Biology Unit >Department of Biochemistry >University of Pretoria >fourie.joubert at up.ac.za >http://www.bi.up.ac.za >Tel. +27-12-420-5825 >Fax. +27-12-420-5800 > >------------------------------------------------------------------------- >This message and attachments are subject to a disclaimer. Please refer >to www.it.up.ac.za/documentation/governance/disclaimer/ for full details. > > >_______________________________________________ >maker-devel mailing list >maker-devel at box290.bluehost.com >http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org From mike.thon at gmail.com Tue Sep 4 02:59:06 2012 From: mike.thon at gmail.com (Michael Thon) Date: Tue, 4 Sep 2012 10:59:06 +0200 Subject: [maker-devel] model_gff not in output Message-ID: <1A01E0C5-E60A-42AA-BD7B-A6429F435645@gmail.com> I'm using maker to update a legacy annotation. As input I'm using RNA-Seq aligned with cufflinks, ESTs, provided in fasta format, and proteins downloaded from UniProt.SwissProt. I have done two runs of maker so far. The first one using the legacy annotations in both the model_gff and pred_gff parameters. In the second run I used the legacy annotations in model_gff and in pred_gff I included gene models created with GeneMark-ES. In both runs 1 and 2 I have found two genes (so far) that exist in the legacy annotations but are not in the final gene models output by maker. Both genes have overlapping cufflinks annotations, in addition to having annotations in model_gff. I thought maker was supposed to keep all the annotations in model_gff, only replacing ones in which it could find an alternative model with better support. Is there any case in which is will remove a model? Another discrepency I found in run1 is a gene that maker 'moved' upstream approx. 150 bases. The gene locus annotated by maker covers the original annotation, but the CDS does not. The site of the original CDS is covered by an annotation in model_gff, pred_gff, two ESTs and a cufflinks annotation. Maker still seems to have moved is is upstream where it only has an overlapping cufflinks annotation. the three-prime utr annotated by cufflinks still covers the legacy annotation though. Here's a link to download the maker gff file I'm looking at: https://dl.dropbox.com/u/320712/supercont1%252E1.gff.zip The genes that are in the legacy annotation but missing in the maker annotation are: GLRG_00074 and GLRG_00092 the 'moved' gene model I described is model GLRG_00081. they all within the first 350 K of sequence. mike From chrisi.hahni at gmail.com Wed Sep 5 05:59:48 2012 From: chrisi.hahni at gmail.com (Christoph Hahn) Date: Wed, 05 Sep 2012 13:59:48 +0200 Subject: [maker-devel] keep_preds option? In-Reply-To: References: Message-ID: <50473EB4.7070501@gmail.com> Hello Barry and Carson, Thank you very much for the extensive replies!! Very helpful!! > > 2. I tried to use EST data of an alternative organism in altest= > (#EST/cDNA sequence file in fasta format from an alternate organism). > The organism is quite distantly related, but its the closest I have so > I thought I d give it a shot. I ran maker twice with identical settigs > expect in altest and est2genome=0/1. The number of genes predicted is > identical with both approaches, so I am not sure whether or not the > EST data was actually used or its just to distantly related. Any easy > way to assess this? > Typically EST evidence from another organism with alt_est will add little in the way of additional support (compared to just using protein evidence from say Swiss-prot) and this would be especially true if your alt_est is > distantly related. I'm not sure I really understand you alt_est/est2genome combo's to comment in more detail. I could see four possible combinations there: which two gave identical results? What I meant was that I ran maker once without any alt_est evidence and est2genome=0 and a second time with alt_est=some.fasta and est2genome=1. The result was the same. Sorry, for not making myself clear enough. I thought that the est2genome=1 switch is is just enabling physical est evidence to be used. Therefore, I thought neither alt_est=some.fasta, est2genome=0 nor alt_est=nothing, est2genome=1 would make any sense. I had misunderstood this. Will follow Carsons advice and will try to use more protein evidence from related species (in addition to uniprot). Running right now - Let s see where that leaves me. The IPRScan approach suggested by Barry to assess gene models without physical evidence sounds very interesting. I will definitely look into that. A question concerning an issue I just discovered: Ran maker twice with the same physical evidence. First time using SNAP and Genemark, second time using SNAP, Genemark and AUGUSTUS (set to the closest related species available - same phylum, different class). Second run gives less gene models. IN another context I found that the second pass of Maker using SNAP and Genemark (after training SNAP on the predictions of the first Pass) and the same physical evidence yields less gene annotations. How can that be given the same physical evidence? Thanks again for your help! It is much appreciated! cheers, Christoph Am 31.08.2012 21:03, schrieb Carson Holt: > I concur with everything Barry said. Also let me add that alt-ESTs do > not get polished around splice sites (exonerate won't handle them). > However ESTs and proteins do. This means that the utility of > alt-ESTs in adding UTR, and splice information is zero. They just > function as an anchor to maintain gene models that might have > otherwise been rejected. This also means alt_est=some.fasta together > with est2genome=1 will produce virtually no additional results because > est2genome requires that the splice site makes sense. You are better > off using proteins with protein2genome=1 if you don't have ESTs and > want partial models for training. Once you have a trained ab initio > gene predictor, turn the est2genome and protein2genome options off. > Otherwise they will give weird partial models that decrease the > quality of your final annotations. (partial models are ok for training > but that's about it). > > If you are getting too low a gene count with keep_preds=0, then you > probably need to add more evidence. Try adding all proteins from a > couple of related species (the protein= option accepts comma separated > lists of files). If your genome is a fungi, oomycete, or a prokaryote, > then setting keep_preds=1 is usually safe. Theses are genomes with > high gene density and simple gene structure, so ab initio predictors > do really well and don't need as much help from the evidence. For > other organisms, leave it set to 0 or you will get a lot of false > positives (false positives on some genomes with complex gene structure > can outnumber the genes by 10 to 1 if you turn this on). > > Thanks, > Carson > > > > > From: Barry Moore > > Date: Friday, 31 August, 2012 12:52 PM > To: Christoph Hahn > > Cc: > > Subject: Re: [maker-devel] keep_preds option? > > Hi Christopher, > > Comments below: > > On Aug 31, 2012, at 6:43 AM, Christoph Hahn wrote: > >> Hello maker users and developers, >> >> I am new to gene prediction and I am trying to use maker 2.25 on a >> newly assembled non-model organisms draft genome. Within maker I use >> genemark, SNAP and Augustus. I have a few questions: >> > > Welcome! > >> 1. I was wondering what the keep_preds option means exactly. >> >> I found two slightly different explanations on the option >> #Add unsupported gene prediction to final annotation set (maker2.25) >> #Add non-overlapping ab-inito gene prediction to final annotation set >> (found on the net - probably older maker version) >> > > It means to keep ab initio gene predictions for which there is no > physical evidence. There are two pieces of information that are > required for every MAKER annotation (by default). MAKER runs the ab > initio gene predictors and aligns transcript (EST/cDNA/mRNASeq > transcripts) and protein sequences to the genome. For each locus > where one or more gene predictions exist MAKER checks to see if there > is any physical evidence for gene expression at that locus > (RNA/protein sequence alignments) and if there is (splice EST or > protein alignments) evidence overlapping the predictions, MAKER > decides which prediction best matches the evidence and promotes that > prediction to an annotation. If there is no evidence overlapping any > of the predictions then those predictions are not included in the > output annotation file (although they are saved). If you set > keep_preds=1 then for each locus where prediction(s) exist maker keeps > one and promotes it to an annotation even though there is no physical > evidence. The description of 'non-overlapping ab-initio' means that > MAKER has clustered all ab-initio predictions at one locus and chose > one representative transcript to output. > >> As far as I understood keep_preds=0 only retains gene models for >> which the ab initio predictions agree. But how many, all three? two >> of three? >> keep_preds=1 instead keeps all gene models regardless if the >> different programs agree, right? >> > > MAKER does not take the presence of multiple ab initio predictions as > evidence and thus in the absence of aligned physical evidence MAKER > will not output an annotation even if all three ab initio tools > predict a gene at that locus. > >> In my case I get substantial differences in the number of gene models >> found between the two settings, while with =1 I get a number that is >> close to what we would expect. How would you interpret that? What >> would you recommend me to do? Obiously =0 is the saver option. > > If you think that the number of genes you are getting from a MAKER run > is too few, you could run MAKER with keep_preds=1. After the run is > finished, use a tool like IPRScan to search all MAKER predictions for > protein domain content and push that IPRScan output back into the > MAKER GFF file with the ipr_update_gff script. Then as a final step > you can run over the GFF file and remove any gene model that doesn't > have either physical evidence (AED < 1) or protein domain content > (Dbxref=PFAM:XXX etc...) sorry there's not a script prepackaged with > MAKER for that yet. > >> >> 2. I tried to use EST data of an alternative organism in altest= >> (#EST/cDNA sequence file in fasta format from an alternate organism). >> The organism is quite distantly related, but its the closest I have >> so I thought I d give it a shot. I ran maker twice with identical >> settigs expect in altest and est2genome=0/1. The number of genes >> predicted is identical with both approaches, so I am not sure whether >> or not the EST data was actually used or its just to distantly >> related. Any easy way to assess this? > > Typically EST evidence from another organism with alt_est will add > little in the way of additional support (compared to just using > protein evidence from say Swiss-prot) and this would be especially > true if your alt_est is distantly related. I'm not sure I really > understand you alt_est/est2genome combo's to comment in more detail. > I could see four possible combinations there: which two gave > identical results? > >> >> 3. I am running maker in several passes and after each pass I am >> training SNAP using the result of the previous pass. Then for every >> pass I run maker from scratch. Would you recommend to supply the gff >> of the previous pass in "#-----Re-annotation Using MAKER Derived GFF3 >> maker_gff= #re-annotate genome based on this gff3 file", instead? >> > > No, 'Re-annotation using MAKER Derived GFF3' is used for re-annotation > of a genome when you want certain parts of the previous run to be > passed through unchanged, but with retraining SNAP you want MAKER to > re-evaluate each annotation in light of the new predictions made by > the retrained SNAP. MAKER should run really fast in all of the runs > after the first one because as long as you haven't changed the > evidence files it won't have to redo any of the alignments. > > > B > >> Thanks in advance for any thoughts/advice on these things! I >> appreciate your help! >> >> much obliged, >> Christoph >> >> _______________________________________________ >> maker-devel mailing list >> maker-devel at box290.bluehost.com >> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org > > Barry Moore > Research Scientist > Dept. of Human Genetics > University of Utah > Salt Lake City, UT 84112 > -------------------------------------------- > (801) 585-3543 > > > > > _______________________________________________ maker-devel mailing > list maker-devel at box290.bluehost.com > > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org -------------- next part -------------- An HTML attachment was scrubbed... URL: From muntjaczhou at gmail.com Wed Sep 5 20:26:38 2012 From: muntjaczhou at gmail.com (Zhou Qi) Date: Wed, 5 Sep 2012 19:26:38 -0700 Subject: [maker-devel] gene duplicates and track the query protein Message-ID: Dear maker users and developers: I'm new to maker and trying to use it to annotate a Drosophila genome given protein sequences of its closely related species. I have two questions: 1. How maker decide which one to keep if one query protein has two similarly best hits in the target genome, e.g., gene duplication? 2. Is there any way to track the maker gene to its corresponding query proteins through setting up some parameters in maker? Or is it possible to directly let maker name the gene model based on its query protein? I looked through the previous threads, one possible way seems to use model_gff and map_forward option combined. I guess people more experienced than me using maker might know other ways? Many thanks! Qi From barry.moore at genetics.utah.edu Thu Sep 6 10:35:02 2012 From: barry.moore at genetics.utah.edu (Barry Moore) Date: Thu, 6 Sep 2012 10:35:02 -0600 Subject: [maker-devel] gene duplicates and track the query protein In-Reply-To: References: Message-ID: On Sep 5, 2012, at 8:26 PM, Zhou Qi wrote: > Dear maker users and developers: > > I'm new to maker and trying to use it to annotate a Drosophila genome given protein sequences of its closely related species. I have two questions: > > 1. How maker decide which one to keep if one query protein has two similarly best hits in the target genome, e.g., gene duplication? MAKER uses the aligned proteins as evidence to support gene predictions (i.e. from SNAP). If the supporting protein can align within the specified parameters (as defined in maker_bopts.ctl) then all of the valid alignments could be used as evidence for gene predictions at those loci. > > 2. Is there any way to track the maker gene to its corresponding query proteins through setting up some parameters in maker? Or is it possible to directly let maker name the gene model based on its query protein? > I don't know of a way to do this by setting parameters in the MAKER control file - maybe Carson has some idea for you here? B > I looked through the previous threads, one possible way seems to use model_gff and map_forward option combined. I guess people more experienced than me using maker might know other ways? > > Many thanks! > > Qi > _______________________________________________ > maker-devel mailing list > maker-devel at box290.bluehost.com > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org Barry Moore Research Scientist Dept. of Human Genetics University of Utah Salt Lake City, UT 84112 -------------------------------------------- (801) 585-3543 -------------- next part -------------- An HTML attachment was scrubbed... URL: From david.powell at monash.edu Thu Sep 6 18:23:57 2012 From: david.powell at monash.edu (David Powell) Date: Fri, 7 Sep 2012 10:23:57 +1000 Subject: [maker-devel] Problem with cegma2zff Message-ID: Greetings, I am using CEGMA to train SNAP for use with maker. However, I had a problem with the cegma2zff script that comes with maker. This script converts the gff file from CEGMA into a zff file for SNAP. The problem is that it was producing a zff file with every multi-exon gene as being "invalid" from SNAPs point of view. My fix was to modify cegma2zff to ignore any feature with the tag "Exon" - as these are always duplicated by cegma as another feature (one of First, Internal, Terminal, Single). Just wanted to post this here in case this fix is useful to anyone else. Cheers, -- David Powell diff --git a/cegma2zff b/cegma2zff index c795da8..a3bbb77 100755 --- a/cegma2zff +++ b/cegma2zff @@ -39,6 +39,8 @@ while(my $line = ){ my @F = split("\t", $line); ($F[3], $F[4]) = ($F[4], $F[3]) if($F[6] eq '-'); + next if $F[2] =~ /Exon/; + $F[2] =~ s/First/Einit/; $F[2] =~ s/Terminal/Eterm/; $F[2] =~ s/Internal/Exon/; -------------- next part -------------- An HTML attachment was scrubbed... URL: From guoyunfei1989 at gmail.com Fri Sep 7 11:54:12 2012 From: guoyunfei1989 at gmail.com (Yunfei Guo) Date: Fri, 7 Sep 2012 10:54:12 -0700 Subject: [maker-devel] maker annotate two species, same evidence, same settings Message-ID: Hi Carson, I have a quick question about maker annotations. I want to annotate two sets of assemblies from two related species using the same sets of evidence and settings except that the est assemblies would be specified as 'est' for one species (along with 'altest' evidence from other species) and as 'altest' (combined with est evidence from other species) for the other, would the annotation reflect the real difference between these two species? Or there might be some variations within the annotations themselves which might make the real difference more or less significant? Thank you! Yunfei From carsonhh at gmail.com Fri Sep 7 12:35:50 2012 From: carsonhh at gmail.com (Carson Holt) Date: Fri, 07 Sep 2012 14:35:50 -0400 Subject: [maker-devel] maker annotate two species, same evidence, same settings In-Reply-To: Message-ID: Let me explain how ESTs and alt-ESTs are use and maybe that will answer your question. ESTs will be polished around splice sites to give information on intron boundaries and UTR location. The polished ESTs can override ab initio gene predictor structure and be used to extend gene models by what is basically an exon cut and paste operation. The alt-ESTs are not polished (exoneerate can't handle them). So the splice site boundaries will be off. Maker will only try and infer UTR and intron boundaries from these if the alignment produces canonical splice sites (almost never happens). So they are relegated to the same status as the unpolished protein alignment (lower scoring hints to the gene predictor as to exon boundaries). They will also contribute to AED score with a little less accuracy than ESTs. When possible use protein models rather than alt-ESTs, primarily because they are computationally less intense than a tblastx type alignment that occurs with alt-ESTs. Exonerate will also polish protein alignments. Thanks, Carson On 12-09-07 1:54 PM, "Yunfei Guo" wrote: >Hi Carson, > >I have a quick question about maker annotations. I want to annotate >two sets of assemblies from two related species using the same sets of >evidence and settings except that the est assemblies would be >specified as 'est' for one species (along with 'altest' evidence from >other species) and as 'altest' (combined with est evidence from other >species) for the other, would the annotation reflect the real >difference between these two species? Or there might be some >variations within the annotations themselves which might make the real >difference more or less significant? > >Thank you! > >Yunfei > >_______________________________________________ >maker-devel mailing list >maker-devel at box290.bluehost.com >http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org From carsonhh at gmail.com Fri Sep 7 20:33:49 2012 From: carsonhh at gmail.com (Carson Holt) Date: Fri, 07 Sep 2012 22:33:49 -0400 Subject: [maker-devel] Problem with cegma2zff In-Reply-To: Message-ID: Yes. There was an update for CEGMA that causes features to be duplicated in it's output. Thanks for the post and the fix. --Carson From: David Powell Date: Thursday, 6 September, 2012 8:23 PM To: Subject: [maker-devel] Problem with cegma2zff Greetings, I am using CEGMA to train SNAP for use with maker. However, I had a problem with the cegma2zff script that comes with maker. This script converts the gff file from CEGMA into a zff file for SNAP. The problem is that it was producing a zff file with every multi-exon gene as being "invalid" from SNAPs point of view. My fix was to modify cegma2zff to ignore any feature with the tag "Exon" - as these are always duplicated by cegma as another feature (one of First, Internal, Terminal, Single). Just wanted to post this here in case this fix is useful to anyone else. Cheers, -- David Powell diff --git a/cegma2zff b/cegma2zff index c795da8..a3bbb77 100755 --- a/cegma2zff +++ b/cegma2zff @@ -39,6 +39,8 @@ while(my $line = ){ my @F = split("\t", $line); ($F[3], $F[4]) = ($F[4], $F[3]) if($F[6] eq '-'); + next if $F[2] =~ /Exon/; + $F[2] =~ s/First/Einit/; $F[2] =~ s/Terminal/Eterm/; $F[2] =~ s/Internal/Exon/; _______________________________________________ maker-devel mailing list maker-devel at box290.bluehost.com http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org -------------- next part -------------- An HTML attachment was scrubbed... URL: From jeremy.semeiks at utsw.edu Sun Sep 9 13:49:36 2012 From: jeremy.semeiks at utsw.edu (Jeremy Semeiks) Date: Sun, 9 Sep 2012 14:49:36 -0500 Subject: [maker-devel] How to preserve human-friendly IDs when reannotating Message-ID: Hi all, I have sequenced some novel fungal genomes, and I am annotating them with maker-2.26-beta. The entire project is pretty iterative, in the sense that I first get some seemingly-sane annotation sets, then analyze and compare the proteomes biologically, then reannotate when new data comes in or as I learn more about how maker works. Because I have already attached biological meaning to some of my proteins, I would like to retain the same human-friendly IDs across annotations. Eg, if maker suddenly finds 1,000 new proteins on a reannotation run because I turned on keep_preds, then I don't want the transcript formerly known as mymold_09652T0 to become mymold_10698T0 when I run maker_map_ids; I want to keep it named mymold_09652T0. So, is there any built-in way to preserve human-friendly IDs, or do I need to write my own script for this? I have tried setting map_forward=1 and maker_gff=, but setting these seems to preserve neither the human-friendly IDs nor even the original IDs. (Eg, protein "genemark-scaffold353-processed-gene-0.9-mRNA-1" changed its name to "genemark-scaffold353-processed-gene-0.6-mRNA-1" when reannotated.) I haven't turned on any of the *_pass options, eg protein_pass; would this be relevant? Extra credit question: I am making some mate-pair libraries for these fungi; when I re-assemble, that will completely change my scaffold names. Is there any easy way to preserve human-friendly transcript names in this case? As with the above simpler case, I think it would be pretty easy to transfer 90% of the names just by doing an all-vs-all blastp between two annotation sets and fishing out the best hits, but the remaining 10% might be a headache. Thanks, Jeremy Grad student, Grishin lab UT Southwestern, Dallas TX 510.385.8959 -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Mon Sep 10 05:01:46 2012 From: carsonhh at gmail.com (Carson Holt) Date: Mon, 10 Sep 2012 07:01:46 -0400 Subject: [maker-devel] How to preserve human-friendly IDs when reannotating In-Reply-To: Message-ID: The map_forward option requires that the pass option for the gene models be turned on. Otherwise you will have to do some spacial overlap test outside of MAKER. If you have a new assembly, you can try mapping the old models onto the new assembly using the old transcripts as input to the est= and setting est2genome=1 (nothing else set, i.e no repeat masking etc.). Then there is an undocumented option that is still a little buggy (hence why it is still undocumented). Add the line est_forward=1 to your control files. This tells MAKER to copy names from the ESTs, build the models directly from their alignment, and to do other things to try and make a 1 to 1 match across the genome. You will have to manually check that it is 1 to 1 in the end (as I said still a little buggy and hence undocumented). Use the resulting file as input to the model_gff option on a separate run with map_forward=1 for additional reannotation wil more evidence, etc. where you want to still be able to map names forward. From: Jeremy Semeiks Date: Sunday, 9 September, 2012 3:49 PM To: Subject: [maker-devel] How to preserve human-friendly IDs when reannotating Hi all, I have sequenced some novel fungal genomes, and I am annotating them with maker-2.26-beta. The entire project is pretty iterative, in the sense that I first get some seemingly-sane annotation sets, then analyze and compare the proteomes biologically, then reannotate when new data comes in or as I learn more about how maker works. Because I have already attached biological meaning to some of my proteins, I would like to retain the same human-friendly IDs across annotations. Eg, if maker suddenly finds 1,000 new proteins on a reannotation run because I turned on keep_preds, then I don't want the transcript formerly known as mymold_09652T0 to become mymold_10698T0 when I run maker_map_ids; I want to keep it named mymold_09652T0. So, is there any built-in way to preserve human-friendly IDs, or do I need to write my own script for this? I have tried setting map_forward=1 and maker_gff=, but setting these seems to preserve neither the human-friendly IDs nor even the original IDs. (Eg, protein "genemark-scaffold353-processed-gene-0.9-mRNA-1" changed its name to "genemark-scaffold353-processed-gene-0.6-mRNA-1" when reannotated.) I haven't turned on any of the *_pass options, eg protein_pass; would this be relevant? Extra credit question: I am making some mate-pair libraries for these fungi; when I re-assemble, that will completely change my scaffold names. Is there any easy way to preserve human-friendly transcript names in this case? As with the above simpler case, I think it would be pretty easy to transfer 90% of the names just by doing an all-vs-all blastp between two annotation sets and fishing out the best hits, but the remaining 10% might be a headache. Thanks, Jeremy Grad student, Grishin lab UT Southwestern, Dallas TX 510.385.8959 _______________________________________________ maker-devel mailing list maker-devel at box290.bluehost.com http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Mon Sep 10 05:10:33 2012 From: carsonhh at gmail.com (Carson Holt) Date: Mon, 10 Sep 2012 07:10:33 -0400 Subject: [maker-devel] keep_preds option? In-Reply-To: <50473EB4.7070501@gmail.com> Message-ID: The final annotations are really produced by GeneMark, SNAP, Augustus etc. MAKER basically takes the physical evidence, turns it into 'hints' for these programs (I.e. Exon and CDS scoring bonuses), and then lets them run again. If you retrain them they will behave different. If you add a new one you may also get a model from the third algorithm that seems to match the evidence better. Sometimes one algorithm will call one gene where another thinks it should be two genes while the third thinks it is really a larger gene merged with exons from a neighboring gene. MAKER will add hints to try and improve the ab initio predictors performance and choose the model that seems to be make sense given the evidence. The source of a gene model is eventually inherent from the name MAKER gives it. If snap is in the name, then the model was derived from snap. If maker and snap are in the name, then it is a model derived from snap with MAKER hints (otherwise it was derived completely from SNAP's training with no MAKER input). Thanks, Carson From: Christoph Hahn Date: Wednesday, 5 September, 2012 7:59 AM To: Carson Holt , Barry Moore Cc: Subject: Re: [maker-devel] keep_preds option? Hello Barry and Carson, Thank you very much for the extensive replies!! Very helpful!! > > > 2. I tried to use EST data of an alternative organism in altest= (#EST/cDNA > sequence file in fasta format from an alternate organism). The organism is > quite distantly related, but its the closest I have so I thought I d give it a > shot. I ran maker twice with identical settigs expect in altest and > est2genome=0/1. The number of genes predicted is identical with both > approaches, so I am not sure whether or not the EST data was actually used or > its just to distantly related. Any easy way to assess this? > > > Typically EST evidence from another organism with alt_est will add little in the way of additional support (compared to just using protein evidence from say Swiss-prot) and this would be especially true if your alt_est is > distantly related. I'm not sure I really understand you alt_est/est2genome combo's to comment in more detail. I could see four possible combinations there: which two gave identical results? What I meant was that I ran maker once without any alt_est evidence and est2genome=0 and a second time with alt_est=some.fasta and est2genome=1. The result was the same. Sorry, for not making myself clear enough. I thought that the est2genome=1 switch is is just enabling physical est evidence to be used. Therefore, I thought neither alt_est=some.fasta, est2genome=0 nor alt_est=nothing, est2genome=1 would make any sense. I had misunderstood this. Will follow Carsons advice and will try to use more protein evidence from related species (in addition to uniprot). Running right now - Let s see where that leaves me. The IPRScan approach suggested by Barry to assess gene models without physical evidence sounds very interesting. I will definitely look into that. A question concerning an issue I just discovered: Ran maker twice with the same physical evidence. First time using SNAP and Genemark, second time using SNAP, Genemark and AUGUSTUS (set to the closest related species available - same phylum, different class). Second run gives less gene models. IN another context I found that the second pass of Maker using SNAP and Genemark (after training SNAP on the predictions of the first Pass) and the same physical evidence yields less gene annotations. How can that be given the same physical evidence? Thanks again for your help! It is much appreciated! cheers, Christoph Am 31.08.2012 21:03, schrieb Carson Holt: > > I concur with everything Barry said. Also let me add that alt-ESTs do not get > polished around splice sites (exonerate won't handle them). However ESTs and > proteins do. This means that the utility of alt-ESTs in adding UTR, and > splice information is zero. They just function as an anchor to maintain gene > models that might have otherwise been rejected. This also means > alt_est=some.fasta together with est2genome=1 will produce virtually no > additional results because est2genome requires that the splice site makes > sense. You are better off using proteins with protein2genome=1 if you don?t > have ESTs and want partial models for training. Once you have a trained ab > initio gene predictor, turn the est2genome and protein2genome options off. > Otherwise they will give weird partial models that decrease the quality of > your final annotations. (partial models are ok for training but that's about > it). > > > > > If you are getting too low a gene count with keep_preds=0, then you probably > need to add more evidence. Try adding all proteins from a couple of related > species (the protein= option accepts comma separated lists of files). If your > genome is a fungi, oomycete, or a prokaryote, then setting keep_preds=1 is > usually safe. Theses are genomes with high gene density and simple gene > structure, so ab initio predictors do really well and don't need as much help > from the evidence. For other organisms, leave it set to 0 or you will get a > lot of false positives (false positives on some genomes with complex gene > structure can outnumber the genes by 10 to 1 if you turn this on). > > > > > Thanks, > > Carson > > > > > > > > > > > > > > From: Barry Moore > Date: Friday, 31 August, 2012 12:52 PM > To: Christoph Hahn > Cc: > Subject: Re: [maker-devel] keep_preds option? > > > > > > > Hi Christopher, > > > > Comments below: > > > > > On Aug 31, 2012, at 6:43 AM, Christoph Hahn wrote: > > >> >> Hello maker users and developers, >> >> I am new to gene prediction and I am trying to use maker 2.25 on a newly >> assembled non-model organisms draft genome. Within maker I use genemark, SNAP >> and Augustus. I have a few questions: >> >> >> > > > > > Welcome! > > >> >> 1. I was wondering what the keep_preds option means exactly. >> >> I found two slightly different explanations on the option >> #Add unsupported gene prediction to final annotation set (maker2.25) >> #Add non-overlapping ab-inito gene prediction to final annotation set (found >> on the net - probably older maker version) >> >> >> > > > > > It means to keep ab initio gene predictions for which there is no physical > evidence. There are two pieces of information that are required for every > MAKER annotation (by default). MAKER runs the ab initio gene predictors and > aligns transcript (EST/cDNA/mRNASeq transcripts) and protein sequences to the > genome. For each locus where one or more gene predictions exist MAKER checks > to see if there is any physical evidence for gene expression at that locus > (RNA/protein sequence alignments) and if there is (splice EST or protein > alignments) evidence overlapping the predictions, MAKER decides which > prediction best matches the evidence and promotes that prediction to an > annotation. If there is no evidence overlapping any of the predictions then > those predictions are not included in the output annotation file (although > they are saved). If you set keep_preds=1 then for each locus where > prediction(s) exist maker keeps one and promotes it to an annotation even > though there is no physical evidence. The description of 'non-overlapping > ab-initio' means that MAKER has clustered all ab-initio predictions at one > locus and chose one representative transcript to output. > > >> >> As far as I understood keep_preds=0 only retains gene models for which the ab >> initio predictions agree. But how many, all three? two of three? >> keep_preds=1 instead keeps all gene models regardless if the different >> programs agree, right? >> >> >> > > > > > MAKER does not take the presence of multiple ab initio predictions as evidence > and thus in the absence of aligned physical evidence MAKER will not output an > annotation even if all three ab initio tools predict a gene at that locus. > > >> >> In my case I get substantial differences in the number of gene models found >> between the two settings, while with =1 I get a number that is close to what >> we would expect. How would you interpret that? What would you recommend me to >> do? Obiously =0 is the saver option. >> >> > > > > > If you think that the number of genes you are getting from a MAKER run is too > few, you could run MAKER with keep_preds=1. After the run is finished, use a > tool like IPRScan to search all MAKER predictions for protein domain content > and push that IPRScan output back into the MAKER GFF file with the > ipr_update_gff script. Then as a final step you can run over the GFF file and > remove any gene model that doesn't have either physical evidence (AED < 1) or > protein domain content (Dbxref=PFAM:XXX etc?) sorry there's not a script > prepackaged with MAKER for that yet. > > > > >> >> >> 2. I tried to use EST data of an alternative organism in altest= (#EST/cDNA >> sequence file in fasta format from an alternate organism). The organism is >> quite distantly related, but its the closest I have so I thought I d give it >> a shot. I ran maker twice with identical settigs expect in altest and >> est2genome=0/1. The number of genes predicted is identical with both >> approaches, so I am not sure whether or not the EST data was actually used or >> its just to distantly related. Any easy way to assess this? >> >> > > > > > Typically EST evidence from another organism with alt_est will add little in > the way of additional support (compared to just using protein evidence from > say Swiss-prot) and this would be especially true if your alt_est is distantly > related. I'm not sure I really understand you alt_est/est2genome combo's to > comment in more detail. I could see four possible combinations there: which > two gave identical results? > > >> >> >> 3. I am running maker in several passes and after each pass I am training >> SNAP using the result of the previous pass. Then for every pass I run maker >> from scratch. Would you recommend to supply the gff of the previous pass in >> "#-----Re-annotation Using MAKER Derived GFF3 >> maker_gff= #re-annotate genome based on this gff3 file", instead? >> >> >> > > > > > No, 'Re-annotation using MAKER Derived GFF3' is used for re-annotation of a > genome when you want certain parts of the previous run to be passed through > unchanged, but with retraining SNAP you want MAKER to re-evaluate each > annotation in light of the new predictions made by the retrained SNAP. MAKER > should run really fast in all of the runs after the first one because as long > as you haven't changed the evidence files it won't have to redo any of the > alignments. > > > > > > > B > > > >> >> Thanks in advance for any thoughts/advice on these things! I appreciate your >> help! >> >> much obliged, >> Christoph >> >> _______________________________________________ >> maker-devel mailing list >> maker-devel at box290.bluehost.com >> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org >> >> > > > > > > Barry Moore > > Research Scientist > > Dept. of Human Genetics > > University of Utah > > Salt Lake City, UT 84112 > > -------------------------------------------- > > (801) 585-3543 > > > > > > > > > > > > > > _______________________________________________ maker-devel mailing list > maker-devel at box290.bluehost.com > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Mon Sep 10 05:17:26 2012 From: carsonhh at gmail.com (Carson Holt) Date: Mon, 10 Sep 2012 07:17:26 -0400 Subject: [maker-devel] model_gff not in output In-Reply-To: <1A01E0C5-E60A-42AA-BD7B-A6429F435645@gmail.com> Message-ID: The only way MAKER should ignore a legacy annotation (only what's in model_gff is considered legacy by MAKER) is if, you also set one of the ab iniio predictors to run simultaneously or provide a pred_gff file and one of those models scores higher and would overlap the legacy model. Then MAKER chooses that model instead. Also if you have two overlapping legacy models MAKER will only keep one or the other under these same conditions. MAKER will only keep all legacy models regardless of overlap if you only supply model_gff with no other predictors turned on. Once you turn a predictor on, MAKER takes this as a cue that you are letting it make changes. Legacy models should always be kept under all circumstances if there is nothing overlapping them with a higher score. Are the missing models partially overlapped by anything in the resulting MAKER annotations? Thanks, Carson On 12-09-04 4:59 AM, "Michael Thon" wrote: >I'm using maker to update a legacy annotation. As input I'm using >RNA-Seq aligned with cufflinks, ESTs, provided in fasta format, and >proteins downloaded from UniProt.SwissProt. I have done two runs of >maker so far. The first one using the legacy annotations in both the >model_gff and pred_gff parameters. In the second run I used the legacy >annotations in model_gff and in pred_gff I included gene models created >with GeneMark-ES. > >In both runs 1 and 2 I have found two genes (so far) that exist in the >legacy annotations but are not in the final gene models output by maker. >Both genes have overlapping cufflinks annotations, in addition to having >annotations in model_gff. I thought maker was supposed to keep all the >annotations in model_gff, only replacing ones in which it could find an >alternative model with better support. Is there any case in which is >will remove a model? > > >Another discrepency I found in run1 is a gene that maker 'moved' upstream >approx. 150 bases. The gene locus annotated by maker covers the original >annotation, but the CDS does not. The site of the original CDS is covered >by an annotation in model_gff, pred_gff, two ESTs and a cufflinks >annotation. Maker still seems to have moved is is upstream where it only >has an overlapping cufflinks annotation. the three-prime utr annotated >by cufflinks still covers the legacy annotation though. > >Here's a link to download the maker gff file I'm looking at: > >https://dl.dropbox.com/u/320712/supercont1%252E1.gff.zip > >The genes that are in the legacy annotation but missing in the maker >annotation are: >GLRG_00074 and GLRG_00092 > >the 'moved' gene model I described is model GLRG_00081. they all within >the first 350 K of sequence. >mike > > > > > >_______________________________________________ >maker-devel mailing list >maker-devel at box290.bluehost.com >http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org From carsonhh at gmail.com Mon Sep 10 05:18:34 2012 From: carsonhh at gmail.com (Carson Holt) Date: Mon, 10 Sep 2012 07:18:34 -0400 Subject: [maker-devel] Maker Re-tries In-Reply-To: <1E417039-68CF-4EFE-90BF-964DC86B1864@uchicago.edu> Message-ID: Killing a job yourself should not increase the failure count for a contig. Thanks, Carson From: Kipp Johnson Date: Tuesday, 21 August, 2012 5:25 PM To: Carson Holt Cc: Kipp Johnson , Subject: Re: Maker Re-tries Hi Carson, Simple question: If I start maker and then kill the job before a thread finishes processing a contig, does this failure to complete the contig count in the number of tries maker will try to complete the contig before skipping to another? Basically, does the "tries=2 #number of times to try a contig if there is a failure for some reason" parameter take into account failures resulting from me killing the job? Best, Kipp Johnson kippjohnson at uchicago.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: From Carson.Holt at oicr.on.ca Mon Sep 10 04:50:09 2012 From: Carson.Holt at oicr.on.ca (Carson Holt) Date: Mon, 10 Sep 2012 10:50:09 +0000 Subject: [maker-devel] gene duplicates and track the query protein In-Reply-To: Message-ID: 2. Is there any way to track the maker gene to its corresponding query proteins through setting up some parameters in maker? Or is it possible to directly let maker name the gene model based on its query protein? Not directly. Proteins can align to multiple locations, so you will get more than one protein overlapping a gene. A reciprocal BLAST would probably be the best thing to do here. If the MAKER derived annotation, and a gene are both each others best hit in separate blast jobs, then you could usually safely call them the same gene. You would have to do that outside of MAKER. Thanks, Carson From: Barry Moore > Date: Thursday, 6 September, 2012 12:35 PM To: Zhou Qi > Cc: > Subject: Re: [maker-devel] gene duplicates and track the query protein On Sep 5, 2012, at 8:26 PM, Zhou Qi wrote: Dear maker users and developers: I'm new to maker and trying to use it to annotate a Drosophila genome given protein sequences of its closely related species. I have two questions: 1. How maker decide which one to keep if one query protein has two similarly best hits in the target genome, e.g., gene duplication? MAKER uses the aligned proteins as evidence to support gene predictions (i.e. from SNAP). If the supporting protein can align within the specified parameters (as defined in maker_bopts.ctl) then all of the valid alignments could be used as evidence for gene predictions at those loci. 2. Is there any way to track the maker gene to its corresponding query proteins through setting up some parameters in maker? Or is it possible to directly let maker name the gene model based on its query protein? I don't know of a way to do this by setting parameters in the MAKER control file - maybe Carson has some idea for you here? B I looked through the previous threads, one possible way seems to use model_gff and map_forward option combined. I guess people more experienced than me using maker might know other ways? Many thanks! Qi _______________________________________________ maker-devel mailing list maker-devel at box290.bluehost.com http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org Barry Moore Research Scientist Dept. of Human Genetics University of Utah Salt Lake City, UT 84112 -------------------------------------------- (801) 585-3543 _______________________________________________ maker-devel mailing list maker-devel at box290.bluehost.com http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org -------------- next part -------------- An HTML attachment was scrubbed... URL: From jeremy.semeiks at utsw.edu Mon Sep 10 09:02:25 2012 From: jeremy.semeiks at utsw.edu (Jeremy Semeiks) Date: Mon, 10 Sep 2012 10:02:25 -0500 Subject: [maker-devel] How to preserve human-friendly IDs when reannotating In-Reply-To: References: Message-ID: OK, thanks. So if I understand correctly, to preserve human-friendly IDs requires setting just three options: map_forward=1, maker_gff=, and model_pass=1. (Or instead of the last two I could equivalently just set model_gff to a GFF containing only models.) A couple new issues came up when I tried to run with these options. I started maker like this: /usr/bin/time mpiexec -n 10 maker -q < /dev/null > maker.oe 2>&1 1. I get a bunch of messages as follows, but with variable line number: DBD::SQLite::db do failed: database is locked at /home/jrs/maker-2.26-beta/bin/../lib/GFFDB.pm line 186. I saw that this came up in another thread < https://groups.google.com/forum/?fromgroups=#!topic/maker-devel/TscBgbQfBX4>, but I'm not sure it was ever resolved, nor whether it will affect my reannotation results (as I'm not sure what "your GFF3 results will not be integrated" means). This error did not come up the last time I ran maker for reannotation with similar options in a different directory. And both my current directory and my tmp directory are locally mounted, ie not NFS. 2. Both in this run and in previous runs, I get a lot of lines like this, seemingly at random: Warning: unable to close filehandle DF properly. On Mon, Sep 10, 2012 at 6:01 AM, Carson Holt wrote: > The map_forward option requires that the pass option for the gene models > be turned on. Otherwise you will have to do some spacial overlap test > outside of MAKER. > > If you have a new assembly, you can try mapping the old models onto the > new assembly using the old transcripts as input to the est= and setting > est2genome=1 (nothing else set, i.e no repeat masking etc.). Then there is > an undocumented option that is still a little buggy (hence why it is still > undocumented). Add the line est_forward=1 to your control files. This > tells MAKER to copy names from the ESTs, build the models directly from > their alignment, and to do other things to try and make a 1 to 1 match > across the genome. You will have to manually check that it is 1 to 1 in > the end (as I said still a little buggy and hence undocumented). Use the > resulting file as input to the model_gff option on a separate run with > map_forward=1 for additional reannotation wil more evidence, etc. where you > want to still be able to map names forward. > > From: Jeremy Semeiks > Date: Sunday, 9 September, 2012 3:49 PM > To: > Subject: [maker-devel] How to preserve human-friendly IDs when > reannotating > > Hi all, > > I have sequenced some novel fungal genomes, and I am annotating them with > maker-2.26-beta. The entire project is pretty iterative, in the sense that > I first get some seemingly-sane annotation sets, then analyze and compare > the proteomes biologically, then reannotate when new data comes in or as I > learn more about how maker works. Because I have already attached > biological meaning to some of my proteins, I would like to retain the same > human-friendly IDs across annotations. Eg, if maker suddenly finds 1,000 > new proteins on a reannotation run because I turned on keep_preds, then I > don't want the transcript formerly known as mymold_09652T0 to become > mymold_10698T0 when I run maker_map_ids; I want to keep it named > mymold_09652T0. > > So, is there any built-in way to preserve human-friendly IDs, or do I need > to write my own script for this? I have tried setting map_forward=1 and > maker_gff=, but > setting these seems to preserve neither the human-friendly IDs nor even the > original IDs. (Eg, protein "genemark-scaffold353-processed-gene-0.9-mRNA-1" > changed its name to "genemark-scaffold353-processed-gene-0.6-mRNA-1" when > reannotated.) I haven't turned on any of the *_pass options, eg > protein_pass; would this be relevant? > > Extra credit question: I am making some mate-pair libraries for these > fungi; when I re-assemble, that will completely change my scaffold names. > Is there any easy way to preserve human-friendly transcript names in this > case? As with the above simpler case, I think it would be pretty easy to > transfer 90% of the names just by doing an all-vs-all blastp between two > annotation sets and fishing out the best hits, but the remaining 10% might > be a headache. > > Thanks, > Jeremy > Grad student, Grishin lab > UT Southwestern, Dallas TX > 510.385.8959 > _______________________________________________ maker-devel mailing list > maker-devel at box290.bluehost.com > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org > -------------- next part -------------- An HTML attachment was scrubbed... URL: From carson.holt at genetics.utah.edu Mon Sep 10 11:21:05 2012 From: carson.holt at genetics.utah.edu (Carson Holt) Date: Mon, 10 Sep 2012 17:21:05 +0000 Subject: [maker-devel] MWAS: User Feedback In-Reply-To: Message-ID: MAKER won't really annotate those. Transcriptome annotation is a very different problem from genome annotation. I'm CC'ing this to the MAKER mailing list to see if anyone has good suggestion for transcriptome annotation. I would recommend using Repeatmasker to remove transposons from your transcriptome set, and then InterProScan for domain identification and maybe blast2go for GO term association. --Carson On 12-09-10 1:10 PM, "grind001 at umn.edu" wrote: >I have assembled RNAseq transcripts. There's no genome assembly for our >species right now, so I was trying to do an organized assembly pipeline >and >use your system. > >On Sep 10 2012, Carson Holt wrote: > >>Tell me a little more about your project. Based on your brief >>description >>I think you might need a different tool. MAKER doesn't assemble or >>annotate transcriptomes (i.e. RNA only). It works with de novo genome >>assemblies to identify the genes from them (I.e entire chromosomes or >>large fragments of chromosomes). It can use RNA-seq result to help >>annotate the genome but still requires a genome assembly. >> >>The online server will annotate maximum of 5 Mb at a time and it's slow >>(mostly built for small jobs). You will get 10-20 faster performance >>locally. >> >>Thanks, >>Carson >> >> >> >>On 12-09-10 12:17 PM, "grind001 at umn.edu" wrote: >> >>>Maker Web Annotation Service - User Feedback: >>>--------------------------------------------- >>>Hi, >>> >>>I'm working on getting your software installed on my systems, and have >>>done a test run on your web page with a portion of my data. >>>I have 150,000 contigs from a de novo assembly of our transcriptome. Do >>>you have room on your server for a large run? or is this just a sample >>>space to test the software? I'm under some time constraints and an just >>>checking and hoping to push this forward a bit faster. >>> >>> >>> >>>Best, >>>Suzanne >>>University of MN >>> >>> >>>--------------------------------------------- >>>User: 1440 >>>First: Suzanne >>>Last: Grindle >>>Institution: University of Minnesota >>>E-mail: grind001 at umn.edu >>> >> >> From felix.bemm at uni-wuerzburg.de Mon Sep 10 13:15:22 2012 From: felix.bemm at uni-wuerzburg.de (Felix Bemm) Date: Mon, 10 Sep 2012 21:15:22 +0200 Subject: [maker-devel] MWAS: User Feedback In-Reply-To: References: Message-ID: <504E3C4A.2040401@uni-wuerzburg.de> hi suzanne, the trinity assembler mailing list has some good ideas for that. You could think about using an "intelligent" orf finder like transdecoder (transdecoder.sourceforge.net). the predicted orfs can than be used for an interpro and blast2go run. merge the interpro and the b2g run with the built-in tool of blast2go. simply put the interpro xml's for each orf of a given transcript into one file for that and use the built-in import function of blast2go. this might help you to improve the GO annotation. it also works with the b2g pipeline tool (which is much faster). In addition, you could try to use interproscan standalone 5 (http://code.google.com/p/interproscan/) since it has an improved support for nucleic acid sequences. cheers felix Am 10.09.2012 19:21, schrieb Carson Holt: > MAKER won't really annotate those. Transcriptome annotation is a very > different problem from genome annotation. I'm CC'ing this to the MAKER > mailing list to see if anyone has good suggestion for transcriptome > annotation. > > I would recommend using Repeatmasker to remove transposons from your > transcriptome set, and then InterProScan for domain identification and > maybe blast2go for GO term association. > > --Carson > > > > > On 12-09-10 1:10 PM, "grind001 at umn.edu" wrote: > >> I have assembled RNAseq transcripts. There's no genome assembly for our >> species right now, so I was trying to do an organized assembly pipeline >> and >> use your system. >> >> On Sep 10 2012, Carson Holt wrote: >> >>> Tell me a little more about your project. Based on your brief >>> description >>> I think you might need a different tool. MAKER doesn't assemble or >>> annotate transcriptomes (i.e. RNA only). It works with de novo genome >>> assemblies to identify the genes from them (I.e entire chromosomes or >>> large fragments of chromosomes). It can use RNA-seq result to help >>> annotate the genome but still requires a genome assembly. >>> >>> The online server will annotate maximum of 5 Mb at a time and it's slow >>> (mostly built for small jobs). You will get 10-20 faster performance >>> locally. >>> >>> Thanks, >>> Carson >>> >>> >>> >>> On 12-09-10 12:17 PM, "grind001 at umn.edu" wrote: >>> >>>> Maker Web Annotation Service - User Feedback: >>>> --------------------------------------------- >>>> Hi, >>>> >>>> I'm working on getting your software installed on my systems, and have >>>> done a test run on your web page with a portion of my data. >>>> I have 150,000 contigs from a de novo assembly of our transcriptome. Do >>>> you have room on your server for a large run? or is this just a sample >>>> space to test the software? I'm under some time constraints and an just >>>> checking and hoping to push this forward a bit faster. >>>> >>>> >>>> >>>> Best, >>>> Suzanne >>>> University of MN >>>> >>>> >>>> --------------------------------------------- >>>> User: 1440 >>>> First: Suzanne >>>> Last: Grindle >>>> Institution: University of Minnesota >>>> E-mail: grind001 at umn.edu >>>> >>> >>> > > > _______________________________________________ > maker-devel mailing list > maker-devel at box290.bluehost.com > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org > -- Felix Bemm Department of Bioinformatics University of W?rzburg, Germany Tel: +49 931 - 31 83696 Fax: +49 931 - 31 84552 felix.bemm at uni-wuerzburg.de From ranjani at uga.edu Tue Sep 11 09:38:33 2012 From: ranjani at uga.edu (Sivaranjani Namasivayam) Date: Tue, 11 Sep 2012 15:38:33 +0000 Subject: [maker-devel] MAKER training Message-ID: Hi, I am using MAKER to annotate a newly sequenced genome. I have trained and retrained with datasets but I would like some advice on assessing the output and how this is affected by the input provided. - I have transcriptome data from 454 and Illumina platforms. Illumina is from a single time point and 454 from multiple time point. 454 was assembled using Newbler(dataset 1) and Illumina using Tophat-Cufflinks (dataset 2) and the denovo Trinity pipeline (dataset 3). I now have3 assemblies - 454 and Illumina will have some redunant transcripts (because of one overlapping time point); TopHat-Cufflinks and Trinity will have highly redundant transcripts (because they use same raw reads). Is it OK to provide all 3 datasets as EST evidence, how does it affect the quality of annotation. (For now I have used dataset 1 and dataset 2 as EST evidence) - I used the above model to retrain, I passed through everything except the abinitio gene predictions. I also provided a set a manually annotated genes , many of which have EST evidence. Is this OK to do? [ For proteins evidence, I gave a set from related organisms, same as above] - In my third retraining, I used the above retrained model, but this time I only provided the genome_gff but did not pass through any other data. However I did provide the manually annotated genes as EST evidence and related proteins as protein_evidence. Can you please give me some advice on which of these could give me the best prediction, or if I can alter something to get a better prediction. - A quick question about Augustus - I used a Augustus model (trained for a closely related organism) for ab-initio prediction. Does MAKER adjust this model based on the evidence provided, or use the model as such for a prediction. Greatly appreciate your help! Thanks! Ranjani -------------- next part -------------- An HTML attachment was scrubbed... URL: From dence at genetics.utah.edu Tue Sep 11 09:46:04 2012 From: dence at genetics.utah.edu (Daniel Ence) Date: Tue, 11 Sep 2012 15:46:04 +0000 Subject: [maker-devel] MAKER training In-Reply-To: References: Message-ID: Hi Ranjani, It is fine to include all three of those transcriptome datatsets. The more (relevant) evidence the better. I'm not certain what you mean when you say "you used the above model to retrain". Did you train an abinitio gene predictor using the results from your first maker run? Daniel Ence Graduate Student Eccles Institute of Human Genetics University of Utah 15 North 2030 East, Room 2100 Salt Lake City, UT 84112-5330 ________________________________ From: maker-devel-bounces at yandell-lab.org [maker-devel-bounces at yandell-lab.org] on behalf of Sivaranjani Namasivayam [ranjani at uga.edu] Sent: Tuesday, September 11, 2012 9:38 AM To: maker-devel at yandell-lab.org Subject: [maker-devel] MAKER training Hi, I am using MAKER to annotate a newly sequenced genome. I have trained and retrained with datasets but I would like some advice on assessing the output and how this is affected by the input provided. - I have transcriptome data from 454 and Illumina platforms. Illumina is from a single time point and 454 from multiple time point. 454 was assembled using Newbler(dataset 1) and Illumina using Tophat-Cufflinks (dataset 2) and the denovo Trinity pipeline (dataset 3). I now have3 assemblies - 454 and Illumina will have some redunant transcripts (because of one overlapping time point); TopHat-Cufflinks and Trinity will have highly redundant transcripts (because they use same raw reads). Is it OK to provide all 3 datasets as EST evidence, how does it affect the quality of annotation. (For now I have used dataset 1 and dataset 2 as EST evidence) - I used the above model to retrain, I passed through everything except the abinitio gene predictions. I also provided a set a manually annotated genes , many of which have EST evidence. Is this OK to do? [ For proteins evidence, I gave a set from related organisms, same as above] - In my third retraining, I used the above retrained model, but this time I only provided the genome_gff but did not pass through any other data. However I did provide the manually annotated genes as EST evidence and related proteins as protein_evidence. Can you please give me some advice on which of these could give me the best prediction, or if I can alter something to get a better prediction. - A quick question about Augustus - I used a Augustus model (trained for a closely related organism) for ab-initio prediction. Does MAKER adjust this model based on the evidence provided, or use the model as such for a prediction. Greatly appreciate your help! Thanks! Ranjani -------------- next part -------------- An HTML attachment was scrubbed... URL: From ranjani at uga.edu Tue Sep 11 09:57:31 2012 From: ranjani at uga.edu (Sivaranjani Namasivayam) Date: Tue, 11 Sep 2012 15:57:31 +0000 Subject: [maker-devel] MAKER training In-Reply-To: References: , Message-ID: Hey, I used the MAKER model to retrain MAKER itself. I read somewhere it improves MAKER's predictions. I did train abinitio gene predictors using MAKERs output, but I wanted to identify the best prediction before using it to train other gene predictors. Thanks, Ranjani ________________________________ From: Daniel Ence [dence at genetics.utah.edu] Sent: Tuesday, September 11, 2012 11:46 AM To: Sivaranjani Namasivayam; maker-devel at yandell-lab.org Subject: RE: MAKER training Hi Ranjani, It is fine to include all three of those transcriptome datatsets. The more (relevant) evidence the better. I'm not certain what you mean when you say "you used the above model to retrain". Did you train an abinitio gene predictor using the results from your first maker run? Daniel Ence Graduate Student Eccles Institute of Human Genetics University of Utah 15 North 2030 East, Room 2100 Salt Lake City, UT 84112-5330 ________________________________ From: maker-devel-bounces at yandell-lab.org [maker-devel-bounces at yandell-lab.org] on behalf of Sivaranjani Namasivayam [ranjani at uga.edu] Sent: Tuesday, September 11, 2012 9:38 AM To: maker-devel at yandell-lab.org Subject: [maker-devel] MAKER training Hi, I am using MAKER to annotate a newly sequenced genome. I have trained and retrained with datasets but I would like some advice on assessing the output and how this is affected by the input provided. - I have transcriptome data from 454 and Illumina platforms. Illumina is from a single time point and 454 from multiple time point. 454 was assembled using Newbler(dataset 1) and Illumina using Tophat-Cufflinks (dataset 2) and the denovo Trinity pipeline (dataset 3). I now have3 assemblies - 454 and Illumina will have some redunant transcripts (because of one overlapping time point); TopHat-Cufflinks and Trinity will have highly redundant transcripts (because they use same raw reads). Is it OK to provide all 3 datasets as EST evidence, how does it affect the quality of annotation. (For now I have used dataset 1 and dataset 2 as EST evidence) - I used the above model to retrain, I passed through everything except the abinitio gene predictions. I also provided a set a manually annotated genes , many of which have EST evidence. Is this OK to do? [ For proteins evidence, I gave a set from related organisms, same as above] - In my third retraining, I used the above retrained model, but this time I only provided the genome_gff but did not pass through any other data. However I did provide the manually annotated genes as EST evidence and related proteins as protein_evidence. Can you please give me some advice on which of these could give me the best prediction, or if I can alter something to get a better prediction. - A quick question about Augustus - I used a Augustus model (trained for a closely related organism) for ab-initio prediction. Does MAKER adjust this model based on the evidence provided, or use the model as such for a prediction. Greatly appreciate your help! Thanks! Ranjani -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Tue Sep 11 10:04:53 2012 From: carsonhh at gmail.com (Carson Holt) Date: Tue, 11 Sep 2012 12:04:53 -0400 Subject: [maker-devel] MAKER training In-Reply-To: Message-ID: > - I have transcriptome data from 454 and Illumina platforms. Illumina is from > a single time point and 454 from multiple time point. 454 was assembled using > Newbler(dataset 1) and Illumina using Tophat-Cufflinks (dataset 2) and the > denovo Trinity pipeline (dataset 3). I now have3 assemblies - 454 and > Illumina will have some redunant transcripts (because of one overlapping time > point); TopHat-Cufflinks and Trinity will have highly redundant transcripts > (because they use same raw reads). Is it OK to provide all 3 datasets as EST > evidence, how does it affect the quality of annotation. (For now I have used > dataset 1 and dataset 2 as EST evidence) This is fine. You can give them as a comma separated list est=file1,file2,file3 > - I used the above model to retrain, I passed through everything except the > abinitio gene predictions. I also provided a set a manually annotated genes , > many of which have EST evidence. Is this OK to do? [ For proteins evidence, I > gave a set from related organisms, same as above] > > - In my third retraining, I used the above retrained model, but this time I > only provided the genome_gff but did not pass through any other data. However > I did provide the manually annotated genes as EST evidence and related > proteins as protein_evidence. > > Can you please give me some advice on which of these could give me the best > prediction, or if I can alter something to get a better prediction. > Everything you've done sounds reasonable. Better training comes from having the most correct models to train with, so providing the manual annotations as training works, or you can also select MAKER models with the lowest AED score (i.e. models that most closely match evidence). The goal is to try and make the process as unbias as possible, so a consistent usually automated selection method is often the easiest to justify justifiable. > > - A quick question about Augustus - I used a Augustus model (trained for a > closely related organism) for ab-initio prediction. Does MAKER adjust this > model based on the evidence provided, or use the model as such for a > prediction. MAKER will provide hints to Augustus during the run to make it perform better. MAKER will report the raw unaided augustus results in the GFF3 file as a reference, but will use evidence to improve performance where it can. The gene name will let you know if it is a hint based or ab initio model prediction. When 'maker', is part of the gene name it is hint based. Thanks, Carson -------------- next part -------------- An HTML attachment was scrubbed... URL: From dence at genetics.utah.edu Tue Sep 11 10:29:21 2012 From: dence at genetics.utah.edu (Daniel Ence) Date: Tue, 11 Sep 2012 16:29:21 +0000 Subject: [maker-devel] MAKER training In-Reply-To: References: , , Message-ID: So, MAKER itself isn't probabilistic. If you give it the same data and the same options, it will give you the same outputs. The iterative approach for MAKER is to get gene models on the first round using the est2genome option and the Augustus model that you mentioned. After that first round, you train the ab-initio predictors and tell maker to use those newly trained gene predictors in the second round. Regarding the set of manually annotated genes, I think you should put those in the model_gff option. Thanks, Daniel Daniel Ence Graduate Student Eccles Institute of Human Genetics University of Utah 15 North 2030 East, Room 2100 Salt Lake City, UT 84112-5330 ________________________________ From: Sivaranjani Namasivayam [ranjani at uga.edu] Sent: Tuesday, September 11, 2012 9:57 AM To: Daniel Ence; maker-devel at yandell-lab.org Subject: RE: MAKER training Hey, I used the MAKER model to retrain MAKER itself. I read somewhere it improves MAKER's predictions. I did train abinitio gene predictors using MAKERs output, but I wanted to identify the best prediction before using it to train other gene predictors. Thanks, Ranjani ________________________________ From: Daniel Ence [dence at genetics.utah.edu] Sent: Tuesday, September 11, 2012 11:46 AM To: Sivaranjani Namasivayam; maker-devel at yandell-lab.org Subject: RE: MAKER training Hi Ranjani, It is fine to include all three of those transcriptome datatsets. The more (relevant) evidence the better. I'm not certain what you mean when you say "you used the above model to retrain". Did you train an abinitio gene predictor using the results from your first maker run? Daniel Ence Graduate Student Eccles Institute of Human Genetics University of Utah 15 North 2030 East, Room 2100 Salt Lake City, UT 84112-5330 ________________________________ From: maker-devel-bounces at yandell-lab.org [maker-devel-bounces at yandell-lab.org] on behalf of Sivaranjani Namasivayam [ranjani at uga.edu] Sent: Tuesday, September 11, 2012 9:38 AM To: maker-devel at yandell-lab.org Subject: [maker-devel] MAKER training Hi, I am using MAKER to annotate a newly sequenced genome. I have trained and retrained with datasets but I would like some advice on assessing the output and how this is affected by the input provided. - I have transcriptome data from 454 and Illumina platforms. Illumina is from a single time point and 454 from multiple time point. 454 was assembled using Newbler(dataset 1) and Illumina using Tophat-Cufflinks (dataset 2) and the denovo Trinity pipeline (dataset 3). I now have3 assemblies - 454 and Illumina will have some redunant transcripts (because of one overlapping time point); TopHat-Cufflinks and Trinity will have highly redundant transcripts (because they use same raw reads). Is it OK to provide all 3 datasets as EST evidence, how does it affect the quality of annotation. (For now I have used dataset 1 and dataset 2 as EST evidence) - I used the above model to retrain, I passed through everything except the abinitio gene predictions. I also provided a set a manually annotated genes , many of which have EST evidence. Is this OK to do? [ For proteins evidence, I gave a set from related organisms, same as above] - In my third retraining, I used the above retrained model, but this time I only provided the genome_gff but did not pass through any other data. However I did provide the manually annotated genes as EST evidence and related proteins as protein_evidence. Can you please give me some advice on which of these could give me the best prediction, or if I can alter something to get a better prediction. - A quick question about Augustus - I used a Augustus model (trained for a closely related organism) for ab-initio prediction. Does MAKER adjust this model based on the evidence provided, or use the model as such for a prediction. Greatly appreciate your help! Thanks! Ranjani -------------- next part -------------- An HTML attachment was scrubbed... URL: From ranjani at uga.edu Tue Sep 11 10:45:42 2012 From: ranjani at uga.edu (Sivaranjani Namasivayam) Date: Tue, 11 Sep 2012 16:45:42 +0000 Subject: [maker-devel] MAKER training In-Reply-To: References: , , , Message-ID: I will try the model_gff option. For the retraining I noticed the count of the annotated genes vary, I haven't examined if the gene structure varies. I will use the models to train ab-initio predictions and providing that as input. But I did notice the number of genes output by MAKER is fairly lower when compared to the transcriptome. I understand this is because MAKER annotations are based on good evidence but can this improve/increase with ab-initio gene models input. Thanks, Ranjani ________________________________ From: Daniel Ence [dence at genetics.utah.edu] Sent: Tuesday, September 11, 2012 12:29 PM To: Sivaranjani Namasivayam; maker-devel at yandell-lab.org Subject: RE: MAKER training So, MAKER itself isn't probabilistic. If you give it the same data and the same options, it will give you the same outputs. The iterative approach for MAKER is to get gene models on the first round using the est2genome option and the Augustus model that you mentioned. After that first round, you train the ab-initio predictors and tell maker to use those newly trained gene predictors in the second round. Regarding the set of manually annotated genes, I think you should put those in the model_gff option. Thanks, Daniel Daniel Ence Graduate Student Eccles Institute of Human Genetics University of Utah 15 North 2030 East, Room 2100 Salt Lake City, UT 84112-5330 ________________________________ From: Sivaranjani Namasivayam [ranjani at uga.edu] Sent: Tuesday, September 11, 2012 9:57 AM To: Daniel Ence; maker-devel at yandell-lab.org Subject: RE: MAKER training Hey, I used the MAKER model to retrain MAKER itself. I read somewhere it improves MAKER's predictions. I did train abinitio gene predictors using MAKERs output, but I wanted to identify the best prediction before using it to train other gene predictors. Thanks, Ranjani ________________________________ From: Daniel Ence [dence at genetics.utah.edu] Sent: Tuesday, September 11, 2012 11:46 AM To: Sivaranjani Namasivayam; maker-devel at yandell-lab.org Subject: RE: MAKER training Hi Ranjani, It is fine to include all three of those transcriptome datatsets. The more (relevant) evidence the better. I'm not certain what you mean when you say "you used the above model to retrain". Did you train an abinitio gene predictor using the results from your first maker run? Daniel Ence Graduate Student Eccles Institute of Human Genetics University of Utah 15 North 2030 East, Room 2100 Salt Lake City, UT 84112-5330 ________________________________ From: maker-devel-bounces at yandell-lab.org [maker-devel-bounces at yandell-lab.org] on behalf of Sivaranjani Namasivayam [ranjani at uga.edu] Sent: Tuesday, September 11, 2012 9:38 AM To: maker-devel at yandell-lab.org Subject: [maker-devel] MAKER training Hi, I am using MAKER to annotate a newly sequenced genome. I have trained and retrained with datasets but I would like some advice on assessing the output and how this is affected by the input provided. - I have transcriptome data from 454 and Illumina platforms. Illumina is from a single time point and 454 from multiple time point. 454 was assembled using Newbler(dataset 1) and Illumina using Tophat-Cufflinks (dataset 2) and the denovo Trinity pipeline (dataset 3). I now have3 assemblies - 454 and Illumina will have some redunant transcripts (because of one overlapping time point); TopHat-Cufflinks and Trinity will have highly redundant transcripts (because they use same raw reads). Is it OK to provide all 3 datasets as EST evidence, how does it affect the quality of annotation. (For now I have used dataset 1 and dataset 2 as EST evidence) - I used the above model to retrain, I passed through everything except the abinitio gene predictions. I also provided a set a manually annotated genes , many of which have EST evidence. Is this OK to do? [ For proteins evidence, I gave a set from related organisms, same as above] - In my third retraining, I used the above retrained model, but this time I only provided the genome_gff but did not pass through any other data. However I did provide the manually annotated genes as EST evidence and related proteins as protein_evidence. Can you please give me some advice on which of these could give me the best prediction, or if I can alter something to get a better prediction. - A quick question about Augustus - I used a Augustus model (trained for a closely related organism) for ab-initio prediction. Does MAKER adjust this model based on the evidence provided, or use the model as such for a prediction. Greatly appreciate your help! Thanks! Ranjani -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Tue Sep 11 14:33:11 2012 From: carsonhh at gmail.com (Carson Holt) Date: Tue, 11 Sep 2012 16:33:11 -0400 Subject: [maker-devel] How to preserve human-friendly IDs when reannotating In-Reply-To: Message-ID: Which version of MAKER are you running (maker --version)? --Carson From: Jeremy Semeiks Date: Monday, 10 September, 2012 11:02 AM To: Carson Holt Cc: Subject: Re: [maker-devel] How to preserve human-friendly IDs when reannotating OK, thanks. So if I understand correctly, to preserve human-friendly IDs requires setting just three options: map_forward=1, maker_gff=, and model_pass=1. (Or instead of the last two I could equivalently just set model_gff to a GFF containing only models.) A couple new issues came up when I tried to run with these options. I started maker like this: /usr/bin/time mpiexec -n 10 maker -q < /dev/null > maker.oe 2>&1 1. I get a bunch of messages as follows, but with variable line number: DBD::SQLite::db do failed: database is locked at /home/jrs/maker-2.26-beta/bin/../lib/GFFDB.pm line 186. I saw that this came up in another thread , but I'm not sure it was ever resolved, nor whether it will affect my reannotation results (as I'm not sure what "your GFF3 results will not be integrated" means). This error did not come up the last time I ran maker for reannotation with similar options in a different directory. And both my current directory and my tmp directory are locally mounted, ie not NFS. 2. Both in this run and in previous runs, I get a lot of lines like this, seemingly at random: Warning: unable to close filehandle DF properly. On Mon, Sep 10, 2012 at 6:01 AM, Carson Holt wrote: > The map_forward option requires that the pass option for the gene models be > turned on. Otherwise you will have to do some spacial overlap test outside of > MAKER. > > If you have a new assembly, you can try mapping the old models onto the new > assembly using the old transcripts as input to the est= and setting > est2genome=1 (nothing else set, i.e no repeat masking etc.). Then there is an > undocumented option that is still a little buggy (hence why it is still > undocumented). Add the line est_forward=1 to your control files. This tells > MAKER to copy names from the ESTs, build the models directly from their > alignment, and to do other things to try and make a 1 to 1 match across the > genome. You will have to manually check that it is 1 to 1 in the end (as I > said still a little buggy and hence undocumented). Use the resulting file as > input to the model_gff option on a separate run with map_forward=1 for > additional reannotation wil more evidence, etc. where you want to still be > able to map names forward. > > From: Jeremy Semeiks > Date: Sunday, 9 September, 2012 3:49 PM > To: > Subject: [maker-devel] How to preserve human-friendly IDs when reannotating > > Hi all, > > I have sequenced some novel fungal genomes, and I am annotating them with > maker-2.26-beta. The entire project is pretty iterative, in the sense that I > first get some seemingly-sane annotation sets, then analyze and compare the > proteomes biologically, then reannotate when new data comes in or as I learn > more about how maker works. Because I have already attached biological meaning > to some of my proteins, I would like to retain the same human-friendly IDs > across annotations. Eg, if maker suddenly finds 1,000 new proteins on a > reannotation run because I turned on keep_preds, then I don't want the > transcript formerly known as mymold_09652T0 to become mymold_10698T0 when I > run maker_map_ids; I want to keep it named mymold_09652T0. > > So, is there any built-in way to preserve human-friendly IDs, or do I need to > write my own script for this? I have tried setting map_forward=1 and > maker_gff=, but > setting these seems to preserve neither the human-friendly IDs nor even the > original IDs. (Eg, protein "genemark-scaffold353-processed-gene-0.9-mRNA-1" > changed its name to "genemark-scaffold353-processed-gene-0.6-mRNA-1" when > reannotated.) I haven't turned on any of the *_pass options, eg protein_pass; > would this be relevant? > > Extra credit question: I am making some mate-pair libraries for these fungi; > when I re-assemble, that will completely change my scaffold names. Is there > any easy way to preserve human-friendly transcript names in this case? As with > the above simpler case, I think it would be pretty easy to transfer 90% of the > names just by doing an all-vs-all blastp between two annotation sets and > fishing out the best hits, but the remaining 10% might be a headache. > > Thanks, > Jeremy > Grad student, Grishin lab > UT Southwestern, Dallas TX > 510.385.8959 > _______________________________________________ maker-devel mailing list > maker-devel at box290.bluehost.comhttp://box290.bluehost.com/mailman/listinfo/mak > er-devel_yandell-lab.org -------------- next part -------------- An HTML attachment was scrubbed... URL: From jeremy.semeiks at utsw.edu Tue Sep 11 17:56:23 2012 From: jeremy.semeiks at utsw.edu (Jeremy Semeiks) Date: Tue, 11 Sep 2012 18:56:23 -0500 Subject: [maker-devel] How to preserve human-friendly IDs when reannotating In-Reply-To: References: Message-ID: maker 2.26. And I have verified for myself that the three options I mentioned below suffice to preserve human-friendly IDs when reannotating. Thanks, J On Tue, Sep 11, 2012 at 3:33 PM, Carson Holt wrote: > Which version of MAKER are you running (maker --version)? > > --Carson > > > > From: Jeremy Semeiks > Date: Monday, 10 September, 2012 11:02 AM > To: Carson Holt > Cc: > Subject: Re: [maker-devel] How to preserve human-friendly IDs when > reannotating > > OK, thanks. So if I understand correctly, to preserve human-friendly IDs > requires setting just three options: map_forward=1, > maker_gff=, and model_pass=1. (Or instead of the > last two I could equivalently just set model_gff to a GFF containing only > models.) > > A couple new issues came up when I tried to run with these options. I > started maker like this: > > /usr/bin/time mpiexec -n 10 maker -q < /dev/null > maker.oe 2>&1 > > 1. I get a bunch of messages as follows, but with variable line number: > > DBD::SQLite::db do failed: database is locked at > /home/jrs/maker-2.26-beta/bin/../lib/GFFDB.pm line 186. > > I saw that this came up in another thread < > https://groups.google.com/forum/?fromgroups=#!topic/maker-devel/TscBgbQfBX4>, > but I'm not sure it was ever resolved, nor whether it will affect my > reannotation results (as I'm not sure what "your GFF3 results will not be > integrated" means). This error did not come up the last time I ran maker > for reannotation with similar options in a different directory. And both my > current directory and my tmp directory are locally mounted, ie not NFS. > > 2. Both in this run and in previous runs, I get a lot of lines like this, > seemingly at random: > > Warning: unable to close filehandle DF properly. > > > On Mon, Sep 10, 2012 at 6:01 AM, Carson Holt wrote: > >> The map_forward option requires that the pass option for the gene models >> be turned on. Otherwise you will have to do some spacial overlap test >> outside of MAKER. >> >> If you have a new assembly, you can try mapping the old models onto the >> new assembly using the old transcripts as input to the est= and setting >> est2genome=1 (nothing else set, i.e no repeat masking etc.). Then there is >> an undocumented option that is still a little buggy (hence why it is still >> undocumented). Add the line est_forward=1 to your control files. This >> tells MAKER to copy names from the ESTs, build the models directly from >> their alignment, and to do other things to try and make a 1 to 1 match >> across the genome. You will have to manually check that it is 1 to 1 in >> the end (as I said still a little buggy and hence undocumented). Use the >> resulting file as input to the model_gff option on a separate run with >> map_forward=1 for additional reannotation wil more evidence, etc. where you >> want to still be able to map names forward. >> >> From: Jeremy Semeiks >> Date: Sunday, 9 September, 2012 3:49 PM >> To: >> Subject: [maker-devel] How to preserve human-friendly IDs when >> reannotating >> >> Hi all, >> >> I have sequenced some novel fungal genomes, and I am annotating them with >> maker-2.26-beta. The entire project is pretty iterative, in the sense that >> I first get some seemingly-sane annotation sets, then analyze and compare >> the proteomes biologically, then reannotate when new data comes in or as I >> learn more about how maker works. Because I have already attached >> biological meaning to some of my proteins, I would like to retain the same >> human-friendly IDs across annotations. Eg, if maker suddenly finds 1,000 >> new proteins on a reannotation run because I turned on keep_preds, then I >> don't want the transcript formerly known as mymold_09652T0 to become >> mymold_10698T0 when I run maker_map_ids; I want to keep it named >> mymold_09652T0. >> >> So, is there any built-in way to preserve human-friendly IDs, or do I >> need to write my own script for this? I have tried setting map_forward=1 >> and maker_gff=, >> but setting these seems to preserve neither the human-friendly IDs nor even >> the original IDs. (Eg, protein >> "genemark-scaffold353-processed-gene-0.9-mRNA-1" changed its name to >> "genemark-scaffold353-processed-gene-0.6-mRNA-1" when reannotated.) I >> haven't turned on any of the *_pass options, eg protein_pass; would this be >> relevant? >> >> Extra credit question: I am making some mate-pair libraries for these >> fungi; when I re-assemble, that will completely change my scaffold names. >> Is there any easy way to preserve human-friendly transcript names in this >> case? As with the above simpler case, I think it would be pretty easy to >> transfer 90% of the names just by doing an all-vs-all blastp between two >> annotation sets and fishing out the best hits, but the remaining 10% might >> be a headache. >> >> Thanks, >> Jeremy >> Grad student, Grishin lab >> UT Southwestern, Dallas TX >> 510.385.8959 >> _______________________________________________ maker-devel mailing list >> maker-devel at box290.bluehost.com >> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org >> > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From ranjani at uga.edu Wed Sep 12 11:53:37 2012 From: ranjani at uga.edu (Sivaranjani Namasivayam) Date: Wed, 12 Sep 2012 17:53:37 +0000 Subject: [maker-devel] MAKER training In-Reply-To: References: , Message-ID: I have a few questions based on your comment about augustus/MAKER naming convention. I have been sorting the data using the second column of the GFF file, I wanted to be sure I have it right - Doesn't 'maker' in the second column signify MAKER's final annotations based on all evidence (EST, protein and abinitio prediction) ? I noticed two types of gene IDs, example 1. augustus_masked-scaffold00030-abinit-gene-3.2 2. maker-scaffold00030-augustus-gene-3.7 Is the first one, a direct augustus prediction without a hints file and the second based on a hints file (made from the EST and protein evidence)? If this is the case, could 2 be a better annotation than 1? - In case of augustus_masked in the 2nd column, I believe all are predictions are without a hints file. Thanks, Ranjani ________________________________ From: Carson Holt [carsonhh at gmail.com] Sent: Tuesday, September 11, 2012 12:04 PM To: Sivaranjani Namasivayam; maker-devel at yandell-lab.org Subject: Re: [maker-devel] MAKER training - I have transcriptome data from 454 and Illumina platforms. Illumina is from a single time point and 454 from multiple time point. 454 was assembled using Newbler(dataset 1) and Illumina using Tophat-Cufflinks (dataset 2) and the denovo Trinity pipeline (dataset 3). I now have3 assemblies - 454 and Illumina will have some redunant transcripts (because of one overlapping time point); TopHat-Cufflinks and Trinity will have highly redundant transcripts (because they use same raw reads). Is it OK to provide all 3 datasets as EST evidence, how does it affect the quality of annotation. (For now I have used dataset 1 and dataset 2 as EST evidence) This is fine. You can give them as a comma separated list est=file1,file2,file3 - I used the above model to retrain, I passed through everything except the abinitio gene predictions. I also provided a set a manually annotated genes , many of which have EST evidence. Is this OK to do? [ For proteins evidence, I gave a set from related organisms, same as above] - In my third retraining, I used the above retrained model, but this time I only provided the genome_gff but did not pass through any other data. However I did provide the manually annotated genes as EST evidence and related proteins as protein_evidence. Can you please give me some advice on which of these could give me the best prediction, or if I can alter something to get a better prediction. Everything you've done sounds reasonable. Better training comes from having the most correct models to train with, so providing the manual annotations as training works, or you can also select MAKER models with the lowest AED score (i.e. models that most closely match evidence). The goal is to try and make the process as unbias as possible, so a consistent usually automated selection method is often the easiest to justify justifiable. - A quick question about Augustus - I used a Augustus model (trained for a closely related organism) for ab-initio prediction. Does MAKER adjust this model based on the evidence provided, or use the model as such for a prediction. MAKER will provide hints to Augustus during the run to make it perform better. MAKER will report the raw unaided augustus results in the GFF3 file as a reference, but will use evidence to improve performance where it can. The gene name will let you know if it is a hint based or ab initio model prediction. When 'maker', is part of the gene name it is hint based. Thanks, Carson -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Thu Sep 13 07:11:27 2012 From: carsonhh at gmail.com (Carson Holt) Date: Thu, 13 Sep 2012 09:11:27 -0400 Subject: [maker-devel] How to preserve human-friendly IDs when reannotating In-Reply-To: Message-ID: The error --> DBD::SQLite::db do failed: database is locked at /home/jrs/maker-2.26-beta/bin/../lib/GFFDB.pm line 186. The location of the specific error you are getting is probably benign. It is a failure to alter the default cache size for the database. The database should already be populated. I'm planning removing the SQLlite database entirely in the future. Perhaps in favor of something like tabix based indexing of the GFF3 file. Thanks, Carson From: Jeremy Semeiks Date: Tuesday, 11 September, 2012 7:56 PM To: Carson Holt Cc: Subject: Re: [maker-devel] How to preserve human-friendly IDs when reannotating maker 2.26. And I have verified for myself that the three options I mentioned below suffice to preserve human-friendly IDs when reannotating. Thanks, J On Tue, Sep 11, 2012 at 3:33 PM, Carson Holt wrote: > Which version of MAKER are you running (maker --version)? > > --Carson > > > > From: Jeremy Semeiks > Date: Monday, 10 September, 2012 11:02 AM > To: Carson Holt > Cc: > Subject: Re: [maker-devel] How to preserve human-friendly IDs when > reannotating > > OK, thanks. So if I understand correctly, to preserve human-friendly IDs > requires setting just three options: map_forward=1, > maker_gff=, and model_pass=1. (Or instead of the last > two I could equivalently just set model_gff to a GFF containing only models.) > > A couple new issues came up when I tried to run with these options. I started > maker like this: > > /usr/bin/time mpiexec -n 10 maker -q < /dev/null > maker.oe 2>&1 > > 1. I get a bunch of messages as follows, but with variable line number: > > DBD::SQLite::db do failed: database is locked at > /home/jrs/maker-2.26-beta/bin/../lib/GFFDB.pm line 186. > > I saw that this came up in another thread > , > but I'm not sure it was ever resolved, nor whether it will affect my > reannotation results (as I'm not sure what "your GFF3 results will not be > integrated" means). This error did not come up the last time I ran maker for > reannotation with similar options in a different directory. And both my > current directory and my tmp directory are locally mounted, ie not NFS. > > 2. Both in this run and in previous runs, I get a lot of lines like this, > seemingly at random: > > Warning: unable to close filehandle DF properly. > > > On Mon, Sep 10, 2012 at 6:01 AM, Carson Holt wrote: >> The map_forward option requires that the pass option for the gene models be >> turned on. Otherwise you will have to do some spacial overlap test outside >> of MAKER. >> >> If you have a new assembly, you can try mapping the old models onto the new >> assembly using the old transcripts as input to the est= and setting >> est2genome=1 (nothing else set, i.e no repeat masking etc.). Then there is >> an undocumented option that is still a little buggy (hence why it is still >> undocumented). Add the line est_forward=1 to your control files. This tells >> MAKER to copy names from the ESTs, build the models directly from their >> alignment, and to do other things to try and make a 1 to 1 match across the >> genome. You will have to manually check that it is 1 to 1 in the end (as I >> said still a little buggy and hence undocumented). Use the resulting file as >> input to the model_gff option on a separate run with map_forward=1 for >> additional reannotation wil more evidence, etc. where you want to still be >> able to map names forward. >> >> From: Jeremy Semeiks >> Date: Sunday, 9 September, 2012 3:49 PM >> To: >> Subject: [maker-devel] How to preserve human-friendly IDs when reannotating >> >> Hi all, >> >> I have sequenced some novel fungal genomes, and I am annotating them with >> maker-2.26-beta. The entire project is pretty iterative, in the sense that I >> first get some seemingly-sane annotation sets, then analyze and compare the >> proteomes biologically, then reannotate when new data comes in or as I learn >> more about how maker works. Because I have already attached biological >> meaning to some of my proteins, I would like to retain the same >> human-friendly IDs across annotations. Eg, if maker suddenly finds 1,000 new >> proteins on a reannotation run because I turned on keep_preds, then I don't >> want the transcript formerly known as mymold_09652T0 to become mymold_10698T0 >> when I run maker_map_ids; I want to keep it named mymold_09652T0. >> >> So, is there any built-in way to preserve human-friendly IDs, or do I need to >> write my own script for this? I have tried setting map_forward=1 and >> maker_gff=, but >> setting these seems to preserve neither the human-friendly IDs nor even the >> original IDs. (Eg, protein "genemark-scaffold353-processed-gene-0.9-mRNA-1" >> changed its name to "genemark-scaffold353-processed-gene-0.6-mRNA-1" when >> reannotated.) I haven't turned on any of the *_pass options, eg protein_pass; >> would this be relevant? >> >> Extra credit question: I am making some mate-pair libraries for these fungi; >> when I re-assemble, that will completely change my scaffold names. Is there >> any easy way to preserve human-friendly transcript names in this case? As >> with the above simpler case, I think it would be pretty easy to transfer 90% >> of the names just by doing an all-vs-all blastp between two annotation sets >> and fishing out the best hits, but the remaining 10% might be a headache. >> >> Thanks, >> Jeremy >> Grad student, Grishin lab >> UT Southwestern, Dallas TX >> 510.385.8959 >> _______________________________________________ maker-devel mailing list >> maker-devel at box290.bluehost.comhttp://box290.bluehost.com/mailman/listinfo/ma >> ker-devel_yandell-lab.org > -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Thu Sep 13 07:30:22 2012 From: carsonhh at gmail.com (Carson Holt) Date: Thu, 13 Sep 2012 09:30:22 -0400 Subject: [maker-devel] MAKER training In-Reply-To: Message-ID: Yes, those are the final annotations, and yes one is derived from the ab initio model and one from hint based models. The selection between hint based models and ab initio models is based on evidence overlap, so either can be better than the other or vice versa. The bets models will have lower AED scores. So if for a given locus I have both hint based and ab initio based models, I keep the one that best matches the evidence (lowest AED score). augustus_masked means the genome was masked for repeats before running augustus. Anything with augustus_masked in the second column will be ab initio models kept for reference purposes. Every ab initio model produced by augustus will have an entry there. Thanks, Carson From: Sivaranjani Namasivayam Date: Wednesday, 12 September, 2012 1:53 PM To: Carson Holt , "maker-devel at yandell-lab.org" Subject: RE: [maker-devel] MAKER training I have a few questions based on your comment about augustus/MAKER naming convention. I have been sorting the data using the second column of the GFF file, I wanted to be sure I have it right - Doesn't 'maker' in the second column signify MAKER's final annotations based on all evidence (EST, protein and abinitio prediction) ? I noticed two types of gene IDs, example 1. augustus_masked-scaffold00030-abinit-gene-3.2 2. maker-scaffold00030-augustus-gene-3.7 Is the first one, a direct augustus prediction without a hints file and the second based on a hints file (made from the EST and protein evidence)? If this is the case, could 2 be a better annotation than 1? - In case of augustus_masked in the 2nd column, I believe all are predictions are without a hints file. Thanks, Ranjani From: Carson Holt [carsonhh at gmail.com] Sent: Tuesday, September 11, 2012 12:04 PM To: Sivaranjani Namasivayam; maker-devel at yandell-lab.org Subject: Re: [maker-devel] MAKER training > - I have transcriptome data from 454 and Illumina platforms. Illumina is from > a single time point and 454 from multiple time point. 454 was assembled using > Newbler(dataset 1) and Illumina using Tophat-Cufflinks (dataset 2) and the > denovo Trinity pipeline (dataset 3). I now have3 assemblies - 454 and > Illumina will have some redunant transcripts (because of one overlapping time > point); TopHat-Cufflinks and Trinity will have highly redundant transcripts > (because they use same raw reads). Is it OK to provide all 3 datasets as EST > evidence, how does it affect the quality of annotation. (For now I have used > dataset 1 and dataset 2 as EST evidence) This is fine. You can give them as a comma separated list est=file1,file2,file3 > - I used the above model to retrain, I passed through everything except the > abinitio gene predictions. I also provided a set a manually annotated genes , > many of which have EST evidence. Is this OK to do? [ For proteins evidence, I > gave a set from related organisms, same as above] > > - In my third retraining, I used the above retrained model, but this time I > only provided the genome_gff but did not pass through any other data. However > I did provide the manually annotated genes as EST evidence and related > proteins as protein_evidence. > > Can you please give me some advice on which of these could give me the best > prediction, or if I can alter something to get a better prediction. > Everything you've done sounds reasonable. Better training comes from having the most correct models to train with, so providing the manual annotations as training works, or you can also select MAKER models with the lowest AED score (i.e. models that most closely match evidence). The goal is to try and make the process as unbias as possible, so a consistent usually automated selection method is often the easiest to justify justifiable. > > - A quick question about Augustus - I used a Augustus model (trained for a > closely related organism) for ab-initio prediction. Does MAKER adjust this > model based on the evidence provided, or use the model as such for a > prediction. MAKER will provide hints to Augustus during the run to make it perform better. MAKER will report the raw unaided augustus results in the GFF3 file as a reference, but will use evidence to improve performance where it can. The gene name will let you know if it is a hint based or ab initio model prediction. When 'maker', is part of the gene name it is hint based. Thanks, Carson -------------- next part -------------- An HTML attachment was scrubbed... URL: From guoyunfei1989 at gmail.com Wed Sep 19 10:41:40 2012 From: guoyunfei1989 at gmail.com (Yunfei Guo) Date: Wed, 19 Sep 2012 09:41:40 -0700 Subject: [maker-devel] open3: fork failed: Cannot allocate memory Message-ID: Hi Carson, Sorry to bother you again because I really can't find a solution to it. Have you seen this error before? I simply started multiple jobs in the same directory and got the following msg after hours of running. >From Admin: "Your batch job 2511011 encountered the following error: open3: fork failed: Cannot allocate memory ERROR: Failed while polishig ESTs ERROR: Chunk failed at level:2, tier_type:2 FAILED CONTIG:scaffold740 It continued generating errors in a loop until the /var filesystem filled. I will cancel the job. You may find it useful within your job script to check for errors and exit if present." And this is not because of lack of memory since this job has exclusive access to the node. Let me know if you want the entire stderr file. Thanks. From carsonhh at gmail.com Fri Sep 21 07:28:34 2012 From: carsonhh at gmail.com (Carson Holt) Date: Fri, 21 Sep 2012 09:28:34 -0400 Subject: [maker-devel] open3: fork failed: Cannot allocate memory In-Reply-To: Message-ID: Exclusive access doesn't necessarily mean that memory is not full, especially if you are running via MPI. Under MPI each MAKER instance will have a separate memory footprint (the sum of which may be too high for your system). You can lower the memory footprint per instance by setting all the blast_depth options in the maker_bopt.ctl file. Set them to 30 for example. Also in you have set max_dna_len to a value greater than 100000, bring it back down. A value of 200000 for example will cause MAEKR to use twice as much memory as 100000. The primary cause of high memory is too much evidence aligning in a region. Setting the depth parameter to 30 will cause MAKER to sort the alignments as they come in and drop all but the best 30 alignments. Each instance of MAKER will usually take up 500Mb to 1Gb of RAM when max_dna_len is set to 100,000. It will take up twice that when max_dna_len is set to 200,000. Alternatively, if you are also using MPI, you can set the job up to launch fewer instances of MAKER, but allow each instance to use more CPUs. You do this by halving the value of the -n option given to mpiexec and then setting cpus=2 in the maker_opts file. The result in that BLAST analyses will run on 2 cpus each but MAKER will only keep the results for 6 jobs in memory at a time rather than 12 jobs (I.e. Lower memory footprint). When using this technique, make sure the hostfile used by mpiexec is set to follow a round robin distribution or all instances will start on half your nodes while the other half of your nodes will be left idle. Example - this is correct: host1 host2 host3 host1 host2 host3 host1 host2 host3 This is incorrect: host1 host1 host1 host2 host2 host2 host3 host3 host3 FYI when using MPI the -n parameter given to mpiexec and the -cpus parameter given to MAKER have a multiplicative affect on CPU usage. Example: mpiexec -n 12 maker -cpus 1 (will launch 12 maker instances and use a total of 12 cpus) mpiexec -n 12 maker -cpus 2 (will launch 12 maker instances but use a total of 24 cpus) mpiexec -n 6 maker -cpus 4 (will launch 6 maker instances but use a total of 24 cpus) Why is this? It's because CPUs affects how many processors to use to solve a single 100,000 bp chunk (per instance). But mpiexec -n sets how many simultaneous instances and as a result how many chunks to run together. So mpiexec -n will cause memory usage to increase in a way that -cpus doesn't. But mpiexec also scales across machines for parallelization where -cpus can't (it's use applies to a single machine). Thanks, Carson On 12-09-19 12:41 PM, "Yunfei Guo" wrote: >Hi Carson, > >Sorry to bother you again because I really can't find a solution to >it. Have you seen this error before? I simply started multiple jobs in >the same directory and got the following msg after hours of running. > >From Admin: >"Your batch job 2511011 encountered the following error: > open3: fork failed: Cannot allocate memory > ERROR: Failed while polishig ESTs > ERROR: Chunk failed at level:2, tier_type:2 > FAILED CONTIG:scaffold740 >It continued generating errors in a loop until the /var filesystem filled. >I will cancel the job. You may find it useful within your job script to >check for errors and exit if present." > >And this is not because of lack of memory since this job has exclusive >access to the node. Let me know if you want the entire stderr file. >Thanks. > >_______________________________________________ >maker-devel mailing list >maker-devel at box290.bluehost.com >http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org From fourie.joubert at up.ac.za Fri Sep 21 07:58:26 2012 From: fourie.joubert at up.ac.za (Fourie Joubert) Date: Fri, 21 Sep 2012 15:58:26 +0200 Subject: [maker-devel] Problems parsing iprscan results with iprscan2gff3 Message-ID: <505C7282.3090107@up.ac.za> Hi Folks I am running into some problems parsing iprscan results. I run iprscan as follows: > iprscan -cli -i bot.all.maker.proteins.fasta -o bot.all.maker.proteins.raw -format raw -goterms -iprlookup and obtain the iprscan output (the iprscan output file is at http://www.bi.up.ac.za/~fourie/bot.all.maker.proteins.raw if anyone is interested in the detailed output, and the initial maker gff3 file is at http://www.bi.up.ac.za/~fourie/bot.all.gff). I then try to run the conversion to gff3, but I get very long list of errors: > iprscan2gff3 bot.all.maker.proteins.raw bot.all.gff > domains.gff ERROR: In maker-NODE_4797_length_138874_cov_96.632576-augustus-gene-0.113 Use of uninitialized value $seqid in concatenation (.) or string at /usr/local/maker/bin/iprscan2gff3 line 255. Use of uninitialized value $start in concatenation (.) or string at /usr/local/maker/bin/iprscan2gff3 line 255. Use of uninitialized value $end in concatenation (.) or string at /usr/local/maker/bin/iprscan2gff3 line 255. Use of uninitialized value $strand in concatenation (.) or string at /usr/local/maker/bin/iprscan2gff3 line 255. Use of uninitialized value $off in subtraction (-) at /usr/local/maker/bin/iprscan2gff3 line 267. Use of uninitialized value $pB in subtraction (-) at /usr/local/maker/bin/iprscan2gff3 line 267. Use of uninitialized value $off in subtraction (-) at /usr/local/maker/bin/iprscan2gff3 line 267. Use of uninitialized value $pE in subtraction (-) at /usr/local/maker/bin/iprscan2gff3 line 267. Use of uninitialized value $seqid in concatenation (.) or string at /usr/local/maker/bin/iprscan2gff3 line 269. Use of uninitialized value $start in concatenation (.) or string at /usr/local/maker/bin/iprscan2gff3 line 269. Use of uninitialized value $end in concatenation (.) or string at /usr/local/maker/bin/iprscan2gff3 line 269. Use of uninitialized value $strand in concatenation (.) or string at /usr/local/maker/bin/iprscan2gff3 line 269. ....... ....... ....... for most of the entries. Any advice or help would be sincerely appreciated! Best regards! Fourie -- -------------- Prof Fourie Joubert Bioinformatics and Computational Biology Unit Department of Biochemistry University of Pretoria fourie.joubert at up.ac.za http://www.bi.up.ac.za Tel. +27-12-420-5825 Fax. +27-12-420-5800 ------------------------------------------------------------------------- This message and attachments are subject to a disclaimer. Please refer to www.it.up.ac.za/documentation/governance/disclaimer/ for full details. -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Fri Sep 21 08:10:21 2012 From: carsonhh at gmail.com (Carson Holt) Date: Fri, 21 Sep 2012 10:10:21 -0400 Subject: [maker-devel] Problems parsing iprscan results with iprscan2gff3 In-Reply-To: <505C7282.3090107@up.ac.za> Message-ID: Some of your iprscan results contain truncated names Example: maker-NODE_5172_length_118591_cov_102.277115-snap-gene-0.100-mR This seems to be the case for almost all HMMPanther and HMMSmart results. Try just removing those two groups of results from your file for now. Then use the iprscan_wrap script that comes with maker to just re-run just those two application within iprscan it will fix the truncation issue (it creates temporary short names and then converts back to the longer names when it parses the results). Thanks, Carson From: Fourie Joubert Date: Friday, 21 September, 2012 9:58 AM To: "maker-devel at yandell-lab.org" Subject: [maker-devel] Problems parsing iprscan results with iprscan2gff3 Hi Folks I am running into some problems parsing iprscan results. I run iprscan as follows: > iprscan -cli -i bot.all.maker.proteins.fasta -o bot.all.maker.proteins.raw -format raw -goterms -iprlookup and obtain the iprscan output (the iprscan output file is at http://www.bi.up.ac.za/~fourie/bot.all.maker.proteins.raw if anyone is interested in the detailed output, and the initial maker gff3 file is at http://www.bi.up.ac.za/~fourie/bot.all.gff). I then try to run the conversion to gff3, but I get very long list of errors: > iprscan2gff3 bot.all.maker.proteins.raw bot.all.gff > domains.gff ERROR: In maker-NODE_4797_length_138874_cov_96.632576-augustus-gene-0.113 Use of uninitialized value $seqid in concatenation (.) or string at /usr/local/maker/bin/iprscan2gff3 line 255. Use of uninitialized value $start in concatenation (.) or string at /usr/local/maker/bin/iprscan2gff3 line 255. Use of uninitialized value $end in concatenation (.) or string at /usr/local/maker/bin/iprscan2gff3 line 255. Use of uninitialized value $strand in concatenation (.) or string at /usr/local/maker/bin/iprscan2gff3 line 255. Use of uninitialized value $off in subtraction (-) at /usr/local/maker/bin/iprscan2gff3 line 267. Use of uninitialized value $pB in subtraction (-) at /usr/local/maker/bin/iprscan2gff3 line 267. Use of uninitialized value $off in subtraction (-) at /usr/local/maker/bin/iprscan2gff3 line 267. Use of uninitialized value $pE in subtraction (-) at /usr/local/maker/bin/iprscan2gff3 line 267. Use of uninitialized value $seqid in concatenation (.) or string at /usr/local/maker/bin/iprscan2gff3 line 269. Use of uninitialized value $start in concatenation (.) or string at /usr/local/maker/bin/iprscan2gff3 line 269. Use of uninitialized value $end in concatenation (.) or string at /usr/local/maker/bin/iprscan2gff3 line 269. Use of uninitialized value $strand in concatenation (.) or string at /usr/local/maker/bin/iprscan2gff3 line 269. ....... ....... ....... for most of the entries. Any advice or help would be sincerely appreciated! Best regards! Fourie -- -------------- Prof Fourie Joubert Bioinformatics and Computational Biology Unit Department of Biochemistry University of Pretoria fourie.joubert at up.ac.zahttp://www.bi.up.ac.za Tel. +27-12-420-5825 Fax. +27-12-420-5800 ------------------------------------------------------------------------- This message and attachments are subject to a disclaimer. Please refer to www.it.up.ac.za/documentation/governance/disclaimer/ for full details. _______________________________________________ maker-devel mailing list maker-devel at box290.bluehost.com http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org -------------- next part -------------- An HTML attachment was scrubbed... URL: From jeremy.semeiks at utsw.edu Fri Sep 21 09:39:15 2012 From: jeremy.semeiks at utsw.edu (Jeremy Semeiks) Date: Fri, 21 Sep 2012 10:39:15 -0500 Subject: [maker-devel] How to preserve human-friendly IDs when reannotating In-Reply-To: References: Message-ID: For the record: After analyzing these runs, I have confirmed that neither error I described (ie, "DBD::SQLite::db do failed" and "Warning: unable to close filehandle DF properly") affects maker's protein output in any way I can detect. Thanks, J On Thu, Sep 13, 2012 at 8:11 AM, Carson Holt wrote: > The error --> DBD::SQLite::db do failed: database is locked at > /home/jrs/maker-2.26-beta/bin/../lib/GFFDB.pm line 186. > > The location of the specific error you are getting is probably benign. It > is a failure to alter the default cache size for the database. The > database should already be populated. I'm planning removing the SQLlite > database entirely in the future. Perhaps in favor of something like tabix > based indexing of the GFF3 file. > > Thanks, > Carson > > > > From: Jeremy Semeiks > Date: Tuesday, 11 September, 2012 7:56 PM > > To: Carson Holt > Cc: > Subject: Re: [maker-devel] How to preserve human-friendly IDs when > reannotating > > maker 2.26. > > And I have verified for myself that the three options I mentioned below > suffice to preserve human-friendly IDs when reannotating. > > Thanks, > J > > On Tue, Sep 11, 2012 at 3:33 PM, Carson Holt wrote: > >> Which version of MAKER are you running (maker --version)? >> >> --Carson >> >> >> >> From: Jeremy Semeiks >> Date: Monday, 10 September, 2012 11:02 AM >> To: Carson Holt >> Cc: >> Subject: Re: [maker-devel] How to preserve human-friendly IDs when >> reannotating >> >> OK, thanks. So if I understand correctly, to preserve human-friendly IDs >> requires setting just three options: map_forward=1, >> maker_gff=, and model_pass=1. (Or instead of the >> last two I could equivalently just set model_gff to a GFF containing only >> models.) >> >> A couple new issues came up when I tried to run with these options. I >> started maker like this: >> >> /usr/bin/time mpiexec -n 10 maker -q < /dev/null > maker.oe 2>&1 >> >> 1. I get a bunch of messages as follows, but with variable line number: >> >> DBD::SQLite::db do failed: database is locked at >> /home/jrs/maker-2.26-beta/bin/../lib/GFFDB.pm line 186. >> >> I saw that this came up in another thread < >> https://groups.google.com/forum/?fromgroups=#!topic/maker-devel/TscBgbQfBX4>, >> but I'm not sure it was ever resolved, nor whether it will affect my >> reannotation results (as I'm not sure what "your GFF3 results will not be >> integrated" means). This error did not come up the last time I ran maker >> for reannotation with similar options in a different directory. And both my >> current directory and my tmp directory are locally mounted, ie not NFS. >> >> 2. Both in this run and in previous runs, I get a lot of lines like this, >> seemingly at random: >> >> Warning: unable to close filehandle DF properly. >> >> >> On Mon, Sep 10, 2012 at 6:01 AM, Carson Holt wrote: >> >>> The map_forward option requires that the pass option for the gene models >>> be turned on. Otherwise you will have to do some spacial overlap test >>> outside of MAKER. >>> >>> If you have a new assembly, you can try mapping the old models onto the >>> new assembly using the old transcripts as input to the est= and setting >>> est2genome=1 (nothing else set, i.e no repeat masking etc.). Then there is >>> an undocumented option that is still a little buggy (hence why it is still >>> undocumented). Add the line est_forward=1 to your control files. This >>> tells MAKER to copy names from the ESTs, build the models directly from >>> their alignment, and to do other things to try and make a 1 to 1 match >>> across the genome. You will have to manually check that it is 1 to 1 in >>> the end (as I said still a little buggy and hence undocumented). Use the >>> resulting file as input to the model_gff option on a separate run with >>> map_forward=1 for additional reannotation wil more evidence, etc. where you >>> want to still be able to map names forward. >>> >>> From: Jeremy Semeiks >>> Date: Sunday, 9 September, 2012 3:49 PM >>> To: >>> Subject: [maker-devel] How to preserve human-friendly IDs when >>> reannotating >>> >>> Hi all, >>> >>> I have sequenced some novel fungal genomes, and I am annotating them >>> with maker-2.26-beta. The entire project is pretty iterative, in the sense >>> that I first get some seemingly-sane annotation sets, then analyze and >>> compare the proteomes biologically, then reannotate when new data comes in >>> or as I learn more about how maker works. Because I have already attached >>> biological meaning to some of my proteins, I would like to retain the same >>> human-friendly IDs across annotations. Eg, if maker suddenly finds 1,000 >>> new proteins on a reannotation run because I turned on keep_preds, then I >>> don't want the transcript formerly known as mymold_09652T0 to become >>> mymold_10698T0 when I run maker_map_ids; I want to keep it named >>> mymold_09652T0. >>> >>> So, is there any built-in way to preserve human-friendly IDs, or do I >>> need to write my own script for this? I have tried setting map_forward=1 >>> and maker_gff=, >>> but setting these seems to preserve neither the human-friendly IDs nor even >>> the original IDs. (Eg, protein >>> "genemark-scaffold353-processed-gene-0.9-mRNA-1" changed its name to >>> "genemark-scaffold353-processed-gene-0.6-mRNA-1" when reannotated.) I >>> haven't turned on any of the *_pass options, eg protein_pass; would this be >>> relevant? >>> >>> Extra credit question: I am making some mate-pair libraries for these >>> fungi; when I re-assemble, that will completely change my scaffold names. >>> Is there any easy way to preserve human-friendly transcript names in this >>> case? As with the above simpler case, I think it would be pretty easy to >>> transfer 90% of the names just by doing an all-vs-all blastp between two >>> annotation sets and fishing out the best hits, but the remaining 10% might >>> be a headache. >>> >>> Thanks, >>> Jeremy >>> Grad student, Grishin lab >>> UT Southwestern, Dallas TX >>> 510.385.8959 >>> _______________________________________________ maker-devel mailing list >>> maker-devel at box290.bluehost.com >>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org >>> >> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Fri Sep 21 09:42:46 2012 From: carsonhh at gmail.com (Carson Holt) Date: Fri, 21 Sep 2012 11:42:46 -0400 Subject: [maker-devel] How to preserve human-friendly IDs when reannotating In-Reply-To: Message-ID: That's good to know :-) --Carson From: Jeremy Semeiks Date: Friday, 21 September, 2012 11:39 AM To: Carson Holt Cc: Subject: Re: [maker-devel] How to preserve human-friendly IDs when reannotating For the record: After analyzing these runs, I have confirmed that neither error I described (ie, "DBD::SQLite::db do failed" and "Warning: unable to close filehandle DF properly") affects maker's protein output in any way I can detect. Thanks, J On Thu, Sep 13, 2012 at 8:11 AM, Carson Holt wrote: > The error --> DBD::SQLite::db do failed: database is locked at > /home/jrs/maker-2.26-beta/bin/../lib/GFFDB.pm line 186. > > The location of the specific error you are getting is probably benign. It is > a failure to alter the default cache size for the database. The database > should already be populated. I'm planning removing the SQLlite database > entirely in the future. Perhaps in favor of something like tabix based > indexing of the GFF3 file. > > Thanks, > Carson > > > > From: Jeremy Semeiks > Date: Tuesday, 11 September, 2012 7:56 PM > > To: Carson Holt > Cc: > Subject: Re: [maker-devel] How to preserve human-friendly IDs when > reannotating > > maker 2.26. > > And I have verified for myself that the three options I mentioned below > suffice to preserve human-friendly IDs when reannotating. > > Thanks, > J > > On Tue, Sep 11, 2012 at 3:33 PM, Carson Holt wrote: >> Which version of MAKER are you running (maker --version)? >> >> --Carson >> >> >> >> From: Jeremy Semeiks >> Date: Monday, 10 September, 2012 11:02 AM >> To: Carson Holt >> Cc: >> Subject: Re: [maker-devel] How to preserve human-friendly IDs when >> reannotating >> >> OK, thanks. So if I understand correctly, to preserve human-friendly IDs >> requires setting just three options: map_forward=1, >> maker_gff=, and model_pass=1. (Or instead of the last >> two I could equivalently just set model_gff to a GFF containing only models.) >> >> A couple new issues came up when I tried to run with these options. I started >> maker like this: >> >> /usr/bin/time mpiexec -n 10 maker -q < /dev/null > maker.oe 2>&1 >> >> 1. I get a bunch of messages as follows, but with variable line number: >> >> DBD::SQLite::db do failed: database is locked at >> /home/jrs/maker-2.26-beta/bin/../lib/GFFDB.pm line 186. >> >> I saw that this came up in another thread >> >> , but I'm not sure it was ever resolved, nor whether it will affect my >> reannotation results (as I'm not sure what "your GFF3 results will not be >> integrated" means). This error did not come up the last time I ran maker for >> reannotation with similar options in a different directory. And both my >> current directory and my tmp directory are locally mounted, ie not NFS. >> >> 2. Both in this run and in previous runs, I get a lot of lines like this, >> seemingly at random: >> >> Warning: unable to close filehandle DF properly. >> >> >> On Mon, Sep 10, 2012 at 6:01 AM, Carson Holt wrote: >>> The map_forward option requires that the pass option for the gene models be >>> turned on. Otherwise you will have to do some spacial overlap test outside >>> of MAKER. >>> >>> If you have a new assembly, you can try mapping the old models onto the new >>> assembly using the old transcripts as input to the est= and setting >>> est2genome=1 (nothing else set, i.e no repeat masking etc.). Then there is >>> an undocumented option that is still a little buggy (hence why it is still >>> undocumented). Add the line est_forward=1 to your control files. This >>> tells MAKER to copy names from the ESTs, build the models directly from >>> their alignment, and to do other things to try and make a 1 to 1 match >>> across the genome. You will have to manually check that it is 1 to 1 in the >>> end (as I said still a little buggy and hence undocumented). Use the >>> resulting file as input to the model_gff option on a separate run with >>> map_forward=1 for additional reannotation wil more evidence, etc. where you >>> want to still be able to map names forward. >>> >>> From: Jeremy Semeiks >>> Date: Sunday, 9 September, 2012 3:49 PM >>> To: >>> Subject: [maker-devel] How to preserve human-friendly IDs when reannotating >>> >>> Hi all, >>> >>> I have sequenced some novel fungal genomes, and I am annotating them with >>> maker-2.26-beta. The entire project is pretty iterative, in the sense that I >>> first get some seemingly-sane annotation sets, then analyze and compare the >>> proteomes biologically, then reannotate when new data comes in or as I learn >>> more about how maker works. Because I have already attached biological >>> meaning to some of my proteins, I would like to retain the same >>> human-friendly IDs across annotations. Eg, if maker suddenly finds 1,000 new >>> proteins on a reannotation run because I turned on keep_preds, then I don't >>> want the transcript formerly known as mymold_09652T0 to become >>> mymold_10698T0 when I run maker_map_ids; I want to keep it named >>> mymold_09652T0. >>> >>> So, is there any built-in way to preserve human-friendly IDs, or do I need >>> to write my own script for this? I have tried setting map_forward=1 and >>> maker_gff=, but >>> setting these seems to preserve neither the human-friendly IDs nor even the >>> original IDs. (Eg, protein "genemark-scaffold353-processed-gene-0.9-mRNA-1" >>> changed its name to "genemark-scaffold353-processed-gene-0.6-mRNA-1" when >>> reannotated.) I haven't turned on any of the *_pass options, eg >>> protein_pass; would this be relevant? >>> >>> Extra credit question: I am making some mate-pair libraries for these fungi; >>> when I re-assemble, that will completely change my scaffold names. Is there >>> any easy way to preserve human-friendly transcript names in this case? As >>> with the above simpler case, I think it would be pretty easy to transfer 90% >>> of the names just by doing an all-vs-all blastp between two annotation sets >>> and fishing out the best hits, but the remaining 10% might be a headache. >>> >>> Thanks, >>> Jeremy >>> Grad student, Grishin lab >>> UT Southwestern, Dallas TX >>> 510.385.8959 >>> _______________________________________________ maker-devel mailing list >>> maker-devel at box290.bluehost.comhttp://box290.bluehost.com/mailman/listinfo/m >>> aker-devel_yandell-lab.org >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From ianmisner17 at aim.com Tue Sep 25 06:27:04 2012 From: ianmisner17 at aim.com (Ian Misner) Date: Tue, 25 Sep 2012 08:27:04 -0400 Subject: [maker-devel] problem with maker_map_ids Message-ID: Hello, I'm trying to create human friendly ids and I'm getting an error when I use the -sort_file option. Without the sort file it runs fine just not numbered from the first contig. I have had some programers at our cluster look at the script and they attempted a fix but it did not work. They mentioned the script was "buggy" so this might be part of the problem. I've attached the error as well as the sort file. I can send more files if necessary. Thanks for you time. Cheers Ian $ maker_map_ids --prefix THRCLA_ --justify 5 --sort_order 34112_sort.txt 34112_3June11Ass.gff > 34112_3June11Ass_named.txt Can't use string ("34112_sort.txt") as a HASH ref while "strict refs" in use at /gpfs/runtime/opt/maker/2.10/maker/bin/maker_map_ids line 311, <$IN> line 499186. -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: 34112_sort.txt URL: From ianmisner at my.uri.edu Tue Sep 25 06:31:23 2012 From: ianmisner at my.uri.edu (Ian Misner) Date: Tue, 25 Sep 2012 08:31:23 -0400 Subject: [maker-devel] Problem with maker_map_ids Message-ID: <0FCB8ACD-35A0-4ED8-BAE2-02C2621E3F65@my.uri.edu> Hello, I'm trying to create human friendly ids and I'm getting an error when I use the -sort_file option. Without the sort file it runs fine just not numbered from the first contig. I have had some programers at our cluster look at the script and they attempted a fix but it did not work. They mentioned the script was "buggy" so this might be part of the problem. I've attached the error as well as the sort file. I can send more files if necessary. Thanks for you time. Cheers Ian $ maker_map_ids --prefix THRCLA_ --justify 5 --sort_order 34112_sort.txt 34112_3June11Ass.gff > 34112_3June11Ass_named.txt Can't use string ("34112_sort.txt") as a HASH ref while "strict refs" in use at /gpfs/runtime/opt/maker/2.10/maker/bin/maker_map_ids line 311, <$IN> line 499186. -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: 34112_sort.txt URL: From carsonhh at gmail.com Tue Sep 25 06:44:02 2012 From: carsonhh at gmail.com (Carson Holt) Date: Tue, 25 Sep 2012 08:44:02 -0400 Subject: [maker-devel] Problem with maker_map_ids In-Reply-To: <0FCB8ACD-35A0-4ED8-BAE2-02C2621E3F65@my.uri.edu> Message-ID: Could you also provide 34112_3June11Ass.gff? Thanks, Carson On 12-09-25 8:31 AM, "Ian Misner" wrote: >Hello, > >I'm trying to create human friendly ids and I'm getting an error when I >use the -sort_file option. Without the sort file it runs fine just not >numbered from the first contig. I have had some programers at our cluster >look at the script and they attempted a fix but it did not work. They >mentioned the script was "buggy" so this might be part of the problem. >I've attached the error as well as the sort file. I can send more files >if necessary. Thanks for you time. > >Cheers >Ian > >$ maker_map_ids --prefix THRCLA_ --justify 5 --sort_order 34112_sort.txt >34112_3June11Ass.gff > 34112_3June11Ass_named.txt >Can't use string ("34112_sort.txt") as a HASH ref while "strict refs" in >use at /gpfs/runtime/opt/maker/2.10/maker/bin/maker_map_ids line 311, ><$IN> line 499186._______________________________________________ >maker-devel mailing list >maker-devel at box290.bluehost.com >http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org From carsonhh at gmail.com Tue Sep 25 07:01:31 2012 From: carsonhh at gmail.com (Carson Holt) Date: Tue, 25 Sep 2012 09:01:31 -0400 Subject: [maker-devel] Problem with maker_map_ids In-Reply-To: Message-ID: While you are sending me the GFF3 file also try the sort order file attached. I found a number of illegal meta character contaminating the file. Sometimes those can be introduced by text editors or sometimes e-mail clients. In case it wasn't the e-mail client I'm sending you this fixed version. Also I see you are using maker_map_ids from version 2.10. Try the 2.26 version. They are different. Thanks, Carson On 12-09-25 8:44 AM, "Carson Holt" wrote: >Could you also provide 34112_3June11Ass.gff? > >Thanks, >Carson > > >On 12-09-25 8:31 AM, "Ian Misner" wrote: > >>Hello, >> >>I'm trying to create human friendly ids and I'm getting an error when I >>use the -sort_file option. Without the sort file it runs fine just not >>numbered from the first contig. I have had some programers at our >>cluster >>look at the script and they attempted a fix but it did not work. They >>mentioned the script was "buggy" so this might be part of the problem. >>I've attached the error as well as the sort file. I can send more files >>if necessary. Thanks for you time. >> >>Cheers >>Ian >> >>$ maker_map_ids --prefix THRCLA_ --justify 5 --sort_order 34112_sort.txt >>34112_3June11Ass.gff > 34112_3June11Ass_named.txt >>Can't use string ("34112_sort.txt") as a HASH ref while "strict refs" in >>use at /gpfs/runtime/opt/maker/2.10/maker/bin/maker_map_ids line 311, >><$IN> line 499186._______________________________________________ >>maker-devel mailing list >>maker-devel at box290.bluehost.com >>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org -------------- next part -------------- A non-text attachment was scrubbed... Name: 34112_sort.txt.gz Type: application/x-gzip Size: 27598 bytes Desc: not available URL: From carsonhh at gmail.com Tue Sep 25 07:13:54 2012 From: carsonhh at gmail.com (Carson Holt) Date: Tue, 25 Sep 2012 09:13:54 -0400 Subject: [maker-devel] Problem with maker_map_ids In-Reply-To: Message-ID: Thanks for the GFF3 file. The meta character came across in the GFF3 as well, so I think it's safe to assume they are being introduced by the e-mail client used to add the attachment (so ignore the last file I sent). I've attached the fixed maker_map_ids. Thanks, Carson On 12-09-25 9:01 AM, "Carson Holt" wrote: >While you are sending me the GFF3 file also try the sort order file >attached. I found a number of illegal meta character contaminating the >file. Sometimes those can be introduced by text editors or sometimes >e-mail clients. In case it wasn't the e-mail client I'm sending you this >fixed version. > >Also I see you are using maker_map_ids from version 2.10. Try the 2.26 >version. They are different. > >Thanks, >Carson > > >On 12-09-25 8:44 AM, "Carson Holt" wrote: > >>Could you also provide 34112_3June11Ass.gff? >> >>Thanks, >>Carson >> >> >>On 12-09-25 8:31 AM, "Ian Misner" wrote: >> >>>Hello, >>> >>>I'm trying to create human friendly ids and I'm getting an error when I >>>use the -sort_file option. Without the sort file it runs fine just not >>>numbered from the first contig. I have had some programers at our >>>cluster >>>look at the script and they attempted a fix but it did not work. They >>>mentioned the script was "buggy" so this might be part of the problem. >>>I've attached the error as well as the sort file. I can send more files >>>if necessary. Thanks for you time. >>> >>>Cheers >>>Ian >>> >>>$ maker_map_ids --prefix THRCLA_ --justify 5 --sort_order >>>34112_sort.txt >>>34112_3June11Ass.gff > 34112_3June11Ass_named.txt >>>Can't use string ("34112_sort.txt") as a HASH ref while "strict refs" >>>in >>>use at /gpfs/runtime/opt/maker/2.10/maker/bin/maker_map_ids line 311, >>><$IN> line 499186._______________________________________________ >>>maker-devel mailing list >>>maker-devel at box290.bluehost.com >>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org -------------- next part -------------- A non-text attachment was scrubbed... Name: maker_map_ids.gz Type: application/x-gzip Size: 3216 bytes Desc: not available URL: From fourie.joubert at up.ac.za Thu Sep 27 08:37:53 2012 From: fourie.joubert at up.ac.za (Fourie Joubert) Date: Thu, 27 Sep 2012 16:37:53 +0200 Subject: [maker-devel] Problem with maker2chado Message-ID: <506464C1.40103@up.ac.za> Hi I am trying to load a maker gff file into chado using maker2chado, but I am seeing the following type of error: Can't locate object method "value" via package "NODE_1002_length_51300_cov_98.972473" (perhaps you forgot to load "NODE_1002_length_51300_cov_98.972473"?) at /usr/local/bin/gmod_bulk_load_gff3.pl line 722, line 2. Any advice would be sincerely appreciated! Best regards! Fourie -- -------------- Prof Fourie Joubert Bioinformatics and Computational Biology Unit Department of Biochemistry University of Pretoria fourie.joubert at up.ac.za http://www.bi.up.ac.za Tel. +27-12-420-5825 Fax. +27-12-420-5800 ------------------------------------------------------------------------- This message and attachments are subject to a disclaimer. Please refer to www.it.up.ac.za/documentation/governance/disclaimer/ for full details. From carsonhh at gmail.com Thu Sep 27 10:27:14 2012 From: carsonhh at gmail.com (Carson Holt) Date: Thu, 27 Sep 2012 12:27:14 -0400 Subject: [maker-devel] Problem with maker2chado In-Reply-To: <506464C1.40103@up.ac.za> Message-ID: The error is being thrown by /usr/local/bin/gmod_bulk_load_gff3.pl It is called by MAKER and is part of the chado install. Try getting the latest version of chado from the SVN repository and then reinstalling it. Command to use --> svn co https://gmod.svn.sourceforge.net/svnroot/gmod/schema/trunk chado --Carson On 12-09-27 10:37 AM, "Fourie Joubert" wrote: >Hi > >I am trying to load a maker gff file into chado using maker2chado, but I >am seeing the following type of error: > >Can't locate object method "value" via package >"NODE_1002_length_51300_cov_98.972473" (perhaps you forgot to load >"NODE_1002_length_51300_cov_98.972473"?) at >/usr/local/bin/gmod_bulk_load_gff3.pl line 722, line 2. > >Any advice would be sincerely appreciated! > >Best regards! > >Fourie > >-- >-------------- >Prof Fourie Joubert >Bioinformatics and Computational Biology Unit >Department of Biochemistry >University of Pretoria >fourie.joubert at up.ac.za >http://www.bi.up.ac.za >Tel. +27-12-420-5825 >Fax. +27-12-420-5800 > >------------------------------------------------------------------------- >This message and attachments are subject to a disclaimer. Please refer >to www.it.up.ac.za/documentation/governance/disclaimer/ for full details. > > >_______________________________________________ >maker-devel mailing list >maker-devel at box290.bluehost.com >http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org From mike.thon at gmail.com Sun Sep 30 23:53:23 2012 From: mike.thon at gmail.com (Michael Thon) Date: Mon, 1 Oct 2012 07:53:23 +0200 Subject: [maker-devel] model_gff question Message-ID: Under what circumstances will maker not include a gene model from the model_gff file in its final output? It was my understanding from this post: https://groups.google.com/d/topic/maker-devel/Y5jSdZ1Olcc/discussion That maker will keep or replace models in model_gff and never remove them. I'm reannotating a fungal genome and in model_gff I'm providing the gene models originally made by the sequencing center. I have 12006 models in the file I specify in model_gff but maker's final annotation has only 10727 models in it. -Mike -------------- next part -------------- An HTML attachment was scrubbed... URL: From mike.thon at gmail.com Tue Sep 4 02:59:06 2012 From: mike.thon at gmail.com (Michael Thon) Date: Tue, 4 Sep 2012 10:59:06 +0200 Subject: [maker-devel] model_gff not in output Message-ID: <1A01E0C5-E60A-42AA-BD7B-A6429F435645@gmail.com> I'm using maker to update a legacy annotation. As input I'm using RNA-Seq aligned with cufflinks, ESTs, provided in fasta format, and proteins downloaded from UniProt.SwissProt. I have done two runs of maker so far. The first one using the legacy annotations in both the model_gff and pred_gff parameters. In the second run I used the legacy annotations in model_gff and in pred_gff I included gene models created with GeneMark-ES. In both runs 1 and 2 I have found two genes (so far) that exist in the legacy annotations but are not in the final gene models output by maker. Both genes have overlapping cufflinks annotations, in addition to having annotations in model_gff. I thought maker was supposed to keep all the annotations in model_gff, only replacing ones in which it could find an alternative model with better support. Is there any case in which is will remove a model? Another discrepency I found in run1 is a gene that maker 'moved' upstream approx. 150 bases. The gene locus annotated by maker covers the original annotation, but the CDS does not. The site of the original CDS is covered by an annotation in model_gff, pred_gff, two ESTs and a cufflinks annotation. Maker still seems to have moved is is upstream where it only has an overlapping cufflinks annotation. the three-prime utr annotated by cufflinks still covers the legacy annotation though. Here's a link to download the maker gff file I'm looking at: https://dl.dropbox.com/u/320712/supercont1%252E1.gff.zip The genes that are in the legacy annotation but missing in the maker annotation are: GLRG_00074 and GLRG_00092 the 'moved' gene model I described is model GLRG_00081. they all within the first 350 K of sequence. mike From chrisi.hahni at gmail.com Wed Sep 5 05:59:48 2012 From: chrisi.hahni at gmail.com (Christoph Hahn) Date: Wed, 05 Sep 2012 13:59:48 +0200 Subject: [maker-devel] keep_preds option? In-Reply-To: References: Message-ID: <50473EB4.7070501@gmail.com> Hello Barry and Carson, Thank you very much for the extensive replies!! Very helpful!! > > 2. I tried to use EST data of an alternative organism in altest= > (#EST/cDNA sequence file in fasta format from an alternate organism). > The organism is quite distantly related, but its the closest I have so > I thought I d give it a shot. I ran maker twice with identical settigs > expect in altest and est2genome=0/1. The number of genes predicted is > identical with both approaches, so I am not sure whether or not the > EST data was actually used or its just to distantly related. Any easy > way to assess this? > Typically EST evidence from another organism with alt_est will add little in the way of additional support (compared to just using protein evidence from say Swiss-prot) and this would be especially true if your alt_est is > distantly related. I'm not sure I really understand you alt_est/est2genome combo's to comment in more detail. I could see four possible combinations there: which two gave identical results? What I meant was that I ran maker once without any alt_est evidence and est2genome=0 and a second time with alt_est=some.fasta and est2genome=1. The result was the same. Sorry, for not making myself clear enough. I thought that the est2genome=1 switch is is just enabling physical est evidence to be used. Therefore, I thought neither alt_est=some.fasta, est2genome=0 nor alt_est=nothing, est2genome=1 would make any sense. I had misunderstood this. Will follow Carsons advice and will try to use more protein evidence from related species (in addition to uniprot). Running right now - Let s see where that leaves me. The IPRScan approach suggested by Barry to assess gene models without physical evidence sounds very interesting. I will definitely look into that. A question concerning an issue I just discovered: Ran maker twice with the same physical evidence. First time using SNAP and Genemark, second time using SNAP, Genemark and AUGUSTUS (set to the closest related species available - same phylum, different class). Second run gives less gene models. IN another context I found that the second pass of Maker using SNAP and Genemark (after training SNAP on the predictions of the first Pass) and the same physical evidence yields less gene annotations. How can that be given the same physical evidence? Thanks again for your help! It is much appreciated! cheers, Christoph Am 31.08.2012 21:03, schrieb Carson Holt: > I concur with everything Barry said. Also let me add that alt-ESTs do > not get polished around splice sites (exonerate won't handle them). > However ESTs and proteins do. This means that the utility of > alt-ESTs in adding UTR, and splice information is zero. They just > function as an anchor to maintain gene models that might have > otherwise been rejected. This also means alt_est=some.fasta together > with est2genome=1 will produce virtually no additional results because > est2genome requires that the splice site makes sense. You are better > off using proteins with protein2genome=1 if you don't have ESTs and > want partial models for training. Once you have a trained ab initio > gene predictor, turn the est2genome and protein2genome options off. > Otherwise they will give weird partial models that decrease the > quality of your final annotations. (partial models are ok for training > but that's about it). > > If you are getting too low a gene count with keep_preds=0, then you > probably need to add more evidence. Try adding all proteins from a > couple of related species (the protein= option accepts comma separated > lists of files). If your genome is a fungi, oomycete, or a prokaryote, > then setting keep_preds=1 is usually safe. Theses are genomes with > high gene density and simple gene structure, so ab initio predictors > do really well and don't need as much help from the evidence. For > other organisms, leave it set to 0 or you will get a lot of false > positives (false positives on some genomes with complex gene structure > can outnumber the genes by 10 to 1 if you turn this on). > > Thanks, > Carson > > > > > From: Barry Moore > > Date: Friday, 31 August, 2012 12:52 PM > To: Christoph Hahn > > Cc: > > Subject: Re: [maker-devel] keep_preds option? > > Hi Christopher, > > Comments below: > > On Aug 31, 2012, at 6:43 AM, Christoph Hahn wrote: > >> Hello maker users and developers, >> >> I am new to gene prediction and I am trying to use maker 2.25 on a >> newly assembled non-model organisms draft genome. Within maker I use >> genemark, SNAP and Augustus. I have a few questions: >> > > Welcome! > >> 1. I was wondering what the keep_preds option means exactly. >> >> I found two slightly different explanations on the option >> #Add unsupported gene prediction to final annotation set (maker2.25) >> #Add non-overlapping ab-inito gene prediction to final annotation set >> (found on the net - probably older maker version) >> > > It means to keep ab initio gene predictions for which there is no > physical evidence. There are two pieces of information that are > required for every MAKER annotation (by default). MAKER runs the ab > initio gene predictors and aligns transcript (EST/cDNA/mRNASeq > transcripts) and protein sequences to the genome. For each locus > where one or more gene predictions exist MAKER checks to see if there > is any physical evidence for gene expression at that locus > (RNA/protein sequence alignments) and if there is (splice EST or > protein alignments) evidence overlapping the predictions, MAKER > decides which prediction best matches the evidence and promotes that > prediction to an annotation. If there is no evidence overlapping any > of the predictions then those predictions are not included in the > output annotation file (although they are saved). If you set > keep_preds=1 then for each locus where prediction(s) exist maker keeps > one and promotes it to an annotation even though there is no physical > evidence. The description of 'non-overlapping ab-initio' means that > MAKER has clustered all ab-initio predictions at one locus and chose > one representative transcript to output. > >> As far as I understood keep_preds=0 only retains gene models for >> which the ab initio predictions agree. But how many, all three? two >> of three? >> keep_preds=1 instead keeps all gene models regardless if the >> different programs agree, right? >> > > MAKER does not take the presence of multiple ab initio predictions as > evidence and thus in the absence of aligned physical evidence MAKER > will not output an annotation even if all three ab initio tools > predict a gene at that locus. > >> In my case I get substantial differences in the number of gene models >> found between the two settings, while with =1 I get a number that is >> close to what we would expect. How would you interpret that? What >> would you recommend me to do? Obiously =0 is the saver option. > > If you think that the number of genes you are getting from a MAKER run > is too few, you could run MAKER with keep_preds=1. After the run is > finished, use a tool like IPRScan to search all MAKER predictions for > protein domain content and push that IPRScan output back into the > MAKER GFF file with the ipr_update_gff script. Then as a final step > you can run over the GFF file and remove any gene model that doesn't > have either physical evidence (AED < 1) or protein domain content > (Dbxref=PFAM:XXX etc...) sorry there's not a script prepackaged with > MAKER for that yet. > >> >> 2. I tried to use EST data of an alternative organism in altest= >> (#EST/cDNA sequence file in fasta format from an alternate organism). >> The organism is quite distantly related, but its the closest I have >> so I thought I d give it a shot. I ran maker twice with identical >> settigs expect in altest and est2genome=0/1. The number of genes >> predicted is identical with both approaches, so I am not sure whether >> or not the EST data was actually used or its just to distantly >> related. Any easy way to assess this? > > Typically EST evidence from another organism with alt_est will add > little in the way of additional support (compared to just using > protein evidence from say Swiss-prot) and this would be especially > true if your alt_est is distantly related. I'm not sure I really > understand you alt_est/est2genome combo's to comment in more detail. > I could see four possible combinations there: which two gave > identical results? > >> >> 3. I am running maker in several passes and after each pass I am >> training SNAP using the result of the previous pass. Then for every >> pass I run maker from scratch. Would you recommend to supply the gff >> of the previous pass in "#-----Re-annotation Using MAKER Derived GFF3 >> maker_gff= #re-annotate genome based on this gff3 file", instead? >> > > No, 'Re-annotation using MAKER Derived GFF3' is used for re-annotation > of a genome when you want certain parts of the previous run to be > passed through unchanged, but with retraining SNAP you want MAKER to > re-evaluate each annotation in light of the new predictions made by > the retrained SNAP. MAKER should run really fast in all of the runs > after the first one because as long as you haven't changed the > evidence files it won't have to redo any of the alignments. > > > B > >> Thanks in advance for any thoughts/advice on these things! I >> appreciate your help! >> >> much obliged, >> Christoph >> >> _______________________________________________ >> maker-devel mailing list >> maker-devel at box290.bluehost.com >> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org > > Barry Moore > Research Scientist > Dept. of Human Genetics > University of Utah > Salt Lake City, UT 84112 > -------------------------------------------- > (801) 585-3543 > > > > > _______________________________________________ maker-devel mailing > list maker-devel at box290.bluehost.com > > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org -------------- next part -------------- An HTML attachment was scrubbed... URL: From muntjaczhou at gmail.com Wed Sep 5 20:26:38 2012 From: muntjaczhou at gmail.com (Zhou Qi) Date: Wed, 5 Sep 2012 19:26:38 -0700 Subject: [maker-devel] gene duplicates and track the query protein Message-ID: Dear maker users and developers: I'm new to maker and trying to use it to annotate a Drosophila genome given protein sequences of its closely related species. I have two questions: 1. How maker decide which one to keep if one query protein has two similarly best hits in the target genome, e.g., gene duplication? 2. Is there any way to track the maker gene to its corresponding query proteins through setting up some parameters in maker? Or is it possible to directly let maker name the gene model based on its query protein? I looked through the previous threads, one possible way seems to use model_gff and map_forward option combined. I guess people more experienced than me using maker might know other ways? Many thanks! Qi From barry.moore at genetics.utah.edu Thu Sep 6 10:35:02 2012 From: barry.moore at genetics.utah.edu (Barry Moore) Date: Thu, 6 Sep 2012 10:35:02 -0600 Subject: [maker-devel] gene duplicates and track the query protein In-Reply-To: References: Message-ID: On Sep 5, 2012, at 8:26 PM, Zhou Qi wrote: > Dear maker users and developers: > > I'm new to maker and trying to use it to annotate a Drosophila genome given protein sequences of its closely related species. I have two questions: > > 1. How maker decide which one to keep if one query protein has two similarly best hits in the target genome, e.g., gene duplication? MAKER uses the aligned proteins as evidence to support gene predictions (i.e. from SNAP). If the supporting protein can align within the specified parameters (as defined in maker_bopts.ctl) then all of the valid alignments could be used as evidence for gene predictions at those loci. > > 2. Is there any way to track the maker gene to its corresponding query proteins through setting up some parameters in maker? Or is it possible to directly let maker name the gene model based on its query protein? > I don't know of a way to do this by setting parameters in the MAKER control file - maybe Carson has some idea for you here? B > I looked through the previous threads, one possible way seems to use model_gff and map_forward option combined. I guess people more experienced than me using maker might know other ways? > > Many thanks! > > Qi > _______________________________________________ > maker-devel mailing list > maker-devel at box290.bluehost.com > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org Barry Moore Research Scientist Dept. of Human Genetics University of Utah Salt Lake City, UT 84112 -------------------------------------------- (801) 585-3543 -------------- next part -------------- An HTML attachment was scrubbed... URL: From david.powell at monash.edu Thu Sep 6 18:23:57 2012 From: david.powell at monash.edu (David Powell) Date: Fri, 7 Sep 2012 10:23:57 +1000 Subject: [maker-devel] Problem with cegma2zff Message-ID: Greetings, I am using CEGMA to train SNAP for use with maker. However, I had a problem with the cegma2zff script that comes with maker. This script converts the gff file from CEGMA into a zff file for SNAP. The problem is that it was producing a zff file with every multi-exon gene as being "invalid" from SNAPs point of view. My fix was to modify cegma2zff to ignore any feature with the tag "Exon" - as these are always duplicated by cegma as another feature (one of First, Internal, Terminal, Single). Just wanted to post this here in case this fix is useful to anyone else. Cheers, -- David Powell diff --git a/cegma2zff b/cegma2zff index c795da8..a3bbb77 100755 --- a/cegma2zff +++ b/cegma2zff @@ -39,6 +39,8 @@ while(my $line = ){ my @F = split("\t", $line); ($F[3], $F[4]) = ($F[4], $F[3]) if($F[6] eq '-'); + next if $F[2] =~ /Exon/; + $F[2] =~ s/First/Einit/; $F[2] =~ s/Terminal/Eterm/; $F[2] =~ s/Internal/Exon/; -------------- next part -------------- An HTML attachment was scrubbed... URL: From guoyunfei1989 at gmail.com Fri Sep 7 11:54:12 2012 From: guoyunfei1989 at gmail.com (Yunfei Guo) Date: Fri, 7 Sep 2012 10:54:12 -0700 Subject: [maker-devel] maker annotate two species, same evidence, same settings Message-ID: Hi Carson, I have a quick question about maker annotations. I want to annotate two sets of assemblies from two related species using the same sets of evidence and settings except that the est assemblies would be specified as 'est' for one species (along with 'altest' evidence from other species) and as 'altest' (combined with est evidence from other species) for the other, would the annotation reflect the real difference between these two species? Or there might be some variations within the annotations themselves which might make the real difference more or less significant? Thank you! Yunfei From carsonhh at gmail.com Fri Sep 7 12:35:50 2012 From: carsonhh at gmail.com (Carson Holt) Date: Fri, 07 Sep 2012 14:35:50 -0400 Subject: [maker-devel] maker annotate two species, same evidence, same settings In-Reply-To: Message-ID: Let me explain how ESTs and alt-ESTs are use and maybe that will answer your question. ESTs will be polished around splice sites to give information on intron boundaries and UTR location. The polished ESTs can override ab initio gene predictor structure and be used to extend gene models by what is basically an exon cut and paste operation. The alt-ESTs are not polished (exoneerate can't handle them). So the splice site boundaries will be off. Maker will only try and infer UTR and intron boundaries from these if the alignment produces canonical splice sites (almost never happens). So they are relegated to the same status as the unpolished protein alignment (lower scoring hints to the gene predictor as to exon boundaries). They will also contribute to AED score with a little less accuracy than ESTs. When possible use protein models rather than alt-ESTs, primarily because they are computationally less intense than a tblastx type alignment that occurs with alt-ESTs. Exonerate will also polish protein alignments. Thanks, Carson On 12-09-07 1:54 PM, "Yunfei Guo" wrote: >Hi Carson, > >I have a quick question about maker annotations. I want to annotate >two sets of assemblies from two related species using the same sets of >evidence and settings except that the est assemblies would be >specified as 'est' for one species (along with 'altest' evidence from >other species) and as 'altest' (combined with est evidence from other >species) for the other, would the annotation reflect the real >difference between these two species? Or there might be some >variations within the annotations themselves which might make the real >difference more or less significant? > >Thank you! > >Yunfei > >_______________________________________________ >maker-devel mailing list >maker-devel at box290.bluehost.com >http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org From carsonhh at gmail.com Fri Sep 7 20:33:49 2012 From: carsonhh at gmail.com (Carson Holt) Date: Fri, 07 Sep 2012 22:33:49 -0400 Subject: [maker-devel] Problem with cegma2zff In-Reply-To: Message-ID: Yes. There was an update for CEGMA that causes features to be duplicated in it's output. Thanks for the post and the fix. --Carson From: David Powell Date: Thursday, 6 September, 2012 8:23 PM To: Subject: [maker-devel] Problem with cegma2zff Greetings, I am using CEGMA to train SNAP for use with maker. However, I had a problem with the cegma2zff script that comes with maker. This script converts the gff file from CEGMA into a zff file for SNAP. The problem is that it was producing a zff file with every multi-exon gene as being "invalid" from SNAPs point of view. My fix was to modify cegma2zff to ignore any feature with the tag "Exon" - as these are always duplicated by cegma as another feature (one of First, Internal, Terminal, Single). Just wanted to post this here in case this fix is useful to anyone else. Cheers, -- David Powell diff --git a/cegma2zff b/cegma2zff index c795da8..a3bbb77 100755 --- a/cegma2zff +++ b/cegma2zff @@ -39,6 +39,8 @@ while(my $line = ){ my @F = split("\t", $line); ($F[3], $F[4]) = ($F[4], $F[3]) if($F[6] eq '-'); + next if $F[2] =~ /Exon/; + $F[2] =~ s/First/Einit/; $F[2] =~ s/Terminal/Eterm/; $F[2] =~ s/Internal/Exon/; _______________________________________________ maker-devel mailing list maker-devel at box290.bluehost.com http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org -------------- next part -------------- An HTML attachment was scrubbed... URL: From jeremy.semeiks at utsw.edu Sun Sep 9 13:49:36 2012 From: jeremy.semeiks at utsw.edu (Jeremy Semeiks) Date: Sun, 9 Sep 2012 14:49:36 -0500 Subject: [maker-devel] How to preserve human-friendly IDs when reannotating Message-ID: Hi all, I have sequenced some novel fungal genomes, and I am annotating them with maker-2.26-beta. The entire project is pretty iterative, in the sense that I first get some seemingly-sane annotation sets, then analyze and compare the proteomes biologically, then reannotate when new data comes in or as I learn more about how maker works. Because I have already attached biological meaning to some of my proteins, I would like to retain the same human-friendly IDs across annotations. Eg, if maker suddenly finds 1,000 new proteins on a reannotation run because I turned on keep_preds, then I don't want the transcript formerly known as mymold_09652T0 to become mymold_10698T0 when I run maker_map_ids; I want to keep it named mymold_09652T0. So, is there any built-in way to preserve human-friendly IDs, or do I need to write my own script for this? I have tried setting map_forward=1 and maker_gff=, but setting these seems to preserve neither the human-friendly IDs nor even the original IDs. (Eg, protein "genemark-scaffold353-processed-gene-0.9-mRNA-1" changed its name to "genemark-scaffold353-processed-gene-0.6-mRNA-1" when reannotated.) I haven't turned on any of the *_pass options, eg protein_pass; would this be relevant? Extra credit question: I am making some mate-pair libraries for these fungi; when I re-assemble, that will completely change my scaffold names. Is there any easy way to preserve human-friendly transcript names in this case? As with the above simpler case, I think it would be pretty easy to transfer 90% of the names just by doing an all-vs-all blastp between two annotation sets and fishing out the best hits, but the remaining 10% might be a headache. Thanks, Jeremy Grad student, Grishin lab UT Southwestern, Dallas TX 510.385.8959 -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Mon Sep 10 05:01:46 2012 From: carsonhh at gmail.com (Carson Holt) Date: Mon, 10 Sep 2012 07:01:46 -0400 Subject: [maker-devel] How to preserve human-friendly IDs when reannotating In-Reply-To: Message-ID: The map_forward option requires that the pass option for the gene models be turned on. Otherwise you will have to do some spacial overlap test outside of MAKER. If you have a new assembly, you can try mapping the old models onto the new assembly using the old transcripts as input to the est= and setting est2genome=1 (nothing else set, i.e no repeat masking etc.). Then there is an undocumented option that is still a little buggy (hence why it is still undocumented). Add the line est_forward=1 to your control files. This tells MAKER to copy names from the ESTs, build the models directly from their alignment, and to do other things to try and make a 1 to 1 match across the genome. You will have to manually check that it is 1 to 1 in the end (as I said still a little buggy and hence undocumented). Use the resulting file as input to the model_gff option on a separate run with map_forward=1 for additional reannotation wil more evidence, etc. where you want to still be able to map names forward. From: Jeremy Semeiks Date: Sunday, 9 September, 2012 3:49 PM To: Subject: [maker-devel] How to preserve human-friendly IDs when reannotating Hi all, I have sequenced some novel fungal genomes, and I am annotating them with maker-2.26-beta. The entire project is pretty iterative, in the sense that I first get some seemingly-sane annotation sets, then analyze and compare the proteomes biologically, then reannotate when new data comes in or as I learn more about how maker works. Because I have already attached biological meaning to some of my proteins, I would like to retain the same human-friendly IDs across annotations. Eg, if maker suddenly finds 1,000 new proteins on a reannotation run because I turned on keep_preds, then I don't want the transcript formerly known as mymold_09652T0 to become mymold_10698T0 when I run maker_map_ids; I want to keep it named mymold_09652T0. So, is there any built-in way to preserve human-friendly IDs, or do I need to write my own script for this? I have tried setting map_forward=1 and maker_gff=, but setting these seems to preserve neither the human-friendly IDs nor even the original IDs. (Eg, protein "genemark-scaffold353-processed-gene-0.9-mRNA-1" changed its name to "genemark-scaffold353-processed-gene-0.6-mRNA-1" when reannotated.) I haven't turned on any of the *_pass options, eg protein_pass; would this be relevant? Extra credit question: I am making some mate-pair libraries for these fungi; when I re-assemble, that will completely change my scaffold names. Is there any easy way to preserve human-friendly transcript names in this case? As with the above simpler case, I think it would be pretty easy to transfer 90% of the names just by doing an all-vs-all blastp between two annotation sets and fishing out the best hits, but the remaining 10% might be a headache. Thanks, Jeremy Grad student, Grishin lab UT Southwestern, Dallas TX 510.385.8959 _______________________________________________ maker-devel mailing list maker-devel at box290.bluehost.com http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Mon Sep 10 05:10:33 2012 From: carsonhh at gmail.com (Carson Holt) Date: Mon, 10 Sep 2012 07:10:33 -0400 Subject: [maker-devel] keep_preds option? In-Reply-To: <50473EB4.7070501@gmail.com> Message-ID: The final annotations are really produced by GeneMark, SNAP, Augustus etc. MAKER basically takes the physical evidence, turns it into 'hints' for these programs (I.e. Exon and CDS scoring bonuses), and then lets them run again. If you retrain them they will behave different. If you add a new one you may also get a model from the third algorithm that seems to match the evidence better. Sometimes one algorithm will call one gene where another thinks it should be two genes while the third thinks it is really a larger gene merged with exons from a neighboring gene. MAKER will add hints to try and improve the ab initio predictors performance and choose the model that seems to be make sense given the evidence. The source of a gene model is eventually inherent from the name MAKER gives it. If snap is in the name, then the model was derived from snap. If maker and snap are in the name, then it is a model derived from snap with MAKER hints (otherwise it was derived completely from SNAP's training with no MAKER input). Thanks, Carson From: Christoph Hahn Date: Wednesday, 5 September, 2012 7:59 AM To: Carson Holt , Barry Moore Cc: Subject: Re: [maker-devel] keep_preds option? Hello Barry and Carson, Thank you very much for the extensive replies!! Very helpful!! > > > 2. I tried to use EST data of an alternative organism in altest= (#EST/cDNA > sequence file in fasta format from an alternate organism). The organism is > quite distantly related, but its the closest I have so I thought I d give it a > shot. I ran maker twice with identical settigs expect in altest and > est2genome=0/1. The number of genes predicted is identical with both > approaches, so I am not sure whether or not the EST data was actually used or > its just to distantly related. Any easy way to assess this? > > > Typically EST evidence from another organism with alt_est will add little in the way of additional support (compared to just using protein evidence from say Swiss-prot) and this would be especially true if your alt_est is > distantly related. I'm not sure I really understand you alt_est/est2genome combo's to comment in more detail. I could see four possible combinations there: which two gave identical results? What I meant was that I ran maker once without any alt_est evidence and est2genome=0 and a second time with alt_est=some.fasta and est2genome=1. The result was the same. Sorry, for not making myself clear enough. I thought that the est2genome=1 switch is is just enabling physical est evidence to be used. Therefore, I thought neither alt_est=some.fasta, est2genome=0 nor alt_est=nothing, est2genome=1 would make any sense. I had misunderstood this. Will follow Carsons advice and will try to use more protein evidence from related species (in addition to uniprot). Running right now - Let s see where that leaves me. The IPRScan approach suggested by Barry to assess gene models without physical evidence sounds very interesting. I will definitely look into that. A question concerning an issue I just discovered: Ran maker twice with the same physical evidence. First time using SNAP and Genemark, second time using SNAP, Genemark and AUGUSTUS (set to the closest related species available - same phylum, different class). Second run gives less gene models. IN another context I found that the second pass of Maker using SNAP and Genemark (after training SNAP on the predictions of the first Pass) and the same physical evidence yields less gene annotations. How can that be given the same physical evidence? Thanks again for your help! It is much appreciated! cheers, Christoph Am 31.08.2012 21:03, schrieb Carson Holt: > > I concur with everything Barry said. Also let me add that alt-ESTs do not get > polished around splice sites (exonerate won't handle them). However ESTs and > proteins do. This means that the utility of alt-ESTs in adding UTR, and > splice information is zero. They just function as an anchor to maintain gene > models that might have otherwise been rejected. This also means > alt_est=some.fasta together with est2genome=1 will produce virtually no > additional results because est2genome requires that the splice site makes > sense. You are better off using proteins with protein2genome=1 if you don?t > have ESTs and want partial models for training. Once you have a trained ab > initio gene predictor, turn the est2genome and protein2genome options off. > Otherwise they will give weird partial models that decrease the quality of > your final annotations. (partial models are ok for training but that's about > it). > > > > > If you are getting too low a gene count with keep_preds=0, then you probably > need to add more evidence. Try adding all proteins from a couple of related > species (the protein= option accepts comma separated lists of files). If your > genome is a fungi, oomycete, or a prokaryote, then setting keep_preds=1 is > usually safe. Theses are genomes with high gene density and simple gene > structure, so ab initio predictors do really well and don't need as much help > from the evidence. For other organisms, leave it set to 0 or you will get a > lot of false positives (false positives on some genomes with complex gene > structure can outnumber the genes by 10 to 1 if you turn this on). > > > > > Thanks, > > Carson > > > > > > > > > > > > > > From: Barry Moore > Date: Friday, 31 August, 2012 12:52 PM > To: Christoph Hahn > Cc: > Subject: Re: [maker-devel] keep_preds option? > > > > > > > Hi Christopher, > > > > Comments below: > > > > > On Aug 31, 2012, at 6:43 AM, Christoph Hahn wrote: > > >> >> Hello maker users and developers, >> >> I am new to gene prediction and I am trying to use maker 2.25 on a newly >> assembled non-model organisms draft genome. Within maker I use genemark, SNAP >> and Augustus. I have a few questions: >> >> >> > > > > > Welcome! > > >> >> 1. I was wondering what the keep_preds option means exactly. >> >> I found two slightly different explanations on the option >> #Add unsupported gene prediction to final annotation set (maker2.25) >> #Add non-overlapping ab-inito gene prediction to final annotation set (found >> on the net - probably older maker version) >> >> >> > > > > > It means to keep ab initio gene predictions for which there is no physical > evidence. There are two pieces of information that are required for every > MAKER annotation (by default). MAKER runs the ab initio gene predictors and > aligns transcript (EST/cDNA/mRNASeq transcripts) and protein sequences to the > genome. For each locus where one or more gene predictions exist MAKER checks > to see if there is any physical evidence for gene expression at that locus > (RNA/protein sequence alignments) and if there is (splice EST or protein > alignments) evidence overlapping the predictions, MAKER decides which > prediction best matches the evidence and promotes that prediction to an > annotation. If there is no evidence overlapping any of the predictions then > those predictions are not included in the output annotation file (although > they are saved). If you set keep_preds=1 then for each locus where > prediction(s) exist maker keeps one and promotes it to an annotation even > though there is no physical evidence. The description of 'non-overlapping > ab-initio' means that MAKER has clustered all ab-initio predictions at one > locus and chose one representative transcript to output. > > >> >> As far as I understood keep_preds=0 only retains gene models for which the ab >> initio predictions agree. But how many, all three? two of three? >> keep_preds=1 instead keeps all gene models regardless if the different >> programs agree, right? >> >> >> > > > > > MAKER does not take the presence of multiple ab initio predictions as evidence > and thus in the absence of aligned physical evidence MAKER will not output an > annotation even if all three ab initio tools predict a gene at that locus. > > >> >> In my case I get substantial differences in the number of gene models found >> between the two settings, while with =1 I get a number that is close to what >> we would expect. How would you interpret that? What would you recommend me to >> do? Obiously =0 is the saver option. >> >> > > > > > If you think that the number of genes you are getting from a MAKER run is too > few, you could run MAKER with keep_preds=1. After the run is finished, use a > tool like IPRScan to search all MAKER predictions for protein domain content > and push that IPRScan output back into the MAKER GFF file with the > ipr_update_gff script. Then as a final step you can run over the GFF file and > remove any gene model that doesn't have either physical evidence (AED < 1) or > protein domain content (Dbxref=PFAM:XXX etc?) sorry there's not a script > prepackaged with MAKER for that yet. > > > > >> >> >> 2. I tried to use EST data of an alternative organism in altest= (#EST/cDNA >> sequence file in fasta format from an alternate organism). The organism is >> quite distantly related, but its the closest I have so I thought I d give it >> a shot. I ran maker twice with identical settigs expect in altest and >> est2genome=0/1. The number of genes predicted is identical with both >> approaches, so I am not sure whether or not the EST data was actually used or >> its just to distantly related. Any easy way to assess this? >> >> > > > > > Typically EST evidence from another organism with alt_est will add little in > the way of additional support (compared to just using protein evidence from > say Swiss-prot) and this would be especially true if your alt_est is distantly > related. I'm not sure I really understand you alt_est/est2genome combo's to > comment in more detail. I could see four possible combinations there: which > two gave identical results? > > >> >> >> 3. I am running maker in several passes and after each pass I am training >> SNAP using the result of the previous pass. Then for every pass I run maker >> from scratch. Would you recommend to supply the gff of the previous pass in >> "#-----Re-annotation Using MAKER Derived GFF3 >> maker_gff= #re-annotate genome based on this gff3 file", instead? >> >> >> > > > > > No, 'Re-annotation using MAKER Derived GFF3' is used for re-annotation of a > genome when you want certain parts of the previous run to be passed through > unchanged, but with retraining SNAP you want MAKER to re-evaluate each > annotation in light of the new predictions made by the retrained SNAP. MAKER > should run really fast in all of the runs after the first one because as long > as you haven't changed the evidence files it won't have to redo any of the > alignments. > > > > > > > B > > > >> >> Thanks in advance for any thoughts/advice on these things! I appreciate your >> help! >> >> much obliged, >> Christoph >> >> _______________________________________________ >> maker-devel mailing list >> maker-devel at box290.bluehost.com >> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org >> >> > > > > > > Barry Moore > > Research Scientist > > Dept. of Human Genetics > > University of Utah > > Salt Lake City, UT 84112 > > -------------------------------------------- > > (801) 585-3543 > > > > > > > > > > > > > > _______________________________________________ maker-devel mailing list > maker-devel at box290.bluehost.com > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Mon Sep 10 05:17:26 2012 From: carsonhh at gmail.com (Carson Holt) Date: Mon, 10 Sep 2012 07:17:26 -0400 Subject: [maker-devel] model_gff not in output In-Reply-To: <1A01E0C5-E60A-42AA-BD7B-A6429F435645@gmail.com> Message-ID: The only way MAKER should ignore a legacy annotation (only what's in model_gff is considered legacy by MAKER) is if, you also set one of the ab iniio predictors to run simultaneously or provide a pred_gff file and one of those models scores higher and would overlap the legacy model. Then MAKER chooses that model instead. Also if you have two overlapping legacy models MAKER will only keep one or the other under these same conditions. MAKER will only keep all legacy models regardless of overlap if you only supply model_gff with no other predictors turned on. Once you turn a predictor on, MAKER takes this as a cue that you are letting it make changes. Legacy models should always be kept under all circumstances if there is nothing overlapping them with a higher score. Are the missing models partially overlapped by anything in the resulting MAKER annotations? Thanks, Carson On 12-09-04 4:59 AM, "Michael Thon" wrote: >I'm using maker to update a legacy annotation. As input I'm using >RNA-Seq aligned with cufflinks, ESTs, provided in fasta format, and >proteins downloaded from UniProt.SwissProt. I have done two runs of >maker so far. The first one using the legacy annotations in both the >model_gff and pred_gff parameters. In the second run I used the legacy >annotations in model_gff and in pred_gff I included gene models created >with GeneMark-ES. > >In both runs 1 and 2 I have found two genes (so far) that exist in the >legacy annotations but are not in the final gene models output by maker. >Both genes have overlapping cufflinks annotations, in addition to having >annotations in model_gff. I thought maker was supposed to keep all the >annotations in model_gff, only replacing ones in which it could find an >alternative model with better support. Is there any case in which is >will remove a model? > > >Another discrepency I found in run1 is a gene that maker 'moved' upstream >approx. 150 bases. The gene locus annotated by maker covers the original >annotation, but the CDS does not. The site of the original CDS is covered >by an annotation in model_gff, pred_gff, two ESTs and a cufflinks >annotation. Maker still seems to have moved is is upstream where it only >has an overlapping cufflinks annotation. the three-prime utr annotated >by cufflinks still covers the legacy annotation though. > >Here's a link to download the maker gff file I'm looking at: > >https://dl.dropbox.com/u/320712/supercont1%252E1.gff.zip > >The genes that are in the legacy annotation but missing in the maker >annotation are: >GLRG_00074 and GLRG_00092 > >the 'moved' gene model I described is model GLRG_00081. they all within >the first 350 K of sequence. >mike > > > > > >_______________________________________________ >maker-devel mailing list >maker-devel at box290.bluehost.com >http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org From carsonhh at gmail.com Mon Sep 10 05:18:34 2012 From: carsonhh at gmail.com (Carson Holt) Date: Mon, 10 Sep 2012 07:18:34 -0400 Subject: [maker-devel] Maker Re-tries In-Reply-To: <1E417039-68CF-4EFE-90BF-964DC86B1864@uchicago.edu> Message-ID: Killing a job yourself should not increase the failure count for a contig. Thanks, Carson From: Kipp Johnson Date: Tuesday, 21 August, 2012 5:25 PM To: Carson Holt Cc: Kipp Johnson , Subject: Re: Maker Re-tries Hi Carson, Simple question: If I start maker and then kill the job before a thread finishes processing a contig, does this failure to complete the contig count in the number of tries maker will try to complete the contig before skipping to another? Basically, does the "tries=2 #number of times to try a contig if there is a failure for some reason" parameter take into account failures resulting from me killing the job? Best, Kipp Johnson kippjohnson at uchicago.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: From Carson.Holt at oicr.on.ca Mon Sep 10 04:50:09 2012 From: Carson.Holt at oicr.on.ca (Carson Holt) Date: Mon, 10 Sep 2012 10:50:09 +0000 Subject: [maker-devel] gene duplicates and track the query protein In-Reply-To: Message-ID: 2. Is there any way to track the maker gene to its corresponding query proteins through setting up some parameters in maker? Or is it possible to directly let maker name the gene model based on its query protein? Not directly. Proteins can align to multiple locations, so you will get more than one protein overlapping a gene. A reciprocal BLAST would probably be the best thing to do here. If the MAKER derived annotation, and a gene are both each others best hit in separate blast jobs, then you could usually safely call them the same gene. You would have to do that outside of MAKER. Thanks, Carson From: Barry Moore > Date: Thursday, 6 September, 2012 12:35 PM To: Zhou Qi > Cc: > Subject: Re: [maker-devel] gene duplicates and track the query protein On Sep 5, 2012, at 8:26 PM, Zhou Qi wrote: Dear maker users and developers: I'm new to maker and trying to use it to annotate a Drosophila genome given protein sequences of its closely related species. I have two questions: 1. How maker decide which one to keep if one query protein has two similarly best hits in the target genome, e.g., gene duplication? MAKER uses the aligned proteins as evidence to support gene predictions (i.e. from SNAP). If the supporting protein can align within the specified parameters (as defined in maker_bopts.ctl) then all of the valid alignments could be used as evidence for gene predictions at those loci. 2. Is there any way to track the maker gene to its corresponding query proteins through setting up some parameters in maker? Or is it possible to directly let maker name the gene model based on its query protein? I don't know of a way to do this by setting parameters in the MAKER control file - maybe Carson has some idea for you here? B I looked through the previous threads, one possible way seems to use model_gff and map_forward option combined. I guess people more experienced than me using maker might know other ways? Many thanks! Qi _______________________________________________ maker-devel mailing list maker-devel at box290.bluehost.com http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org Barry Moore Research Scientist Dept. of Human Genetics University of Utah Salt Lake City, UT 84112 -------------------------------------------- (801) 585-3543 _______________________________________________ maker-devel mailing list maker-devel at box290.bluehost.com http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org -------------- next part -------------- An HTML attachment was scrubbed... URL: From jeremy.semeiks at utsw.edu Mon Sep 10 09:02:25 2012 From: jeremy.semeiks at utsw.edu (Jeremy Semeiks) Date: Mon, 10 Sep 2012 10:02:25 -0500 Subject: [maker-devel] How to preserve human-friendly IDs when reannotating In-Reply-To: References: Message-ID: OK, thanks. So if I understand correctly, to preserve human-friendly IDs requires setting just three options: map_forward=1, maker_gff=, and model_pass=1. (Or instead of the last two I could equivalently just set model_gff to a GFF containing only models.) A couple new issues came up when I tried to run with these options. I started maker like this: /usr/bin/time mpiexec -n 10 maker -q < /dev/null > maker.oe 2>&1 1. I get a bunch of messages as follows, but with variable line number: DBD::SQLite::db do failed: database is locked at /home/jrs/maker-2.26-beta/bin/../lib/GFFDB.pm line 186. I saw that this came up in another thread < https://groups.google.com/forum/?fromgroups=#!topic/maker-devel/TscBgbQfBX4>, but I'm not sure it was ever resolved, nor whether it will affect my reannotation results (as I'm not sure what "your GFF3 results will not be integrated" means). This error did not come up the last time I ran maker for reannotation with similar options in a different directory. And both my current directory and my tmp directory are locally mounted, ie not NFS. 2. Both in this run and in previous runs, I get a lot of lines like this, seemingly at random: Warning: unable to close filehandle DF properly. On Mon, Sep 10, 2012 at 6:01 AM, Carson Holt wrote: > The map_forward option requires that the pass option for the gene models > be turned on. Otherwise you will have to do some spacial overlap test > outside of MAKER. > > If you have a new assembly, you can try mapping the old models onto the > new assembly using the old transcripts as input to the est= and setting > est2genome=1 (nothing else set, i.e no repeat masking etc.). Then there is > an undocumented option that is still a little buggy (hence why it is still > undocumented). Add the line est_forward=1 to your control files. This > tells MAKER to copy names from the ESTs, build the models directly from > their alignment, and to do other things to try and make a 1 to 1 match > across the genome. You will have to manually check that it is 1 to 1 in > the end (as I said still a little buggy and hence undocumented). Use the > resulting file as input to the model_gff option on a separate run with > map_forward=1 for additional reannotation wil more evidence, etc. where you > want to still be able to map names forward. > > From: Jeremy Semeiks > Date: Sunday, 9 September, 2012 3:49 PM > To: > Subject: [maker-devel] How to preserve human-friendly IDs when > reannotating > > Hi all, > > I have sequenced some novel fungal genomes, and I am annotating them with > maker-2.26-beta. The entire project is pretty iterative, in the sense that > I first get some seemingly-sane annotation sets, then analyze and compare > the proteomes biologically, then reannotate when new data comes in or as I > learn more about how maker works. Because I have already attached > biological meaning to some of my proteins, I would like to retain the same > human-friendly IDs across annotations. Eg, if maker suddenly finds 1,000 > new proteins on a reannotation run because I turned on keep_preds, then I > don't want the transcript formerly known as mymold_09652T0 to become > mymold_10698T0 when I run maker_map_ids; I want to keep it named > mymold_09652T0. > > So, is there any built-in way to preserve human-friendly IDs, or do I need > to write my own script for this? I have tried setting map_forward=1 and > maker_gff=, but > setting these seems to preserve neither the human-friendly IDs nor even the > original IDs. (Eg, protein "genemark-scaffold353-processed-gene-0.9-mRNA-1" > changed its name to "genemark-scaffold353-processed-gene-0.6-mRNA-1" when > reannotated.) I haven't turned on any of the *_pass options, eg > protein_pass; would this be relevant? > > Extra credit question: I am making some mate-pair libraries for these > fungi; when I re-assemble, that will completely change my scaffold names. > Is there any easy way to preserve human-friendly transcript names in this > case? As with the above simpler case, I think it would be pretty easy to > transfer 90% of the names just by doing an all-vs-all blastp between two > annotation sets and fishing out the best hits, but the remaining 10% might > be a headache. > > Thanks, > Jeremy > Grad student, Grishin lab > UT Southwestern, Dallas TX > 510.385.8959 > _______________________________________________ maker-devel mailing list > maker-devel at box290.bluehost.com > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org > -------------- next part -------------- An HTML attachment was scrubbed... URL: From carson.holt at genetics.utah.edu Mon Sep 10 11:21:05 2012 From: carson.holt at genetics.utah.edu (Carson Holt) Date: Mon, 10 Sep 2012 17:21:05 +0000 Subject: [maker-devel] MWAS: User Feedback In-Reply-To: Message-ID: MAKER won't really annotate those. Transcriptome annotation is a very different problem from genome annotation. I'm CC'ing this to the MAKER mailing list to see if anyone has good suggestion for transcriptome annotation. I would recommend using Repeatmasker to remove transposons from your transcriptome set, and then InterProScan for domain identification and maybe blast2go for GO term association. --Carson On 12-09-10 1:10 PM, "grind001 at umn.edu" wrote: >I have assembled RNAseq transcripts. There's no genome assembly for our >species right now, so I was trying to do an organized assembly pipeline >and >use your system. > >On Sep 10 2012, Carson Holt wrote: > >>Tell me a little more about your project. Based on your brief >>description >>I think you might need a different tool. MAKER doesn't assemble or >>annotate transcriptomes (i.e. RNA only). It works with de novo genome >>assemblies to identify the genes from them (I.e entire chromosomes or >>large fragments of chromosomes). It can use RNA-seq result to help >>annotate the genome but still requires a genome assembly. >> >>The online server will annotate maximum of 5 Mb at a time and it's slow >>(mostly built for small jobs). You will get 10-20 faster performance >>locally. >> >>Thanks, >>Carson >> >> >> >>On 12-09-10 12:17 PM, "grind001 at umn.edu" wrote: >> >>>Maker Web Annotation Service - User Feedback: >>>--------------------------------------------- >>>Hi, >>> >>>I'm working on getting your software installed on my systems, and have >>>done a test run on your web page with a portion of my data. >>>I have 150,000 contigs from a de novo assembly of our transcriptome. Do >>>you have room on your server for a large run? or is this just a sample >>>space to test the software? I'm under some time constraints and an just >>>checking and hoping to push this forward a bit faster. >>> >>> >>> >>>Best, >>>Suzanne >>>University of MN >>> >>> >>>--------------------------------------------- >>>User: 1440 >>>First: Suzanne >>>Last: Grindle >>>Institution: University of Minnesota >>>E-mail: grind001 at umn.edu >>> >> >> From felix.bemm at uni-wuerzburg.de Mon Sep 10 13:15:22 2012 From: felix.bemm at uni-wuerzburg.de (Felix Bemm) Date: Mon, 10 Sep 2012 21:15:22 +0200 Subject: [maker-devel] MWAS: User Feedback In-Reply-To: References: Message-ID: <504E3C4A.2040401@uni-wuerzburg.de> hi suzanne, the trinity assembler mailing list has some good ideas for that. You could think about using an "intelligent" orf finder like transdecoder (transdecoder.sourceforge.net). the predicted orfs can than be used for an interpro and blast2go run. merge the interpro and the b2g run with the built-in tool of blast2go. simply put the interpro xml's for each orf of a given transcript into one file for that and use the built-in import function of blast2go. this might help you to improve the GO annotation. it also works with the b2g pipeline tool (which is much faster). In addition, you could try to use interproscan standalone 5 (http://code.google.com/p/interproscan/) since it has an improved support for nucleic acid sequences. cheers felix Am 10.09.2012 19:21, schrieb Carson Holt: > MAKER won't really annotate those. Transcriptome annotation is a very > different problem from genome annotation. I'm CC'ing this to the MAKER > mailing list to see if anyone has good suggestion for transcriptome > annotation. > > I would recommend using Repeatmasker to remove transposons from your > transcriptome set, and then InterProScan for domain identification and > maybe blast2go for GO term association. > > --Carson > > > > > On 12-09-10 1:10 PM, "grind001 at umn.edu" wrote: > >> I have assembled RNAseq transcripts. There's no genome assembly for our >> species right now, so I was trying to do an organized assembly pipeline >> and >> use your system. >> >> On Sep 10 2012, Carson Holt wrote: >> >>> Tell me a little more about your project. Based on your brief >>> description >>> I think you might need a different tool. MAKER doesn't assemble or >>> annotate transcriptomes (i.e. RNA only). It works with de novo genome >>> assemblies to identify the genes from them (I.e entire chromosomes or >>> large fragments of chromosomes). It can use RNA-seq result to help >>> annotate the genome but still requires a genome assembly. >>> >>> The online server will annotate maximum of 5 Mb at a time and it's slow >>> (mostly built for small jobs). You will get 10-20 faster performance >>> locally. >>> >>> Thanks, >>> Carson >>> >>> >>> >>> On 12-09-10 12:17 PM, "grind001 at umn.edu" wrote: >>> >>>> Maker Web Annotation Service - User Feedback: >>>> --------------------------------------------- >>>> Hi, >>>> >>>> I'm working on getting your software installed on my systems, and have >>>> done a test run on your web page with a portion of my data. >>>> I have 150,000 contigs from a de novo assembly of our transcriptome. Do >>>> you have room on your server for a large run? or is this just a sample >>>> space to test the software? I'm under some time constraints and an just >>>> checking and hoping to push this forward a bit faster. >>>> >>>> >>>> >>>> Best, >>>> Suzanne >>>> University of MN >>>> >>>> >>>> --------------------------------------------- >>>> User: 1440 >>>> First: Suzanne >>>> Last: Grindle >>>> Institution: University of Minnesota >>>> E-mail: grind001 at umn.edu >>>> >>> >>> > > > _______________________________________________ > maker-devel mailing list > maker-devel at box290.bluehost.com > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org > -- Felix Bemm Department of Bioinformatics University of W?rzburg, Germany Tel: +49 931 - 31 83696 Fax: +49 931 - 31 84552 felix.bemm at uni-wuerzburg.de From ranjani at uga.edu Tue Sep 11 09:38:33 2012 From: ranjani at uga.edu (Sivaranjani Namasivayam) Date: Tue, 11 Sep 2012 15:38:33 +0000 Subject: [maker-devel] MAKER training Message-ID: Hi, I am using MAKER to annotate a newly sequenced genome. I have trained and retrained with datasets but I would like some advice on assessing the output and how this is affected by the input provided. - I have transcriptome data from 454 and Illumina platforms. Illumina is from a single time point and 454 from multiple time point. 454 was assembled using Newbler(dataset 1) and Illumina using Tophat-Cufflinks (dataset 2) and the denovo Trinity pipeline (dataset 3). I now have3 assemblies - 454 and Illumina will have some redunant transcripts (because of one overlapping time point); TopHat-Cufflinks and Trinity will have highly redundant transcripts (because they use same raw reads). Is it OK to provide all 3 datasets as EST evidence, how does it affect the quality of annotation. (For now I have used dataset 1 and dataset 2 as EST evidence) - I used the above model to retrain, I passed through everything except the abinitio gene predictions. I also provided a set a manually annotated genes , many of which have EST evidence. Is this OK to do? [ For proteins evidence, I gave a set from related organisms, same as above] - In my third retraining, I used the above retrained model, but this time I only provided the genome_gff but did not pass through any other data. However I did provide the manually annotated genes as EST evidence and related proteins as protein_evidence. Can you please give me some advice on which of these could give me the best prediction, or if I can alter something to get a better prediction. - A quick question about Augustus - I used a Augustus model (trained for a closely related organism) for ab-initio prediction. Does MAKER adjust this model based on the evidence provided, or use the model as such for a prediction. Greatly appreciate your help! Thanks! Ranjani -------------- next part -------------- An HTML attachment was scrubbed... URL: From dence at genetics.utah.edu Tue Sep 11 09:46:04 2012 From: dence at genetics.utah.edu (Daniel Ence) Date: Tue, 11 Sep 2012 15:46:04 +0000 Subject: [maker-devel] MAKER training In-Reply-To: References: Message-ID: Hi Ranjani, It is fine to include all three of those transcriptome datatsets. The more (relevant) evidence the better. I'm not certain what you mean when you say "you used the above model to retrain". Did you train an abinitio gene predictor using the results from your first maker run? Daniel Ence Graduate Student Eccles Institute of Human Genetics University of Utah 15 North 2030 East, Room 2100 Salt Lake City, UT 84112-5330 ________________________________ From: maker-devel-bounces at yandell-lab.org [maker-devel-bounces at yandell-lab.org] on behalf of Sivaranjani Namasivayam [ranjani at uga.edu] Sent: Tuesday, September 11, 2012 9:38 AM To: maker-devel at yandell-lab.org Subject: [maker-devel] MAKER training Hi, I am using MAKER to annotate a newly sequenced genome. I have trained and retrained with datasets but I would like some advice on assessing the output and how this is affected by the input provided. - I have transcriptome data from 454 and Illumina platforms. Illumina is from a single time point and 454 from multiple time point. 454 was assembled using Newbler(dataset 1) and Illumina using Tophat-Cufflinks (dataset 2) and the denovo Trinity pipeline (dataset 3). I now have3 assemblies - 454 and Illumina will have some redunant transcripts (because of one overlapping time point); TopHat-Cufflinks and Trinity will have highly redundant transcripts (because they use same raw reads). Is it OK to provide all 3 datasets as EST evidence, how does it affect the quality of annotation. (For now I have used dataset 1 and dataset 2 as EST evidence) - I used the above model to retrain, I passed through everything except the abinitio gene predictions. I also provided a set a manually annotated genes , many of which have EST evidence. Is this OK to do? [ For proteins evidence, I gave a set from related organisms, same as above] - In my third retraining, I used the above retrained model, but this time I only provided the genome_gff but did not pass through any other data. However I did provide the manually annotated genes as EST evidence and related proteins as protein_evidence. Can you please give me some advice on which of these could give me the best prediction, or if I can alter something to get a better prediction. - A quick question about Augustus - I used a Augustus model (trained for a closely related organism) for ab-initio prediction. Does MAKER adjust this model based on the evidence provided, or use the model as such for a prediction. Greatly appreciate your help! Thanks! Ranjani -------------- next part -------------- An HTML attachment was scrubbed... URL: From ranjani at uga.edu Tue Sep 11 09:57:31 2012 From: ranjani at uga.edu (Sivaranjani Namasivayam) Date: Tue, 11 Sep 2012 15:57:31 +0000 Subject: [maker-devel] MAKER training In-Reply-To: References: , Message-ID: Hey, I used the MAKER model to retrain MAKER itself. I read somewhere it improves MAKER's predictions. I did train abinitio gene predictors using MAKERs output, but I wanted to identify the best prediction before using it to train other gene predictors. Thanks, Ranjani ________________________________ From: Daniel Ence [dence at genetics.utah.edu] Sent: Tuesday, September 11, 2012 11:46 AM To: Sivaranjani Namasivayam; maker-devel at yandell-lab.org Subject: RE: MAKER training Hi Ranjani, It is fine to include all three of those transcriptome datatsets. The more (relevant) evidence the better. I'm not certain what you mean when you say "you used the above model to retrain". Did you train an abinitio gene predictor using the results from your first maker run? Daniel Ence Graduate Student Eccles Institute of Human Genetics University of Utah 15 North 2030 East, Room 2100 Salt Lake City, UT 84112-5330 ________________________________ From: maker-devel-bounces at yandell-lab.org [maker-devel-bounces at yandell-lab.org] on behalf of Sivaranjani Namasivayam [ranjani at uga.edu] Sent: Tuesday, September 11, 2012 9:38 AM To: maker-devel at yandell-lab.org Subject: [maker-devel] MAKER training Hi, I am using MAKER to annotate a newly sequenced genome. I have trained and retrained with datasets but I would like some advice on assessing the output and how this is affected by the input provided. - I have transcriptome data from 454 and Illumina platforms. Illumina is from a single time point and 454 from multiple time point. 454 was assembled using Newbler(dataset 1) and Illumina using Tophat-Cufflinks (dataset 2) and the denovo Trinity pipeline (dataset 3). I now have3 assemblies - 454 and Illumina will have some redunant transcripts (because of one overlapping time point); TopHat-Cufflinks and Trinity will have highly redundant transcripts (because they use same raw reads). Is it OK to provide all 3 datasets as EST evidence, how does it affect the quality of annotation. (For now I have used dataset 1 and dataset 2 as EST evidence) - I used the above model to retrain, I passed through everything except the abinitio gene predictions. I also provided a set a manually annotated genes , many of which have EST evidence. Is this OK to do? [ For proteins evidence, I gave a set from related organisms, same as above] - In my third retraining, I used the above retrained model, but this time I only provided the genome_gff but did not pass through any other data. However I did provide the manually annotated genes as EST evidence and related proteins as protein_evidence. Can you please give me some advice on which of these could give me the best prediction, or if I can alter something to get a better prediction. - A quick question about Augustus - I used a Augustus model (trained for a closely related organism) for ab-initio prediction. Does MAKER adjust this model based on the evidence provided, or use the model as such for a prediction. Greatly appreciate your help! Thanks! Ranjani -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Tue Sep 11 10:04:53 2012 From: carsonhh at gmail.com (Carson Holt) Date: Tue, 11 Sep 2012 12:04:53 -0400 Subject: [maker-devel] MAKER training In-Reply-To: Message-ID: > - I have transcriptome data from 454 and Illumina platforms. Illumina is from > a single time point and 454 from multiple time point. 454 was assembled using > Newbler(dataset 1) and Illumina using Tophat-Cufflinks (dataset 2) and the > denovo Trinity pipeline (dataset 3). I now have3 assemblies - 454 and > Illumina will have some redunant transcripts (because of one overlapping time > point); TopHat-Cufflinks and Trinity will have highly redundant transcripts > (because they use same raw reads). Is it OK to provide all 3 datasets as EST > evidence, how does it affect the quality of annotation. (For now I have used > dataset 1 and dataset 2 as EST evidence) This is fine. You can give them as a comma separated list est=file1,file2,file3 > - I used the above model to retrain, I passed through everything except the > abinitio gene predictions. I also provided a set a manually annotated genes , > many of which have EST evidence. Is this OK to do? [ For proteins evidence, I > gave a set from related organisms, same as above] > > - In my third retraining, I used the above retrained model, but this time I > only provided the genome_gff but did not pass through any other data. However > I did provide the manually annotated genes as EST evidence and related > proteins as protein_evidence. > > Can you please give me some advice on which of these could give me the best > prediction, or if I can alter something to get a better prediction. > Everything you've done sounds reasonable. Better training comes from having the most correct models to train with, so providing the manual annotations as training works, or you can also select MAKER models with the lowest AED score (i.e. models that most closely match evidence). The goal is to try and make the process as unbias as possible, so a consistent usually automated selection method is often the easiest to justify justifiable. > > - A quick question about Augustus - I used a Augustus model (trained for a > closely related organism) for ab-initio prediction. Does MAKER adjust this > model based on the evidence provided, or use the model as such for a > prediction. MAKER will provide hints to Augustus during the run to make it perform better. MAKER will report the raw unaided augustus results in the GFF3 file as a reference, but will use evidence to improve performance where it can. The gene name will let you know if it is a hint based or ab initio model prediction. When 'maker', is part of the gene name it is hint based. Thanks, Carson -------------- next part -------------- An HTML attachment was scrubbed... URL: From dence at genetics.utah.edu Tue Sep 11 10:29:21 2012 From: dence at genetics.utah.edu (Daniel Ence) Date: Tue, 11 Sep 2012 16:29:21 +0000 Subject: [maker-devel] MAKER training In-Reply-To: References: , , Message-ID: So, MAKER itself isn't probabilistic. If you give it the same data and the same options, it will give you the same outputs. The iterative approach for MAKER is to get gene models on the first round using the est2genome option and the Augustus model that you mentioned. After that first round, you train the ab-initio predictors and tell maker to use those newly trained gene predictors in the second round. Regarding the set of manually annotated genes, I think you should put those in the model_gff option. Thanks, Daniel Daniel Ence Graduate Student Eccles Institute of Human Genetics University of Utah 15 North 2030 East, Room 2100 Salt Lake City, UT 84112-5330 ________________________________ From: Sivaranjani Namasivayam [ranjani at uga.edu] Sent: Tuesday, September 11, 2012 9:57 AM To: Daniel Ence; maker-devel at yandell-lab.org Subject: RE: MAKER training Hey, I used the MAKER model to retrain MAKER itself. I read somewhere it improves MAKER's predictions. I did train abinitio gene predictors using MAKERs output, but I wanted to identify the best prediction before using it to train other gene predictors. Thanks, Ranjani ________________________________ From: Daniel Ence [dence at genetics.utah.edu] Sent: Tuesday, September 11, 2012 11:46 AM To: Sivaranjani Namasivayam; maker-devel at yandell-lab.org Subject: RE: MAKER training Hi Ranjani, It is fine to include all three of those transcriptome datatsets. The more (relevant) evidence the better. I'm not certain what you mean when you say "you used the above model to retrain". Did you train an abinitio gene predictor using the results from your first maker run? Daniel Ence Graduate Student Eccles Institute of Human Genetics University of Utah 15 North 2030 East, Room 2100 Salt Lake City, UT 84112-5330 ________________________________ From: maker-devel-bounces at yandell-lab.org [maker-devel-bounces at yandell-lab.org] on behalf of Sivaranjani Namasivayam [ranjani at uga.edu] Sent: Tuesday, September 11, 2012 9:38 AM To: maker-devel at yandell-lab.org Subject: [maker-devel] MAKER training Hi, I am using MAKER to annotate a newly sequenced genome. I have trained and retrained with datasets but I would like some advice on assessing the output and how this is affected by the input provided. - I have transcriptome data from 454 and Illumina platforms. Illumina is from a single time point and 454 from multiple time point. 454 was assembled using Newbler(dataset 1) and Illumina using Tophat-Cufflinks (dataset 2) and the denovo Trinity pipeline (dataset 3). I now have3 assemblies - 454 and Illumina will have some redunant transcripts (because of one overlapping time point); TopHat-Cufflinks and Trinity will have highly redundant transcripts (because they use same raw reads). Is it OK to provide all 3 datasets as EST evidence, how does it affect the quality of annotation. (For now I have used dataset 1 and dataset 2 as EST evidence) - I used the above model to retrain, I passed through everything except the abinitio gene predictions. I also provided a set a manually annotated genes , many of which have EST evidence. Is this OK to do? [ For proteins evidence, I gave a set from related organisms, same as above] - In my third retraining, I used the above retrained model, but this time I only provided the genome_gff but did not pass through any other data. However I did provide the manually annotated genes as EST evidence and related proteins as protein_evidence. Can you please give me some advice on which of these could give me the best prediction, or if I can alter something to get a better prediction. - A quick question about Augustus - I used a Augustus model (trained for a closely related organism) for ab-initio prediction. Does MAKER adjust this model based on the evidence provided, or use the model as such for a prediction. Greatly appreciate your help! Thanks! Ranjani -------------- next part -------------- An HTML attachment was scrubbed... URL: From ranjani at uga.edu Tue Sep 11 10:45:42 2012 From: ranjani at uga.edu (Sivaranjani Namasivayam) Date: Tue, 11 Sep 2012 16:45:42 +0000 Subject: [maker-devel] MAKER training In-Reply-To: References: , , , Message-ID: I will try the model_gff option. For the retraining I noticed the count of the annotated genes vary, I haven't examined if the gene structure varies. I will use the models to train ab-initio predictions and providing that as input. But I did notice the number of genes output by MAKER is fairly lower when compared to the transcriptome. I understand this is because MAKER annotations are based on good evidence but can this improve/increase with ab-initio gene models input. Thanks, Ranjani ________________________________ From: Daniel Ence [dence at genetics.utah.edu] Sent: Tuesday, September 11, 2012 12:29 PM To: Sivaranjani Namasivayam; maker-devel at yandell-lab.org Subject: RE: MAKER training So, MAKER itself isn't probabilistic. If you give it the same data and the same options, it will give you the same outputs. The iterative approach for MAKER is to get gene models on the first round using the est2genome option and the Augustus model that you mentioned. After that first round, you train the ab-initio predictors and tell maker to use those newly trained gene predictors in the second round. Regarding the set of manually annotated genes, I think you should put those in the model_gff option. Thanks, Daniel Daniel Ence Graduate Student Eccles Institute of Human Genetics University of Utah 15 North 2030 East, Room 2100 Salt Lake City, UT 84112-5330 ________________________________ From: Sivaranjani Namasivayam [ranjani at uga.edu] Sent: Tuesday, September 11, 2012 9:57 AM To: Daniel Ence; maker-devel at yandell-lab.org Subject: RE: MAKER training Hey, I used the MAKER model to retrain MAKER itself. I read somewhere it improves MAKER's predictions. I did train abinitio gene predictors using MAKERs output, but I wanted to identify the best prediction before using it to train other gene predictors. Thanks, Ranjani ________________________________ From: Daniel Ence [dence at genetics.utah.edu] Sent: Tuesday, September 11, 2012 11:46 AM To: Sivaranjani Namasivayam; maker-devel at yandell-lab.org Subject: RE: MAKER training Hi Ranjani, It is fine to include all three of those transcriptome datatsets. The more (relevant) evidence the better. I'm not certain what you mean when you say "you used the above model to retrain". Did you train an abinitio gene predictor using the results from your first maker run? Daniel Ence Graduate Student Eccles Institute of Human Genetics University of Utah 15 North 2030 East, Room 2100 Salt Lake City, UT 84112-5330 ________________________________ From: maker-devel-bounces at yandell-lab.org [maker-devel-bounces at yandell-lab.org] on behalf of Sivaranjani Namasivayam [ranjani at uga.edu] Sent: Tuesday, September 11, 2012 9:38 AM To: maker-devel at yandell-lab.org Subject: [maker-devel] MAKER training Hi, I am using MAKER to annotate a newly sequenced genome. I have trained and retrained with datasets but I would like some advice on assessing the output and how this is affected by the input provided. - I have transcriptome data from 454 and Illumina platforms. Illumina is from a single time point and 454 from multiple time point. 454 was assembled using Newbler(dataset 1) and Illumina using Tophat-Cufflinks (dataset 2) and the denovo Trinity pipeline (dataset 3). I now have3 assemblies - 454 and Illumina will have some redunant transcripts (because of one overlapping time point); TopHat-Cufflinks and Trinity will have highly redundant transcripts (because they use same raw reads). Is it OK to provide all 3 datasets as EST evidence, how does it affect the quality of annotation. (For now I have used dataset 1 and dataset 2 as EST evidence) - I used the above model to retrain, I passed through everything except the abinitio gene predictions. I also provided a set a manually annotated genes , many of which have EST evidence. Is this OK to do? [ For proteins evidence, I gave a set from related organisms, same as above] - In my third retraining, I used the above retrained model, but this time I only provided the genome_gff but did not pass through any other data. However I did provide the manually annotated genes as EST evidence and related proteins as protein_evidence. Can you please give me some advice on which of these could give me the best prediction, or if I can alter something to get a better prediction. - A quick question about Augustus - I used a Augustus model (trained for a closely related organism) for ab-initio prediction. Does MAKER adjust this model based on the evidence provided, or use the model as such for a prediction. Greatly appreciate your help! Thanks! Ranjani -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Tue Sep 11 14:33:11 2012 From: carsonhh at gmail.com (Carson Holt) Date: Tue, 11 Sep 2012 16:33:11 -0400 Subject: [maker-devel] How to preserve human-friendly IDs when reannotating In-Reply-To: Message-ID: Which version of MAKER are you running (maker --version)? --Carson From: Jeremy Semeiks Date: Monday, 10 September, 2012 11:02 AM To: Carson Holt Cc: Subject: Re: [maker-devel] How to preserve human-friendly IDs when reannotating OK, thanks. So if I understand correctly, to preserve human-friendly IDs requires setting just three options: map_forward=1, maker_gff=, and model_pass=1. (Or instead of the last two I could equivalently just set model_gff to a GFF containing only models.) A couple new issues came up when I tried to run with these options. I started maker like this: /usr/bin/time mpiexec -n 10 maker -q < /dev/null > maker.oe 2>&1 1. I get a bunch of messages as follows, but with variable line number: DBD::SQLite::db do failed: database is locked at /home/jrs/maker-2.26-beta/bin/../lib/GFFDB.pm line 186. I saw that this came up in another thread , but I'm not sure it was ever resolved, nor whether it will affect my reannotation results (as I'm not sure what "your GFF3 results will not be integrated" means). This error did not come up the last time I ran maker for reannotation with similar options in a different directory. And both my current directory and my tmp directory are locally mounted, ie not NFS. 2. Both in this run and in previous runs, I get a lot of lines like this, seemingly at random: Warning: unable to close filehandle DF properly. On Mon, Sep 10, 2012 at 6:01 AM, Carson Holt wrote: > The map_forward option requires that the pass option for the gene models be > turned on. Otherwise you will have to do some spacial overlap test outside of > MAKER. > > If you have a new assembly, you can try mapping the old models onto the new > assembly using the old transcripts as input to the est= and setting > est2genome=1 (nothing else set, i.e no repeat masking etc.). Then there is an > undocumented option that is still a little buggy (hence why it is still > undocumented). Add the line est_forward=1 to your control files. This tells > MAKER to copy names from the ESTs, build the models directly from their > alignment, and to do other things to try and make a 1 to 1 match across the > genome. You will have to manually check that it is 1 to 1 in the end (as I > said still a little buggy and hence undocumented). Use the resulting file as > input to the model_gff option on a separate run with map_forward=1 for > additional reannotation wil more evidence, etc. where you want to still be > able to map names forward. > > From: Jeremy Semeiks > Date: Sunday, 9 September, 2012 3:49 PM > To: > Subject: [maker-devel] How to preserve human-friendly IDs when reannotating > > Hi all, > > I have sequenced some novel fungal genomes, and I am annotating them with > maker-2.26-beta. The entire project is pretty iterative, in the sense that I > first get some seemingly-sane annotation sets, then analyze and compare the > proteomes biologically, then reannotate when new data comes in or as I learn > more about how maker works. Because I have already attached biological meaning > to some of my proteins, I would like to retain the same human-friendly IDs > across annotations. Eg, if maker suddenly finds 1,000 new proteins on a > reannotation run because I turned on keep_preds, then I don't want the > transcript formerly known as mymold_09652T0 to become mymold_10698T0 when I > run maker_map_ids; I want to keep it named mymold_09652T0. > > So, is there any built-in way to preserve human-friendly IDs, or do I need to > write my own script for this? I have tried setting map_forward=1 and > maker_gff=, but > setting these seems to preserve neither the human-friendly IDs nor even the > original IDs. (Eg, protein "genemark-scaffold353-processed-gene-0.9-mRNA-1" > changed its name to "genemark-scaffold353-processed-gene-0.6-mRNA-1" when > reannotated.) I haven't turned on any of the *_pass options, eg protein_pass; > would this be relevant? > > Extra credit question: I am making some mate-pair libraries for these fungi; > when I re-assemble, that will completely change my scaffold names. Is there > any easy way to preserve human-friendly transcript names in this case? As with > the above simpler case, I think it would be pretty easy to transfer 90% of the > names just by doing an all-vs-all blastp between two annotation sets and > fishing out the best hits, but the remaining 10% might be a headache. > > Thanks, > Jeremy > Grad student, Grishin lab > UT Southwestern, Dallas TX > 510.385.8959 > _______________________________________________ maker-devel mailing list > maker-devel at box290.bluehost.comhttp://box290.bluehost.com/mailman/listinfo/mak > er-devel_yandell-lab.org -------------- next part -------------- An HTML attachment was scrubbed... URL: From jeremy.semeiks at utsw.edu Tue Sep 11 17:56:23 2012 From: jeremy.semeiks at utsw.edu (Jeremy Semeiks) Date: Tue, 11 Sep 2012 18:56:23 -0500 Subject: [maker-devel] How to preserve human-friendly IDs when reannotating In-Reply-To: References: Message-ID: maker 2.26. And I have verified for myself that the three options I mentioned below suffice to preserve human-friendly IDs when reannotating. Thanks, J On Tue, Sep 11, 2012 at 3:33 PM, Carson Holt wrote: > Which version of MAKER are you running (maker --version)? > > --Carson > > > > From: Jeremy Semeiks > Date: Monday, 10 September, 2012 11:02 AM > To: Carson Holt > Cc: > Subject: Re: [maker-devel] How to preserve human-friendly IDs when > reannotating > > OK, thanks. So if I understand correctly, to preserve human-friendly IDs > requires setting just three options: map_forward=1, > maker_gff=, and model_pass=1. (Or instead of the > last two I could equivalently just set model_gff to a GFF containing only > models.) > > A couple new issues came up when I tried to run with these options. I > started maker like this: > > /usr/bin/time mpiexec -n 10 maker -q < /dev/null > maker.oe 2>&1 > > 1. I get a bunch of messages as follows, but with variable line number: > > DBD::SQLite::db do failed: database is locked at > /home/jrs/maker-2.26-beta/bin/../lib/GFFDB.pm line 186. > > I saw that this came up in another thread < > https://groups.google.com/forum/?fromgroups=#!topic/maker-devel/TscBgbQfBX4>, > but I'm not sure it was ever resolved, nor whether it will affect my > reannotation results (as I'm not sure what "your GFF3 results will not be > integrated" means). This error did not come up the last time I ran maker > for reannotation with similar options in a different directory. And both my > current directory and my tmp directory are locally mounted, ie not NFS. > > 2. Both in this run and in previous runs, I get a lot of lines like this, > seemingly at random: > > Warning: unable to close filehandle DF properly. > > > On Mon, Sep 10, 2012 at 6:01 AM, Carson Holt wrote: > >> The map_forward option requires that the pass option for the gene models >> be turned on. Otherwise you will have to do some spacial overlap test >> outside of MAKER. >> >> If you have a new assembly, you can try mapping the old models onto the >> new assembly using the old transcripts as input to the est= and setting >> est2genome=1 (nothing else set, i.e no repeat masking etc.). Then there is >> an undocumented option that is still a little buggy (hence why it is still >> undocumented). Add the line est_forward=1 to your control files. This >> tells MAKER to copy names from the ESTs, build the models directly from >> their alignment, and to do other things to try and make a 1 to 1 match >> across the genome. You will have to manually check that it is 1 to 1 in >> the end (as I said still a little buggy and hence undocumented). Use the >> resulting file as input to the model_gff option on a separate run with >> map_forward=1 for additional reannotation wil more evidence, etc. where you >> want to still be able to map names forward. >> >> From: Jeremy Semeiks >> Date: Sunday, 9 September, 2012 3:49 PM >> To: >> Subject: [maker-devel] How to preserve human-friendly IDs when >> reannotating >> >> Hi all, >> >> I have sequenced some novel fungal genomes, and I am annotating them with >> maker-2.26-beta. The entire project is pretty iterative, in the sense that >> I first get some seemingly-sane annotation sets, then analyze and compare >> the proteomes biologically, then reannotate when new data comes in or as I >> learn more about how maker works. Because I have already attached >> biological meaning to some of my proteins, I would like to retain the same >> human-friendly IDs across annotations. Eg, if maker suddenly finds 1,000 >> new proteins on a reannotation run because I turned on keep_preds, then I >> don't want the transcript formerly known as mymold_09652T0 to become >> mymold_10698T0 when I run maker_map_ids; I want to keep it named >> mymold_09652T0. >> >> So, is there any built-in way to preserve human-friendly IDs, or do I >> need to write my own script for this? I have tried setting map_forward=1 >> and maker_gff=, >> but setting these seems to preserve neither the human-friendly IDs nor even >> the original IDs. (Eg, protein >> "genemark-scaffold353-processed-gene-0.9-mRNA-1" changed its name to >> "genemark-scaffold353-processed-gene-0.6-mRNA-1" when reannotated.) I >> haven't turned on any of the *_pass options, eg protein_pass; would this be >> relevant? >> >> Extra credit question: I am making some mate-pair libraries for these >> fungi; when I re-assemble, that will completely change my scaffold names. >> Is there any easy way to preserve human-friendly transcript names in this >> case? As with the above simpler case, I think it would be pretty easy to >> transfer 90% of the names just by doing an all-vs-all blastp between two >> annotation sets and fishing out the best hits, but the remaining 10% might >> be a headache. >> >> Thanks, >> Jeremy >> Grad student, Grishin lab >> UT Southwestern, Dallas TX >> 510.385.8959 >> _______________________________________________ maker-devel mailing list >> maker-devel at box290.bluehost.com >> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org >> > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From ranjani at uga.edu Wed Sep 12 11:53:37 2012 From: ranjani at uga.edu (Sivaranjani Namasivayam) Date: Wed, 12 Sep 2012 17:53:37 +0000 Subject: [maker-devel] MAKER training In-Reply-To: References: , Message-ID: I have a few questions based on your comment about augustus/MAKER naming convention. I have been sorting the data using the second column of the GFF file, I wanted to be sure I have it right - Doesn't 'maker' in the second column signify MAKER's final annotations based on all evidence (EST, protein and abinitio prediction) ? I noticed two types of gene IDs, example 1. augustus_masked-scaffold00030-abinit-gene-3.2 2. maker-scaffold00030-augustus-gene-3.7 Is the first one, a direct augustus prediction without a hints file and the second based on a hints file (made from the EST and protein evidence)? If this is the case, could 2 be a better annotation than 1? - In case of augustus_masked in the 2nd column, I believe all are predictions are without a hints file. Thanks, Ranjani ________________________________ From: Carson Holt [carsonhh at gmail.com] Sent: Tuesday, September 11, 2012 12:04 PM To: Sivaranjani Namasivayam; maker-devel at yandell-lab.org Subject: Re: [maker-devel] MAKER training - I have transcriptome data from 454 and Illumina platforms. Illumina is from a single time point and 454 from multiple time point. 454 was assembled using Newbler(dataset 1) and Illumina using Tophat-Cufflinks (dataset 2) and the denovo Trinity pipeline (dataset 3). I now have3 assemblies - 454 and Illumina will have some redunant transcripts (because of one overlapping time point); TopHat-Cufflinks and Trinity will have highly redundant transcripts (because they use same raw reads). Is it OK to provide all 3 datasets as EST evidence, how does it affect the quality of annotation. (For now I have used dataset 1 and dataset 2 as EST evidence) This is fine. You can give them as a comma separated list est=file1,file2,file3 - I used the above model to retrain, I passed through everything except the abinitio gene predictions. I also provided a set a manually annotated genes , many of which have EST evidence. Is this OK to do? [ For proteins evidence, I gave a set from related organisms, same as above] - In my third retraining, I used the above retrained model, but this time I only provided the genome_gff but did not pass through any other data. However I did provide the manually annotated genes as EST evidence and related proteins as protein_evidence. Can you please give me some advice on which of these could give me the best prediction, or if I can alter something to get a better prediction. Everything you've done sounds reasonable. Better training comes from having the most correct models to train with, so providing the manual annotations as training works, or you can also select MAKER models with the lowest AED score (i.e. models that most closely match evidence). The goal is to try and make the process as unbias as possible, so a consistent usually automated selection method is often the easiest to justify justifiable. - A quick question about Augustus - I used a Augustus model (trained for a closely related organism) for ab-initio prediction. Does MAKER adjust this model based on the evidence provided, or use the model as such for a prediction. MAKER will provide hints to Augustus during the run to make it perform better. MAKER will report the raw unaided augustus results in the GFF3 file as a reference, but will use evidence to improve performance where it can. The gene name will let you know if it is a hint based or ab initio model prediction. When 'maker', is part of the gene name it is hint based. Thanks, Carson -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Thu Sep 13 07:11:27 2012 From: carsonhh at gmail.com (Carson Holt) Date: Thu, 13 Sep 2012 09:11:27 -0400 Subject: [maker-devel] How to preserve human-friendly IDs when reannotating In-Reply-To: Message-ID: The error --> DBD::SQLite::db do failed: database is locked at /home/jrs/maker-2.26-beta/bin/../lib/GFFDB.pm line 186. The location of the specific error you are getting is probably benign. It is a failure to alter the default cache size for the database. The database should already be populated. I'm planning removing the SQLlite database entirely in the future. Perhaps in favor of something like tabix based indexing of the GFF3 file. Thanks, Carson From: Jeremy Semeiks Date: Tuesday, 11 September, 2012 7:56 PM To: Carson Holt Cc: Subject: Re: [maker-devel] How to preserve human-friendly IDs when reannotating maker 2.26. And I have verified for myself that the three options I mentioned below suffice to preserve human-friendly IDs when reannotating. Thanks, J On Tue, Sep 11, 2012 at 3:33 PM, Carson Holt wrote: > Which version of MAKER are you running (maker --version)? > > --Carson > > > > From: Jeremy Semeiks > Date: Monday, 10 September, 2012 11:02 AM > To: Carson Holt > Cc: > Subject: Re: [maker-devel] How to preserve human-friendly IDs when > reannotating > > OK, thanks. So if I understand correctly, to preserve human-friendly IDs > requires setting just three options: map_forward=1, > maker_gff=, and model_pass=1. (Or instead of the last > two I could equivalently just set model_gff to a GFF containing only models.) > > A couple new issues came up when I tried to run with these options. I started > maker like this: > > /usr/bin/time mpiexec -n 10 maker -q < /dev/null > maker.oe 2>&1 > > 1. I get a bunch of messages as follows, but with variable line number: > > DBD::SQLite::db do failed: database is locked at > /home/jrs/maker-2.26-beta/bin/../lib/GFFDB.pm line 186. > > I saw that this came up in another thread > , > but I'm not sure it was ever resolved, nor whether it will affect my > reannotation results (as I'm not sure what "your GFF3 results will not be > integrated" means). This error did not come up the last time I ran maker for > reannotation with similar options in a different directory. And both my > current directory and my tmp directory are locally mounted, ie not NFS. > > 2. Both in this run and in previous runs, I get a lot of lines like this, > seemingly at random: > > Warning: unable to close filehandle DF properly. > > > On Mon, Sep 10, 2012 at 6:01 AM, Carson Holt wrote: >> The map_forward option requires that the pass option for the gene models be >> turned on. Otherwise you will have to do some spacial overlap test outside >> of MAKER. >> >> If you have a new assembly, you can try mapping the old models onto the new >> assembly using the old transcripts as input to the est= and setting >> est2genome=1 (nothing else set, i.e no repeat masking etc.). Then there is >> an undocumented option that is still a little buggy (hence why it is still >> undocumented). Add the line est_forward=1 to your control files. This tells >> MAKER to copy names from the ESTs, build the models directly from their >> alignment, and to do other things to try and make a 1 to 1 match across the >> genome. You will have to manually check that it is 1 to 1 in the end (as I >> said still a little buggy and hence undocumented). Use the resulting file as >> input to the model_gff option on a separate run with map_forward=1 for >> additional reannotation wil more evidence, etc. where you want to still be >> able to map names forward. >> >> From: Jeremy Semeiks >> Date: Sunday, 9 September, 2012 3:49 PM >> To: >> Subject: [maker-devel] How to preserve human-friendly IDs when reannotating >> >> Hi all, >> >> I have sequenced some novel fungal genomes, and I am annotating them with >> maker-2.26-beta. The entire project is pretty iterative, in the sense that I >> first get some seemingly-sane annotation sets, then analyze and compare the >> proteomes biologically, then reannotate when new data comes in or as I learn >> more about how maker works. Because I have already attached biological >> meaning to some of my proteins, I would like to retain the same >> human-friendly IDs across annotations. Eg, if maker suddenly finds 1,000 new >> proteins on a reannotation run because I turned on keep_preds, then I don't >> want the transcript formerly known as mymold_09652T0 to become mymold_10698T0 >> when I run maker_map_ids; I want to keep it named mymold_09652T0. >> >> So, is there any built-in way to preserve human-friendly IDs, or do I need to >> write my own script for this? I have tried setting map_forward=1 and >> maker_gff=, but >> setting these seems to preserve neither the human-friendly IDs nor even the >> original IDs. (Eg, protein "genemark-scaffold353-processed-gene-0.9-mRNA-1" >> changed its name to "genemark-scaffold353-processed-gene-0.6-mRNA-1" when >> reannotated.) I haven't turned on any of the *_pass options, eg protein_pass; >> would this be relevant? >> >> Extra credit question: I am making some mate-pair libraries for these fungi; >> when I re-assemble, that will completely change my scaffold names. Is there >> any easy way to preserve human-friendly transcript names in this case? As >> with the above simpler case, I think it would be pretty easy to transfer 90% >> of the names just by doing an all-vs-all blastp between two annotation sets >> and fishing out the best hits, but the remaining 10% might be a headache. >> >> Thanks, >> Jeremy >> Grad student, Grishin lab >> UT Southwestern, Dallas TX >> 510.385.8959 >> _______________________________________________ maker-devel mailing list >> maker-devel at box290.bluehost.comhttp://box290.bluehost.com/mailman/listinfo/ma >> ker-devel_yandell-lab.org > -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Thu Sep 13 07:30:22 2012 From: carsonhh at gmail.com (Carson Holt) Date: Thu, 13 Sep 2012 09:30:22 -0400 Subject: [maker-devel] MAKER training In-Reply-To: Message-ID: Yes, those are the final annotations, and yes one is derived from the ab initio model and one from hint based models. The selection between hint based models and ab initio models is based on evidence overlap, so either can be better than the other or vice versa. The bets models will have lower AED scores. So if for a given locus I have both hint based and ab initio based models, I keep the one that best matches the evidence (lowest AED score). augustus_masked means the genome was masked for repeats before running augustus. Anything with augustus_masked in the second column will be ab initio models kept for reference purposes. Every ab initio model produced by augustus will have an entry there. Thanks, Carson From: Sivaranjani Namasivayam Date: Wednesday, 12 September, 2012 1:53 PM To: Carson Holt , "maker-devel at yandell-lab.org" Subject: RE: [maker-devel] MAKER training I have a few questions based on your comment about augustus/MAKER naming convention. I have been sorting the data using the second column of the GFF file, I wanted to be sure I have it right - Doesn't 'maker' in the second column signify MAKER's final annotations based on all evidence (EST, protein and abinitio prediction) ? I noticed two types of gene IDs, example 1. augustus_masked-scaffold00030-abinit-gene-3.2 2. maker-scaffold00030-augustus-gene-3.7 Is the first one, a direct augustus prediction without a hints file and the second based on a hints file (made from the EST and protein evidence)? If this is the case, could 2 be a better annotation than 1? - In case of augustus_masked in the 2nd column, I believe all are predictions are without a hints file. Thanks, Ranjani From: Carson Holt [carsonhh at gmail.com] Sent: Tuesday, September 11, 2012 12:04 PM To: Sivaranjani Namasivayam; maker-devel at yandell-lab.org Subject: Re: [maker-devel] MAKER training > - I have transcriptome data from 454 and Illumina platforms. Illumina is from > a single time point and 454 from multiple time point. 454 was assembled using > Newbler(dataset 1) and Illumina using Tophat-Cufflinks (dataset 2) and the > denovo Trinity pipeline (dataset 3). I now have3 assemblies - 454 and > Illumina will have some redunant transcripts (because of one overlapping time > point); TopHat-Cufflinks and Trinity will have highly redundant transcripts > (because they use same raw reads). Is it OK to provide all 3 datasets as EST > evidence, how does it affect the quality of annotation. (For now I have used > dataset 1 and dataset 2 as EST evidence) This is fine. You can give them as a comma separated list est=file1,file2,file3 > - I used the above model to retrain, I passed through everything except the > abinitio gene predictions. I also provided a set a manually annotated genes , > many of which have EST evidence. Is this OK to do? [ For proteins evidence, I > gave a set from related organisms, same as above] > > - In my third retraining, I used the above retrained model, but this time I > only provided the genome_gff but did not pass through any other data. However > I did provide the manually annotated genes as EST evidence and related > proteins as protein_evidence. > > Can you please give me some advice on which of these could give me the best > prediction, or if I can alter something to get a better prediction. > Everything you've done sounds reasonable. Better training comes from having the most correct models to train with, so providing the manual annotations as training works, or you can also select MAKER models with the lowest AED score (i.e. models that most closely match evidence). The goal is to try and make the process as unbias as possible, so a consistent usually automated selection method is often the easiest to justify justifiable. > > - A quick question about Augustus - I used a Augustus model (trained for a > closely related organism) for ab-initio prediction. Does MAKER adjust this > model based on the evidence provided, or use the model as such for a > prediction. MAKER will provide hints to Augustus during the run to make it perform better. MAKER will report the raw unaided augustus results in the GFF3 file as a reference, but will use evidence to improve performance where it can. The gene name will let you know if it is a hint based or ab initio model prediction. When 'maker', is part of the gene name it is hint based. Thanks, Carson -------------- next part -------------- An HTML attachment was scrubbed... URL: From guoyunfei1989 at gmail.com Wed Sep 19 10:41:40 2012 From: guoyunfei1989 at gmail.com (Yunfei Guo) Date: Wed, 19 Sep 2012 09:41:40 -0700 Subject: [maker-devel] open3: fork failed: Cannot allocate memory Message-ID: Hi Carson, Sorry to bother you again because I really can't find a solution to it. Have you seen this error before? I simply started multiple jobs in the same directory and got the following msg after hours of running. >From Admin: "Your batch job 2511011 encountered the following error: open3: fork failed: Cannot allocate memory ERROR: Failed while polishig ESTs ERROR: Chunk failed at level:2, tier_type:2 FAILED CONTIG:scaffold740 It continued generating errors in a loop until the /var filesystem filled. I will cancel the job. You may find it useful within your job script to check for errors and exit if present." And this is not because of lack of memory since this job has exclusive access to the node. Let me know if you want the entire stderr file. Thanks. From carsonhh at gmail.com Fri Sep 21 07:28:34 2012 From: carsonhh at gmail.com (Carson Holt) Date: Fri, 21 Sep 2012 09:28:34 -0400 Subject: [maker-devel] open3: fork failed: Cannot allocate memory In-Reply-To: Message-ID: Exclusive access doesn't necessarily mean that memory is not full, especially if you are running via MPI. Under MPI each MAKER instance will have a separate memory footprint (the sum of which may be too high for your system). You can lower the memory footprint per instance by setting all the blast_depth options in the maker_bopt.ctl file. Set them to 30 for example. Also in you have set max_dna_len to a value greater than 100000, bring it back down. A value of 200000 for example will cause MAEKR to use twice as much memory as 100000. The primary cause of high memory is too much evidence aligning in a region. Setting the depth parameter to 30 will cause MAKER to sort the alignments as they come in and drop all but the best 30 alignments. Each instance of MAKER will usually take up 500Mb to 1Gb of RAM when max_dna_len is set to 100,000. It will take up twice that when max_dna_len is set to 200,000. Alternatively, if you are also using MPI, you can set the job up to launch fewer instances of MAKER, but allow each instance to use more CPUs. You do this by halving the value of the -n option given to mpiexec and then setting cpus=2 in the maker_opts file. The result in that BLAST analyses will run on 2 cpus each but MAKER will only keep the results for 6 jobs in memory at a time rather than 12 jobs (I.e. Lower memory footprint). When using this technique, make sure the hostfile used by mpiexec is set to follow a round robin distribution or all instances will start on half your nodes while the other half of your nodes will be left idle. Example - this is correct: host1 host2 host3 host1 host2 host3 host1 host2 host3 This is incorrect: host1 host1 host1 host2 host2 host2 host3 host3 host3 FYI when using MPI the -n parameter given to mpiexec and the -cpus parameter given to MAKER have a multiplicative affect on CPU usage. Example: mpiexec -n 12 maker -cpus 1 (will launch 12 maker instances and use a total of 12 cpus) mpiexec -n 12 maker -cpus 2 (will launch 12 maker instances but use a total of 24 cpus) mpiexec -n 6 maker -cpus 4 (will launch 6 maker instances but use a total of 24 cpus) Why is this? It's because CPUs affects how many processors to use to solve a single 100,000 bp chunk (per instance). But mpiexec -n sets how many simultaneous instances and as a result how many chunks to run together. So mpiexec -n will cause memory usage to increase in a way that -cpus doesn't. But mpiexec also scales across machines for parallelization where -cpus can't (it's use applies to a single machine). Thanks, Carson On 12-09-19 12:41 PM, "Yunfei Guo" wrote: >Hi Carson, > >Sorry to bother you again because I really can't find a solution to >it. Have you seen this error before? I simply started multiple jobs in >the same directory and got the following msg after hours of running. > >From Admin: >"Your batch job 2511011 encountered the following error: > open3: fork failed: Cannot allocate memory > ERROR: Failed while polishig ESTs > ERROR: Chunk failed at level:2, tier_type:2 > FAILED CONTIG:scaffold740 >It continued generating errors in a loop until the /var filesystem filled. >I will cancel the job. You may find it useful within your job script to >check for errors and exit if present." > >And this is not because of lack of memory since this job has exclusive >access to the node. Let me know if you want the entire stderr file. >Thanks. > >_______________________________________________ >maker-devel mailing list >maker-devel at box290.bluehost.com >http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org From fourie.joubert at up.ac.za Fri Sep 21 07:58:26 2012 From: fourie.joubert at up.ac.za (Fourie Joubert) Date: Fri, 21 Sep 2012 15:58:26 +0200 Subject: [maker-devel] Problems parsing iprscan results with iprscan2gff3 Message-ID: <505C7282.3090107@up.ac.za> Hi Folks I am running into some problems parsing iprscan results. I run iprscan as follows: > iprscan -cli -i bot.all.maker.proteins.fasta -o bot.all.maker.proteins.raw -format raw -goterms -iprlookup and obtain the iprscan output (the iprscan output file is at http://www.bi.up.ac.za/~fourie/bot.all.maker.proteins.raw if anyone is interested in the detailed output, and the initial maker gff3 file is at http://www.bi.up.ac.za/~fourie/bot.all.gff). I then try to run the conversion to gff3, but I get very long list of errors: > iprscan2gff3 bot.all.maker.proteins.raw bot.all.gff > domains.gff ERROR: In maker-NODE_4797_length_138874_cov_96.632576-augustus-gene-0.113 Use of uninitialized value $seqid in concatenation (.) or string at /usr/local/maker/bin/iprscan2gff3 line 255. Use of uninitialized value $start in concatenation (.) or string at /usr/local/maker/bin/iprscan2gff3 line 255. Use of uninitialized value $end in concatenation (.) or string at /usr/local/maker/bin/iprscan2gff3 line 255. Use of uninitialized value $strand in concatenation (.) or string at /usr/local/maker/bin/iprscan2gff3 line 255. Use of uninitialized value $off in subtraction (-) at /usr/local/maker/bin/iprscan2gff3 line 267. Use of uninitialized value $pB in subtraction (-) at /usr/local/maker/bin/iprscan2gff3 line 267. Use of uninitialized value $off in subtraction (-) at /usr/local/maker/bin/iprscan2gff3 line 267. Use of uninitialized value $pE in subtraction (-) at /usr/local/maker/bin/iprscan2gff3 line 267. Use of uninitialized value $seqid in concatenation (.) or string at /usr/local/maker/bin/iprscan2gff3 line 269. Use of uninitialized value $start in concatenation (.) or string at /usr/local/maker/bin/iprscan2gff3 line 269. Use of uninitialized value $end in concatenation (.) or string at /usr/local/maker/bin/iprscan2gff3 line 269. Use of uninitialized value $strand in concatenation (.) or string at /usr/local/maker/bin/iprscan2gff3 line 269. ....... ....... ....... for most of the entries. Any advice or help would be sincerely appreciated! Best regards! Fourie -- -------------- Prof Fourie Joubert Bioinformatics and Computational Biology Unit Department of Biochemistry University of Pretoria fourie.joubert at up.ac.za http://www.bi.up.ac.za Tel. +27-12-420-5825 Fax. +27-12-420-5800 ------------------------------------------------------------------------- This message and attachments are subject to a disclaimer. Please refer to www.it.up.ac.za/documentation/governance/disclaimer/ for full details. -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Fri Sep 21 08:10:21 2012 From: carsonhh at gmail.com (Carson Holt) Date: Fri, 21 Sep 2012 10:10:21 -0400 Subject: [maker-devel] Problems parsing iprscan results with iprscan2gff3 In-Reply-To: <505C7282.3090107@up.ac.za> Message-ID: Some of your iprscan results contain truncated names Example: maker-NODE_5172_length_118591_cov_102.277115-snap-gene-0.100-mR This seems to be the case for almost all HMMPanther and HMMSmart results. Try just removing those two groups of results from your file for now. Then use the iprscan_wrap script that comes with maker to just re-run just those two application within iprscan it will fix the truncation issue (it creates temporary short names and then converts back to the longer names when it parses the results). Thanks, Carson From: Fourie Joubert Date: Friday, 21 September, 2012 9:58 AM To: "maker-devel at yandell-lab.org" Subject: [maker-devel] Problems parsing iprscan results with iprscan2gff3 Hi Folks I am running into some problems parsing iprscan results. I run iprscan as follows: > iprscan -cli -i bot.all.maker.proteins.fasta -o bot.all.maker.proteins.raw -format raw -goterms -iprlookup and obtain the iprscan output (the iprscan output file is at http://www.bi.up.ac.za/~fourie/bot.all.maker.proteins.raw if anyone is interested in the detailed output, and the initial maker gff3 file is at http://www.bi.up.ac.za/~fourie/bot.all.gff). I then try to run the conversion to gff3, but I get very long list of errors: > iprscan2gff3 bot.all.maker.proteins.raw bot.all.gff > domains.gff ERROR: In maker-NODE_4797_length_138874_cov_96.632576-augustus-gene-0.113 Use of uninitialized value $seqid in concatenation (.) or string at /usr/local/maker/bin/iprscan2gff3 line 255. Use of uninitialized value $start in concatenation (.) or string at /usr/local/maker/bin/iprscan2gff3 line 255. Use of uninitialized value $end in concatenation (.) or string at /usr/local/maker/bin/iprscan2gff3 line 255. Use of uninitialized value $strand in concatenation (.) or string at /usr/local/maker/bin/iprscan2gff3 line 255. Use of uninitialized value $off in subtraction (-) at /usr/local/maker/bin/iprscan2gff3 line 267. Use of uninitialized value $pB in subtraction (-) at /usr/local/maker/bin/iprscan2gff3 line 267. Use of uninitialized value $off in subtraction (-) at /usr/local/maker/bin/iprscan2gff3 line 267. Use of uninitialized value $pE in subtraction (-) at /usr/local/maker/bin/iprscan2gff3 line 267. Use of uninitialized value $seqid in concatenation (.) or string at /usr/local/maker/bin/iprscan2gff3 line 269. Use of uninitialized value $start in concatenation (.) or string at /usr/local/maker/bin/iprscan2gff3 line 269. Use of uninitialized value $end in concatenation (.) or string at /usr/local/maker/bin/iprscan2gff3 line 269. Use of uninitialized value $strand in concatenation (.) or string at /usr/local/maker/bin/iprscan2gff3 line 269. ....... ....... ....... for most of the entries. Any advice or help would be sincerely appreciated! Best regards! Fourie -- -------------- Prof Fourie Joubert Bioinformatics and Computational Biology Unit Department of Biochemistry University of Pretoria fourie.joubert at up.ac.zahttp://www.bi.up.ac.za Tel. +27-12-420-5825 Fax. +27-12-420-5800 ------------------------------------------------------------------------- This message and attachments are subject to a disclaimer. Please refer to www.it.up.ac.za/documentation/governance/disclaimer/ for full details. _______________________________________________ maker-devel mailing list maker-devel at box290.bluehost.com http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org -------------- next part -------------- An HTML attachment was scrubbed... URL: From jeremy.semeiks at utsw.edu Fri Sep 21 09:39:15 2012 From: jeremy.semeiks at utsw.edu (Jeremy Semeiks) Date: Fri, 21 Sep 2012 10:39:15 -0500 Subject: [maker-devel] How to preserve human-friendly IDs when reannotating In-Reply-To: References: Message-ID: For the record: After analyzing these runs, I have confirmed that neither error I described (ie, "DBD::SQLite::db do failed" and "Warning: unable to close filehandle DF properly") affects maker's protein output in any way I can detect. Thanks, J On Thu, Sep 13, 2012 at 8:11 AM, Carson Holt wrote: > The error --> DBD::SQLite::db do failed: database is locked at > /home/jrs/maker-2.26-beta/bin/../lib/GFFDB.pm line 186. > > The location of the specific error you are getting is probably benign. It > is a failure to alter the default cache size for the database. The > database should already be populated. I'm planning removing the SQLlite > database entirely in the future. Perhaps in favor of something like tabix > based indexing of the GFF3 file. > > Thanks, > Carson > > > > From: Jeremy Semeiks > Date: Tuesday, 11 September, 2012 7:56 PM > > To: Carson Holt > Cc: > Subject: Re: [maker-devel] How to preserve human-friendly IDs when > reannotating > > maker 2.26. > > And I have verified for myself that the three options I mentioned below > suffice to preserve human-friendly IDs when reannotating. > > Thanks, > J > > On Tue, Sep 11, 2012 at 3:33 PM, Carson Holt wrote: > >> Which version of MAKER are you running (maker --version)? >> >> --Carson >> >> >> >> From: Jeremy Semeiks >> Date: Monday, 10 September, 2012 11:02 AM >> To: Carson Holt >> Cc: >> Subject: Re: [maker-devel] How to preserve human-friendly IDs when >> reannotating >> >> OK, thanks. So if I understand correctly, to preserve human-friendly IDs >> requires setting just three options: map_forward=1, >> maker_gff=, and model_pass=1. (Or instead of the >> last two I could equivalently just set model_gff to a GFF containing only >> models.) >> >> A couple new issues came up when I tried to run with these options. I >> started maker like this: >> >> /usr/bin/time mpiexec -n 10 maker -q < /dev/null > maker.oe 2>&1 >> >> 1. I get a bunch of messages as follows, but with variable line number: >> >> DBD::SQLite::db do failed: database is locked at >> /home/jrs/maker-2.26-beta/bin/../lib/GFFDB.pm line 186. >> >> I saw that this came up in another thread < >> https://groups.google.com/forum/?fromgroups=#!topic/maker-devel/TscBgbQfBX4>, >> but I'm not sure it was ever resolved, nor whether it will affect my >> reannotation results (as I'm not sure what "your GFF3 results will not be >> integrated" means). This error did not come up the last time I ran maker >> for reannotation with similar options in a different directory. And both my >> current directory and my tmp directory are locally mounted, ie not NFS. >> >> 2. Both in this run and in previous runs, I get a lot of lines like this, >> seemingly at random: >> >> Warning: unable to close filehandle DF properly. >> >> >> On Mon, Sep 10, 2012 at 6:01 AM, Carson Holt wrote: >> >>> The map_forward option requires that the pass option for the gene models >>> be turned on. Otherwise you will have to do some spacial overlap test >>> outside of MAKER. >>> >>> If you have a new assembly, you can try mapping the old models onto the >>> new assembly using the old transcripts as input to the est= and setting >>> est2genome=1 (nothing else set, i.e no repeat masking etc.). Then there is >>> an undocumented option that is still a little buggy (hence why it is still >>> undocumented). Add the line est_forward=1 to your control files. This >>> tells MAKER to copy names from the ESTs, build the models directly from >>> their alignment, and to do other things to try and make a 1 to 1 match >>> across the genome. You will have to manually check that it is 1 to 1 in >>> the end (as I said still a little buggy and hence undocumented). Use the >>> resulting file as input to the model_gff option on a separate run with >>> map_forward=1 for additional reannotation wil more evidence, etc. where you >>> want to still be able to map names forward. >>> >>> From: Jeremy Semeiks >>> Date: Sunday, 9 September, 2012 3:49 PM >>> To: >>> Subject: [maker-devel] How to preserve human-friendly IDs when >>> reannotating >>> >>> Hi all, >>> >>> I have sequenced some novel fungal genomes, and I am annotating them >>> with maker-2.26-beta. The entire project is pretty iterative, in the sense >>> that I first get some seemingly-sane annotation sets, then analyze and >>> compare the proteomes biologically, then reannotate when new data comes in >>> or as I learn more about how maker works. Because I have already attached >>> biological meaning to some of my proteins, I would like to retain the same >>> human-friendly IDs across annotations. Eg, if maker suddenly finds 1,000 >>> new proteins on a reannotation run because I turned on keep_preds, then I >>> don't want the transcript formerly known as mymold_09652T0 to become >>> mymold_10698T0 when I run maker_map_ids; I want to keep it named >>> mymold_09652T0. >>> >>> So, is there any built-in way to preserve human-friendly IDs, or do I >>> need to write my own script for this? I have tried setting map_forward=1 >>> and maker_gff=, >>> but setting these seems to preserve neither the human-friendly IDs nor even >>> the original IDs. (Eg, protein >>> "genemark-scaffold353-processed-gene-0.9-mRNA-1" changed its name to >>> "genemark-scaffold353-processed-gene-0.6-mRNA-1" when reannotated.) I >>> haven't turned on any of the *_pass options, eg protein_pass; would this be >>> relevant? >>> >>> Extra credit question: I am making some mate-pair libraries for these >>> fungi; when I re-assemble, that will completely change my scaffold names. >>> Is there any easy way to preserve human-friendly transcript names in this >>> case? As with the above simpler case, I think it would be pretty easy to >>> transfer 90% of the names just by doing an all-vs-all blastp between two >>> annotation sets and fishing out the best hits, but the remaining 10% might >>> be a headache. >>> >>> Thanks, >>> Jeremy >>> Grad student, Grishin lab >>> UT Southwestern, Dallas TX >>> 510.385.8959 >>> _______________________________________________ maker-devel mailing list >>> maker-devel at box290.bluehost.com >>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org >>> >> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Fri Sep 21 09:42:46 2012 From: carsonhh at gmail.com (Carson Holt) Date: Fri, 21 Sep 2012 11:42:46 -0400 Subject: [maker-devel] How to preserve human-friendly IDs when reannotating In-Reply-To: Message-ID: That's good to know :-) --Carson From: Jeremy Semeiks Date: Friday, 21 September, 2012 11:39 AM To: Carson Holt Cc: Subject: Re: [maker-devel] How to preserve human-friendly IDs when reannotating For the record: After analyzing these runs, I have confirmed that neither error I described (ie, "DBD::SQLite::db do failed" and "Warning: unable to close filehandle DF properly") affects maker's protein output in any way I can detect. Thanks, J On Thu, Sep 13, 2012 at 8:11 AM, Carson Holt wrote: > The error --> DBD::SQLite::db do failed: database is locked at > /home/jrs/maker-2.26-beta/bin/../lib/GFFDB.pm line 186. > > The location of the specific error you are getting is probably benign. It is > a failure to alter the default cache size for the database. The database > should already be populated. I'm planning removing the SQLlite database > entirely in the future. Perhaps in favor of something like tabix based > indexing of the GFF3 file. > > Thanks, > Carson > > > > From: Jeremy Semeiks > Date: Tuesday, 11 September, 2012 7:56 PM > > To: Carson Holt > Cc: > Subject: Re: [maker-devel] How to preserve human-friendly IDs when > reannotating > > maker 2.26. > > And I have verified for myself that the three options I mentioned below > suffice to preserve human-friendly IDs when reannotating. > > Thanks, > J > > On Tue, Sep 11, 2012 at 3:33 PM, Carson Holt wrote: >> Which version of MAKER are you running (maker --version)? >> >> --Carson >> >> >> >> From: Jeremy Semeiks >> Date: Monday, 10 September, 2012 11:02 AM >> To: Carson Holt >> Cc: >> Subject: Re: [maker-devel] How to preserve human-friendly IDs when >> reannotating >> >> OK, thanks. So if I understand correctly, to preserve human-friendly IDs >> requires setting just three options: map_forward=1, >> maker_gff=, and model_pass=1. (Or instead of the last >> two I could equivalently just set model_gff to a GFF containing only models.) >> >> A couple new issues came up when I tried to run with these options. I started >> maker like this: >> >> /usr/bin/time mpiexec -n 10 maker -q < /dev/null > maker.oe 2>&1 >> >> 1. I get a bunch of messages as follows, but with variable line number: >> >> DBD::SQLite::db do failed: database is locked at >> /home/jrs/maker-2.26-beta/bin/../lib/GFFDB.pm line 186. >> >> I saw that this came up in another thread >> >> , but I'm not sure it was ever resolved, nor whether it will affect my >> reannotation results (as I'm not sure what "your GFF3 results will not be >> integrated" means). This error did not come up the last time I ran maker for >> reannotation with similar options in a different directory. And both my >> current directory and my tmp directory are locally mounted, ie not NFS. >> >> 2. Both in this run and in previous runs, I get a lot of lines like this, >> seemingly at random: >> >> Warning: unable to close filehandle DF properly. >> >> >> On Mon, Sep 10, 2012 at 6:01 AM, Carson Holt wrote: >>> The map_forward option requires that the pass option for the gene models be >>> turned on. Otherwise you will have to do some spacial overlap test outside >>> of MAKER. >>> >>> If you have a new assembly, you can try mapping the old models onto the new >>> assembly using the old transcripts as input to the est= and setting >>> est2genome=1 (nothing else set, i.e no repeat masking etc.). Then there is >>> an undocumented option that is still a little buggy (hence why it is still >>> undocumented). Add the line est_forward=1 to your control files. This >>> tells MAKER to copy names from the ESTs, build the models directly from >>> their alignment, and to do other things to try and make a 1 to 1 match >>> across the genome. You will have to manually check that it is 1 to 1 in the >>> end (as I said still a little buggy and hence undocumented). Use the >>> resulting file as input to the model_gff option on a separate run with >>> map_forward=1 for additional reannotation wil more evidence, etc. where you >>> want to still be able to map names forward. >>> >>> From: Jeremy Semeiks >>> Date: Sunday, 9 September, 2012 3:49 PM >>> To: >>> Subject: [maker-devel] How to preserve human-friendly IDs when reannotating >>> >>> Hi all, >>> >>> I have sequenced some novel fungal genomes, and I am annotating them with >>> maker-2.26-beta. The entire project is pretty iterative, in the sense that I >>> first get some seemingly-sane annotation sets, then analyze and compare the >>> proteomes biologically, then reannotate when new data comes in or as I learn >>> more about how maker works. Because I have already attached biological >>> meaning to some of my proteins, I would like to retain the same >>> human-friendly IDs across annotations. Eg, if maker suddenly finds 1,000 new >>> proteins on a reannotation run because I turned on keep_preds, then I don't >>> want the transcript formerly known as mymold_09652T0 to become >>> mymold_10698T0 when I run maker_map_ids; I want to keep it named >>> mymold_09652T0. >>> >>> So, is there any built-in way to preserve human-friendly IDs, or do I need >>> to write my own script for this? I have tried setting map_forward=1 and >>> maker_gff=, but >>> setting these seems to preserve neither the human-friendly IDs nor even the >>> original IDs. (Eg, protein "genemark-scaffold353-processed-gene-0.9-mRNA-1" >>> changed its name to "genemark-scaffold353-processed-gene-0.6-mRNA-1" when >>> reannotated.) I haven't turned on any of the *_pass options, eg >>> protein_pass; would this be relevant? >>> >>> Extra credit question: I am making some mate-pair libraries for these fungi; >>> when I re-assemble, that will completely change my scaffold names. Is there >>> any easy way to preserve human-friendly transcript names in this case? As >>> with the above simpler case, I think it would be pretty easy to transfer 90% >>> of the names just by doing an all-vs-all blastp between two annotation sets >>> and fishing out the best hits, but the remaining 10% might be a headache. >>> >>> Thanks, >>> Jeremy >>> Grad student, Grishin lab >>> UT Southwestern, Dallas TX >>> 510.385.8959 >>> _______________________________________________ maker-devel mailing list >>> maker-devel at box290.bluehost.comhttp://box290.bluehost.com/mailman/listinfo/m >>> aker-devel_yandell-lab.org >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From ianmisner17 at aim.com Tue Sep 25 06:27:04 2012 From: ianmisner17 at aim.com (Ian Misner) Date: Tue, 25 Sep 2012 08:27:04 -0400 Subject: [maker-devel] problem with maker_map_ids Message-ID: Hello, I'm trying to create human friendly ids and I'm getting an error when I use the -sort_file option. Without the sort file it runs fine just not numbered from the first contig. I have had some programers at our cluster look at the script and they attempted a fix but it did not work. They mentioned the script was "buggy" so this might be part of the problem. I've attached the error as well as the sort file. I can send more files if necessary. Thanks for you time. Cheers Ian $ maker_map_ids --prefix THRCLA_ --justify 5 --sort_order 34112_sort.txt 34112_3June11Ass.gff > 34112_3June11Ass_named.txt Can't use string ("34112_sort.txt") as a HASH ref while "strict refs" in use at /gpfs/runtime/opt/maker/2.10/maker/bin/maker_map_ids line 311, <$IN> line 499186. -------------- next part -------------- THRCLA_contig1 1 THRCLA_contig2 2 THRCLA_contig3 3 THRCLA_contig4 4 THRCLA_contig5 5 THRCLA_contig6 6 THRCLA_contig7 7 THRCLA_contig8 8 THRCLA_contig9 9 THRCLA_contig10 10 THRCLA_contig11 11 THRCLA_contig12 12 THRCLA_contig13 13 THRCLA_contig14 14 THRCLA_contig15 15 THRCLA_contig16 16 THRCLA_contig17 17 THRCLA_contig18 18 THRCLA_contig19 19 THRCLA_contig20 20 THRCLA_contig21 21 THRCLA_contig22 22 THRCLA_contig23 23 THRCLA_contig24 24 THRCLA_contig25 25 THRCLA_contig26 26 THRCLA_contig27 27 THRCLA_contig28 28 THRCLA_contig29 29 THRCLA_contig30 30 THRCLA_contig31 31 THRCLA_contig32 32 THRCLA_contig33 33 THRCLA_contig34 34 THRCLA_contig35 35 THRCLA_contig36 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THRCLA_contig466 466 THRCLA_contig467 467 THRCLA_contig468 468 THRCLA_contig469 469 THRCLA_contig470 470 THRCLA_contig471 471 THRCLA_contig472 472 THRCLA_contig473 473 THRCLA_contig474 474 THRCLA_contig475 475 THRCLA_contig476 476 THRCLA_contig477 477 THRCLA_contig478 478 THRCLA_contig479 479 THRCLA_contig480 480 THRCLA_contig481 481 THRCLA_contig482 482 THRCLA_contig483 483 THRCLA_contig484 484 THRCLA_contig485 485 THRCLA_contig486 486 THRCLA_contig487 487 THRCLA_contig488 488 THRCLA_contig489 489 THRCLA_contig490 490 THRCLA_contig491 491 THRCLA_contig492 492 THRCLA_contig493 493 THRCLA_contig494 494 THRCLA_contig495 495 THRCLA_contig496 496 THRCLA_contig497 497 THRCLA_contig498 498 THRCLA_contig499 499 THRCLA_contig500 500 THRCLA_contig501 501 THRCLA_contig502 502 THRCLA_contig503 503 THRCLA_contig504 504 THRCLA_contig505 505 THRCLA_contig506 506 THRCLA_contig507 507 THRCLA_contig508 508 THRCLA_contig509 509 THRCLA_contig510 510 THRCLA_contig511 511 THRCLA_contig512 512 THRCLA_contig513 513 THRCLA_contig514 514 THRCLA_contig515 515 THRCLA_contig516 516 THRCLA_contig517 517 THRCLA_contig518 518 THRCLA_contig519 519 THRCLA_contig520 520 THRCLA_contig521 521 THRCLA_contig522 522 THRCLA_contig523 523 THRCLA_contig524 524 THRCLA_contig525 525 THRCLA_contig526 526 THRCLA_contig527 527 THRCLA_contig528 528 THRCLA_contig529 529 THRCLA_contig530 530 THRCLA_contig531 531 THRCLA_contig532 532 THRCLA_contig533 533 THRCLA_contig534 534 THRCLA_contig535 535 THRCLA_contig536 536 THRCLA_contig537 537 THRCLA_contig538 538 THRCLA_contig539 539 THRCLA_contig540 540 THRCLA_contig541 541 THRCLA_contig542 542 THRCLA_contig543 543 THRCLA_contig544 544 THRCLA_contig545 545 THRCLA_contig546 546 THRCLA_contig547 547 THRCLA_contig548 548 THRCLA_contig549 549 THRCLA_contig550 550 THRCLA_contig551 551 THRCLA_contig552 552 THRCLA_contig553 553 THRCLA_contig554 554 THRCLA_contig555 555 THRCLA_contig556 556 THRCLA_contig557 557 THRCLA_contig558 558 THRCLA_contig559 559 THRCLA_contig560 560 THRCLA_contig561 561 THRCLA_contig562 562 THRCLA_contig563 563 THRCLA_contig564 564 THRCLA_contig565 565 THRCLA_contig566 566 THRCLA_contig567 567 THRCLA_contig568 568 THRCLA_contig569 569 THRCLA_contig570 570 THRCLA_contig571 571 THRCLA_contig572 572 THRCLA_contig573 573 THRCLA_contig574 574 THRCLA_contig575 575 THRCLA_contig576 576 THRCLA_contig577 577 THRCLA_contig578 578 THRCLA_contig579 579 THRCLA_contig580 580 THRCLA_contig581 581 THRCLA_contig582 582 THRCLA_contig583 583 THRCLA_contig584 584 THRCLA_contig585 585 THRCLA_contig586 586 THRCLA_contig587 587 THRCLA_contig588 588 THRCLA_contig589 589 THRCLA_contig590 590 THRCLA_contig591 591 THRCLA_contig592 592 THRCLA_contig593 593 THRCLA_contig594 594 THRCLA_contig595 595 THRCLA_contig596 596 THRCLA_contig597 597 THRCLA_contig598 598 THRCLA_contig599 599 THRCLA_contig600 600 THRCLA_contig601 601 THRCLA_contig602 602 THRCLA_contig603 603 THRCLA_contig604 604 THRCLA_contig605 605 THRCLA_contig606 606 THRCLA_contig607 607 THRCLA_contig608 608 THRCLA_contig609 609 THRCLA_contig610 610 THRCLA_contig611 611 THRCLA_contig612 612 THRCLA_contig613 613 THRCLA_contig614 614 THRCLA_contig615 615 THRCLA_contig616 616 THRCLA_contig617 617 THRCLA_contig618 618 THRCLA_contig619 619 THRCLA_contig620 620 THRCLA_contig621 621 THRCLA_contig622 622 THRCLA_contig623 623 THRCLA_contig624 624 THRCLA_contig625 625 THRCLA_contig626 626 THRCLA_contig627 627 THRCLA_contig628 628 THRCLA_contig629 629 THRCLA_contig630 630 THRCLA_contig631 631 THRCLA_contig632 632 THRCLA_contig633 633 THRCLA_contig634 634 THRCLA_contig635 635 THRCLA_contig636 636 THRCLA_contig637 637 THRCLA_contig638 638 THRCLA_contig639 639 THRCLA_contig640 640 THRCLA_contig641 641 THRCLA_contig642 642 THRCLA_contig643 643 THRCLA_contig644 644 THRCLA_contig645 645 THRCLA_contig646 646 THRCLA_contig647 647 THRCLA_contig648 648 THRCLA_contig649 649 THRCLA_contig650 650 THRCLA_contig651 651 THRCLA_contig652 652 THRCLA_contig653 653 THRCLA_contig654 654 THRCLA_contig655 655 THRCLA_contig656 656 THRCLA_contig657 657 THRCLA_contig658 658 THRCLA_contig659 659 THRCLA_contig660 660 THRCLA_contig661 661 THRCLA_contig662 662 THRCLA_contig663 663 THRCLA_contig664 664 THRCLA_contig665 665 THRCLA_contig666 666 THRCLA_contig667 667 THRCLA_contig668 668 THRCLA_contig669 669 THRCLA_contig670 670 THRCLA_contig671 671 THRCLA_contig672 672 THRCLA_contig673 673 THRCLA_contig674 674 THRCLA_contig675 675 THRCLA_contig676 676 THRCLA_contig677 677 THRCLA_contig678 678 THRCLA_contig679 679 THRCLA_contig680 680 THRCLA_contig681 681 THRCLA_contig682 682 THRCLA_contig683 683 THRCLA_contig684 684 THRCLA_contig685 685 THRCLA_contig686 686 THRCLA_contig687 687 THRCLA_contig688 688 THRCLA_contig689 689 THRCLA_contig690 690 THRCLA_contig691 691 THRCLA_contig692 692 THRCLA_contig693 693 THRCLA_contig694 694 THRCLA_contig695 695 THRCLA_contig696 696 THRCLA_contig697 697 THRCLA_contig698 698 THRCLA_contig699 699 THRCLA_contig700 700 THRCLA_contig701 701 THRCLA_contig702 702 THRCLA_contig703 703 THRCLA_contig704 704 THRCLA_contig705 705 THRCLA_contig706 706 THRCLA_contig707 707 THRCLA_contig708 708 THRCLA_contig709 709 THRCLA_contig710 710 THRCLA_contig711 711 THRCLA_contig712 712 THRCLA_contig713 713 THRCLA_contig714 714 THRCLA_contig715 715 THRCLA_contig716 716 THRCLA_contig717 717 THRCLA_contig718 718 THRCLA_contig719 719 THRCLA_contig720 720 THRCLA_contig721 721 THRCLA_contig722 722 THRCLA_contig723 723 THRCLA_contig724 724 THRCLA_contig725 725 THRCLA_contig726 726 THRCLA_contig727 727 THRCLA_contig728 728 THRCLA_contig729 729 THRCLA_contig730 730 THRCLA_contig731 731 THRCLA_contig732 732 THRCLA_contig733 733 THRCLA_contig734 734 THRCLA_contig735 735 THRCLA_contig736 736 THRCLA_contig737 737 THRCLA_contig738 738 THRCLA_contig739 739 THRCLA_contig740 740 THRCLA_contig741 741 THRCLA_contig742 742 THRCLA_contig743 743 THRCLA_contig744 744 THRCLA_contig745 745 THRCLA_contig746 746 THRCLA_contig747 747 THRCLA_contig748 748 THRCLA_contig749 749 THRCLA_contig750 750 THRCLA_contig751 751 THRCLA_contig752 752 THRCLA_contig753 753 THRCLA_contig754 754 THRCLA_contig755 755 THRCLA_contig756 756 THRCLA_contig757 757 THRCLA_contig758 758 THRCLA_contig759 759 THRCLA_contig760 760 THRCLA_contig761 761 THRCLA_contig762 762 THRCLA_contig763 763 THRCLA_contig764 764 THRCLA_contig765 765 THRCLA_contig766 766 THRCLA_contig767 767 THRCLA_contig768 768 THRCLA_contig769 769 THRCLA_contig770 770 THRCLA_contig771 771 THRCLA_contig772 772 THRCLA_contig773 773 THRCLA_contig774 774 THRCLA_contig775 775 THRCLA_contig776 776 THRCLA_contig777 777 THRCLA_contig778 778 THRCLA_contig779 779 THRCLA_contig780 780 THRCLA_contig781 781 THRCLA_contig782 782 THRCLA_contig783 783 THRCLA_contig784 784 THRCLA_contig785 785 THRCLA_contig786 786 THRCLA_contig787 787 THRCLA_contig788 788 THRCLA_contig789 789 THRCLA_contig790 790 THRCLA_contig791 791 THRCLA_contig792 792 THRCLA_contig793 793 THRCLA_contig794 794 THRCLA_contig795 795 THRCLA_contig796 796 THRCLA_contig797 797 THRCLA_contig798 798 THRCLA_contig799 799 THRCLA_contig800 800 THRCLA_contig801 801 THRCLA_contig802 802 THRCLA_contig803 803 THRCLA_contig804 804 THRCLA_contig805 805 THRCLA_contig806 806 THRCLA_contig807 807 THRCLA_contig808 808 THRCLA_contig809 809 THRCLA_contig810 810 THRCLA_contig811 811 THRCLA_contig812 812 THRCLA_contig813 813 THRCLA_contig814 814 THRCLA_contig815 815 THRCLA_contig816 816 THRCLA_contig817 817 THRCLA_contig818 818 THRCLA_contig819 819 THRCLA_contig820 820 THRCLA_contig821 821 THRCLA_contig822 822 THRCLA_contig823 823 THRCLA_contig824 824 THRCLA_contig825 825 THRCLA_contig826 826 THRCLA_contig827 827 THRCLA_contig828 828 THRCLA_contig829 829 THRCLA_contig830 830 THRCLA_contig831 831 THRCLA_contig832 832 THRCLA_contig833 833 THRCLA_contig834 834 THRCLA_contig835 835 THRCLA_contig836 836 THRCLA_contig837 837 THRCLA_contig838 838 THRCLA_contig839 839 THRCLA_contig840 840 THRCLA_contig841 841 THRCLA_contig842 842 THRCLA_contig843 843 THRCLA_contig844 844 THRCLA_contig845 845 THRCLA_contig846 846 THRCLA_contig847 847 THRCLA_contig848 848 THRCLA_contig849 849 THRCLA_contig850 850 THRCLA_contig851 851 THRCLA_contig852 852 THRCLA_contig853 853 THRCLA_contig854 854 THRCLA_contig855 855 THRCLA_contig856 856 THRCLA_contig857 857 THRCLA_contig858 858 THRCLA_contig859 859 THRCLA_contig860 860 THRCLA_contig861 861 THRCLA_contig862 862 THRCLA_contig863 863 THRCLA_contig864 864 THRCLA_contig865 865 THRCLA_contig866 866 THRCLA_contig867 867 THRCLA_contig868 868 THRCLA_contig869 869 THRCLA_contig870 870 THRCLA_contig871 871 THRCLA_contig872 872 THRCLA_contig873 873 THRCLA_contig874 874 THRCLA_contig875 875 THRCLA_contig876 876 THRCLA_contig877 877 THRCLA_contig878 878 THRCLA_contig879 879 THRCLA_contig880 880 THRCLA_contig881 881 THRCLA_contig882 882 THRCLA_contig883 883 THRCLA_contig884 884 THRCLA_contig885 885 THRCLA_contig886 886 THRCLA_contig887 887 THRCLA_contig888 888 THRCLA_contig889 889 THRCLA_contig890 890 THRCLA_contig891 891 THRCLA_contig892 892 THRCLA_contig893 893 THRCLA_contig894 894 THRCLA_contig895 895 THRCLA_contig896 896 THRCLA_contig897 897 THRCLA_contig898 898 THRCLA_contig899 899 THRCLA_contig900 900 THRCLA_contig901 901 THRCLA_contig902 902 THRCLA_contig903 903 THRCLA_contig904 904 THRCLA_contig905 905 THRCLA_contig906 906 THRCLA_contig907 907 THRCLA_contig908 908 THRCLA_contig909 909 THRCLA_contig910 910 THRCLA_contig911 911 THRCLA_contig912 912 THRCLA_contig913 913 THRCLA_contig914 914 THRCLA_contig915 915 THRCLA_contig916 916 THRCLA_contig917 917 THRCLA_contig918 918 THRCLA_contig919 919 THRCLA_contig920 920 THRCLA_contig921 921 THRCLA_contig922 922 THRCLA_contig923 923 THRCLA_contig924 924 THRCLA_contig925 925 THRCLA_contig926 926 THRCLA_contig927 927 THRCLA_contig928 928 THRCLA_contig929 929 THRCLA_contig930 930 THRCLA_contig931 931 THRCLA_contig932 932 THRCLA_contig933 933 THRCLA_contig934 934 THRCLA_contig935 935 THRCLA_contig936 936 THRCLA_contig937 937 THRCLA_contig938 938 THRCLA_contig939 939 THRCLA_contig940 940 THRCLA_contig941 941 THRCLA_contig942 942 THRCLA_contig943 943 THRCLA_contig944 944 THRCLA_contig945 945 THRCLA_contig946 946 THRCLA_contig947 947 THRCLA_contig948 948 THRCLA_contig949 949 THRCLA_contig950 950 THRCLA_contig951 951 THRCLA_contig952 952 THRCLA_contig953 953 THRCLA_contig954 954 THRCLA_contig955 955 THRCLA_contig956 956 THRCLA_contig957 957 THRCLA_contig958 958 THRCLA_contig959 959 THRCLA_contig960 960 THRCLA_contig961 961 THRCLA_contig962 962 THRCLA_contig963 963 THRCLA_contig964 964 THRCLA_contig965 965 THRCLA_contig966 966 THRCLA_contig967 967 THRCLA_contig968 968 THRCLA_contig969 969 THRCLA_contig970 970 THRCLA_contig971 971 THRCLA_contig972 972 THRCLA_contig973 973 THRCLA_contig974 974 THRCLA_contig975 975 THRCLA_contig976 976 THRCLA_contig977 977 THRCLA_contig978 978 THRCLA_contig979 979 THRCLA_contig980 980 THRCLA_contig981 981 THRCLA_contig982 982 THRCLA_contig983 983 THRCLA_contig984 984 THRCLA_contig985 985 THRCLA_contig986 986 THRCLA_contig987 987 THRCLA_contig988 988 THRCLA_contig989 989 THRCLA_contig990 990 THRCLA_contig991 991 THRCLA_contig992 992 THRCLA_contig993 993 THRCLA_contig994 994 THRCLA_contig995 995 THRCLA_contig996 996 THRCLA_contig997 997 THRCLA_contig998 998 THRCLA_contig999 999 THRCLA_contig1000 1000 THRCLA_contig1001 1001 THRCLA_contig1002 1002 THRCLA_contig1003 1003 THRCLA_contig1004 1004 THRCLA_contig1005 1005 THRCLA_contig1006 1006 THRCLA_contig1007 1007 THRCLA_contig1008 1008 THRCLA_contig1009 1009 THRCLA_contig1010 1010 THRCLA_contig1011 1011 THRCLA_contig1012 1012 THRCLA_contig1013 1013 THRCLA_contig1014 1014 THRCLA_contig1015 1015 THRCLA_contig1016 1016 THRCLA_contig1017 1017 THRCLA_contig1018 1018 THRCLA_contig1019 1019 THRCLA_contig1020 1020 THRCLA_contig1021 1021 THRCLA_contig1022 1022 THRCLA_contig1023 1023 THRCLA_contig1024 1024 THRCLA_contig1025 1025 THRCLA_contig1026 1026 THRCLA_contig1027 1027 THRCLA_contig1028 1028 THRCLA_contig1029 1029 THRCLA_contig1030 1030 THRCLA_contig1031 1031 THRCLA_contig1032 1032 THRCLA_contig1033 1033 THRCLA_contig1034 1034 THRCLA_contig1035 1035 THRCLA_contig1036 1036 THRCLA_contig1037 1037 THRCLA_contig1038 1038 THRCLA_contig1039 1039 THRCLA_contig1040 1040 THRCLA_contig1041 1041 THRCLA_contig1042 1042 THRCLA_contig1043 1043 THRCLA_contig1044 1044 THRCLA_contig1045 1045 THRCLA_contig1046 1046 THRCLA_contig1047 1047 THRCLA_contig1048 1048 THRCLA_contig1049 1049 THRCLA_contig1050 1050 THRCLA_contig1051 1051 THRCLA_contig1052 1052 THRCLA_contig1053 1053 THRCLA_contig1054 1054 THRCLA_contig1055 1055 THRCLA_contig1056 1056 THRCLA_contig1057 1057 THRCLA_contig1058 1058 THRCLA_contig1059 1059 THRCLA_contig1060 1060 THRCLA_contig1061 1061 THRCLA_contig1062 1062 THRCLA_contig1063 1063 THRCLA_contig1064 1064 THRCLA_contig1065 1065 THRCLA_contig1066 1066 THRCLA_contig1067 1067 THRCLA_contig1068 1068 THRCLA_contig1069 1069 THRCLA_contig1070 1070 THRCLA_contig1071 1071 THRCLA_contig1072 1072 THRCLA_contig1073 1073 THRCLA_contig1074 1074 THRCLA_contig1075 1075 THRCLA_contig1076 1076 THRCLA_contig1077 1077 THRCLA_contig1078 1078 THRCLA_contig1079 1079 THRCLA_contig1080 1080 THRCLA_contig1081 1081 THRCLA_contig1082 1082 THRCLA_contig1083 1083 THRCLA_contig1084 1084 THRCLA_contig1085 1085 THRCLA_contig1086 1086 THRCLA_contig1087 1087 THRCLA_contig1088 1088 THRCLA_contig1089 1089 THRCLA_contig1090 1090 THRCLA_contig1091 1091 THRCLA_contig1092 1092 THRCLA_contig1093 1093 THRCLA_contig1094 1094 THRCLA_contig1095 1095 THRCLA_contig1096 1096 THRCLA_contig1097 1097 THRCLA_contig1098 1098 THRCLA_contig1099 1099 THRCLA_contig1100 1100 THRCLA_contig1101 1101 THRCLA_contig1102 1102 THRCLA_contig1103 1103 THRCLA_contig1104 1104 THRCLA_contig1105 1105 THRCLA_contig1106 1106 THRCLA_contig1107 1107 THRCLA_contig1108 1108 THRCLA_contig1109 1109 THRCLA_contig1110 1110 THRCLA_contig1111 1111 THRCLA_contig1112 1112 THRCLA_contig1113 1113 THRCLA_contig1114 1114 THRCLA_contig1115 1115 THRCLA_contig1116 1116 THRCLA_contig1117 1117 THRCLA_contig1118 1118 THRCLA_contig1119 1119 THRCLA_contig1120 1120 THRCLA_contig1121 1121 THRCLA_contig1122 1122 THRCLA_contig1123 1123 THRCLA_contig1124 1124 THRCLA_contig1125 1125 THRCLA_contig1126 1126 THRCLA_contig1127 1127 THRCLA_contig1128 1128 THRCLA_contig1129 1129 THRCLA_contig1130 1130 THRCLA_contig1131 1131 THRCLA_contig1132 1132 THRCLA_contig1133 1133 THRCLA_contig1134 1134 THRCLA_contig1135 1135 THRCLA_contig1136 1136 THRCLA_contig1137 1137 THRCLA_contig1138 1138 THRCLA_contig1139 1139 THRCLA_contig1140 1140 THRCLA_contig1141 1141 THRCLA_contig1142 1142 THRCLA_contig1143 1143 THRCLA_contig1144 1144 THRCLA_contig1145 1145 THRCLA_contig1146 1146 THRCLA_contig1147 1147 THRCLA_contig1148 1148 THRCLA_contig1149 1149 THRCLA_contig1150 1150 THRCLA_contig1151 1151 THRCLA_contig1152 1152 THRCLA_contig1153 1153 THRCLA_contig1154 1154 THRCLA_contig1155 1155 THRCLA_contig1156 1156 THRCLA_contig1157 1157 THRCLA_contig1158 1158 THRCLA_contig1159 1159 THRCLA_contig1160 1160 THRCLA_contig1161 1161 THRCLA_contig1162 1162 THRCLA_contig1163 1163 THRCLA_contig1164 1164 THRCLA_contig1165 1165 THRCLA_contig1166 1166 THRCLA_contig1167 1167 THRCLA_contig1168 1168 THRCLA_contig1169 1169 THRCLA_contig1170 1170 THRCLA_contig1171 1171 THRCLA_contig1172 1172 THRCLA_contig1173 1173 THRCLA_contig1174 1174 THRCLA_contig1175 1175 THRCLA_contig1176 1176 THRCLA_contig1177 1177 THRCLA_contig1178 1178 THRCLA_contig1179 1179 THRCLA_contig1180 1180 THRCLA_contig1181 1181 THRCLA_contig1182 1182 THRCLA_contig1183 1183 THRCLA_contig1184 1184 THRCLA_contig1185 1185 THRCLA_contig1186 1186 THRCLA_contig1187 1187 THRCLA_contig1188 1188 THRCLA_contig1189 1189 THRCLA_contig1190 1190 THRCLA_contig1191 1191 THRCLA_contig1192 1192 THRCLA_contig1193 1193 THRCLA_contig1194 1194 THRCLA_contig1195 1195 THRCLA_contig1196 1196 THRCLA_contig1197 1197 THRCLA_contig1198 1198 THRCLA_contig1199 1199 THRCLA_contig1200 1200 THRCLA_contig1201 1201 THRCLA_contig1202 1202 THRCLA_contig1203 1203 THRCLA_contig1204 1204 THRCLA_contig1205 1205 THRCLA_contig1206 1206 THRCLA_contig1207 1207 THRCLA_contig1208 1208 THRCLA_contig1209 1209 THRCLA_contig1210 1210 THRCLA_contig1211 1211 THRCLA_contig1212 1212 THRCLA_contig1213 1213 THRCLA_contig1214 1214 THRCLA_contig1215 1215 THRCLA_contig1216 1216 THRCLA_contig1217 1217 THRCLA_contig1218 1218 THRCLA_contig1219 1219 THRCLA_contig1220 1220 THRCLA_contig1221 1221 THRCLA_contig1222 1222 THRCLA_contig1223 1223 THRCLA_contig1224 1224 THRCLA_contig1225 1225 THRCLA_contig1226 1226 THRCLA_contig1227 1227 THRCLA_contig1228 1228 THRCLA_contig1229 1229 THRCLA_contig1230 1230 THRCLA_contig1231 1231 THRCLA_contig1232 1232 THRCLA_contig1233 1233 THRCLA_contig1234 1234 THRCLA_contig1235 1235 THRCLA_contig1236 1236 THRCLA_contig1237 1237 THRCLA_contig1238 1238 THRCLA_contig1239 1239 THRCLA_contig1240 1240 THRCLA_contig1241 1241 THRCLA_contig1242 1242 THRCLA_contig1243 1243 THRCLA_contig1244 1244 THRCLA_contig1245 1245 THRCLA_contig1246 1246 THRCLA_contig1247 1247 THRCLA_contig1248 1248 THRCLA_contig1249 1249 THRCLA_contig1250 1250 THRCLA_contig1251 1251 THRCLA_contig1252 1252 THRCLA_contig1253 1253 THRCLA_contig1254 1254 THRCLA_contig1255 1255 THRCLA_contig1256 1256 THRCLA_contig1257 1257 THRCLA_contig1258 1258 THRCLA_contig1259 1259 THRCLA_contig1260 1260 THRCLA_contig1261 1261 THRCLA_contig1262 1262 THRCLA_contig1263 1263 THRCLA_contig1264 1264 THRCLA_contig1265 1265 THRCLA_contig1266 1266 THRCLA_contig1267 1267 THRCLA_contig1268 1268 THRCLA_contig1269 1269 THRCLA_contig1270 1270 THRCLA_contig1271 1271 THRCLA_contig1272 1272 THRCLA_contig1273 1273 THRCLA_contig1274 1274 THRCLA_contig1275 1275 THRCLA_contig1276 1276 THRCLA_contig1277 1277 THRCLA_contig1278 1278 THRCLA_contig1279 1279 THRCLA_contig1280 1280 THRCLA_contig1281 1281 THRCLA_contig1282 1282 THRCLA_contig1283 1283 THRCLA_contig1284 1284 THRCLA_contig1285 1285 THRCLA_contig1286 1286 THRCLA_contig1287 1287 THRCLA_contig1288 1288 THRCLA_contig1289 1289 THRCLA_contig1290 1290 THRCLA_contig1291 1291 THRCLA_contig1292 1292 THRCLA_contig1293 1293 THRCLA_contig1294 1294 THRCLA_contig1295 1295 THRCLA_contig1296 1296 THRCLA_contig1297 1297 THRCLA_contig1298 1298 THRCLA_contig1299 1299 THRCLA_contig1300 1300 THRCLA_contig1301 1301 THRCLA_contig1302 1302 THRCLA_contig1303 1303 THRCLA_contig1304 1304 THRCLA_contig1305 1305 THRCLA_contig1306 1306 THRCLA_contig1307 1307 THRCLA_contig1308 1308 THRCLA_contig1309 1309 THRCLA_contig1310 1310 THRCLA_contig1311 1311 THRCLA_contig1312 1312 THRCLA_contig1313 1313 THRCLA_contig1314 1314 THRCLA_contig1315 1315 THRCLA_contig1316 1316 THRCLA_contig1317 1317 THRCLA_contig1318 1318 THRCLA_contig1319 1319 THRCLA_contig1320 1320 THRCLA_contig1321 1321 THRCLA_contig1322 1322 THRCLA_contig1323 1323 THRCLA_contig1324 1324 THRCLA_contig1325 1325 THRCLA_contig1326 1326 THRCLA_contig1327 1327 THRCLA_contig1328 1328 THRCLA_contig1329 1329 THRCLA_contig1330 1330 THRCLA_contig1331 1331 THRCLA_contig1332 1332 THRCLA_contig1333 1333 THRCLA_contig1334 1334 THRCLA_contig1335 1335 THRCLA_contig1336 1336 THRCLA_contig1337 1337 THRCLA_contig1338 1338 THRCLA_contig1339 1339 THRCLA_contig1340 1340 THRCLA_contig1341 1341 THRCLA_contig1342 1342 THRCLA_contig1343 1343 THRCLA_contig1344 1344 THRCLA_contig1345 1345 THRCLA_contig1346 1346 THRCLA_contig1347 1347 THRCLA_contig1348 1348 THRCLA_contig1349 1349 THRCLA_contig1350 1350 THRCLA_contig1351 1351 THRCLA_contig1352 1352 THRCLA_contig1353 1353 THRCLA_contig1354 1354 THRCLA_contig1355 1355 THRCLA_contig1356 1356 THRCLA_contig1357 1357 THRCLA_contig1358 1358 THRCLA_contig1359 1359 THRCLA_contig1360 1360 THRCLA_contig1361 1361 THRCLA_contig1362 1362 THRCLA_contig1363 1363 THRCLA_contig1364 1364 THRCLA_contig1365 1365 THRCLA_contig1366 1366 THRCLA_contig1367 1367 THRCLA_contig1368 1368 THRCLA_contig1369 1369 THRCLA_contig1370 1370 THRCLA_contig1371 1371 THRCLA_contig1372 1372 THRCLA_contig1373 1373 THRCLA_contig1374 1374 THRCLA_contig1375 1375 THRCLA_contig1376 1376 THRCLA_contig1377 1377 THRCLA_contig1378 1378 THRCLA_contig1379 1379 THRCLA_contig1380 1380 THRCLA_contig1381 1381 THRCLA_contig1382 1382 THRCLA_contig1383 1383 THRCLA_contig1384 1384 THRCLA_contig1385 1385 THRCLA_contig1386 1386 THRCLA_contig1387 1387 THRCLA_contig1388 1388 THRCLA_contig1389 1389 THRCLA_contig1390 1390 THRCLA_contig1391 1391 THRCLA_contig1392 1392 THRCLA_contig1393 1393 THRCLA_contig1394 1394 THRCLA_contig1395 1395 THRCLA_contig1396 1396 THRCLA_contig1397 1397 THRCLA_contig1398 1398 THRCLA_contig1399 1399 THRCLA_contig1400 1400 THRCLA_contig1401 1401 THRCLA_contig1402 1402 THRCLA_contig1403 1403 THRCLA_contig1404 1404 THRCLA_contig1405 1405 THRCLA_contig1406 1406 THRCLA_contig1407 1407 THRCLA_contig1408 1408 THRCLA_contig1409 1409 THRCLA_contig1410 1410 THRCLA_contig1411 1411 THRCLA_contig1412 1412 THRCLA_contig1413 1413 THRCLA_contig1414 1414 THRCLA_contig1415 1415 THRCLA_contig1416 1416 THRCLA_contig1417 1417 THRCLA_contig1418 1418 THRCLA_contig1419 1419 THRCLA_contig1420 1420 THRCLA_contig1421 1421 THRCLA_contig1422 1422 THRCLA_contig1423 1423 THRCLA_contig1424 1424 THRCLA_contig1425 1425 THRCLA_contig1426 1426 THRCLA_contig1427 1427 THRCLA_contig1428 1428 THRCLA_contig1429 1429 THRCLA_contig1430 1430 THRCLA_contig1431 1431 THRCLA_contig1432 1432 THRCLA_contig1433 1433 THRCLA_contig1434 1434 THRCLA_contig1435 1435 THRCLA_contig1436 1436 THRCLA_contig1437 1437 THRCLA_contig1438 1438 THRCLA_contig1439 1439 THRCLA_contig1440 1440 THRCLA_contig1441 1441 THRCLA_contig1442 1442 THRCLA_contig1443 1443 THRCLA_contig1444 1444 THRCLA_contig1445 1445 THRCLA_contig1446 1446 THRCLA_contig1447 1447 THRCLA_contig1448 1448 THRCLA_contig1449 1449 THRCLA_contig1450 1450 THRCLA_contig1451 1451 THRCLA_contig1452 1452 THRCLA_contig1453 1453 THRCLA_contig1454 1454 THRCLA_contig1455 1455 THRCLA_contig1456 1456 THRCLA_contig1457 1457 THRCLA_contig1458 1458 THRCLA_contig1459 1459 THRCLA_contig1460 1460 THRCLA_contig1461 1461 THRCLA_contig1462 1462 THRCLA_contig1463 1463 THRCLA_contig1464 1464 THRCLA_contig1465 1465 THRCLA_contig1466 1466 THRCLA_contig1467 1467 THRCLA_contig1468 1468 THRCLA_contig1469 1469 THRCLA_contig1470 1470 THRCLA_contig1471 1471 THRCLA_contig1472 1472 THRCLA_contig1473 1473 THRCLA_contig1474 1474 THRCLA_contig1475 1475 THRCLA_contig1476 1476 THRCLA_contig1477 1477 THRCLA_contig1478 1478 THRCLA_contig1479 1479 THRCLA_contig1480 1480 THRCLA_contig1481 1481 THRCLA_contig1482 1482 THRCLA_contig1483 1483 THRCLA_contig1484 1484 THRCLA_contig1485 1485 THRCLA_contig1486 1486 THRCLA_contig1487 1487 THRCLA_contig1488 1488 THRCLA_contig1489 1489 THRCLA_contig1490 1490 THRCLA_contig1491 1491 THRCLA_contig1492 1492 THRCLA_contig1493 1493 THRCLA_contig1494 1494 THRCLA_contig1495 1495 THRCLA_contig1496 1496 THRCLA_contig1497 1497 THRCLA_contig1498 1498 THRCLA_contig1499 1499 THRCLA_contig1500 1500 THRCLA_contig1501 1501 THRCLA_contig1502 1502 THRCLA_contig1503 1503 THRCLA_contig1504 1504 THRCLA_contig1505 1505 THRCLA_contig1506 1506 THRCLA_contig1507 1507 THRCLA_contig1508 1508 THRCLA_contig1509 1509 THRCLA_contig1510 1510 THRCLA_contig1511 1511 THRCLA_contig1512 1512 THRCLA_contig1513 1513 THRCLA_contig1514 1514 THRCLA_contig1515 1515 THRCLA_contig1516 1516 THRCLA_contig1517 1517 THRCLA_contig1518 1518 THRCLA_contig1519 1519 THRCLA_contig1520 1520 THRCLA_contig1521 1521 THRCLA_contig1522 1522 THRCLA_contig1523 1523 THRCLA_contig1524 1524 THRCLA_contig1525 1525 THRCLA_contig1526 1526 THRCLA_contig1527 1527 THRCLA_contig1528 1528 THRCLA_contig1529 1529 THRCLA_contig1530 1530 THRCLA_contig1531 1531 THRCLA_contig1532 1532 THRCLA_contig1533 1533 THRCLA_contig1534 1534 THRCLA_contig1535 1535 THRCLA_contig1536 1536 THRCLA_contig1537 1537 THRCLA_contig1538 1538 THRCLA_contig1539 1539 THRCLA_contig1540 1540 THRCLA_contig1541 1541 THRCLA_contig1542 1542 THRCLA_contig1543 1543 THRCLA_contig1544 1544 THRCLA_contig1545 1545 THRCLA_contig1546 1546 THRCLA_contig1547 1547 THRCLA_contig1548 1548 THRCLA_contig1549 1549 THRCLA_contig1550 1550 THRCLA_contig1551 1551 THRCLA_contig1552 1552 THRCLA_contig1553 1553 THRCLA_contig1554 1554 THRCLA_contig1555 1555 THRCLA_contig1556 1556 THRCLA_contig1557 1557 THRCLA_contig1558 1558 THRCLA_contig1559 1559 THRCLA_contig1560 1560 THRCLA_contig1561 1561 THRCLA_contig1562 1562 THRCLA_contig1563 1563 THRCLA_contig1564 1564 THRCLA_contig1565 1565 THRCLA_contig1566 1566 THRCLA_contig1567 1567 THRCLA_contig1568 1568 THRCLA_contig1569 1569 THRCLA_contig1570 1570 THRCLA_contig1571 1571 THRCLA_contig1572 1572 THRCLA_contig1573 1573 THRCLA_contig1574 1574 THRCLA_contig1575 1575 THRCLA_contig1576 1576 THRCLA_contig1577 1577 THRCLA_contig1578 1578 THRCLA_contig1579 1579 THRCLA_contig1580 1580 THRCLA_contig1581 1581 THRCLA_contig1582 1582 THRCLA_contig1583 1583 THRCLA_contig1584 1584 THRCLA_contig1585 1585 THRCLA_contig1586 1586 THRCLA_contig1587 1587 THRCLA_contig1588 1588 THRCLA_contig1589 1589 THRCLA_contig1590 1590 THRCLA_contig1591 1591 THRCLA_contig1592 1592 THRCLA_contig1593 1593 THRCLA_contig1594 1594 THRCLA_contig1595 1595 THRCLA_contig1596 1596 THRCLA_contig1597 1597 THRCLA_contig1598 1598 THRCLA_contig1599 1599 THRCLA_contig1600 1600 THRCLA_contig1601 1601 THRCLA_contig1602 1602 THRCLA_contig1603 1603 THRCLA_contig1604 1604 THRCLA_contig1605 1605 THRCLA_contig1606 1606 THRCLA_contig1607 1607 THRCLA_contig1608 1608 THRCLA_contig1609 1609 THRCLA_contig1610 1610 THRCLA_contig1611 1611 THRCLA_contig1612 1612 THRCLA_contig1613 1613 THRCLA_contig1614 1614 THRCLA_contig1615 1615 THRCLA_contig1616 1616 THRCLA_contig1617 1617 THRCLA_contig1618 1618 THRCLA_contig1619 1619 THRCLA_contig1620 1620 THRCLA_contig1621 1621 THRCLA_contig1622 1622 THRCLA_contig1623 1623 THRCLA_contig1624 1624 THRCLA_contig1625 1625 THRCLA_contig1626 1626 THRCLA_contig1627 1627 THRCLA_contig1628 1628 THRCLA_contig1629 1629 THRCLA_contig1630 1630 THRCLA_contig1631 1631 THRCLA_contig1632 1632 THRCLA_contig1633 1633 THRCLA_contig1634 1634 THRCLA_contig1635 1635 THRCLA_contig1636 1636 THRCLA_contig1637 1637 THRCLA_contig1638 1638 THRCLA_contig1639 1639 THRCLA_contig1640 1640 THRCLA_contig1641 1641 THRCLA_contig1642 1642 THRCLA_contig1643 1643 THRCLA_contig1644 1644 THRCLA_contig1645 1645 THRCLA_contig1646 1646 THRCLA_contig1647 1647 THRCLA_contig1648 1648 THRCLA_contig1649 1649 THRCLA_contig1650 1650 THRCLA_contig1651 1651 THRCLA_contig1652 1652 THRCLA_contig1653 1653 THRCLA_contig1654 1654 THRCLA_contig1655 1655 THRCLA_contig1656 1656 THRCLA_contig1657 1657 THRCLA_contig1658 1658 THRCLA_contig1659 1659 THRCLA_contig1660 1660 THRCLA_contig1661 1661 THRCLA_contig1662 1662 THRCLA_contig1663 1663 THRCLA_contig1664 1664 THRCLA_contig1665 1665 THRCLA_contig1666 1666 THRCLA_contig1667 1667 THRCLA_contig1668 1668 THRCLA_contig1669 1669 THRCLA_contig1670 1670 THRCLA_contig1671 1671 THRCLA_contig1672 1672 THRCLA_contig1673 1673 THRCLA_contig1674 1674 THRCLA_contig1675 1675 THRCLA_contig1676 1676 THRCLA_contig1677 1677 THRCLA_contig1678 1678 THRCLA_contig1679 1679 THRCLA_contig1680 1680 THRCLA_contig1681 1681 THRCLA_contig1682 1682 THRCLA_contig1683 1683 THRCLA_contig1684 1684 THRCLA_contig1685 1685 THRCLA_contig1686 1686 THRCLA_contig1687 1687 THRCLA_contig1688 1688 THRCLA_contig1689 1689 THRCLA_contig1690 1690 THRCLA_contig1691 1691 THRCLA_contig1692 1692 THRCLA_contig1693 1693 THRCLA_contig1694 1694 THRCLA_contig1695 1695 THRCLA_contig1696 1696 THRCLA_contig1697 1697 THRCLA_contig1698 1698 THRCLA_contig1699 1699 THRCLA_contig1700 1700 THRCLA_contig1701 1701 THRCLA_contig1702 1702 THRCLA_contig1703 1703 THRCLA_contig1704 1704 THRCLA_contig1705 1705 THRCLA_contig1706 1706 THRCLA_contig1707 1707 THRCLA_contig1708 1708 THRCLA_contig1709 1709 THRCLA_contig1710 1710 THRCLA_contig1711 1711 THRCLA_contig1712 1712 THRCLA_contig1713 1713 THRCLA_contig1714 1714 THRCLA_contig1715 1715 THRCLA_contig1716 1716 THRCLA_contig1717 1717 THRCLA_contig1718 1718 THRCLA_contig1719 1719 THRCLA_contig1720 1720 THRCLA_contig1721 1721 THRCLA_contig1722 1722 THRCLA_contig1723 1723 THRCLA_contig1724 1724 THRCLA_contig1725 1725 THRCLA_contig1726 1726 THRCLA_contig1727 1727 THRCLA_contig1728 1728 THRCLA_contig1729 1729 THRCLA_contig1730 1730 THRCLA_contig1731 1731 THRCLA_contig1732 1732 THRCLA_contig1733 1733 THRCLA_contig1734 1734 THRCLA_contig1735 1735 THRCLA_contig1736 1736 THRCLA_contig1737 1737 THRCLA_contig1738 1738 THRCLA_contig1739 1739 THRCLA_contig1740 1740 THRCLA_contig1741 1741 THRCLA_contig1742 1742 THRCLA_contig1743 1743 THRCLA_contig1744 1744 THRCLA_contig1745 1745 THRCLA_contig1746 1746 THRCLA_contig1747 1747 THRCLA_contig1748 1748 THRCLA_contig1749 1749 THRCLA_contig1750 1750 THRCLA_contig1751 1751 THRCLA_contig1752 1752 THRCLA_contig1753 1753 THRCLA_contig1754 1754 THRCLA_contig1755 1755 THRCLA_contig1756 1756 THRCLA_contig1757 1757 THRCLA_contig1758 1758 THRCLA_contig1759 1759 THRCLA_contig1760 1760 THRCLA_contig1761 1761 THRCLA_contig1762 1762 THRCLA_contig1763 1763 THRCLA_contig1764 1764 THRCLA_contig1765 1765 THRCLA_contig1766 1766 THRCLA_contig1767 1767 THRCLA_contig1768 1768 THRCLA_contig1769 1769 THRCLA_contig1770 1770 THRCLA_contig1771 1771 THRCLA_contig1772 1772 THRCLA_contig1773 1773 THRCLA_contig1774 1774 THRCLA_contig1775 1775 THRCLA_contig1776 1776 THRCLA_contig1777 1777 THRCLA_contig1778 1778 THRCLA_contig1779 1779 THRCLA_contig1780 1780 THRCLA_contig1781 1781 THRCLA_contig1782 1782 THRCLA_contig1783 1783 THRCLA_contig1784 1784 THRCLA_contig1785 1785 THRCLA_contig1786 1786 THRCLA_contig1787 1787 THRCLA_contig1788 1788 THRCLA_contig1789 1789 THRCLA_contig1790 1790 THRCLA_contig1791 1791 THRCLA_contig1792 1792 THRCLA_contig1793 1793 THRCLA_contig1794 1794 THRCLA_contig1795 1795 THRCLA_contig1796 1796 THRCLA_contig1797 1797 THRCLA_contig1798 1798 THRCLA_contig1799 1799 THRCLA_contig1800 1800 THRCLA_contig1801 1801 THRCLA_contig1802 1802 THRCLA_contig1803 1803 THRCLA_contig1804 1804 THRCLA_contig1805 1805 THRCLA_contig1806 1806 THRCLA_contig1807 1807 THRCLA_contig1808 1808 THRCLA_contig1809 1809 THRCLA_contig1810 1810 THRCLA_contig1811 1811 THRCLA_contig1812 1812 THRCLA_contig1813 1813 THRCLA_contig1814 1814 THRCLA_contig1815 1815 THRCLA_contig1816 1816 THRCLA_contig1817 1817 THRCLA_contig1818 1818 THRCLA_contig1819 1819 THRCLA_contig1820 1820 THRCLA_contig1821 1821 THRCLA_contig1822 1822 THRCLA_contig1823 1823 THRCLA_contig1824 1824 THRCLA_contig1825 1825 THRCLA_contig1826 1826 THRCLA_contig1827 1827 THRCLA_contig1828 1828 THRCLA_contig1829 1829 THRCLA_contig1830 1830 THRCLA_contig1831 1831 THRCLA_contig1832 1832 THRCLA_contig1833 1833 THRCLA_contig1834 1834 THRCLA_contig1835 1835 THRCLA_contig1836 1836 THRCLA_contig1837 1837 THRCLA_contig1838 1838 THRCLA_contig1839 1839 THRCLA_contig1840 1840 THRCLA_contig1841 1841 THRCLA_contig1842 1842 THRCLA_contig1843 1843 THRCLA_contig1844 1844 THRCLA_contig1845 1845 THRCLA_contig1846 1846 THRCLA_contig1847 1847 THRCLA_contig1848 1848 THRCLA_contig1849 1849 THRCLA_contig1850 1850 THRCLA_contig1851 1851 THRCLA_contig1852 1852 THRCLA_contig1853 1853 THRCLA_contig1854 1854 THRCLA_contig1855 1855 THRCLA_contig1856 1856 THRCLA_contig1857 1857 THRCLA_contig1858 1858 THRCLA_contig1859 1859 THRCLA_contig1860 1860 THRCLA_contig1861 1861 THRCLA_contig1862 1862 THRCLA_contig1863 1863 THRCLA_contig1864 1864 THRCLA_contig1865 1865 THRCLA_contig1866 1866 THRCLA_contig1867 1867 THRCLA_contig1868 1868 THRCLA_contig1869 1869 THRCLA_contig1870 1870 THRCLA_contig1871 1871 THRCLA_contig1872 1872 THRCLA_contig1873 1873 THRCLA_contig1874 1874 THRCLA_contig1875 1875 THRCLA_contig1876 1876 THRCLA_contig1877 1877 THRCLA_contig1878 1878 THRCLA_contig1879 1879 THRCLA_contig1880 1880 THRCLA_contig1881 1881 THRCLA_contig1882 1882 THRCLA_contig1883 1883 THRCLA_contig1884 1884 THRCLA_contig1885 1885 THRCLA_contig1886 1886 THRCLA_contig1887 1887 THRCLA_contig1888 1888 THRCLA_contig1889 1889 THRCLA_contig1890 1890 THRCLA_contig1891 1891 THRCLA_contig1892 1892 THRCLA_contig1893 1893 THRCLA_contig1894 1894 THRCLA_contig1895 1895 THRCLA_contig1896 1896 THRCLA_contig1897 1897 THRCLA_contig1898 1898 THRCLA_contig1899 1899 THRCLA_contig1900 1900 THRCLA_contig1901 1901 THRCLA_contig1902 1902 THRCLA_contig1903 1903 THRCLA_contig1904 1904 THRCLA_contig1905 1905 THRCLA_contig1906 1906 THRCLA_contig1907 1907 THRCLA_contig1908 1908 THRCLA_contig1909 1909 THRCLA_contig1910 1910 THRCLA_contig1911 1911 THRCLA_contig1912 1912 THRCLA_contig1913 1913 THRCLA_contig1914 1914 THRCLA_contig1915 1915 THRCLA_contig1916 1916 THRCLA_contig1917 1917 THRCLA_contig1918 1918 THRCLA_contig1919 1919 THRCLA_contig1920 1920 THRCLA_contig1921 1921 THRCLA_contig1922 1922 THRCLA_contig1923 1923 THRCLA_contig1924 1924 THRCLA_contig1925 1925 THRCLA_contig1926 1926 THRCLA_contig1927 1927 THRCLA_contig1928 1928 THRCLA_contig1929 1929 THRCLA_contig1930 1930 THRCLA_contig1931 1931 THRCLA_contig1932 1932 THRCLA_contig1933 1933 THRCLA_contig1934 1934 THRCLA_contig1935 1935 THRCLA_contig1936 1936 THRCLA_contig1937 1937 THRCLA_contig1938 1938 THRCLA_contig1939 1939 THRCLA_contig1940 1940 THRCLA_contig1941 1941 THRCLA_contig1942 1942 THRCLA_contig1943 1943 THRCLA_contig1944 1944 THRCLA_contig1945 1945 THRCLA_contig1946 1946 THRCLA_contig1947 1947 THRCLA_contig1948 1948 THRCLA_contig1949 1949 THRCLA_contig1950 1950 THRCLA_contig1951 1951 THRCLA_contig1952 1952 THRCLA_contig1953 1953 THRCLA_contig1954 1954 THRCLA_contig1955 1955 THRCLA_contig1956 1956 THRCLA_contig1957 1957 THRCLA_contig1958 1958 THRCLA_contig1959 1959 THRCLA_contig1960 1960 THRCLA_contig1961 1961 THRCLA_contig1962 1962 THRCLA_contig1963 1963 THRCLA_contig1964 1964 THRCLA_contig1965 1965 THRCLA_contig1966 1966 THRCLA_contig1967 1967 THRCLA_contig1968 1968 THRCLA_contig1969 1969 THRCLA_contig1970 1970 THRCLA_contig1971 1971 THRCLA_contig1972 1972 THRCLA_contig1973 1973 THRCLA_contig1974 1974 THRCLA_contig1975 1975 THRCLA_contig1976 1976 THRCLA_contig1977 1977 THRCLA_contig1978 1978 THRCLA_contig1979 1979 THRCLA_contig1980 1980 THRCLA_contig1981 1981 THRCLA_contig1982 1982 THRCLA_contig1983 1983 THRCLA_contig1984 1984 THRCLA_contig1985 1985 THRCLA_contig1986 1986 THRCLA_contig1987 1987 THRCLA_contig1988 1988 THRCLA_contig1989 1989 THRCLA_contig1990 1990 THRCLA_contig1991 1991 THRCLA_contig1992 1992 THRCLA_contig1993 1993 THRCLA_contig1994 1994 THRCLA_contig1995 1995 THRCLA_contig1996 1996 THRCLA_contig1997 1997 THRCLA_contig1998 1998 THRCLA_contig1999 1999 THRCLA_contig2000 2000 THRCLA_contig2001 2001 THRCLA_contig2002 2002 THRCLA_contig2003 2003 THRCLA_contig2004 2004 THRCLA_contig2005 2005 THRCLA_contig2006 2006 THRCLA_contig2007 2007 THRCLA_contig2008 2008 THRCLA_contig2009 2009 THRCLA_contig2010 2010 THRCLA_contig2011 2011 THRCLA_contig2012 2012 THRCLA_contig2013 2013 THRCLA_contig2014 2014 THRCLA_contig2015 2015 THRCLA_contig2016 2016 THRCLA_contig2017 2017 THRCLA_contig2018 2018 THRCLA_contig2019 2019 THRCLA_contig2020 2020 THRCLA_contig2021 2021 THRCLA_contig2022 2022 THRCLA_contig2023 2023 THRCLA_contig2024 2024 THRCLA_contig2025 2025 THRCLA_contig2026 2026 THRCLA_contig2027 2027 THRCLA_contig2028 2028 THRCLA_contig2029 2029 THRCLA_contig2030 2030 THRCLA_contig2031 2031 THRCLA_contig2032 2032 THRCLA_contig2033 2033 THRCLA_contig2034 2034 THRCLA_contig2035 2035 THRCLA_contig2036 2036 THRCLA_contig2037 2037 THRCLA_contig2038 2038 THRCLA_contig2039 2039 THRCLA_contig2040 2040 THRCLA_contig2041 2041 THRCLA_contig2042 2042 THRCLA_contig2043 2043 THRCLA_contig2044 2044 THRCLA_contig2045 2045 THRCLA_contig2046 2046 THRCLA_contig2047 2047 THRCLA_contig2048 2048 THRCLA_contig2049 2049 THRCLA_contig2050 2050 THRCLA_contig2051 2051 THRCLA_contig2052 2052 THRCLA_contig2053 2053 THRCLA_contig2054 2054 THRCLA_contig2055 2055 THRCLA_contig2056 2056 THRCLA_contig2057 2057 THRCLA_contig2058 2058 THRCLA_contig2059 2059 THRCLA_contig2060 2060 THRCLA_contig2061 2061 THRCLA_contig2062 2062 THRCLA_contig2063 2063 THRCLA_contig2064 2064 THRCLA_contig2065 2065 THRCLA_contig2066 2066 THRCLA_contig2067 2067 THRCLA_contig2068 2068 THRCLA_contig2069 2069 THRCLA_contig2070 2070 THRCLA_contig2071 2071 THRCLA_contig2072 2072 THRCLA_contig2073 2073 THRCLA_contig2074 2074 THRCLA_contig2075 2075 THRCLA_contig2076 2076 THRCLA_contig2077 2077 THRCLA_contig2078 2078 THRCLA_contig2079 2079 THRCLA_contig2080 2080 THRCLA_contig2081 2081 THRCLA_contig2082 2082 THRCLA_contig2083 2083 THRCLA_contig2084 2084 THRCLA_contig2085 2085 THRCLA_contig2086 2086 THRCLA_contig2087 2087 THRCLA_contig2088 2088 THRCLA_contig2089 2089 THRCLA_contig2090 2090 THRCLA_contig2091 2091 THRCLA_contig2092 2092 THRCLA_contig2093 2093 THRCLA_contig2094 2094 THRCLA_contig2095 2095 THRCLA_contig2096 2096 THRCLA_contig2097 2097 THRCLA_contig2098 2098 THRCLA_contig2099 2099 THRCLA_contig2100 2100 THRCLA_contig2101 2101 THRCLA_contig2102 2102 THRCLA_contig2103 2103 THRCLA_contig2104 2104 THRCLA_contig2105 2105 THRCLA_contig2106 2106 THRCLA_contig2107 2107 THRCLA_contig2108 2108 THRCLA_contig2109 2109 THRCLA_contig2110 2110 THRCLA_contig2111 2111 THRCLA_contig2112 2112 THRCLA_contig2113 2113 THRCLA_contig2114 2114 THRCLA_contig2115 2115 THRCLA_contig2116 2116 THRCLA_contig2117 2117 THRCLA_contig2118 2118 THRCLA_contig2119 2119 THRCLA_contig2120 2120 THRCLA_contig2121 2121 THRCLA_contig2122 2122 THRCLA_contig2123 2123 THRCLA_contig2124 2124 THRCLA_contig2125 2125 THRCLA_contig2126 2126 THRCLA_contig2127 2127 THRCLA_contig2128 2128 THRCLA_contig2129 2129 THRCLA_contig2130 2130 THRCLA_contig2131 2131 THRCLA_contig2132 2132 THRCLA_contig2133 2133 THRCLA_contig2134 2134 THRCLA_contig2135 2135 THRCLA_contig2136 2136 THRCLA_contig2137 2137 THRCLA_contig2138 2138 THRCLA_contig2139 2139 THRCLA_contig2140 2140 THRCLA_contig2141 2141 THRCLA_contig2142 2142 THRCLA_contig2143 2143 THRCLA_contig2144 2144 THRCLA_contig2145 2145 THRCLA_contig2146 2146 THRCLA_contig2147 2147 THRCLA_contig2148 2148 THRCLA_contig2149 2149 THRCLA_contig2150 2150 THRCLA_contig2151 2151 THRCLA_contig2152 2152 THRCLA_contig2153 2153 THRCLA_contig2154 2154 THRCLA_contig2155 2155 THRCLA_contig2156 2156 THRCLA_contig2157 2157 THRCLA_contig2158 2158 THRCLA_contig2159 2159 THRCLA_contig2160 2160 THRCLA_contig2161 2161 THRCLA_contig2162 2162 THRCLA_contig2163 2163 THRCLA_contig2164 2164 THRCLA_contig2165 2165 THRCLA_contig2166 2166 THRCLA_contig2167 2167 THRCLA_contig2168 2168 THRCLA_contig2169 2169 THRCLA_contig2170 2170 THRCLA_contig2171 2171 THRCLA_contig2172 2172 THRCLA_contig2173 2173 THRCLA_contig2174 2174 THRCLA_contig2175 2175 THRCLA_contig2176 2176 THRCLA_contig2177 2177 THRCLA_contig2178 2178 THRCLA_contig2179 2179 THRCLA_contig2180 2180 THRCLA_contig2181 2181 THRCLA_contig2182 2182 THRCLA_contig2183 2183 THRCLA_contig2184 2184 THRCLA_contig2185 2185 THRCLA_contig2186 2186 THRCLA_contig2187 2187 THRCLA_contig2188 2188 THRCLA_contig2189 2189 THRCLA_contig2190 2190 THRCLA_contig2191 2191 THRCLA_contig2192 2192 THRCLA_contig2193 2193 THRCLA_contig2194 2194 THRCLA_contig2195 2195 THRCLA_contig2196 2196 THRCLA_contig2197 2197 THRCLA_contig2198 2198 THRCLA_contig2199 2199 THRCLA_contig2200 2200 THRCLA_contig2201 2201 THRCLA_contig2202 2202 THRCLA_contig2203 2203 THRCLA_contig2204 2204 THRCLA_contig2205 2205 THRCLA_contig2206 2206 THRCLA_contig2207 2207 THRCLA_contig2208 2208 THRCLA_contig2209 2209 THRCLA_contig2210 2210 THRCLA_contig2211 2211 THRCLA_contig2212 2212 THRCLA_contig2213 2213 THRCLA_contig2214 2214 THRCLA_contig2215 2215 THRCLA_contig2216 2216 THRCLA_contig2217 2217 THRCLA_contig2218 2218 THRCLA_contig2219 2219 THRCLA_contig2220 2220 THRCLA_contig2221 2221 THRCLA_contig2222 2222 THRCLA_contig2223 2223 THRCLA_contig2224 2224 THRCLA_contig2225 2225 THRCLA_contig2226 2226 THRCLA_contig2227 2227 THRCLA_contig2228 2228 THRCLA_contig2229 2229 THRCLA_contig2230 2230 THRCLA_contig2231 2231 THRCLA_contig2232 2232 THRCLA_contig2233 2233 THRCLA_contig2234 2234 THRCLA_contig2235 2235 THRCLA_contig2236 2236 THRCLA_contig2237 2237 THRCLA_contig2238 2238 THRCLA_contig2239 2239 THRCLA_contig2240 2240 THRCLA_contig2241 2241 THRCLA_contig2242 2242 THRCLA_contig2243 2243 THRCLA_contig2244 2244 THRCLA_contig2245 2245 THRCLA_contig2246 2246 THRCLA_contig2247 2247 THRCLA_contig2248 2248 THRCLA_contig2249 2249 THRCLA_contig2250 2250 THRCLA_contig2251 2251 THRCLA_contig2252 2252 THRCLA_contig2253 2253 THRCLA_contig2254 2254 THRCLA_contig2255 2255 THRCLA_contig2256 2256 THRCLA_contig2257 2257 THRCLA_contig2258 2258 THRCLA_contig2259 2259 THRCLA_contig2260 2260 THRCLA_contig2261 2261 THRCLA_contig2262 2262 THRCLA_contig2263 2263 THRCLA_contig2264 2264 THRCLA_contig2265 2265 THRCLA_contig2266 2266 THRCLA_contig2267 2267 THRCLA_contig2268 2268 THRCLA_contig2269 2269 THRCLA_contig2270 2270 THRCLA_contig2271 2271 THRCLA_contig2272 2272 THRCLA_contig2273 2273 THRCLA_contig2274 2274 THRCLA_contig2275 2275 THRCLA_contig2276 2276 THRCLA_contig2277 2277 THRCLA_contig2278 2278 THRCLA_contig2279 2279 THRCLA_contig2280 2280 THRCLA_contig2281 2281 THRCLA_contig2282 2282 THRCLA_contig2283 2283 THRCLA_contig2284 2284 THRCLA_contig2285 2285 THRCLA_contig2286 2286 THRCLA_contig2287 2287 THRCLA_contig2288 2288 THRCLA_contig2289 2289 THRCLA_contig2290 2290 THRCLA_contig2291 2291 THRCLA_contig2292 2292 THRCLA_contig2293 2293 THRCLA_contig2294 2294 THRCLA_contig2295 2295 THRCLA_contig2296 2296 THRCLA_contig2297 2297 THRCLA_contig2298 2298 THRCLA_contig2299 2299 THRCLA_contig2300 2300 THRCLA_contig2301 2301 THRCLA_contig2302 2302 THRCLA_contig2303 2303 THRCLA_contig2304 2304 THRCLA_contig2305 2305 THRCLA_contig2306 2306 THRCLA_contig2307 2307 THRCLA_contig2308 2308 THRCLA_contig2309 2309 THRCLA_contig2310 2310 THRCLA_contig2311 2311 THRCLA_contig2312 2312 THRCLA_contig2313 2313 THRCLA_contig2314 2314 THRCLA_contig2315 2315 THRCLA_contig2316 2316 THRCLA_contig2317 2317 THRCLA_contig2318 2318 THRCLA_contig2319 2319 THRCLA_contig2320 2320 THRCLA_contig2321 2321 THRCLA_contig2322 2322 THRCLA_contig2323 2323 THRCLA_contig2324 2324 THRCLA_contig2325 2325 THRCLA_contig2326 2326 THRCLA_contig2327 2327 THRCLA_contig2328 2328 THRCLA_contig2329 2329 THRCLA_contig2330 2330 THRCLA_contig2331 2331 THRCLA_contig2332 2332 THRCLA_contig2333 2333 THRCLA_contig2334 2334 THRCLA_contig2335 2335 THRCLA_contig2336 2336 THRCLA_contig2337 2337 THRCLA_contig2338 2338 THRCLA_contig2339 2339 THRCLA_contig2340 2340 THRCLA_contig2341 2341 THRCLA_contig2342 2342 THRCLA_contig2343 2343 THRCLA_contig2344 2344 THRCLA_contig2345 2345 THRCLA_contig2346 2346 THRCLA_contig2347 2347 THRCLA_contig2348 2348 THRCLA_contig2349 2349 THRCLA_contig2350 2350 THRCLA_contig2351 2351 THRCLA_contig2352 2352 THRCLA_contig2353 2353 THRCLA_contig2354 2354 THRCLA_contig2355 2355 THRCLA_contig2356 2356 THRCLA_contig2357 2357 THRCLA_contig2358 2358 THRCLA_contig2359 2359 THRCLA_contig2360 2360 THRCLA_contig2361 2361 THRCLA_contig2362 2362 THRCLA_contig2363 2363 THRCLA_contig2364 2364 THRCLA_contig2365 2365 THRCLA_contig2366 2366 THRCLA_contig2367 2367 THRCLA_contig2368 2368 THRCLA_contig2369 2369 THRCLA_contig2370 2370 THRCLA_contig2371 2371 THRCLA_contig2372 2372 THRCLA_contig2373 2373 THRCLA_contig2374 2374 THRCLA_contig2375 2375 THRCLA_contig2376 2376 THRCLA_contig2377 2377 THRCLA_contig2378 2378 THRCLA_contig2379 2379 THRCLA_contig2380 2380 THRCLA_contig2381 2381 THRCLA_contig2382 2382 THRCLA_contig2383 2383 THRCLA_contig2384 2384 THRCLA_contig2385 2385 THRCLA_contig2386 2386 THRCLA_contig2387 2387 THRCLA_contig2388 2388 THRCLA_contig2389 2389 THRCLA_contig2390 2390 THRCLA_contig2391 2391 THRCLA_contig2392 2392 THRCLA_contig2393 2393 THRCLA_contig2394 2394 THRCLA_contig2395 2395 THRCLA_contig2396 2396 THRCLA_contig2397 2397 THRCLA_contig2398 2398 THRCLA_contig2399 2399 THRCLA_contig2400 2400 THRCLA_contig2401 2401 THRCLA_contig2402 2402 THRCLA_contig2403 2403 THRCLA_contig2404 2404 THRCLA_contig2405 2405 THRCLA_contig2406 2406 THRCLA_contig2407 2407 THRCLA_contig2408 2408 THRCLA_contig2409 2409 THRCLA_contig2410 2410 THRCLA_contig2411 2411 THRCLA_contig2412 2412 THRCLA_contig2413 2413 THRCLA_contig2414 2414 THRCLA_contig2415 2415 THRCLA_contig2416 2416 THRCLA_contig2417 2417 THRCLA_contig2418 2418 THRCLA_contig2419 2419 THRCLA_contig2420 2420 THRCLA_contig2421 2421 THRCLA_contig2422 2422 THRCLA_contig2423 2423 THRCLA_contig2424 2424 THRCLA_contig2425 2425 THRCLA_contig2426 2426 THRCLA_contig2427 2427 THRCLA_contig2428 2428 THRCLA_contig2429 2429 THRCLA_contig2430 2430 THRCLA_contig2431 2431 THRCLA_contig2432 2432 THRCLA_contig2433 2433 THRCLA_contig2434 2434 THRCLA_contig2435 2435 THRCLA_contig2436 2436 THRCLA_contig2437 2437 THRCLA_contig2438 2438 THRCLA_contig2439 2439 THRCLA_contig2440 2440 THRCLA_contig2441 2441 THRCLA_contig2442 2442 THRCLA_contig2443 2443 THRCLA_contig2444 2444 THRCLA_contig2445 2445 THRCLA_contig2446 2446 THRCLA_contig2447 2447 THRCLA_contig2448 2448 THRCLA_contig2449 2449 THRCLA_contig2450 2450 THRCLA_contig2451 2451 THRCLA_contig2452 2452 THRCLA_contig2453 2453 THRCLA_contig2454 2454 THRCLA_contig2455 2455 THRCLA_contig2456 2456 THRCLA_contig2457 2457 THRCLA_contig2458 2458 THRCLA_contig2459 2459 THRCLA_contig2460 2460 THRCLA_contig2461 2461 THRCLA_contig2462 2462 THRCLA_contig2463 2463 THRCLA_contig2464 2464 THRCLA_contig2465 2465 THRCLA_contig2466 2466 THRCLA_contig2467 2467 THRCLA_contig2468 2468 THRCLA_contig2469 2469 THRCLA_contig2470 2470 THRCLA_contig2471 2471 THRCLA_contig2472 2472 THRCLA_contig2473 2473 THRCLA_contig2474 2474 THRCLA_contig2475 2475 THRCLA_contig2476 2476 THRCLA_contig2477 2477 THRCLA_contig2478 2478 THRCLA_contig2479 2479 THRCLA_contig2480 2480 THRCLA_contig2481 2481 THRCLA_contig2482 2482 THRCLA_contig2483 2483 THRCLA_contig2484 2484 THRCLA_contig2485 2485 THRCLA_contig2486 2486 THRCLA_contig2487 2487 THRCLA_contig2488 2488 THRCLA_contig2489 2489 THRCLA_contig2490 2490 THRCLA_contig2491 2491 THRCLA_contig2492 2492 THRCLA_contig2493 2493 THRCLA_contig2494 2494 THRCLA_contig2495 2495 THRCLA_contig2496 2496 THRCLA_contig2497 2497 THRCLA_contig2498 2498 THRCLA_contig2499 2499 THRCLA_contig2500 2500 THRCLA_contig2501 2501 THRCLA_contig2502 2502 THRCLA_contig2503 2503 THRCLA_contig2504 2504 THRCLA_contig2505 2505 THRCLA_contig2506 2506 THRCLA_contig2507 2507 THRCLA_contig2508 2508 THRCLA_contig2509 2509 THRCLA_contig2510 2510 THRCLA_contig2511 2511 THRCLA_contig2512 2512 THRCLA_contig2513 2513 THRCLA_contig2514 2514 THRCLA_contig2515 2515 THRCLA_contig2516 2516 THRCLA_contig2517 2517 THRCLA_contig2518 2518 THRCLA_contig2519 2519 THRCLA_contig2520 2520 THRCLA_contig2521 2521 THRCLA_contig2522 2522 THRCLA_contig2523 2523 THRCLA_contig2524 2524 THRCLA_contig2525 2525 THRCLA_contig2526 2526 THRCLA_contig2527 2527 THRCLA_contig2528 2528 THRCLA_contig2529 2529 THRCLA_contig2530 2530 THRCLA_contig2531 2531 THRCLA_contig2532 2532 THRCLA_contig2533 2533 THRCLA_contig2534 2534 THRCLA_contig2535 2535 THRCLA_contig2536 2536 THRCLA_contig2537 2537 THRCLA_contig2538 2538 THRCLA_contig2539 2539 THRCLA_contig2540 2540 THRCLA_contig2541 2541 THRCLA_contig2542 2542 THRCLA_contig2543 2543 THRCLA_contig2544 2544 THRCLA_contig2545 2545 THRCLA_contig2546 2546 THRCLA_contig2547 2547 THRCLA_contig2548 2548 THRCLA_contig2549 2549 THRCLA_contig2550 2550 THRCLA_contig2551 2551 THRCLA_contig2552 2552 THRCLA_contig2553 2553 THRCLA_contig2554 2554 THRCLA_contig2555 2555 THRCLA_contig2556 2556 THRCLA_contig2557 2557 THRCLA_contig2558 2558 THRCLA_contig2559 2559 THRCLA_contig2560 2560 THRCLA_contig2561 2561 THRCLA_contig2562 2562 THRCLA_contig2563 2563 THRCLA_contig2564 2564 THRCLA_contig2565 2565 THRCLA_contig2566 2566 THRCLA_contig2567 2567 THRCLA_contig2568 2568 THRCLA_contig2569 2569 THRCLA_contig2570 2570 THRCLA_contig2571 2571 THRCLA_contig2572 2572 THRCLA_contig2573 2573 THRCLA_contig2574 2574 THRCLA_contig2575 2575 THRCLA_contig2576 2576 THRCLA_contig2577 2577 THRCLA_contig2578 2578 THRCLA_contig2579 2579 THRCLA_contig2580 2580 THRCLA_contig2581 2581 THRCLA_contig2582 2582 THRCLA_contig2583 2583 THRCLA_contig2584 2584 THRCLA_contig2585 2585 THRCLA_contig2586 2586 THRCLA_contig2587 2587 THRCLA_contig2588 2588 THRCLA_contig2589 2589 THRCLA_contig2590 2590 THRCLA_contig2591 2591 THRCLA_contig2592 2592 THRCLA_contig2593 2593 THRCLA_contig2594 2594 THRCLA_contig2595 2595 THRCLA_contig2596 2596 THRCLA_contig2597 2597 THRCLA_contig2598 2598 THRCLA_contig2599 2599 THRCLA_contig2600 2600 THRCLA_contig2601 2601 THRCLA_contig2602 2602 THRCLA_contig2603 2603 THRCLA_contig2604 2604 THRCLA_contig2605 2605 THRCLA_contig2606 2606 THRCLA_contig2607 2607 THRCLA_contig2608 2608 THRCLA_contig2609 2609 THRCLA_contig2610 2610 THRCLA_contig2611 2611 THRCLA_contig2612 2612 THRCLA_contig2613 2613 THRCLA_contig2614 2614 THRCLA_contig2615 2615 THRCLA_contig2616 2616 THRCLA_contig2617 2617 THRCLA_contig2618 2618 THRCLA_contig2619 2619 THRCLA_contig2620 2620 THRCLA_contig2621 2621 THRCLA_contig2622 2622 THRCLA_contig2623 2623 THRCLA_contig2624 2624 THRCLA_contig2625 2625 THRCLA_contig2626 2626 THRCLA_contig2627 2627 THRCLA_contig2628 2628 THRCLA_contig2629 2629 THRCLA_contig2630 2630 THRCLA_contig2631 2631 THRCLA_contig2632 2632 THRCLA_contig2633 2633 THRCLA_contig2634 2634 THRCLA_contig2635 2635 THRCLA_contig2636 2636 THRCLA_contig2637 2637 THRCLA_contig2638 2638 THRCLA_contig2639 2639 THRCLA_contig2640 2640 THRCLA_contig2641 2641 THRCLA_contig2642 2642 THRCLA_contig2643 2643 THRCLA_contig2644 2644 THRCLA_contig2645 2645 THRCLA_contig2646 2646 THRCLA_contig2647 2647 THRCLA_contig2648 2648 THRCLA_contig2649 2649 THRCLA_contig2650 2650 THRCLA_contig2651 2651 THRCLA_contig2652 2652 THRCLA_contig2653 2653 THRCLA_contig2654 2654 THRCLA_contig2655 2655 THRCLA_contig2656 2656 THRCLA_contig2657 2657 THRCLA_contig2658 2658 THRCLA_contig2659 2659 THRCLA_contig2660 2660 THRCLA_contig2661 2661 THRCLA_contig2662 2662 THRCLA_contig2663 2663 THRCLA_contig2664 2664 THRCLA_contig2665 2665 THRCLA_contig2666 2666 THRCLA_contig2667 2667 THRCLA_contig2668 2668 THRCLA_contig2669 2669 THRCLA_contig2670 2670 THRCLA_contig2671 2671 THRCLA_contig2672 2672 THRCLA_contig2673 2673 THRCLA_contig2674 2674 THRCLA_contig2675 2675 THRCLA_contig2676 2676 THRCLA_contig2677 2677 THRCLA_contig2678 2678 THRCLA_contig2679 2679 THRCLA_contig2680 2680 THRCLA_contig2681 2681 THRCLA_contig2682 2682 THRCLA_contig2683 2683 THRCLA_contig2684 2684 THRCLA_contig2685 2685 THRCLA_contig2686 2686 THRCLA_contig2687 2687 THRCLA_contig2688 2688 THRCLA_contig2689 2689 THRCLA_contig2690 2690 THRCLA_contig2691 2691 THRCLA_contig2692 2692 THRCLA_contig2693 2693 THRCLA_contig2694 2694 THRCLA_contig2695 2695 THRCLA_contig2696 2696 THRCLA_contig2697 2697 THRCLA_contig2698 2698 THRCLA_contig2699 2699 THRCLA_contig2700 2700 THRCLA_contig2701 2701 THRCLA_contig2702 2702 THRCLA_contig2703 2703 THRCLA_contig2704 2704 THRCLA_contig2705 2705 THRCLA_contig2706 2706 THRCLA_contig2707 2707 THRCLA_contig2708 2708 THRCLA_contig2709 2709 THRCLA_contig2710 2710 THRCLA_contig2711 2711 THRCLA_contig2712 2712 THRCLA_contig2713 2713 THRCLA_contig2714 2714 THRCLA_contig2715 2715 THRCLA_contig2716 2716 THRCLA_contig2717 2717 THRCLA_contig2718 2718 THRCLA_contig2719 2719 THRCLA_contig2720 2720 THRCLA_contig2721 2721 THRCLA_contig2722 2722 THRCLA_contig2723 2723 THRCLA_contig2724 2724 THRCLA_contig2725 2725 THRCLA_contig2726 2726 THRCLA_contig2727 2727 THRCLA_contig2728 2728 THRCLA_contig2729 2729 THRCLA_contig2730 2730 THRCLA_contig2731 2731 THRCLA_contig2732 2732 THRCLA_contig2733 2733 THRCLA_contig2734 2734 THRCLA_contig2735 2735 THRCLA_contig2736 2736 THRCLA_contig2737 2737 THRCLA_contig2738 2738 THRCLA_contig2739 2739 THRCLA_contig2740 2740 THRCLA_contig2741 2741 THRCLA_contig2742 2742 THRCLA_contig2743 2743 THRCLA_contig2744 2744 THRCLA_contig2745 2745 THRCLA_contig2746 2746 THRCLA_contig2747 2747 THRCLA_contig2748 2748 THRCLA_contig2749 2749 THRCLA_contig2750 2750 THRCLA_contig2751 2751 THRCLA_contig2752 2752 THRCLA_contig2753 2753 THRCLA_contig2754 2754 THRCLA_contig2755 2755 THRCLA_contig2756 2756 THRCLA_contig2757 2757 THRCLA_contig2758 2758 THRCLA_contig2759 2759 THRCLA_contig2760 2760 THRCLA_contig2761 2761 THRCLA_contig2762 2762 THRCLA_contig2763 2763 THRCLA_contig2764 2764 THRCLA_contig2765 2765 THRCLA_contig2766 2766 THRCLA_contig2767 2767 THRCLA_contig2768 2768 THRCLA_contig2769 2769 THRCLA_contig2770 2770 THRCLA_contig2771 2771 THRCLA_contig2772 2772 THRCLA_contig2773 2773 THRCLA_contig2774 2774 THRCLA_contig2775 2775 THRCLA_contig2776 2776 THRCLA_contig2777 2777 THRCLA_contig2778 2778 THRCLA_contig2779 2779 THRCLA_contig2780 2780 THRCLA_contig2781 2781 THRCLA_contig2782 2782 THRCLA_contig2783 2783 THRCLA_contig2784 2784 THRCLA_contig2785 2785 THRCLA_contig2786 2786 THRCLA_contig2787 2787 THRCLA_contig2788 2788 THRCLA_contig2789 2789 THRCLA_contig2790 2790 THRCLA_contig2791 2791 THRCLA_contig2792 2792 THRCLA_contig2793 2793 THRCLA_contig2794 2794 THRCLA_contig2795 2795 THRCLA_contig2796 2796 THRCLA_contig2797 2797 THRCLA_contig2798 2798 THRCLA_contig2799 2799 THRCLA_contig2800 2800 THRCLA_contig2801 2801 THRCLA_contig2802 2802 THRCLA_contig2803 2803 THRCLA_contig2804 2804 THRCLA_contig2805 2805 THRCLA_contig2806 2806 THRCLA_contig2807 2807 THRCLA_contig2808 2808 THRCLA_contig2809 2809 THRCLA_contig2810 2810 THRCLA_contig2811 2811 THRCLA_contig2812 2812 THRCLA_contig2813 2813 THRCLA_contig2814 2814 THRCLA_contig2815 2815 THRCLA_contig2816 2816 THRCLA_contig2817 2817 THRCLA_contig2818 2818 THRCLA_contig2819 2819 THRCLA_contig2820 2820 THRCLA_contig2821 2821 THRCLA_contig2822 2822 THRCLA_contig2823 2823 THRCLA_contig2824 2824 THRCLA_contig2825 2825 THRCLA_contig2826 2826 THRCLA_contig2827 2827 THRCLA_contig2828 2828 THRCLA_contig2829 2829 THRCLA_contig2830 2830 THRCLA_contig2831 2831 THRCLA_contig2832 2832 THRCLA_contig2833 2833 THRCLA_contig2834 2834 THRCLA_contig2835 2835 THRCLA_contig2836 2836 THRCLA_contig2837 2837 THRCLA_contig2838 2838 THRCLA_contig2839 2839 THRCLA_contig2840 2840 THRCLA_contig2841 2841 THRCLA_contig2842 2842 THRCLA_contig2843 2843 THRCLA_contig2844 2844 THRCLA_contig2845 2845 THRCLA_contig2846 2846 THRCLA_contig2847 2847 THRCLA_contig2848 2848 THRCLA_contig2849 2849 THRCLA_contig2850 2850 THRCLA_contig2851 2851 THRCLA_contig2852 2852 THRCLA_contig2853 2853 THRCLA_contig2854 2854 THRCLA_contig2855 2855 THRCLA_contig2856 2856 THRCLA_contig2857 2857 THRCLA_contig2858 2858 THRCLA_contig2859 2859 THRCLA_contig2860 2860 THRCLA_contig2861 2861 THRCLA_contig2862 2862 THRCLA_contig2863 2863 THRCLA_contig2864 2864 THRCLA_contig2865 2865 THRCLA_contig2866 2866 THRCLA_contig2867 2867 THRCLA_contig2868 2868 THRCLA_contig2869 2869 THRCLA_contig2870 2870 THRCLA_contig2871 2871 THRCLA_contig2872 2872 THRCLA_contig2873 2873 THRCLA_contig2874 2874 THRCLA_contig2875 2875 THRCLA_contig2876 2876 THRCLA_contig2877 2877 THRCLA_contig2878 2878 THRCLA_contig2879 2879 THRCLA_contig2880 2880 THRCLA_contig2881 2881 THRCLA_contig2882 2882 THRCLA_contig2883 2883 THRCLA_contig2884 2884 THRCLA_contig2885 2885 THRCLA_contig2886 2886 THRCLA_contig2887 2887 THRCLA_contig2888 2888 THRCLA_contig2889 2889 THRCLA_contig2890 2890 THRCLA_contig2891 2891 THRCLA_contig2892 2892 THRCLA_contig2893 2893 THRCLA_contig2894 2894 THRCLA_contig2895 2895 THRCLA_contig2896 2896 THRCLA_contig2897 2897 THRCLA_contig2898 2898 THRCLA_contig2899 2899 THRCLA_contig2900 2900 THRCLA_contig2901 2901 THRCLA_contig2902 2902 THRCLA_contig2903 2903 THRCLA_contig2904 2904 THRCLA_contig2905 2905 THRCLA_contig2906 2906 THRCLA_contig2907 2907 THRCLA_contig2908 2908 THRCLA_contig2909 2909 THRCLA_contig2910 2910 THRCLA_contig2911 2911 THRCLA_contig2912 2912 THRCLA_contig2913 2913 THRCLA_contig2914 2914 THRCLA_contig2915 2915 THRCLA_contig2916 2916 THRCLA_contig2917 2917 THRCLA_contig2918 2918 THRCLA_contig2919 2919 THRCLA_contig2920 2920 THRCLA_contig2921 2921 THRCLA_contig2922 2922 THRCLA_contig2923 2923 THRCLA_contig2924 2924 THRCLA_contig2925 2925 THRCLA_contig2926 2926 THRCLA_contig2927 2927 THRCLA_contig2928 2928 THRCLA_contig2929 2929 THRCLA_contig2930 2930 THRCLA_contig2931 2931 THRCLA_contig2932 2932 THRCLA_contig2933 2933 THRCLA_contig2934 2934 THRCLA_contig2935 2935 THRCLA_contig2936 2936 THRCLA_contig2937 2937 THRCLA_contig2938 2938 THRCLA_contig2939 2939 THRCLA_contig2940 2940 THRCLA_contig2941 2941 THRCLA_contig2942 2942 THRCLA_contig2943 2943 THRCLA_contig2944 2944 THRCLA_contig2945 2945 THRCLA_contig2946 2946 THRCLA_contig2947 2947 THRCLA_contig2948 2948 THRCLA_contig2949 2949 THRCLA_contig2950 2950 THRCLA_contig2951 2951 THRCLA_contig2952 2952 THRCLA_contig2953 2953 THRCLA_contig2954 2954 THRCLA_contig2955 2955 THRCLA_contig2956 2956 THRCLA_contig2957 2957 THRCLA_contig2958 2958 THRCLA_contig2959 2959 THRCLA_contig2960 2960 THRCLA_contig2961 2961 THRCLA_contig2962 2962 THRCLA_contig2963 2963 THRCLA_contig2964 2964 THRCLA_contig2965 2965 THRCLA_contig2966 2966 THRCLA_contig2967 2967 THRCLA_contig2968 2968 THRCLA_contig2969 2969 THRCLA_contig2970 2970 THRCLA_contig2971 2971 THRCLA_contig2972 2972 THRCLA_contig2973 2973 THRCLA_contig2974 2974 THRCLA_contig2975 2975 THRCLA_contig2976 2976 THRCLA_contig2977 2977 THRCLA_contig2978 2978 THRCLA_contig2979 2979 THRCLA_contig2980 2980 THRCLA_contig2981 2981 THRCLA_contig2982 2982 THRCLA_contig2983 2983 THRCLA_contig2984 2984 THRCLA_contig2985 2985 THRCLA_contig2986 2986 THRCLA_contig2987 2987 THRCLA_contig2988 2988 THRCLA_contig2989 2989 THRCLA_contig2990 2990 THRCLA_contig2991 2991 THRCLA_contig2992 2992 THRCLA_contig2993 2993 THRCLA_contig2994 2994 THRCLA_contig2995 2995 THRCLA_contig2996 2996 THRCLA_contig2997 2997 THRCLA_contig2998 2998 THRCLA_contig2999 2999 THRCLA_contig3000 3000 THRCLA_contig3001 3001 THRCLA_contig3002 3002 THRCLA_contig3003 3003 THRCLA_contig3004 3004 THRCLA_contig3005 3005 THRCLA_contig3006 3006 THRCLA_contig3007 3007 THRCLA_contig3008 3008 THRCLA_contig3009 3009 THRCLA_contig3010 3010 THRCLA_contig3011 3011 THRCLA_contig3012 3012 THRCLA_contig3013 3013 THRCLA_contig3014 3014 THRCLA_contig3015 3015 THRCLA_contig3016 3016 THRCLA_contig3017 3017 THRCLA_contig3018 3018 THRCLA_contig3019 3019 THRCLA_contig3020 3020 THRCLA_contig3021 3021 THRCLA_contig3022 3022 THRCLA_contig3023 3023 THRCLA_contig3024 3024 THRCLA_contig3025 3025 THRCLA_contig3026 3026 THRCLA_contig3027 3027 THRCLA_contig3028 3028 THRCLA_contig3029 3029 THRCLA_contig3030 3030 THRCLA_contig3031 3031 THRCLA_contig3032 3032 THRCLA_contig3033 3033 THRCLA_contig3034 3034 THRCLA_contig3035 3035 THRCLA_contig3036 3036 THRCLA_contig3037 3037 THRCLA_contig3038 3038 THRCLA_contig3039 3039 THRCLA_contig3040 3040 THRCLA_contig3041 3041 THRCLA_contig3042 3042 THRCLA_contig3043 3043 THRCLA_contig3044 3044 THRCLA_contig3045 3045 THRCLA_contig3046 3046 THRCLA_contig3047 3047 THRCLA_contig3048 3048 THRCLA_contig3049 3049 THRCLA_contig3050 3050 THRCLA_contig3051 3051 THRCLA_contig3052 3052 THRCLA_contig3053 3053 THRCLA_contig3054 3054 THRCLA_contig3055 3055 THRCLA_contig3056 3056 THRCLA_contig3057 3057 THRCLA_contig3058 3058 THRCLA_contig3059 3059 THRCLA_contig3060 3060 THRCLA_contig3061 3061 THRCLA_contig3062 3062 THRCLA_contig3063 3063 THRCLA_contig3064 3064 THRCLA_contig3065 3065 THRCLA_contig3066 3066 THRCLA_contig3067 3067 THRCLA_contig3068 3068 THRCLA_contig3069 3069 THRCLA_contig3070 3070 THRCLA_contig3071 3071 THRCLA_contig3072 3072 THRCLA_contig3073 3073 THRCLA_contig3074 3074 THRCLA_contig3075 3075 THRCLA_contig3076 3076 THRCLA_contig3077 3077 THRCLA_contig3078 3078 THRCLA_contig3079 3079 THRCLA_contig3080 3080 THRCLA_contig3081 3081 THRCLA_contig3082 3082 THRCLA_contig3083 3083 THRCLA_contig3084 3084 THRCLA_contig3085 3085 THRCLA_contig3086 3086 THRCLA_contig3087 3087 THRCLA_contig3088 3088 THRCLA_contig3089 3089 THRCLA_contig3090 3090 THRCLA_contig3091 3091 THRCLA_contig3092 3092 THRCLA_contig3093 3093 THRCLA_contig3094 3094 THRCLA_contig3095 3095 THRCLA_contig3096 3096 THRCLA_contig3097 3097 THRCLA_contig3098 3098 THRCLA_contig3099 3099 THRCLA_contig3100 3100 THRCLA_contig3101 3101 THRCLA_contig3102 3102 THRCLA_contig3103 3103 THRCLA_contig3104 3104 THRCLA_contig3105 3105 THRCLA_contig3106 3106 THRCLA_contig3107 3107 THRCLA_contig3108 3108 THRCLA_contig3109 3109 THRCLA_contig3110 3110 THRCLA_contig3111 3111 THRCLA_contig3112 3112 THRCLA_contig3113 3113 THRCLA_contig3114 3114 THRCLA_contig3115 3115 THRCLA_contig3116 3116 THRCLA_contig3117 3117 THRCLA_contig3118 3118 THRCLA_contig3119 3119 THRCLA_contig3120 3120 THRCLA_contig3121 3121 THRCLA_contig3122 3122 THRCLA_contig3123 3123 THRCLA_contig3124 3124 THRCLA_contig3125 3125 THRCLA_contig3126 3126 THRCLA_contig3127 3127 THRCLA_contig3128 3128 THRCLA_contig3129 3129 THRCLA_contig3130 3130 THRCLA_contig3131 3131 THRCLA_contig3132 3132 THRCLA_contig3133 3133 THRCLA_contig3134 3134 THRCLA_contig3135 3135 THRCLA_contig3136 3136 THRCLA_contig3137 3137 THRCLA_contig3138 3138 THRCLA_contig3139 3139 THRCLA_contig3140 3140 THRCLA_contig3141 3141 THRCLA_contig3142 3142 THRCLA_contig3143 3143 THRCLA_contig3144 3144 THRCLA_contig3145 3145 THRCLA_contig3146 3146 THRCLA_contig3147 3147 THRCLA_contig3148 3148 THRCLA_contig3149 3149 THRCLA_contig3150 3150 THRCLA_contig3151 3151 THRCLA_contig3152 3152 THRCLA_contig3153 3153 THRCLA_contig3154 3154 THRCLA_contig3155 3155 THRCLA_contig3156 3156 THRCLA_contig3157 3157 THRCLA_contig3158 3158 THRCLA_contig3159 3159 THRCLA_contig3160 3160 THRCLA_contig3161 3161 THRCLA_contig3162 3162 THRCLA_contig3163 3163 THRCLA_contig3164 3164 THRCLA_contig3165 3165 THRCLA_contig3166 3166 THRCLA_contig3167 3167 THRCLA_contig3168 3168 THRCLA_contig3169 3169 THRCLA_contig3170 3170 THRCLA_contig3171 3171 THRCLA_contig3172 3172 THRCLA_contig3173 3173 THRCLA_contig3174 3174 THRCLA_contig3175 3175 THRCLA_contig3176 3176 THRCLA_contig3177 3177 THRCLA_contig3178 3178 THRCLA_contig3179 3179 THRCLA_contig3180 3180 THRCLA_contig3181 3181 THRCLA_contig3182 3182 THRCLA_contig3183 3183 THRCLA_contig3184 3184 THRCLA_contig3185 3185 THRCLA_contig3186 3186 THRCLA_contig3187 3187 THRCLA_contig3188 3188 THRCLA_contig3189 3189 THRCLA_contig3190 3190 THRCLA_contig3191 3191 THRCLA_contig3192 3192 THRCLA_contig3193 3193 THRCLA_contig3194 3194 THRCLA_contig3195 3195 THRCLA_contig3196 3196 THRCLA_contig3197 3197 THRCLA_contig3198 3198 THRCLA_contig3199 3199 THRCLA_contig3200 3200 THRCLA_contig3201 3201 THRCLA_contig3202 3202 THRCLA_contig3203 3203 THRCLA_contig3204 3204 THRCLA_contig3205 3205 THRCLA_contig3206 3206 THRCLA_contig3207 3207 THRCLA_contig3208 3208 THRCLA_contig3209 3209 THRCLA_contig3210 3210 THRCLA_contig3211 3211 THRCLA_contig3212 3212 THRCLA_contig3213 3213 THRCLA_contig3214 3214 THRCLA_contig3215 3215 THRCLA_contig3216 3216 THRCLA_contig3217 3217 THRCLA_contig3218 3218 THRCLA_contig3219 3219 THRCLA_contig3220 3220 THRCLA_contig3221 3221 THRCLA_contig3222 3222 THRCLA_contig3223 3223 THRCLA_contig3224 3224 THRCLA_contig3225 3225 THRCLA_contig3226 3226 THRCLA_contig3227 3227 THRCLA_contig3228 3228 THRCLA_contig3229 3229 THRCLA_contig3230 3230 THRCLA_contig3231 3231 THRCLA_contig3232 3232 THRCLA_contig3233 3233 THRCLA_contig3234 3234 THRCLA_contig3235 3235 THRCLA_contig3236 3236 THRCLA_contig3237 3237 THRCLA_contig3238 3238 THRCLA_contig3239 3239 THRCLA_contig3240 3240 THRCLA_contig3241 3241 THRCLA_contig3242 3242 THRCLA_contig3243 3243 THRCLA_contig3244 3244 THRCLA_contig3245 3245 THRCLA_contig3246 3246 THRCLA_contig3247 3247 THRCLA_contig3248 3248 THRCLA_contig3249 3249 THRCLA_contig3250 3250 THRCLA_contig3251 3251 THRCLA_contig3252 3252 THRCLA_contig3253 3253 THRCLA_contig3254 3254 THRCLA_contig3255 3255 THRCLA_contig3256 3256 THRCLA_contig3257 3257 THRCLA_contig3258 3258 THRCLA_contig3259 3259 THRCLA_contig3260 3260 THRCLA_contig3261 3261 THRCLA_contig3262 3262 THRCLA_contig3263 3263 THRCLA_contig3264 3264 THRCLA_contig3265 3265 THRCLA_contig3266 3266 THRCLA_contig3267 3267 THRCLA_contig3268 3268 THRCLA_contig3269 3269 THRCLA_contig3270 3270 THRCLA_contig3271 3271 THRCLA_contig3272 3272 THRCLA_contig3273 3273 THRCLA_contig3274 3274 THRCLA_contig3275 3275 THRCLA_contig3276 3276 THRCLA_contig3277 3277 THRCLA_contig3278 3278 THRCLA_contig3279 3279 THRCLA_contig3280 3280 THRCLA_contig3281 3281 THRCLA_contig3282 3282 THRCLA_contig3283 3283 THRCLA_contig3284 3284 THRCLA_contig3285 3285 THRCLA_contig3286 3286 THRCLA_contig3287 3287 THRCLA_contig3288 3288 THRCLA_contig3289 3289 THRCLA_contig3290 3290 THRCLA_contig3291 3291 THRCLA_contig3292 3292 THRCLA_contig3293 3293 THRCLA_contig3294 3294 THRCLA_contig3295 3295 THRCLA_contig3296 3296 THRCLA_contig3297 3297 THRCLA_contig3298 3298 THRCLA_contig3299 3299 THRCLA_contig3300 3300 THRCLA_contig3301 3301 THRCLA_contig3302 3302 THRCLA_contig3303 3303 THRCLA_contig3304 3304 THRCLA_contig3305 3305 THRCLA_contig3306 3306 THRCLA_contig3307 3307 THRCLA_contig3308 3308 THRCLA_contig3309 3309 THRCLA_contig3310 3310 THRCLA_contig3311 3311 THRCLA_contig3312 3312 THRCLA_contig3313 3313 THRCLA_contig3314 3314 THRCLA_contig3315 3315 THRCLA_contig3316 3316 THRCLA_contig3317 3317 THRCLA_contig3318 3318 THRCLA_contig3319 3319 THRCLA_contig3320 3320 THRCLA_contig3321 3321 THRCLA_contig3322 3322 THRCLA_contig3323 3323 THRCLA_contig3324 3324 THRCLA_contig3325 3325 THRCLA_contig3326 3326 THRCLA_contig3327 3327 THRCLA_contig3328 3328 THRCLA_contig3329 3329 THRCLA_contig3330 3330 THRCLA_contig3331 3331 THRCLA_contig3332 3332 THRCLA_contig3333 3333 THRCLA_contig3334 3334 THRCLA_contig3335 3335 THRCLA_contig3336 3336 THRCLA_contig3337 3337 THRCLA_contig3338 3338 THRCLA_contig3339 3339 THRCLA_contig3340 3340 THRCLA_contig3341 3341 THRCLA_contig3342 3342 THRCLA_contig3343 3343 THRCLA_contig3344 3344 THRCLA_contig3345 3345 THRCLA_contig3346 3346 THRCLA_contig3347 3347 THRCLA_contig3348 3348 THRCLA_contig3349 3349 THRCLA_contig3350 3350 THRCLA_contig3351 3351 THRCLA_contig3352 3352 THRCLA_contig3353 3353 THRCLA_contig3354 3354 THRCLA_contig3355 3355 THRCLA_contig3356 3356 THRCLA_contig3357 3357 THRCLA_contig3358 3358 THRCLA_contig3359 3359 THRCLA_contig3360 3360 THRCLA_contig3361 3361 THRCLA_contig3362 3362 THRCLA_contig3363 3363 THRCLA_contig3364 3364 THRCLA_contig3365 3365 THRCLA_contig3366 3366 THRCLA_contig3367 3367 THRCLA_contig3368 3368 THRCLA_contig3369 3369 THRCLA_contig3370 3370 THRCLA_contig3371 3371 THRCLA_contig3372 3372 THRCLA_contig3373 3373 THRCLA_contig3374 3374 THRCLA_contig3375 3375 THRCLA_contig3376 3376 THRCLA_contig3377 3377 THRCLA_contig3378 3378 THRCLA_contig3379 3379 THRCLA_contig3380 3380 THRCLA_contig3381 3381 THRCLA_contig3382 3382 THRCLA_contig3383 3383 THRCLA_contig3384 3384 THRCLA_contig3385 3385 THRCLA_contig3386 3386 THRCLA_contig3387 3387 THRCLA_contig3388 3388 THRCLA_contig3389 3389 THRCLA_contig3390 3390 THRCLA_contig3391 3391 THRCLA_contig3392 3392 THRCLA_contig3393 3393 THRCLA_contig3394 3394 THRCLA_contig3395 3395 THRCLA_contig3396 3396 THRCLA_contig3397 3397 THRCLA_contig3398 3398 THRCLA_contig3399 3399 THRCLA_contig3400 3400 THRCLA_contig3401 3401 THRCLA_contig3402 3402 THRCLA_contig3403 3403 THRCLA_contig3404 3404 THRCLA_contig3405 3405 THRCLA_contig3406 3406 THRCLA_contig3407 3407 THRCLA_contig3408 3408 THRCLA_contig3409 3409 THRCLA_contig3410 3410 THRCLA_contig3411 3411 THRCLA_contig3412 3412 THRCLA_contig3413 3413 THRCLA_contig3414 3414 THRCLA_contig3415 3415 THRCLA_contig3416 3416 THRCLA_contig3417 3417 THRCLA_contig3418 3418 THRCLA_contig3419 3419 THRCLA_contig3420 3420 THRCLA_contig3421 3421 THRCLA_contig3422 3422 THRCLA_contig3423 3423 THRCLA_contig3424 3424 THRCLA_contig3425 3425 THRCLA_contig3426 3426 THRCLA_contig3427 3427 THRCLA_contig3428 3428 THRCLA_contig3429 3429 THRCLA_contig3430 3430 THRCLA_contig3431 3431 THRCLA_contig3432 3432 THRCLA_contig3433 3433 THRCLA_contig3434 3434 THRCLA_contig3435 3435 THRCLA_contig3436 3436 THRCLA_contig3437 3437 THRCLA_contig3438 3438 THRCLA_contig3439 3439 THRCLA_contig3440 3440 THRCLA_contig3441 3441 THRCLA_contig3442 3442 THRCLA_contig3443 3443 THRCLA_contig3444 3444 THRCLA_contig3445 3445 THRCLA_contig3446 3446 THRCLA_contig3447 3447 THRCLA_contig3448 3448 THRCLA_contig3449 3449 THRCLA_contig3450 3450 THRCLA_contig3451 3451 THRCLA_contig3452 3452 THRCLA_contig3453 3453 THRCLA_contig3454 3454 THRCLA_contig3455 3455 THRCLA_contig3456 3456 THRCLA_contig3457 3457 THRCLA_contig3458 3458 THRCLA_contig3459 3459 THRCLA_contig3460 3460 THRCLA_contig3461 3461 THRCLA_contig3462 3462 THRCLA_contig3463 3463 THRCLA_contig3464 3464 THRCLA_contig3465 3465 THRCLA_contig3466 3466 THRCLA_contig3467 3467 THRCLA_contig3468 3468 THRCLA_contig3469 3469 THRCLA_contig3470 3470 THRCLA_contig3471 3471 THRCLA_contig3472 3472 THRCLA_contig3473 3473 THRCLA_contig3474 3474 THRCLA_contig3475 3475 THRCLA_contig3476 3476 THRCLA_contig3477 3477 THRCLA_contig3478 3478 THRCLA_contig3479 3479 THRCLA_contig3480 3480 THRCLA_contig3481 3481 THRCLA_contig3482 3482 THRCLA_contig3483 3483 THRCLA_contig3484 3484 THRCLA_contig3485 3485 THRCLA_contig3486 3486 THRCLA_contig3487 3487 THRCLA_contig3488 3488 THRCLA_contig3489 3489 THRCLA_contig3490 3490 THRCLA_contig3491 3491 THRCLA_contig3492 3492 THRCLA_contig3493 3493 THRCLA_contig3494 3494 THRCLA_contig3495 3495 THRCLA_contig3496 3496 THRCLA_contig3497 3497 THRCLA_contig3498 3498 THRCLA_contig3499 3499 THRCLA_contig3500 3500 THRCLA_contig3501 3501 THRCLA_contig3502 3502 THRCLA_contig3503 3503 THRCLA_contig3504 3504 THRCLA_contig3505 3505 THRCLA_contig3506 3506 THRCLA_contig3507 3507 THRCLA_contig3508 3508 THRCLA_contig3509 3509 THRCLA_contig3510 3510 THRCLA_contig3511 3511 THRCLA_contig3512 3512 THRCLA_contig3513 3513 THRCLA_contig3514 3514 THRCLA_contig3515 3515 THRCLA_contig3516 3516 THRCLA_contig3517 3517 THRCLA_contig3518 3518 THRCLA_contig3519 3519 THRCLA_contig3520 3520 THRCLA_contig3521 3521 THRCLA_contig3522 3522 THRCLA_contig3523 3523 THRCLA_contig3524 3524 THRCLA_contig3525 3525 THRCLA_contig3526 3526 THRCLA_contig3527 3527 THRCLA_contig3528 3528 THRCLA_contig3529 3529 THRCLA_contig3530 3530 THRCLA_contig3531 3531 THRCLA_contig3532 3532 THRCLA_contig3533 3533 THRCLA_contig3534 3534 THRCLA_contig3535 3535 THRCLA_contig3536 3536 THRCLA_contig3537 3537 THRCLA_contig3538 3538 THRCLA_contig3539 3539 THRCLA_contig3540 3540 THRCLA_contig3541 3541 THRCLA_contig3542 3542 THRCLA_contig3543 3543 THRCLA_contig3544 3544 THRCLA_contig3545 3545 THRCLA_contig3546 3546 THRCLA_contig3547 3547 THRCLA_contig3548 3548 THRCLA_contig3549 3549 THRCLA_contig3550 3550 THRCLA_contig3551 3551 THRCLA_contig3552 3552 THRCLA_contig3553 3553 THRCLA_contig3554 3554 THRCLA_contig3555 3555 THRCLA_contig3556 3556 THRCLA_contig3557 3557 THRCLA_contig3558 3558 THRCLA_contig3559 3559 THRCLA_contig3560 3560 THRCLA_contig3561 3561 THRCLA_contig3562 3562 THRCLA_contig3563 3563 THRCLA_contig3564 3564 THRCLA_contig3565 3565 THRCLA_contig3566 3566 THRCLA_contig3567 3567 THRCLA_contig3568 3568 THRCLA_contig3569 3569 THRCLA_contig3570 3570 THRCLA_contig3571 3571 THRCLA_contig3572 3572 THRCLA_contig3573 3573 THRCLA_contig3574 3574 THRCLA_contig3575 3575 THRCLA_contig3576 3576 THRCLA_contig3577 3577 THRCLA_contig3578 3578 THRCLA_contig3579 3579 THRCLA_contig3580 3580 THRCLA_contig3581 3581 THRCLA_contig3582 3582 THRCLA_contig3583 3583 THRCLA_contig3584 3584 THRCLA_contig3585 3585 THRCLA_contig3586 3586 THRCLA_contig3587 3587 THRCLA_contig3588 3588 THRCLA_contig3589 3589 THRCLA_contig3590 3590 THRCLA_contig3591 3591 THRCLA_contig3592 3592 THRCLA_contig3593 3593 THRCLA_contig3594 3594 THRCLA_contig3595 3595 THRCLA_contig3596 3596 THRCLA_contig3597 3597 THRCLA_contig3598 3598 THRCLA_contig3599 3599 THRCLA_contig3600 3600 THRCLA_contig3601 3601 THRCLA_contig3602 3602 THRCLA_contig3603 3603 THRCLA_contig3604 3604 THRCLA_contig3605 3605 THRCLA_contig3606 3606 THRCLA_contig3607 3607 THRCLA_contig3608 3608 THRCLA_contig3609 3609 THRCLA_contig3610 3610 THRCLA_contig3611 3611 THRCLA_contig3612 3612 THRCLA_contig3613 3613 THRCLA_contig3614 3614 THRCLA_contig3615 3615 THRCLA_contig3616 3616 THRCLA_contig3617 3617 THRCLA_contig3618 3618 THRCLA_contig3619 3619 THRCLA_contig3620 3620 THRCLA_contig3621 3621 THRCLA_contig3622 3622 THRCLA_contig3623 3623 THRCLA_contig3624 3624 THRCLA_contig3625 3625 THRCLA_contig3626 3626 THRCLA_contig3627 3627 THRCLA_contig3628 3628 THRCLA_contig3629 3629 THRCLA_contig3630 3630 THRCLA_contig3631 3631 THRCLA_contig3632 3632 THRCLA_contig3633 3633 THRCLA_contig3634 3634 THRCLA_contig3635 3635 THRCLA_contig3636 3636 THRCLA_contig3637 3637 THRCLA_contig3638 3638 THRCLA_contig3639 3639 THRCLA_contig3640 3640 THRCLA_contig3641 3641 THRCLA_contig3642 3642 THRCLA_contig3643 3643 THRCLA_contig3644 3644 THRCLA_contig3645 3645 THRCLA_contig3646 3646 THRCLA_contig3647 3647 THRCLA_contig3648 3648 THRCLA_contig3649 3649 THRCLA_contig3650 3650 THRCLA_contig3651 3651 THRCLA_contig3652 3652 THRCLA_contig3653 3653 THRCLA_contig3654 3654 THRCLA_contig3655 3655 THRCLA_contig3656 3656 THRCLA_contig3657 3657 THRCLA_contig3658 3658 THRCLA_contig3659 3659 THRCLA_contig3660 3660 THRCLA_contig3661 3661 THRCLA_contig3662 3662 THRCLA_contig3663 3663 THRCLA_contig3664 3664 THRCLA_contig3665 3665 THRCLA_contig3666 3666 THRCLA_contig3667 3667 THRCLA_contig3668 3668 THRCLA_contig3669 3669 THRCLA_contig3670 3670 THRCLA_contig3671 3671 THRCLA_contig3672 3672 THRCLA_contig3673 3673 THRCLA_contig3674 3674 THRCLA_contig3675 3675 THRCLA_contig3676 3676 THRCLA_contig3677 3677 THRCLA_contig3678 3678 THRCLA_contig3679 3679 THRCLA_contig3680 3680 THRCLA_contig3681 3681 THRCLA_contig3682 3682 THRCLA_contig3683 3683 THRCLA_contig3684 3684 THRCLA_contig3685 3685 THRCLA_contig3686 3686 THRCLA_contig3687 3687 THRCLA_contig3688 3688 THRCLA_contig3689 3689 THRCLA_contig3690 3690 THRCLA_contig3691 3691 THRCLA_contig3692 3692 THRCLA_contig3693 3693 THRCLA_contig3694 3694 THRCLA_contig3695 3695 THRCLA_contig3696 3696 THRCLA_contig3697 3697 THRCLA_contig3698 3698 THRCLA_contig3699 3699 THRCLA_contig3700 3700 THRCLA_contig3701 3701 THRCLA_contig3702 3702 THRCLA_contig3703 3703 THRCLA_contig3704 3704 THRCLA_contig3705 3705 THRCLA_contig3706 3706 THRCLA_contig3707 3707 THRCLA_contig3708 3708 THRCLA_contig3709 3709 THRCLA_contig3710 3710 THRCLA_contig3711 3711 THRCLA_contig3712 3712 THRCLA_contig3713 3713 THRCLA_contig3714 3714 THRCLA_contig3715 3715 THRCLA_contig3716 3716 THRCLA_contig3717 3717 THRCLA_contig3718 3718 THRCLA_contig3719 3719 THRCLA_contig3720 3720 THRCLA_contig3721 3721 THRCLA_contig3722 3722 THRCLA_contig3723 3723 THRCLA_contig3724 3724 THRCLA_contig3725 3725 THRCLA_contig3726 3726 THRCLA_contig3727 3727 THRCLA_contig3728 3728 THRCLA_contig3729 3729 THRCLA_contig3730 3730 THRCLA_contig3731 3731 THRCLA_contig3732 3732 THRCLA_contig3733 3733 THRCLA_contig3734 3734 THRCLA_contig3735 3735 THRCLA_contig3736 3736 THRCLA_contig3737 3737 THRCLA_contig3738 3738 THRCLA_contig3739 3739 THRCLA_contig3740 3740 THRCLA_contig3741 3741 THRCLA_contig3742 3742 THRCLA_contig3743 3743 THRCLA_contig3744 3744 THRCLA_contig3745 3745 THRCLA_contig3746 3746 THRCLA_contig3747 3747 THRCLA_contig3748 3748 THRCLA_contig3749 3749 THRCLA_contig3750 3750 THRCLA_contig3751 3751 THRCLA_contig3752 3752 THRCLA_contig3753 3753 THRCLA_contig3754 3754 THRCLA_contig3755 3755 THRCLA_contig3756 3756 THRCLA_contig3757 3757 THRCLA_contig3758 3758 THRCLA_contig3759 3759 THRCLA_contig3760 3760 THRCLA_contig3761 3761 THRCLA_contig3762 3762 THRCLA_contig3763 3763 THRCLA_contig3764 3764 THRCLA_contig3765 3765 THRCLA_contig3766 3766 THRCLA_contig3767 3767 THRCLA_contig3768 3768 THRCLA_contig3769 3769 THRCLA_contig3770 3770 THRCLA_contig3771 3771 THRCLA_contig3772 3772 THRCLA_contig3773 3773 THRCLA_contig3774 3774 THRCLA_contig3775 3775 THRCLA_contig3776 3776 THRCLA_contig3777 3777 THRCLA_contig3778 3778 THRCLA_contig3779 3779 THRCLA_contig3780 3780 THRCLA_contig3781 3781 THRCLA_contig3782 3782 THRCLA_contig3783 3783 THRCLA_contig3784 3784 THRCLA_contig3785 3785 THRCLA_contig3786 3786 THRCLA_contig3787 3787 THRCLA_contig3788 3788 THRCLA_contig3789 3789 THRCLA_contig3790 3790 THRCLA_contig3791 3791 THRCLA_contig3792 3792 THRCLA_contig3793 3793 THRCLA_contig3794 3794 THRCLA_contig3795 3795 THRCLA_contig3796 3796 THRCLA_contig3797 3797 THRCLA_contig3798 3798 THRCLA_contig3799 3799 THRCLA_contig3800 3800 THRCLA_contig3801 3801 THRCLA_contig3802 3802 THRCLA_contig3803 3803 THRCLA_contig3804 3804 THRCLA_contig3805 3805 THRCLA_contig3806 3806 THRCLA_contig3807 3807 THRCLA_contig3808 3808 THRCLA_contig3809 3809 THRCLA_contig3810 3810 THRCLA_contig3811 3811 THRCLA_contig3812 3812 THRCLA_contig3813 3813 THRCLA_contig3814 3814 THRCLA_contig3815 3815 THRCLA_contig3816 3816 THRCLA_contig3817 3817 THRCLA_contig3818 3818 THRCLA_contig3819 3819 THRCLA_contig3820 3820 THRCLA_contig3821 3821 THRCLA_contig3822 3822 THRCLA_contig3823 3823 THRCLA_contig3824 3824 THRCLA_contig3825 3825 THRCLA_contig3826 3826 THRCLA_contig3827 3827 THRCLA_contig3828 3828 THRCLA_contig3829 3829 THRCLA_contig3830 3830 THRCLA_contig3831 3831 THRCLA_contig3832 3832 THRCLA_contig3833 3833 THRCLA_contig3834 3834 THRCLA_contig3835 3835 THRCLA_contig3836 3836 THRCLA_contig3837 3837 THRCLA_contig3838 3838 THRCLA_contig3839 3839 THRCLA_contig3840 3840 THRCLA_contig3841 3841 THRCLA_contig3842 3842 THRCLA_contig3843 3843 THRCLA_contig3844 3844 THRCLA_contig3845 3845 THRCLA_contig3846 3846 THRCLA_contig3847 3847 THRCLA_contig3848 3848 THRCLA_contig3849 3849 THRCLA_contig3850 3850 THRCLA_contig3851 3851 THRCLA_contig3852 3852 THRCLA_contig3853 3853 THRCLA_contig3854 3854 THRCLA_contig3855 3855 THRCLA_contig3856 3856 THRCLA_contig3857 3857 THRCLA_contig3858 3858 THRCLA_contig3859 3859 THRCLA_contig3860 3860 THRCLA_contig3861 3861 THRCLA_contig3862 3862 THRCLA_contig3863 3863 THRCLA_contig3864 3864 THRCLA_contig3865 3865 THRCLA_contig3866 3866 THRCLA_contig3867 3867 THRCLA_contig3868 3868 THRCLA_contig3869 3869 THRCLA_contig3870 3870 THRCLA_contig3871 3871 THRCLA_contig3872 3872 THRCLA_contig3873 3873 THRCLA_contig3874 3874 THRCLA_contig3875 3875 THRCLA_contig3876 3876 THRCLA_contig3877 3877 THRCLA_contig3878 3878 THRCLA_contig3879 3879 THRCLA_contig3880 3880 THRCLA_contig3881 3881 THRCLA_contig3882 3882 THRCLA_contig3883 3883 THRCLA_contig3884 3884 THRCLA_contig3885 3885 THRCLA_contig3886 3886 THRCLA_contig3887 3887 THRCLA_contig3888 3888 THRCLA_contig3889 3889 THRCLA_contig3890 3890 THRCLA_contig3891 3891 THRCLA_contig3892 3892 THRCLA_contig3893 3893 THRCLA_contig3894 3894 THRCLA_contig3895 3895 THRCLA_contig3896 3896 THRCLA_contig3897 3897 THRCLA_contig3898 3898 THRCLA_contig3899 3899 THRCLA_contig3900 3900 THRCLA_contig3901 3901 THRCLA_contig3902 3902 THRCLA_contig3903 3903 THRCLA_contig3904 3904 THRCLA_contig3905 3905 THRCLA_contig3906 3906 THRCLA_contig3907 3907 THRCLA_contig3908 3908 THRCLA_contig3909 3909 THRCLA_contig3910 3910 THRCLA_contig3911 3911 THRCLA_contig3912 3912 THRCLA_contig3913 3913 THRCLA_contig3914 3914 THRCLA_contig3915 3915 THRCLA_contig3916 3916 THRCLA_contig3917 3917 THRCLA_contig3918 3918 THRCLA_contig3919 3919 THRCLA_contig3920 3920 THRCLA_contig3921 3921 THRCLA_contig3922 3922 THRCLA_contig3923 3923 THRCLA_contig3924 3924 THRCLA_contig3925 3925 THRCLA_contig3926 3926 THRCLA_contig3927 3927 THRCLA_contig3928 3928 THRCLA_contig3929 3929 THRCLA_contig3930 3930 THRCLA_contig3931 3931 THRCLA_contig3932 3932 THRCLA_contig3933 3933 THRCLA_contig3934 3934 THRCLA_contig3935 3935 THRCLA_contig3936 3936 THRCLA_contig3937 3937 THRCLA_contig3938 3938 THRCLA_contig3939 3939 THRCLA_contig3940 3940 THRCLA_contig3941 3941 THRCLA_contig3942 3942 THRCLA_contig3943 3943 THRCLA_contig3944 3944 THRCLA_contig3945 3945 THRCLA_contig3946 3946 THRCLA_contig3947 3947 THRCLA_contig3948 3948 THRCLA_contig3949 3949 THRCLA_contig3950 3950 THRCLA_contig3951 3951 THRCLA_contig3952 3952 THRCLA_contig3953 3953 THRCLA_contig3954 3954 THRCLA_contig3955 3955 THRCLA_contig3956 3956 THRCLA_contig3957 3957 THRCLA_contig3958 3958 THRCLA_contig3959 3959 THRCLA_contig3960 3960 THRCLA_contig3961 3961 THRCLA_contig3962 3962 THRCLA_contig3963 3963 THRCLA_contig3964 3964 THRCLA_contig3965 3965 THRCLA_contig3966 3966 THRCLA_contig3967 3967 THRCLA_contig3968 3968 THRCLA_contig3969 3969 THRCLA_contig3970 3970 THRCLA_contig3971 3971 THRCLA_contig3972 3972 THRCLA_contig3973 3973 THRCLA_contig3974 3974 THRCLA_contig3975 3975 THRCLA_contig3976 3976 THRCLA_contig3977 3977 THRCLA_contig3978 3978 THRCLA_contig3979 3979 THRCLA_contig3980 3980 THRCLA_contig3981 3981 THRCLA_contig3982 3982 THRCLA_contig3983 3983 THRCLA_contig3984 3984 THRCLA_contig3985 3985 THRCLA_contig3986 3986 THRCLA_contig3987 3987 THRCLA_contig3988 3988 THRCLA_contig3989 3989 THRCLA_contig3990 3990 THRCLA_contig3991 3991 THRCLA_contig3992 3992 THRCLA_contig3993 3993 THRCLA_contig3994 3994 THRCLA_contig3995 3995 THRCLA_contig3996 3996 THRCLA_contig3997 3997 THRCLA_contig3998 3998 THRCLA_contig3999 3999 THRCLA_contig4000 4000 THRCLA_contig4001 4001 THRCLA_contig4002 4002 THRCLA_contig4003 4003 THRCLA_contig4004 4004 THRCLA_contig4005 4005 THRCLA_contig4006 4006 THRCLA_contig4007 4007 THRCLA_contig4008 4008 THRCLA_contig4009 4009 THRCLA_contig4010 4010 THRCLA_contig4011 4011 THRCLA_contig4012 4012 THRCLA_contig4013 4013 THRCLA_contig4014 4014 THRCLA_contig4015 4015 THRCLA_contig4016 4016 THRCLA_contig4017 4017 THRCLA_contig4018 4018 THRCLA_contig4019 4019 THRCLA_contig4020 4020 THRCLA_contig4021 4021 THRCLA_contig4022 4022 THRCLA_contig4023 4023 THRCLA_contig4024 4024 THRCLA_contig4025 4025 THRCLA_contig4026 4026 THRCLA_contig4027 4027 THRCLA_contig4028 4028 THRCLA_contig4029 4029 THRCLA_contig4030 4030 THRCLA_contig4031 4031 THRCLA_contig4032 4032 THRCLA_contig4033 4033 THRCLA_contig4034 4034 THRCLA_contig4035 4035 THRCLA_contig4036 4036 THRCLA_contig4037 4037 THRCLA_contig4038 4038 THRCLA_contig4039 4039 THRCLA_contig4040 4040 THRCLA_contig4041 4041 THRCLA_contig4042 4042 THRCLA_contig4043 4043 THRCLA_contig4044 4044 THRCLA_contig4045 4045 THRCLA_contig4046 4046 THRCLA_contig4047 4047 THRCLA_contig4048 4048 THRCLA_contig4049 4049 THRCLA_contig4050 4050 THRCLA_contig4051 4051 THRCLA_contig4052 4052 THRCLA_contig4053 4053 THRCLA_contig4054 4054 THRCLA_contig4055 4055 THRCLA_contig4056 4056 THRCLA_contig4057 4057 THRCLA_contig4058 4058 THRCLA_contig4059 4059 THRCLA_contig4060 4060 THRCLA_contig4061 4061 THRCLA_contig4062 4062 THRCLA_contig4063 4063 THRCLA_contig4064 4064 THRCLA_contig4065 4065 THRCLA_contig4066 4066 THRCLA_contig4067 4067 THRCLA_contig4068 4068 THRCLA_contig4069 4069 THRCLA_contig4070 4070 THRCLA_contig4071 4071 THRCLA_contig4072 4072 THRCLA_contig4073 4073 THRCLA_contig4074 4074 THRCLA_contig4075 4075 THRCLA_contig4076 4076 THRCLA_contig4077 4077 THRCLA_contig4078 4078 THRCLA_contig4079 4079 THRCLA_contig4080 4080 THRCLA_contig4081 4081 THRCLA_contig4082 4082 THRCLA_contig4083 4083 THRCLA_contig4084 4084 THRCLA_contig4085 4085 THRCLA_contig4086 4086 THRCLA_contig4087 4087 THRCLA_contig4088 4088 THRCLA_contig4089 4089 THRCLA_contig4090 4090 THRCLA_contig4091 4091 THRCLA_contig4092 4092 THRCLA_contig4093 4093 THRCLA_contig4094 4094 THRCLA_contig4095 4095 THRCLA_contig4096 4096 THRCLA_contig4097 4097 THRCLA_contig4098 4098 THRCLA_contig4099 4099 THRCLA_contig4100 4100 THRCLA_contig4101 4101 THRCLA_contig4102 4102 THRCLA_contig4103 4103 THRCLA_contig4104 4104 THRCLA_contig4105 4105 THRCLA_contig4106 4106 THRCLA_contig4107 4107 THRCLA_contig4108 4108 THRCLA_contig4109 4109 THRCLA_contig4110 4110 THRCLA_contig4111 4111 THRCLA_contig4112 4112 THRCLA_contig4113 4113 THRCLA_contig4114 4114 THRCLA_contig4115 4115 THRCLA_contig4116 4116 THRCLA_contig4117 4117 THRCLA_contig4118 4118 THRCLA_contig4119 4119 THRCLA_contig4120 4120 THRCLA_contig4121 4121 THRCLA_contig4122 4122 THRCLA_contig4123 4123 THRCLA_contig4124 4124 THRCLA_contig4125 4125 THRCLA_contig4126 4126 THRCLA_contig4127 4127 THRCLA_contig4128 4128 THRCLA_contig4129 4129 THRCLA_contig4130 4130 THRCLA_contig4131 4131 THRCLA_contig4132 4132 THRCLA_contig4133 4133 THRCLA_contig4134 4134 THRCLA_contig4135 4135 THRCLA_contig4136 4136 THRCLA_contig4137 4137 THRCLA_contig4138 4138 THRCLA_contig4139 4139 THRCLA_contig4140 4140 THRCLA_contig4141 4141 THRCLA_contig4142 4142 THRCLA_contig4143 4143 THRCLA_contig4144 4144 THRCLA_contig4145 4145 THRCLA_contig4146 4146 THRCLA_contig4147 4147 THRCLA_contig4148 4148 THRCLA_contig4149 4149 THRCLA_contig4150 4150 THRCLA_contig4151 4151 THRCLA_contig4152 4152 THRCLA_contig4153 4153 THRCLA_contig4154 4154 THRCLA_contig4155 4155 THRCLA_contig4156 4156 THRCLA_contig4157 4157 THRCLA_contig4158 4158 THRCLA_contig4159 4159 THRCLA_contig4160 4160 THRCLA_contig4161 4161 THRCLA_contig4162 4162 THRCLA_contig4163 4163 THRCLA_contig4164 4164 THRCLA_contig4165 4165 THRCLA_contig4166 4166 THRCLA_contig4167 4167 THRCLA_contig4168 4168 THRCLA_contig4169 4169 THRCLA_contig4170 4170 THRCLA_contig4171 4171 THRCLA_contig4172 4172 THRCLA_contig4173 4173 THRCLA_contig4174 4174 THRCLA_contig4175 4175 THRCLA_contig4176 4176 THRCLA_contig4177 4177 THRCLA_contig4178 4178 THRCLA_contig4179 4179 THRCLA_contig4180 4180 THRCLA_contig4181 4181 THRCLA_contig4182 4182 THRCLA_contig4183 4183 THRCLA_contig4184 4184 THRCLA_contig4185 4185 THRCLA_contig4186 4186 THRCLA_contig4187 4187 THRCLA_contig4188 4188 THRCLA_contig4189 4189 THRCLA_contig4190 4190 THRCLA_contig4191 4191 THRCLA_contig4192 4192 THRCLA_contig4193 4193 THRCLA_contig4194 4194 THRCLA_contig4195 4195 THRCLA_contig4196 4196 THRCLA_contig4197 4197 THRCLA_contig4198 4198 THRCLA_contig4199 4199 THRCLA_contig4200 4200 THRCLA_contig4201 4201 THRCLA_contig4202 4202 THRCLA_contig4203 4203 THRCLA_contig4204 4204 THRCLA_contig4205 4205 THRCLA_contig4206 4206 THRCLA_contig4207 4207 THRCLA_contig4208 4208 THRCLA_contig4209 4209 THRCLA_contig4210 4210 THRCLA_contig4211 4211 THRCLA_contig4212 4212 THRCLA_contig4213 4213 THRCLA_contig4214 4214 THRCLA_contig4215 4215 THRCLA_contig4216 4216 THRCLA_contig4217 4217 THRCLA_contig4218 4218 THRCLA_contig4219 4219 THRCLA_contig4220 4220 THRCLA_contig4221 4221 THRCLA_contig4222 4222 THRCLA_contig4223 4223 THRCLA_contig4224 4224 THRCLA_contig4225 4225 THRCLA_contig4226 4226 THRCLA_contig4227 4227 THRCLA_contig4228 4228 THRCLA_contig4229 4229 THRCLA_contig4230 4230 THRCLA_contig4231 4231 THRCLA_contig4232 4232 THRCLA_contig4233 4233 THRCLA_contig4234 4234 THRCLA_contig4235 4235 THRCLA_contig4236 4236 THRCLA_contig4237 4237 THRCLA_contig4238 4238 THRCLA_contig4239 4239 THRCLA_contig4240 4240 THRCLA_contig4241 4241 THRCLA_contig4242 4242 THRCLA_contig4243 4243 THRCLA_contig4244 4244 THRCLA_contig4245 4245 THRCLA_contig4246 4246 THRCLA_contig4247 4247 THRCLA_contig4248 4248 THRCLA_contig4249 4249 THRCLA_contig4250 4250 THRCLA_contig4251 4251 THRCLA_contig4252 4252 THRCLA_contig4253 4253 THRCLA_contig4254 4254 THRCLA_contig4255 4255 THRCLA_contig4256 4256 THRCLA_contig4257 4257 THRCLA_contig4258 4258 THRCLA_contig4259 4259 THRCLA_contig4260 4260 THRCLA_contig4261 4261 THRCLA_contig4262 4262 THRCLA_contig4263 4263 THRCLA_contig4264 4264 THRCLA_contig4265 4265 THRCLA_contig4266 4266 THRCLA_contig4267 4267 THRCLA_contig4268 4268 THRCLA_contig4269 4269 THRCLA_contig4270 4270 THRCLA_contig4271 4271 THRCLA_contig4272 4272 THRCLA_contig4273 4273 THRCLA_contig4274 4274 THRCLA_contig4275 4275 THRCLA_contig4276 4276 THRCLA_contig4277 4277 THRCLA_contig4278 4278 THRCLA_contig4279 4279 THRCLA_contig4280 4280 THRCLA_contig4281 4281 THRCLA_contig4282 4282 THRCLA_contig4283 4283 THRCLA_contig4284 4284 THRCLA_contig4285 4285 THRCLA_contig4286 4286 THRCLA_contig4287 4287 THRCLA_contig4288 4288 THRCLA_contig4289 4289 THRCLA_contig4290 4290 THRCLA_contig4291 4291 THRCLA_contig4292 4292 THRCLA_contig4293 4293 THRCLA_contig4294 4294 THRCLA_contig4295 4295 THRCLA_contig4296 4296 THRCLA_contig4297 4297 THRCLA_contig4298 4298 THRCLA_contig4299 4299 THRCLA_contig4300 4300 THRCLA_contig4301 4301 THRCLA_contig4302 4302 THRCLA_contig4303 4303 THRCLA_contig4304 4304 THRCLA_contig4305 4305 THRCLA_contig4306 4306 THRCLA_contig4307 4307 THRCLA_contig4308 4308 THRCLA_contig4309 4309 THRCLA_contig4310 4310 THRCLA_contig4311 4311 THRCLA_contig4312 4312 THRCLA_contig4313 4313 THRCLA_contig4314 4314 THRCLA_contig4315 4315 THRCLA_contig4316 4316 THRCLA_contig4317 4317 THRCLA_contig4318 4318 THRCLA_contig4319 4319 THRCLA_contig4320 4320 THRCLA_contig4321 4321 THRCLA_contig4322 4322 THRCLA_contig4323 4323 THRCLA_contig4324 4324 THRCLA_contig4325 4325 THRCLA_contig4326 4326 THRCLA_contig4327 4327 THRCLA_contig4328 4328 THRCLA_contig4329 4329 THRCLA_contig4330 4330 THRCLA_contig4331 4331 THRCLA_contig4332 4332 THRCLA_contig4333 4333 THRCLA_contig4334 4334 THRCLA_contig4335 4335 THRCLA_contig4336 4336 THRCLA_contig4337 4337 THRCLA_contig4338 4338 THRCLA_contig4339 4339 THRCLA_contig4340 4340 THRCLA_contig4341 4341 THRCLA_contig4342 4342 THRCLA_contig4343 4343 THRCLA_contig4344 4344 THRCLA_contig4345 4345 THRCLA_contig4346 4346 THRCLA_contig4347 4347 THRCLA_contig4348 4348 THRCLA_contig4349 4349 THRCLA_contig4350 4350 THRCLA_contig4351 4351 THRCLA_contig4352 4352 THRCLA_contig4353 4353 THRCLA_contig4354 4354 THRCLA_contig4355 4355 THRCLA_contig4356 4356 THRCLA_contig4357 4357 THRCLA_contig4358 4358 THRCLA_contig4359 4359 THRCLA_contig4360 4360 THRCLA_contig4361 4361 THRCLA_contig4362 4362 THRCLA_contig4363 4363 THRCLA_contig4364 4364 THRCLA_contig4365 4365 THRCLA_contig4366 4366 THRCLA_contig4367 4367 THRCLA_contig4368 4368 THRCLA_contig4369 4369 THRCLA_contig4370 4370 THRCLA_contig4371 4371 THRCLA_contig4372 4372 THRCLA_contig4373 4373 THRCLA_contig4374 4374 THRCLA_contig4375 4375 THRCLA_contig4376 4376 THRCLA_contig4377 4377 THRCLA_contig4378 4378 THRCLA_contig4379 4379 THRCLA_contig4380 4380 THRCLA_contig4381 4381 THRCLA_contig4382 4382 THRCLA_contig4383 4383 THRCLA_contig4384 4384 THRCLA_contig4385 4385 THRCLA_contig4386 4386 THRCLA_contig4387 4387 THRCLA_contig4388 4388 THRCLA_contig4389 4389 THRCLA_contig4390 4390 THRCLA_contig4391 4391 THRCLA_contig4392 4392 THRCLA_contig4393 4393 THRCLA_contig4394 4394 THRCLA_contig4395 4395 THRCLA_contig4396 4396 THRCLA_contig4397 4397 THRCLA_contig4398 4398 THRCLA_contig4399 4399 THRCLA_contig4400 4400 THRCLA_contig4401 4401 THRCLA_contig4402 4402 THRCLA_contig4403 4403 THRCLA_contig4404 4404 THRCLA_contig4405 4405 THRCLA_contig4406 4406 THRCLA_contig4407 4407 THRCLA_contig4408 4408 THRCLA_contig4409 4409 THRCLA_contig4410 4410 THRCLA_contig4411 4411 THRCLA_contig4412 4412 THRCLA_contig4413 4413 THRCLA_contig4414 4414 THRCLA_contig4415 4415 THRCLA_contig4416 4416 THRCLA_contig4417 4417 THRCLA_contig4418 4418 THRCLA_contig4419 4419 THRCLA_contig4420 4420 THRCLA_contig4421 4421 THRCLA_contig4422 4422 THRCLA_contig4423 4423 THRCLA_contig4424 4424 THRCLA_contig4425 4425 THRCLA_contig4426 4426 THRCLA_contig4427 4427 THRCLA_contig4428 4428 THRCLA_contig4429 4429 THRCLA_contig4430 4430 THRCLA_contig4431 4431 THRCLA_contig4432 4432 THRCLA_contig4433 4433 THRCLA_contig4434 4434 THRCLA_contig4435 4435 THRCLA_contig4436 4436 THRCLA_contig4437 4437 THRCLA_contig4438 4438 THRCLA_contig4439 4439 THRCLA_contig4440 4440 THRCLA_contig4441 4441 THRCLA_contig4442 4442 THRCLA_contig4443 4443 THRCLA_contig4444 4444 THRCLA_contig4445 4445 THRCLA_contig4446 4446 THRCLA_contig4447 4447 THRCLA_contig4448 4448 THRCLA_contig4449 4449 THRCLA_contig4450 4450 THRCLA_contig4451 4451 THRCLA_contig4452 4452 THRCLA_contig4453 4453 THRCLA_contig4454 4454 THRCLA_contig4455 4455 THRCLA_contig4456 4456 THRCLA_contig4457 4457 THRCLA_contig4458 4458 THRCLA_contig4459 4459 THRCLA_contig4460 4460 THRCLA_contig4461 4461 THRCLA_contig4462 4462 THRCLA_contig4463 4463 THRCLA_contig4464 4464 THRCLA_contig4465 4465 THRCLA_contig4466 4466 THRCLA_contig4467 4467 THRCLA_contig4468 4468 THRCLA_contig4469 4469 THRCLA_contig4470 4470 THRCLA_contig4471 4471 THRCLA_contig4472 4472 THRCLA_contig4473 4473 THRCLA_contig4474 4474 THRCLA_contig4475 4475 THRCLA_contig4476 4476 THRCLA_contig4477 4477 THRCLA_contig4478 4478 THRCLA_contig4479 4479 THRCLA_contig4480 4480 THRCLA_contig4481 4481 THRCLA_contig4482 4482 THRCLA_contig4483 4483 THRCLA_contig4484 4484 THRCLA_contig4485 4485 THRCLA_contig4486 4486 THRCLA_contig4487 4487 THRCLA_contig4488 4488 THRCLA_contig4489 4489 THRCLA_contig4490 4490 THRCLA_contig4491 4491 THRCLA_contig4492 4492 THRCLA_contig4493 4493 THRCLA_contig4494 4494 THRCLA_contig4495 4495 THRCLA_contig4496 4496 THRCLA_contig4497 4497 THRCLA_contig4498 4498 THRCLA_contig4499 4499 THRCLA_contig4500 4500 THRCLA_contig4501 4501 THRCLA_contig4502 4502 THRCLA_contig4503 4503 THRCLA_contig4504 4504 THRCLA_contig4505 4505 THRCLA_contig4506 4506 THRCLA_contig4507 4507 THRCLA_contig4508 4508 THRCLA_contig4509 4509 THRCLA_contig4510 4510 THRCLA_contig4511 4511 THRCLA_contig4512 4512 THRCLA_contig4513 4513 THRCLA_contig4514 4514 THRCLA_contig4515 4515 THRCLA_contig4516 4516 THRCLA_contig4517 4517 THRCLA_contig4518 4518 THRCLA_contig4519 4519 THRCLA_contig4520 4520 THRCLA_contig4521 4521 THRCLA_contig4522 4522 THRCLA_contig4523 4523 THRCLA_contig4524 4524 THRCLA_contig4525 4525 THRCLA_contig4526 4526 THRCLA_contig4527 4527 THRCLA_contig4528 4528 THRCLA_contig4529 4529 THRCLA_contig4530 4530 THRCLA_contig4531 4531 THRCLA_contig4532 4532 THRCLA_contig4533 4533 THRCLA_contig4534 4534 THRCLA_contig4535 4535 THRCLA_contig4536 4536 THRCLA_contig4537 4537 THRCLA_contig4538 4538 THRCLA_contig4539 4539 THRCLA_contig4540 4540 THRCLA_contig4541 4541 THRCLA_contig4542 4542 THRCLA_contig4543 4543 THRCLA_contig4544 4544 THRCLA_contig4545 4545 THRCLA_contig4546 4546 THRCLA_contig4547 4547 THRCLA_contig4548 4548 THRCLA_contig4549 4549 THRCLA_contig4550 4550 THRCLA_contig4551 4551 THRCLA_contig4552 4552 THRCLA_contig4553 4553 THRCLA_contig4554 4554 THRCLA_contig4555 4555 THRCLA_contig4556 4556 THRCLA_contig4557 4557 THRCLA_contig4558 4558 THRCLA_contig4559 4559 THRCLA_contig4560 4560 THRCLA_contig4561 4561 THRCLA_contig4562 4562 THRCLA_contig4563 4563 THRCLA_contig4564 4564 THRCLA_contig4565 4565 THRCLA_contig4566 4566 THRCLA_contig4567 4567 THRCLA_contig4568 4568 THRCLA_contig4569 4569 THRCLA_contig4570 4570 THRCLA_contig4571 4571 THRCLA_contig4572 4572 THRCLA_contig4573 4573 THRCLA_contig4574 4574 THRCLA_contig4575 4575 THRCLA_contig4576 4576 THRCLA_contig4577 4577 THRCLA_contig4578 4578 THRCLA_contig4579 4579 THRCLA_contig4580 4580 THRCLA_contig4581 4581 THRCLA_contig4582 4582 THRCLA_contig4583 4583 THRCLA_contig4584 4584 THRCLA_contig4585 4585 THRCLA_contig4586 4586 THRCLA_contig4587 4587 THRCLA_contig4588 4588 THRCLA_contig4589 4589 THRCLA_contig4590 4590 THRCLA_contig4591 4591 THRCLA_contig4592 4592 THRCLA_contig4593 4593 THRCLA_contig4594 4594 THRCLA_contig4595 4595 THRCLA_contig4596 4596 THRCLA_contig4597 4597 THRCLA_contig4598 4598 THRCLA_contig4599 4599 THRCLA_contig4600 4600 THRCLA_contig4601 4601 THRCLA_contig4602 4602 THRCLA_contig4603 4603 THRCLA_contig4604 4604 THRCLA_contig4605 4605 THRCLA_contig4606 4606 THRCLA_contig4607 4607 THRCLA_contig4608 4608 THRCLA_contig4609 4609 THRCLA_contig4610 4610 THRCLA_contig4611 4611 THRCLA_contig4612 4612 THRCLA_contig4613 4613 THRCLA_contig4614 4614 THRCLA_contig4615 4615 THRCLA_contig4616 4616 THRCLA_contig4617 4617 THRCLA_contig4618 4618 THRCLA_contig4619 4619 THRCLA_contig4620 4620 THRCLA_contig4621 4621 THRCLA_contig4622 4622 THRCLA_contig4623 4623 THRCLA_contig4624 4624 THRCLA_contig4625 4625 THRCLA_contig4626 4626 THRCLA_contig4627 4627 THRCLA_contig4628 4628 THRCLA_contig4629 4629 THRCLA_contig4630 4630 THRCLA_contig4631 4631 THRCLA_contig4632 4632 THRCLA_contig4633 4633 THRCLA_contig4634 4634 THRCLA_contig4635 4635 THRCLA_contig4636 4636 THRCLA_contig4637 4637 THRCLA_contig4638 4638 THRCLA_contig4639 4639 THRCLA_contig4640 4640 THRCLA_contig4641 4641 THRCLA_contig4642 4642 THRCLA_contig4643 4643 THRCLA_contig4644 4644 THRCLA_contig4645 4645 THRCLA_contig4646 4646 THRCLA_contig4647 4647 THRCLA_contig4648 4648 THRCLA_contig4649 4649 THRCLA_contig4650 4650 THRCLA_contig4651 4651 THRCLA_contig4652 4652 THRCLA_contig4653 4653 THRCLA_contig4654 4654 THRCLA_contig4655 4655 THRCLA_contig4656 4656 THRCLA_contig4657 4657 THRCLA_contig4658 4658 THRCLA_contig4659 4659 THRCLA_contig4660 4660 THRCLA_contig4661 4661 THRCLA_contig4662 4662 THRCLA_contig4663 4663 THRCLA_contig4664 4664 THRCLA_contig4665 4665 THRCLA_contig4666 4666 THRCLA_contig4667 4667 THRCLA_contig4668 4668 THRCLA_contig4669 4669 THRCLA_contig4670 4670 THRCLA_contig4671 4671 THRCLA_contig4672 4672 THRCLA_contig4673 4673 THRCLA_contig4674 4674 THRCLA_contig4675 4675 THRCLA_contig4676 4676 THRCLA_contig4677 4677 THRCLA_contig4678 4678 THRCLA_contig4679 4679 THRCLA_contig4680 4680 THRCLA_contig4681 4681 THRCLA_contig4682 4682 THRCLA_contig4683 4683 THRCLA_contig4684 4684 THRCLA_contig4685 4685 THRCLA_contig4686 4686 THRCLA_contig4687 4687 THRCLA_contig4688 4688 THRCLA_contig4689 4689 THRCLA_contig4690 4690 THRCLA_contig4691 4691 THRCLA_contig4692 4692 THRCLA_contig4693 4693 THRCLA_contig4694 4694 THRCLA_contig4695 4695 THRCLA_contig4696 4696 THRCLA_contig4697 4697 THRCLA_contig4698 4698 THRCLA_contig4699 4699 THRCLA_contig4700 4700 THRCLA_contig4701 4701 THRCLA_contig4702 4702 THRCLA_contig4703 4703 THRCLA_contig4704 4704 THRCLA_contig4705 4705 THRCLA_contig4706 4706 THRCLA_contig4707 4707 THRCLA_contig4708 4708 THRCLA_contig4709 4709 THRCLA_contig4710 4710 THRCLA_contig4711 4711 THRCLA_contig4712 4712 THRCLA_contig4713 4713 THRCLA_contig4714 4714 THRCLA_contig4715 4715 THRCLA_contig4716 4716 THRCLA_contig4717 4717 THRCLA_contig4718 4718 THRCLA_contig4719 4719 THRCLA_contig4720 4720 THRCLA_contig4721 4721 THRCLA_contig4722 4722 THRCLA_contig4723 4723 THRCLA_contig4724 4724 THRCLA_contig4725 4725 THRCLA_contig4726 4726 THRCLA_contig4727 4727 THRCLA_contig4728 4728 THRCLA_contig4729 4729 THRCLA_contig4730 4730 THRCLA_contig4731 4731 THRCLA_contig4732 4732 THRCLA_contig4733 4733 THRCLA_contig4734 4734 THRCLA_contig4735 4735 THRCLA_contig4736 4736 THRCLA_contig4737 4737 THRCLA_contig4738 4738 THRCLA_contig4739 4739 THRCLA_contig4740 4740 THRCLA_contig4741 4741 THRCLA_contig4742 4742 THRCLA_contig4743 4743 THRCLA_contig4744 4744 THRCLA_contig4745 4745 THRCLA_contig4746 4746 THRCLA_contig4747 4747 THRCLA_contig4748 4748 THRCLA_contig4749 4749 THRCLA_contig4750 4750 THRCLA_contig4751 4751 THRCLA_contig4752 4752 THRCLA_contig4753 4753 THRCLA_contig4754 4754 THRCLA_contig4755 4755 THRCLA_contig4756 4756 THRCLA_contig4757 4757 THRCLA_contig4758 4758 THRCLA_contig4759 4759 THRCLA_contig4760 4760 THRCLA_contig4761 4761 THRCLA_contig4762 4762 THRCLA_contig4763 4763 THRCLA_contig4764 4764 THRCLA_contig4765 4765 THRCLA_contig4766 4766 THRCLA_contig4767 4767 THRCLA_contig4768 4768 THRCLA_contig4769 4769 THRCLA_contig4770 4770 THRCLA_contig4771 4771 THRCLA_contig4772 4772 THRCLA_contig4773 4773 THRCLA_contig4774 4774 THRCLA_contig4775 4775 THRCLA_contig4776 4776 THRCLA_contig4777 4777 THRCLA_contig4778 4778 THRCLA_contig4779 4779 THRCLA_contig4780 4780 THRCLA_contig4781 4781 THRCLA_contig4782 4782 THRCLA_contig4783 4783 THRCLA_contig4784 4784 THRCLA_contig4785 4785 THRCLA_contig4786 4786 THRCLA_contig4787 4787 THRCLA_contig4788 4788 THRCLA_contig4789 4789 THRCLA_contig4790 4790 THRCLA_contig4791 4791 THRCLA_contig4792 4792 THRCLA_contig4793 4793 THRCLA_contig4794 4794 THRCLA_contig4795 4795 THRCLA_contig4796 4796 THRCLA_contig4797 4797 THRCLA_contig4798 4798 THRCLA_contig4799 4799 THRCLA_contig4800 4800 THRCLA_contig4801 4801 THRCLA_contig4802 4802 THRCLA_contig4803 4803 THRCLA_contig4804 4804 THRCLA_contig4805 4805 THRCLA_contig4806 4806 THRCLA_contig4807 4807 THRCLA_contig4808 4808 THRCLA_contig4809 4809 THRCLA_contig4810 4810 THRCLA_contig4811 4811 THRCLA_contig4812 4812 THRCLA_contig4813 4813 THRCLA_contig4814 4814 THRCLA_contig4815 4815 THRCLA_contig4816 4816 THRCLA_contig4817 4817 THRCLA_contig4818 4818 THRCLA_contig4819 4819 THRCLA_contig4820 4820 THRCLA_contig4821 4821 THRCLA_contig4822 4822 THRCLA_contig4823 4823 THRCLA_contig4824 4824 THRCLA_contig4825 4825 THRCLA_contig4826 4826 THRCLA_contig4827 4827 THRCLA_contig4828 4828 THRCLA_contig4829 4829 THRCLA_contig4830 4830 THRCLA_contig4831 4831 THRCLA_contig4832 4832 THRCLA_contig4833 4833 THRCLA_contig4834 4834 THRCLA_contig4835 4835 THRCLA_contig4836 4836 THRCLA_contig4837 4837 THRCLA_contig4838 4838 THRCLA_contig4839 4839 THRCLA_contig4840 4840 THRCLA_contig4841 4841 THRCLA_contig4842 4842 THRCLA_contig4843 4843 THRCLA_contig4844 4844 THRCLA_contig4845 4845 THRCLA_contig4846 4846 THRCLA_contig4847 4847 THRCLA_contig4848 4848 THRCLA_contig4849 4849 THRCLA_contig4850 4850 THRCLA_contig4851 4851 THRCLA_contig4852 4852 THRCLA_contig4853 4853 THRCLA_contig4854 4854 THRCLA_contig4855 4855 THRCLA_contig4856 4856 THRCLA_contig4857 4857 THRCLA_contig4858 4858 THRCLA_contig4859 4859 THRCLA_contig4860 4860 THRCLA_contig4861 4861 THRCLA_contig4862 4862 THRCLA_contig4863 4863 THRCLA_contig4864 4864 THRCLA_contig4865 4865 THRCLA_contig4866 4866 THRCLA_contig4867 4867 THRCLA_contig4868 4868 THRCLA_contig4869 4869 THRCLA_contig4870 4870 THRCLA_contig4871 4871 THRCLA_contig4872 4872 THRCLA_contig4873 4873 THRCLA_contig4874 4874 THRCLA_contig4875 4875 THRCLA_contig4876 4876 THRCLA_contig4877 4877 THRCLA_contig4878 4878 THRCLA_contig4879 4879 THRCLA_contig4880 4880 THRCLA_contig4881 4881 THRCLA_contig4882 4882 THRCLA_contig4883 4883 THRCLA_contig4884 4884 THRCLA_contig4885 4885 THRCLA_contig4886 4886 THRCLA_contig4887 4887 THRCLA_contig4888 4888 THRCLA_contig4889 4889 THRCLA_contig4890 4890 THRCLA_contig4891 4891 THRCLA_contig4892 4892 THRCLA_contig4893 4893 THRCLA_contig4894 4894 THRCLA_contig4895 4895 THRCLA_contig4896 4896 THRCLA_contig4897 4897 THRCLA_contig4898 4898 THRCLA_contig4899 4899 THRCLA_contig4900 4900 THRCLA_contig4901 4901 THRCLA_contig4902 4902 THRCLA_contig4903 4903 THRCLA_contig4904 4904 THRCLA_contig4905 4905 THRCLA_contig4906 4906 THRCLA_contig4907 4907 THRCLA_contig4908 4908 THRCLA_contig4909 4909 THRCLA_contig4910 4910 THRCLA_contig4911 4911 THRCLA_contig4912 4912 THRCLA_contig4913 4913 THRCLA_contig4914 4914 THRCLA_contig4915 4915 THRCLA_contig4916 4916 THRCLA_contig4917 4917 THRCLA_contig4918 4918 THRCLA_contig4919 4919 THRCLA_contig4920 4920 THRCLA_contig4921 4921 THRCLA_contig4922 4922 THRCLA_contig4923 4923 THRCLA_contig4924 4924 THRCLA_contig4925 4925 THRCLA_contig4926 4926 THRCLA_contig4927 4927 THRCLA_contig4928 4928 THRCLA_contig4929 4929 THRCLA_contig4930 4930 THRCLA_contig4931 4931 THRCLA_contig4932 4932 THRCLA_contig4933 4933 THRCLA_contig4934 4934 THRCLA_contig4935 4935 THRCLA_contig4936 4936 THRCLA_contig4937 4937 THRCLA_contig4938 4938 THRCLA_contig4939 4939 THRCLA_contig4940 4940 THRCLA_contig4941 4941 THRCLA_contig4942 4942 THRCLA_contig4943 4943 THRCLA_contig4944 4944 THRCLA_contig4945 4945 THRCLA_contig4946 4946 THRCLA_contig4947 4947 THRCLA_contig4948 4948 THRCLA_contig4949 4949 THRCLA_contig4950 4950 THRCLA_contig4951 4951 THRCLA_contig4952 4952 THRCLA_contig4953 4953 THRCLA_contig4954 4954 THRCLA_contig4955 4955 THRCLA_contig4956 4956 THRCLA_contig4957 4957 THRCLA_contig4958 4958 THRCLA_contig4959 4959 THRCLA_contig4960 4960 THRCLA_contig4961 4961 THRCLA_contig4962 4962 THRCLA_contig4963 4963 THRCLA_contig4964 4964 THRCLA_contig4965 4965 THRCLA_contig4966 4966 THRCLA_contig4967 4967 THRCLA_contig4968 4968 THRCLA_contig4969 4969 THRCLA_contig4970 4970 THRCLA_contig4971 4971 THRCLA_contig4972 4972 THRCLA_contig4973 4973 THRCLA_contig4974 4974 THRCLA_contig4975 4975 THRCLA_contig4976 4976 THRCLA_contig4977 4977 THRCLA_contig4978 4978 THRCLA_contig4979 4979 THRCLA_contig4980 4980 THRCLA_contig4981 4981 THRCLA_contig4982 4982 THRCLA_contig4983 4983 THRCLA_contig4984 4984 THRCLA_contig4985 4985 THRCLA_contig4986 4986 THRCLA_contig4987 4987 THRCLA_contig4988 4988 THRCLA_contig4989 4989 THRCLA_contig4990 4990 THRCLA_contig4991 4991 THRCLA_contig4992 4992 THRCLA_contig4993 4993 THRCLA_contig4994 4994 THRCLA_contig4995 4995 THRCLA_contig4996 4996 THRCLA_contig4997 4997 THRCLA_contig4998 4998 THRCLA_contig4999 4999 THRCLA_contig5000 5000 THRCLA_contig5001 5001 THRCLA_contig5002 5002 THRCLA_contig5003 5003 THRCLA_contig5004 5004 THRCLA_contig5005 5005 THRCLA_contig5006 5006 THRCLA_contig5007 5007 THRCLA_contig5008 5008 THRCLA_contig5009 5009 THRCLA_contig5010 5010 THRCLA_contig5011 5011 THRCLA_contig5012 5012 THRCLA_contig5013 5013 THRCLA_contig5014 5014 THRCLA_contig5015 5015 THRCLA_contig5016 5016 THRCLA_contig5017 5017 THRCLA_contig5018 5018 THRCLA_contig5019 5019 THRCLA_contig5020 5020 THRCLA_contig5021 5021 THRCLA_contig5022 5022 THRCLA_contig5023 5023 THRCLA_contig5024 5024 THRCLA_contig5025 5025 THRCLA_contig5026 5026 THRCLA_contig5027 5027 THRCLA_contig5028 5028 THRCLA_contig5029 5029 THRCLA_contig5030 5030 THRCLA_contig5031 5031 THRCLA_contig5032 5032 THRCLA_contig5033 5033 THRCLA_contig5034 5034 THRCLA_contig5035 5035 THRCLA_contig5036 5036 THRCLA_contig5037 5037 THRCLA_contig5038 5038 THRCLA_contig5039 5039 THRCLA_contig5040 5040 THRCLA_contig5041 5041 THRCLA_contig5042 5042 THRCLA_contig5043 5043 THRCLA_contig5044 5044 THRCLA_contig5045 5045 THRCLA_contig5046 5046 THRCLA_contig5047 5047 THRCLA_contig5048 5048 THRCLA_contig5049 5049 THRCLA_contig5050 5050 THRCLA_contig5051 5051 THRCLA_contig5052 5052 THRCLA_contig5053 5053 THRCLA_contig5054 5054 THRCLA_contig5055 5055 THRCLA_contig5056 5056 THRCLA_contig5057 5057 THRCLA_contig5058 5058 THRCLA_contig5059 5059 THRCLA_contig5060 5060 THRCLA_contig5061 5061 THRCLA_contig5062 5062 THRCLA_contig5063 5063 THRCLA_contig5064 5064 THRCLA_contig5065 5065 THRCLA_contig5066 5066 THRCLA_contig5067 5067 THRCLA_contig5068 5068 THRCLA_contig5069 5069 THRCLA_contig5070 5070 THRCLA_contig5071 5071 THRCLA_contig5072 5072 THRCLA_contig5073 5073 THRCLA_contig5074 5074 THRCLA_contig5075 5075 THRCLA_contig5076 5076 THRCLA_contig5077 5077 THRCLA_contig5078 5078 THRCLA_contig5079 5079 THRCLA_contig5080 5080 THRCLA_contig5081 5081 THRCLA_contig5082 5082 THRCLA_contig5083 5083 THRCLA_contig5084 5084 THRCLA_contig5085 5085 THRCLA_contig5086 5086 THRCLA_contig5087 5087 THRCLA_contig5088 5088 THRCLA_contig5089 5089 THRCLA_contig5090 5090 THRCLA_contig5091 5091 THRCLA_contig5092 5092 THRCLA_contig5093 5093 THRCLA_contig5094 5094 THRCLA_contig5095 5095 THRCLA_contig5096 5096 THRCLA_contig5097 5097 THRCLA_contig5098 5098 THRCLA_contig5099 5099 THRCLA_contig5100 5100 THRCLA_contig5101 5101 THRCLA_contig5102 5102 THRCLA_contig5103 5103 THRCLA_contig5104 5104 THRCLA_contig5105 5105 THRCLA_contig5106 5106 THRCLA_contig5107 5107 THRCLA_contig5108 5108 THRCLA_contig5109 5109 THRCLA_contig5110 5110 THRCLA_contig5111 5111 THRCLA_contig5112 5112 THRCLA_contig5113 5113 THRCLA_contig5114 5114 THRCLA_contig5115 5115 THRCLA_contig5116 5116 THRCLA_contig5117 5117 THRCLA_contig5118 5118 THRCLA_contig5119 5119 THRCLA_contig5120 5120 THRCLA_contig5121 5121 THRCLA_contig5122 5122 THRCLA_contig5123 5123 THRCLA_contig5124 5124 THRCLA_contig5125 5125 THRCLA_contig5126 5126 THRCLA_contig5127 5127 THRCLA_contig5128 5128 THRCLA_contig5129 5129 THRCLA_contig5130 5130 THRCLA_contig5131 5131 THRCLA_contig5132 5132 THRCLA_contig5133 5133 THRCLA_contig5134 5134 THRCLA_contig5135 5135 THRCLA_contig5136 5136 THRCLA_contig5137 5137 THRCLA_contig5138 5138 THRCLA_contig5139 5139 THRCLA_contig5140 5140 THRCLA_contig5141 5141 THRCLA_contig5142 5142 THRCLA_contig5143 5143 THRCLA_contig5144 5144 THRCLA_contig5145 5145 THRCLA_contig5146 5146 THRCLA_contig5147 5147 THRCLA_contig5148 5148 THRCLA_contig5149 5149 THRCLA_contig5150 5150 THRCLA_contig5151 5151 THRCLA_contig5152 5152 THRCLA_contig5153 5153 THRCLA_contig5154 5154 THRCLA_contig5155 5155 THRCLA_contig5156 5156 THRCLA_contig5157 5157 THRCLA_contig5158 5158 THRCLA_contig5159 5159 THRCLA_contig5160 5160 THRCLA_contig5161 5161 THRCLA_contig5162 5162 THRCLA_contig5163 5163 THRCLA_contig5164 5164 THRCLA_contig5165 5165 THRCLA_contig5166 5166 THRCLA_contig5167 5167 THRCLA_contig5168 5168 THRCLA_contig5169 5169 THRCLA_contig5170 5170 THRCLA_contig5171 5171 THRCLA_contig5172 5172 THRCLA_contig5173 5173 THRCLA_contig5174 5174 THRCLA_contig5175 5175 THRCLA_contig5176 5176 THRCLA_contig5177 5177 THRCLA_contig5178 5178 THRCLA_contig5179 5179 THRCLA_contig5180 5180 THRCLA_contig5181 5181 THRCLA_contig5182 5182 THRCLA_contig5183 5183 THRCLA_contig5184 5184 THRCLA_contig5185 5185 THRCLA_contig5186 5186 THRCLA_contig5187 5187 THRCLA_contig5188 5188 THRCLA_contig5189 5189 THRCLA_contig5190 5190 THRCLA_contig5191 5191 THRCLA_contig5192 5192 THRCLA_contig5193 5193 THRCLA_contig5194 5194 THRCLA_contig5195 5195 THRCLA_contig5196 5196 THRCLA_contig5197 5197 THRCLA_contig5198 5198 THRCLA_contig5199 5199 THRCLA_contig5200 5200 THRCLA_contig5201 5201 THRCLA_contig5202 5202 THRCLA_contig5203 5203 THRCLA_contig5204 5204 THRCLA_contig5205 5205 THRCLA_contig5206 5206 THRCLA_contig5207 5207 THRCLA_contig5208 5208 THRCLA_contig5209 5209 THRCLA_contig5210 5210 THRCLA_contig5211 5211 THRCLA_contig5212 5212 THRCLA_contig5213 5213 THRCLA_contig5214 5214 THRCLA_contig5215 5215 THRCLA_contig5216 5216 THRCLA_contig5217 5217 THRCLA_contig5218 5218 THRCLA_contig5219 5219 THRCLA_contig5220 5220 THRCLA_contig5221 5221 THRCLA_contig5222 5222 THRCLA_contig5223 5223 THRCLA_contig5224 5224 THRCLA_contig5225 5225 THRCLA_contig5226 5226 THRCLA_contig5227 5227 THRCLA_contig5228 5228 THRCLA_contig5229 5229 THRCLA_contig5230 5230 THRCLA_contig5231 5231 THRCLA_contig5232 5232 THRCLA_contig5233 5233 THRCLA_contig5234 5234 THRCLA_contig5235 5235 THRCLA_contig5236 5236 THRCLA_contig5237 5237 THRCLA_contig5238 5238 THRCLA_contig5239 5239 THRCLA_contig5240 5240 THRCLA_contig5241 5241 THRCLA_contig5242 5242 THRCLA_contig5243 5243 THRCLA_contig5244 5244 THRCLA_contig5245 5245 THRCLA_contig5246 5246 THRCLA_contig5247 5247 THRCLA_contig5248 5248 THRCLA_contig5249 5249 THRCLA_contig5250 5250 THRCLA_contig5251 5251 THRCLA_contig5252 5252 THRCLA_contig5253 5253 THRCLA_contig5254 5254 THRCLA_contig5255 5255 THRCLA_contig5256 5256 THRCLA_contig5257 5257 THRCLA_contig5258 5258 THRCLA_contig5259 5259 THRCLA_contig5260 5260 THRCLA_contig5261 5261 THRCLA_contig5262 5262 THRCLA_contig5263 5263 THRCLA_contig5264 5264 THRCLA_contig5265 5265 THRCLA_contig5266 5266 THRCLA_contig5267 5267 THRCLA_contig5268 5268 THRCLA_contig5269 5269 THRCLA_contig5270 5270 THRCLA_contig5271 5271 THRCLA_contig5272 5272 THRCLA_contig5273 5273 THRCLA_contig5274 5274 THRCLA_contig5275 5275 THRCLA_contig5276 5276 THRCLA_contig5277 5277 THRCLA_contig5278 5278 THRCLA_contig5279 5279 THRCLA_contig5280 5280 THRCLA_contig5281 5281 THRCLA_contig5282 5282 THRCLA_contig5283 5283 THRCLA_contig5284 5284 THRCLA_contig5285 5285 THRCLA_contig5286 5286 THRCLA_contig5287 5287 THRCLA_contig5288 5288 THRCLA_contig5289 5289 THRCLA_contig5290 5290 THRCLA_contig5291 5291 THRCLA_contig5292 5292 THRCLA_contig5293 5293 THRCLA_contig5294 5294 THRCLA_contig5295 5295 THRCLA_contig5296 5296 THRCLA_contig5297 5297 THRCLA_contig5298 5298 THRCLA_contig5299 5299 THRCLA_contig5300 5300 THRCLA_contig5301 5301 THRCLA_contig5302 5302 THRCLA_contig5303 5303 THRCLA_contig5304 5304 THRCLA_contig5305 5305 THRCLA_contig5306 5306 THRCLA_contig5307 5307 THRCLA_contig5308 5308 THRCLA_contig5309 5309 THRCLA_contig5310 5310 THRCLA_contig5311 5311 THRCLA_contig5312 5312 THRCLA_contig5313 5313 THRCLA_contig5314 5314 THRCLA_contig5315 5315 THRCLA_contig5316 5316 THRCLA_contig5317 5317 THRCLA_contig5318 5318 THRCLA_contig5319 5319 THRCLA_contig5320 5320 THRCLA_contig5321 5321 THRCLA_contig5322 5322 THRCLA_contig5323 5323 THRCLA_contig5324 5324 THRCLA_contig5325 5325 THRCLA_contig5326 5326 THRCLA_contig5327 5327 THRCLA_contig5328 5328 THRCLA_contig5329 5329 THRCLA_contig5330 5330 THRCLA_contig5331 5331 THRCLA_contig5332 5332 THRCLA_contig5333 5333 THRCLA_contig5334 5334 THRCLA_contig5335 5335 THRCLA_contig5336 5336 THRCLA_contig5337 5337 THRCLA_contig5338 5338 From ianmisner at my.uri.edu Tue Sep 25 06:31:23 2012 From: ianmisner at my.uri.edu (Ian Misner) Date: Tue, 25 Sep 2012 08:31:23 -0400 Subject: [maker-devel] Problem with maker_map_ids Message-ID: <0FCB8ACD-35A0-4ED8-BAE2-02C2621E3F65@my.uri.edu> Hello, I'm trying to create human friendly ids and I'm getting an error when I use the -sort_file option. Without the sort file it runs fine just not numbered from the first contig. I have had some programers at our cluster look at the script and they attempted a fix but it did not work. They mentioned the script was "buggy" so this might be part of the problem. I've attached the error as well as the sort file. I can send more files if necessary. Thanks for you time. Cheers Ian $ maker_map_ids --prefix THRCLA_ --justify 5 --sort_order 34112_sort.txt 34112_3June11Ass.gff > 34112_3June11Ass_named.txt Can't use string ("34112_sort.txt") as a HASH ref while "strict refs" in use at /gpfs/runtime/opt/maker/2.10/maker/bin/maker_map_ids line 311, <$IN> line 499186. -------------- next part -------------- THRCLA_contig1 1 THRCLA_contig2 2 THRCLA_contig3 3 THRCLA_contig4 4 THRCLA_contig5 5 THRCLA_contig6 6 THRCLA_contig7 7 THRCLA_contig8 8 THRCLA_contig9 9 THRCLA_contig10 10 THRCLA_contig11 11 THRCLA_contig12 12 THRCLA_contig13 13 THRCLA_contig14 14 THRCLA_contig15 15 THRCLA_contig16 16 THRCLA_contig17 17 THRCLA_contig18 18 THRCLA_contig19 19 THRCLA_contig20 20 THRCLA_contig21 21 THRCLA_contig22 22 THRCLA_contig23 23 THRCLA_contig24 24 THRCLA_contig25 25 THRCLA_contig26 26 THRCLA_contig27 27 THRCLA_contig28 28 THRCLA_contig29 29 THRCLA_contig30 30 THRCLA_contig31 31 THRCLA_contig32 32 THRCLA_contig33 33 THRCLA_contig34 34 THRCLA_contig35 35 THRCLA_contig36 36 THRCLA_contig37 37 THRCLA_contig38 38 THRCLA_contig39 39 THRCLA_contig40 40 THRCLA_contig41 41 THRCLA_contig42 42 THRCLA_contig43 43 THRCLA_contig44 44 THRCLA_contig45 45 THRCLA_contig46 46 THRCLA_contig47 47 THRCLA_contig48 48 THRCLA_contig49 49 THRCLA_contig50 50 THRCLA_contig51 51 THRCLA_contig52 52 THRCLA_contig53 53 THRCLA_contig54 54 THRCLA_contig55 55 THRCLA_contig56 56 THRCLA_contig57 57 THRCLA_contig58 58 THRCLA_contig59 59 THRCLA_contig60 60 THRCLA_contig61 61 THRCLA_contig62 62 THRCLA_contig63 63 THRCLA_contig64 64 THRCLA_contig65 65 THRCLA_contig66 66 THRCLA_contig67 67 THRCLA_contig68 68 THRCLA_contig69 69 THRCLA_contig70 70 THRCLA_contig71 71 THRCLA_contig72 72 THRCLA_contig73 73 THRCLA_contig74 74 THRCLA_contig75 75 THRCLA_contig76 76 THRCLA_contig77 77 THRCLA_contig78 78 THRCLA_contig79 79 THRCLA_contig80 80 THRCLA_contig81 81 THRCLA_contig82 82 THRCLA_contig83 83 THRCLA_contig84 84 THRCLA_contig85 85 THRCLA_contig86 86 THRCLA_contig87 87 THRCLA_contig88 88 THRCLA_contig89 89 THRCLA_contig90 90 THRCLA_contig91 91 THRCLA_contig92 92 THRCLA_contig93 93 THRCLA_contig94 94 THRCLA_contig95 95 THRCLA_contig96 96 THRCLA_contig97 97 THRCLA_contig98 98 THRCLA_contig99 99 THRCLA_contig100 100 THRCLA_contig101 101 THRCLA_contig102 102 THRCLA_contig103 103 THRCLA_contig104 104 THRCLA_contig105 105 THRCLA_contig106 106 THRCLA_contig107 107 THRCLA_contig108 108 THRCLA_contig109 109 THRCLA_contig110 110 THRCLA_contig111 111 THRCLA_contig112 112 THRCLA_contig113 113 THRCLA_contig114 114 THRCLA_contig115 115 THRCLA_contig116 116 THRCLA_contig117 117 THRCLA_contig118 118 THRCLA_contig119 119 THRCLA_contig120 120 THRCLA_contig121 121 THRCLA_contig122 122 THRCLA_contig123 123 THRCLA_contig124 124 THRCLA_contig125 125 THRCLA_contig126 126 THRCLA_contig127 127 THRCLA_contig128 128 THRCLA_contig129 129 THRCLA_contig130 130 THRCLA_contig131 131 THRCLA_contig132 132 THRCLA_contig133 133 THRCLA_contig134 134 THRCLA_contig135 135 THRCLA_contig136 136 THRCLA_contig137 137 THRCLA_contig138 138 THRCLA_contig139 139 THRCLA_contig140 140 THRCLA_contig141 141 THRCLA_contig142 142 THRCLA_contig143 143 THRCLA_contig144 144 THRCLA_contig145 145 THRCLA_contig146 146 THRCLA_contig147 147 THRCLA_contig148 148 THRCLA_contig149 149 THRCLA_contig150 150 THRCLA_contig151 151 THRCLA_contig152 152 THRCLA_contig153 153 THRCLA_contig154 154 THRCLA_contig155 155 THRCLA_contig156 156 THRCLA_contig157 157 THRCLA_contig158 158 THRCLA_contig159 159 THRCLA_contig160 160 THRCLA_contig161 161 THRCLA_contig162 162 THRCLA_contig163 163 THRCLA_contig164 164 THRCLA_contig165 165 THRCLA_contig166 166 THRCLA_contig167 167 THRCLA_contig168 168 THRCLA_contig169 169 THRCLA_contig170 170 THRCLA_contig171 171 THRCLA_contig172 172 THRCLA_contig173 173 THRCLA_contig174 174 THRCLA_contig175 175 THRCLA_contig176 176 THRCLA_contig177 177 THRCLA_contig178 178 THRCLA_contig179 179 THRCLA_contig180 180 THRCLA_contig181 181 THRCLA_contig182 182 THRCLA_contig183 183 THRCLA_contig184 184 THRCLA_contig185 185 THRCLA_contig186 186 THRCLA_contig187 187 THRCLA_contig188 188 THRCLA_contig189 189 THRCLA_contig190 190 THRCLA_contig191 191 THRCLA_contig192 192 THRCLA_contig193 193 THRCLA_contig194 194 THRCLA_contig195 195 THRCLA_contig196 196 THRCLA_contig197 197 THRCLA_contig198 198 THRCLA_contig199 199 THRCLA_contig200 200 THRCLA_contig201 201 THRCLA_contig202 202 THRCLA_contig203 203 THRCLA_contig204 204 THRCLA_contig205 205 THRCLA_contig206 206 THRCLA_contig207 207 THRCLA_contig208 208 THRCLA_contig209 209 THRCLA_contig210 210 THRCLA_contig211 211 THRCLA_contig212 212 THRCLA_contig213 213 THRCLA_contig214 214 THRCLA_contig215 215 THRCLA_contig216 216 THRCLA_contig217 217 THRCLA_contig218 218 THRCLA_contig219 219 THRCLA_contig220 220 THRCLA_contig221 221 THRCLA_contig222 222 THRCLA_contig223 223 THRCLA_contig224 224 THRCLA_contig225 225 THRCLA_contig226 226 THRCLA_contig227 227 THRCLA_contig228 228 THRCLA_contig229 229 THRCLA_contig230 230 THRCLA_contig231 231 THRCLA_contig232 232 THRCLA_contig233 233 THRCLA_contig234 234 THRCLA_contig235 235 THRCLA_contig236 236 THRCLA_contig237 237 THRCLA_contig238 238 THRCLA_contig239 239 THRCLA_contig240 240 THRCLA_contig241 241 THRCLA_contig242 242 THRCLA_contig243 243 THRCLA_contig244 244 THRCLA_contig245 245 THRCLA_contig246 246 THRCLA_contig247 247 THRCLA_contig248 248 THRCLA_contig249 249 THRCLA_contig250 250 THRCLA_contig251 251 THRCLA_contig252 252 THRCLA_contig253 253 THRCLA_contig254 254 THRCLA_contig255 255 THRCLA_contig256 256 THRCLA_contig257 257 THRCLA_contig258 258 THRCLA_contig259 259 THRCLA_contig260 260 THRCLA_contig261 261 THRCLA_contig262 262 THRCLA_contig263 263 THRCLA_contig264 264 THRCLA_contig265 265 THRCLA_contig266 266 THRCLA_contig267 267 THRCLA_contig268 268 THRCLA_contig269 269 THRCLA_contig270 270 THRCLA_contig271 271 THRCLA_contig272 272 THRCLA_contig273 273 THRCLA_contig274 274 THRCLA_contig275 275 THRCLA_contig276 276 THRCLA_contig277 277 THRCLA_contig278 278 THRCLA_contig279 279 THRCLA_contig280 280 THRCLA_contig281 281 THRCLA_contig282 282 THRCLA_contig283 283 THRCLA_contig284 284 THRCLA_contig285 285 THRCLA_contig286 286 THRCLA_contig287 287 THRCLA_contig288 288 THRCLA_contig289 289 THRCLA_contig290 290 THRCLA_contig291 291 THRCLA_contig292 292 THRCLA_contig293 293 THRCLA_contig294 294 THRCLA_contig295 295 THRCLA_contig296 296 THRCLA_contig297 297 THRCLA_contig298 298 THRCLA_contig299 299 THRCLA_contig300 300 THRCLA_contig301 301 THRCLA_contig302 302 THRCLA_contig303 303 THRCLA_contig304 304 THRCLA_contig305 305 THRCLA_contig306 306 THRCLA_contig307 307 THRCLA_contig308 308 THRCLA_contig309 309 THRCLA_contig310 310 THRCLA_contig311 311 THRCLA_contig312 312 THRCLA_contig313 313 THRCLA_contig314 314 THRCLA_contig315 315 THRCLA_contig316 316 THRCLA_contig317 317 THRCLA_contig318 318 THRCLA_contig319 319 THRCLA_contig320 320 THRCLA_contig321 321 THRCLA_contig322 322 THRCLA_contig323 323 THRCLA_contig324 324 THRCLA_contig325 325 THRCLA_contig326 326 THRCLA_contig327 327 THRCLA_contig328 328 THRCLA_contig329 329 THRCLA_contig330 330 THRCLA_contig331 331 THRCLA_contig332 332 THRCLA_contig333 333 THRCLA_contig334 334 THRCLA_contig335 335 THRCLA_contig336 336 THRCLA_contig337 337 THRCLA_contig338 338 THRCLA_contig339 339 THRCLA_contig340 340 THRCLA_contig341 341 THRCLA_contig342 342 THRCLA_contig343 343 THRCLA_contig344 344 THRCLA_contig345 345 THRCLA_contig346 346 THRCLA_contig347 347 THRCLA_contig348 348 THRCLA_contig349 349 THRCLA_contig350 350 THRCLA_contig351 351 THRCLA_contig352 352 THRCLA_contig353 353 THRCLA_contig354 354 THRCLA_contig355 355 THRCLA_contig356 356 THRCLA_contig357 357 THRCLA_contig358 358 THRCLA_contig359 359 THRCLA_contig360 360 THRCLA_contig361 361 THRCLA_contig362 362 THRCLA_contig363 363 THRCLA_contig364 364 THRCLA_contig365 365 THRCLA_contig366 366 THRCLA_contig367 367 THRCLA_contig368 368 THRCLA_contig369 369 THRCLA_contig370 370 THRCLA_contig371 371 THRCLA_contig372 372 THRCLA_contig373 373 THRCLA_contig374 374 THRCLA_contig375 375 THRCLA_contig376 376 THRCLA_contig377 377 THRCLA_contig378 378 THRCLA_contig379 379 THRCLA_contig380 380 THRCLA_contig381 381 THRCLA_contig382 382 THRCLA_contig383 383 THRCLA_contig384 384 THRCLA_contig385 385 THRCLA_contig386 386 THRCLA_contig387 387 THRCLA_contig388 388 THRCLA_contig389 389 THRCLA_contig390 390 THRCLA_contig391 391 THRCLA_contig392 392 THRCLA_contig393 393 THRCLA_contig394 394 THRCLA_contig395 395 THRCLA_contig396 396 THRCLA_contig397 397 THRCLA_contig398 398 THRCLA_contig399 399 THRCLA_contig400 400 THRCLA_contig401 401 THRCLA_contig402 402 THRCLA_contig403 403 THRCLA_contig404 404 THRCLA_contig405 405 THRCLA_contig406 406 THRCLA_contig407 407 THRCLA_contig408 408 THRCLA_contig409 409 THRCLA_contig410 410 THRCLA_contig411 411 THRCLA_contig412 412 THRCLA_contig413 413 THRCLA_contig414 414 THRCLA_contig415 415 THRCLA_contig416 416 THRCLA_contig417 417 THRCLA_contig418 418 THRCLA_contig419 419 THRCLA_contig420 420 THRCLA_contig421 421 THRCLA_contig422 422 THRCLA_contig423 423 THRCLA_contig424 424 THRCLA_contig425 425 THRCLA_contig426 426 THRCLA_contig427 427 THRCLA_contig428 428 THRCLA_contig429 429 THRCLA_contig430 430 THRCLA_contig431 431 THRCLA_contig432 432 THRCLA_contig433 433 THRCLA_contig434 434 THRCLA_contig435 435 THRCLA_contig436 436 THRCLA_contig437 437 THRCLA_contig438 438 THRCLA_contig439 439 THRCLA_contig440 440 THRCLA_contig441 441 THRCLA_contig442 442 THRCLA_contig443 443 THRCLA_contig444 444 THRCLA_contig445 445 THRCLA_contig446 446 THRCLA_contig447 447 THRCLA_contig448 448 THRCLA_contig449 449 THRCLA_contig450 450 THRCLA_contig451 451 THRCLA_contig452 452 THRCLA_contig453 453 THRCLA_contig454 454 THRCLA_contig455 455 THRCLA_contig456 456 THRCLA_contig457 457 THRCLA_contig458 458 THRCLA_contig459 459 THRCLA_contig460 460 THRCLA_contig461 461 THRCLA_contig462 462 THRCLA_contig463 463 THRCLA_contig464 464 THRCLA_contig465 465 THRCLA_contig466 466 THRCLA_contig467 467 THRCLA_contig468 468 THRCLA_contig469 469 THRCLA_contig470 470 THRCLA_contig471 471 THRCLA_contig472 472 THRCLA_contig473 473 THRCLA_contig474 474 THRCLA_contig475 475 THRCLA_contig476 476 THRCLA_contig477 477 THRCLA_contig478 478 THRCLA_contig479 479 THRCLA_contig480 480 THRCLA_contig481 481 THRCLA_contig482 482 THRCLA_contig483 483 THRCLA_contig484 484 THRCLA_contig485 485 THRCLA_contig486 486 THRCLA_contig487 487 THRCLA_contig488 488 THRCLA_contig489 489 THRCLA_contig490 490 THRCLA_contig491 491 THRCLA_contig492 492 THRCLA_contig493 493 THRCLA_contig494 494 THRCLA_contig495 495 THRCLA_contig496 496 THRCLA_contig497 497 THRCLA_contig498 498 THRCLA_contig499 499 THRCLA_contig500 500 THRCLA_contig501 501 THRCLA_contig502 502 THRCLA_contig503 503 THRCLA_contig504 504 THRCLA_contig505 505 THRCLA_contig506 506 THRCLA_contig507 507 THRCLA_contig508 508 THRCLA_contig509 509 THRCLA_contig510 510 THRCLA_contig511 511 THRCLA_contig512 512 THRCLA_contig513 513 THRCLA_contig514 514 THRCLA_contig515 515 THRCLA_contig516 516 THRCLA_contig517 517 THRCLA_contig518 518 THRCLA_contig519 519 THRCLA_contig520 520 THRCLA_contig521 521 THRCLA_contig522 522 THRCLA_contig523 523 THRCLA_contig524 524 THRCLA_contig525 525 THRCLA_contig526 526 THRCLA_contig527 527 THRCLA_contig528 528 THRCLA_contig529 529 THRCLA_contig530 530 THRCLA_contig531 531 THRCLA_contig532 532 THRCLA_contig533 533 THRCLA_contig534 534 THRCLA_contig535 535 THRCLA_contig536 536 THRCLA_contig537 537 THRCLA_contig538 538 THRCLA_contig539 539 THRCLA_contig540 540 THRCLA_contig541 541 THRCLA_contig542 542 THRCLA_contig543 543 THRCLA_contig544 544 THRCLA_contig545 545 THRCLA_contig546 546 THRCLA_contig547 547 THRCLA_contig548 548 THRCLA_contig549 549 THRCLA_contig550 550 THRCLA_contig551 551 THRCLA_contig552 552 THRCLA_contig553 553 THRCLA_contig554 554 THRCLA_contig555 555 THRCLA_contig556 556 THRCLA_contig557 557 THRCLA_contig558 558 THRCLA_contig559 559 THRCLA_contig560 560 THRCLA_contig561 561 THRCLA_contig562 562 THRCLA_contig563 563 THRCLA_contig564 564 THRCLA_contig565 565 THRCLA_contig566 566 THRCLA_contig567 567 THRCLA_contig568 568 THRCLA_contig569 569 THRCLA_contig570 570 THRCLA_contig571 571 THRCLA_contig572 572 THRCLA_contig573 573 THRCLA_contig574 574 THRCLA_contig575 575 THRCLA_contig576 576 THRCLA_contig577 577 THRCLA_contig578 578 THRCLA_contig579 579 THRCLA_contig580 580 THRCLA_contig581 581 THRCLA_contig582 582 THRCLA_contig583 583 THRCLA_contig584 584 THRCLA_contig585 585 THRCLA_contig586 586 THRCLA_contig587 587 THRCLA_contig588 588 THRCLA_contig589 589 THRCLA_contig590 590 THRCLA_contig591 591 THRCLA_contig592 592 THRCLA_contig593 593 THRCLA_contig594 594 THRCLA_contig595 595 THRCLA_contig596 596 THRCLA_contig597 597 THRCLA_contig598 598 THRCLA_contig599 599 THRCLA_contig600 600 THRCLA_contig601 601 THRCLA_contig602 602 THRCLA_contig603 603 THRCLA_contig604 604 THRCLA_contig605 605 THRCLA_contig606 606 THRCLA_contig607 607 THRCLA_contig608 608 THRCLA_contig609 609 THRCLA_contig610 610 THRCLA_contig611 611 THRCLA_contig612 612 THRCLA_contig613 613 THRCLA_contig614 614 THRCLA_contig615 615 THRCLA_contig616 616 THRCLA_contig617 617 THRCLA_contig618 618 THRCLA_contig619 619 THRCLA_contig620 620 THRCLA_contig621 621 THRCLA_contig622 622 THRCLA_contig623 623 THRCLA_contig624 624 THRCLA_contig625 625 THRCLA_contig626 626 THRCLA_contig627 627 THRCLA_contig628 628 THRCLA_contig629 629 THRCLA_contig630 630 THRCLA_contig631 631 THRCLA_contig632 632 THRCLA_contig633 633 THRCLA_contig634 634 THRCLA_contig635 635 THRCLA_contig636 636 THRCLA_contig637 637 THRCLA_contig638 638 THRCLA_contig639 639 THRCLA_contig640 640 THRCLA_contig641 641 THRCLA_contig642 642 THRCLA_contig643 643 THRCLA_contig644 644 THRCLA_contig645 645 THRCLA_contig646 646 THRCLA_contig647 647 THRCLA_contig648 648 THRCLA_contig649 649 THRCLA_contig650 650 THRCLA_contig651 651 THRCLA_contig652 652 THRCLA_contig653 653 THRCLA_contig654 654 THRCLA_contig655 655 THRCLA_contig656 656 THRCLA_contig657 657 THRCLA_contig658 658 THRCLA_contig659 659 THRCLA_contig660 660 THRCLA_contig661 661 THRCLA_contig662 662 THRCLA_contig663 663 THRCLA_contig664 664 THRCLA_contig665 665 THRCLA_contig666 666 THRCLA_contig667 667 THRCLA_contig668 668 THRCLA_contig669 669 THRCLA_contig670 670 THRCLA_contig671 671 THRCLA_contig672 672 THRCLA_contig673 673 THRCLA_contig674 674 THRCLA_contig675 675 THRCLA_contig676 676 THRCLA_contig677 677 THRCLA_contig678 678 THRCLA_contig679 679 THRCLA_contig680 680 THRCLA_contig681 681 THRCLA_contig682 682 THRCLA_contig683 683 THRCLA_contig684 684 THRCLA_contig685 685 THRCLA_contig686 686 THRCLA_contig687 687 THRCLA_contig688 688 THRCLA_contig689 689 THRCLA_contig690 690 THRCLA_contig691 691 THRCLA_contig692 692 THRCLA_contig693 693 THRCLA_contig694 694 THRCLA_contig695 695 THRCLA_contig696 696 THRCLA_contig697 697 THRCLA_contig698 698 THRCLA_contig699 699 THRCLA_contig700 700 THRCLA_contig701 701 THRCLA_contig702 702 THRCLA_contig703 703 THRCLA_contig704 704 THRCLA_contig705 705 THRCLA_contig706 706 THRCLA_contig707 707 THRCLA_contig708 708 THRCLA_contig709 709 THRCLA_contig710 710 THRCLA_contig711 711 THRCLA_contig712 712 THRCLA_contig713 713 THRCLA_contig714 714 THRCLA_contig715 715 THRCLA_contig716 716 THRCLA_contig717 717 THRCLA_contig718 718 THRCLA_contig719 719 THRCLA_contig720 720 THRCLA_contig721 721 THRCLA_contig722 722 THRCLA_contig723 723 THRCLA_contig724 724 THRCLA_contig725 725 THRCLA_contig726 726 THRCLA_contig727 727 THRCLA_contig728 728 THRCLA_contig729 729 THRCLA_contig730 730 THRCLA_contig731 731 THRCLA_contig732 732 THRCLA_contig733 733 THRCLA_contig734 734 THRCLA_contig735 735 THRCLA_contig736 736 THRCLA_contig737 737 THRCLA_contig738 738 THRCLA_contig739 739 THRCLA_contig740 740 THRCLA_contig741 741 THRCLA_contig742 742 THRCLA_contig743 743 THRCLA_contig744 744 THRCLA_contig745 745 THRCLA_contig746 746 THRCLA_contig747 747 THRCLA_contig748 748 THRCLA_contig749 749 THRCLA_contig750 750 THRCLA_contig751 751 THRCLA_contig752 752 THRCLA_contig753 753 THRCLA_contig754 754 THRCLA_contig755 755 THRCLA_contig756 756 THRCLA_contig757 757 THRCLA_contig758 758 THRCLA_contig759 759 THRCLA_contig760 760 THRCLA_contig761 761 THRCLA_contig762 762 THRCLA_contig763 763 THRCLA_contig764 764 THRCLA_contig765 765 THRCLA_contig766 766 THRCLA_contig767 767 THRCLA_contig768 768 THRCLA_contig769 769 THRCLA_contig770 770 THRCLA_contig771 771 THRCLA_contig772 772 THRCLA_contig773 773 THRCLA_contig774 774 THRCLA_contig775 775 THRCLA_contig776 776 THRCLA_contig777 777 THRCLA_contig778 778 THRCLA_contig779 779 THRCLA_contig780 780 THRCLA_contig781 781 THRCLA_contig782 782 THRCLA_contig783 783 THRCLA_contig784 784 THRCLA_contig785 785 THRCLA_contig786 786 THRCLA_contig787 787 THRCLA_contig788 788 THRCLA_contig789 789 THRCLA_contig790 790 THRCLA_contig791 791 THRCLA_contig792 792 THRCLA_contig793 793 THRCLA_contig794 794 THRCLA_contig795 795 THRCLA_contig796 796 THRCLA_contig797 797 THRCLA_contig798 798 THRCLA_contig799 799 THRCLA_contig800 800 THRCLA_contig801 801 THRCLA_contig802 802 THRCLA_contig803 803 THRCLA_contig804 804 THRCLA_contig805 805 THRCLA_contig806 806 THRCLA_contig807 807 THRCLA_contig808 808 THRCLA_contig809 809 THRCLA_contig810 810 THRCLA_contig811 811 THRCLA_contig812 812 THRCLA_contig813 813 THRCLA_contig814 814 THRCLA_contig815 815 THRCLA_contig816 816 THRCLA_contig817 817 THRCLA_contig818 818 THRCLA_contig819 819 THRCLA_contig820 820 THRCLA_contig821 821 THRCLA_contig822 822 THRCLA_contig823 823 THRCLA_contig824 824 THRCLA_contig825 825 THRCLA_contig826 826 THRCLA_contig827 827 THRCLA_contig828 828 THRCLA_contig829 829 THRCLA_contig830 830 THRCLA_contig831 831 THRCLA_contig832 832 THRCLA_contig833 833 THRCLA_contig834 834 THRCLA_contig835 835 THRCLA_contig836 836 THRCLA_contig837 837 THRCLA_contig838 838 THRCLA_contig839 839 THRCLA_contig840 840 THRCLA_contig841 841 THRCLA_contig842 842 THRCLA_contig843 843 THRCLA_contig844 844 THRCLA_contig845 845 THRCLA_contig846 846 THRCLA_contig847 847 THRCLA_contig848 848 THRCLA_contig849 849 THRCLA_contig850 850 THRCLA_contig851 851 THRCLA_contig852 852 THRCLA_contig853 853 THRCLA_contig854 854 THRCLA_contig855 855 THRCLA_contig856 856 THRCLA_contig857 857 THRCLA_contig858 858 THRCLA_contig859 859 THRCLA_contig860 860 THRCLA_contig861 861 THRCLA_contig862 862 THRCLA_contig863 863 THRCLA_contig864 864 THRCLA_contig865 865 THRCLA_contig866 866 THRCLA_contig867 867 THRCLA_contig868 868 THRCLA_contig869 869 THRCLA_contig870 870 THRCLA_contig871 871 THRCLA_contig872 872 THRCLA_contig873 873 THRCLA_contig874 874 THRCLA_contig875 875 THRCLA_contig876 876 THRCLA_contig877 877 THRCLA_contig878 878 THRCLA_contig879 879 THRCLA_contig880 880 THRCLA_contig881 881 THRCLA_contig882 882 THRCLA_contig883 883 THRCLA_contig884 884 THRCLA_contig885 885 THRCLA_contig886 886 THRCLA_contig887 887 THRCLA_contig888 888 THRCLA_contig889 889 THRCLA_contig890 890 THRCLA_contig891 891 THRCLA_contig892 892 THRCLA_contig893 893 THRCLA_contig894 894 THRCLA_contig895 895 THRCLA_contig896 896 THRCLA_contig897 897 THRCLA_contig898 898 THRCLA_contig899 899 THRCLA_contig900 900 THRCLA_contig901 901 THRCLA_contig902 902 THRCLA_contig903 903 THRCLA_contig904 904 THRCLA_contig905 905 THRCLA_contig906 906 THRCLA_contig907 907 THRCLA_contig908 908 THRCLA_contig909 909 THRCLA_contig910 910 THRCLA_contig911 911 THRCLA_contig912 912 THRCLA_contig913 913 THRCLA_contig914 914 THRCLA_contig915 915 THRCLA_contig916 916 THRCLA_contig917 917 THRCLA_contig918 918 THRCLA_contig919 919 THRCLA_contig920 920 THRCLA_contig921 921 THRCLA_contig922 922 THRCLA_contig923 923 THRCLA_contig924 924 THRCLA_contig925 925 THRCLA_contig926 926 THRCLA_contig927 927 THRCLA_contig928 928 THRCLA_contig929 929 THRCLA_contig930 930 THRCLA_contig931 931 THRCLA_contig932 932 THRCLA_contig933 933 THRCLA_contig934 934 THRCLA_contig935 935 THRCLA_contig936 936 THRCLA_contig937 937 THRCLA_contig938 938 THRCLA_contig939 939 THRCLA_contig940 940 THRCLA_contig941 941 THRCLA_contig942 942 THRCLA_contig943 943 THRCLA_contig944 944 THRCLA_contig945 945 THRCLA_contig946 946 THRCLA_contig947 947 THRCLA_contig948 948 THRCLA_contig949 949 THRCLA_contig950 950 THRCLA_contig951 951 THRCLA_contig952 952 THRCLA_contig953 953 THRCLA_contig954 954 THRCLA_contig955 955 THRCLA_contig956 956 THRCLA_contig957 957 THRCLA_contig958 958 THRCLA_contig959 959 THRCLA_contig960 960 THRCLA_contig961 961 THRCLA_contig962 962 THRCLA_contig963 963 THRCLA_contig964 964 THRCLA_contig965 965 THRCLA_contig966 966 THRCLA_contig967 967 THRCLA_contig968 968 THRCLA_contig969 969 THRCLA_contig970 970 THRCLA_contig971 971 THRCLA_contig972 972 THRCLA_contig973 973 THRCLA_contig974 974 THRCLA_contig975 975 THRCLA_contig976 976 THRCLA_contig977 977 THRCLA_contig978 978 THRCLA_contig979 979 THRCLA_contig980 980 THRCLA_contig981 981 THRCLA_contig982 982 THRCLA_contig983 983 THRCLA_contig984 984 THRCLA_contig985 985 THRCLA_contig986 986 THRCLA_contig987 987 THRCLA_contig988 988 THRCLA_contig989 989 THRCLA_contig990 990 THRCLA_contig991 991 THRCLA_contig992 992 THRCLA_contig993 993 THRCLA_contig994 994 THRCLA_contig995 995 THRCLA_contig996 996 THRCLA_contig997 997 THRCLA_contig998 998 THRCLA_contig999 999 THRCLA_contig1000 1000 THRCLA_contig1001 1001 THRCLA_contig1002 1002 THRCLA_contig1003 1003 THRCLA_contig1004 1004 THRCLA_contig1005 1005 THRCLA_contig1006 1006 THRCLA_contig1007 1007 THRCLA_contig1008 1008 THRCLA_contig1009 1009 THRCLA_contig1010 1010 THRCLA_contig1011 1011 THRCLA_contig1012 1012 THRCLA_contig1013 1013 THRCLA_contig1014 1014 THRCLA_contig1015 1015 THRCLA_contig1016 1016 THRCLA_contig1017 1017 THRCLA_contig1018 1018 THRCLA_contig1019 1019 THRCLA_contig1020 1020 THRCLA_contig1021 1021 THRCLA_contig1022 1022 THRCLA_contig1023 1023 THRCLA_contig1024 1024 THRCLA_contig1025 1025 THRCLA_contig1026 1026 THRCLA_contig1027 1027 THRCLA_contig1028 1028 THRCLA_contig1029 1029 THRCLA_contig1030 1030 THRCLA_contig1031 1031 THRCLA_contig1032 1032 THRCLA_contig1033 1033 THRCLA_contig1034 1034 THRCLA_contig1035 1035 THRCLA_contig1036 1036 THRCLA_contig1037 1037 THRCLA_contig1038 1038 THRCLA_contig1039 1039 THRCLA_contig1040 1040 THRCLA_contig1041 1041 THRCLA_contig1042 1042 THRCLA_contig1043 1043 THRCLA_contig1044 1044 THRCLA_contig1045 1045 THRCLA_contig1046 1046 THRCLA_contig1047 1047 THRCLA_contig1048 1048 THRCLA_contig1049 1049 THRCLA_contig1050 1050 THRCLA_contig1051 1051 THRCLA_contig1052 1052 THRCLA_contig1053 1053 THRCLA_contig1054 1054 THRCLA_contig1055 1055 THRCLA_contig1056 1056 THRCLA_contig1057 1057 THRCLA_contig1058 1058 THRCLA_contig1059 1059 THRCLA_contig1060 1060 THRCLA_contig1061 1061 THRCLA_contig1062 1062 THRCLA_contig1063 1063 THRCLA_contig1064 1064 THRCLA_contig1065 1065 THRCLA_contig1066 1066 THRCLA_contig1067 1067 THRCLA_contig1068 1068 THRCLA_contig1069 1069 THRCLA_contig1070 1070 THRCLA_contig1071 1071 THRCLA_contig1072 1072 THRCLA_contig1073 1073 THRCLA_contig1074 1074 THRCLA_contig1075 1075 THRCLA_contig1076 1076 THRCLA_contig1077 1077 THRCLA_contig1078 1078 THRCLA_contig1079 1079 THRCLA_contig1080 1080 THRCLA_contig1081 1081 THRCLA_contig1082 1082 THRCLA_contig1083 1083 THRCLA_contig1084 1084 THRCLA_contig1085 1085 THRCLA_contig1086 1086 THRCLA_contig1087 1087 THRCLA_contig1088 1088 THRCLA_contig1089 1089 THRCLA_contig1090 1090 THRCLA_contig1091 1091 THRCLA_contig1092 1092 THRCLA_contig1093 1093 THRCLA_contig1094 1094 THRCLA_contig1095 1095 THRCLA_contig1096 1096 THRCLA_contig1097 1097 THRCLA_contig1098 1098 THRCLA_contig1099 1099 THRCLA_contig1100 1100 THRCLA_contig1101 1101 THRCLA_contig1102 1102 THRCLA_contig1103 1103 THRCLA_contig1104 1104 THRCLA_contig1105 1105 THRCLA_contig1106 1106 THRCLA_contig1107 1107 THRCLA_contig1108 1108 THRCLA_contig1109 1109 THRCLA_contig1110 1110 THRCLA_contig1111 1111 THRCLA_contig1112 1112 THRCLA_contig1113 1113 THRCLA_contig1114 1114 THRCLA_contig1115 1115 THRCLA_contig1116 1116 THRCLA_contig1117 1117 THRCLA_contig1118 1118 THRCLA_contig1119 1119 THRCLA_contig1120 1120 THRCLA_contig1121 1121 THRCLA_contig1122 1122 THRCLA_contig1123 1123 THRCLA_contig1124 1124 THRCLA_contig1125 1125 THRCLA_contig1126 1126 THRCLA_contig1127 1127 THRCLA_contig1128 1128 THRCLA_contig1129 1129 THRCLA_contig1130 1130 THRCLA_contig1131 1131 THRCLA_contig1132 1132 THRCLA_contig1133 1133 THRCLA_contig1134 1134 THRCLA_contig1135 1135 THRCLA_contig1136 1136 THRCLA_contig1137 1137 THRCLA_contig1138 1138 THRCLA_contig1139 1139 THRCLA_contig1140 1140 THRCLA_contig1141 1141 THRCLA_contig1142 1142 THRCLA_contig1143 1143 THRCLA_contig1144 1144 THRCLA_contig1145 1145 THRCLA_contig1146 1146 THRCLA_contig1147 1147 THRCLA_contig1148 1148 THRCLA_contig1149 1149 THRCLA_contig1150 1150 THRCLA_contig1151 1151 THRCLA_contig1152 1152 THRCLA_contig1153 1153 THRCLA_contig1154 1154 THRCLA_contig1155 1155 THRCLA_contig1156 1156 THRCLA_contig1157 1157 THRCLA_contig1158 1158 THRCLA_contig1159 1159 THRCLA_contig1160 1160 THRCLA_contig1161 1161 THRCLA_contig1162 1162 THRCLA_contig1163 1163 THRCLA_contig1164 1164 THRCLA_contig1165 1165 THRCLA_contig1166 1166 THRCLA_contig1167 1167 THRCLA_contig1168 1168 THRCLA_contig1169 1169 THRCLA_contig1170 1170 THRCLA_contig1171 1171 THRCLA_contig1172 1172 THRCLA_contig1173 1173 THRCLA_contig1174 1174 THRCLA_contig1175 1175 THRCLA_contig1176 1176 THRCLA_contig1177 1177 THRCLA_contig1178 1178 THRCLA_contig1179 1179 THRCLA_contig1180 1180 THRCLA_contig1181 1181 THRCLA_contig1182 1182 THRCLA_contig1183 1183 THRCLA_contig1184 1184 THRCLA_contig1185 1185 THRCLA_contig1186 1186 THRCLA_contig1187 1187 THRCLA_contig1188 1188 THRCLA_contig1189 1189 THRCLA_contig1190 1190 THRCLA_contig1191 1191 THRCLA_contig1192 1192 THRCLA_contig1193 1193 THRCLA_contig1194 1194 THRCLA_contig1195 1195 THRCLA_contig1196 1196 THRCLA_contig1197 1197 THRCLA_contig1198 1198 THRCLA_contig1199 1199 THRCLA_contig1200 1200 THRCLA_contig1201 1201 THRCLA_contig1202 1202 THRCLA_contig1203 1203 THRCLA_contig1204 1204 THRCLA_contig1205 1205 THRCLA_contig1206 1206 THRCLA_contig1207 1207 THRCLA_contig1208 1208 THRCLA_contig1209 1209 THRCLA_contig1210 1210 THRCLA_contig1211 1211 THRCLA_contig1212 1212 THRCLA_contig1213 1213 THRCLA_contig1214 1214 THRCLA_contig1215 1215 THRCLA_contig1216 1216 THRCLA_contig1217 1217 THRCLA_contig1218 1218 THRCLA_contig1219 1219 THRCLA_contig1220 1220 THRCLA_contig1221 1221 THRCLA_contig1222 1222 THRCLA_contig1223 1223 THRCLA_contig1224 1224 THRCLA_contig1225 1225 THRCLA_contig1226 1226 THRCLA_contig1227 1227 THRCLA_contig1228 1228 THRCLA_contig1229 1229 THRCLA_contig1230 1230 THRCLA_contig1231 1231 THRCLA_contig1232 1232 THRCLA_contig1233 1233 THRCLA_contig1234 1234 THRCLA_contig1235 1235 THRCLA_contig1236 1236 THRCLA_contig1237 1237 THRCLA_contig1238 1238 THRCLA_contig1239 1239 THRCLA_contig1240 1240 THRCLA_contig1241 1241 THRCLA_contig1242 1242 THRCLA_contig1243 1243 THRCLA_contig1244 1244 THRCLA_contig1245 1245 THRCLA_contig1246 1246 THRCLA_contig1247 1247 THRCLA_contig1248 1248 THRCLA_contig1249 1249 THRCLA_contig1250 1250 THRCLA_contig1251 1251 THRCLA_contig1252 1252 THRCLA_contig1253 1253 THRCLA_contig1254 1254 THRCLA_contig1255 1255 THRCLA_contig1256 1256 THRCLA_contig1257 1257 THRCLA_contig1258 1258 THRCLA_contig1259 1259 THRCLA_contig1260 1260 THRCLA_contig1261 1261 THRCLA_contig1262 1262 THRCLA_contig1263 1263 THRCLA_contig1264 1264 THRCLA_contig1265 1265 THRCLA_contig1266 1266 THRCLA_contig1267 1267 THRCLA_contig1268 1268 THRCLA_contig1269 1269 THRCLA_contig1270 1270 THRCLA_contig1271 1271 THRCLA_contig1272 1272 THRCLA_contig1273 1273 THRCLA_contig1274 1274 THRCLA_contig1275 1275 THRCLA_contig1276 1276 THRCLA_contig1277 1277 THRCLA_contig1278 1278 THRCLA_contig1279 1279 THRCLA_contig1280 1280 THRCLA_contig1281 1281 THRCLA_contig1282 1282 THRCLA_contig1283 1283 THRCLA_contig1284 1284 THRCLA_contig1285 1285 THRCLA_contig1286 1286 THRCLA_contig1287 1287 THRCLA_contig1288 1288 THRCLA_contig1289 1289 THRCLA_contig1290 1290 THRCLA_contig1291 1291 THRCLA_contig1292 1292 THRCLA_contig1293 1293 THRCLA_contig1294 1294 THRCLA_contig1295 1295 THRCLA_contig1296 1296 THRCLA_contig1297 1297 THRCLA_contig1298 1298 THRCLA_contig1299 1299 THRCLA_contig1300 1300 THRCLA_contig1301 1301 THRCLA_contig1302 1302 THRCLA_contig1303 1303 THRCLA_contig1304 1304 THRCLA_contig1305 1305 THRCLA_contig1306 1306 THRCLA_contig1307 1307 THRCLA_contig1308 1308 THRCLA_contig1309 1309 THRCLA_contig1310 1310 THRCLA_contig1311 1311 THRCLA_contig1312 1312 THRCLA_contig1313 1313 THRCLA_contig1314 1314 THRCLA_contig1315 1315 THRCLA_contig1316 1316 THRCLA_contig1317 1317 THRCLA_contig1318 1318 THRCLA_contig1319 1319 THRCLA_contig1320 1320 THRCLA_contig1321 1321 THRCLA_contig1322 1322 THRCLA_contig1323 1323 THRCLA_contig1324 1324 THRCLA_contig1325 1325 THRCLA_contig1326 1326 THRCLA_contig1327 1327 THRCLA_contig1328 1328 THRCLA_contig1329 1329 THRCLA_contig1330 1330 THRCLA_contig1331 1331 THRCLA_contig1332 1332 THRCLA_contig1333 1333 THRCLA_contig1334 1334 THRCLA_contig1335 1335 THRCLA_contig1336 1336 THRCLA_contig1337 1337 THRCLA_contig1338 1338 THRCLA_contig1339 1339 THRCLA_contig1340 1340 THRCLA_contig1341 1341 THRCLA_contig1342 1342 THRCLA_contig1343 1343 THRCLA_contig1344 1344 THRCLA_contig1345 1345 THRCLA_contig1346 1346 THRCLA_contig1347 1347 THRCLA_contig1348 1348 THRCLA_contig1349 1349 THRCLA_contig1350 1350 THRCLA_contig1351 1351 THRCLA_contig1352 1352 THRCLA_contig1353 1353 THRCLA_contig1354 1354 THRCLA_contig1355 1355 THRCLA_contig1356 1356 THRCLA_contig1357 1357 THRCLA_contig1358 1358 THRCLA_contig1359 1359 THRCLA_contig1360 1360 THRCLA_contig1361 1361 THRCLA_contig1362 1362 THRCLA_contig1363 1363 THRCLA_contig1364 1364 THRCLA_contig1365 1365 THRCLA_contig1366 1366 THRCLA_contig1367 1367 THRCLA_contig1368 1368 THRCLA_contig1369 1369 THRCLA_contig1370 1370 THRCLA_contig1371 1371 THRCLA_contig1372 1372 THRCLA_contig1373 1373 THRCLA_contig1374 1374 THRCLA_contig1375 1375 THRCLA_contig1376 1376 THRCLA_contig1377 1377 THRCLA_contig1378 1378 THRCLA_contig1379 1379 THRCLA_contig1380 1380 THRCLA_contig1381 1381 THRCLA_contig1382 1382 THRCLA_contig1383 1383 THRCLA_contig1384 1384 THRCLA_contig1385 1385 THRCLA_contig1386 1386 THRCLA_contig1387 1387 THRCLA_contig1388 1388 THRCLA_contig1389 1389 THRCLA_contig1390 1390 THRCLA_contig1391 1391 THRCLA_contig1392 1392 THRCLA_contig1393 1393 THRCLA_contig1394 1394 THRCLA_contig1395 1395 THRCLA_contig1396 1396 THRCLA_contig1397 1397 THRCLA_contig1398 1398 THRCLA_contig1399 1399 THRCLA_contig1400 1400 THRCLA_contig1401 1401 THRCLA_contig1402 1402 THRCLA_contig1403 1403 THRCLA_contig1404 1404 THRCLA_contig1405 1405 THRCLA_contig1406 1406 THRCLA_contig1407 1407 THRCLA_contig1408 1408 THRCLA_contig1409 1409 THRCLA_contig1410 1410 THRCLA_contig1411 1411 THRCLA_contig1412 1412 THRCLA_contig1413 1413 THRCLA_contig1414 1414 THRCLA_contig1415 1415 THRCLA_contig1416 1416 THRCLA_contig1417 1417 THRCLA_contig1418 1418 THRCLA_contig1419 1419 THRCLA_contig1420 1420 THRCLA_contig1421 1421 THRCLA_contig1422 1422 THRCLA_contig1423 1423 THRCLA_contig1424 1424 THRCLA_contig1425 1425 THRCLA_contig1426 1426 THRCLA_contig1427 1427 THRCLA_contig1428 1428 THRCLA_contig1429 1429 THRCLA_contig1430 1430 THRCLA_contig1431 1431 THRCLA_contig1432 1432 THRCLA_contig1433 1433 THRCLA_contig1434 1434 THRCLA_contig1435 1435 THRCLA_contig1436 1436 THRCLA_contig1437 1437 THRCLA_contig1438 1438 THRCLA_contig1439 1439 THRCLA_contig1440 1440 THRCLA_contig1441 1441 THRCLA_contig1442 1442 THRCLA_contig1443 1443 THRCLA_contig1444 1444 THRCLA_contig1445 1445 THRCLA_contig1446 1446 THRCLA_contig1447 1447 THRCLA_contig1448 1448 THRCLA_contig1449 1449 THRCLA_contig1450 1450 THRCLA_contig1451 1451 THRCLA_contig1452 1452 THRCLA_contig1453 1453 THRCLA_contig1454 1454 THRCLA_contig1455 1455 THRCLA_contig1456 1456 THRCLA_contig1457 1457 THRCLA_contig1458 1458 THRCLA_contig1459 1459 THRCLA_contig1460 1460 THRCLA_contig1461 1461 THRCLA_contig1462 1462 THRCLA_contig1463 1463 THRCLA_contig1464 1464 THRCLA_contig1465 1465 THRCLA_contig1466 1466 THRCLA_contig1467 1467 THRCLA_contig1468 1468 THRCLA_contig1469 1469 THRCLA_contig1470 1470 THRCLA_contig1471 1471 THRCLA_contig1472 1472 THRCLA_contig1473 1473 THRCLA_contig1474 1474 THRCLA_contig1475 1475 THRCLA_contig1476 1476 THRCLA_contig1477 1477 THRCLA_contig1478 1478 THRCLA_contig1479 1479 THRCLA_contig1480 1480 THRCLA_contig1481 1481 THRCLA_contig1482 1482 THRCLA_contig1483 1483 THRCLA_contig1484 1484 THRCLA_contig1485 1485 THRCLA_contig1486 1486 THRCLA_contig1487 1487 THRCLA_contig1488 1488 THRCLA_contig1489 1489 THRCLA_contig1490 1490 THRCLA_contig1491 1491 THRCLA_contig1492 1492 THRCLA_contig1493 1493 THRCLA_contig1494 1494 THRCLA_contig1495 1495 THRCLA_contig1496 1496 THRCLA_contig1497 1497 THRCLA_contig1498 1498 THRCLA_contig1499 1499 THRCLA_contig1500 1500 THRCLA_contig1501 1501 THRCLA_contig1502 1502 THRCLA_contig1503 1503 THRCLA_contig1504 1504 THRCLA_contig1505 1505 THRCLA_contig1506 1506 THRCLA_contig1507 1507 THRCLA_contig1508 1508 THRCLA_contig1509 1509 THRCLA_contig1510 1510 THRCLA_contig1511 1511 THRCLA_contig1512 1512 THRCLA_contig1513 1513 THRCLA_contig1514 1514 THRCLA_contig1515 1515 THRCLA_contig1516 1516 THRCLA_contig1517 1517 THRCLA_contig1518 1518 THRCLA_contig1519 1519 THRCLA_contig1520 1520 THRCLA_contig1521 1521 THRCLA_contig1522 1522 THRCLA_contig1523 1523 THRCLA_contig1524 1524 THRCLA_contig1525 1525 THRCLA_contig1526 1526 THRCLA_contig1527 1527 THRCLA_contig1528 1528 THRCLA_contig1529 1529 THRCLA_contig1530 1530 THRCLA_contig1531 1531 THRCLA_contig1532 1532 THRCLA_contig1533 1533 THRCLA_contig1534 1534 THRCLA_contig1535 1535 THRCLA_contig1536 1536 THRCLA_contig1537 1537 THRCLA_contig1538 1538 THRCLA_contig1539 1539 THRCLA_contig1540 1540 THRCLA_contig1541 1541 THRCLA_contig1542 1542 THRCLA_contig1543 1543 THRCLA_contig1544 1544 THRCLA_contig1545 1545 THRCLA_contig1546 1546 THRCLA_contig1547 1547 THRCLA_contig1548 1548 THRCLA_contig1549 1549 THRCLA_contig1550 1550 THRCLA_contig1551 1551 THRCLA_contig1552 1552 THRCLA_contig1553 1553 THRCLA_contig1554 1554 THRCLA_contig1555 1555 THRCLA_contig1556 1556 THRCLA_contig1557 1557 THRCLA_contig1558 1558 THRCLA_contig1559 1559 THRCLA_contig1560 1560 THRCLA_contig1561 1561 THRCLA_contig1562 1562 THRCLA_contig1563 1563 THRCLA_contig1564 1564 THRCLA_contig1565 1565 THRCLA_contig1566 1566 THRCLA_contig1567 1567 THRCLA_contig1568 1568 THRCLA_contig1569 1569 THRCLA_contig1570 1570 THRCLA_contig1571 1571 THRCLA_contig1572 1572 THRCLA_contig1573 1573 THRCLA_contig1574 1574 THRCLA_contig1575 1575 THRCLA_contig1576 1576 THRCLA_contig1577 1577 THRCLA_contig1578 1578 THRCLA_contig1579 1579 THRCLA_contig1580 1580 THRCLA_contig1581 1581 THRCLA_contig1582 1582 THRCLA_contig1583 1583 THRCLA_contig1584 1584 THRCLA_contig1585 1585 THRCLA_contig1586 1586 THRCLA_contig1587 1587 THRCLA_contig1588 1588 THRCLA_contig1589 1589 THRCLA_contig1590 1590 THRCLA_contig1591 1591 THRCLA_contig1592 1592 THRCLA_contig1593 1593 THRCLA_contig1594 1594 THRCLA_contig1595 1595 THRCLA_contig1596 1596 THRCLA_contig1597 1597 THRCLA_contig1598 1598 THRCLA_contig1599 1599 THRCLA_contig1600 1600 THRCLA_contig1601 1601 THRCLA_contig1602 1602 THRCLA_contig1603 1603 THRCLA_contig1604 1604 THRCLA_contig1605 1605 THRCLA_contig1606 1606 THRCLA_contig1607 1607 THRCLA_contig1608 1608 THRCLA_contig1609 1609 THRCLA_contig1610 1610 THRCLA_contig1611 1611 THRCLA_contig1612 1612 THRCLA_contig1613 1613 THRCLA_contig1614 1614 THRCLA_contig1615 1615 THRCLA_contig1616 1616 THRCLA_contig1617 1617 THRCLA_contig1618 1618 THRCLA_contig1619 1619 THRCLA_contig1620 1620 THRCLA_contig1621 1621 THRCLA_contig1622 1622 THRCLA_contig1623 1623 THRCLA_contig1624 1624 THRCLA_contig1625 1625 THRCLA_contig1626 1626 THRCLA_contig1627 1627 THRCLA_contig1628 1628 THRCLA_contig1629 1629 THRCLA_contig1630 1630 THRCLA_contig1631 1631 THRCLA_contig1632 1632 THRCLA_contig1633 1633 THRCLA_contig1634 1634 THRCLA_contig1635 1635 THRCLA_contig1636 1636 THRCLA_contig1637 1637 THRCLA_contig1638 1638 THRCLA_contig1639 1639 THRCLA_contig1640 1640 THRCLA_contig1641 1641 THRCLA_contig1642 1642 THRCLA_contig1643 1643 THRCLA_contig1644 1644 THRCLA_contig1645 1645 THRCLA_contig1646 1646 THRCLA_contig1647 1647 THRCLA_contig1648 1648 THRCLA_contig1649 1649 THRCLA_contig1650 1650 THRCLA_contig1651 1651 THRCLA_contig1652 1652 THRCLA_contig1653 1653 THRCLA_contig1654 1654 THRCLA_contig1655 1655 THRCLA_contig1656 1656 THRCLA_contig1657 1657 THRCLA_contig1658 1658 THRCLA_contig1659 1659 THRCLA_contig1660 1660 THRCLA_contig1661 1661 THRCLA_contig1662 1662 THRCLA_contig1663 1663 THRCLA_contig1664 1664 THRCLA_contig1665 1665 THRCLA_contig1666 1666 THRCLA_contig1667 1667 THRCLA_contig1668 1668 THRCLA_contig1669 1669 THRCLA_contig1670 1670 THRCLA_contig1671 1671 THRCLA_contig1672 1672 THRCLA_contig1673 1673 THRCLA_contig1674 1674 THRCLA_contig1675 1675 THRCLA_contig1676 1676 THRCLA_contig1677 1677 THRCLA_contig1678 1678 THRCLA_contig1679 1679 THRCLA_contig1680 1680 THRCLA_contig1681 1681 THRCLA_contig1682 1682 THRCLA_contig1683 1683 THRCLA_contig1684 1684 THRCLA_contig1685 1685 THRCLA_contig1686 1686 THRCLA_contig1687 1687 THRCLA_contig1688 1688 THRCLA_contig1689 1689 THRCLA_contig1690 1690 THRCLA_contig1691 1691 THRCLA_contig1692 1692 THRCLA_contig1693 1693 THRCLA_contig1694 1694 THRCLA_contig1695 1695 THRCLA_contig1696 1696 THRCLA_contig1697 1697 THRCLA_contig1698 1698 THRCLA_contig1699 1699 THRCLA_contig1700 1700 THRCLA_contig1701 1701 THRCLA_contig1702 1702 THRCLA_contig1703 1703 THRCLA_contig1704 1704 THRCLA_contig1705 1705 THRCLA_contig1706 1706 THRCLA_contig1707 1707 THRCLA_contig1708 1708 THRCLA_contig1709 1709 THRCLA_contig1710 1710 THRCLA_contig1711 1711 THRCLA_contig1712 1712 THRCLA_contig1713 1713 THRCLA_contig1714 1714 THRCLA_contig1715 1715 THRCLA_contig1716 1716 THRCLA_contig1717 1717 THRCLA_contig1718 1718 THRCLA_contig1719 1719 THRCLA_contig1720 1720 THRCLA_contig1721 1721 THRCLA_contig1722 1722 THRCLA_contig1723 1723 THRCLA_contig1724 1724 THRCLA_contig1725 1725 THRCLA_contig1726 1726 THRCLA_contig1727 1727 THRCLA_contig1728 1728 THRCLA_contig1729 1729 THRCLA_contig1730 1730 THRCLA_contig1731 1731 THRCLA_contig1732 1732 THRCLA_contig1733 1733 THRCLA_contig1734 1734 THRCLA_contig1735 1735 THRCLA_contig1736 1736 THRCLA_contig1737 1737 THRCLA_contig1738 1738 THRCLA_contig1739 1739 THRCLA_contig1740 1740 THRCLA_contig1741 1741 THRCLA_contig1742 1742 THRCLA_contig1743 1743 THRCLA_contig1744 1744 THRCLA_contig1745 1745 THRCLA_contig1746 1746 THRCLA_contig1747 1747 THRCLA_contig1748 1748 THRCLA_contig1749 1749 THRCLA_contig1750 1750 THRCLA_contig1751 1751 THRCLA_contig1752 1752 THRCLA_contig1753 1753 THRCLA_contig1754 1754 THRCLA_contig1755 1755 THRCLA_contig1756 1756 THRCLA_contig1757 1757 THRCLA_contig1758 1758 THRCLA_contig1759 1759 THRCLA_contig1760 1760 THRCLA_contig1761 1761 THRCLA_contig1762 1762 THRCLA_contig1763 1763 THRCLA_contig1764 1764 THRCLA_contig1765 1765 THRCLA_contig1766 1766 THRCLA_contig1767 1767 THRCLA_contig1768 1768 THRCLA_contig1769 1769 THRCLA_contig1770 1770 THRCLA_contig1771 1771 THRCLA_contig1772 1772 THRCLA_contig1773 1773 THRCLA_contig1774 1774 THRCLA_contig1775 1775 THRCLA_contig1776 1776 THRCLA_contig1777 1777 THRCLA_contig1778 1778 THRCLA_contig1779 1779 THRCLA_contig1780 1780 THRCLA_contig1781 1781 THRCLA_contig1782 1782 THRCLA_contig1783 1783 THRCLA_contig1784 1784 THRCLA_contig1785 1785 THRCLA_contig1786 1786 THRCLA_contig1787 1787 THRCLA_contig1788 1788 THRCLA_contig1789 1789 THRCLA_contig1790 1790 THRCLA_contig1791 1791 THRCLA_contig1792 1792 THRCLA_contig1793 1793 THRCLA_contig1794 1794 THRCLA_contig1795 1795 THRCLA_contig1796 1796 THRCLA_contig1797 1797 THRCLA_contig1798 1798 THRCLA_contig1799 1799 THRCLA_contig1800 1800 THRCLA_contig1801 1801 THRCLA_contig1802 1802 THRCLA_contig1803 1803 THRCLA_contig1804 1804 THRCLA_contig1805 1805 THRCLA_contig1806 1806 THRCLA_contig1807 1807 THRCLA_contig1808 1808 THRCLA_contig1809 1809 THRCLA_contig1810 1810 THRCLA_contig1811 1811 THRCLA_contig1812 1812 THRCLA_contig1813 1813 THRCLA_contig1814 1814 THRCLA_contig1815 1815 THRCLA_contig1816 1816 THRCLA_contig1817 1817 THRCLA_contig1818 1818 THRCLA_contig1819 1819 THRCLA_contig1820 1820 THRCLA_contig1821 1821 THRCLA_contig1822 1822 THRCLA_contig1823 1823 THRCLA_contig1824 1824 THRCLA_contig1825 1825 THRCLA_contig1826 1826 THRCLA_contig1827 1827 THRCLA_contig1828 1828 THRCLA_contig1829 1829 THRCLA_contig1830 1830 THRCLA_contig1831 1831 THRCLA_contig1832 1832 THRCLA_contig1833 1833 THRCLA_contig1834 1834 THRCLA_contig1835 1835 THRCLA_contig1836 1836 THRCLA_contig1837 1837 THRCLA_contig1838 1838 THRCLA_contig1839 1839 THRCLA_contig1840 1840 THRCLA_contig1841 1841 THRCLA_contig1842 1842 THRCLA_contig1843 1843 THRCLA_contig1844 1844 THRCLA_contig1845 1845 THRCLA_contig1846 1846 THRCLA_contig1847 1847 THRCLA_contig1848 1848 THRCLA_contig1849 1849 THRCLA_contig1850 1850 THRCLA_contig1851 1851 THRCLA_contig1852 1852 THRCLA_contig1853 1853 THRCLA_contig1854 1854 THRCLA_contig1855 1855 THRCLA_contig1856 1856 THRCLA_contig1857 1857 THRCLA_contig1858 1858 THRCLA_contig1859 1859 THRCLA_contig1860 1860 THRCLA_contig1861 1861 THRCLA_contig1862 1862 THRCLA_contig1863 1863 THRCLA_contig1864 1864 THRCLA_contig1865 1865 THRCLA_contig1866 1866 THRCLA_contig1867 1867 THRCLA_contig1868 1868 THRCLA_contig1869 1869 THRCLA_contig1870 1870 THRCLA_contig1871 1871 THRCLA_contig1872 1872 THRCLA_contig1873 1873 THRCLA_contig1874 1874 THRCLA_contig1875 1875 THRCLA_contig1876 1876 THRCLA_contig1877 1877 THRCLA_contig1878 1878 THRCLA_contig1879 1879 THRCLA_contig1880 1880 THRCLA_contig1881 1881 THRCLA_contig1882 1882 THRCLA_contig1883 1883 THRCLA_contig1884 1884 THRCLA_contig1885 1885 THRCLA_contig1886 1886 THRCLA_contig1887 1887 THRCLA_contig1888 1888 THRCLA_contig1889 1889 THRCLA_contig1890 1890 THRCLA_contig1891 1891 THRCLA_contig1892 1892 THRCLA_contig1893 1893 THRCLA_contig1894 1894 THRCLA_contig1895 1895 THRCLA_contig1896 1896 THRCLA_contig1897 1897 THRCLA_contig1898 1898 THRCLA_contig1899 1899 THRCLA_contig1900 1900 THRCLA_contig1901 1901 THRCLA_contig1902 1902 THRCLA_contig1903 1903 THRCLA_contig1904 1904 THRCLA_contig1905 1905 THRCLA_contig1906 1906 THRCLA_contig1907 1907 THRCLA_contig1908 1908 THRCLA_contig1909 1909 THRCLA_contig1910 1910 THRCLA_contig1911 1911 THRCLA_contig1912 1912 THRCLA_contig1913 1913 THRCLA_contig1914 1914 THRCLA_contig1915 1915 THRCLA_contig1916 1916 THRCLA_contig1917 1917 THRCLA_contig1918 1918 THRCLA_contig1919 1919 THRCLA_contig1920 1920 THRCLA_contig1921 1921 THRCLA_contig1922 1922 THRCLA_contig1923 1923 THRCLA_contig1924 1924 THRCLA_contig1925 1925 THRCLA_contig1926 1926 THRCLA_contig1927 1927 THRCLA_contig1928 1928 THRCLA_contig1929 1929 THRCLA_contig1930 1930 THRCLA_contig1931 1931 THRCLA_contig1932 1932 THRCLA_contig1933 1933 THRCLA_contig1934 1934 THRCLA_contig1935 1935 THRCLA_contig1936 1936 THRCLA_contig1937 1937 THRCLA_contig1938 1938 THRCLA_contig1939 1939 THRCLA_contig1940 1940 THRCLA_contig1941 1941 THRCLA_contig1942 1942 THRCLA_contig1943 1943 THRCLA_contig1944 1944 THRCLA_contig1945 1945 THRCLA_contig1946 1946 THRCLA_contig1947 1947 THRCLA_contig1948 1948 THRCLA_contig1949 1949 THRCLA_contig1950 1950 THRCLA_contig1951 1951 THRCLA_contig1952 1952 THRCLA_contig1953 1953 THRCLA_contig1954 1954 THRCLA_contig1955 1955 THRCLA_contig1956 1956 THRCLA_contig1957 1957 THRCLA_contig1958 1958 THRCLA_contig1959 1959 THRCLA_contig1960 1960 THRCLA_contig1961 1961 THRCLA_contig1962 1962 THRCLA_contig1963 1963 THRCLA_contig1964 1964 THRCLA_contig1965 1965 THRCLA_contig1966 1966 THRCLA_contig1967 1967 THRCLA_contig1968 1968 THRCLA_contig1969 1969 THRCLA_contig1970 1970 THRCLA_contig1971 1971 THRCLA_contig1972 1972 THRCLA_contig1973 1973 THRCLA_contig1974 1974 THRCLA_contig1975 1975 THRCLA_contig1976 1976 THRCLA_contig1977 1977 THRCLA_contig1978 1978 THRCLA_contig1979 1979 THRCLA_contig1980 1980 THRCLA_contig1981 1981 THRCLA_contig1982 1982 THRCLA_contig1983 1983 THRCLA_contig1984 1984 THRCLA_contig1985 1985 THRCLA_contig1986 1986 THRCLA_contig1987 1987 THRCLA_contig1988 1988 THRCLA_contig1989 1989 THRCLA_contig1990 1990 THRCLA_contig1991 1991 THRCLA_contig1992 1992 THRCLA_contig1993 1993 THRCLA_contig1994 1994 THRCLA_contig1995 1995 THRCLA_contig1996 1996 THRCLA_contig1997 1997 THRCLA_contig1998 1998 THRCLA_contig1999 1999 THRCLA_contig2000 2000 THRCLA_contig2001 2001 THRCLA_contig2002 2002 THRCLA_contig2003 2003 THRCLA_contig2004 2004 THRCLA_contig2005 2005 THRCLA_contig2006 2006 THRCLA_contig2007 2007 THRCLA_contig2008 2008 THRCLA_contig2009 2009 THRCLA_contig2010 2010 THRCLA_contig2011 2011 THRCLA_contig2012 2012 THRCLA_contig2013 2013 THRCLA_contig2014 2014 THRCLA_contig2015 2015 THRCLA_contig2016 2016 THRCLA_contig2017 2017 THRCLA_contig2018 2018 THRCLA_contig2019 2019 THRCLA_contig2020 2020 THRCLA_contig2021 2021 THRCLA_contig2022 2022 THRCLA_contig2023 2023 THRCLA_contig2024 2024 THRCLA_contig2025 2025 THRCLA_contig2026 2026 THRCLA_contig2027 2027 THRCLA_contig2028 2028 THRCLA_contig2029 2029 THRCLA_contig2030 2030 THRCLA_contig2031 2031 THRCLA_contig2032 2032 THRCLA_contig2033 2033 THRCLA_contig2034 2034 THRCLA_contig2035 2035 THRCLA_contig2036 2036 THRCLA_contig2037 2037 THRCLA_contig2038 2038 THRCLA_contig2039 2039 THRCLA_contig2040 2040 THRCLA_contig2041 2041 THRCLA_contig2042 2042 THRCLA_contig2043 2043 THRCLA_contig2044 2044 THRCLA_contig2045 2045 THRCLA_contig2046 2046 THRCLA_contig2047 2047 THRCLA_contig2048 2048 THRCLA_contig2049 2049 THRCLA_contig2050 2050 THRCLA_contig2051 2051 THRCLA_contig2052 2052 THRCLA_contig2053 2053 THRCLA_contig2054 2054 THRCLA_contig2055 2055 THRCLA_contig2056 2056 THRCLA_contig2057 2057 THRCLA_contig2058 2058 THRCLA_contig2059 2059 THRCLA_contig2060 2060 THRCLA_contig2061 2061 THRCLA_contig2062 2062 THRCLA_contig2063 2063 THRCLA_contig2064 2064 THRCLA_contig2065 2065 THRCLA_contig2066 2066 THRCLA_contig2067 2067 THRCLA_contig2068 2068 THRCLA_contig2069 2069 THRCLA_contig2070 2070 THRCLA_contig2071 2071 THRCLA_contig2072 2072 THRCLA_contig2073 2073 THRCLA_contig2074 2074 THRCLA_contig2075 2075 THRCLA_contig2076 2076 THRCLA_contig2077 2077 THRCLA_contig2078 2078 THRCLA_contig2079 2079 THRCLA_contig2080 2080 THRCLA_contig2081 2081 THRCLA_contig2082 2082 THRCLA_contig2083 2083 THRCLA_contig2084 2084 THRCLA_contig2085 2085 THRCLA_contig2086 2086 THRCLA_contig2087 2087 THRCLA_contig2088 2088 THRCLA_contig2089 2089 THRCLA_contig2090 2090 THRCLA_contig2091 2091 THRCLA_contig2092 2092 THRCLA_contig2093 2093 THRCLA_contig2094 2094 THRCLA_contig2095 2095 THRCLA_contig2096 2096 THRCLA_contig2097 2097 THRCLA_contig2098 2098 THRCLA_contig2099 2099 THRCLA_contig2100 2100 THRCLA_contig2101 2101 THRCLA_contig2102 2102 THRCLA_contig2103 2103 THRCLA_contig2104 2104 THRCLA_contig2105 2105 THRCLA_contig2106 2106 THRCLA_contig2107 2107 THRCLA_contig2108 2108 THRCLA_contig2109 2109 THRCLA_contig2110 2110 THRCLA_contig2111 2111 THRCLA_contig2112 2112 THRCLA_contig2113 2113 THRCLA_contig2114 2114 THRCLA_contig2115 2115 THRCLA_contig2116 2116 THRCLA_contig2117 2117 THRCLA_contig2118 2118 THRCLA_contig2119 2119 THRCLA_contig2120 2120 THRCLA_contig2121 2121 THRCLA_contig2122 2122 THRCLA_contig2123 2123 THRCLA_contig2124 2124 THRCLA_contig2125 2125 THRCLA_contig2126 2126 THRCLA_contig2127 2127 THRCLA_contig2128 2128 THRCLA_contig2129 2129 THRCLA_contig2130 2130 THRCLA_contig2131 2131 THRCLA_contig2132 2132 THRCLA_contig2133 2133 THRCLA_contig2134 2134 THRCLA_contig2135 2135 THRCLA_contig2136 2136 THRCLA_contig2137 2137 THRCLA_contig2138 2138 THRCLA_contig2139 2139 THRCLA_contig2140 2140 THRCLA_contig2141 2141 THRCLA_contig2142 2142 THRCLA_contig2143 2143 THRCLA_contig2144 2144 THRCLA_contig2145 2145 THRCLA_contig2146 2146 THRCLA_contig2147 2147 THRCLA_contig2148 2148 THRCLA_contig2149 2149 THRCLA_contig2150 2150 THRCLA_contig2151 2151 THRCLA_contig2152 2152 THRCLA_contig2153 2153 THRCLA_contig2154 2154 THRCLA_contig2155 2155 THRCLA_contig2156 2156 THRCLA_contig2157 2157 THRCLA_contig2158 2158 THRCLA_contig2159 2159 THRCLA_contig2160 2160 THRCLA_contig2161 2161 THRCLA_contig2162 2162 THRCLA_contig2163 2163 THRCLA_contig2164 2164 THRCLA_contig2165 2165 THRCLA_contig2166 2166 THRCLA_contig2167 2167 THRCLA_contig2168 2168 THRCLA_contig2169 2169 THRCLA_contig2170 2170 THRCLA_contig2171 2171 THRCLA_contig2172 2172 THRCLA_contig2173 2173 THRCLA_contig2174 2174 THRCLA_contig2175 2175 THRCLA_contig2176 2176 THRCLA_contig2177 2177 THRCLA_contig2178 2178 THRCLA_contig2179 2179 THRCLA_contig2180 2180 THRCLA_contig2181 2181 THRCLA_contig2182 2182 THRCLA_contig2183 2183 THRCLA_contig2184 2184 THRCLA_contig2185 2185 THRCLA_contig2186 2186 THRCLA_contig2187 2187 THRCLA_contig2188 2188 THRCLA_contig2189 2189 THRCLA_contig2190 2190 THRCLA_contig2191 2191 THRCLA_contig2192 2192 THRCLA_contig2193 2193 THRCLA_contig2194 2194 THRCLA_contig2195 2195 THRCLA_contig2196 2196 THRCLA_contig2197 2197 THRCLA_contig2198 2198 THRCLA_contig2199 2199 THRCLA_contig2200 2200 THRCLA_contig2201 2201 THRCLA_contig2202 2202 THRCLA_contig2203 2203 THRCLA_contig2204 2204 THRCLA_contig2205 2205 THRCLA_contig2206 2206 THRCLA_contig2207 2207 THRCLA_contig2208 2208 THRCLA_contig2209 2209 THRCLA_contig2210 2210 THRCLA_contig2211 2211 THRCLA_contig2212 2212 THRCLA_contig2213 2213 THRCLA_contig2214 2214 THRCLA_contig2215 2215 THRCLA_contig2216 2216 THRCLA_contig2217 2217 THRCLA_contig2218 2218 THRCLA_contig2219 2219 THRCLA_contig2220 2220 THRCLA_contig2221 2221 THRCLA_contig2222 2222 THRCLA_contig2223 2223 THRCLA_contig2224 2224 THRCLA_contig2225 2225 THRCLA_contig2226 2226 THRCLA_contig2227 2227 THRCLA_contig2228 2228 THRCLA_contig2229 2229 THRCLA_contig2230 2230 THRCLA_contig2231 2231 THRCLA_contig2232 2232 THRCLA_contig2233 2233 THRCLA_contig2234 2234 THRCLA_contig2235 2235 THRCLA_contig2236 2236 THRCLA_contig2237 2237 THRCLA_contig2238 2238 THRCLA_contig2239 2239 THRCLA_contig2240 2240 THRCLA_contig2241 2241 THRCLA_contig2242 2242 THRCLA_contig2243 2243 THRCLA_contig2244 2244 THRCLA_contig2245 2245 THRCLA_contig2246 2246 THRCLA_contig2247 2247 THRCLA_contig2248 2248 THRCLA_contig2249 2249 THRCLA_contig2250 2250 THRCLA_contig2251 2251 THRCLA_contig2252 2252 THRCLA_contig2253 2253 THRCLA_contig2254 2254 THRCLA_contig2255 2255 THRCLA_contig2256 2256 THRCLA_contig2257 2257 THRCLA_contig2258 2258 THRCLA_contig2259 2259 THRCLA_contig2260 2260 THRCLA_contig2261 2261 THRCLA_contig2262 2262 THRCLA_contig2263 2263 THRCLA_contig2264 2264 THRCLA_contig2265 2265 THRCLA_contig2266 2266 THRCLA_contig2267 2267 THRCLA_contig2268 2268 THRCLA_contig2269 2269 THRCLA_contig2270 2270 THRCLA_contig2271 2271 THRCLA_contig2272 2272 THRCLA_contig2273 2273 THRCLA_contig2274 2274 THRCLA_contig2275 2275 THRCLA_contig2276 2276 THRCLA_contig2277 2277 THRCLA_contig2278 2278 THRCLA_contig2279 2279 THRCLA_contig2280 2280 THRCLA_contig2281 2281 THRCLA_contig2282 2282 THRCLA_contig2283 2283 THRCLA_contig2284 2284 THRCLA_contig2285 2285 THRCLA_contig2286 2286 THRCLA_contig2287 2287 THRCLA_contig2288 2288 THRCLA_contig2289 2289 THRCLA_contig2290 2290 THRCLA_contig2291 2291 THRCLA_contig2292 2292 THRCLA_contig2293 2293 THRCLA_contig2294 2294 THRCLA_contig2295 2295 THRCLA_contig2296 2296 THRCLA_contig2297 2297 THRCLA_contig2298 2298 THRCLA_contig2299 2299 THRCLA_contig2300 2300 THRCLA_contig2301 2301 THRCLA_contig2302 2302 THRCLA_contig2303 2303 THRCLA_contig2304 2304 THRCLA_contig2305 2305 THRCLA_contig2306 2306 THRCLA_contig2307 2307 THRCLA_contig2308 2308 THRCLA_contig2309 2309 THRCLA_contig2310 2310 THRCLA_contig2311 2311 THRCLA_contig2312 2312 THRCLA_contig2313 2313 THRCLA_contig2314 2314 THRCLA_contig2315 2315 THRCLA_contig2316 2316 THRCLA_contig2317 2317 THRCLA_contig2318 2318 THRCLA_contig2319 2319 THRCLA_contig2320 2320 THRCLA_contig2321 2321 THRCLA_contig2322 2322 THRCLA_contig2323 2323 THRCLA_contig2324 2324 THRCLA_contig2325 2325 THRCLA_contig2326 2326 THRCLA_contig2327 2327 THRCLA_contig2328 2328 THRCLA_contig2329 2329 THRCLA_contig2330 2330 THRCLA_contig2331 2331 THRCLA_contig2332 2332 THRCLA_contig2333 2333 THRCLA_contig2334 2334 THRCLA_contig2335 2335 THRCLA_contig2336 2336 THRCLA_contig2337 2337 THRCLA_contig2338 2338 THRCLA_contig2339 2339 THRCLA_contig2340 2340 THRCLA_contig2341 2341 THRCLA_contig2342 2342 THRCLA_contig2343 2343 THRCLA_contig2344 2344 THRCLA_contig2345 2345 THRCLA_contig2346 2346 THRCLA_contig2347 2347 THRCLA_contig2348 2348 THRCLA_contig2349 2349 THRCLA_contig2350 2350 THRCLA_contig2351 2351 THRCLA_contig2352 2352 THRCLA_contig2353 2353 THRCLA_contig2354 2354 THRCLA_contig2355 2355 THRCLA_contig2356 2356 THRCLA_contig2357 2357 THRCLA_contig2358 2358 THRCLA_contig2359 2359 THRCLA_contig2360 2360 THRCLA_contig2361 2361 THRCLA_contig2362 2362 THRCLA_contig2363 2363 THRCLA_contig2364 2364 THRCLA_contig2365 2365 THRCLA_contig2366 2366 THRCLA_contig2367 2367 THRCLA_contig2368 2368 THRCLA_contig2369 2369 THRCLA_contig2370 2370 THRCLA_contig2371 2371 THRCLA_contig2372 2372 THRCLA_contig2373 2373 THRCLA_contig2374 2374 THRCLA_contig2375 2375 THRCLA_contig2376 2376 THRCLA_contig2377 2377 THRCLA_contig2378 2378 THRCLA_contig2379 2379 THRCLA_contig2380 2380 THRCLA_contig2381 2381 THRCLA_contig2382 2382 THRCLA_contig2383 2383 THRCLA_contig2384 2384 THRCLA_contig2385 2385 THRCLA_contig2386 2386 THRCLA_contig2387 2387 THRCLA_contig2388 2388 THRCLA_contig2389 2389 THRCLA_contig2390 2390 THRCLA_contig2391 2391 THRCLA_contig2392 2392 THRCLA_contig2393 2393 THRCLA_contig2394 2394 THRCLA_contig2395 2395 THRCLA_contig2396 2396 THRCLA_contig2397 2397 THRCLA_contig2398 2398 THRCLA_contig2399 2399 THRCLA_contig2400 2400 THRCLA_contig2401 2401 THRCLA_contig2402 2402 THRCLA_contig2403 2403 THRCLA_contig2404 2404 THRCLA_contig2405 2405 THRCLA_contig2406 2406 THRCLA_contig2407 2407 THRCLA_contig2408 2408 THRCLA_contig2409 2409 THRCLA_contig2410 2410 THRCLA_contig2411 2411 THRCLA_contig2412 2412 THRCLA_contig2413 2413 THRCLA_contig2414 2414 THRCLA_contig2415 2415 THRCLA_contig2416 2416 THRCLA_contig2417 2417 THRCLA_contig2418 2418 THRCLA_contig2419 2419 THRCLA_contig2420 2420 THRCLA_contig2421 2421 THRCLA_contig2422 2422 THRCLA_contig2423 2423 THRCLA_contig2424 2424 THRCLA_contig2425 2425 THRCLA_contig2426 2426 THRCLA_contig2427 2427 THRCLA_contig2428 2428 THRCLA_contig2429 2429 THRCLA_contig2430 2430 THRCLA_contig2431 2431 THRCLA_contig2432 2432 THRCLA_contig2433 2433 THRCLA_contig2434 2434 THRCLA_contig2435 2435 THRCLA_contig2436 2436 THRCLA_contig2437 2437 THRCLA_contig2438 2438 THRCLA_contig2439 2439 THRCLA_contig2440 2440 THRCLA_contig2441 2441 THRCLA_contig2442 2442 THRCLA_contig2443 2443 THRCLA_contig2444 2444 THRCLA_contig2445 2445 THRCLA_contig2446 2446 THRCLA_contig2447 2447 THRCLA_contig2448 2448 THRCLA_contig2449 2449 THRCLA_contig2450 2450 THRCLA_contig2451 2451 THRCLA_contig2452 2452 THRCLA_contig2453 2453 THRCLA_contig2454 2454 THRCLA_contig2455 2455 THRCLA_contig2456 2456 THRCLA_contig2457 2457 THRCLA_contig2458 2458 THRCLA_contig2459 2459 THRCLA_contig2460 2460 THRCLA_contig2461 2461 THRCLA_contig2462 2462 THRCLA_contig2463 2463 THRCLA_contig2464 2464 THRCLA_contig2465 2465 THRCLA_contig2466 2466 THRCLA_contig2467 2467 THRCLA_contig2468 2468 THRCLA_contig2469 2469 THRCLA_contig2470 2470 THRCLA_contig2471 2471 THRCLA_contig2472 2472 THRCLA_contig2473 2473 THRCLA_contig2474 2474 THRCLA_contig2475 2475 THRCLA_contig2476 2476 THRCLA_contig2477 2477 THRCLA_contig2478 2478 THRCLA_contig2479 2479 THRCLA_contig2480 2480 THRCLA_contig2481 2481 THRCLA_contig2482 2482 THRCLA_contig2483 2483 THRCLA_contig2484 2484 THRCLA_contig2485 2485 THRCLA_contig2486 2486 THRCLA_contig2487 2487 THRCLA_contig2488 2488 THRCLA_contig2489 2489 THRCLA_contig2490 2490 THRCLA_contig2491 2491 THRCLA_contig2492 2492 THRCLA_contig2493 2493 THRCLA_contig2494 2494 THRCLA_contig2495 2495 THRCLA_contig2496 2496 THRCLA_contig2497 2497 THRCLA_contig2498 2498 THRCLA_contig2499 2499 THRCLA_contig2500 2500 THRCLA_contig2501 2501 THRCLA_contig2502 2502 THRCLA_contig2503 2503 THRCLA_contig2504 2504 THRCLA_contig2505 2505 THRCLA_contig2506 2506 THRCLA_contig2507 2507 THRCLA_contig2508 2508 THRCLA_contig2509 2509 THRCLA_contig2510 2510 THRCLA_contig2511 2511 THRCLA_contig2512 2512 THRCLA_contig2513 2513 THRCLA_contig2514 2514 THRCLA_contig2515 2515 THRCLA_contig2516 2516 THRCLA_contig2517 2517 THRCLA_contig2518 2518 THRCLA_contig2519 2519 THRCLA_contig2520 2520 THRCLA_contig2521 2521 THRCLA_contig2522 2522 THRCLA_contig2523 2523 THRCLA_contig2524 2524 THRCLA_contig2525 2525 THRCLA_contig2526 2526 THRCLA_contig2527 2527 THRCLA_contig2528 2528 THRCLA_contig2529 2529 THRCLA_contig2530 2530 THRCLA_contig2531 2531 THRCLA_contig2532 2532 THRCLA_contig2533 2533 THRCLA_contig2534 2534 THRCLA_contig2535 2535 THRCLA_contig2536 2536 THRCLA_contig2537 2537 THRCLA_contig2538 2538 THRCLA_contig2539 2539 THRCLA_contig2540 2540 THRCLA_contig2541 2541 THRCLA_contig2542 2542 THRCLA_contig2543 2543 THRCLA_contig2544 2544 THRCLA_contig2545 2545 THRCLA_contig2546 2546 THRCLA_contig2547 2547 THRCLA_contig2548 2548 THRCLA_contig2549 2549 THRCLA_contig2550 2550 THRCLA_contig2551 2551 THRCLA_contig2552 2552 THRCLA_contig2553 2553 THRCLA_contig2554 2554 THRCLA_contig2555 2555 THRCLA_contig2556 2556 THRCLA_contig2557 2557 THRCLA_contig2558 2558 THRCLA_contig2559 2559 THRCLA_contig2560 2560 THRCLA_contig2561 2561 THRCLA_contig2562 2562 THRCLA_contig2563 2563 THRCLA_contig2564 2564 THRCLA_contig2565 2565 THRCLA_contig2566 2566 THRCLA_contig2567 2567 THRCLA_contig2568 2568 THRCLA_contig2569 2569 THRCLA_contig2570 2570 THRCLA_contig2571 2571 THRCLA_contig2572 2572 THRCLA_contig2573 2573 THRCLA_contig2574 2574 THRCLA_contig2575 2575 THRCLA_contig2576 2576 THRCLA_contig2577 2577 THRCLA_contig2578 2578 THRCLA_contig2579 2579 THRCLA_contig2580 2580 THRCLA_contig2581 2581 THRCLA_contig2582 2582 THRCLA_contig2583 2583 THRCLA_contig2584 2584 THRCLA_contig2585 2585 THRCLA_contig2586 2586 THRCLA_contig2587 2587 THRCLA_contig2588 2588 THRCLA_contig2589 2589 THRCLA_contig2590 2590 THRCLA_contig2591 2591 THRCLA_contig2592 2592 THRCLA_contig2593 2593 THRCLA_contig2594 2594 THRCLA_contig2595 2595 THRCLA_contig2596 2596 THRCLA_contig2597 2597 THRCLA_contig2598 2598 THRCLA_contig2599 2599 THRCLA_contig2600 2600 THRCLA_contig2601 2601 THRCLA_contig2602 2602 THRCLA_contig2603 2603 THRCLA_contig2604 2604 THRCLA_contig2605 2605 THRCLA_contig2606 2606 THRCLA_contig2607 2607 THRCLA_contig2608 2608 THRCLA_contig2609 2609 THRCLA_contig2610 2610 THRCLA_contig2611 2611 THRCLA_contig2612 2612 THRCLA_contig2613 2613 THRCLA_contig2614 2614 THRCLA_contig2615 2615 THRCLA_contig2616 2616 THRCLA_contig2617 2617 THRCLA_contig2618 2618 THRCLA_contig2619 2619 THRCLA_contig2620 2620 THRCLA_contig2621 2621 THRCLA_contig2622 2622 THRCLA_contig2623 2623 THRCLA_contig2624 2624 THRCLA_contig2625 2625 THRCLA_contig2626 2626 THRCLA_contig2627 2627 THRCLA_contig2628 2628 THRCLA_contig2629 2629 THRCLA_contig2630 2630 THRCLA_contig2631 2631 THRCLA_contig2632 2632 THRCLA_contig2633 2633 THRCLA_contig2634 2634 THRCLA_contig2635 2635 THRCLA_contig2636 2636 THRCLA_contig2637 2637 THRCLA_contig2638 2638 THRCLA_contig2639 2639 THRCLA_contig2640 2640 THRCLA_contig2641 2641 THRCLA_contig2642 2642 THRCLA_contig2643 2643 THRCLA_contig2644 2644 THRCLA_contig2645 2645 THRCLA_contig2646 2646 THRCLA_contig2647 2647 THRCLA_contig2648 2648 THRCLA_contig2649 2649 THRCLA_contig2650 2650 THRCLA_contig2651 2651 THRCLA_contig2652 2652 THRCLA_contig2653 2653 THRCLA_contig2654 2654 THRCLA_contig2655 2655 THRCLA_contig2656 2656 THRCLA_contig2657 2657 THRCLA_contig2658 2658 THRCLA_contig2659 2659 THRCLA_contig2660 2660 THRCLA_contig2661 2661 THRCLA_contig2662 2662 THRCLA_contig2663 2663 THRCLA_contig2664 2664 THRCLA_contig2665 2665 THRCLA_contig2666 2666 THRCLA_contig2667 2667 THRCLA_contig2668 2668 THRCLA_contig2669 2669 THRCLA_contig2670 2670 THRCLA_contig2671 2671 THRCLA_contig2672 2672 THRCLA_contig2673 2673 THRCLA_contig2674 2674 THRCLA_contig2675 2675 THRCLA_contig2676 2676 THRCLA_contig2677 2677 THRCLA_contig2678 2678 THRCLA_contig2679 2679 THRCLA_contig2680 2680 THRCLA_contig2681 2681 THRCLA_contig2682 2682 THRCLA_contig2683 2683 THRCLA_contig2684 2684 THRCLA_contig2685 2685 THRCLA_contig2686 2686 THRCLA_contig2687 2687 THRCLA_contig2688 2688 THRCLA_contig2689 2689 THRCLA_contig2690 2690 THRCLA_contig2691 2691 THRCLA_contig2692 2692 THRCLA_contig2693 2693 THRCLA_contig2694 2694 THRCLA_contig2695 2695 THRCLA_contig2696 2696 THRCLA_contig2697 2697 THRCLA_contig2698 2698 THRCLA_contig2699 2699 THRCLA_contig2700 2700 THRCLA_contig2701 2701 THRCLA_contig2702 2702 THRCLA_contig2703 2703 THRCLA_contig2704 2704 THRCLA_contig2705 2705 THRCLA_contig2706 2706 THRCLA_contig2707 2707 THRCLA_contig2708 2708 THRCLA_contig2709 2709 THRCLA_contig2710 2710 THRCLA_contig2711 2711 THRCLA_contig2712 2712 THRCLA_contig2713 2713 THRCLA_contig2714 2714 THRCLA_contig2715 2715 THRCLA_contig2716 2716 THRCLA_contig2717 2717 THRCLA_contig2718 2718 THRCLA_contig2719 2719 THRCLA_contig2720 2720 THRCLA_contig2721 2721 THRCLA_contig2722 2722 THRCLA_contig2723 2723 THRCLA_contig2724 2724 THRCLA_contig2725 2725 THRCLA_contig2726 2726 THRCLA_contig2727 2727 THRCLA_contig2728 2728 THRCLA_contig2729 2729 THRCLA_contig2730 2730 THRCLA_contig2731 2731 THRCLA_contig2732 2732 THRCLA_contig2733 2733 THRCLA_contig2734 2734 THRCLA_contig2735 2735 THRCLA_contig2736 2736 THRCLA_contig2737 2737 THRCLA_contig2738 2738 THRCLA_contig2739 2739 THRCLA_contig2740 2740 THRCLA_contig2741 2741 THRCLA_contig2742 2742 THRCLA_contig2743 2743 THRCLA_contig2744 2744 THRCLA_contig2745 2745 THRCLA_contig2746 2746 THRCLA_contig2747 2747 THRCLA_contig2748 2748 THRCLA_contig2749 2749 THRCLA_contig2750 2750 THRCLA_contig2751 2751 THRCLA_contig2752 2752 THRCLA_contig2753 2753 THRCLA_contig2754 2754 THRCLA_contig2755 2755 THRCLA_contig2756 2756 THRCLA_contig2757 2757 THRCLA_contig2758 2758 THRCLA_contig2759 2759 THRCLA_contig2760 2760 THRCLA_contig2761 2761 THRCLA_contig2762 2762 THRCLA_contig2763 2763 THRCLA_contig2764 2764 THRCLA_contig2765 2765 THRCLA_contig2766 2766 THRCLA_contig2767 2767 THRCLA_contig2768 2768 THRCLA_contig2769 2769 THRCLA_contig2770 2770 THRCLA_contig2771 2771 THRCLA_contig2772 2772 THRCLA_contig2773 2773 THRCLA_contig2774 2774 THRCLA_contig2775 2775 THRCLA_contig2776 2776 THRCLA_contig2777 2777 THRCLA_contig2778 2778 THRCLA_contig2779 2779 THRCLA_contig2780 2780 THRCLA_contig2781 2781 THRCLA_contig2782 2782 THRCLA_contig2783 2783 THRCLA_contig2784 2784 THRCLA_contig2785 2785 THRCLA_contig2786 2786 THRCLA_contig2787 2787 THRCLA_contig2788 2788 THRCLA_contig2789 2789 THRCLA_contig2790 2790 THRCLA_contig2791 2791 THRCLA_contig2792 2792 THRCLA_contig2793 2793 THRCLA_contig2794 2794 THRCLA_contig2795 2795 THRCLA_contig2796 2796 THRCLA_contig2797 2797 THRCLA_contig2798 2798 THRCLA_contig2799 2799 THRCLA_contig2800 2800 THRCLA_contig2801 2801 THRCLA_contig2802 2802 THRCLA_contig2803 2803 THRCLA_contig2804 2804 THRCLA_contig2805 2805 THRCLA_contig2806 2806 THRCLA_contig2807 2807 THRCLA_contig2808 2808 THRCLA_contig2809 2809 THRCLA_contig2810 2810 THRCLA_contig2811 2811 THRCLA_contig2812 2812 THRCLA_contig2813 2813 THRCLA_contig2814 2814 THRCLA_contig2815 2815 THRCLA_contig2816 2816 THRCLA_contig2817 2817 THRCLA_contig2818 2818 THRCLA_contig2819 2819 THRCLA_contig2820 2820 THRCLA_contig2821 2821 THRCLA_contig2822 2822 THRCLA_contig2823 2823 THRCLA_contig2824 2824 THRCLA_contig2825 2825 THRCLA_contig2826 2826 THRCLA_contig2827 2827 THRCLA_contig2828 2828 THRCLA_contig2829 2829 THRCLA_contig2830 2830 THRCLA_contig2831 2831 THRCLA_contig2832 2832 THRCLA_contig2833 2833 THRCLA_contig2834 2834 THRCLA_contig2835 2835 THRCLA_contig2836 2836 THRCLA_contig2837 2837 THRCLA_contig2838 2838 THRCLA_contig2839 2839 THRCLA_contig2840 2840 THRCLA_contig2841 2841 THRCLA_contig2842 2842 THRCLA_contig2843 2843 THRCLA_contig2844 2844 THRCLA_contig2845 2845 THRCLA_contig2846 2846 THRCLA_contig2847 2847 THRCLA_contig2848 2848 THRCLA_contig2849 2849 THRCLA_contig2850 2850 THRCLA_contig2851 2851 THRCLA_contig2852 2852 THRCLA_contig2853 2853 THRCLA_contig2854 2854 THRCLA_contig2855 2855 THRCLA_contig2856 2856 THRCLA_contig2857 2857 THRCLA_contig2858 2858 THRCLA_contig2859 2859 THRCLA_contig2860 2860 THRCLA_contig2861 2861 THRCLA_contig2862 2862 THRCLA_contig2863 2863 THRCLA_contig2864 2864 THRCLA_contig2865 2865 THRCLA_contig2866 2866 THRCLA_contig2867 2867 THRCLA_contig2868 2868 THRCLA_contig2869 2869 THRCLA_contig2870 2870 THRCLA_contig2871 2871 THRCLA_contig2872 2872 THRCLA_contig2873 2873 THRCLA_contig2874 2874 THRCLA_contig2875 2875 THRCLA_contig2876 2876 THRCLA_contig2877 2877 THRCLA_contig2878 2878 THRCLA_contig2879 2879 THRCLA_contig2880 2880 THRCLA_contig2881 2881 THRCLA_contig2882 2882 THRCLA_contig2883 2883 THRCLA_contig2884 2884 THRCLA_contig2885 2885 THRCLA_contig2886 2886 THRCLA_contig2887 2887 THRCLA_contig2888 2888 THRCLA_contig2889 2889 THRCLA_contig2890 2890 THRCLA_contig2891 2891 THRCLA_contig2892 2892 THRCLA_contig2893 2893 THRCLA_contig2894 2894 THRCLA_contig2895 2895 THRCLA_contig2896 2896 THRCLA_contig2897 2897 THRCLA_contig2898 2898 THRCLA_contig2899 2899 THRCLA_contig2900 2900 THRCLA_contig2901 2901 THRCLA_contig2902 2902 THRCLA_contig2903 2903 THRCLA_contig2904 2904 THRCLA_contig2905 2905 THRCLA_contig2906 2906 THRCLA_contig2907 2907 THRCLA_contig2908 2908 THRCLA_contig2909 2909 THRCLA_contig2910 2910 THRCLA_contig2911 2911 THRCLA_contig2912 2912 THRCLA_contig2913 2913 THRCLA_contig2914 2914 THRCLA_contig2915 2915 THRCLA_contig2916 2916 THRCLA_contig2917 2917 THRCLA_contig2918 2918 THRCLA_contig2919 2919 THRCLA_contig2920 2920 THRCLA_contig2921 2921 THRCLA_contig2922 2922 THRCLA_contig2923 2923 THRCLA_contig2924 2924 THRCLA_contig2925 2925 THRCLA_contig2926 2926 THRCLA_contig2927 2927 THRCLA_contig2928 2928 THRCLA_contig2929 2929 THRCLA_contig2930 2930 THRCLA_contig2931 2931 THRCLA_contig2932 2932 THRCLA_contig2933 2933 THRCLA_contig2934 2934 THRCLA_contig2935 2935 THRCLA_contig2936 2936 THRCLA_contig2937 2937 THRCLA_contig2938 2938 THRCLA_contig2939 2939 THRCLA_contig2940 2940 THRCLA_contig2941 2941 THRCLA_contig2942 2942 THRCLA_contig2943 2943 THRCLA_contig2944 2944 THRCLA_contig2945 2945 THRCLA_contig2946 2946 THRCLA_contig2947 2947 THRCLA_contig2948 2948 THRCLA_contig2949 2949 THRCLA_contig2950 2950 THRCLA_contig2951 2951 THRCLA_contig2952 2952 THRCLA_contig2953 2953 THRCLA_contig2954 2954 THRCLA_contig2955 2955 THRCLA_contig2956 2956 THRCLA_contig2957 2957 THRCLA_contig2958 2958 THRCLA_contig2959 2959 THRCLA_contig2960 2960 THRCLA_contig2961 2961 THRCLA_contig2962 2962 THRCLA_contig2963 2963 THRCLA_contig2964 2964 THRCLA_contig2965 2965 THRCLA_contig2966 2966 THRCLA_contig2967 2967 THRCLA_contig2968 2968 THRCLA_contig2969 2969 THRCLA_contig2970 2970 THRCLA_contig2971 2971 THRCLA_contig2972 2972 THRCLA_contig2973 2973 THRCLA_contig2974 2974 THRCLA_contig2975 2975 THRCLA_contig2976 2976 THRCLA_contig2977 2977 THRCLA_contig2978 2978 THRCLA_contig2979 2979 THRCLA_contig2980 2980 THRCLA_contig2981 2981 THRCLA_contig2982 2982 THRCLA_contig2983 2983 THRCLA_contig2984 2984 THRCLA_contig2985 2985 THRCLA_contig2986 2986 THRCLA_contig2987 2987 THRCLA_contig2988 2988 THRCLA_contig2989 2989 THRCLA_contig2990 2990 THRCLA_contig2991 2991 THRCLA_contig2992 2992 THRCLA_contig2993 2993 THRCLA_contig2994 2994 THRCLA_contig2995 2995 THRCLA_contig2996 2996 THRCLA_contig2997 2997 THRCLA_contig2998 2998 THRCLA_contig2999 2999 THRCLA_contig3000 3000 THRCLA_contig3001 3001 THRCLA_contig3002 3002 THRCLA_contig3003 3003 THRCLA_contig3004 3004 THRCLA_contig3005 3005 THRCLA_contig3006 3006 THRCLA_contig3007 3007 THRCLA_contig3008 3008 THRCLA_contig3009 3009 THRCLA_contig3010 3010 THRCLA_contig3011 3011 THRCLA_contig3012 3012 THRCLA_contig3013 3013 THRCLA_contig3014 3014 THRCLA_contig3015 3015 THRCLA_contig3016 3016 THRCLA_contig3017 3017 THRCLA_contig3018 3018 THRCLA_contig3019 3019 THRCLA_contig3020 3020 THRCLA_contig3021 3021 THRCLA_contig3022 3022 THRCLA_contig3023 3023 THRCLA_contig3024 3024 THRCLA_contig3025 3025 THRCLA_contig3026 3026 THRCLA_contig3027 3027 THRCLA_contig3028 3028 THRCLA_contig3029 3029 THRCLA_contig3030 3030 THRCLA_contig3031 3031 THRCLA_contig3032 3032 THRCLA_contig3033 3033 THRCLA_contig3034 3034 THRCLA_contig3035 3035 THRCLA_contig3036 3036 THRCLA_contig3037 3037 THRCLA_contig3038 3038 THRCLA_contig3039 3039 THRCLA_contig3040 3040 THRCLA_contig3041 3041 THRCLA_contig3042 3042 THRCLA_contig3043 3043 THRCLA_contig3044 3044 THRCLA_contig3045 3045 THRCLA_contig3046 3046 THRCLA_contig3047 3047 THRCLA_contig3048 3048 THRCLA_contig3049 3049 THRCLA_contig3050 3050 THRCLA_contig3051 3051 THRCLA_contig3052 3052 THRCLA_contig3053 3053 THRCLA_contig3054 3054 THRCLA_contig3055 3055 THRCLA_contig3056 3056 THRCLA_contig3057 3057 THRCLA_contig3058 3058 THRCLA_contig3059 3059 THRCLA_contig3060 3060 THRCLA_contig3061 3061 THRCLA_contig3062 3062 THRCLA_contig3063 3063 THRCLA_contig3064 3064 THRCLA_contig3065 3065 THRCLA_contig3066 3066 THRCLA_contig3067 3067 THRCLA_contig3068 3068 THRCLA_contig3069 3069 THRCLA_contig3070 3070 THRCLA_contig3071 3071 THRCLA_contig3072 3072 THRCLA_contig3073 3073 THRCLA_contig3074 3074 THRCLA_contig3075 3075 THRCLA_contig3076 3076 THRCLA_contig3077 3077 THRCLA_contig3078 3078 THRCLA_contig3079 3079 THRCLA_contig3080 3080 THRCLA_contig3081 3081 THRCLA_contig3082 3082 THRCLA_contig3083 3083 THRCLA_contig3084 3084 THRCLA_contig3085 3085 THRCLA_contig3086 3086 THRCLA_contig3087 3087 THRCLA_contig3088 3088 THRCLA_contig3089 3089 THRCLA_contig3090 3090 THRCLA_contig3091 3091 THRCLA_contig3092 3092 THRCLA_contig3093 3093 THRCLA_contig3094 3094 THRCLA_contig3095 3095 THRCLA_contig3096 3096 THRCLA_contig3097 3097 THRCLA_contig3098 3098 THRCLA_contig3099 3099 THRCLA_contig3100 3100 THRCLA_contig3101 3101 THRCLA_contig3102 3102 THRCLA_contig3103 3103 THRCLA_contig3104 3104 THRCLA_contig3105 3105 THRCLA_contig3106 3106 THRCLA_contig3107 3107 THRCLA_contig3108 3108 THRCLA_contig3109 3109 THRCLA_contig3110 3110 THRCLA_contig3111 3111 THRCLA_contig3112 3112 THRCLA_contig3113 3113 THRCLA_contig3114 3114 THRCLA_contig3115 3115 THRCLA_contig3116 3116 THRCLA_contig3117 3117 THRCLA_contig3118 3118 THRCLA_contig3119 3119 THRCLA_contig3120 3120 THRCLA_contig3121 3121 THRCLA_contig3122 3122 THRCLA_contig3123 3123 THRCLA_contig3124 3124 THRCLA_contig3125 3125 THRCLA_contig3126 3126 THRCLA_contig3127 3127 THRCLA_contig3128 3128 THRCLA_contig3129 3129 THRCLA_contig3130 3130 THRCLA_contig3131 3131 THRCLA_contig3132 3132 THRCLA_contig3133 3133 THRCLA_contig3134 3134 THRCLA_contig3135 3135 THRCLA_contig3136 3136 THRCLA_contig3137 3137 THRCLA_contig3138 3138 THRCLA_contig3139 3139 THRCLA_contig3140 3140 THRCLA_contig3141 3141 THRCLA_contig3142 3142 THRCLA_contig3143 3143 THRCLA_contig3144 3144 THRCLA_contig3145 3145 THRCLA_contig3146 3146 THRCLA_contig3147 3147 THRCLA_contig3148 3148 THRCLA_contig3149 3149 THRCLA_contig3150 3150 THRCLA_contig3151 3151 THRCLA_contig3152 3152 THRCLA_contig3153 3153 THRCLA_contig3154 3154 THRCLA_contig3155 3155 THRCLA_contig3156 3156 THRCLA_contig3157 3157 THRCLA_contig3158 3158 THRCLA_contig3159 3159 THRCLA_contig3160 3160 THRCLA_contig3161 3161 THRCLA_contig3162 3162 THRCLA_contig3163 3163 THRCLA_contig3164 3164 THRCLA_contig3165 3165 THRCLA_contig3166 3166 THRCLA_contig3167 3167 THRCLA_contig3168 3168 THRCLA_contig3169 3169 THRCLA_contig3170 3170 THRCLA_contig3171 3171 THRCLA_contig3172 3172 THRCLA_contig3173 3173 THRCLA_contig3174 3174 THRCLA_contig3175 3175 THRCLA_contig3176 3176 THRCLA_contig3177 3177 THRCLA_contig3178 3178 THRCLA_contig3179 3179 THRCLA_contig3180 3180 THRCLA_contig3181 3181 THRCLA_contig3182 3182 THRCLA_contig3183 3183 THRCLA_contig3184 3184 THRCLA_contig3185 3185 THRCLA_contig3186 3186 THRCLA_contig3187 3187 THRCLA_contig3188 3188 THRCLA_contig3189 3189 THRCLA_contig3190 3190 THRCLA_contig3191 3191 THRCLA_contig3192 3192 THRCLA_contig3193 3193 THRCLA_contig3194 3194 THRCLA_contig3195 3195 THRCLA_contig3196 3196 THRCLA_contig3197 3197 THRCLA_contig3198 3198 THRCLA_contig3199 3199 THRCLA_contig3200 3200 THRCLA_contig3201 3201 THRCLA_contig3202 3202 THRCLA_contig3203 3203 THRCLA_contig3204 3204 THRCLA_contig3205 3205 THRCLA_contig3206 3206 THRCLA_contig3207 3207 THRCLA_contig3208 3208 THRCLA_contig3209 3209 THRCLA_contig3210 3210 THRCLA_contig3211 3211 THRCLA_contig3212 3212 THRCLA_contig3213 3213 THRCLA_contig3214 3214 THRCLA_contig3215 3215 THRCLA_contig3216 3216 THRCLA_contig3217 3217 THRCLA_contig3218 3218 THRCLA_contig3219 3219 THRCLA_contig3220 3220 THRCLA_contig3221 3221 THRCLA_contig3222 3222 THRCLA_contig3223 3223 THRCLA_contig3224 3224 THRCLA_contig3225 3225 THRCLA_contig3226 3226 THRCLA_contig3227 3227 THRCLA_contig3228 3228 THRCLA_contig3229 3229 THRCLA_contig3230 3230 THRCLA_contig3231 3231 THRCLA_contig3232 3232 THRCLA_contig3233 3233 THRCLA_contig3234 3234 THRCLA_contig3235 3235 THRCLA_contig3236 3236 THRCLA_contig3237 3237 THRCLA_contig3238 3238 THRCLA_contig3239 3239 THRCLA_contig3240 3240 THRCLA_contig3241 3241 THRCLA_contig3242 3242 THRCLA_contig3243 3243 THRCLA_contig3244 3244 THRCLA_contig3245 3245 THRCLA_contig3246 3246 THRCLA_contig3247 3247 THRCLA_contig3248 3248 THRCLA_contig3249 3249 THRCLA_contig3250 3250 THRCLA_contig3251 3251 THRCLA_contig3252 3252 THRCLA_contig3253 3253 THRCLA_contig3254 3254 THRCLA_contig3255 3255 THRCLA_contig3256 3256 THRCLA_contig3257 3257 THRCLA_contig3258 3258 THRCLA_contig3259 3259 THRCLA_contig3260 3260 THRCLA_contig3261 3261 THRCLA_contig3262 3262 THRCLA_contig3263 3263 THRCLA_contig3264 3264 THRCLA_contig3265 3265 THRCLA_contig3266 3266 THRCLA_contig3267 3267 THRCLA_contig3268 3268 THRCLA_contig3269 3269 THRCLA_contig3270 3270 THRCLA_contig3271 3271 THRCLA_contig3272 3272 THRCLA_contig3273 3273 THRCLA_contig3274 3274 THRCLA_contig3275 3275 THRCLA_contig3276 3276 THRCLA_contig3277 3277 THRCLA_contig3278 3278 THRCLA_contig3279 3279 THRCLA_contig3280 3280 THRCLA_contig3281 3281 THRCLA_contig3282 3282 THRCLA_contig3283 3283 THRCLA_contig3284 3284 THRCLA_contig3285 3285 THRCLA_contig3286 3286 THRCLA_contig3287 3287 THRCLA_contig3288 3288 THRCLA_contig3289 3289 THRCLA_contig3290 3290 THRCLA_contig3291 3291 THRCLA_contig3292 3292 THRCLA_contig3293 3293 THRCLA_contig3294 3294 THRCLA_contig3295 3295 THRCLA_contig3296 3296 THRCLA_contig3297 3297 THRCLA_contig3298 3298 THRCLA_contig3299 3299 THRCLA_contig3300 3300 THRCLA_contig3301 3301 THRCLA_contig3302 3302 THRCLA_contig3303 3303 THRCLA_contig3304 3304 THRCLA_contig3305 3305 THRCLA_contig3306 3306 THRCLA_contig3307 3307 THRCLA_contig3308 3308 THRCLA_contig3309 3309 THRCLA_contig3310 3310 THRCLA_contig3311 3311 THRCLA_contig3312 3312 THRCLA_contig3313 3313 THRCLA_contig3314 3314 THRCLA_contig3315 3315 THRCLA_contig3316 3316 THRCLA_contig3317 3317 THRCLA_contig3318 3318 THRCLA_contig3319 3319 THRCLA_contig3320 3320 THRCLA_contig3321 3321 THRCLA_contig3322 3322 THRCLA_contig3323 3323 THRCLA_contig3324 3324 THRCLA_contig3325 3325 THRCLA_contig3326 3326 THRCLA_contig3327 3327 THRCLA_contig3328 3328 THRCLA_contig3329 3329 THRCLA_contig3330 3330 THRCLA_contig3331 3331 THRCLA_contig3332 3332 THRCLA_contig3333 3333 THRCLA_contig3334 3334 THRCLA_contig3335 3335 THRCLA_contig3336 3336 THRCLA_contig3337 3337 THRCLA_contig3338 3338 THRCLA_contig3339 3339 THRCLA_contig3340 3340 THRCLA_contig3341 3341 THRCLA_contig3342 3342 THRCLA_contig3343 3343 THRCLA_contig3344 3344 THRCLA_contig3345 3345 THRCLA_contig3346 3346 THRCLA_contig3347 3347 THRCLA_contig3348 3348 THRCLA_contig3349 3349 THRCLA_contig3350 3350 THRCLA_contig3351 3351 THRCLA_contig3352 3352 THRCLA_contig3353 3353 THRCLA_contig3354 3354 THRCLA_contig3355 3355 THRCLA_contig3356 3356 THRCLA_contig3357 3357 THRCLA_contig3358 3358 THRCLA_contig3359 3359 THRCLA_contig3360 3360 THRCLA_contig3361 3361 THRCLA_contig3362 3362 THRCLA_contig3363 3363 THRCLA_contig3364 3364 THRCLA_contig3365 3365 THRCLA_contig3366 3366 THRCLA_contig3367 3367 THRCLA_contig3368 3368 THRCLA_contig3369 3369 THRCLA_contig3370 3370 THRCLA_contig3371 3371 THRCLA_contig3372 3372 THRCLA_contig3373 3373 THRCLA_contig3374 3374 THRCLA_contig3375 3375 THRCLA_contig3376 3376 THRCLA_contig3377 3377 THRCLA_contig3378 3378 THRCLA_contig3379 3379 THRCLA_contig3380 3380 THRCLA_contig3381 3381 THRCLA_contig3382 3382 THRCLA_contig3383 3383 THRCLA_contig3384 3384 THRCLA_contig3385 3385 THRCLA_contig3386 3386 THRCLA_contig3387 3387 THRCLA_contig3388 3388 THRCLA_contig3389 3389 THRCLA_contig3390 3390 THRCLA_contig3391 3391 THRCLA_contig3392 3392 THRCLA_contig3393 3393 THRCLA_contig3394 3394 THRCLA_contig3395 3395 THRCLA_contig3396 3396 THRCLA_contig3397 3397 THRCLA_contig3398 3398 THRCLA_contig3399 3399 THRCLA_contig3400 3400 THRCLA_contig3401 3401 THRCLA_contig3402 3402 THRCLA_contig3403 3403 THRCLA_contig3404 3404 THRCLA_contig3405 3405 THRCLA_contig3406 3406 THRCLA_contig3407 3407 THRCLA_contig3408 3408 THRCLA_contig3409 3409 THRCLA_contig3410 3410 THRCLA_contig3411 3411 THRCLA_contig3412 3412 THRCLA_contig3413 3413 THRCLA_contig3414 3414 THRCLA_contig3415 3415 THRCLA_contig3416 3416 THRCLA_contig3417 3417 THRCLA_contig3418 3418 THRCLA_contig3419 3419 THRCLA_contig3420 3420 THRCLA_contig3421 3421 THRCLA_contig3422 3422 THRCLA_contig3423 3423 THRCLA_contig3424 3424 THRCLA_contig3425 3425 THRCLA_contig3426 3426 THRCLA_contig3427 3427 THRCLA_contig3428 3428 THRCLA_contig3429 3429 THRCLA_contig3430 3430 THRCLA_contig3431 3431 THRCLA_contig3432 3432 THRCLA_contig3433 3433 THRCLA_contig3434 3434 THRCLA_contig3435 3435 THRCLA_contig3436 3436 THRCLA_contig3437 3437 THRCLA_contig3438 3438 THRCLA_contig3439 3439 THRCLA_contig3440 3440 THRCLA_contig3441 3441 THRCLA_contig3442 3442 THRCLA_contig3443 3443 THRCLA_contig3444 3444 THRCLA_contig3445 3445 THRCLA_contig3446 3446 THRCLA_contig3447 3447 THRCLA_contig3448 3448 THRCLA_contig3449 3449 THRCLA_contig3450 3450 THRCLA_contig3451 3451 THRCLA_contig3452 3452 THRCLA_contig3453 3453 THRCLA_contig3454 3454 THRCLA_contig3455 3455 THRCLA_contig3456 3456 THRCLA_contig3457 3457 THRCLA_contig3458 3458 THRCLA_contig3459 3459 THRCLA_contig3460 3460 THRCLA_contig3461 3461 THRCLA_contig3462 3462 THRCLA_contig3463 3463 THRCLA_contig3464 3464 THRCLA_contig3465 3465 THRCLA_contig3466 3466 THRCLA_contig3467 3467 THRCLA_contig3468 3468 THRCLA_contig3469 3469 THRCLA_contig3470 3470 THRCLA_contig3471 3471 THRCLA_contig3472 3472 THRCLA_contig3473 3473 THRCLA_contig3474 3474 THRCLA_contig3475 3475 THRCLA_contig3476 3476 THRCLA_contig3477 3477 THRCLA_contig3478 3478 THRCLA_contig3479 3479 THRCLA_contig3480 3480 THRCLA_contig3481 3481 THRCLA_contig3482 3482 THRCLA_contig3483 3483 THRCLA_contig3484 3484 THRCLA_contig3485 3485 THRCLA_contig3486 3486 THRCLA_contig3487 3487 THRCLA_contig3488 3488 THRCLA_contig3489 3489 THRCLA_contig3490 3490 THRCLA_contig3491 3491 THRCLA_contig3492 3492 THRCLA_contig3493 3493 THRCLA_contig3494 3494 THRCLA_contig3495 3495 THRCLA_contig3496 3496 THRCLA_contig3497 3497 THRCLA_contig3498 3498 THRCLA_contig3499 3499 THRCLA_contig3500 3500 THRCLA_contig3501 3501 THRCLA_contig3502 3502 THRCLA_contig3503 3503 THRCLA_contig3504 3504 THRCLA_contig3505 3505 THRCLA_contig3506 3506 THRCLA_contig3507 3507 THRCLA_contig3508 3508 THRCLA_contig3509 3509 THRCLA_contig3510 3510 THRCLA_contig3511 3511 THRCLA_contig3512 3512 THRCLA_contig3513 3513 THRCLA_contig3514 3514 THRCLA_contig3515 3515 THRCLA_contig3516 3516 THRCLA_contig3517 3517 THRCLA_contig3518 3518 THRCLA_contig3519 3519 THRCLA_contig3520 3520 THRCLA_contig3521 3521 THRCLA_contig3522 3522 THRCLA_contig3523 3523 THRCLA_contig3524 3524 THRCLA_contig3525 3525 THRCLA_contig3526 3526 THRCLA_contig3527 3527 THRCLA_contig3528 3528 THRCLA_contig3529 3529 THRCLA_contig3530 3530 THRCLA_contig3531 3531 THRCLA_contig3532 3532 THRCLA_contig3533 3533 THRCLA_contig3534 3534 THRCLA_contig3535 3535 THRCLA_contig3536 3536 THRCLA_contig3537 3537 THRCLA_contig3538 3538 THRCLA_contig3539 3539 THRCLA_contig3540 3540 THRCLA_contig3541 3541 THRCLA_contig3542 3542 THRCLA_contig3543 3543 THRCLA_contig3544 3544 THRCLA_contig3545 3545 THRCLA_contig3546 3546 THRCLA_contig3547 3547 THRCLA_contig3548 3548 THRCLA_contig3549 3549 THRCLA_contig3550 3550 THRCLA_contig3551 3551 THRCLA_contig3552 3552 THRCLA_contig3553 3553 THRCLA_contig3554 3554 THRCLA_contig3555 3555 THRCLA_contig3556 3556 THRCLA_contig3557 3557 THRCLA_contig3558 3558 THRCLA_contig3559 3559 THRCLA_contig3560 3560 THRCLA_contig3561 3561 THRCLA_contig3562 3562 THRCLA_contig3563 3563 THRCLA_contig3564 3564 THRCLA_contig3565 3565 THRCLA_contig3566 3566 THRCLA_contig3567 3567 THRCLA_contig3568 3568 THRCLA_contig3569 3569 THRCLA_contig3570 3570 THRCLA_contig3571 3571 THRCLA_contig3572 3572 THRCLA_contig3573 3573 THRCLA_contig3574 3574 THRCLA_contig3575 3575 THRCLA_contig3576 3576 THRCLA_contig3577 3577 THRCLA_contig3578 3578 THRCLA_contig3579 3579 THRCLA_contig3580 3580 THRCLA_contig3581 3581 THRCLA_contig3582 3582 THRCLA_contig3583 3583 THRCLA_contig3584 3584 THRCLA_contig3585 3585 THRCLA_contig3586 3586 THRCLA_contig3587 3587 THRCLA_contig3588 3588 THRCLA_contig3589 3589 THRCLA_contig3590 3590 THRCLA_contig3591 3591 THRCLA_contig3592 3592 THRCLA_contig3593 3593 THRCLA_contig3594 3594 THRCLA_contig3595 3595 THRCLA_contig3596 3596 THRCLA_contig3597 3597 THRCLA_contig3598 3598 THRCLA_contig3599 3599 THRCLA_contig3600 3600 THRCLA_contig3601 3601 THRCLA_contig3602 3602 THRCLA_contig3603 3603 THRCLA_contig3604 3604 THRCLA_contig3605 3605 THRCLA_contig3606 3606 THRCLA_contig3607 3607 THRCLA_contig3608 3608 THRCLA_contig3609 3609 THRCLA_contig3610 3610 THRCLA_contig3611 3611 THRCLA_contig3612 3612 THRCLA_contig3613 3613 THRCLA_contig3614 3614 THRCLA_contig3615 3615 THRCLA_contig3616 3616 THRCLA_contig3617 3617 THRCLA_contig3618 3618 THRCLA_contig3619 3619 THRCLA_contig3620 3620 THRCLA_contig3621 3621 THRCLA_contig3622 3622 THRCLA_contig3623 3623 THRCLA_contig3624 3624 THRCLA_contig3625 3625 THRCLA_contig3626 3626 THRCLA_contig3627 3627 THRCLA_contig3628 3628 THRCLA_contig3629 3629 THRCLA_contig3630 3630 THRCLA_contig3631 3631 THRCLA_contig3632 3632 THRCLA_contig3633 3633 THRCLA_contig3634 3634 THRCLA_contig3635 3635 THRCLA_contig3636 3636 THRCLA_contig3637 3637 THRCLA_contig3638 3638 THRCLA_contig3639 3639 THRCLA_contig3640 3640 THRCLA_contig3641 3641 THRCLA_contig3642 3642 THRCLA_contig3643 3643 THRCLA_contig3644 3644 THRCLA_contig3645 3645 THRCLA_contig3646 3646 THRCLA_contig3647 3647 THRCLA_contig3648 3648 THRCLA_contig3649 3649 THRCLA_contig3650 3650 THRCLA_contig3651 3651 THRCLA_contig3652 3652 THRCLA_contig3653 3653 THRCLA_contig3654 3654 THRCLA_contig3655 3655 THRCLA_contig3656 3656 THRCLA_contig3657 3657 THRCLA_contig3658 3658 THRCLA_contig3659 3659 THRCLA_contig3660 3660 THRCLA_contig3661 3661 THRCLA_contig3662 3662 THRCLA_contig3663 3663 THRCLA_contig3664 3664 THRCLA_contig3665 3665 THRCLA_contig3666 3666 THRCLA_contig3667 3667 THRCLA_contig3668 3668 THRCLA_contig3669 3669 THRCLA_contig3670 3670 THRCLA_contig3671 3671 THRCLA_contig3672 3672 THRCLA_contig3673 3673 THRCLA_contig3674 3674 THRCLA_contig3675 3675 THRCLA_contig3676 3676 THRCLA_contig3677 3677 THRCLA_contig3678 3678 THRCLA_contig3679 3679 THRCLA_contig3680 3680 THRCLA_contig3681 3681 THRCLA_contig3682 3682 THRCLA_contig3683 3683 THRCLA_contig3684 3684 THRCLA_contig3685 3685 THRCLA_contig3686 3686 THRCLA_contig3687 3687 THRCLA_contig3688 3688 THRCLA_contig3689 3689 THRCLA_contig3690 3690 THRCLA_contig3691 3691 THRCLA_contig3692 3692 THRCLA_contig3693 3693 THRCLA_contig3694 3694 THRCLA_contig3695 3695 THRCLA_contig3696 3696 THRCLA_contig3697 3697 THRCLA_contig3698 3698 THRCLA_contig3699 3699 THRCLA_contig3700 3700 THRCLA_contig3701 3701 THRCLA_contig3702 3702 THRCLA_contig3703 3703 THRCLA_contig3704 3704 THRCLA_contig3705 3705 THRCLA_contig3706 3706 THRCLA_contig3707 3707 THRCLA_contig3708 3708 THRCLA_contig3709 3709 THRCLA_contig3710 3710 THRCLA_contig3711 3711 THRCLA_contig3712 3712 THRCLA_contig3713 3713 THRCLA_contig3714 3714 THRCLA_contig3715 3715 THRCLA_contig3716 3716 THRCLA_contig3717 3717 THRCLA_contig3718 3718 THRCLA_contig3719 3719 THRCLA_contig3720 3720 THRCLA_contig3721 3721 THRCLA_contig3722 3722 THRCLA_contig3723 3723 THRCLA_contig3724 3724 THRCLA_contig3725 3725 THRCLA_contig3726 3726 THRCLA_contig3727 3727 THRCLA_contig3728 3728 THRCLA_contig3729 3729 THRCLA_contig3730 3730 THRCLA_contig3731 3731 THRCLA_contig3732 3732 THRCLA_contig3733 3733 THRCLA_contig3734 3734 THRCLA_contig3735 3735 THRCLA_contig3736 3736 THRCLA_contig3737 3737 THRCLA_contig3738 3738 THRCLA_contig3739 3739 THRCLA_contig3740 3740 THRCLA_contig3741 3741 THRCLA_contig3742 3742 THRCLA_contig3743 3743 THRCLA_contig3744 3744 THRCLA_contig3745 3745 THRCLA_contig3746 3746 THRCLA_contig3747 3747 THRCLA_contig3748 3748 THRCLA_contig3749 3749 THRCLA_contig3750 3750 THRCLA_contig3751 3751 THRCLA_contig3752 3752 THRCLA_contig3753 3753 THRCLA_contig3754 3754 THRCLA_contig3755 3755 THRCLA_contig3756 3756 THRCLA_contig3757 3757 THRCLA_contig3758 3758 THRCLA_contig3759 3759 THRCLA_contig3760 3760 THRCLA_contig3761 3761 THRCLA_contig3762 3762 THRCLA_contig3763 3763 THRCLA_contig3764 3764 THRCLA_contig3765 3765 THRCLA_contig3766 3766 THRCLA_contig3767 3767 THRCLA_contig3768 3768 THRCLA_contig3769 3769 THRCLA_contig3770 3770 THRCLA_contig3771 3771 THRCLA_contig3772 3772 THRCLA_contig3773 3773 THRCLA_contig3774 3774 THRCLA_contig3775 3775 THRCLA_contig3776 3776 THRCLA_contig3777 3777 THRCLA_contig3778 3778 THRCLA_contig3779 3779 THRCLA_contig3780 3780 THRCLA_contig3781 3781 THRCLA_contig3782 3782 THRCLA_contig3783 3783 THRCLA_contig3784 3784 THRCLA_contig3785 3785 THRCLA_contig3786 3786 THRCLA_contig3787 3787 THRCLA_contig3788 3788 THRCLA_contig3789 3789 THRCLA_contig3790 3790 THRCLA_contig3791 3791 THRCLA_contig3792 3792 THRCLA_contig3793 3793 THRCLA_contig3794 3794 THRCLA_contig3795 3795 THRCLA_contig3796 3796 THRCLA_contig3797 3797 THRCLA_contig3798 3798 THRCLA_contig3799 3799 THRCLA_contig3800 3800 THRCLA_contig3801 3801 THRCLA_contig3802 3802 THRCLA_contig3803 3803 THRCLA_contig3804 3804 THRCLA_contig3805 3805 THRCLA_contig3806 3806 THRCLA_contig3807 3807 THRCLA_contig3808 3808 THRCLA_contig3809 3809 THRCLA_contig3810 3810 THRCLA_contig3811 3811 THRCLA_contig3812 3812 THRCLA_contig3813 3813 THRCLA_contig3814 3814 THRCLA_contig3815 3815 THRCLA_contig3816 3816 THRCLA_contig3817 3817 THRCLA_contig3818 3818 THRCLA_contig3819 3819 THRCLA_contig3820 3820 THRCLA_contig3821 3821 THRCLA_contig3822 3822 THRCLA_contig3823 3823 THRCLA_contig3824 3824 THRCLA_contig3825 3825 THRCLA_contig3826 3826 THRCLA_contig3827 3827 THRCLA_contig3828 3828 THRCLA_contig3829 3829 THRCLA_contig3830 3830 THRCLA_contig3831 3831 THRCLA_contig3832 3832 THRCLA_contig3833 3833 THRCLA_contig3834 3834 THRCLA_contig3835 3835 THRCLA_contig3836 3836 THRCLA_contig3837 3837 THRCLA_contig3838 3838 THRCLA_contig3839 3839 THRCLA_contig3840 3840 THRCLA_contig3841 3841 THRCLA_contig3842 3842 THRCLA_contig3843 3843 THRCLA_contig3844 3844 THRCLA_contig3845 3845 THRCLA_contig3846 3846 THRCLA_contig3847 3847 THRCLA_contig3848 3848 THRCLA_contig3849 3849 THRCLA_contig3850 3850 THRCLA_contig3851 3851 THRCLA_contig3852 3852 THRCLA_contig3853 3853 THRCLA_contig3854 3854 THRCLA_contig3855 3855 THRCLA_contig3856 3856 THRCLA_contig3857 3857 THRCLA_contig3858 3858 THRCLA_contig3859 3859 THRCLA_contig3860 3860 THRCLA_contig3861 3861 THRCLA_contig3862 3862 THRCLA_contig3863 3863 THRCLA_contig3864 3864 THRCLA_contig3865 3865 THRCLA_contig3866 3866 THRCLA_contig3867 3867 THRCLA_contig3868 3868 THRCLA_contig3869 3869 THRCLA_contig3870 3870 THRCLA_contig3871 3871 THRCLA_contig3872 3872 THRCLA_contig3873 3873 THRCLA_contig3874 3874 THRCLA_contig3875 3875 THRCLA_contig3876 3876 THRCLA_contig3877 3877 THRCLA_contig3878 3878 THRCLA_contig3879 3879 THRCLA_contig3880 3880 THRCLA_contig3881 3881 THRCLA_contig3882 3882 THRCLA_contig3883 3883 THRCLA_contig3884 3884 THRCLA_contig3885 3885 THRCLA_contig3886 3886 THRCLA_contig3887 3887 THRCLA_contig3888 3888 THRCLA_contig3889 3889 THRCLA_contig3890 3890 THRCLA_contig3891 3891 THRCLA_contig3892 3892 THRCLA_contig3893 3893 THRCLA_contig3894 3894 THRCLA_contig3895 3895 THRCLA_contig3896 3896 THRCLA_contig3897 3897 THRCLA_contig3898 3898 THRCLA_contig3899 3899 THRCLA_contig3900 3900 THRCLA_contig3901 3901 THRCLA_contig3902 3902 THRCLA_contig3903 3903 THRCLA_contig3904 3904 THRCLA_contig3905 3905 THRCLA_contig3906 3906 THRCLA_contig3907 3907 THRCLA_contig3908 3908 THRCLA_contig3909 3909 THRCLA_contig3910 3910 THRCLA_contig3911 3911 THRCLA_contig3912 3912 THRCLA_contig3913 3913 THRCLA_contig3914 3914 THRCLA_contig3915 3915 THRCLA_contig3916 3916 THRCLA_contig3917 3917 THRCLA_contig3918 3918 THRCLA_contig3919 3919 THRCLA_contig3920 3920 THRCLA_contig3921 3921 THRCLA_contig3922 3922 THRCLA_contig3923 3923 THRCLA_contig3924 3924 THRCLA_contig3925 3925 THRCLA_contig3926 3926 THRCLA_contig3927 3927 THRCLA_contig3928 3928 THRCLA_contig3929 3929 THRCLA_contig3930 3930 THRCLA_contig3931 3931 THRCLA_contig3932 3932 THRCLA_contig3933 3933 THRCLA_contig3934 3934 THRCLA_contig3935 3935 THRCLA_contig3936 3936 THRCLA_contig3937 3937 THRCLA_contig3938 3938 THRCLA_contig3939 3939 THRCLA_contig3940 3940 THRCLA_contig3941 3941 THRCLA_contig3942 3942 THRCLA_contig3943 3943 THRCLA_contig3944 3944 THRCLA_contig3945 3945 THRCLA_contig3946 3946 THRCLA_contig3947 3947 THRCLA_contig3948 3948 THRCLA_contig3949 3949 THRCLA_contig3950 3950 THRCLA_contig3951 3951 THRCLA_contig3952 3952 THRCLA_contig3953 3953 THRCLA_contig3954 3954 THRCLA_contig3955 3955 THRCLA_contig3956 3956 THRCLA_contig3957 3957 THRCLA_contig3958 3958 THRCLA_contig3959 3959 THRCLA_contig3960 3960 THRCLA_contig3961 3961 THRCLA_contig3962 3962 THRCLA_contig3963 3963 THRCLA_contig3964 3964 THRCLA_contig3965 3965 THRCLA_contig3966 3966 THRCLA_contig3967 3967 THRCLA_contig3968 3968 THRCLA_contig3969 3969 THRCLA_contig3970 3970 THRCLA_contig3971 3971 THRCLA_contig3972 3972 THRCLA_contig3973 3973 THRCLA_contig3974 3974 THRCLA_contig3975 3975 THRCLA_contig3976 3976 THRCLA_contig3977 3977 THRCLA_contig3978 3978 THRCLA_contig3979 3979 THRCLA_contig3980 3980 THRCLA_contig3981 3981 THRCLA_contig3982 3982 THRCLA_contig3983 3983 THRCLA_contig3984 3984 THRCLA_contig3985 3985 THRCLA_contig3986 3986 THRCLA_contig3987 3987 THRCLA_contig3988 3988 THRCLA_contig3989 3989 THRCLA_contig3990 3990 THRCLA_contig3991 3991 THRCLA_contig3992 3992 THRCLA_contig3993 3993 THRCLA_contig3994 3994 THRCLA_contig3995 3995 THRCLA_contig3996 3996 THRCLA_contig3997 3997 THRCLA_contig3998 3998 THRCLA_contig3999 3999 THRCLA_contig4000 4000 THRCLA_contig4001 4001 THRCLA_contig4002 4002 THRCLA_contig4003 4003 THRCLA_contig4004 4004 THRCLA_contig4005 4005 THRCLA_contig4006 4006 THRCLA_contig4007 4007 THRCLA_contig4008 4008 THRCLA_contig4009 4009 THRCLA_contig4010 4010 THRCLA_contig4011 4011 THRCLA_contig4012 4012 THRCLA_contig4013 4013 THRCLA_contig4014 4014 THRCLA_contig4015 4015 THRCLA_contig4016 4016 THRCLA_contig4017 4017 THRCLA_contig4018 4018 THRCLA_contig4019 4019 THRCLA_contig4020 4020 THRCLA_contig4021 4021 THRCLA_contig4022 4022 THRCLA_contig4023 4023 THRCLA_contig4024 4024 THRCLA_contig4025 4025 THRCLA_contig4026 4026 THRCLA_contig4027 4027 THRCLA_contig4028 4028 THRCLA_contig4029 4029 THRCLA_contig4030 4030 THRCLA_contig4031 4031 THRCLA_contig4032 4032 THRCLA_contig4033 4033 THRCLA_contig4034 4034 THRCLA_contig4035 4035 THRCLA_contig4036 4036 THRCLA_contig4037 4037 THRCLA_contig4038 4038 THRCLA_contig4039 4039 THRCLA_contig4040 4040 THRCLA_contig4041 4041 THRCLA_contig4042 4042 THRCLA_contig4043 4043 THRCLA_contig4044 4044 THRCLA_contig4045 4045 THRCLA_contig4046 4046 THRCLA_contig4047 4047 THRCLA_contig4048 4048 THRCLA_contig4049 4049 THRCLA_contig4050 4050 THRCLA_contig4051 4051 THRCLA_contig4052 4052 THRCLA_contig4053 4053 THRCLA_contig4054 4054 THRCLA_contig4055 4055 THRCLA_contig4056 4056 THRCLA_contig4057 4057 THRCLA_contig4058 4058 THRCLA_contig4059 4059 THRCLA_contig4060 4060 THRCLA_contig4061 4061 THRCLA_contig4062 4062 THRCLA_contig4063 4063 THRCLA_contig4064 4064 THRCLA_contig4065 4065 THRCLA_contig4066 4066 THRCLA_contig4067 4067 THRCLA_contig4068 4068 THRCLA_contig4069 4069 THRCLA_contig4070 4070 THRCLA_contig4071 4071 THRCLA_contig4072 4072 THRCLA_contig4073 4073 THRCLA_contig4074 4074 THRCLA_contig4075 4075 THRCLA_contig4076 4076 THRCLA_contig4077 4077 THRCLA_contig4078 4078 THRCLA_contig4079 4079 THRCLA_contig4080 4080 THRCLA_contig4081 4081 THRCLA_contig4082 4082 THRCLA_contig4083 4083 THRCLA_contig4084 4084 THRCLA_contig4085 4085 THRCLA_contig4086 4086 THRCLA_contig4087 4087 THRCLA_contig4088 4088 THRCLA_contig4089 4089 THRCLA_contig4090 4090 THRCLA_contig4091 4091 THRCLA_contig4092 4092 THRCLA_contig4093 4093 THRCLA_contig4094 4094 THRCLA_contig4095 4095 THRCLA_contig4096 4096 THRCLA_contig4097 4097 THRCLA_contig4098 4098 THRCLA_contig4099 4099 THRCLA_contig4100 4100 THRCLA_contig4101 4101 THRCLA_contig4102 4102 THRCLA_contig4103 4103 THRCLA_contig4104 4104 THRCLA_contig4105 4105 THRCLA_contig4106 4106 THRCLA_contig4107 4107 THRCLA_contig4108 4108 THRCLA_contig4109 4109 THRCLA_contig4110 4110 THRCLA_contig4111 4111 THRCLA_contig4112 4112 THRCLA_contig4113 4113 THRCLA_contig4114 4114 THRCLA_contig4115 4115 THRCLA_contig4116 4116 THRCLA_contig4117 4117 THRCLA_contig4118 4118 THRCLA_contig4119 4119 THRCLA_contig4120 4120 THRCLA_contig4121 4121 THRCLA_contig4122 4122 THRCLA_contig4123 4123 THRCLA_contig4124 4124 THRCLA_contig4125 4125 THRCLA_contig4126 4126 THRCLA_contig4127 4127 THRCLA_contig4128 4128 THRCLA_contig4129 4129 THRCLA_contig4130 4130 THRCLA_contig4131 4131 THRCLA_contig4132 4132 THRCLA_contig4133 4133 THRCLA_contig4134 4134 THRCLA_contig4135 4135 THRCLA_contig4136 4136 THRCLA_contig4137 4137 THRCLA_contig4138 4138 THRCLA_contig4139 4139 THRCLA_contig4140 4140 THRCLA_contig4141 4141 THRCLA_contig4142 4142 THRCLA_contig4143 4143 THRCLA_contig4144 4144 THRCLA_contig4145 4145 THRCLA_contig4146 4146 THRCLA_contig4147 4147 THRCLA_contig4148 4148 THRCLA_contig4149 4149 THRCLA_contig4150 4150 THRCLA_contig4151 4151 THRCLA_contig4152 4152 THRCLA_contig4153 4153 THRCLA_contig4154 4154 THRCLA_contig4155 4155 THRCLA_contig4156 4156 THRCLA_contig4157 4157 THRCLA_contig4158 4158 THRCLA_contig4159 4159 THRCLA_contig4160 4160 THRCLA_contig4161 4161 THRCLA_contig4162 4162 THRCLA_contig4163 4163 THRCLA_contig4164 4164 THRCLA_contig4165 4165 THRCLA_contig4166 4166 THRCLA_contig4167 4167 THRCLA_contig4168 4168 THRCLA_contig4169 4169 THRCLA_contig4170 4170 THRCLA_contig4171 4171 THRCLA_contig4172 4172 THRCLA_contig4173 4173 THRCLA_contig4174 4174 THRCLA_contig4175 4175 THRCLA_contig4176 4176 THRCLA_contig4177 4177 THRCLA_contig4178 4178 THRCLA_contig4179 4179 THRCLA_contig4180 4180 THRCLA_contig4181 4181 THRCLA_contig4182 4182 THRCLA_contig4183 4183 THRCLA_contig4184 4184 THRCLA_contig4185 4185 THRCLA_contig4186 4186 THRCLA_contig4187 4187 THRCLA_contig4188 4188 THRCLA_contig4189 4189 THRCLA_contig4190 4190 THRCLA_contig4191 4191 THRCLA_contig4192 4192 THRCLA_contig4193 4193 THRCLA_contig4194 4194 THRCLA_contig4195 4195 THRCLA_contig4196 4196 THRCLA_contig4197 4197 THRCLA_contig4198 4198 THRCLA_contig4199 4199 THRCLA_contig4200 4200 THRCLA_contig4201 4201 THRCLA_contig4202 4202 THRCLA_contig4203 4203 THRCLA_contig4204 4204 THRCLA_contig4205 4205 THRCLA_contig4206 4206 THRCLA_contig4207 4207 THRCLA_contig4208 4208 THRCLA_contig4209 4209 THRCLA_contig4210 4210 THRCLA_contig4211 4211 THRCLA_contig4212 4212 THRCLA_contig4213 4213 THRCLA_contig4214 4214 THRCLA_contig4215 4215 THRCLA_contig4216 4216 THRCLA_contig4217 4217 THRCLA_contig4218 4218 THRCLA_contig4219 4219 THRCLA_contig4220 4220 THRCLA_contig4221 4221 THRCLA_contig4222 4222 THRCLA_contig4223 4223 THRCLA_contig4224 4224 THRCLA_contig4225 4225 THRCLA_contig4226 4226 THRCLA_contig4227 4227 THRCLA_contig4228 4228 THRCLA_contig4229 4229 THRCLA_contig4230 4230 THRCLA_contig4231 4231 THRCLA_contig4232 4232 THRCLA_contig4233 4233 THRCLA_contig4234 4234 THRCLA_contig4235 4235 THRCLA_contig4236 4236 THRCLA_contig4237 4237 THRCLA_contig4238 4238 THRCLA_contig4239 4239 THRCLA_contig4240 4240 THRCLA_contig4241 4241 THRCLA_contig4242 4242 THRCLA_contig4243 4243 THRCLA_contig4244 4244 THRCLA_contig4245 4245 THRCLA_contig4246 4246 THRCLA_contig4247 4247 THRCLA_contig4248 4248 THRCLA_contig4249 4249 THRCLA_contig4250 4250 THRCLA_contig4251 4251 THRCLA_contig4252 4252 THRCLA_contig4253 4253 THRCLA_contig4254 4254 THRCLA_contig4255 4255 THRCLA_contig4256 4256 THRCLA_contig4257 4257 THRCLA_contig4258 4258 THRCLA_contig4259 4259 THRCLA_contig4260 4260 THRCLA_contig4261 4261 THRCLA_contig4262 4262 THRCLA_contig4263 4263 THRCLA_contig4264 4264 THRCLA_contig4265 4265 THRCLA_contig4266 4266 THRCLA_contig4267 4267 THRCLA_contig4268 4268 THRCLA_contig4269 4269 THRCLA_contig4270 4270 THRCLA_contig4271 4271 THRCLA_contig4272 4272 THRCLA_contig4273 4273 THRCLA_contig4274 4274 THRCLA_contig4275 4275 THRCLA_contig4276 4276 THRCLA_contig4277 4277 THRCLA_contig4278 4278 THRCLA_contig4279 4279 THRCLA_contig4280 4280 THRCLA_contig4281 4281 THRCLA_contig4282 4282 THRCLA_contig4283 4283 THRCLA_contig4284 4284 THRCLA_contig4285 4285 THRCLA_contig4286 4286 THRCLA_contig4287 4287 THRCLA_contig4288 4288 THRCLA_contig4289 4289 THRCLA_contig4290 4290 THRCLA_contig4291 4291 THRCLA_contig4292 4292 THRCLA_contig4293 4293 THRCLA_contig4294 4294 THRCLA_contig4295 4295 THRCLA_contig4296 4296 THRCLA_contig4297 4297 THRCLA_contig4298 4298 THRCLA_contig4299 4299 THRCLA_contig4300 4300 THRCLA_contig4301 4301 THRCLA_contig4302 4302 THRCLA_contig4303 4303 THRCLA_contig4304 4304 THRCLA_contig4305 4305 THRCLA_contig4306 4306 THRCLA_contig4307 4307 THRCLA_contig4308 4308 THRCLA_contig4309 4309 THRCLA_contig4310 4310 THRCLA_contig4311 4311 THRCLA_contig4312 4312 THRCLA_contig4313 4313 THRCLA_contig4314 4314 THRCLA_contig4315 4315 THRCLA_contig4316 4316 THRCLA_contig4317 4317 THRCLA_contig4318 4318 THRCLA_contig4319 4319 THRCLA_contig4320 4320 THRCLA_contig4321 4321 THRCLA_contig4322 4322 THRCLA_contig4323 4323 THRCLA_contig4324 4324 THRCLA_contig4325 4325 THRCLA_contig4326 4326 THRCLA_contig4327 4327 THRCLA_contig4328 4328 THRCLA_contig4329 4329 THRCLA_contig4330 4330 THRCLA_contig4331 4331 THRCLA_contig4332 4332 THRCLA_contig4333 4333 THRCLA_contig4334 4334 THRCLA_contig4335 4335 THRCLA_contig4336 4336 THRCLA_contig4337 4337 THRCLA_contig4338 4338 THRCLA_contig4339 4339 THRCLA_contig4340 4340 THRCLA_contig4341 4341 THRCLA_contig4342 4342 THRCLA_contig4343 4343 THRCLA_contig4344 4344 THRCLA_contig4345 4345 THRCLA_contig4346 4346 THRCLA_contig4347 4347 THRCLA_contig4348 4348 THRCLA_contig4349 4349 THRCLA_contig4350 4350 THRCLA_contig4351 4351 THRCLA_contig4352 4352 THRCLA_contig4353 4353 THRCLA_contig4354 4354 THRCLA_contig4355 4355 THRCLA_contig4356 4356 THRCLA_contig4357 4357 THRCLA_contig4358 4358 THRCLA_contig4359 4359 THRCLA_contig4360 4360 THRCLA_contig4361 4361 THRCLA_contig4362 4362 THRCLA_contig4363 4363 THRCLA_contig4364 4364 THRCLA_contig4365 4365 THRCLA_contig4366 4366 THRCLA_contig4367 4367 THRCLA_contig4368 4368 THRCLA_contig4369 4369 THRCLA_contig4370 4370 THRCLA_contig4371 4371 THRCLA_contig4372 4372 THRCLA_contig4373 4373 THRCLA_contig4374 4374 THRCLA_contig4375 4375 THRCLA_contig4376 4376 THRCLA_contig4377 4377 THRCLA_contig4378 4378 THRCLA_contig4379 4379 THRCLA_contig4380 4380 THRCLA_contig4381 4381 THRCLA_contig4382 4382 THRCLA_contig4383 4383 THRCLA_contig4384 4384 THRCLA_contig4385 4385 THRCLA_contig4386 4386 THRCLA_contig4387 4387 THRCLA_contig4388 4388 THRCLA_contig4389 4389 THRCLA_contig4390 4390 THRCLA_contig4391 4391 THRCLA_contig4392 4392 THRCLA_contig4393 4393 THRCLA_contig4394 4394 THRCLA_contig4395 4395 THRCLA_contig4396 4396 THRCLA_contig4397 4397 THRCLA_contig4398 4398 THRCLA_contig4399 4399 THRCLA_contig4400 4400 THRCLA_contig4401 4401 THRCLA_contig4402 4402 THRCLA_contig4403 4403 THRCLA_contig4404 4404 THRCLA_contig4405 4405 THRCLA_contig4406 4406 THRCLA_contig4407 4407 THRCLA_contig4408 4408 THRCLA_contig4409 4409 THRCLA_contig4410 4410 THRCLA_contig4411 4411 THRCLA_contig4412 4412 THRCLA_contig4413 4413 THRCLA_contig4414 4414 THRCLA_contig4415 4415 THRCLA_contig4416 4416 THRCLA_contig4417 4417 THRCLA_contig4418 4418 THRCLA_contig4419 4419 THRCLA_contig4420 4420 THRCLA_contig4421 4421 THRCLA_contig4422 4422 THRCLA_contig4423 4423 THRCLA_contig4424 4424 THRCLA_contig4425 4425 THRCLA_contig4426 4426 THRCLA_contig4427 4427 THRCLA_contig4428 4428 THRCLA_contig4429 4429 THRCLA_contig4430 4430 THRCLA_contig4431 4431 THRCLA_contig4432 4432 THRCLA_contig4433 4433 THRCLA_contig4434 4434 THRCLA_contig4435 4435 THRCLA_contig4436 4436 THRCLA_contig4437 4437 THRCLA_contig4438 4438 THRCLA_contig4439 4439 THRCLA_contig4440 4440 THRCLA_contig4441 4441 THRCLA_contig4442 4442 THRCLA_contig4443 4443 THRCLA_contig4444 4444 THRCLA_contig4445 4445 THRCLA_contig4446 4446 THRCLA_contig4447 4447 THRCLA_contig4448 4448 THRCLA_contig4449 4449 THRCLA_contig4450 4450 THRCLA_contig4451 4451 THRCLA_contig4452 4452 THRCLA_contig4453 4453 THRCLA_contig4454 4454 THRCLA_contig4455 4455 THRCLA_contig4456 4456 THRCLA_contig4457 4457 THRCLA_contig4458 4458 THRCLA_contig4459 4459 THRCLA_contig4460 4460 THRCLA_contig4461 4461 THRCLA_contig4462 4462 THRCLA_contig4463 4463 THRCLA_contig4464 4464 THRCLA_contig4465 4465 THRCLA_contig4466 4466 THRCLA_contig4467 4467 THRCLA_contig4468 4468 THRCLA_contig4469 4469 THRCLA_contig4470 4470 THRCLA_contig4471 4471 THRCLA_contig4472 4472 THRCLA_contig4473 4473 THRCLA_contig4474 4474 THRCLA_contig4475 4475 THRCLA_contig4476 4476 THRCLA_contig4477 4477 THRCLA_contig4478 4478 THRCLA_contig4479 4479 THRCLA_contig4480 4480 THRCLA_contig4481 4481 THRCLA_contig4482 4482 THRCLA_contig4483 4483 THRCLA_contig4484 4484 THRCLA_contig4485 4485 THRCLA_contig4486 4486 THRCLA_contig4487 4487 THRCLA_contig4488 4488 THRCLA_contig4489 4489 THRCLA_contig4490 4490 THRCLA_contig4491 4491 THRCLA_contig4492 4492 THRCLA_contig4493 4493 THRCLA_contig4494 4494 THRCLA_contig4495 4495 THRCLA_contig4496 4496 THRCLA_contig4497 4497 THRCLA_contig4498 4498 THRCLA_contig4499 4499 THRCLA_contig4500 4500 THRCLA_contig4501 4501 THRCLA_contig4502 4502 THRCLA_contig4503 4503 THRCLA_contig4504 4504 THRCLA_contig4505 4505 THRCLA_contig4506 4506 THRCLA_contig4507 4507 THRCLA_contig4508 4508 THRCLA_contig4509 4509 THRCLA_contig4510 4510 THRCLA_contig4511 4511 THRCLA_contig4512 4512 THRCLA_contig4513 4513 THRCLA_contig4514 4514 THRCLA_contig4515 4515 THRCLA_contig4516 4516 THRCLA_contig4517 4517 THRCLA_contig4518 4518 THRCLA_contig4519 4519 THRCLA_contig4520 4520 THRCLA_contig4521 4521 THRCLA_contig4522 4522 THRCLA_contig4523 4523 THRCLA_contig4524 4524 THRCLA_contig4525 4525 THRCLA_contig4526 4526 THRCLA_contig4527 4527 THRCLA_contig4528 4528 THRCLA_contig4529 4529 THRCLA_contig4530 4530 THRCLA_contig4531 4531 THRCLA_contig4532 4532 THRCLA_contig4533 4533 THRCLA_contig4534 4534 THRCLA_contig4535 4535 THRCLA_contig4536 4536 THRCLA_contig4537 4537 THRCLA_contig4538 4538 THRCLA_contig4539 4539 THRCLA_contig4540 4540 THRCLA_contig4541 4541 THRCLA_contig4542 4542 THRCLA_contig4543 4543 THRCLA_contig4544 4544 THRCLA_contig4545 4545 THRCLA_contig4546 4546 THRCLA_contig4547 4547 THRCLA_contig4548 4548 THRCLA_contig4549 4549 THRCLA_contig4550 4550 THRCLA_contig4551 4551 THRCLA_contig4552 4552 THRCLA_contig4553 4553 THRCLA_contig4554 4554 THRCLA_contig4555 4555 THRCLA_contig4556 4556 THRCLA_contig4557 4557 THRCLA_contig4558 4558 THRCLA_contig4559 4559 THRCLA_contig4560 4560 THRCLA_contig4561 4561 THRCLA_contig4562 4562 THRCLA_contig4563 4563 THRCLA_contig4564 4564 THRCLA_contig4565 4565 THRCLA_contig4566 4566 THRCLA_contig4567 4567 THRCLA_contig4568 4568 THRCLA_contig4569 4569 THRCLA_contig4570 4570 THRCLA_contig4571 4571 THRCLA_contig4572 4572 THRCLA_contig4573 4573 THRCLA_contig4574 4574 THRCLA_contig4575 4575 THRCLA_contig4576 4576 THRCLA_contig4577 4577 THRCLA_contig4578 4578 THRCLA_contig4579 4579 THRCLA_contig4580 4580 THRCLA_contig4581 4581 THRCLA_contig4582 4582 THRCLA_contig4583 4583 THRCLA_contig4584 4584 THRCLA_contig4585 4585 THRCLA_contig4586 4586 THRCLA_contig4587 4587 THRCLA_contig4588 4588 THRCLA_contig4589 4589 THRCLA_contig4590 4590 THRCLA_contig4591 4591 THRCLA_contig4592 4592 THRCLA_contig4593 4593 THRCLA_contig4594 4594 THRCLA_contig4595 4595 THRCLA_contig4596 4596 THRCLA_contig4597 4597 THRCLA_contig4598 4598 THRCLA_contig4599 4599 THRCLA_contig4600 4600 THRCLA_contig4601 4601 THRCLA_contig4602 4602 THRCLA_contig4603 4603 THRCLA_contig4604 4604 THRCLA_contig4605 4605 THRCLA_contig4606 4606 THRCLA_contig4607 4607 THRCLA_contig4608 4608 THRCLA_contig4609 4609 THRCLA_contig4610 4610 THRCLA_contig4611 4611 THRCLA_contig4612 4612 THRCLA_contig4613 4613 THRCLA_contig4614 4614 THRCLA_contig4615 4615 THRCLA_contig4616 4616 THRCLA_contig4617 4617 THRCLA_contig4618 4618 THRCLA_contig4619 4619 THRCLA_contig4620 4620 THRCLA_contig4621 4621 THRCLA_contig4622 4622 THRCLA_contig4623 4623 THRCLA_contig4624 4624 THRCLA_contig4625 4625 THRCLA_contig4626 4626 THRCLA_contig4627 4627 THRCLA_contig4628 4628 THRCLA_contig4629 4629 THRCLA_contig4630 4630 THRCLA_contig4631 4631 THRCLA_contig4632 4632 THRCLA_contig4633 4633 THRCLA_contig4634 4634 THRCLA_contig4635 4635 THRCLA_contig4636 4636 THRCLA_contig4637 4637 THRCLA_contig4638 4638 THRCLA_contig4639 4639 THRCLA_contig4640 4640 THRCLA_contig4641 4641 THRCLA_contig4642 4642 THRCLA_contig4643 4643 THRCLA_contig4644 4644 THRCLA_contig4645 4645 THRCLA_contig4646 4646 THRCLA_contig4647 4647 THRCLA_contig4648 4648 THRCLA_contig4649 4649 THRCLA_contig4650 4650 THRCLA_contig4651 4651 THRCLA_contig4652 4652 THRCLA_contig4653 4653 THRCLA_contig4654 4654 THRCLA_contig4655 4655 THRCLA_contig4656 4656 THRCLA_contig4657 4657 THRCLA_contig4658 4658 THRCLA_contig4659 4659 THRCLA_contig4660 4660 THRCLA_contig4661 4661 THRCLA_contig4662 4662 THRCLA_contig4663 4663 THRCLA_contig4664 4664 THRCLA_contig4665 4665 THRCLA_contig4666 4666 THRCLA_contig4667 4667 THRCLA_contig4668 4668 THRCLA_contig4669 4669 THRCLA_contig4670 4670 THRCLA_contig4671 4671 THRCLA_contig4672 4672 THRCLA_contig4673 4673 THRCLA_contig4674 4674 THRCLA_contig4675 4675 THRCLA_contig4676 4676 THRCLA_contig4677 4677 THRCLA_contig4678 4678 THRCLA_contig4679 4679 THRCLA_contig4680 4680 THRCLA_contig4681 4681 THRCLA_contig4682 4682 THRCLA_contig4683 4683 THRCLA_contig4684 4684 THRCLA_contig4685 4685 THRCLA_contig4686 4686 THRCLA_contig4687 4687 THRCLA_contig4688 4688 THRCLA_contig4689 4689 THRCLA_contig4690 4690 THRCLA_contig4691 4691 THRCLA_contig4692 4692 THRCLA_contig4693 4693 THRCLA_contig4694 4694 THRCLA_contig4695 4695 THRCLA_contig4696 4696 THRCLA_contig4697 4697 THRCLA_contig4698 4698 THRCLA_contig4699 4699 THRCLA_contig4700 4700 THRCLA_contig4701 4701 THRCLA_contig4702 4702 THRCLA_contig4703 4703 THRCLA_contig4704 4704 THRCLA_contig4705 4705 THRCLA_contig4706 4706 THRCLA_contig4707 4707 THRCLA_contig4708 4708 THRCLA_contig4709 4709 THRCLA_contig4710 4710 THRCLA_contig4711 4711 THRCLA_contig4712 4712 THRCLA_contig4713 4713 THRCLA_contig4714 4714 THRCLA_contig4715 4715 THRCLA_contig4716 4716 THRCLA_contig4717 4717 THRCLA_contig4718 4718 THRCLA_contig4719 4719 THRCLA_contig4720 4720 THRCLA_contig4721 4721 THRCLA_contig4722 4722 THRCLA_contig4723 4723 THRCLA_contig4724 4724 THRCLA_contig4725 4725 THRCLA_contig4726 4726 THRCLA_contig4727 4727 THRCLA_contig4728 4728 THRCLA_contig4729 4729 THRCLA_contig4730 4730 THRCLA_contig4731 4731 THRCLA_contig4732 4732 THRCLA_contig4733 4733 THRCLA_contig4734 4734 THRCLA_contig4735 4735 THRCLA_contig4736 4736 THRCLA_contig4737 4737 THRCLA_contig4738 4738 THRCLA_contig4739 4739 THRCLA_contig4740 4740 THRCLA_contig4741 4741 THRCLA_contig4742 4742 THRCLA_contig4743 4743 THRCLA_contig4744 4744 THRCLA_contig4745 4745 THRCLA_contig4746 4746 THRCLA_contig4747 4747 THRCLA_contig4748 4748 THRCLA_contig4749 4749 THRCLA_contig4750 4750 THRCLA_contig4751 4751 THRCLA_contig4752 4752 THRCLA_contig4753 4753 THRCLA_contig4754 4754 THRCLA_contig4755 4755 THRCLA_contig4756 4756 THRCLA_contig4757 4757 THRCLA_contig4758 4758 THRCLA_contig4759 4759 THRCLA_contig4760 4760 THRCLA_contig4761 4761 THRCLA_contig4762 4762 THRCLA_contig4763 4763 THRCLA_contig4764 4764 THRCLA_contig4765 4765 THRCLA_contig4766 4766 THRCLA_contig4767 4767 THRCLA_contig4768 4768 THRCLA_contig4769 4769 THRCLA_contig4770 4770 THRCLA_contig4771 4771 THRCLA_contig4772 4772 THRCLA_contig4773 4773 THRCLA_contig4774 4774 THRCLA_contig4775 4775 THRCLA_contig4776 4776 THRCLA_contig4777 4777 THRCLA_contig4778 4778 THRCLA_contig4779 4779 THRCLA_contig4780 4780 THRCLA_contig4781 4781 THRCLA_contig4782 4782 THRCLA_contig4783 4783 THRCLA_contig4784 4784 THRCLA_contig4785 4785 THRCLA_contig4786 4786 THRCLA_contig4787 4787 THRCLA_contig4788 4788 THRCLA_contig4789 4789 THRCLA_contig4790 4790 THRCLA_contig4791 4791 THRCLA_contig4792 4792 THRCLA_contig4793 4793 THRCLA_contig4794 4794 THRCLA_contig4795 4795 THRCLA_contig4796 4796 THRCLA_contig4797 4797 THRCLA_contig4798 4798 THRCLA_contig4799 4799 THRCLA_contig4800 4800 THRCLA_contig4801 4801 THRCLA_contig4802 4802 THRCLA_contig4803 4803 THRCLA_contig4804 4804 THRCLA_contig4805 4805 THRCLA_contig4806 4806 THRCLA_contig4807 4807 THRCLA_contig4808 4808 THRCLA_contig4809 4809 THRCLA_contig4810 4810 THRCLA_contig4811 4811 THRCLA_contig4812 4812 THRCLA_contig4813 4813 THRCLA_contig4814 4814 THRCLA_contig4815 4815 THRCLA_contig4816 4816 THRCLA_contig4817 4817 THRCLA_contig4818 4818 THRCLA_contig4819 4819 THRCLA_contig4820 4820 THRCLA_contig4821 4821 THRCLA_contig4822 4822 THRCLA_contig4823 4823 THRCLA_contig4824 4824 THRCLA_contig4825 4825 THRCLA_contig4826 4826 THRCLA_contig4827 4827 THRCLA_contig4828 4828 THRCLA_contig4829 4829 THRCLA_contig4830 4830 THRCLA_contig4831 4831 THRCLA_contig4832 4832 THRCLA_contig4833 4833 THRCLA_contig4834 4834 THRCLA_contig4835 4835 THRCLA_contig4836 4836 THRCLA_contig4837 4837 THRCLA_contig4838 4838 THRCLA_contig4839 4839 THRCLA_contig4840 4840 THRCLA_contig4841 4841 THRCLA_contig4842 4842 THRCLA_contig4843 4843 THRCLA_contig4844 4844 THRCLA_contig4845 4845 THRCLA_contig4846 4846 THRCLA_contig4847 4847 THRCLA_contig4848 4848 THRCLA_contig4849 4849 THRCLA_contig4850 4850 THRCLA_contig4851 4851 THRCLA_contig4852 4852 THRCLA_contig4853 4853 THRCLA_contig4854 4854 THRCLA_contig4855 4855 THRCLA_contig4856 4856 THRCLA_contig4857 4857 THRCLA_contig4858 4858 THRCLA_contig4859 4859 THRCLA_contig4860 4860 THRCLA_contig4861 4861 THRCLA_contig4862 4862 THRCLA_contig4863 4863 THRCLA_contig4864 4864 THRCLA_contig4865 4865 THRCLA_contig4866 4866 THRCLA_contig4867 4867 THRCLA_contig4868 4868 THRCLA_contig4869 4869 THRCLA_contig4870 4870 THRCLA_contig4871 4871 THRCLA_contig4872 4872 THRCLA_contig4873 4873 THRCLA_contig4874 4874 THRCLA_contig4875 4875 THRCLA_contig4876 4876 THRCLA_contig4877 4877 THRCLA_contig4878 4878 THRCLA_contig4879 4879 THRCLA_contig4880 4880 THRCLA_contig4881 4881 THRCLA_contig4882 4882 THRCLA_contig4883 4883 THRCLA_contig4884 4884 THRCLA_contig4885 4885 THRCLA_contig4886 4886 THRCLA_contig4887 4887 THRCLA_contig4888 4888 THRCLA_contig4889 4889 THRCLA_contig4890 4890 THRCLA_contig4891 4891 THRCLA_contig4892 4892 THRCLA_contig4893 4893 THRCLA_contig4894 4894 THRCLA_contig4895 4895 THRCLA_contig4896 4896 THRCLA_contig4897 4897 THRCLA_contig4898 4898 THRCLA_contig4899 4899 THRCLA_contig4900 4900 THRCLA_contig4901 4901 THRCLA_contig4902 4902 THRCLA_contig4903 4903 THRCLA_contig4904 4904 THRCLA_contig4905 4905 THRCLA_contig4906 4906 THRCLA_contig4907 4907 THRCLA_contig4908 4908 THRCLA_contig4909 4909 THRCLA_contig4910 4910 THRCLA_contig4911 4911 THRCLA_contig4912 4912 THRCLA_contig4913 4913 THRCLA_contig4914 4914 THRCLA_contig4915 4915 THRCLA_contig4916 4916 THRCLA_contig4917 4917 THRCLA_contig4918 4918 THRCLA_contig4919 4919 THRCLA_contig4920 4920 THRCLA_contig4921 4921 THRCLA_contig4922 4922 THRCLA_contig4923 4923 THRCLA_contig4924 4924 THRCLA_contig4925 4925 THRCLA_contig4926 4926 THRCLA_contig4927 4927 THRCLA_contig4928 4928 THRCLA_contig4929 4929 THRCLA_contig4930 4930 THRCLA_contig4931 4931 THRCLA_contig4932 4932 THRCLA_contig4933 4933 THRCLA_contig4934 4934 THRCLA_contig4935 4935 THRCLA_contig4936 4936 THRCLA_contig4937 4937 THRCLA_contig4938 4938 THRCLA_contig4939 4939 THRCLA_contig4940 4940 THRCLA_contig4941 4941 THRCLA_contig4942 4942 THRCLA_contig4943 4943 THRCLA_contig4944 4944 THRCLA_contig4945 4945 THRCLA_contig4946 4946 THRCLA_contig4947 4947 THRCLA_contig4948 4948 THRCLA_contig4949 4949 THRCLA_contig4950 4950 THRCLA_contig4951 4951 THRCLA_contig4952 4952 THRCLA_contig4953 4953 THRCLA_contig4954 4954 THRCLA_contig4955 4955 THRCLA_contig4956 4956 THRCLA_contig4957 4957 THRCLA_contig4958 4958 THRCLA_contig4959 4959 THRCLA_contig4960 4960 THRCLA_contig4961 4961 THRCLA_contig4962 4962 THRCLA_contig4963 4963 THRCLA_contig4964 4964 THRCLA_contig4965 4965 THRCLA_contig4966 4966 THRCLA_contig4967 4967 THRCLA_contig4968 4968 THRCLA_contig4969 4969 THRCLA_contig4970 4970 THRCLA_contig4971 4971 THRCLA_contig4972 4972 THRCLA_contig4973 4973 THRCLA_contig4974 4974 THRCLA_contig4975 4975 THRCLA_contig4976 4976 THRCLA_contig4977 4977 THRCLA_contig4978 4978 THRCLA_contig4979 4979 THRCLA_contig4980 4980 THRCLA_contig4981 4981 THRCLA_contig4982 4982 THRCLA_contig4983 4983 THRCLA_contig4984 4984 THRCLA_contig4985 4985 THRCLA_contig4986 4986 THRCLA_contig4987 4987 THRCLA_contig4988 4988 THRCLA_contig4989 4989 THRCLA_contig4990 4990 THRCLA_contig4991 4991 THRCLA_contig4992 4992 THRCLA_contig4993 4993 THRCLA_contig4994 4994 THRCLA_contig4995 4995 THRCLA_contig4996 4996 THRCLA_contig4997 4997 THRCLA_contig4998 4998 THRCLA_contig4999 4999 THRCLA_contig5000 5000 THRCLA_contig5001 5001 THRCLA_contig5002 5002 THRCLA_contig5003 5003 THRCLA_contig5004 5004 THRCLA_contig5005 5005 THRCLA_contig5006 5006 THRCLA_contig5007 5007 THRCLA_contig5008 5008 THRCLA_contig5009 5009 THRCLA_contig5010 5010 THRCLA_contig5011 5011 THRCLA_contig5012 5012 THRCLA_contig5013 5013 THRCLA_contig5014 5014 THRCLA_contig5015 5015 THRCLA_contig5016 5016 THRCLA_contig5017 5017 THRCLA_contig5018 5018 THRCLA_contig5019 5019 THRCLA_contig5020 5020 THRCLA_contig5021 5021 THRCLA_contig5022 5022 THRCLA_contig5023 5023 THRCLA_contig5024 5024 THRCLA_contig5025 5025 THRCLA_contig5026 5026 THRCLA_contig5027 5027 THRCLA_contig5028 5028 THRCLA_contig5029 5029 THRCLA_contig5030 5030 THRCLA_contig5031 5031 THRCLA_contig5032 5032 THRCLA_contig5033 5033 THRCLA_contig5034 5034 THRCLA_contig5035 5035 THRCLA_contig5036 5036 THRCLA_contig5037 5037 THRCLA_contig5038 5038 THRCLA_contig5039 5039 THRCLA_contig5040 5040 THRCLA_contig5041 5041 THRCLA_contig5042 5042 THRCLA_contig5043 5043 THRCLA_contig5044 5044 THRCLA_contig5045 5045 THRCLA_contig5046 5046 THRCLA_contig5047 5047 THRCLA_contig5048 5048 THRCLA_contig5049 5049 THRCLA_contig5050 5050 THRCLA_contig5051 5051 THRCLA_contig5052 5052 THRCLA_contig5053 5053 THRCLA_contig5054 5054 THRCLA_contig5055 5055 THRCLA_contig5056 5056 THRCLA_contig5057 5057 THRCLA_contig5058 5058 THRCLA_contig5059 5059 THRCLA_contig5060 5060 THRCLA_contig5061 5061 THRCLA_contig5062 5062 THRCLA_contig5063 5063 THRCLA_contig5064 5064 THRCLA_contig5065 5065 THRCLA_contig5066 5066 THRCLA_contig5067 5067 THRCLA_contig5068 5068 THRCLA_contig5069 5069 THRCLA_contig5070 5070 THRCLA_contig5071 5071 THRCLA_contig5072 5072 THRCLA_contig5073 5073 THRCLA_contig5074 5074 THRCLA_contig5075 5075 THRCLA_contig5076 5076 THRCLA_contig5077 5077 THRCLA_contig5078 5078 THRCLA_contig5079 5079 THRCLA_contig5080 5080 THRCLA_contig5081 5081 THRCLA_contig5082 5082 THRCLA_contig5083 5083 THRCLA_contig5084 5084 THRCLA_contig5085 5085 THRCLA_contig5086 5086 THRCLA_contig5087 5087 THRCLA_contig5088 5088 THRCLA_contig5089 5089 THRCLA_contig5090 5090 THRCLA_contig5091 5091 THRCLA_contig5092 5092 THRCLA_contig5093 5093 THRCLA_contig5094 5094 THRCLA_contig5095 5095 THRCLA_contig5096 5096 THRCLA_contig5097 5097 THRCLA_contig5098 5098 THRCLA_contig5099 5099 THRCLA_contig5100 5100 THRCLA_contig5101 5101 THRCLA_contig5102 5102 THRCLA_contig5103 5103 THRCLA_contig5104 5104 THRCLA_contig5105 5105 THRCLA_contig5106 5106 THRCLA_contig5107 5107 THRCLA_contig5108 5108 THRCLA_contig5109 5109 THRCLA_contig5110 5110 THRCLA_contig5111 5111 THRCLA_contig5112 5112 THRCLA_contig5113 5113 THRCLA_contig5114 5114 THRCLA_contig5115 5115 THRCLA_contig5116 5116 THRCLA_contig5117 5117 THRCLA_contig5118 5118 THRCLA_contig5119 5119 THRCLA_contig5120 5120 THRCLA_contig5121 5121 THRCLA_contig5122 5122 THRCLA_contig5123 5123 THRCLA_contig5124 5124 THRCLA_contig5125 5125 THRCLA_contig5126 5126 THRCLA_contig5127 5127 THRCLA_contig5128 5128 THRCLA_contig5129 5129 THRCLA_contig5130 5130 THRCLA_contig5131 5131 THRCLA_contig5132 5132 THRCLA_contig5133 5133 THRCLA_contig5134 5134 THRCLA_contig5135 5135 THRCLA_contig5136 5136 THRCLA_contig5137 5137 THRCLA_contig5138 5138 THRCLA_contig5139 5139 THRCLA_contig5140 5140 THRCLA_contig5141 5141 THRCLA_contig5142 5142 THRCLA_contig5143 5143 THRCLA_contig5144 5144 THRCLA_contig5145 5145 THRCLA_contig5146 5146 THRCLA_contig5147 5147 THRCLA_contig5148 5148 THRCLA_contig5149 5149 THRCLA_contig5150 5150 THRCLA_contig5151 5151 THRCLA_contig5152 5152 THRCLA_contig5153 5153 THRCLA_contig5154 5154 THRCLA_contig5155 5155 THRCLA_contig5156 5156 THRCLA_contig5157 5157 THRCLA_contig5158 5158 THRCLA_contig5159 5159 THRCLA_contig5160 5160 THRCLA_contig5161 5161 THRCLA_contig5162 5162 THRCLA_contig5163 5163 THRCLA_contig5164 5164 THRCLA_contig5165 5165 THRCLA_contig5166 5166 THRCLA_contig5167 5167 THRCLA_contig5168 5168 THRCLA_contig5169 5169 THRCLA_contig5170 5170 THRCLA_contig5171 5171 THRCLA_contig5172 5172 THRCLA_contig5173 5173 THRCLA_contig5174 5174 THRCLA_contig5175 5175 THRCLA_contig5176 5176 THRCLA_contig5177 5177 THRCLA_contig5178 5178 THRCLA_contig5179 5179 THRCLA_contig5180 5180 THRCLA_contig5181 5181 THRCLA_contig5182 5182 THRCLA_contig5183 5183 THRCLA_contig5184 5184 THRCLA_contig5185 5185 THRCLA_contig5186 5186 THRCLA_contig5187 5187 THRCLA_contig5188 5188 THRCLA_contig5189 5189 THRCLA_contig5190 5190 THRCLA_contig5191 5191 THRCLA_contig5192 5192 THRCLA_contig5193 5193 THRCLA_contig5194 5194 THRCLA_contig5195 5195 THRCLA_contig5196 5196 THRCLA_contig5197 5197 THRCLA_contig5198 5198 THRCLA_contig5199 5199 THRCLA_contig5200 5200 THRCLA_contig5201 5201 THRCLA_contig5202 5202 THRCLA_contig5203 5203 THRCLA_contig5204 5204 THRCLA_contig5205 5205 THRCLA_contig5206 5206 THRCLA_contig5207 5207 THRCLA_contig5208 5208 THRCLA_contig5209 5209 THRCLA_contig5210 5210 THRCLA_contig5211 5211 THRCLA_contig5212 5212 THRCLA_contig5213 5213 THRCLA_contig5214 5214 THRCLA_contig5215 5215 THRCLA_contig5216 5216 THRCLA_contig5217 5217 THRCLA_contig5218 5218 THRCLA_contig5219 5219 THRCLA_contig5220 5220 THRCLA_contig5221 5221 THRCLA_contig5222 5222 THRCLA_contig5223 5223 THRCLA_contig5224 5224 THRCLA_contig5225 5225 THRCLA_contig5226 5226 THRCLA_contig5227 5227 THRCLA_contig5228 5228 THRCLA_contig5229 5229 THRCLA_contig5230 5230 THRCLA_contig5231 5231 THRCLA_contig5232 5232 THRCLA_contig5233 5233 THRCLA_contig5234 5234 THRCLA_contig5235 5235 THRCLA_contig5236 5236 THRCLA_contig5237 5237 THRCLA_contig5238 5238 THRCLA_contig5239 5239 THRCLA_contig5240 5240 THRCLA_contig5241 5241 THRCLA_contig5242 5242 THRCLA_contig5243 5243 THRCLA_contig5244 5244 THRCLA_contig5245 5245 THRCLA_contig5246 5246 THRCLA_contig5247 5247 THRCLA_contig5248 5248 THRCLA_contig5249 5249 THRCLA_contig5250 5250 THRCLA_contig5251 5251 THRCLA_contig5252 5252 THRCLA_contig5253 5253 THRCLA_contig5254 5254 THRCLA_contig5255 5255 THRCLA_contig5256 5256 THRCLA_contig5257 5257 THRCLA_contig5258 5258 THRCLA_contig5259 5259 THRCLA_contig5260 5260 THRCLA_contig5261 5261 THRCLA_contig5262 5262 THRCLA_contig5263 5263 THRCLA_contig5264 5264 THRCLA_contig5265 5265 THRCLA_contig5266 5266 THRCLA_contig5267 5267 THRCLA_contig5268 5268 THRCLA_contig5269 5269 THRCLA_contig5270 5270 THRCLA_contig5271 5271 THRCLA_contig5272 5272 THRCLA_contig5273 5273 THRCLA_contig5274 5274 THRCLA_contig5275 5275 THRCLA_contig5276 5276 THRCLA_contig5277 5277 THRCLA_contig5278 5278 THRCLA_contig5279 5279 THRCLA_contig5280 5280 THRCLA_contig5281 5281 THRCLA_contig5282 5282 THRCLA_contig5283 5283 THRCLA_contig5284 5284 THRCLA_contig5285 5285 THRCLA_contig5286 5286 THRCLA_contig5287 5287 THRCLA_contig5288 5288 THRCLA_contig5289 5289 THRCLA_contig5290 5290 THRCLA_contig5291 5291 THRCLA_contig5292 5292 THRCLA_contig5293 5293 THRCLA_contig5294 5294 THRCLA_contig5295 5295 THRCLA_contig5296 5296 THRCLA_contig5297 5297 THRCLA_contig5298 5298 THRCLA_contig5299 5299 THRCLA_contig5300 5300 THRCLA_contig5301 5301 THRCLA_contig5302 5302 THRCLA_contig5303 5303 THRCLA_contig5304 5304 THRCLA_contig5305 5305 THRCLA_contig5306 5306 THRCLA_contig5307 5307 THRCLA_contig5308 5308 THRCLA_contig5309 5309 THRCLA_contig5310 5310 THRCLA_contig5311 5311 THRCLA_contig5312 5312 THRCLA_contig5313 5313 THRCLA_contig5314 5314 THRCLA_contig5315 5315 THRCLA_contig5316 5316 THRCLA_contig5317 5317 THRCLA_contig5318 5318 THRCLA_contig5319 5319 THRCLA_contig5320 5320 THRCLA_contig5321 5321 THRCLA_contig5322 5322 THRCLA_contig5323 5323 THRCLA_contig5324 5324 THRCLA_contig5325 5325 THRCLA_contig5326 5326 THRCLA_contig5327 5327 THRCLA_contig5328 5328 THRCLA_contig5329 5329 THRCLA_contig5330 5330 THRCLA_contig5331 5331 THRCLA_contig5332 5332 THRCLA_contig5333 5333 THRCLA_contig5334 5334 THRCLA_contig5335 5335 THRCLA_contig5336 5336 THRCLA_contig5337 5337 THRCLA_contig5338 5338 From carsonhh at gmail.com Tue Sep 25 06:44:02 2012 From: carsonhh at gmail.com (Carson Holt) Date: Tue, 25 Sep 2012 08:44:02 -0400 Subject: [maker-devel] Problem with maker_map_ids In-Reply-To: <0FCB8ACD-35A0-4ED8-BAE2-02C2621E3F65@my.uri.edu> Message-ID: Could you also provide 34112_3June11Ass.gff? Thanks, Carson On 12-09-25 8:31 AM, "Ian Misner" wrote: >Hello, > >I'm trying to create human friendly ids and I'm getting an error when I >use the -sort_file option. Without the sort file it runs fine just not >numbered from the first contig. I have had some programers at our cluster >look at the script and they attempted a fix but it did not work. They >mentioned the script was "buggy" so this might be part of the problem. >I've attached the error as well as the sort file. I can send more files >if necessary. Thanks for you time. > >Cheers >Ian > >$ maker_map_ids --prefix THRCLA_ --justify 5 --sort_order 34112_sort.txt >34112_3June11Ass.gff > 34112_3June11Ass_named.txt >Can't use string ("34112_sort.txt") as a HASH ref while "strict refs" in >use at /gpfs/runtime/opt/maker/2.10/maker/bin/maker_map_ids line 311, ><$IN> line 499186._______________________________________________ >maker-devel mailing list >maker-devel at box290.bluehost.com >http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org From carsonhh at gmail.com Tue Sep 25 07:01:31 2012 From: carsonhh at gmail.com (Carson Holt) Date: Tue, 25 Sep 2012 09:01:31 -0400 Subject: [maker-devel] Problem with maker_map_ids In-Reply-To: Message-ID: While you are sending me the GFF3 file also try the sort order file attached. I found a number of illegal meta character contaminating the file. Sometimes those can be introduced by text editors or sometimes e-mail clients. In case it wasn't the e-mail client I'm sending you this fixed version. Also I see you are using maker_map_ids from version 2.10. Try the 2.26 version. They are different. Thanks, Carson On 12-09-25 8:44 AM, "Carson Holt" wrote: >Could you also provide 34112_3June11Ass.gff? > >Thanks, >Carson > > >On 12-09-25 8:31 AM, "Ian Misner" wrote: > >>Hello, >> >>I'm trying to create human friendly ids and I'm getting an error when I >>use the -sort_file option. Without the sort file it runs fine just not >>numbered from the first contig. I have had some programers at our >>cluster >>look at the script and they attempted a fix but it did not work. They >>mentioned the script was "buggy" so this might be part of the problem. >>I've attached the error as well as the sort file. I can send more files >>if necessary. Thanks for you time. >> >>Cheers >>Ian >> >>$ maker_map_ids --prefix THRCLA_ --justify 5 --sort_order 34112_sort.txt >>34112_3June11Ass.gff > 34112_3June11Ass_named.txt >>Can't use string ("34112_sort.txt") as a HASH ref while "strict refs" in >>use at /gpfs/runtime/opt/maker/2.10/maker/bin/maker_map_ids line 311, >><$IN> line 499186._______________________________________________ >>maker-devel mailing list >>maker-devel at box290.bluehost.com >>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org -------------- next part -------------- A non-text attachment was scrubbed... Name: 34112_sort.txt.gz Type: application/x-gzip Size: 27598 bytes Desc: not available URL: From carsonhh at gmail.com Tue Sep 25 07:13:54 2012 From: carsonhh at gmail.com (Carson Holt) Date: Tue, 25 Sep 2012 09:13:54 -0400 Subject: [maker-devel] Problem with maker_map_ids In-Reply-To: Message-ID: Thanks for the GFF3 file. The meta character came across in the GFF3 as well, so I think it's safe to assume they are being introduced by the e-mail client used to add the attachment (so ignore the last file I sent). I've attached the fixed maker_map_ids. Thanks, Carson On 12-09-25 9:01 AM, "Carson Holt" wrote: >While you are sending me the GFF3 file also try the sort order file >attached. I found a number of illegal meta character contaminating the >file. Sometimes those can be introduced by text editors or sometimes >e-mail clients. In case it wasn't the e-mail client I'm sending you this >fixed version. > >Also I see you are using maker_map_ids from version 2.10. Try the 2.26 >version. They are different. > >Thanks, >Carson > > >On 12-09-25 8:44 AM, "Carson Holt" wrote: > >>Could you also provide 34112_3June11Ass.gff? >> >>Thanks, >>Carson >> >> >>On 12-09-25 8:31 AM, "Ian Misner" wrote: >> >>>Hello, >>> >>>I'm trying to create human friendly ids and I'm getting an error when I >>>use the -sort_file option. Without the sort file it runs fine just not >>>numbered from the first contig. I have had some programers at our >>>cluster >>>look at the script and they attempted a fix but it did not work. They >>>mentioned the script was "buggy" so this might be part of the problem. >>>I've attached the error as well as the sort file. I can send more files >>>if necessary. Thanks for you time. >>> >>>Cheers >>>Ian >>> >>>$ maker_map_ids --prefix THRCLA_ --justify 5 --sort_order >>>34112_sort.txt >>>34112_3June11Ass.gff > 34112_3June11Ass_named.txt >>>Can't use string ("34112_sort.txt") as a HASH ref while "strict refs" >>>in >>>use at /gpfs/runtime/opt/maker/2.10/maker/bin/maker_map_ids line 311, >>><$IN> line 499186._______________________________________________ >>>maker-devel mailing list >>>maker-devel at box290.bluehost.com >>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org -------------- next part -------------- A non-text attachment was scrubbed... Name: maker_map_ids.gz Type: application/x-gzip Size: 3216 bytes Desc: not available URL: From fourie.joubert at up.ac.za Thu Sep 27 08:37:53 2012 From: fourie.joubert at up.ac.za (Fourie Joubert) Date: Thu, 27 Sep 2012 16:37:53 +0200 Subject: [maker-devel] Problem with maker2chado Message-ID: <506464C1.40103@up.ac.za> Hi I am trying to load a maker gff file into chado using maker2chado, but I am seeing the following type of error: Can't locate object method "value" via package "NODE_1002_length_51300_cov_98.972473" (perhaps you forgot to load "NODE_1002_length_51300_cov_98.972473"?) at /usr/local/bin/gmod_bulk_load_gff3.pl line 722, line 2. Any advice would be sincerely appreciated! Best regards! Fourie -- -------------- Prof Fourie Joubert Bioinformatics and Computational Biology Unit Department of Biochemistry University of Pretoria fourie.joubert at up.ac.za http://www.bi.up.ac.za Tel. +27-12-420-5825 Fax. +27-12-420-5800 ------------------------------------------------------------------------- This message and attachments are subject to a disclaimer. Please refer to www.it.up.ac.za/documentation/governance/disclaimer/ for full details. From carsonhh at gmail.com Thu Sep 27 10:27:14 2012 From: carsonhh at gmail.com (Carson Holt) Date: Thu, 27 Sep 2012 12:27:14 -0400 Subject: [maker-devel] Problem with maker2chado In-Reply-To: <506464C1.40103@up.ac.za> Message-ID: The error is being thrown by /usr/local/bin/gmod_bulk_load_gff3.pl It is called by MAKER and is part of the chado install. Try getting the latest version of chado from the SVN repository and then reinstalling it. Command to use --> svn co https://gmod.svn.sourceforge.net/svnroot/gmod/schema/trunk chado --Carson On 12-09-27 10:37 AM, "Fourie Joubert" wrote: >Hi > >I am trying to load a maker gff file into chado using maker2chado, but I >am seeing the following type of error: > >Can't locate object method "value" via package >"NODE_1002_length_51300_cov_98.972473" (perhaps you forgot to load >"NODE_1002_length_51300_cov_98.972473"?) at >/usr/local/bin/gmod_bulk_load_gff3.pl line 722, line 2. > >Any advice would be sincerely appreciated! > >Best regards! > >Fourie > >-- >-------------- >Prof Fourie Joubert >Bioinformatics and Computational Biology Unit >Department of Biochemistry >University of Pretoria >fourie.joubert at up.ac.za >http://www.bi.up.ac.za >Tel. +27-12-420-5825 >Fax. +27-12-420-5800 > >------------------------------------------------------------------------- >This message and attachments are subject to a disclaimer. Please refer >to www.it.up.ac.za/documentation/governance/disclaimer/ for full details. > > >_______________________________________________ >maker-devel mailing list >maker-devel at box290.bluehost.com >http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org From mike.thon at gmail.com Sun Sep 30 23:53:23 2012 From: mike.thon at gmail.com (Michael Thon) Date: Mon, 1 Oct 2012 07:53:23 +0200 Subject: [maker-devel] model_gff question Message-ID: Under what circumstances will maker not include a gene model from the model_gff file in its final output? It was my understanding from this post: https://groups.google.com/d/topic/maker-devel/Y5jSdZ1Olcc/discussion That maker will keep or replace models in model_gff and never remove them. I'm reannotating a fungal genome and in model_gff I'm providing the gene models originally made by the sequencing center. I have 12006 models in the file I specify in model_gff but maker's final annotation has only 10727 models in it. -Mike -------------- next part -------------- An HTML attachment was scrubbed... URL: From mike.thon at gmail.com Tue Sep 4 02:59:06 2012 From: mike.thon at gmail.com (Michael Thon) Date: Tue, 4 Sep 2012 10:59:06 +0200 Subject: [maker-devel] model_gff not in output Message-ID: <1A01E0C5-E60A-42AA-BD7B-A6429F435645@gmail.com> I'm using maker to update a legacy annotation. As input I'm using RNA-Seq aligned with cufflinks, ESTs, provided in fasta format, and proteins downloaded from UniProt.SwissProt. I have done two runs of maker so far. The first one using the legacy annotations in both the model_gff and pred_gff parameters. In the second run I used the legacy annotations in model_gff and in pred_gff I included gene models created with GeneMark-ES. In both runs 1 and 2 I have found two genes (so far) that exist in the legacy annotations but are not in the final gene models output by maker. Both genes have overlapping cufflinks annotations, in addition to having annotations in model_gff. I thought maker was supposed to keep all the annotations in model_gff, only replacing ones in which it could find an alternative model with better support. Is there any case in which is will remove a model? Another discrepency I found in run1 is a gene that maker 'moved' upstream approx. 150 bases. The gene locus annotated by maker covers the original annotation, but the CDS does not. The site of the original CDS is covered by an annotation in model_gff, pred_gff, two ESTs and a cufflinks annotation. Maker still seems to have moved is is upstream where it only has an overlapping cufflinks annotation. the three-prime utr annotated by cufflinks still covers the legacy annotation though. Here's a link to download the maker gff file I'm looking at: https://dl.dropbox.com/u/320712/supercont1%252E1.gff.zip The genes that are in the legacy annotation but missing in the maker annotation are: GLRG_00074 and GLRG_00092 the 'moved' gene model I described is model GLRG_00081. they all within the first 350 K of sequence. mike From chrisi.hahni at gmail.com Wed Sep 5 05:59:48 2012 From: chrisi.hahni at gmail.com (Christoph Hahn) Date: Wed, 05 Sep 2012 13:59:48 +0200 Subject: [maker-devel] keep_preds option? In-Reply-To: References: Message-ID: <50473EB4.7070501@gmail.com> Hello Barry and Carson, Thank you very much for the extensive replies!! Very helpful!! > > 2. I tried to use EST data of an alternative organism in altest= > (#EST/cDNA sequence file in fasta format from an alternate organism). > The organism is quite distantly related, but its the closest I have so > I thought I d give it a shot. I ran maker twice with identical settigs > expect in altest and est2genome=0/1. The number of genes predicted is > identical with both approaches, so I am not sure whether or not the > EST data was actually used or its just to distantly related. Any easy > way to assess this? > Typically EST evidence from another organism with alt_est will add little in the way of additional support (compared to just using protein evidence from say Swiss-prot) and this would be especially true if your alt_est is > distantly related. I'm not sure I really understand you alt_est/est2genome combo's to comment in more detail. I could see four possible combinations there: which two gave identical results? What I meant was that I ran maker once without any alt_est evidence and est2genome=0 and a second time with alt_est=some.fasta and est2genome=1. The result was the same. Sorry, for not making myself clear enough. I thought that the est2genome=1 switch is is just enabling physical est evidence to be used. Therefore, I thought neither alt_est=some.fasta, est2genome=0 nor alt_est=nothing, est2genome=1 would make any sense. I had misunderstood this. Will follow Carsons advice and will try to use more protein evidence from related species (in addition to uniprot). Running right now - Let s see where that leaves me. The IPRScan approach suggested by Barry to assess gene models without physical evidence sounds very interesting. I will definitely look into that. A question concerning an issue I just discovered: Ran maker twice with the same physical evidence. First time using SNAP and Genemark, second time using SNAP, Genemark and AUGUSTUS (set to the closest related species available - same phylum, different class). Second run gives less gene models. IN another context I found that the second pass of Maker using SNAP and Genemark (after training SNAP on the predictions of the first Pass) and the same physical evidence yields less gene annotations. How can that be given the same physical evidence? Thanks again for your help! It is much appreciated! cheers, Christoph Am 31.08.2012 21:03, schrieb Carson Holt: > I concur with everything Barry said. Also let me add that alt-ESTs do > not get polished around splice sites (exonerate won't handle them). > However ESTs and proteins do. This means that the utility of > alt-ESTs in adding UTR, and splice information is zero. They just > function as an anchor to maintain gene models that might have > otherwise been rejected. This also means alt_est=some.fasta together > with est2genome=1 will produce virtually no additional results because > est2genome requires that the splice site makes sense. You are better > off using proteins with protein2genome=1 if you don't have ESTs and > want partial models for training. Once you have a trained ab initio > gene predictor, turn the est2genome and protein2genome options off. > Otherwise they will give weird partial models that decrease the > quality of your final annotations. (partial models are ok for training > but that's about it). > > If you are getting too low a gene count with keep_preds=0, then you > probably need to add more evidence. Try adding all proteins from a > couple of related species (the protein= option accepts comma separated > lists of files). If your genome is a fungi, oomycete, or a prokaryote, > then setting keep_preds=1 is usually safe. Theses are genomes with > high gene density and simple gene structure, so ab initio predictors > do really well and don't need as much help from the evidence. For > other organisms, leave it set to 0 or you will get a lot of false > positives (false positives on some genomes with complex gene structure > can outnumber the genes by 10 to 1 if you turn this on). > > Thanks, > Carson > > > > > From: Barry Moore > > Date: Friday, 31 August, 2012 12:52 PM > To: Christoph Hahn > > Cc: > > Subject: Re: [maker-devel] keep_preds option? > > Hi Christopher, > > Comments below: > > On Aug 31, 2012, at 6:43 AM, Christoph Hahn wrote: > >> Hello maker users and developers, >> >> I am new to gene prediction and I am trying to use maker 2.25 on a >> newly assembled non-model organisms draft genome. Within maker I use >> genemark, SNAP and Augustus. I have a few questions: >> > > Welcome! > >> 1. I was wondering what the keep_preds option means exactly. >> >> I found two slightly different explanations on the option >> #Add unsupported gene prediction to final annotation set (maker2.25) >> #Add non-overlapping ab-inito gene prediction to final annotation set >> (found on the net - probably older maker version) >> > > It means to keep ab initio gene predictions for which there is no > physical evidence. There are two pieces of information that are > required for every MAKER annotation (by default). MAKER runs the ab > initio gene predictors and aligns transcript (EST/cDNA/mRNASeq > transcripts) and protein sequences to the genome. For each locus > where one or more gene predictions exist MAKER checks to see if there > is any physical evidence for gene expression at that locus > (RNA/protein sequence alignments) and if there is (splice EST or > protein alignments) evidence overlapping the predictions, MAKER > decides which prediction best matches the evidence and promotes that > prediction to an annotation. If there is no evidence overlapping any > of the predictions then those predictions are not included in the > output annotation file (although they are saved). If you set > keep_preds=1 then for each locus where prediction(s) exist maker keeps > one and promotes it to an annotation even though there is no physical > evidence. The description of 'non-overlapping ab-initio' means that > MAKER has clustered all ab-initio predictions at one locus and chose > one representative transcript to output. > >> As far as I understood keep_preds=0 only retains gene models for >> which the ab initio predictions agree. But how many, all three? two >> of three? >> keep_preds=1 instead keeps all gene models regardless if the >> different programs agree, right? >> > > MAKER does not take the presence of multiple ab initio predictions as > evidence and thus in the absence of aligned physical evidence MAKER > will not output an annotation even if all three ab initio tools > predict a gene at that locus. > >> In my case I get substantial differences in the number of gene models >> found between the two settings, while with =1 I get a number that is >> close to what we would expect. How would you interpret that? What >> would you recommend me to do? Obiously =0 is the saver option. > > If you think that the number of genes you are getting from a MAKER run > is too few, you could run MAKER with keep_preds=1. After the run is > finished, use a tool like IPRScan to search all MAKER predictions for > protein domain content and push that IPRScan output back into the > MAKER GFF file with the ipr_update_gff script. Then as a final step > you can run over the GFF file and remove any gene model that doesn't > have either physical evidence (AED < 1) or protein domain content > (Dbxref=PFAM:XXX etc...) sorry there's not a script prepackaged with > MAKER for that yet. > >> >> 2. I tried to use EST data of an alternative organism in altest= >> (#EST/cDNA sequence file in fasta format from an alternate organism). >> The organism is quite distantly related, but its the closest I have >> so I thought I d give it a shot. I ran maker twice with identical >> settigs expect in altest and est2genome=0/1. The number of genes >> predicted is identical with both approaches, so I am not sure whether >> or not the EST data was actually used or its just to distantly >> related. Any easy way to assess this? > > Typically EST evidence from another organism with alt_est will add > little in the way of additional support (compared to just using > protein evidence from say Swiss-prot) and this would be especially > true if your alt_est is distantly related. I'm not sure I really > understand you alt_est/est2genome combo's to comment in more detail. > I could see four possible combinations there: which two gave > identical results? > >> >> 3. I am running maker in several passes and after each pass I am >> training SNAP using the result of the previous pass. Then for every >> pass I run maker from scratch. Would you recommend to supply the gff >> of the previous pass in "#-----Re-annotation Using MAKER Derived GFF3 >> maker_gff= #re-annotate genome based on this gff3 file", instead? >> > > No, 'Re-annotation using MAKER Derived GFF3' is used for re-annotation > of a genome when you want certain parts of the previous run to be > passed through unchanged, but with retraining SNAP you want MAKER to > re-evaluate each annotation in light of the new predictions made by > the retrained SNAP. MAKER should run really fast in all of the runs > after the first one because as long as you haven't changed the > evidence files it won't have to redo any of the alignments. > > > B > >> Thanks in advance for any thoughts/advice on these things! I >> appreciate your help! >> >> much obliged, >> Christoph >> >> _______________________________________________ >> maker-devel mailing list >> maker-devel at box290.bluehost.com >> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org > > Barry Moore > Research Scientist > Dept. of Human Genetics > University of Utah > Salt Lake City, UT 84112 > -------------------------------------------- > (801) 585-3543 > > > > > _______________________________________________ maker-devel mailing > list maker-devel at box290.bluehost.com > > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org -------------- next part -------------- An HTML attachment was scrubbed... URL: From muntjaczhou at gmail.com Wed Sep 5 20:26:38 2012 From: muntjaczhou at gmail.com (Zhou Qi) Date: Wed, 5 Sep 2012 19:26:38 -0700 Subject: [maker-devel] gene duplicates and track the query protein Message-ID: Dear maker users and developers: I'm new to maker and trying to use it to annotate a Drosophila genome given protein sequences of its closely related species. I have two questions: 1. How maker decide which one to keep if one query protein has two similarly best hits in the target genome, e.g., gene duplication? 2. Is there any way to track the maker gene to its corresponding query proteins through setting up some parameters in maker? Or is it possible to directly let maker name the gene model based on its query protein? I looked through the previous threads, one possible way seems to use model_gff and map_forward option combined. I guess people more experienced than me using maker might know other ways? Many thanks! Qi From barry.moore at genetics.utah.edu Thu Sep 6 10:35:02 2012 From: barry.moore at genetics.utah.edu (Barry Moore) Date: Thu, 6 Sep 2012 10:35:02 -0600 Subject: [maker-devel] gene duplicates and track the query protein In-Reply-To: References: Message-ID: On Sep 5, 2012, at 8:26 PM, Zhou Qi wrote: > Dear maker users and developers: > > I'm new to maker and trying to use it to annotate a Drosophila genome given protein sequences of its closely related species. I have two questions: > > 1. How maker decide which one to keep if one query protein has two similarly best hits in the target genome, e.g., gene duplication? MAKER uses the aligned proteins as evidence to support gene predictions (i.e. from SNAP). If the supporting protein can align within the specified parameters (as defined in maker_bopts.ctl) then all of the valid alignments could be used as evidence for gene predictions at those loci. > > 2. Is there any way to track the maker gene to its corresponding query proteins through setting up some parameters in maker? Or is it possible to directly let maker name the gene model based on its query protein? > I don't know of a way to do this by setting parameters in the MAKER control file - maybe Carson has some idea for you here? B > I looked through the previous threads, one possible way seems to use model_gff and map_forward option combined. I guess people more experienced than me using maker might know other ways? > > Many thanks! > > Qi > _______________________________________________ > maker-devel mailing list > maker-devel at box290.bluehost.com > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org Barry Moore Research Scientist Dept. of Human Genetics University of Utah Salt Lake City, UT 84112 -------------------------------------------- (801) 585-3543 -------------- next part -------------- An HTML attachment was scrubbed... URL: From david.powell at monash.edu Thu Sep 6 18:23:57 2012 From: david.powell at monash.edu (David Powell) Date: Fri, 7 Sep 2012 10:23:57 +1000 Subject: [maker-devel] Problem with cegma2zff Message-ID: Greetings, I am using CEGMA to train SNAP for use with maker. However, I had a problem with the cegma2zff script that comes with maker. This script converts the gff file from CEGMA into a zff file for SNAP. The problem is that it was producing a zff file with every multi-exon gene as being "invalid" from SNAPs point of view. My fix was to modify cegma2zff to ignore any feature with the tag "Exon" - as these are always duplicated by cegma as another feature (one of First, Internal, Terminal, Single). Just wanted to post this here in case this fix is useful to anyone else. Cheers, -- David Powell diff --git a/cegma2zff b/cegma2zff index c795da8..a3bbb77 100755 --- a/cegma2zff +++ b/cegma2zff @@ -39,6 +39,8 @@ while(my $line = ){ my @F = split("\t", $line); ($F[3], $F[4]) = ($F[4], $F[3]) if($F[6] eq '-'); + next if $F[2] =~ /Exon/; + $F[2] =~ s/First/Einit/; $F[2] =~ s/Terminal/Eterm/; $F[2] =~ s/Internal/Exon/; -------------- next part -------------- An HTML attachment was scrubbed... URL: From guoyunfei1989 at gmail.com Fri Sep 7 11:54:12 2012 From: guoyunfei1989 at gmail.com (Yunfei Guo) Date: Fri, 7 Sep 2012 10:54:12 -0700 Subject: [maker-devel] maker annotate two species, same evidence, same settings Message-ID: Hi Carson, I have a quick question about maker annotations. I want to annotate two sets of assemblies from two related species using the same sets of evidence and settings except that the est assemblies would be specified as 'est' for one species (along with 'altest' evidence from other species) and as 'altest' (combined with est evidence from other species) for the other, would the annotation reflect the real difference between these two species? Or there might be some variations within the annotations themselves which might make the real difference more or less significant? Thank you! Yunfei From carsonhh at gmail.com Fri Sep 7 12:35:50 2012 From: carsonhh at gmail.com (Carson Holt) Date: Fri, 07 Sep 2012 14:35:50 -0400 Subject: [maker-devel] maker annotate two species, same evidence, same settings In-Reply-To: Message-ID: Let me explain how ESTs and alt-ESTs are use and maybe that will answer your question. ESTs will be polished around splice sites to give information on intron boundaries and UTR location. The polished ESTs can override ab initio gene predictor structure and be used to extend gene models by what is basically an exon cut and paste operation. The alt-ESTs are not polished (exoneerate can't handle them). So the splice site boundaries will be off. Maker will only try and infer UTR and intron boundaries from these if the alignment produces canonical splice sites (almost never happens). So they are relegated to the same status as the unpolished protein alignment (lower scoring hints to the gene predictor as to exon boundaries). They will also contribute to AED score with a little less accuracy than ESTs. When possible use protein models rather than alt-ESTs, primarily because they are computationally less intense than a tblastx type alignment that occurs with alt-ESTs. Exonerate will also polish protein alignments. Thanks, Carson On 12-09-07 1:54 PM, "Yunfei Guo" wrote: >Hi Carson, > >I have a quick question about maker annotations. I want to annotate >two sets of assemblies from two related species using the same sets of >evidence and settings except that the est assemblies would be >specified as 'est' for one species (along with 'altest' evidence from >other species) and as 'altest' (combined with est evidence from other >species) for the other, would the annotation reflect the real >difference between these two species? Or there might be some >variations within the annotations themselves which might make the real >difference more or less significant? > >Thank you! > >Yunfei > >_______________________________________________ >maker-devel mailing list >maker-devel at box290.bluehost.com >http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org From carsonhh at gmail.com Fri Sep 7 20:33:49 2012 From: carsonhh at gmail.com (Carson Holt) Date: Fri, 07 Sep 2012 22:33:49 -0400 Subject: [maker-devel] Problem with cegma2zff In-Reply-To: Message-ID: Yes. There was an update for CEGMA that causes features to be duplicated in it's output. Thanks for the post and the fix. --Carson From: David Powell Date: Thursday, 6 September, 2012 8:23 PM To: Subject: [maker-devel] Problem with cegma2zff Greetings, I am using CEGMA to train SNAP for use with maker. However, I had a problem with the cegma2zff script that comes with maker. This script converts the gff file from CEGMA into a zff file for SNAP. The problem is that it was producing a zff file with every multi-exon gene as being "invalid" from SNAPs point of view. My fix was to modify cegma2zff to ignore any feature with the tag "Exon" - as these are always duplicated by cegma as another feature (one of First, Internal, Terminal, Single). Just wanted to post this here in case this fix is useful to anyone else. Cheers, -- David Powell diff --git a/cegma2zff b/cegma2zff index c795da8..a3bbb77 100755 --- a/cegma2zff +++ b/cegma2zff @@ -39,6 +39,8 @@ while(my $line = ){ my @F = split("\t", $line); ($F[3], $F[4]) = ($F[4], $F[3]) if($F[6] eq '-'); + next if $F[2] =~ /Exon/; + $F[2] =~ s/First/Einit/; $F[2] =~ s/Terminal/Eterm/; $F[2] =~ s/Internal/Exon/; _______________________________________________ maker-devel mailing list maker-devel at box290.bluehost.com http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org -------------- next part -------------- An HTML attachment was scrubbed... URL: From jeremy.semeiks at utsw.edu Sun Sep 9 13:49:36 2012 From: jeremy.semeiks at utsw.edu (Jeremy Semeiks) Date: Sun, 9 Sep 2012 14:49:36 -0500 Subject: [maker-devel] How to preserve human-friendly IDs when reannotating Message-ID: Hi all, I have sequenced some novel fungal genomes, and I am annotating them with maker-2.26-beta. The entire project is pretty iterative, in the sense that I first get some seemingly-sane annotation sets, then analyze and compare the proteomes biologically, then reannotate when new data comes in or as I learn more about how maker works. Because I have already attached biological meaning to some of my proteins, I would like to retain the same human-friendly IDs across annotations. Eg, if maker suddenly finds 1,000 new proteins on a reannotation run because I turned on keep_preds, then I don't want the transcript formerly known as mymold_09652T0 to become mymold_10698T0 when I run maker_map_ids; I want to keep it named mymold_09652T0. So, is there any built-in way to preserve human-friendly IDs, or do I need to write my own script for this? I have tried setting map_forward=1 and maker_gff=, but setting these seems to preserve neither the human-friendly IDs nor even the original IDs. (Eg, protein "genemark-scaffold353-processed-gene-0.9-mRNA-1" changed its name to "genemark-scaffold353-processed-gene-0.6-mRNA-1" when reannotated.) I haven't turned on any of the *_pass options, eg protein_pass; would this be relevant? Extra credit question: I am making some mate-pair libraries for these fungi; when I re-assemble, that will completely change my scaffold names. Is there any easy way to preserve human-friendly transcript names in this case? As with the above simpler case, I think it would be pretty easy to transfer 90% of the names just by doing an all-vs-all blastp between two annotation sets and fishing out the best hits, but the remaining 10% might be a headache. Thanks, Jeremy Grad student, Grishin lab UT Southwestern, Dallas TX 510.385.8959 -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Mon Sep 10 05:01:46 2012 From: carsonhh at gmail.com (Carson Holt) Date: Mon, 10 Sep 2012 07:01:46 -0400 Subject: [maker-devel] How to preserve human-friendly IDs when reannotating In-Reply-To: Message-ID: The map_forward option requires that the pass option for the gene models be turned on. Otherwise you will have to do some spacial overlap test outside of MAKER. If you have a new assembly, you can try mapping the old models onto the new assembly using the old transcripts as input to the est= and setting est2genome=1 (nothing else set, i.e no repeat masking etc.). Then there is an undocumented option that is still a little buggy (hence why it is still undocumented). Add the line est_forward=1 to your control files. This tells MAKER to copy names from the ESTs, build the models directly from their alignment, and to do other things to try and make a 1 to 1 match across the genome. You will have to manually check that it is 1 to 1 in the end (as I said still a little buggy and hence undocumented). Use the resulting file as input to the model_gff option on a separate run with map_forward=1 for additional reannotation wil more evidence, etc. where you want to still be able to map names forward. From: Jeremy Semeiks Date: Sunday, 9 September, 2012 3:49 PM To: Subject: [maker-devel] How to preserve human-friendly IDs when reannotating Hi all, I have sequenced some novel fungal genomes, and I am annotating them with maker-2.26-beta. The entire project is pretty iterative, in the sense that I first get some seemingly-sane annotation sets, then analyze and compare the proteomes biologically, then reannotate when new data comes in or as I learn more about how maker works. Because I have already attached biological meaning to some of my proteins, I would like to retain the same human-friendly IDs across annotations. Eg, if maker suddenly finds 1,000 new proteins on a reannotation run because I turned on keep_preds, then I don't want the transcript formerly known as mymold_09652T0 to become mymold_10698T0 when I run maker_map_ids; I want to keep it named mymold_09652T0. So, is there any built-in way to preserve human-friendly IDs, or do I need to write my own script for this? I have tried setting map_forward=1 and maker_gff=, but setting these seems to preserve neither the human-friendly IDs nor even the original IDs. (Eg, protein "genemark-scaffold353-processed-gene-0.9-mRNA-1" changed its name to "genemark-scaffold353-processed-gene-0.6-mRNA-1" when reannotated.) I haven't turned on any of the *_pass options, eg protein_pass; would this be relevant? Extra credit question: I am making some mate-pair libraries for these fungi; when I re-assemble, that will completely change my scaffold names. Is there any easy way to preserve human-friendly transcript names in this case? As with the above simpler case, I think it would be pretty easy to transfer 90% of the names just by doing an all-vs-all blastp between two annotation sets and fishing out the best hits, but the remaining 10% might be a headache. Thanks, Jeremy Grad student, Grishin lab UT Southwestern, Dallas TX 510.385.8959 _______________________________________________ maker-devel mailing list maker-devel at box290.bluehost.com http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Mon Sep 10 05:10:33 2012 From: carsonhh at gmail.com (Carson Holt) Date: Mon, 10 Sep 2012 07:10:33 -0400 Subject: [maker-devel] keep_preds option? In-Reply-To: <50473EB4.7070501@gmail.com> Message-ID: The final annotations are really produced by GeneMark, SNAP, Augustus etc. MAKER basically takes the physical evidence, turns it into 'hints' for these programs (I.e. Exon and CDS scoring bonuses), and then lets them run again. If you retrain them they will behave different. If you add a new one you may also get a model from the third algorithm that seems to match the evidence better. Sometimes one algorithm will call one gene where another thinks it should be two genes while the third thinks it is really a larger gene merged with exons from a neighboring gene. MAKER will add hints to try and improve the ab initio predictors performance and choose the model that seems to be make sense given the evidence. The source of a gene model is eventually inherent from the name MAKER gives it. If snap is in the name, then the model was derived from snap. If maker and snap are in the name, then it is a model derived from snap with MAKER hints (otherwise it was derived completely from SNAP's training with no MAKER input). Thanks, Carson From: Christoph Hahn Date: Wednesday, 5 September, 2012 7:59 AM To: Carson Holt , Barry Moore Cc: Subject: Re: [maker-devel] keep_preds option? Hello Barry and Carson, Thank you very much for the extensive replies!! Very helpful!! > > > 2. I tried to use EST data of an alternative organism in altest= (#EST/cDNA > sequence file in fasta format from an alternate organism). The organism is > quite distantly related, but its the closest I have so I thought I d give it a > shot. I ran maker twice with identical settigs expect in altest and > est2genome=0/1. The number of genes predicted is identical with both > approaches, so I am not sure whether or not the EST data was actually used or > its just to distantly related. Any easy way to assess this? > > > Typically EST evidence from another organism with alt_est will add little in the way of additional support (compared to just using protein evidence from say Swiss-prot) and this would be especially true if your alt_est is > distantly related. I'm not sure I really understand you alt_est/est2genome combo's to comment in more detail. I could see four possible combinations there: which two gave identical results? What I meant was that I ran maker once without any alt_est evidence and est2genome=0 and a second time with alt_est=some.fasta and est2genome=1. The result was the same. Sorry, for not making myself clear enough. I thought that the est2genome=1 switch is is just enabling physical est evidence to be used. Therefore, I thought neither alt_est=some.fasta, est2genome=0 nor alt_est=nothing, est2genome=1 would make any sense. I had misunderstood this. Will follow Carsons advice and will try to use more protein evidence from related species (in addition to uniprot). Running right now - Let s see where that leaves me. The IPRScan approach suggested by Barry to assess gene models without physical evidence sounds very interesting. I will definitely look into that. A question concerning an issue I just discovered: Ran maker twice with the same physical evidence. First time using SNAP and Genemark, second time using SNAP, Genemark and AUGUSTUS (set to the closest related species available - same phylum, different class). Second run gives less gene models. IN another context I found that the second pass of Maker using SNAP and Genemark (after training SNAP on the predictions of the first Pass) and the same physical evidence yields less gene annotations. How can that be given the same physical evidence? Thanks again for your help! It is much appreciated! cheers, Christoph Am 31.08.2012 21:03, schrieb Carson Holt: > > I concur with everything Barry said. Also let me add that alt-ESTs do not get > polished around splice sites (exonerate won't handle them). However ESTs and > proteins do. This means that the utility of alt-ESTs in adding UTR, and > splice information is zero. They just function as an anchor to maintain gene > models that might have otherwise been rejected. This also means > alt_est=some.fasta together with est2genome=1 will produce virtually no > additional results because est2genome requires that the splice site makes > sense. You are better off using proteins with protein2genome=1 if you don?t > have ESTs and want partial models for training. Once you have a trained ab > initio gene predictor, turn the est2genome and protein2genome options off. > Otherwise they will give weird partial models that decrease the quality of > your final annotations. (partial models are ok for training but that's about > it). > > > > > If you are getting too low a gene count with keep_preds=0, then you probably > need to add more evidence. Try adding all proteins from a couple of related > species (the protein= option accepts comma separated lists of files). If your > genome is a fungi, oomycete, or a prokaryote, then setting keep_preds=1 is > usually safe. Theses are genomes with high gene density and simple gene > structure, so ab initio predictors do really well and don't need as much help > from the evidence. For other organisms, leave it set to 0 or you will get a > lot of false positives (false positives on some genomes with complex gene > structure can outnumber the genes by 10 to 1 if you turn this on). > > > > > Thanks, > > Carson > > > > > > > > > > > > > > From: Barry Moore > Date: Friday, 31 August, 2012 12:52 PM > To: Christoph Hahn > Cc: > Subject: Re: [maker-devel] keep_preds option? > > > > > > > Hi Christopher, > > > > Comments below: > > > > > On Aug 31, 2012, at 6:43 AM, Christoph Hahn wrote: > > >> >> Hello maker users and developers, >> >> I am new to gene prediction and I am trying to use maker 2.25 on a newly >> assembled non-model organisms draft genome. Within maker I use genemark, SNAP >> and Augustus. I have a few questions: >> >> >> > > > > > Welcome! > > >> >> 1. I was wondering what the keep_preds option means exactly. >> >> I found two slightly different explanations on the option >> #Add unsupported gene prediction to final annotation set (maker2.25) >> #Add non-overlapping ab-inito gene prediction to final annotation set (found >> on the net - probably older maker version) >> >> >> > > > > > It means to keep ab initio gene predictions for which there is no physical > evidence. There are two pieces of information that are required for every > MAKER annotation (by default). MAKER runs the ab initio gene predictors and > aligns transcript (EST/cDNA/mRNASeq transcripts) and protein sequences to the > genome. For each locus where one or more gene predictions exist MAKER checks > to see if there is any physical evidence for gene expression at that locus > (RNA/protein sequence alignments) and if there is (splice EST or protein > alignments) evidence overlapping the predictions, MAKER decides which > prediction best matches the evidence and promotes that prediction to an > annotation. If there is no evidence overlapping any of the predictions then > those predictions are not included in the output annotation file (although > they are saved). If you set keep_preds=1 then for each locus where > prediction(s) exist maker keeps one and promotes it to an annotation even > though there is no physical evidence. The description of 'non-overlapping > ab-initio' means that MAKER has clustered all ab-initio predictions at one > locus and chose one representative transcript to output. > > >> >> As far as I understood keep_preds=0 only retains gene models for which the ab >> initio predictions agree. But how many, all three? two of three? >> keep_preds=1 instead keeps all gene models regardless if the different >> programs agree, right? >> >> >> > > > > > MAKER does not take the presence of multiple ab initio predictions as evidence > and thus in the absence of aligned physical evidence MAKER will not output an > annotation even if all three ab initio tools predict a gene at that locus. > > >> >> In my case I get substantial differences in the number of gene models found >> between the two settings, while with =1 I get a number that is close to what >> we would expect. How would you interpret that? What would you recommend me to >> do? Obiously =0 is the saver option. >> >> > > > > > If you think that the number of genes you are getting from a MAKER run is too > few, you could run MAKER with keep_preds=1. After the run is finished, use a > tool like IPRScan to search all MAKER predictions for protein domain content > and push that IPRScan output back into the MAKER GFF file with the > ipr_update_gff script. Then as a final step you can run over the GFF file and > remove any gene model that doesn't have either physical evidence (AED < 1) or > protein domain content (Dbxref=PFAM:XXX etc?) sorry there's not a script > prepackaged with MAKER for that yet. > > > > >> >> >> 2. I tried to use EST data of an alternative organism in altest= (#EST/cDNA >> sequence file in fasta format from an alternate organism). The organism is >> quite distantly related, but its the closest I have so I thought I d give it >> a shot. I ran maker twice with identical settigs expect in altest and >> est2genome=0/1. The number of genes predicted is identical with both >> approaches, so I am not sure whether or not the EST data was actually used or >> its just to distantly related. Any easy way to assess this? >> >> > > > > > Typically EST evidence from another organism with alt_est will add little in > the way of additional support (compared to just using protein evidence from > say Swiss-prot) and this would be especially true if your alt_est is distantly > related. I'm not sure I really understand you alt_est/est2genome combo's to > comment in more detail. I could see four possible combinations there: which > two gave identical results? > > >> >> >> 3. I am running maker in several passes and after each pass I am training >> SNAP using the result of the previous pass. Then for every pass I run maker >> from scratch. Would you recommend to supply the gff of the previous pass in >> "#-----Re-annotation Using MAKER Derived GFF3 >> maker_gff= #re-annotate genome based on this gff3 file", instead? >> >> >> > > > > > No, 'Re-annotation using MAKER Derived GFF3' is used for re-annotation of a > genome when you want certain parts of the previous run to be passed through > unchanged, but with retraining SNAP you want MAKER to re-evaluate each > annotation in light of the new predictions made by the retrained SNAP. MAKER > should run really fast in all of the runs after the first one because as long > as you haven't changed the evidence files it won't have to redo any of the > alignments. > > > > > > > B > > > >> >> Thanks in advance for any thoughts/advice on these things! I appreciate your >> help! >> >> much obliged, >> Christoph >> >> _______________________________________________ >> maker-devel mailing list >> maker-devel at box290.bluehost.com >> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org >> >> > > > > > > Barry Moore > > Research Scientist > > Dept. of Human Genetics > > University of Utah > > Salt Lake City, UT 84112 > > -------------------------------------------- > > (801) 585-3543 > > > > > > > > > > > > > > _______________________________________________ maker-devel mailing list > maker-devel at box290.bluehost.com > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Mon Sep 10 05:17:26 2012 From: carsonhh at gmail.com (Carson Holt) Date: Mon, 10 Sep 2012 07:17:26 -0400 Subject: [maker-devel] model_gff not in output In-Reply-To: <1A01E0C5-E60A-42AA-BD7B-A6429F435645@gmail.com> Message-ID: The only way MAKER should ignore a legacy annotation (only what's in model_gff is considered legacy by MAKER) is if, you also set one of the ab iniio predictors to run simultaneously or provide a pred_gff file and one of those models scores higher and would overlap the legacy model. Then MAKER chooses that model instead. Also if you have two overlapping legacy models MAKER will only keep one or the other under these same conditions. MAKER will only keep all legacy models regardless of overlap if you only supply model_gff with no other predictors turned on. Once you turn a predictor on, MAKER takes this as a cue that you are letting it make changes. Legacy models should always be kept under all circumstances if there is nothing overlapping them with a higher score. Are the missing models partially overlapped by anything in the resulting MAKER annotations? Thanks, Carson On 12-09-04 4:59 AM, "Michael Thon" wrote: >I'm using maker to update a legacy annotation. As input I'm using >RNA-Seq aligned with cufflinks, ESTs, provided in fasta format, and >proteins downloaded from UniProt.SwissProt. I have done two runs of >maker so far. The first one using the legacy annotations in both the >model_gff and pred_gff parameters. In the second run I used the legacy >annotations in model_gff and in pred_gff I included gene models created >with GeneMark-ES. > >In both runs 1 and 2 I have found two genes (so far) that exist in the >legacy annotations but are not in the final gene models output by maker. >Both genes have overlapping cufflinks annotations, in addition to having >annotations in model_gff. I thought maker was supposed to keep all the >annotations in model_gff, only replacing ones in which it could find an >alternative model with better support. Is there any case in which is >will remove a model? > > >Another discrepency I found in run1 is a gene that maker 'moved' upstream >approx. 150 bases. The gene locus annotated by maker covers the original >annotation, but the CDS does not. The site of the original CDS is covered >by an annotation in model_gff, pred_gff, two ESTs and a cufflinks >annotation. Maker still seems to have moved is is upstream where it only >has an overlapping cufflinks annotation. the three-prime utr annotated >by cufflinks still covers the legacy annotation though. > >Here's a link to download the maker gff file I'm looking at: > >https://dl.dropbox.com/u/320712/supercont1%252E1.gff.zip > >The genes that are in the legacy annotation but missing in the maker >annotation are: >GLRG_00074 and GLRG_00092 > >the 'moved' gene model I described is model GLRG_00081. they all within >the first 350 K of sequence. >mike > > > > > >_______________________________________________ >maker-devel mailing list >maker-devel at box290.bluehost.com >http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org From carsonhh at gmail.com Mon Sep 10 05:18:34 2012 From: carsonhh at gmail.com (Carson Holt) Date: Mon, 10 Sep 2012 07:18:34 -0400 Subject: [maker-devel] Maker Re-tries In-Reply-To: <1E417039-68CF-4EFE-90BF-964DC86B1864@uchicago.edu> Message-ID: Killing a job yourself should not increase the failure count for a contig. Thanks, Carson From: Kipp Johnson Date: Tuesday, 21 August, 2012 5:25 PM To: Carson Holt Cc: Kipp Johnson , Subject: Re: Maker Re-tries Hi Carson, Simple question: If I start maker and then kill the job before a thread finishes processing a contig, does this failure to complete the contig count in the number of tries maker will try to complete the contig before skipping to another? Basically, does the "tries=2 #number of times to try a contig if there is a failure for some reason" parameter take into account failures resulting from me killing the job? Best, Kipp Johnson kippjohnson at uchicago.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: From Carson.Holt at oicr.on.ca Mon Sep 10 04:50:09 2012 From: Carson.Holt at oicr.on.ca (Carson Holt) Date: Mon, 10 Sep 2012 10:50:09 +0000 Subject: [maker-devel] gene duplicates and track the query protein In-Reply-To: Message-ID: 2. Is there any way to track the maker gene to its corresponding query proteins through setting up some parameters in maker? Or is it possible to directly let maker name the gene model based on its query protein? Not directly. Proteins can align to multiple locations, so you will get more than one protein overlapping a gene. A reciprocal BLAST would probably be the best thing to do here. If the MAKER derived annotation, and a gene are both each others best hit in separate blast jobs, then you could usually safely call them the same gene. You would have to do that outside of MAKER. Thanks, Carson From: Barry Moore > Date: Thursday, 6 September, 2012 12:35 PM To: Zhou Qi > Cc: > Subject: Re: [maker-devel] gene duplicates and track the query protein On Sep 5, 2012, at 8:26 PM, Zhou Qi wrote: Dear maker users and developers: I'm new to maker and trying to use it to annotate a Drosophila genome given protein sequences of its closely related species. I have two questions: 1. How maker decide which one to keep if one query protein has two similarly best hits in the target genome, e.g., gene duplication? MAKER uses the aligned proteins as evidence to support gene predictions (i.e. from SNAP). If the supporting protein can align within the specified parameters (as defined in maker_bopts.ctl) then all of the valid alignments could be used as evidence for gene predictions at those loci. 2. Is there any way to track the maker gene to its corresponding query proteins through setting up some parameters in maker? Or is it possible to directly let maker name the gene model based on its query protein? I don't know of a way to do this by setting parameters in the MAKER control file - maybe Carson has some idea for you here? B I looked through the previous threads, one possible way seems to use model_gff and map_forward option combined. I guess people more experienced than me using maker might know other ways? Many thanks! Qi _______________________________________________ maker-devel mailing list maker-devel at box290.bluehost.com http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org Barry Moore Research Scientist Dept. of Human Genetics University of Utah Salt Lake City, UT 84112 -------------------------------------------- (801) 585-3543 _______________________________________________ maker-devel mailing list maker-devel at box290.bluehost.com http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org -------------- next part -------------- An HTML attachment was scrubbed... URL: From jeremy.semeiks at utsw.edu Mon Sep 10 09:02:25 2012 From: jeremy.semeiks at utsw.edu (Jeremy Semeiks) Date: Mon, 10 Sep 2012 10:02:25 -0500 Subject: [maker-devel] How to preserve human-friendly IDs when reannotating In-Reply-To: References: Message-ID: OK, thanks. So if I understand correctly, to preserve human-friendly IDs requires setting just three options: map_forward=1, maker_gff=, and model_pass=1. (Or instead of the last two I could equivalently just set model_gff to a GFF containing only models.) A couple new issues came up when I tried to run with these options. I started maker like this: /usr/bin/time mpiexec -n 10 maker -q < /dev/null > maker.oe 2>&1 1. I get a bunch of messages as follows, but with variable line number: DBD::SQLite::db do failed: database is locked at /home/jrs/maker-2.26-beta/bin/../lib/GFFDB.pm line 186. I saw that this came up in another thread < https://groups.google.com/forum/?fromgroups=#!topic/maker-devel/TscBgbQfBX4>, but I'm not sure it was ever resolved, nor whether it will affect my reannotation results (as I'm not sure what "your GFF3 results will not be integrated" means). This error did not come up the last time I ran maker for reannotation with similar options in a different directory. And both my current directory and my tmp directory are locally mounted, ie not NFS. 2. Both in this run and in previous runs, I get a lot of lines like this, seemingly at random: Warning: unable to close filehandle DF properly. On Mon, Sep 10, 2012 at 6:01 AM, Carson Holt wrote: > The map_forward option requires that the pass option for the gene models > be turned on. Otherwise you will have to do some spacial overlap test > outside of MAKER. > > If you have a new assembly, you can try mapping the old models onto the > new assembly using the old transcripts as input to the est= and setting > est2genome=1 (nothing else set, i.e no repeat masking etc.). Then there is > an undocumented option that is still a little buggy (hence why it is still > undocumented). Add the line est_forward=1 to your control files. This > tells MAKER to copy names from the ESTs, build the models directly from > their alignment, and to do other things to try and make a 1 to 1 match > across the genome. You will have to manually check that it is 1 to 1 in > the end (as I said still a little buggy and hence undocumented). Use the > resulting file as input to the model_gff option on a separate run with > map_forward=1 for additional reannotation wil more evidence, etc. where you > want to still be able to map names forward. > > From: Jeremy Semeiks > Date: Sunday, 9 September, 2012 3:49 PM > To: > Subject: [maker-devel] How to preserve human-friendly IDs when > reannotating > > Hi all, > > I have sequenced some novel fungal genomes, and I am annotating them with > maker-2.26-beta. The entire project is pretty iterative, in the sense that > I first get some seemingly-sane annotation sets, then analyze and compare > the proteomes biologically, then reannotate when new data comes in or as I > learn more about how maker works. Because I have already attached > biological meaning to some of my proteins, I would like to retain the same > human-friendly IDs across annotations. Eg, if maker suddenly finds 1,000 > new proteins on a reannotation run because I turned on keep_preds, then I > don't want the transcript formerly known as mymold_09652T0 to become > mymold_10698T0 when I run maker_map_ids; I want to keep it named > mymold_09652T0. > > So, is there any built-in way to preserve human-friendly IDs, or do I need > to write my own script for this? I have tried setting map_forward=1 and > maker_gff=, but > setting these seems to preserve neither the human-friendly IDs nor even the > original IDs. (Eg, protein "genemark-scaffold353-processed-gene-0.9-mRNA-1" > changed its name to "genemark-scaffold353-processed-gene-0.6-mRNA-1" when > reannotated.) I haven't turned on any of the *_pass options, eg > protein_pass; would this be relevant? > > Extra credit question: I am making some mate-pair libraries for these > fungi; when I re-assemble, that will completely change my scaffold names. > Is there any easy way to preserve human-friendly transcript names in this > case? As with the above simpler case, I think it would be pretty easy to > transfer 90% of the names just by doing an all-vs-all blastp between two > annotation sets and fishing out the best hits, but the remaining 10% might > be a headache. > > Thanks, > Jeremy > Grad student, Grishin lab > UT Southwestern, Dallas TX > 510.385.8959 > _______________________________________________ maker-devel mailing list > maker-devel at box290.bluehost.com > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org > -------------- next part -------------- An HTML attachment was scrubbed... URL: From carson.holt at genetics.utah.edu Mon Sep 10 11:21:05 2012 From: carson.holt at genetics.utah.edu (Carson Holt) Date: Mon, 10 Sep 2012 17:21:05 +0000 Subject: [maker-devel] MWAS: User Feedback In-Reply-To: Message-ID: MAKER won't really annotate those. Transcriptome annotation is a very different problem from genome annotation. I'm CC'ing this to the MAKER mailing list to see if anyone has good suggestion for transcriptome annotation. I would recommend using Repeatmasker to remove transposons from your transcriptome set, and then InterProScan for domain identification and maybe blast2go for GO term association. --Carson On 12-09-10 1:10 PM, "grind001 at umn.edu" wrote: >I have assembled RNAseq transcripts. There's no genome assembly for our >species right now, so I was trying to do an organized assembly pipeline >and >use your system. > >On Sep 10 2012, Carson Holt wrote: > >>Tell me a little more about your project. Based on your brief >>description >>I think you might need a different tool. MAKER doesn't assemble or >>annotate transcriptomes (i.e. RNA only). It works with de novo genome >>assemblies to identify the genes from them (I.e entire chromosomes or >>large fragments of chromosomes). It can use RNA-seq result to help >>annotate the genome but still requires a genome assembly. >> >>The online server will annotate maximum of 5 Mb at a time and it's slow >>(mostly built for small jobs). You will get 10-20 faster performance >>locally. >> >>Thanks, >>Carson >> >> >> >>On 12-09-10 12:17 PM, "grind001 at umn.edu" wrote: >> >>>Maker Web Annotation Service - User Feedback: >>>--------------------------------------------- >>>Hi, >>> >>>I'm working on getting your software installed on my systems, and have >>>done a test run on your web page with a portion of my data. >>>I have 150,000 contigs from a de novo assembly of our transcriptome. Do >>>you have room on your server for a large run? or is this just a sample >>>space to test the software? I'm under some time constraints and an just >>>checking and hoping to push this forward a bit faster. >>> >>> >>> >>>Best, >>>Suzanne >>>University of MN >>> >>> >>>--------------------------------------------- >>>User: 1440 >>>First: Suzanne >>>Last: Grindle >>>Institution: University of Minnesota >>>E-mail: grind001 at umn.edu >>> >> >> From felix.bemm at uni-wuerzburg.de Mon Sep 10 13:15:22 2012 From: felix.bemm at uni-wuerzburg.de (Felix Bemm) Date: Mon, 10 Sep 2012 21:15:22 +0200 Subject: [maker-devel] MWAS: User Feedback In-Reply-To: References: Message-ID: <504E3C4A.2040401@uni-wuerzburg.de> hi suzanne, the trinity assembler mailing list has some good ideas for that. You could think about using an "intelligent" orf finder like transdecoder (transdecoder.sourceforge.net). the predicted orfs can than be used for an interpro and blast2go run. merge the interpro and the b2g run with the built-in tool of blast2go. simply put the interpro xml's for each orf of a given transcript into one file for that and use the built-in import function of blast2go. this might help you to improve the GO annotation. it also works with the b2g pipeline tool (which is much faster). In addition, you could try to use interproscan standalone 5 (http://code.google.com/p/interproscan/) since it has an improved support for nucleic acid sequences. cheers felix Am 10.09.2012 19:21, schrieb Carson Holt: > MAKER won't really annotate those. Transcriptome annotation is a very > different problem from genome annotation. I'm CC'ing this to the MAKER > mailing list to see if anyone has good suggestion for transcriptome > annotation. > > I would recommend using Repeatmasker to remove transposons from your > transcriptome set, and then InterProScan for domain identification and > maybe blast2go for GO term association. > > --Carson > > > > > On 12-09-10 1:10 PM, "grind001 at umn.edu" wrote: > >> I have assembled RNAseq transcripts. There's no genome assembly for our >> species right now, so I was trying to do an organized assembly pipeline >> and >> use your system. >> >> On Sep 10 2012, Carson Holt wrote: >> >>> Tell me a little more about your project. Based on your brief >>> description >>> I think you might need a different tool. MAKER doesn't assemble or >>> annotate transcriptomes (i.e. RNA only). It works with de novo genome >>> assemblies to identify the genes from them (I.e entire chromosomes or >>> large fragments of chromosomes). It can use RNA-seq result to help >>> annotate the genome but still requires a genome assembly. >>> >>> The online server will annotate maximum of 5 Mb at a time and it's slow >>> (mostly built for small jobs). You will get 10-20 faster performance >>> locally. >>> >>> Thanks, >>> Carson >>> >>> >>> >>> On 12-09-10 12:17 PM, "grind001 at umn.edu" wrote: >>> >>>> Maker Web Annotation Service - User Feedback: >>>> --------------------------------------------- >>>> Hi, >>>> >>>> I'm working on getting your software installed on my systems, and have >>>> done a test run on your web page with a portion of my data. >>>> I have 150,000 contigs from a de novo assembly of our transcriptome. Do >>>> you have room on your server for a large run? or is this just a sample >>>> space to test the software? I'm under some time constraints and an just >>>> checking and hoping to push this forward a bit faster. >>>> >>>> >>>> >>>> Best, >>>> Suzanne >>>> University of MN >>>> >>>> >>>> --------------------------------------------- >>>> User: 1440 >>>> First: Suzanne >>>> Last: Grindle >>>> Institution: University of Minnesota >>>> E-mail: grind001 at umn.edu >>>> >>> >>> > > > _______________________________________________ > maker-devel mailing list > maker-devel at box290.bluehost.com > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org > -- Felix Bemm Department of Bioinformatics University of W?rzburg, Germany Tel: +49 931 - 31 83696 Fax: +49 931 - 31 84552 felix.bemm at uni-wuerzburg.de From ranjani at uga.edu Tue Sep 11 09:38:33 2012 From: ranjani at uga.edu (Sivaranjani Namasivayam) Date: Tue, 11 Sep 2012 15:38:33 +0000 Subject: [maker-devel] MAKER training Message-ID: Hi, I am using MAKER to annotate a newly sequenced genome. I have trained and retrained with datasets but I would like some advice on assessing the output and how this is affected by the input provided. - I have transcriptome data from 454 and Illumina platforms. Illumina is from a single time point and 454 from multiple time point. 454 was assembled using Newbler(dataset 1) and Illumina using Tophat-Cufflinks (dataset 2) and the denovo Trinity pipeline (dataset 3). I now have3 assemblies - 454 and Illumina will have some redunant transcripts (because of one overlapping time point); TopHat-Cufflinks and Trinity will have highly redundant transcripts (because they use same raw reads). Is it OK to provide all 3 datasets as EST evidence, how does it affect the quality of annotation. (For now I have used dataset 1 and dataset 2 as EST evidence) - I used the above model to retrain, I passed through everything except the abinitio gene predictions. I also provided a set a manually annotated genes , many of which have EST evidence. Is this OK to do? [ For proteins evidence, I gave a set from related organisms, same as above] - In my third retraining, I used the above retrained model, but this time I only provided the genome_gff but did not pass through any other data. However I did provide the manually annotated genes as EST evidence and related proteins as protein_evidence. Can you please give me some advice on which of these could give me the best prediction, or if I can alter something to get a better prediction. - A quick question about Augustus - I used a Augustus model (trained for a closely related organism) for ab-initio prediction. Does MAKER adjust this model based on the evidence provided, or use the model as such for a prediction. Greatly appreciate your help! Thanks! Ranjani -------------- next part -------------- An HTML attachment was scrubbed... URL: From dence at genetics.utah.edu Tue Sep 11 09:46:04 2012 From: dence at genetics.utah.edu (Daniel Ence) Date: Tue, 11 Sep 2012 15:46:04 +0000 Subject: [maker-devel] MAKER training In-Reply-To: References: Message-ID: Hi Ranjani, It is fine to include all three of those transcriptome datatsets. The more (relevant) evidence the better. I'm not certain what you mean when you say "you used the above model to retrain". Did you train an abinitio gene predictor using the results from your first maker run? Daniel Ence Graduate Student Eccles Institute of Human Genetics University of Utah 15 North 2030 East, Room 2100 Salt Lake City, UT 84112-5330 ________________________________ From: maker-devel-bounces at yandell-lab.org [maker-devel-bounces at yandell-lab.org] on behalf of Sivaranjani Namasivayam [ranjani at uga.edu] Sent: Tuesday, September 11, 2012 9:38 AM To: maker-devel at yandell-lab.org Subject: [maker-devel] MAKER training Hi, I am using MAKER to annotate a newly sequenced genome. I have trained and retrained with datasets but I would like some advice on assessing the output and how this is affected by the input provided. - I have transcriptome data from 454 and Illumina platforms. Illumina is from a single time point and 454 from multiple time point. 454 was assembled using Newbler(dataset 1) and Illumina using Tophat-Cufflinks (dataset 2) and the denovo Trinity pipeline (dataset 3). I now have3 assemblies - 454 and Illumina will have some redunant transcripts (because of one overlapping time point); TopHat-Cufflinks and Trinity will have highly redundant transcripts (because they use same raw reads). Is it OK to provide all 3 datasets as EST evidence, how does it affect the quality of annotation. (For now I have used dataset 1 and dataset 2 as EST evidence) - I used the above model to retrain, I passed through everything except the abinitio gene predictions. I also provided a set a manually annotated genes , many of which have EST evidence. Is this OK to do? [ For proteins evidence, I gave a set from related organisms, same as above] - In my third retraining, I used the above retrained model, but this time I only provided the genome_gff but did not pass through any other data. However I did provide the manually annotated genes as EST evidence and related proteins as protein_evidence. Can you please give me some advice on which of these could give me the best prediction, or if I can alter something to get a better prediction. - A quick question about Augustus - I used a Augustus model (trained for a closely related organism) for ab-initio prediction. Does MAKER adjust this model based on the evidence provided, or use the model as such for a prediction. Greatly appreciate your help! Thanks! Ranjani -------------- next part -------------- An HTML attachment was scrubbed... URL: From ranjani at uga.edu Tue Sep 11 09:57:31 2012 From: ranjani at uga.edu (Sivaranjani Namasivayam) Date: Tue, 11 Sep 2012 15:57:31 +0000 Subject: [maker-devel] MAKER training In-Reply-To: References: , Message-ID: Hey, I used the MAKER model to retrain MAKER itself. I read somewhere it improves MAKER's predictions. I did train abinitio gene predictors using MAKERs output, but I wanted to identify the best prediction before using it to train other gene predictors. Thanks, Ranjani ________________________________ From: Daniel Ence [dence at genetics.utah.edu] Sent: Tuesday, September 11, 2012 11:46 AM To: Sivaranjani Namasivayam; maker-devel at yandell-lab.org Subject: RE: MAKER training Hi Ranjani, It is fine to include all three of those transcriptome datatsets. The more (relevant) evidence the better. I'm not certain what you mean when you say "you used the above model to retrain". Did you train an abinitio gene predictor using the results from your first maker run? Daniel Ence Graduate Student Eccles Institute of Human Genetics University of Utah 15 North 2030 East, Room 2100 Salt Lake City, UT 84112-5330 ________________________________ From: maker-devel-bounces at yandell-lab.org [maker-devel-bounces at yandell-lab.org] on behalf of Sivaranjani Namasivayam [ranjani at uga.edu] Sent: Tuesday, September 11, 2012 9:38 AM To: maker-devel at yandell-lab.org Subject: [maker-devel] MAKER training Hi, I am using MAKER to annotate a newly sequenced genome. I have trained and retrained with datasets but I would like some advice on assessing the output and how this is affected by the input provided. - I have transcriptome data from 454 and Illumina platforms. Illumina is from a single time point and 454 from multiple time point. 454 was assembled using Newbler(dataset 1) and Illumina using Tophat-Cufflinks (dataset 2) and the denovo Trinity pipeline (dataset 3). I now have3 assemblies - 454 and Illumina will have some redunant transcripts (because of one overlapping time point); TopHat-Cufflinks and Trinity will have highly redundant transcripts (because they use same raw reads). Is it OK to provide all 3 datasets as EST evidence, how does it affect the quality of annotation. (For now I have used dataset 1 and dataset 2 as EST evidence) - I used the above model to retrain, I passed through everything except the abinitio gene predictions. I also provided a set a manually annotated genes , many of which have EST evidence. Is this OK to do? [ For proteins evidence, I gave a set from related organisms, same as above] - In my third retraining, I used the above retrained model, but this time I only provided the genome_gff but did not pass through any other data. However I did provide the manually annotated genes as EST evidence and related proteins as protein_evidence. Can you please give me some advice on which of these could give me the best prediction, or if I can alter something to get a better prediction. - A quick question about Augustus - I used a Augustus model (trained for a closely related organism) for ab-initio prediction. Does MAKER adjust this model based on the evidence provided, or use the model as such for a prediction. Greatly appreciate your help! Thanks! Ranjani -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Tue Sep 11 10:04:53 2012 From: carsonhh at gmail.com (Carson Holt) Date: Tue, 11 Sep 2012 12:04:53 -0400 Subject: [maker-devel] MAKER training In-Reply-To: Message-ID: > - I have transcriptome data from 454 and Illumina platforms. Illumina is from > a single time point and 454 from multiple time point. 454 was assembled using > Newbler(dataset 1) and Illumina using Tophat-Cufflinks (dataset 2) and the > denovo Trinity pipeline (dataset 3). I now have3 assemblies - 454 and > Illumina will have some redunant transcripts (because of one overlapping time > point); TopHat-Cufflinks and Trinity will have highly redundant transcripts > (because they use same raw reads). Is it OK to provide all 3 datasets as EST > evidence, how does it affect the quality of annotation. (For now I have used > dataset 1 and dataset 2 as EST evidence) This is fine. You can give them as a comma separated list est=file1,file2,file3 > - I used the above model to retrain, I passed through everything except the > abinitio gene predictions. I also provided a set a manually annotated genes , > many of which have EST evidence. Is this OK to do? [ For proteins evidence, I > gave a set from related organisms, same as above] > > - In my third retraining, I used the above retrained model, but this time I > only provided the genome_gff but did not pass through any other data. However > I did provide the manually annotated genes as EST evidence and related > proteins as protein_evidence. > > Can you please give me some advice on which of these could give me the best > prediction, or if I can alter something to get a better prediction. > Everything you've done sounds reasonable. Better training comes from having the most correct models to train with, so providing the manual annotations as training works, or you can also select MAKER models with the lowest AED score (i.e. models that most closely match evidence). The goal is to try and make the process as unbias as possible, so a consistent usually automated selection method is often the easiest to justify justifiable. > > - A quick question about Augustus - I used a Augustus model (trained for a > closely related organism) for ab-initio prediction. Does MAKER adjust this > model based on the evidence provided, or use the model as such for a > prediction. MAKER will provide hints to Augustus during the run to make it perform better. MAKER will report the raw unaided augustus results in the GFF3 file as a reference, but will use evidence to improve performance where it can. The gene name will let you know if it is a hint based or ab initio model prediction. When 'maker', is part of the gene name it is hint based. Thanks, Carson -------------- next part -------------- An HTML attachment was scrubbed... URL: From dence at genetics.utah.edu Tue Sep 11 10:29:21 2012 From: dence at genetics.utah.edu (Daniel Ence) Date: Tue, 11 Sep 2012 16:29:21 +0000 Subject: [maker-devel] MAKER training In-Reply-To: References: , , Message-ID: So, MAKER itself isn't probabilistic. If you give it the same data and the same options, it will give you the same outputs. The iterative approach for MAKER is to get gene models on the first round using the est2genome option and the Augustus model that you mentioned. After that first round, you train the ab-initio predictors and tell maker to use those newly trained gene predictors in the second round. Regarding the set of manually annotated genes, I think you should put those in the model_gff option. Thanks, Daniel Daniel Ence Graduate Student Eccles Institute of Human Genetics University of Utah 15 North 2030 East, Room 2100 Salt Lake City, UT 84112-5330 ________________________________ From: Sivaranjani Namasivayam [ranjani at uga.edu] Sent: Tuesday, September 11, 2012 9:57 AM To: Daniel Ence; maker-devel at yandell-lab.org Subject: RE: MAKER training Hey, I used the MAKER model to retrain MAKER itself. I read somewhere it improves MAKER's predictions. I did train abinitio gene predictors using MAKERs output, but I wanted to identify the best prediction before using it to train other gene predictors. Thanks, Ranjani ________________________________ From: Daniel Ence [dence at genetics.utah.edu] Sent: Tuesday, September 11, 2012 11:46 AM To: Sivaranjani Namasivayam; maker-devel at yandell-lab.org Subject: RE: MAKER training Hi Ranjani, It is fine to include all three of those transcriptome datatsets. The more (relevant) evidence the better. I'm not certain what you mean when you say "you used the above model to retrain". Did you train an abinitio gene predictor using the results from your first maker run? Daniel Ence Graduate Student Eccles Institute of Human Genetics University of Utah 15 North 2030 East, Room 2100 Salt Lake City, UT 84112-5330 ________________________________ From: maker-devel-bounces at yandell-lab.org [maker-devel-bounces at yandell-lab.org] on behalf of Sivaranjani Namasivayam [ranjani at uga.edu] Sent: Tuesday, September 11, 2012 9:38 AM To: maker-devel at yandell-lab.org Subject: [maker-devel] MAKER training Hi, I am using MAKER to annotate a newly sequenced genome. I have trained and retrained with datasets but I would like some advice on assessing the output and how this is affected by the input provided. - I have transcriptome data from 454 and Illumina platforms. Illumina is from a single time point and 454 from multiple time point. 454 was assembled using Newbler(dataset 1) and Illumina using Tophat-Cufflinks (dataset 2) and the denovo Trinity pipeline (dataset 3). I now have3 assemblies - 454 and Illumina will have some redunant transcripts (because of one overlapping time point); TopHat-Cufflinks and Trinity will have highly redundant transcripts (because they use same raw reads). Is it OK to provide all 3 datasets as EST evidence, how does it affect the quality of annotation. (For now I have used dataset 1 and dataset 2 as EST evidence) - I used the above model to retrain, I passed through everything except the abinitio gene predictions. I also provided a set a manually annotated genes , many of which have EST evidence. Is this OK to do? [ For proteins evidence, I gave a set from related organisms, same as above] - In my third retraining, I used the above retrained model, but this time I only provided the genome_gff but did not pass through any other data. However I did provide the manually annotated genes as EST evidence and related proteins as protein_evidence. Can you please give me some advice on which of these could give me the best prediction, or if I can alter something to get a better prediction. - A quick question about Augustus - I used a Augustus model (trained for a closely related organism) for ab-initio prediction. Does MAKER adjust this model based on the evidence provided, or use the model as such for a prediction. Greatly appreciate your help! Thanks! Ranjani -------------- next part -------------- An HTML attachment was scrubbed... URL: From ranjani at uga.edu Tue Sep 11 10:45:42 2012 From: ranjani at uga.edu (Sivaranjani Namasivayam) Date: Tue, 11 Sep 2012 16:45:42 +0000 Subject: [maker-devel] MAKER training In-Reply-To: References: , , , Message-ID: I will try the model_gff option. For the retraining I noticed the count of the annotated genes vary, I haven't examined if the gene structure varies. I will use the models to train ab-initio predictions and providing that as input. But I did notice the number of genes output by MAKER is fairly lower when compared to the transcriptome. I understand this is because MAKER annotations are based on good evidence but can this improve/increase with ab-initio gene models input. Thanks, Ranjani ________________________________ From: Daniel Ence [dence at genetics.utah.edu] Sent: Tuesday, September 11, 2012 12:29 PM To: Sivaranjani Namasivayam; maker-devel at yandell-lab.org Subject: RE: MAKER training So, MAKER itself isn't probabilistic. If you give it the same data and the same options, it will give you the same outputs. The iterative approach for MAKER is to get gene models on the first round using the est2genome option and the Augustus model that you mentioned. After that first round, you train the ab-initio predictors and tell maker to use those newly trained gene predictors in the second round. Regarding the set of manually annotated genes, I think you should put those in the model_gff option. Thanks, Daniel Daniel Ence Graduate Student Eccles Institute of Human Genetics University of Utah 15 North 2030 East, Room 2100 Salt Lake City, UT 84112-5330 ________________________________ From: Sivaranjani Namasivayam [ranjani at uga.edu] Sent: Tuesday, September 11, 2012 9:57 AM To: Daniel Ence; maker-devel at yandell-lab.org Subject: RE: MAKER training Hey, I used the MAKER model to retrain MAKER itself. I read somewhere it improves MAKER's predictions. I did train abinitio gene predictors using MAKERs output, but I wanted to identify the best prediction before using it to train other gene predictors. Thanks, Ranjani ________________________________ From: Daniel Ence [dence at genetics.utah.edu] Sent: Tuesday, September 11, 2012 11:46 AM To: Sivaranjani Namasivayam; maker-devel at yandell-lab.org Subject: RE: MAKER training Hi Ranjani, It is fine to include all three of those transcriptome datatsets. The more (relevant) evidence the better. I'm not certain what you mean when you say "you used the above model to retrain". Did you train an abinitio gene predictor using the results from your first maker run? Daniel Ence Graduate Student Eccles Institute of Human Genetics University of Utah 15 North 2030 East, Room 2100 Salt Lake City, UT 84112-5330 ________________________________ From: maker-devel-bounces at yandell-lab.org [maker-devel-bounces at yandell-lab.org] on behalf of Sivaranjani Namasivayam [ranjani at uga.edu] Sent: Tuesday, September 11, 2012 9:38 AM To: maker-devel at yandell-lab.org Subject: [maker-devel] MAKER training Hi, I am using MAKER to annotate a newly sequenced genome. I have trained and retrained with datasets but I would like some advice on assessing the output and how this is affected by the input provided. - I have transcriptome data from 454 and Illumina platforms. Illumina is from a single time point and 454 from multiple time point. 454 was assembled using Newbler(dataset 1) and Illumina using Tophat-Cufflinks (dataset 2) and the denovo Trinity pipeline (dataset 3). I now have3 assemblies - 454 and Illumina will have some redunant transcripts (because of one overlapping time point); TopHat-Cufflinks and Trinity will have highly redundant transcripts (because they use same raw reads). Is it OK to provide all 3 datasets as EST evidence, how does it affect the quality of annotation. (For now I have used dataset 1 and dataset 2 as EST evidence) - I used the above model to retrain, I passed through everything except the abinitio gene predictions. I also provided a set a manually annotated genes , many of which have EST evidence. Is this OK to do? [ For proteins evidence, I gave a set from related organisms, same as above] - In my third retraining, I used the above retrained model, but this time I only provided the genome_gff but did not pass through any other data. However I did provide the manually annotated genes as EST evidence and related proteins as protein_evidence. Can you please give me some advice on which of these could give me the best prediction, or if I can alter something to get a better prediction. - A quick question about Augustus - I used a Augustus model (trained for a closely related organism) for ab-initio prediction. Does MAKER adjust this model based on the evidence provided, or use the model as such for a prediction. Greatly appreciate your help! Thanks! Ranjani -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Tue Sep 11 14:33:11 2012 From: carsonhh at gmail.com (Carson Holt) Date: Tue, 11 Sep 2012 16:33:11 -0400 Subject: [maker-devel] How to preserve human-friendly IDs when reannotating In-Reply-To: Message-ID: Which version of MAKER are you running (maker --version)? --Carson From: Jeremy Semeiks Date: Monday, 10 September, 2012 11:02 AM To: Carson Holt Cc: Subject: Re: [maker-devel] How to preserve human-friendly IDs when reannotating OK, thanks. So if I understand correctly, to preserve human-friendly IDs requires setting just three options: map_forward=1, maker_gff=, and model_pass=1. (Or instead of the last two I could equivalently just set model_gff to a GFF containing only models.) A couple new issues came up when I tried to run with these options. I started maker like this: /usr/bin/time mpiexec -n 10 maker -q < /dev/null > maker.oe 2>&1 1. I get a bunch of messages as follows, but with variable line number: DBD::SQLite::db do failed: database is locked at /home/jrs/maker-2.26-beta/bin/../lib/GFFDB.pm line 186. I saw that this came up in another thread , but I'm not sure it was ever resolved, nor whether it will affect my reannotation results (as I'm not sure what "your GFF3 results will not be integrated" means). This error did not come up the last time I ran maker for reannotation with similar options in a different directory. And both my current directory and my tmp directory are locally mounted, ie not NFS. 2. Both in this run and in previous runs, I get a lot of lines like this, seemingly at random: Warning: unable to close filehandle DF properly. On Mon, Sep 10, 2012 at 6:01 AM, Carson Holt wrote: > The map_forward option requires that the pass option for the gene models be > turned on. Otherwise you will have to do some spacial overlap test outside of > MAKER. > > If you have a new assembly, you can try mapping the old models onto the new > assembly using the old transcripts as input to the est= and setting > est2genome=1 (nothing else set, i.e no repeat masking etc.). Then there is an > undocumented option that is still a little buggy (hence why it is still > undocumented). Add the line est_forward=1 to your control files. This tells > MAKER to copy names from the ESTs, build the models directly from their > alignment, and to do other things to try and make a 1 to 1 match across the > genome. You will have to manually check that it is 1 to 1 in the end (as I > said still a little buggy and hence undocumented). Use the resulting file as > input to the model_gff option on a separate run with map_forward=1 for > additional reannotation wil more evidence, etc. where you want to still be > able to map names forward. > > From: Jeremy Semeiks > Date: Sunday, 9 September, 2012 3:49 PM > To: > Subject: [maker-devel] How to preserve human-friendly IDs when reannotating > > Hi all, > > I have sequenced some novel fungal genomes, and I am annotating them with > maker-2.26-beta. The entire project is pretty iterative, in the sense that I > first get some seemingly-sane annotation sets, then analyze and compare the > proteomes biologically, then reannotate when new data comes in or as I learn > more about how maker works. Because I have already attached biological meaning > to some of my proteins, I would like to retain the same human-friendly IDs > across annotations. Eg, if maker suddenly finds 1,000 new proteins on a > reannotation run because I turned on keep_preds, then I don't want the > transcript formerly known as mymold_09652T0 to become mymold_10698T0 when I > run maker_map_ids; I want to keep it named mymold_09652T0. > > So, is there any built-in way to preserve human-friendly IDs, or do I need to > write my own script for this? I have tried setting map_forward=1 and > maker_gff=, but > setting these seems to preserve neither the human-friendly IDs nor even the > original IDs. (Eg, protein "genemark-scaffold353-processed-gene-0.9-mRNA-1" > changed its name to "genemark-scaffold353-processed-gene-0.6-mRNA-1" when > reannotated.) I haven't turned on any of the *_pass options, eg protein_pass; > would this be relevant? > > Extra credit question: I am making some mate-pair libraries for these fungi; > when I re-assemble, that will completely change my scaffold names. Is there > any easy way to preserve human-friendly transcript names in this case? As with > the above simpler case, I think it would be pretty easy to transfer 90% of the > names just by doing an all-vs-all blastp between two annotation sets and > fishing out the best hits, but the remaining 10% might be a headache. > > Thanks, > Jeremy > Grad student, Grishin lab > UT Southwestern, Dallas TX > 510.385.8959 > _______________________________________________ maker-devel mailing list > maker-devel at box290.bluehost.comhttp://box290.bluehost.com/mailman/listinfo/mak > er-devel_yandell-lab.org -------------- next part -------------- An HTML attachment was scrubbed... URL: From jeremy.semeiks at utsw.edu Tue Sep 11 17:56:23 2012 From: jeremy.semeiks at utsw.edu (Jeremy Semeiks) Date: Tue, 11 Sep 2012 18:56:23 -0500 Subject: [maker-devel] How to preserve human-friendly IDs when reannotating In-Reply-To: References: Message-ID: maker 2.26. And I have verified for myself that the three options I mentioned below suffice to preserve human-friendly IDs when reannotating. Thanks, J On Tue, Sep 11, 2012 at 3:33 PM, Carson Holt wrote: > Which version of MAKER are you running (maker --version)? > > --Carson > > > > From: Jeremy Semeiks > Date: Monday, 10 September, 2012 11:02 AM > To: Carson Holt > Cc: > Subject: Re: [maker-devel] How to preserve human-friendly IDs when > reannotating > > OK, thanks. So if I understand correctly, to preserve human-friendly IDs > requires setting just three options: map_forward=1, > maker_gff=, and model_pass=1. (Or instead of the > last two I could equivalently just set model_gff to a GFF containing only > models.) > > A couple new issues came up when I tried to run with these options. I > started maker like this: > > /usr/bin/time mpiexec -n 10 maker -q < /dev/null > maker.oe 2>&1 > > 1. I get a bunch of messages as follows, but with variable line number: > > DBD::SQLite::db do failed: database is locked at > /home/jrs/maker-2.26-beta/bin/../lib/GFFDB.pm line 186. > > I saw that this came up in another thread < > https://groups.google.com/forum/?fromgroups=#!topic/maker-devel/TscBgbQfBX4>, > but I'm not sure it was ever resolved, nor whether it will affect my > reannotation results (as I'm not sure what "your GFF3 results will not be > integrated" means). This error did not come up the last time I ran maker > for reannotation with similar options in a different directory. And both my > current directory and my tmp directory are locally mounted, ie not NFS. > > 2. Both in this run and in previous runs, I get a lot of lines like this, > seemingly at random: > > Warning: unable to close filehandle DF properly. > > > On Mon, Sep 10, 2012 at 6:01 AM, Carson Holt wrote: > >> The map_forward option requires that the pass option for the gene models >> be turned on. Otherwise you will have to do some spacial overlap test >> outside of MAKER. >> >> If you have a new assembly, you can try mapping the old models onto the >> new assembly using the old transcripts as input to the est= and setting >> est2genome=1 (nothing else set, i.e no repeat masking etc.). Then there is >> an undocumented option that is still a little buggy (hence why it is still >> undocumented). Add the line est_forward=1 to your control files. This >> tells MAKER to copy names from the ESTs, build the models directly from >> their alignment, and to do other things to try and make a 1 to 1 match >> across the genome. You will have to manually check that it is 1 to 1 in >> the end (as I said still a little buggy and hence undocumented). Use the >> resulting file as input to the model_gff option on a separate run with >> map_forward=1 for additional reannotation wil more evidence, etc. where you >> want to still be able to map names forward. >> >> From: Jeremy Semeiks >> Date: Sunday, 9 September, 2012 3:49 PM >> To: >> Subject: [maker-devel] How to preserve human-friendly IDs when >> reannotating >> >> Hi all, >> >> I have sequenced some novel fungal genomes, and I am annotating them with >> maker-2.26-beta. The entire project is pretty iterative, in the sense that >> I first get some seemingly-sane annotation sets, then analyze and compare >> the proteomes biologically, then reannotate when new data comes in or as I >> learn more about how maker works. Because I have already attached >> biological meaning to some of my proteins, I would like to retain the same >> human-friendly IDs across annotations. Eg, if maker suddenly finds 1,000 >> new proteins on a reannotation run because I turned on keep_preds, then I >> don't want the transcript formerly known as mymold_09652T0 to become >> mymold_10698T0 when I run maker_map_ids; I want to keep it named >> mymold_09652T0. >> >> So, is there any built-in way to preserve human-friendly IDs, or do I >> need to write my own script for this? I have tried setting map_forward=1 >> and maker_gff=, >> but setting these seems to preserve neither the human-friendly IDs nor even >> the original IDs. (Eg, protein >> "genemark-scaffold353-processed-gene-0.9-mRNA-1" changed its name to >> "genemark-scaffold353-processed-gene-0.6-mRNA-1" when reannotated.) I >> haven't turned on any of the *_pass options, eg protein_pass; would this be >> relevant? >> >> Extra credit question: I am making some mate-pair libraries for these >> fungi; when I re-assemble, that will completely change my scaffold names. >> Is there any easy way to preserve human-friendly transcript names in this >> case? As with the above simpler case, I think it would be pretty easy to >> transfer 90% of the names just by doing an all-vs-all blastp between two >> annotation sets and fishing out the best hits, but the remaining 10% might >> be a headache. >> >> Thanks, >> Jeremy >> Grad student, Grishin lab >> UT Southwestern, Dallas TX >> 510.385.8959 >> _______________________________________________ maker-devel mailing list >> maker-devel at box290.bluehost.com >> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org >> > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From ranjani at uga.edu Wed Sep 12 11:53:37 2012 From: ranjani at uga.edu (Sivaranjani Namasivayam) Date: Wed, 12 Sep 2012 17:53:37 +0000 Subject: [maker-devel] MAKER training In-Reply-To: References: , Message-ID: I have a few questions based on your comment about augustus/MAKER naming convention. I have been sorting the data using the second column of the GFF file, I wanted to be sure I have it right - Doesn't 'maker' in the second column signify MAKER's final annotations based on all evidence (EST, protein and abinitio prediction) ? I noticed two types of gene IDs, example 1. augustus_masked-scaffold00030-abinit-gene-3.2 2. maker-scaffold00030-augustus-gene-3.7 Is the first one, a direct augustus prediction without a hints file and the second based on a hints file (made from the EST and protein evidence)? If this is the case, could 2 be a better annotation than 1? - In case of augustus_masked in the 2nd column, I believe all are predictions are without a hints file. Thanks, Ranjani ________________________________ From: Carson Holt [carsonhh at gmail.com] Sent: Tuesday, September 11, 2012 12:04 PM To: Sivaranjani Namasivayam; maker-devel at yandell-lab.org Subject: Re: [maker-devel] MAKER training - I have transcriptome data from 454 and Illumina platforms. Illumina is from a single time point and 454 from multiple time point. 454 was assembled using Newbler(dataset 1) and Illumina using Tophat-Cufflinks (dataset 2) and the denovo Trinity pipeline (dataset 3). I now have3 assemblies - 454 and Illumina will have some redunant transcripts (because of one overlapping time point); TopHat-Cufflinks and Trinity will have highly redundant transcripts (because they use same raw reads). Is it OK to provide all 3 datasets as EST evidence, how does it affect the quality of annotation. (For now I have used dataset 1 and dataset 2 as EST evidence) This is fine. You can give them as a comma separated list est=file1,file2,file3 - I used the above model to retrain, I passed through everything except the abinitio gene predictions. I also provided a set a manually annotated genes , many of which have EST evidence. Is this OK to do? [ For proteins evidence, I gave a set from related organisms, same as above] - In my third retraining, I used the above retrained model, but this time I only provided the genome_gff but did not pass through any other data. However I did provide the manually annotated genes as EST evidence and related proteins as protein_evidence. Can you please give me some advice on which of these could give me the best prediction, or if I can alter something to get a better prediction. Everything you've done sounds reasonable. Better training comes from having the most correct models to train with, so providing the manual annotations as training works, or you can also select MAKER models with the lowest AED score (i.e. models that most closely match evidence). The goal is to try and make the process as unbias as possible, so a consistent usually automated selection method is often the easiest to justify justifiable. - A quick question about Augustus - I used a Augustus model (trained for a closely related organism) for ab-initio prediction. Does MAKER adjust this model based on the evidence provided, or use the model as such for a prediction. MAKER will provide hints to Augustus during the run to make it perform better. MAKER will report the raw unaided augustus results in the GFF3 file as a reference, but will use evidence to improve performance where it can. The gene name will let you know if it is a hint based or ab initio model prediction. When 'maker', is part of the gene name it is hint based. Thanks, Carson -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Thu Sep 13 07:11:27 2012 From: carsonhh at gmail.com (Carson Holt) Date: Thu, 13 Sep 2012 09:11:27 -0400 Subject: [maker-devel] How to preserve human-friendly IDs when reannotating In-Reply-To: Message-ID: The error --> DBD::SQLite::db do failed: database is locked at /home/jrs/maker-2.26-beta/bin/../lib/GFFDB.pm line 186. The location of the specific error you are getting is probably benign. It is a failure to alter the default cache size for the database. The database should already be populated. I'm planning removing the SQLlite database entirely in the future. Perhaps in favor of something like tabix based indexing of the GFF3 file. Thanks, Carson From: Jeremy Semeiks Date: Tuesday, 11 September, 2012 7:56 PM To: Carson Holt Cc: Subject: Re: [maker-devel] How to preserve human-friendly IDs when reannotating maker 2.26. And I have verified for myself that the three options I mentioned below suffice to preserve human-friendly IDs when reannotating. Thanks, J On Tue, Sep 11, 2012 at 3:33 PM, Carson Holt wrote: > Which version of MAKER are you running (maker --version)? > > --Carson > > > > From: Jeremy Semeiks > Date: Monday, 10 September, 2012 11:02 AM > To: Carson Holt > Cc: > Subject: Re: [maker-devel] How to preserve human-friendly IDs when > reannotating > > OK, thanks. So if I understand correctly, to preserve human-friendly IDs > requires setting just three options: map_forward=1, > maker_gff=, and model_pass=1. (Or instead of the last > two I could equivalently just set model_gff to a GFF containing only models.) > > A couple new issues came up when I tried to run with these options. I started > maker like this: > > /usr/bin/time mpiexec -n 10 maker -q < /dev/null > maker.oe 2>&1 > > 1. I get a bunch of messages as follows, but with variable line number: > > DBD::SQLite::db do failed: database is locked at > /home/jrs/maker-2.26-beta/bin/../lib/GFFDB.pm line 186. > > I saw that this came up in another thread > , > but I'm not sure it was ever resolved, nor whether it will affect my > reannotation results (as I'm not sure what "your GFF3 results will not be > integrated" means). This error did not come up the last time I ran maker for > reannotation with similar options in a different directory. And both my > current directory and my tmp directory are locally mounted, ie not NFS. > > 2. Both in this run and in previous runs, I get a lot of lines like this, > seemingly at random: > > Warning: unable to close filehandle DF properly. > > > On Mon, Sep 10, 2012 at 6:01 AM, Carson Holt wrote: >> The map_forward option requires that the pass option for the gene models be >> turned on. Otherwise you will have to do some spacial overlap test outside >> of MAKER. >> >> If you have a new assembly, you can try mapping the old models onto the new >> assembly using the old transcripts as input to the est= and setting >> est2genome=1 (nothing else set, i.e no repeat masking etc.). Then there is >> an undocumented option that is still a little buggy (hence why it is still >> undocumented). Add the line est_forward=1 to your control files. This tells >> MAKER to copy names from the ESTs, build the models directly from their >> alignment, and to do other things to try and make a 1 to 1 match across the >> genome. You will have to manually check that it is 1 to 1 in the end (as I >> said still a little buggy and hence undocumented). Use the resulting file as >> input to the model_gff option on a separate run with map_forward=1 for >> additional reannotation wil more evidence, etc. where you want to still be >> able to map names forward. >> >> From: Jeremy Semeiks >> Date: Sunday, 9 September, 2012 3:49 PM >> To: >> Subject: [maker-devel] How to preserve human-friendly IDs when reannotating >> >> Hi all, >> >> I have sequenced some novel fungal genomes, and I am annotating them with >> maker-2.26-beta. The entire project is pretty iterative, in the sense that I >> first get some seemingly-sane annotation sets, then analyze and compare the >> proteomes biologically, then reannotate when new data comes in or as I learn >> more about how maker works. Because I have already attached biological >> meaning to some of my proteins, I would like to retain the same >> human-friendly IDs across annotations. Eg, if maker suddenly finds 1,000 new >> proteins on a reannotation run because I turned on keep_preds, then I don't >> want the transcript formerly known as mymold_09652T0 to become mymold_10698T0 >> when I run maker_map_ids; I want to keep it named mymold_09652T0. >> >> So, is there any built-in way to preserve human-friendly IDs, or do I need to >> write my own script for this? I have tried setting map_forward=1 and >> maker_gff=, but >> setting these seems to preserve neither the human-friendly IDs nor even the >> original IDs. (Eg, protein "genemark-scaffold353-processed-gene-0.9-mRNA-1" >> changed its name to "genemark-scaffold353-processed-gene-0.6-mRNA-1" when >> reannotated.) I haven't turned on any of the *_pass options, eg protein_pass; >> would this be relevant? >> >> Extra credit question: I am making some mate-pair libraries for these fungi; >> when I re-assemble, that will completely change my scaffold names. Is there >> any easy way to preserve human-friendly transcript names in this case? As >> with the above simpler case, I think it would be pretty easy to transfer 90% >> of the names just by doing an all-vs-all blastp between two annotation sets >> and fishing out the best hits, but the remaining 10% might be a headache. >> >> Thanks, >> Jeremy >> Grad student, Grishin lab >> UT Southwestern, Dallas TX >> 510.385.8959 >> _______________________________________________ maker-devel mailing list >> maker-devel at box290.bluehost.comhttp://box290.bluehost.com/mailman/listinfo/ma >> ker-devel_yandell-lab.org > -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Thu Sep 13 07:30:22 2012 From: carsonhh at gmail.com (Carson Holt) Date: Thu, 13 Sep 2012 09:30:22 -0400 Subject: [maker-devel] MAKER training In-Reply-To: Message-ID: Yes, those are the final annotations, and yes one is derived from the ab initio model and one from hint based models. The selection between hint based models and ab initio models is based on evidence overlap, so either can be better than the other or vice versa. The bets models will have lower AED scores. So if for a given locus I have both hint based and ab initio based models, I keep the one that best matches the evidence (lowest AED score). augustus_masked means the genome was masked for repeats before running augustus. Anything with augustus_masked in the second column will be ab initio models kept for reference purposes. Every ab initio model produced by augustus will have an entry there. Thanks, Carson From: Sivaranjani Namasivayam Date: Wednesday, 12 September, 2012 1:53 PM To: Carson Holt , "maker-devel at yandell-lab.org" Subject: RE: [maker-devel] MAKER training I have a few questions based on your comment about augustus/MAKER naming convention. I have been sorting the data using the second column of the GFF file, I wanted to be sure I have it right - Doesn't 'maker' in the second column signify MAKER's final annotations based on all evidence (EST, protein and abinitio prediction) ? I noticed two types of gene IDs, example 1. augustus_masked-scaffold00030-abinit-gene-3.2 2. maker-scaffold00030-augustus-gene-3.7 Is the first one, a direct augustus prediction without a hints file and the second based on a hints file (made from the EST and protein evidence)? If this is the case, could 2 be a better annotation than 1? - In case of augustus_masked in the 2nd column, I believe all are predictions are without a hints file. Thanks, Ranjani From: Carson Holt [carsonhh at gmail.com] Sent: Tuesday, September 11, 2012 12:04 PM To: Sivaranjani Namasivayam; maker-devel at yandell-lab.org Subject: Re: [maker-devel] MAKER training > - I have transcriptome data from 454 and Illumina platforms. Illumina is from > a single time point and 454 from multiple time point. 454 was assembled using > Newbler(dataset 1) and Illumina using Tophat-Cufflinks (dataset 2) and the > denovo Trinity pipeline (dataset 3). I now have3 assemblies - 454 and > Illumina will have some redunant transcripts (because of one overlapping time > point); TopHat-Cufflinks and Trinity will have highly redundant transcripts > (because they use same raw reads). Is it OK to provide all 3 datasets as EST > evidence, how does it affect the quality of annotation. (For now I have used > dataset 1 and dataset 2 as EST evidence) This is fine. You can give them as a comma separated list est=file1,file2,file3 > - I used the above model to retrain, I passed through everything except the > abinitio gene predictions. I also provided a set a manually annotated genes , > many of which have EST evidence. Is this OK to do? [ For proteins evidence, I > gave a set from related organisms, same as above] > > - In my third retraining, I used the above retrained model, but this time I > only provided the genome_gff but did not pass through any other data. However > I did provide the manually annotated genes as EST evidence and related > proteins as protein_evidence. > > Can you please give me some advice on which of these could give me the best > prediction, or if I can alter something to get a better prediction. > Everything you've done sounds reasonable. Better training comes from having the most correct models to train with, so providing the manual annotations as training works, or you can also select MAKER models with the lowest AED score (i.e. models that most closely match evidence). The goal is to try and make the process as unbias as possible, so a consistent usually automated selection method is often the easiest to justify justifiable. > > - A quick question about Augustus - I used a Augustus model (trained for a > closely related organism) for ab-initio prediction. Does MAKER adjust this > model based on the evidence provided, or use the model as such for a > prediction. MAKER will provide hints to Augustus during the run to make it perform better. MAKER will report the raw unaided augustus results in the GFF3 file as a reference, but will use evidence to improve performance where it can. The gene name will let you know if it is a hint based or ab initio model prediction. When 'maker', is part of the gene name it is hint based. Thanks, Carson -------------- next part -------------- An HTML attachment was scrubbed... URL: From guoyunfei1989 at gmail.com Wed Sep 19 10:41:40 2012 From: guoyunfei1989 at gmail.com (Yunfei Guo) Date: Wed, 19 Sep 2012 09:41:40 -0700 Subject: [maker-devel] open3: fork failed: Cannot allocate memory Message-ID: Hi Carson, Sorry to bother you again because I really can't find a solution to it. Have you seen this error before? I simply started multiple jobs in the same directory and got the following msg after hours of running. >From Admin: "Your batch job 2511011 encountered the following error: open3: fork failed: Cannot allocate memory ERROR: Failed while polishig ESTs ERROR: Chunk failed at level:2, tier_type:2 FAILED CONTIG:scaffold740 It continued generating errors in a loop until the /var filesystem filled. I will cancel the job. You may find it useful within your job script to check for errors and exit if present." And this is not because of lack of memory since this job has exclusive access to the node. Let me know if you want the entire stderr file. Thanks. From carsonhh at gmail.com Fri Sep 21 07:28:34 2012 From: carsonhh at gmail.com (Carson Holt) Date: Fri, 21 Sep 2012 09:28:34 -0400 Subject: [maker-devel] open3: fork failed: Cannot allocate memory In-Reply-To: Message-ID: Exclusive access doesn't necessarily mean that memory is not full, especially if you are running via MPI. Under MPI each MAKER instance will have a separate memory footprint (the sum of which may be too high for your system). You can lower the memory footprint per instance by setting all the blast_depth options in the maker_bopt.ctl file. Set them to 30 for example. Also in you have set max_dna_len to a value greater than 100000, bring it back down. A value of 200000 for example will cause MAEKR to use twice as much memory as 100000. The primary cause of high memory is too much evidence aligning in a region. Setting the depth parameter to 30 will cause MAKER to sort the alignments as they come in and drop all but the best 30 alignments. Each instance of MAKER will usually take up 500Mb to 1Gb of RAM when max_dna_len is set to 100,000. It will take up twice that when max_dna_len is set to 200,000. Alternatively, if you are also using MPI, you can set the job up to launch fewer instances of MAKER, but allow each instance to use more CPUs. You do this by halving the value of the -n option given to mpiexec and then setting cpus=2 in the maker_opts file. The result in that BLAST analyses will run on 2 cpus each but MAKER will only keep the results for 6 jobs in memory at a time rather than 12 jobs (I.e. Lower memory footprint). When using this technique, make sure the hostfile used by mpiexec is set to follow a round robin distribution or all instances will start on half your nodes while the other half of your nodes will be left idle. Example - this is correct: host1 host2 host3 host1 host2 host3 host1 host2 host3 This is incorrect: host1 host1 host1 host2 host2 host2 host3 host3 host3 FYI when using MPI the -n parameter given to mpiexec and the -cpus parameter given to MAKER have a multiplicative affect on CPU usage. Example: mpiexec -n 12 maker -cpus 1 (will launch 12 maker instances and use a total of 12 cpus) mpiexec -n 12 maker -cpus 2 (will launch 12 maker instances but use a total of 24 cpus) mpiexec -n 6 maker -cpus 4 (will launch 6 maker instances but use a total of 24 cpus) Why is this? It's because CPUs affects how many processors to use to solve a single 100,000 bp chunk (per instance). But mpiexec -n sets how many simultaneous instances and as a result how many chunks to run together. So mpiexec -n will cause memory usage to increase in a way that -cpus doesn't. But mpiexec also scales across machines for parallelization where -cpus can't (it's use applies to a single machine). Thanks, Carson On 12-09-19 12:41 PM, "Yunfei Guo" wrote: >Hi Carson, > >Sorry to bother you again because I really can't find a solution to >it. Have you seen this error before? I simply started multiple jobs in >the same directory and got the following msg after hours of running. > >From Admin: >"Your batch job 2511011 encountered the following error: > open3: fork failed: Cannot allocate memory > ERROR: Failed while polishig ESTs > ERROR: Chunk failed at level:2, tier_type:2 > FAILED CONTIG:scaffold740 >It continued generating errors in a loop until the /var filesystem filled. >I will cancel the job. You may find it useful within your job script to >check for errors and exit if present." > >And this is not because of lack of memory since this job has exclusive >access to the node. Let me know if you want the entire stderr file. >Thanks. > >_______________________________________________ >maker-devel mailing list >maker-devel at box290.bluehost.com >http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org From fourie.joubert at up.ac.za Fri Sep 21 07:58:26 2012 From: fourie.joubert at up.ac.za (Fourie Joubert) Date: Fri, 21 Sep 2012 15:58:26 +0200 Subject: [maker-devel] Problems parsing iprscan results with iprscan2gff3 Message-ID: <505C7282.3090107@up.ac.za> Hi Folks I am running into some problems parsing iprscan results. I run iprscan as follows: > iprscan -cli -i bot.all.maker.proteins.fasta -o bot.all.maker.proteins.raw -format raw -goterms -iprlookup and obtain the iprscan output (the iprscan output file is at http://www.bi.up.ac.za/~fourie/bot.all.maker.proteins.raw if anyone is interested in the detailed output, and the initial maker gff3 file is at http://www.bi.up.ac.za/~fourie/bot.all.gff). I then try to run the conversion to gff3, but I get very long list of errors: > iprscan2gff3 bot.all.maker.proteins.raw bot.all.gff > domains.gff ERROR: In maker-NODE_4797_length_138874_cov_96.632576-augustus-gene-0.113 Use of uninitialized value $seqid in concatenation (.) or string at /usr/local/maker/bin/iprscan2gff3 line 255. Use of uninitialized value $start in concatenation (.) or string at /usr/local/maker/bin/iprscan2gff3 line 255. Use of uninitialized value $end in concatenation (.) or string at /usr/local/maker/bin/iprscan2gff3 line 255. Use of uninitialized value $strand in concatenation (.) or string at /usr/local/maker/bin/iprscan2gff3 line 255. Use of uninitialized value $off in subtraction (-) at /usr/local/maker/bin/iprscan2gff3 line 267. Use of uninitialized value $pB in subtraction (-) at /usr/local/maker/bin/iprscan2gff3 line 267. Use of uninitialized value $off in subtraction (-) at /usr/local/maker/bin/iprscan2gff3 line 267. Use of uninitialized value $pE in subtraction (-) at /usr/local/maker/bin/iprscan2gff3 line 267. Use of uninitialized value $seqid in concatenation (.) or string at /usr/local/maker/bin/iprscan2gff3 line 269. Use of uninitialized value $start in concatenation (.) or string at /usr/local/maker/bin/iprscan2gff3 line 269. Use of uninitialized value $end in concatenation (.) or string at /usr/local/maker/bin/iprscan2gff3 line 269. Use of uninitialized value $strand in concatenation (.) or string at /usr/local/maker/bin/iprscan2gff3 line 269. ....... ....... ....... for most of the entries. Any advice or help would be sincerely appreciated! Best regards! Fourie -- -------------- Prof Fourie Joubert Bioinformatics and Computational Biology Unit Department of Biochemistry University of Pretoria fourie.joubert at up.ac.za http://www.bi.up.ac.za Tel. +27-12-420-5825 Fax. +27-12-420-5800 ------------------------------------------------------------------------- This message and attachments are subject to a disclaimer. Please refer to www.it.up.ac.za/documentation/governance/disclaimer/ for full details. -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Fri Sep 21 08:10:21 2012 From: carsonhh at gmail.com (Carson Holt) Date: Fri, 21 Sep 2012 10:10:21 -0400 Subject: [maker-devel] Problems parsing iprscan results with iprscan2gff3 In-Reply-To: <505C7282.3090107@up.ac.za> Message-ID: Some of your iprscan results contain truncated names Example: maker-NODE_5172_length_118591_cov_102.277115-snap-gene-0.100-mR This seems to be the case for almost all HMMPanther and HMMSmart results. Try just removing those two groups of results from your file for now. Then use the iprscan_wrap script that comes with maker to just re-run just those two application within iprscan it will fix the truncation issue (it creates temporary short names and then converts back to the longer names when it parses the results). Thanks, Carson From: Fourie Joubert Date: Friday, 21 September, 2012 9:58 AM To: "maker-devel at yandell-lab.org" Subject: [maker-devel] Problems parsing iprscan results with iprscan2gff3 Hi Folks I am running into some problems parsing iprscan results. I run iprscan as follows: > iprscan -cli -i bot.all.maker.proteins.fasta -o bot.all.maker.proteins.raw -format raw -goterms -iprlookup and obtain the iprscan output (the iprscan output file is at http://www.bi.up.ac.za/~fourie/bot.all.maker.proteins.raw if anyone is interested in the detailed output, and the initial maker gff3 file is at http://www.bi.up.ac.za/~fourie/bot.all.gff). I then try to run the conversion to gff3, but I get very long list of errors: > iprscan2gff3 bot.all.maker.proteins.raw bot.all.gff > domains.gff ERROR: In maker-NODE_4797_length_138874_cov_96.632576-augustus-gene-0.113 Use of uninitialized value $seqid in concatenation (.) or string at /usr/local/maker/bin/iprscan2gff3 line 255. Use of uninitialized value $start in concatenation (.) or string at /usr/local/maker/bin/iprscan2gff3 line 255. Use of uninitialized value $end in concatenation (.) or string at /usr/local/maker/bin/iprscan2gff3 line 255. Use of uninitialized value $strand in concatenation (.) or string at /usr/local/maker/bin/iprscan2gff3 line 255. Use of uninitialized value $off in subtraction (-) at /usr/local/maker/bin/iprscan2gff3 line 267. Use of uninitialized value $pB in subtraction (-) at /usr/local/maker/bin/iprscan2gff3 line 267. Use of uninitialized value $off in subtraction (-) at /usr/local/maker/bin/iprscan2gff3 line 267. Use of uninitialized value $pE in subtraction (-) at /usr/local/maker/bin/iprscan2gff3 line 267. Use of uninitialized value $seqid in concatenation (.) or string at /usr/local/maker/bin/iprscan2gff3 line 269. Use of uninitialized value $start in concatenation (.) or string at /usr/local/maker/bin/iprscan2gff3 line 269. Use of uninitialized value $end in concatenation (.) or string at /usr/local/maker/bin/iprscan2gff3 line 269. Use of uninitialized value $strand in concatenation (.) or string at /usr/local/maker/bin/iprscan2gff3 line 269. ....... ....... ....... for most of the entries. Any advice or help would be sincerely appreciated! Best regards! Fourie -- -------------- Prof Fourie Joubert Bioinformatics and Computational Biology Unit Department of Biochemistry University of Pretoria fourie.joubert at up.ac.zahttp://www.bi.up.ac.za Tel. +27-12-420-5825 Fax. +27-12-420-5800 ------------------------------------------------------------------------- This message and attachments are subject to a disclaimer. Please refer to www.it.up.ac.za/documentation/governance/disclaimer/ for full details. _______________________________________________ maker-devel mailing list maker-devel at box290.bluehost.com http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org -------------- next part -------------- An HTML attachment was scrubbed... URL: From jeremy.semeiks at utsw.edu Fri Sep 21 09:39:15 2012 From: jeremy.semeiks at utsw.edu (Jeremy Semeiks) Date: Fri, 21 Sep 2012 10:39:15 -0500 Subject: [maker-devel] How to preserve human-friendly IDs when reannotating In-Reply-To: References: Message-ID: For the record: After analyzing these runs, I have confirmed that neither error I described (ie, "DBD::SQLite::db do failed" and "Warning: unable to close filehandle DF properly") affects maker's protein output in any way I can detect. Thanks, J On Thu, Sep 13, 2012 at 8:11 AM, Carson Holt wrote: > The error --> DBD::SQLite::db do failed: database is locked at > /home/jrs/maker-2.26-beta/bin/../lib/GFFDB.pm line 186. > > The location of the specific error you are getting is probably benign. It > is a failure to alter the default cache size for the database. The > database should already be populated. I'm planning removing the SQLlite > database entirely in the future. Perhaps in favor of something like tabix > based indexing of the GFF3 file. > > Thanks, > Carson > > > > From: Jeremy Semeiks > Date: Tuesday, 11 September, 2012 7:56 PM > > To: Carson Holt > Cc: > Subject: Re: [maker-devel] How to preserve human-friendly IDs when > reannotating > > maker 2.26. > > And I have verified for myself that the three options I mentioned below > suffice to preserve human-friendly IDs when reannotating. > > Thanks, > J > > On Tue, Sep 11, 2012 at 3:33 PM, Carson Holt wrote: > >> Which version of MAKER are you running (maker --version)? >> >> --Carson >> >> >> >> From: Jeremy Semeiks >> Date: Monday, 10 September, 2012 11:02 AM >> To: Carson Holt >> Cc: >> Subject: Re: [maker-devel] How to preserve human-friendly IDs when >> reannotating >> >> OK, thanks. So if I understand correctly, to preserve human-friendly IDs >> requires setting just three options: map_forward=1, >> maker_gff=, and model_pass=1. (Or instead of the >> last two I could equivalently just set model_gff to a GFF containing only >> models.) >> >> A couple new issues came up when I tried to run with these options. I >> started maker like this: >> >> /usr/bin/time mpiexec -n 10 maker -q < /dev/null > maker.oe 2>&1 >> >> 1. I get a bunch of messages as follows, but with variable line number: >> >> DBD::SQLite::db do failed: database is locked at >> /home/jrs/maker-2.26-beta/bin/../lib/GFFDB.pm line 186. >> >> I saw that this came up in another thread < >> https://groups.google.com/forum/?fromgroups=#!topic/maker-devel/TscBgbQfBX4>, >> but I'm not sure it was ever resolved, nor whether it will affect my >> reannotation results (as I'm not sure what "your GFF3 results will not be >> integrated" means). This error did not come up the last time I ran maker >> for reannotation with similar options in a different directory. And both my >> current directory and my tmp directory are locally mounted, ie not NFS. >> >> 2. Both in this run and in previous runs, I get a lot of lines like this, >> seemingly at random: >> >> Warning: unable to close filehandle DF properly. >> >> >> On Mon, Sep 10, 2012 at 6:01 AM, Carson Holt wrote: >> >>> The map_forward option requires that the pass option for the gene models >>> be turned on. Otherwise you will have to do some spacial overlap test >>> outside of MAKER. >>> >>> If you have a new assembly, you can try mapping the old models onto the >>> new assembly using the old transcripts as input to the est= and setting >>> est2genome=1 (nothing else set, i.e no repeat masking etc.). Then there is >>> an undocumented option that is still a little buggy (hence why it is still >>> undocumented). Add the line est_forward=1 to your control files. This >>> tells MAKER to copy names from the ESTs, build the models directly from >>> their alignment, and to do other things to try and make a 1 to 1 match >>> across the genome. You will have to manually check that it is 1 to 1 in >>> the end (as I said still a little buggy and hence undocumented). Use the >>> resulting file as input to the model_gff option on a separate run with >>> map_forward=1 for additional reannotation wil more evidence, etc. where you >>> want to still be able to map names forward. >>> >>> From: Jeremy Semeiks >>> Date: Sunday, 9 September, 2012 3:49 PM >>> To: >>> Subject: [maker-devel] How to preserve human-friendly IDs when >>> reannotating >>> >>> Hi all, >>> >>> I have sequenced some novel fungal genomes, and I am annotating them >>> with maker-2.26-beta. The entire project is pretty iterative, in the sense >>> that I first get some seemingly-sane annotation sets, then analyze and >>> compare the proteomes biologically, then reannotate when new data comes in >>> or as I learn more about how maker works. Because I have already attached >>> biological meaning to some of my proteins, I would like to retain the same >>> human-friendly IDs across annotations. Eg, if maker suddenly finds 1,000 >>> new proteins on a reannotation run because I turned on keep_preds, then I >>> don't want the transcript formerly known as mymold_09652T0 to become >>> mymold_10698T0 when I run maker_map_ids; I want to keep it named >>> mymold_09652T0. >>> >>> So, is there any built-in way to preserve human-friendly IDs, or do I >>> need to write my own script for this? I have tried setting map_forward=1 >>> and maker_gff=, >>> but setting these seems to preserve neither the human-friendly IDs nor even >>> the original IDs. (Eg, protein >>> "genemark-scaffold353-processed-gene-0.9-mRNA-1" changed its name to >>> "genemark-scaffold353-processed-gene-0.6-mRNA-1" when reannotated.) I >>> haven't turned on any of the *_pass options, eg protein_pass; would this be >>> relevant? >>> >>> Extra credit question: I am making some mate-pair libraries for these >>> fungi; when I re-assemble, that will completely change my scaffold names. >>> Is there any easy way to preserve human-friendly transcript names in this >>> case? As with the above simpler case, I think it would be pretty easy to >>> transfer 90% of the names just by doing an all-vs-all blastp between two >>> annotation sets and fishing out the best hits, but the remaining 10% might >>> be a headache. >>> >>> Thanks, >>> Jeremy >>> Grad student, Grishin lab >>> UT Southwestern, Dallas TX >>> 510.385.8959 >>> _______________________________________________ maker-devel mailing list >>> maker-devel at box290.bluehost.com >>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org >>> >> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Fri Sep 21 09:42:46 2012 From: carsonhh at gmail.com (Carson Holt) Date: Fri, 21 Sep 2012 11:42:46 -0400 Subject: [maker-devel] How to preserve human-friendly IDs when reannotating In-Reply-To: Message-ID: That's good to know :-) --Carson From: Jeremy Semeiks Date: Friday, 21 September, 2012 11:39 AM To: Carson Holt Cc: Subject: Re: [maker-devel] How to preserve human-friendly IDs when reannotating For the record: After analyzing these runs, I have confirmed that neither error I described (ie, "DBD::SQLite::db do failed" and "Warning: unable to close filehandle DF properly") affects maker's protein output in any way I can detect. Thanks, J On Thu, Sep 13, 2012 at 8:11 AM, Carson Holt wrote: > The error --> DBD::SQLite::db do failed: database is locked at > /home/jrs/maker-2.26-beta/bin/../lib/GFFDB.pm line 186. > > The location of the specific error you are getting is probably benign. It is > a failure to alter the default cache size for the database. The database > should already be populated. I'm planning removing the SQLlite database > entirely in the future. Perhaps in favor of something like tabix based > indexing of the GFF3 file. > > Thanks, > Carson > > > > From: Jeremy Semeiks > Date: Tuesday, 11 September, 2012 7:56 PM > > To: Carson Holt > Cc: > Subject: Re: [maker-devel] How to preserve human-friendly IDs when > reannotating > > maker 2.26. > > And I have verified for myself that the three options I mentioned below > suffice to preserve human-friendly IDs when reannotating. > > Thanks, > J > > On Tue, Sep 11, 2012 at 3:33 PM, Carson Holt wrote: >> Which version of MAKER are you running (maker --version)? >> >> --Carson >> >> >> >> From: Jeremy Semeiks >> Date: Monday, 10 September, 2012 11:02 AM >> To: Carson Holt >> Cc: >> Subject: Re: [maker-devel] How to preserve human-friendly IDs when >> reannotating >> >> OK, thanks. So if I understand correctly, to preserve human-friendly IDs >> requires setting just three options: map_forward=1, >> maker_gff=, and model_pass=1. (Or instead of the last >> two I could equivalently just set model_gff to a GFF containing only models.) >> >> A couple new issues came up when I tried to run with these options. I started >> maker like this: >> >> /usr/bin/time mpiexec -n 10 maker -q < /dev/null > maker.oe 2>&1 >> >> 1. I get a bunch of messages as follows, but with variable line number: >> >> DBD::SQLite::db do failed: database is locked at >> /home/jrs/maker-2.26-beta/bin/../lib/GFFDB.pm line 186. >> >> I saw that this came up in another thread >> >> , but I'm not sure it was ever resolved, nor whether it will affect my >> reannotation results (as I'm not sure what "your GFF3 results will not be >> integrated" means). This error did not come up the last time I ran maker for >> reannotation with similar options in a different directory. And both my >> current directory and my tmp directory are locally mounted, ie not NFS. >> >> 2. Both in this run and in previous runs, I get a lot of lines like this, >> seemingly at random: >> >> Warning: unable to close filehandle DF properly. >> >> >> On Mon, Sep 10, 2012 at 6:01 AM, Carson Holt wrote: >>> The map_forward option requires that the pass option for the gene models be >>> turned on. Otherwise you will have to do some spacial overlap test outside >>> of MAKER. >>> >>> If you have a new assembly, you can try mapping the old models onto the new >>> assembly using the old transcripts as input to the est= and setting >>> est2genome=1 (nothing else set, i.e no repeat masking etc.). Then there is >>> an undocumented option that is still a little buggy (hence why it is still >>> undocumented). Add the line est_forward=1 to your control files. This >>> tells MAKER to copy names from the ESTs, build the models directly from >>> their alignment, and to do other things to try and make a 1 to 1 match >>> across the genome. You will have to manually check that it is 1 to 1 in the >>> end (as I said still a little buggy and hence undocumented). Use the >>> resulting file as input to the model_gff option on a separate run with >>> map_forward=1 for additional reannotation wil more evidence, etc. where you >>> want to still be able to map names forward. >>> >>> From: Jeremy Semeiks >>> Date: Sunday, 9 September, 2012 3:49 PM >>> To: >>> Subject: [maker-devel] How to preserve human-friendly IDs when reannotating >>> >>> Hi all, >>> >>> I have sequenced some novel fungal genomes, and I am annotating them with >>> maker-2.26-beta. The entire project is pretty iterative, in the sense that I >>> first get some seemingly-sane annotation sets, then analyze and compare the >>> proteomes biologically, then reannotate when new data comes in or as I learn >>> more about how maker works. Because I have already attached biological >>> meaning to some of my proteins, I would like to retain the same >>> human-friendly IDs across annotations. Eg, if maker suddenly finds 1,000 new >>> proteins on a reannotation run because I turned on keep_preds, then I don't >>> want the transcript formerly known as mymold_09652T0 to become >>> mymold_10698T0 when I run maker_map_ids; I want to keep it named >>> mymold_09652T0. >>> >>> So, is there any built-in way to preserve human-friendly IDs, or do I need >>> to write my own script for this? I have tried setting map_forward=1 and >>> maker_gff=, but >>> setting these seems to preserve neither the human-friendly IDs nor even the >>> original IDs. (Eg, protein "genemark-scaffold353-processed-gene-0.9-mRNA-1" >>> changed its name to "genemark-scaffold353-processed-gene-0.6-mRNA-1" when >>> reannotated.) I haven't turned on any of the *_pass options, eg >>> protein_pass; would this be relevant? >>> >>> Extra credit question: I am making some mate-pair libraries for these fungi; >>> when I re-assemble, that will completely change my scaffold names. Is there >>> any easy way to preserve human-friendly transcript names in this case? As >>> with the above simpler case, I think it would be pretty easy to transfer 90% >>> of the names just by doing an all-vs-all blastp between two annotation sets >>> and fishing out the best hits, but the remaining 10% might be a headache. >>> >>> Thanks, >>> Jeremy >>> Grad student, Grishin lab >>> UT Southwestern, Dallas TX >>> 510.385.8959 >>> _______________________________________________ maker-devel mailing list >>> maker-devel at box290.bluehost.comhttp://box290.bluehost.com/mailman/listinfo/m >>> aker-devel_yandell-lab.org >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From ianmisner17 at aim.com Tue Sep 25 06:27:04 2012 From: ianmisner17 at aim.com (Ian Misner) Date: Tue, 25 Sep 2012 08:27:04 -0400 Subject: [maker-devel] problem with maker_map_ids Message-ID: Hello, I'm trying to create human friendly ids and I'm getting an error when I use the -sort_file option. Without the sort file it runs fine just not numbered from the first contig. I have had some programers at our cluster look at the script and they attempted a fix but it did not work. They mentioned the script was "buggy" so this might be part of the problem. I've attached the error as well as the sort file. I can send more files if necessary. Thanks for you time. Cheers Ian $ maker_map_ids --prefix THRCLA_ --justify 5 --sort_order 34112_sort.txt 34112_3June11Ass.gff > 34112_3June11Ass_named.txt Can't use string ("34112_sort.txt") as a HASH ref while "strict refs" in use at /gpfs/runtime/opt/maker/2.10/maker/bin/maker_map_ids line 311, <$IN> line 499186. -------------- next part -------------- THRCLA_contig1 1 THRCLA_contig2 2 THRCLA_contig3 3 THRCLA_contig4 4 THRCLA_contig5 5 THRCLA_contig6 6 THRCLA_contig7 7 THRCLA_contig8 8 THRCLA_contig9 9 THRCLA_contig10 10 THRCLA_contig11 11 THRCLA_contig12 12 THRCLA_contig13 13 THRCLA_contig14 14 THRCLA_contig15 15 THRCLA_contig16 16 THRCLA_contig17 17 THRCLA_contig18 18 THRCLA_contig19 19 THRCLA_contig20 20 THRCLA_contig21 21 THRCLA_contig22 22 THRCLA_contig23 23 THRCLA_contig24 24 THRCLA_contig25 25 THRCLA_contig26 26 THRCLA_contig27 27 THRCLA_contig28 28 THRCLA_contig29 29 THRCLA_contig30 30 THRCLA_contig31 31 THRCLA_contig32 32 THRCLA_contig33 33 THRCLA_contig34 34 THRCLA_contig35 35 THRCLA_contig36 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THRCLA_contig137 137 THRCLA_contig138 138 THRCLA_contig139 139 THRCLA_contig140 140 THRCLA_contig141 141 THRCLA_contig142 142 THRCLA_contig143 143 THRCLA_contig144 144 THRCLA_contig145 145 THRCLA_contig146 146 THRCLA_contig147 147 THRCLA_contig148 148 THRCLA_contig149 149 THRCLA_contig150 150 THRCLA_contig151 151 THRCLA_contig152 152 THRCLA_contig153 153 THRCLA_contig154 154 THRCLA_contig155 155 THRCLA_contig156 156 THRCLA_contig157 157 THRCLA_contig158 158 THRCLA_contig159 159 THRCLA_contig160 160 THRCLA_contig161 161 THRCLA_contig162 162 THRCLA_contig163 163 THRCLA_contig164 164 THRCLA_contig165 165 THRCLA_contig166 166 THRCLA_contig167 167 THRCLA_contig168 168 THRCLA_contig169 169 THRCLA_contig170 170 THRCLA_contig171 171 THRCLA_contig172 172 THRCLA_contig173 173 THRCLA_contig174 174 THRCLA_contig175 175 THRCLA_contig176 176 THRCLA_contig177 177 THRCLA_contig178 178 THRCLA_contig179 179 THRCLA_contig180 180 THRCLA_contig181 181 THRCLA_contig182 182 THRCLA_contig183 183 THRCLA_contig184 184 THRCLA_contig185 185 THRCLA_contig186 186 THRCLA_contig187 187 THRCLA_contig188 188 THRCLA_contig189 189 THRCLA_contig190 190 THRCLA_contig191 191 THRCLA_contig192 192 THRCLA_contig193 193 THRCLA_contig194 194 THRCLA_contig195 195 THRCLA_contig196 196 THRCLA_contig197 197 THRCLA_contig198 198 THRCLA_contig199 199 THRCLA_contig200 200 THRCLA_contig201 201 THRCLA_contig202 202 THRCLA_contig203 203 THRCLA_contig204 204 THRCLA_contig205 205 THRCLA_contig206 206 THRCLA_contig207 207 THRCLA_contig208 208 THRCLA_contig209 209 THRCLA_contig210 210 THRCLA_contig211 211 THRCLA_contig212 212 THRCLA_contig213 213 THRCLA_contig214 214 THRCLA_contig215 215 THRCLA_contig216 216 THRCLA_contig217 217 THRCLA_contig218 218 THRCLA_contig219 219 THRCLA_contig220 220 THRCLA_contig221 221 THRCLA_contig222 222 THRCLA_contig223 223 THRCLA_contig224 224 THRCLA_contig225 225 THRCLA_contig226 226 THRCLA_contig227 227 THRCLA_contig228 228 THRCLA_contig229 229 THRCLA_contig230 230 THRCLA_contig231 231 THRCLA_contig232 232 THRCLA_contig233 233 THRCLA_contig234 234 THRCLA_contig235 235 THRCLA_contig236 236 THRCLA_contig237 237 THRCLA_contig238 238 THRCLA_contig239 239 THRCLA_contig240 240 THRCLA_contig241 241 THRCLA_contig242 242 THRCLA_contig243 243 THRCLA_contig244 244 THRCLA_contig245 245 THRCLA_contig246 246 THRCLA_contig247 247 THRCLA_contig248 248 THRCLA_contig249 249 THRCLA_contig250 250 THRCLA_contig251 251 THRCLA_contig252 252 THRCLA_contig253 253 THRCLA_contig254 254 THRCLA_contig255 255 THRCLA_contig256 256 THRCLA_contig257 257 THRCLA_contig258 258 THRCLA_contig259 259 THRCLA_contig260 260 THRCLA_contig261 261 THRCLA_contig262 262 THRCLA_contig263 263 THRCLA_contig264 264 THRCLA_contig265 265 THRCLA_contig266 266 THRCLA_contig267 267 THRCLA_contig268 268 THRCLA_contig269 269 THRCLA_contig270 270 THRCLA_contig271 271 THRCLA_contig272 272 THRCLA_contig273 273 THRCLA_contig274 274 THRCLA_contig275 275 THRCLA_contig276 276 THRCLA_contig277 277 THRCLA_contig278 278 THRCLA_contig279 279 THRCLA_contig280 280 THRCLA_contig281 281 THRCLA_contig282 282 THRCLA_contig283 283 THRCLA_contig284 284 THRCLA_contig285 285 THRCLA_contig286 286 THRCLA_contig287 287 THRCLA_contig288 288 THRCLA_contig289 289 THRCLA_contig290 290 THRCLA_contig291 291 THRCLA_contig292 292 THRCLA_contig293 293 THRCLA_contig294 294 THRCLA_contig295 295 THRCLA_contig296 296 THRCLA_contig297 297 THRCLA_contig298 298 THRCLA_contig299 299 THRCLA_contig300 300 THRCLA_contig301 301 THRCLA_contig302 302 THRCLA_contig303 303 THRCLA_contig304 304 THRCLA_contig305 305 THRCLA_contig306 306 THRCLA_contig307 307 THRCLA_contig308 308 THRCLA_contig309 309 THRCLA_contig310 310 THRCLA_contig311 311 THRCLA_contig312 312 THRCLA_contig313 313 THRCLA_contig314 314 THRCLA_contig315 315 THRCLA_contig316 316 THRCLA_contig317 317 THRCLA_contig318 318 THRCLA_contig319 319 THRCLA_contig320 320 THRCLA_contig321 321 THRCLA_contig322 322 THRCLA_contig323 323 THRCLA_contig324 324 THRCLA_contig325 325 THRCLA_contig326 326 THRCLA_contig327 327 THRCLA_contig328 328 THRCLA_contig329 329 THRCLA_contig330 330 THRCLA_contig331 331 THRCLA_contig332 332 THRCLA_contig333 333 THRCLA_contig334 334 THRCLA_contig335 335 THRCLA_contig336 336 THRCLA_contig337 337 THRCLA_contig338 338 THRCLA_contig339 339 THRCLA_contig340 340 THRCLA_contig341 341 THRCLA_contig342 342 THRCLA_contig343 343 THRCLA_contig344 344 THRCLA_contig345 345 THRCLA_contig346 346 THRCLA_contig347 347 THRCLA_contig348 348 THRCLA_contig349 349 THRCLA_contig350 350 THRCLA_contig351 351 THRCLA_contig352 352 THRCLA_contig353 353 THRCLA_contig354 354 THRCLA_contig355 355 THRCLA_contig356 356 THRCLA_contig357 357 THRCLA_contig358 358 THRCLA_contig359 359 THRCLA_contig360 360 THRCLA_contig361 361 THRCLA_contig362 362 THRCLA_contig363 363 THRCLA_contig364 364 THRCLA_contig365 365 THRCLA_contig366 366 THRCLA_contig367 367 THRCLA_contig368 368 THRCLA_contig369 369 THRCLA_contig370 370 THRCLA_contig371 371 THRCLA_contig372 372 THRCLA_contig373 373 THRCLA_contig374 374 THRCLA_contig375 375 THRCLA_contig376 376 THRCLA_contig377 377 THRCLA_contig378 378 THRCLA_contig379 379 THRCLA_contig380 380 THRCLA_contig381 381 THRCLA_contig382 382 THRCLA_contig383 383 THRCLA_contig384 384 THRCLA_contig385 385 THRCLA_contig386 386 THRCLA_contig387 387 THRCLA_contig388 388 THRCLA_contig389 389 THRCLA_contig390 390 THRCLA_contig391 391 THRCLA_contig392 392 THRCLA_contig393 393 THRCLA_contig394 394 THRCLA_contig395 395 THRCLA_contig396 396 THRCLA_contig397 397 THRCLA_contig398 398 THRCLA_contig399 399 THRCLA_contig400 400 THRCLA_contig401 401 THRCLA_contig402 402 THRCLA_contig403 403 THRCLA_contig404 404 THRCLA_contig405 405 THRCLA_contig406 406 THRCLA_contig407 407 THRCLA_contig408 408 THRCLA_contig409 409 THRCLA_contig410 410 THRCLA_contig411 411 THRCLA_contig412 412 THRCLA_contig413 413 THRCLA_contig414 414 THRCLA_contig415 415 THRCLA_contig416 416 THRCLA_contig417 417 THRCLA_contig418 418 THRCLA_contig419 419 THRCLA_contig420 420 THRCLA_contig421 421 THRCLA_contig422 422 THRCLA_contig423 423 THRCLA_contig424 424 THRCLA_contig425 425 THRCLA_contig426 426 THRCLA_contig427 427 THRCLA_contig428 428 THRCLA_contig429 429 THRCLA_contig430 430 THRCLA_contig431 431 THRCLA_contig432 432 THRCLA_contig433 433 THRCLA_contig434 434 THRCLA_contig435 435 THRCLA_contig436 436 THRCLA_contig437 437 THRCLA_contig438 438 THRCLA_contig439 439 THRCLA_contig440 440 THRCLA_contig441 441 THRCLA_contig442 442 THRCLA_contig443 443 THRCLA_contig444 444 THRCLA_contig445 445 THRCLA_contig446 446 THRCLA_contig447 447 THRCLA_contig448 448 THRCLA_contig449 449 THRCLA_contig450 450 THRCLA_contig451 451 THRCLA_contig452 452 THRCLA_contig453 453 THRCLA_contig454 454 THRCLA_contig455 455 THRCLA_contig456 456 THRCLA_contig457 457 THRCLA_contig458 458 THRCLA_contig459 459 THRCLA_contig460 460 THRCLA_contig461 461 THRCLA_contig462 462 THRCLA_contig463 463 THRCLA_contig464 464 THRCLA_contig465 465 THRCLA_contig466 466 THRCLA_contig467 467 THRCLA_contig468 468 THRCLA_contig469 469 THRCLA_contig470 470 THRCLA_contig471 471 THRCLA_contig472 472 THRCLA_contig473 473 THRCLA_contig474 474 THRCLA_contig475 475 THRCLA_contig476 476 THRCLA_contig477 477 THRCLA_contig478 478 THRCLA_contig479 479 THRCLA_contig480 480 THRCLA_contig481 481 THRCLA_contig482 482 THRCLA_contig483 483 THRCLA_contig484 484 THRCLA_contig485 485 THRCLA_contig486 486 THRCLA_contig487 487 THRCLA_contig488 488 THRCLA_contig489 489 THRCLA_contig490 490 THRCLA_contig491 491 THRCLA_contig492 492 THRCLA_contig493 493 THRCLA_contig494 494 THRCLA_contig495 495 THRCLA_contig496 496 THRCLA_contig497 497 THRCLA_contig498 498 THRCLA_contig499 499 THRCLA_contig500 500 THRCLA_contig501 501 THRCLA_contig502 502 THRCLA_contig503 503 THRCLA_contig504 504 THRCLA_contig505 505 THRCLA_contig506 506 THRCLA_contig507 507 THRCLA_contig508 508 THRCLA_contig509 509 THRCLA_contig510 510 THRCLA_contig511 511 THRCLA_contig512 512 THRCLA_contig513 513 THRCLA_contig514 514 THRCLA_contig515 515 THRCLA_contig516 516 THRCLA_contig517 517 THRCLA_contig518 518 THRCLA_contig519 519 THRCLA_contig520 520 THRCLA_contig521 521 THRCLA_contig522 522 THRCLA_contig523 523 THRCLA_contig524 524 THRCLA_contig525 525 THRCLA_contig526 526 THRCLA_contig527 527 THRCLA_contig528 528 THRCLA_contig529 529 THRCLA_contig530 530 THRCLA_contig531 531 THRCLA_contig532 532 THRCLA_contig533 533 THRCLA_contig534 534 THRCLA_contig535 535 THRCLA_contig536 536 THRCLA_contig537 537 THRCLA_contig538 538 THRCLA_contig539 539 THRCLA_contig540 540 THRCLA_contig541 541 THRCLA_contig542 542 THRCLA_contig543 543 THRCLA_contig544 544 THRCLA_contig545 545 THRCLA_contig546 546 THRCLA_contig547 547 THRCLA_contig548 548 THRCLA_contig549 549 THRCLA_contig550 550 THRCLA_contig551 551 THRCLA_contig552 552 THRCLA_contig553 553 THRCLA_contig554 554 THRCLA_contig555 555 THRCLA_contig556 556 THRCLA_contig557 557 THRCLA_contig558 558 THRCLA_contig559 559 THRCLA_contig560 560 THRCLA_contig561 561 THRCLA_contig562 562 THRCLA_contig563 563 THRCLA_contig564 564 THRCLA_contig565 565 THRCLA_contig566 566 THRCLA_contig567 567 THRCLA_contig568 568 THRCLA_contig569 569 THRCLA_contig570 570 THRCLA_contig571 571 THRCLA_contig572 572 THRCLA_contig573 573 THRCLA_contig574 574 THRCLA_contig575 575 THRCLA_contig576 576 THRCLA_contig577 577 THRCLA_contig578 578 THRCLA_contig579 579 THRCLA_contig580 580 THRCLA_contig581 581 THRCLA_contig582 582 THRCLA_contig583 583 THRCLA_contig584 584 THRCLA_contig585 585 THRCLA_contig586 586 THRCLA_contig587 587 THRCLA_contig588 588 THRCLA_contig589 589 THRCLA_contig590 590 THRCLA_contig591 591 THRCLA_contig592 592 THRCLA_contig593 593 THRCLA_contig594 594 THRCLA_contig595 595 THRCLA_contig596 596 THRCLA_contig597 597 THRCLA_contig598 598 THRCLA_contig599 599 THRCLA_contig600 600 THRCLA_contig601 601 THRCLA_contig602 602 THRCLA_contig603 603 THRCLA_contig604 604 THRCLA_contig605 605 THRCLA_contig606 606 THRCLA_contig607 607 THRCLA_contig608 608 THRCLA_contig609 609 THRCLA_contig610 610 THRCLA_contig611 611 THRCLA_contig612 612 THRCLA_contig613 613 THRCLA_contig614 614 THRCLA_contig615 615 THRCLA_contig616 616 THRCLA_contig617 617 THRCLA_contig618 618 THRCLA_contig619 619 THRCLA_contig620 620 THRCLA_contig621 621 THRCLA_contig622 622 THRCLA_contig623 623 THRCLA_contig624 624 THRCLA_contig625 625 THRCLA_contig626 626 THRCLA_contig627 627 THRCLA_contig628 628 THRCLA_contig629 629 THRCLA_contig630 630 THRCLA_contig631 631 THRCLA_contig632 632 THRCLA_contig633 633 THRCLA_contig634 634 THRCLA_contig635 635 THRCLA_contig636 636 THRCLA_contig637 637 THRCLA_contig638 638 THRCLA_contig639 639 THRCLA_contig640 640 THRCLA_contig641 641 THRCLA_contig642 642 THRCLA_contig643 643 THRCLA_contig644 644 THRCLA_contig645 645 THRCLA_contig646 646 THRCLA_contig647 647 THRCLA_contig648 648 THRCLA_contig649 649 THRCLA_contig650 650 THRCLA_contig651 651 THRCLA_contig652 652 THRCLA_contig653 653 THRCLA_contig654 654 THRCLA_contig655 655 THRCLA_contig656 656 THRCLA_contig657 657 THRCLA_contig658 658 THRCLA_contig659 659 THRCLA_contig660 660 THRCLA_contig661 661 THRCLA_contig662 662 THRCLA_contig663 663 THRCLA_contig664 664 THRCLA_contig665 665 THRCLA_contig666 666 THRCLA_contig667 667 THRCLA_contig668 668 THRCLA_contig669 669 THRCLA_contig670 670 THRCLA_contig671 671 THRCLA_contig672 672 THRCLA_contig673 673 THRCLA_contig674 674 THRCLA_contig675 675 THRCLA_contig676 676 THRCLA_contig677 677 THRCLA_contig678 678 THRCLA_contig679 679 THRCLA_contig680 680 THRCLA_contig681 681 THRCLA_contig682 682 THRCLA_contig683 683 THRCLA_contig684 684 THRCLA_contig685 685 THRCLA_contig686 686 THRCLA_contig687 687 THRCLA_contig688 688 THRCLA_contig689 689 THRCLA_contig690 690 THRCLA_contig691 691 THRCLA_contig692 692 THRCLA_contig693 693 THRCLA_contig694 694 THRCLA_contig695 695 THRCLA_contig696 696 THRCLA_contig697 697 THRCLA_contig698 698 THRCLA_contig699 699 THRCLA_contig700 700 THRCLA_contig701 701 THRCLA_contig702 702 THRCLA_contig703 703 THRCLA_contig704 704 THRCLA_contig705 705 THRCLA_contig706 706 THRCLA_contig707 707 THRCLA_contig708 708 THRCLA_contig709 709 THRCLA_contig710 710 THRCLA_contig711 711 THRCLA_contig712 712 THRCLA_contig713 713 THRCLA_contig714 714 THRCLA_contig715 715 THRCLA_contig716 716 THRCLA_contig717 717 THRCLA_contig718 718 THRCLA_contig719 719 THRCLA_contig720 720 THRCLA_contig721 721 THRCLA_contig722 722 THRCLA_contig723 723 THRCLA_contig724 724 THRCLA_contig725 725 THRCLA_contig726 726 THRCLA_contig727 727 THRCLA_contig728 728 THRCLA_contig729 729 THRCLA_contig730 730 THRCLA_contig731 731 THRCLA_contig732 732 THRCLA_contig733 733 THRCLA_contig734 734 THRCLA_contig735 735 THRCLA_contig736 736 THRCLA_contig737 737 THRCLA_contig738 738 THRCLA_contig739 739 THRCLA_contig740 740 THRCLA_contig741 741 THRCLA_contig742 742 THRCLA_contig743 743 THRCLA_contig744 744 THRCLA_contig745 745 THRCLA_contig746 746 THRCLA_contig747 747 THRCLA_contig748 748 THRCLA_contig749 749 THRCLA_contig750 750 THRCLA_contig751 751 THRCLA_contig752 752 THRCLA_contig753 753 THRCLA_contig754 754 THRCLA_contig755 755 THRCLA_contig756 756 THRCLA_contig757 757 THRCLA_contig758 758 THRCLA_contig759 759 THRCLA_contig760 760 THRCLA_contig761 761 THRCLA_contig762 762 THRCLA_contig763 763 THRCLA_contig764 764 THRCLA_contig765 765 THRCLA_contig766 766 THRCLA_contig767 767 THRCLA_contig768 768 THRCLA_contig769 769 THRCLA_contig770 770 THRCLA_contig771 771 THRCLA_contig772 772 THRCLA_contig773 773 THRCLA_contig774 774 THRCLA_contig775 775 THRCLA_contig776 776 THRCLA_contig777 777 THRCLA_contig778 778 THRCLA_contig779 779 THRCLA_contig780 780 THRCLA_contig781 781 THRCLA_contig782 782 THRCLA_contig783 783 THRCLA_contig784 784 THRCLA_contig785 785 THRCLA_contig786 786 THRCLA_contig787 787 THRCLA_contig788 788 THRCLA_contig789 789 THRCLA_contig790 790 THRCLA_contig791 791 THRCLA_contig792 792 THRCLA_contig793 793 THRCLA_contig794 794 THRCLA_contig795 795 THRCLA_contig796 796 THRCLA_contig797 797 THRCLA_contig798 798 THRCLA_contig799 799 THRCLA_contig800 800 THRCLA_contig801 801 THRCLA_contig802 802 THRCLA_contig803 803 THRCLA_contig804 804 THRCLA_contig805 805 THRCLA_contig806 806 THRCLA_contig807 807 THRCLA_contig808 808 THRCLA_contig809 809 THRCLA_contig810 810 THRCLA_contig811 811 THRCLA_contig812 812 THRCLA_contig813 813 THRCLA_contig814 814 THRCLA_contig815 815 THRCLA_contig816 816 THRCLA_contig817 817 THRCLA_contig818 818 THRCLA_contig819 819 THRCLA_contig820 820 THRCLA_contig821 821 THRCLA_contig822 822 THRCLA_contig823 823 THRCLA_contig824 824 THRCLA_contig825 825 THRCLA_contig826 826 THRCLA_contig827 827 THRCLA_contig828 828 THRCLA_contig829 829 THRCLA_contig830 830 THRCLA_contig831 831 THRCLA_contig832 832 THRCLA_contig833 833 THRCLA_contig834 834 THRCLA_contig835 835 THRCLA_contig836 836 THRCLA_contig837 837 THRCLA_contig838 838 THRCLA_contig839 839 THRCLA_contig840 840 THRCLA_contig841 841 THRCLA_contig842 842 THRCLA_contig843 843 THRCLA_contig844 844 THRCLA_contig845 845 THRCLA_contig846 846 THRCLA_contig847 847 THRCLA_contig848 848 THRCLA_contig849 849 THRCLA_contig850 850 THRCLA_contig851 851 THRCLA_contig852 852 THRCLA_contig853 853 THRCLA_contig854 854 THRCLA_contig855 855 THRCLA_contig856 856 THRCLA_contig857 857 THRCLA_contig858 858 THRCLA_contig859 859 THRCLA_contig860 860 THRCLA_contig861 861 THRCLA_contig862 862 THRCLA_contig863 863 THRCLA_contig864 864 THRCLA_contig865 865 THRCLA_contig866 866 THRCLA_contig867 867 THRCLA_contig868 868 THRCLA_contig869 869 THRCLA_contig870 870 THRCLA_contig871 871 THRCLA_contig872 872 THRCLA_contig873 873 THRCLA_contig874 874 THRCLA_contig875 875 THRCLA_contig876 876 THRCLA_contig877 877 THRCLA_contig878 878 THRCLA_contig879 879 THRCLA_contig880 880 THRCLA_contig881 881 THRCLA_contig882 882 THRCLA_contig883 883 THRCLA_contig884 884 THRCLA_contig885 885 THRCLA_contig886 886 THRCLA_contig887 887 THRCLA_contig888 888 THRCLA_contig889 889 THRCLA_contig890 890 THRCLA_contig891 891 THRCLA_contig892 892 THRCLA_contig893 893 THRCLA_contig894 894 THRCLA_contig895 895 THRCLA_contig896 896 THRCLA_contig897 897 THRCLA_contig898 898 THRCLA_contig899 899 THRCLA_contig900 900 THRCLA_contig901 901 THRCLA_contig902 902 THRCLA_contig903 903 THRCLA_contig904 904 THRCLA_contig905 905 THRCLA_contig906 906 THRCLA_contig907 907 THRCLA_contig908 908 THRCLA_contig909 909 THRCLA_contig910 910 THRCLA_contig911 911 THRCLA_contig912 912 THRCLA_contig913 913 THRCLA_contig914 914 THRCLA_contig915 915 THRCLA_contig916 916 THRCLA_contig917 917 THRCLA_contig918 918 THRCLA_contig919 919 THRCLA_contig920 920 THRCLA_contig921 921 THRCLA_contig922 922 THRCLA_contig923 923 THRCLA_contig924 924 THRCLA_contig925 925 THRCLA_contig926 926 THRCLA_contig927 927 THRCLA_contig928 928 THRCLA_contig929 929 THRCLA_contig930 930 THRCLA_contig931 931 THRCLA_contig932 932 THRCLA_contig933 933 THRCLA_contig934 934 THRCLA_contig935 935 THRCLA_contig936 936 THRCLA_contig937 937 THRCLA_contig938 938 THRCLA_contig939 939 THRCLA_contig940 940 THRCLA_contig941 941 THRCLA_contig942 942 THRCLA_contig943 943 THRCLA_contig944 944 THRCLA_contig945 945 THRCLA_contig946 946 THRCLA_contig947 947 THRCLA_contig948 948 THRCLA_contig949 949 THRCLA_contig950 950 THRCLA_contig951 951 THRCLA_contig952 952 THRCLA_contig953 953 THRCLA_contig954 954 THRCLA_contig955 955 THRCLA_contig956 956 THRCLA_contig957 957 THRCLA_contig958 958 THRCLA_contig959 959 THRCLA_contig960 960 THRCLA_contig961 961 THRCLA_contig962 962 THRCLA_contig963 963 THRCLA_contig964 964 THRCLA_contig965 965 THRCLA_contig966 966 THRCLA_contig967 967 THRCLA_contig968 968 THRCLA_contig969 969 THRCLA_contig970 970 THRCLA_contig971 971 THRCLA_contig972 972 THRCLA_contig973 973 THRCLA_contig974 974 THRCLA_contig975 975 THRCLA_contig976 976 THRCLA_contig977 977 THRCLA_contig978 978 THRCLA_contig979 979 THRCLA_contig980 980 THRCLA_contig981 981 THRCLA_contig982 982 THRCLA_contig983 983 THRCLA_contig984 984 THRCLA_contig985 985 THRCLA_contig986 986 THRCLA_contig987 987 THRCLA_contig988 988 THRCLA_contig989 989 THRCLA_contig990 990 THRCLA_contig991 991 THRCLA_contig992 992 THRCLA_contig993 993 THRCLA_contig994 994 THRCLA_contig995 995 THRCLA_contig996 996 THRCLA_contig997 997 THRCLA_contig998 998 THRCLA_contig999 999 THRCLA_contig1000 1000 THRCLA_contig1001 1001 THRCLA_contig1002 1002 THRCLA_contig1003 1003 THRCLA_contig1004 1004 THRCLA_contig1005 1005 THRCLA_contig1006 1006 THRCLA_contig1007 1007 THRCLA_contig1008 1008 THRCLA_contig1009 1009 THRCLA_contig1010 1010 THRCLA_contig1011 1011 THRCLA_contig1012 1012 THRCLA_contig1013 1013 THRCLA_contig1014 1014 THRCLA_contig1015 1015 THRCLA_contig1016 1016 THRCLA_contig1017 1017 THRCLA_contig1018 1018 THRCLA_contig1019 1019 THRCLA_contig1020 1020 THRCLA_contig1021 1021 THRCLA_contig1022 1022 THRCLA_contig1023 1023 THRCLA_contig1024 1024 THRCLA_contig1025 1025 THRCLA_contig1026 1026 THRCLA_contig1027 1027 THRCLA_contig1028 1028 THRCLA_contig1029 1029 THRCLA_contig1030 1030 THRCLA_contig1031 1031 THRCLA_contig1032 1032 THRCLA_contig1033 1033 THRCLA_contig1034 1034 THRCLA_contig1035 1035 THRCLA_contig1036 1036 THRCLA_contig1037 1037 THRCLA_contig1038 1038 THRCLA_contig1039 1039 THRCLA_contig1040 1040 THRCLA_contig1041 1041 THRCLA_contig1042 1042 THRCLA_contig1043 1043 THRCLA_contig1044 1044 THRCLA_contig1045 1045 THRCLA_contig1046 1046 THRCLA_contig1047 1047 THRCLA_contig1048 1048 THRCLA_contig1049 1049 THRCLA_contig1050 1050 THRCLA_contig1051 1051 THRCLA_contig1052 1052 THRCLA_contig1053 1053 THRCLA_contig1054 1054 THRCLA_contig1055 1055 THRCLA_contig1056 1056 THRCLA_contig1057 1057 THRCLA_contig1058 1058 THRCLA_contig1059 1059 THRCLA_contig1060 1060 THRCLA_contig1061 1061 THRCLA_contig1062 1062 THRCLA_contig1063 1063 THRCLA_contig1064 1064 THRCLA_contig1065 1065 THRCLA_contig1066 1066 THRCLA_contig1067 1067 THRCLA_contig1068 1068 THRCLA_contig1069 1069 THRCLA_contig1070 1070 THRCLA_contig1071 1071 THRCLA_contig1072 1072 THRCLA_contig1073 1073 THRCLA_contig1074 1074 THRCLA_contig1075 1075 THRCLA_contig1076 1076 THRCLA_contig1077 1077 THRCLA_contig1078 1078 THRCLA_contig1079 1079 THRCLA_contig1080 1080 THRCLA_contig1081 1081 THRCLA_contig1082 1082 THRCLA_contig1083 1083 THRCLA_contig1084 1084 THRCLA_contig1085 1085 THRCLA_contig1086 1086 THRCLA_contig1087 1087 THRCLA_contig1088 1088 THRCLA_contig1089 1089 THRCLA_contig1090 1090 THRCLA_contig1091 1091 THRCLA_contig1092 1092 THRCLA_contig1093 1093 THRCLA_contig1094 1094 THRCLA_contig1095 1095 THRCLA_contig1096 1096 THRCLA_contig1097 1097 THRCLA_contig1098 1098 THRCLA_contig1099 1099 THRCLA_contig1100 1100 THRCLA_contig1101 1101 THRCLA_contig1102 1102 THRCLA_contig1103 1103 THRCLA_contig1104 1104 THRCLA_contig1105 1105 THRCLA_contig1106 1106 THRCLA_contig1107 1107 THRCLA_contig1108 1108 THRCLA_contig1109 1109 THRCLA_contig1110 1110 THRCLA_contig1111 1111 THRCLA_contig1112 1112 THRCLA_contig1113 1113 THRCLA_contig1114 1114 THRCLA_contig1115 1115 THRCLA_contig1116 1116 THRCLA_contig1117 1117 THRCLA_contig1118 1118 THRCLA_contig1119 1119 THRCLA_contig1120 1120 THRCLA_contig1121 1121 THRCLA_contig1122 1122 THRCLA_contig1123 1123 THRCLA_contig1124 1124 THRCLA_contig1125 1125 THRCLA_contig1126 1126 THRCLA_contig1127 1127 THRCLA_contig1128 1128 THRCLA_contig1129 1129 THRCLA_contig1130 1130 THRCLA_contig1131 1131 THRCLA_contig1132 1132 THRCLA_contig1133 1133 THRCLA_contig1134 1134 THRCLA_contig1135 1135 THRCLA_contig1136 1136 THRCLA_contig1137 1137 THRCLA_contig1138 1138 THRCLA_contig1139 1139 THRCLA_contig1140 1140 THRCLA_contig1141 1141 THRCLA_contig1142 1142 THRCLA_contig1143 1143 THRCLA_contig1144 1144 THRCLA_contig1145 1145 THRCLA_contig1146 1146 THRCLA_contig1147 1147 THRCLA_contig1148 1148 THRCLA_contig1149 1149 THRCLA_contig1150 1150 THRCLA_contig1151 1151 THRCLA_contig1152 1152 THRCLA_contig1153 1153 THRCLA_contig1154 1154 THRCLA_contig1155 1155 THRCLA_contig1156 1156 THRCLA_contig1157 1157 THRCLA_contig1158 1158 THRCLA_contig1159 1159 THRCLA_contig1160 1160 THRCLA_contig1161 1161 THRCLA_contig1162 1162 THRCLA_contig1163 1163 THRCLA_contig1164 1164 THRCLA_contig1165 1165 THRCLA_contig1166 1166 THRCLA_contig1167 1167 THRCLA_contig1168 1168 THRCLA_contig1169 1169 THRCLA_contig1170 1170 THRCLA_contig1171 1171 THRCLA_contig1172 1172 THRCLA_contig1173 1173 THRCLA_contig1174 1174 THRCLA_contig1175 1175 THRCLA_contig1176 1176 THRCLA_contig1177 1177 THRCLA_contig1178 1178 THRCLA_contig1179 1179 THRCLA_contig1180 1180 THRCLA_contig1181 1181 THRCLA_contig1182 1182 THRCLA_contig1183 1183 THRCLA_contig1184 1184 THRCLA_contig1185 1185 THRCLA_contig1186 1186 THRCLA_contig1187 1187 THRCLA_contig1188 1188 THRCLA_contig1189 1189 THRCLA_contig1190 1190 THRCLA_contig1191 1191 THRCLA_contig1192 1192 THRCLA_contig1193 1193 THRCLA_contig1194 1194 THRCLA_contig1195 1195 THRCLA_contig1196 1196 THRCLA_contig1197 1197 THRCLA_contig1198 1198 THRCLA_contig1199 1199 THRCLA_contig1200 1200 THRCLA_contig1201 1201 THRCLA_contig1202 1202 THRCLA_contig1203 1203 THRCLA_contig1204 1204 THRCLA_contig1205 1205 THRCLA_contig1206 1206 THRCLA_contig1207 1207 THRCLA_contig1208 1208 THRCLA_contig1209 1209 THRCLA_contig1210 1210 THRCLA_contig1211 1211 THRCLA_contig1212 1212 THRCLA_contig1213 1213 THRCLA_contig1214 1214 THRCLA_contig1215 1215 THRCLA_contig1216 1216 THRCLA_contig1217 1217 THRCLA_contig1218 1218 THRCLA_contig1219 1219 THRCLA_contig1220 1220 THRCLA_contig1221 1221 THRCLA_contig1222 1222 THRCLA_contig1223 1223 THRCLA_contig1224 1224 THRCLA_contig1225 1225 THRCLA_contig1226 1226 THRCLA_contig1227 1227 THRCLA_contig1228 1228 THRCLA_contig1229 1229 THRCLA_contig1230 1230 THRCLA_contig1231 1231 THRCLA_contig1232 1232 THRCLA_contig1233 1233 THRCLA_contig1234 1234 THRCLA_contig1235 1235 THRCLA_contig1236 1236 THRCLA_contig1237 1237 THRCLA_contig1238 1238 THRCLA_contig1239 1239 THRCLA_contig1240 1240 THRCLA_contig1241 1241 THRCLA_contig1242 1242 THRCLA_contig1243 1243 THRCLA_contig1244 1244 THRCLA_contig1245 1245 THRCLA_contig1246 1246 THRCLA_contig1247 1247 THRCLA_contig1248 1248 THRCLA_contig1249 1249 THRCLA_contig1250 1250 THRCLA_contig1251 1251 THRCLA_contig1252 1252 THRCLA_contig1253 1253 THRCLA_contig1254 1254 THRCLA_contig1255 1255 THRCLA_contig1256 1256 THRCLA_contig1257 1257 THRCLA_contig1258 1258 THRCLA_contig1259 1259 THRCLA_contig1260 1260 THRCLA_contig1261 1261 THRCLA_contig1262 1262 THRCLA_contig1263 1263 THRCLA_contig1264 1264 THRCLA_contig1265 1265 THRCLA_contig1266 1266 THRCLA_contig1267 1267 THRCLA_contig1268 1268 THRCLA_contig1269 1269 THRCLA_contig1270 1270 THRCLA_contig1271 1271 THRCLA_contig1272 1272 THRCLA_contig1273 1273 THRCLA_contig1274 1274 THRCLA_contig1275 1275 THRCLA_contig1276 1276 THRCLA_contig1277 1277 THRCLA_contig1278 1278 THRCLA_contig1279 1279 THRCLA_contig1280 1280 THRCLA_contig1281 1281 THRCLA_contig1282 1282 THRCLA_contig1283 1283 THRCLA_contig1284 1284 THRCLA_contig1285 1285 THRCLA_contig1286 1286 THRCLA_contig1287 1287 THRCLA_contig1288 1288 THRCLA_contig1289 1289 THRCLA_contig1290 1290 THRCLA_contig1291 1291 THRCLA_contig1292 1292 THRCLA_contig1293 1293 THRCLA_contig1294 1294 THRCLA_contig1295 1295 THRCLA_contig1296 1296 THRCLA_contig1297 1297 THRCLA_contig1298 1298 THRCLA_contig1299 1299 THRCLA_contig1300 1300 THRCLA_contig1301 1301 THRCLA_contig1302 1302 THRCLA_contig1303 1303 THRCLA_contig1304 1304 THRCLA_contig1305 1305 THRCLA_contig1306 1306 THRCLA_contig1307 1307 THRCLA_contig1308 1308 THRCLA_contig1309 1309 THRCLA_contig1310 1310 THRCLA_contig1311 1311 THRCLA_contig1312 1312 THRCLA_contig1313 1313 THRCLA_contig1314 1314 THRCLA_contig1315 1315 THRCLA_contig1316 1316 THRCLA_contig1317 1317 THRCLA_contig1318 1318 THRCLA_contig1319 1319 THRCLA_contig1320 1320 THRCLA_contig1321 1321 THRCLA_contig1322 1322 THRCLA_contig1323 1323 THRCLA_contig1324 1324 THRCLA_contig1325 1325 THRCLA_contig1326 1326 THRCLA_contig1327 1327 THRCLA_contig1328 1328 THRCLA_contig1329 1329 THRCLA_contig1330 1330 THRCLA_contig1331 1331 THRCLA_contig1332 1332 THRCLA_contig1333 1333 THRCLA_contig1334 1334 THRCLA_contig1335 1335 THRCLA_contig1336 1336 THRCLA_contig1337 1337 THRCLA_contig1338 1338 THRCLA_contig1339 1339 THRCLA_contig1340 1340 THRCLA_contig1341 1341 THRCLA_contig1342 1342 THRCLA_contig1343 1343 THRCLA_contig1344 1344 THRCLA_contig1345 1345 THRCLA_contig1346 1346 THRCLA_contig1347 1347 THRCLA_contig1348 1348 THRCLA_contig1349 1349 THRCLA_contig1350 1350 THRCLA_contig1351 1351 THRCLA_contig1352 1352 THRCLA_contig1353 1353 THRCLA_contig1354 1354 THRCLA_contig1355 1355 THRCLA_contig1356 1356 THRCLA_contig1357 1357 THRCLA_contig1358 1358 THRCLA_contig1359 1359 THRCLA_contig1360 1360 THRCLA_contig1361 1361 THRCLA_contig1362 1362 THRCLA_contig1363 1363 THRCLA_contig1364 1364 THRCLA_contig1365 1365 THRCLA_contig1366 1366 THRCLA_contig1367 1367 THRCLA_contig1368 1368 THRCLA_contig1369 1369 THRCLA_contig1370 1370 THRCLA_contig1371 1371 THRCLA_contig1372 1372 THRCLA_contig1373 1373 THRCLA_contig1374 1374 THRCLA_contig1375 1375 THRCLA_contig1376 1376 THRCLA_contig1377 1377 THRCLA_contig1378 1378 THRCLA_contig1379 1379 THRCLA_contig1380 1380 THRCLA_contig1381 1381 THRCLA_contig1382 1382 THRCLA_contig1383 1383 THRCLA_contig1384 1384 THRCLA_contig1385 1385 THRCLA_contig1386 1386 THRCLA_contig1387 1387 THRCLA_contig1388 1388 THRCLA_contig1389 1389 THRCLA_contig1390 1390 THRCLA_contig1391 1391 THRCLA_contig1392 1392 THRCLA_contig1393 1393 THRCLA_contig1394 1394 THRCLA_contig1395 1395 THRCLA_contig1396 1396 THRCLA_contig1397 1397 THRCLA_contig1398 1398 THRCLA_contig1399 1399 THRCLA_contig1400 1400 THRCLA_contig1401 1401 THRCLA_contig1402 1402 THRCLA_contig1403 1403 THRCLA_contig1404 1404 THRCLA_contig1405 1405 THRCLA_contig1406 1406 THRCLA_contig1407 1407 THRCLA_contig1408 1408 THRCLA_contig1409 1409 THRCLA_contig1410 1410 THRCLA_contig1411 1411 THRCLA_contig1412 1412 THRCLA_contig1413 1413 THRCLA_contig1414 1414 THRCLA_contig1415 1415 THRCLA_contig1416 1416 THRCLA_contig1417 1417 THRCLA_contig1418 1418 THRCLA_contig1419 1419 THRCLA_contig1420 1420 THRCLA_contig1421 1421 THRCLA_contig1422 1422 THRCLA_contig1423 1423 THRCLA_contig1424 1424 THRCLA_contig1425 1425 THRCLA_contig1426 1426 THRCLA_contig1427 1427 THRCLA_contig1428 1428 THRCLA_contig1429 1429 THRCLA_contig1430 1430 THRCLA_contig1431 1431 THRCLA_contig1432 1432 THRCLA_contig1433 1433 THRCLA_contig1434 1434 THRCLA_contig1435 1435 THRCLA_contig1436 1436 THRCLA_contig1437 1437 THRCLA_contig1438 1438 THRCLA_contig1439 1439 THRCLA_contig1440 1440 THRCLA_contig1441 1441 THRCLA_contig1442 1442 THRCLA_contig1443 1443 THRCLA_contig1444 1444 THRCLA_contig1445 1445 THRCLA_contig1446 1446 THRCLA_contig1447 1447 THRCLA_contig1448 1448 THRCLA_contig1449 1449 THRCLA_contig1450 1450 THRCLA_contig1451 1451 THRCLA_contig1452 1452 THRCLA_contig1453 1453 THRCLA_contig1454 1454 THRCLA_contig1455 1455 THRCLA_contig1456 1456 THRCLA_contig1457 1457 THRCLA_contig1458 1458 THRCLA_contig1459 1459 THRCLA_contig1460 1460 THRCLA_contig1461 1461 THRCLA_contig1462 1462 THRCLA_contig1463 1463 THRCLA_contig1464 1464 THRCLA_contig1465 1465 THRCLA_contig1466 1466 THRCLA_contig1467 1467 THRCLA_contig1468 1468 THRCLA_contig1469 1469 THRCLA_contig1470 1470 THRCLA_contig1471 1471 THRCLA_contig1472 1472 THRCLA_contig1473 1473 THRCLA_contig1474 1474 THRCLA_contig1475 1475 THRCLA_contig1476 1476 THRCLA_contig1477 1477 THRCLA_contig1478 1478 THRCLA_contig1479 1479 THRCLA_contig1480 1480 THRCLA_contig1481 1481 THRCLA_contig1482 1482 THRCLA_contig1483 1483 THRCLA_contig1484 1484 THRCLA_contig1485 1485 THRCLA_contig1486 1486 THRCLA_contig1487 1487 THRCLA_contig1488 1488 THRCLA_contig1489 1489 THRCLA_contig1490 1490 THRCLA_contig1491 1491 THRCLA_contig1492 1492 THRCLA_contig1493 1493 THRCLA_contig1494 1494 THRCLA_contig1495 1495 THRCLA_contig1496 1496 THRCLA_contig1497 1497 THRCLA_contig1498 1498 THRCLA_contig1499 1499 THRCLA_contig1500 1500 THRCLA_contig1501 1501 THRCLA_contig1502 1502 THRCLA_contig1503 1503 THRCLA_contig1504 1504 THRCLA_contig1505 1505 THRCLA_contig1506 1506 THRCLA_contig1507 1507 THRCLA_contig1508 1508 THRCLA_contig1509 1509 THRCLA_contig1510 1510 THRCLA_contig1511 1511 THRCLA_contig1512 1512 THRCLA_contig1513 1513 THRCLA_contig1514 1514 THRCLA_contig1515 1515 THRCLA_contig1516 1516 THRCLA_contig1517 1517 THRCLA_contig1518 1518 THRCLA_contig1519 1519 THRCLA_contig1520 1520 THRCLA_contig1521 1521 THRCLA_contig1522 1522 THRCLA_contig1523 1523 THRCLA_contig1524 1524 THRCLA_contig1525 1525 THRCLA_contig1526 1526 THRCLA_contig1527 1527 THRCLA_contig1528 1528 THRCLA_contig1529 1529 THRCLA_contig1530 1530 THRCLA_contig1531 1531 THRCLA_contig1532 1532 THRCLA_contig1533 1533 THRCLA_contig1534 1534 THRCLA_contig1535 1535 THRCLA_contig1536 1536 THRCLA_contig1537 1537 THRCLA_contig1538 1538 THRCLA_contig1539 1539 THRCLA_contig1540 1540 THRCLA_contig1541 1541 THRCLA_contig1542 1542 THRCLA_contig1543 1543 THRCLA_contig1544 1544 THRCLA_contig1545 1545 THRCLA_contig1546 1546 THRCLA_contig1547 1547 THRCLA_contig1548 1548 THRCLA_contig1549 1549 THRCLA_contig1550 1550 THRCLA_contig1551 1551 THRCLA_contig1552 1552 THRCLA_contig1553 1553 THRCLA_contig1554 1554 THRCLA_contig1555 1555 THRCLA_contig1556 1556 THRCLA_contig1557 1557 THRCLA_contig1558 1558 THRCLA_contig1559 1559 THRCLA_contig1560 1560 THRCLA_contig1561 1561 THRCLA_contig1562 1562 THRCLA_contig1563 1563 THRCLA_contig1564 1564 THRCLA_contig1565 1565 THRCLA_contig1566 1566 THRCLA_contig1567 1567 THRCLA_contig1568 1568 THRCLA_contig1569 1569 THRCLA_contig1570 1570 THRCLA_contig1571 1571 THRCLA_contig1572 1572 THRCLA_contig1573 1573 THRCLA_contig1574 1574 THRCLA_contig1575 1575 THRCLA_contig1576 1576 THRCLA_contig1577 1577 THRCLA_contig1578 1578 THRCLA_contig1579 1579 THRCLA_contig1580 1580 THRCLA_contig1581 1581 THRCLA_contig1582 1582 THRCLA_contig1583 1583 THRCLA_contig1584 1584 THRCLA_contig1585 1585 THRCLA_contig1586 1586 THRCLA_contig1587 1587 THRCLA_contig1588 1588 THRCLA_contig1589 1589 THRCLA_contig1590 1590 THRCLA_contig1591 1591 THRCLA_contig1592 1592 THRCLA_contig1593 1593 THRCLA_contig1594 1594 THRCLA_contig1595 1595 THRCLA_contig1596 1596 THRCLA_contig1597 1597 THRCLA_contig1598 1598 THRCLA_contig1599 1599 THRCLA_contig1600 1600 THRCLA_contig1601 1601 THRCLA_contig1602 1602 THRCLA_contig1603 1603 THRCLA_contig1604 1604 THRCLA_contig1605 1605 THRCLA_contig1606 1606 THRCLA_contig1607 1607 THRCLA_contig1608 1608 THRCLA_contig1609 1609 THRCLA_contig1610 1610 THRCLA_contig1611 1611 THRCLA_contig1612 1612 THRCLA_contig1613 1613 THRCLA_contig1614 1614 THRCLA_contig1615 1615 THRCLA_contig1616 1616 THRCLA_contig1617 1617 THRCLA_contig1618 1618 THRCLA_contig1619 1619 THRCLA_contig1620 1620 THRCLA_contig1621 1621 THRCLA_contig1622 1622 THRCLA_contig1623 1623 THRCLA_contig1624 1624 THRCLA_contig1625 1625 THRCLA_contig1626 1626 THRCLA_contig1627 1627 THRCLA_contig1628 1628 THRCLA_contig1629 1629 THRCLA_contig1630 1630 THRCLA_contig1631 1631 THRCLA_contig1632 1632 THRCLA_contig1633 1633 THRCLA_contig1634 1634 THRCLA_contig1635 1635 THRCLA_contig1636 1636 THRCLA_contig1637 1637 THRCLA_contig1638 1638 THRCLA_contig1639 1639 THRCLA_contig1640 1640 THRCLA_contig1641 1641 THRCLA_contig1642 1642 THRCLA_contig1643 1643 THRCLA_contig1644 1644 THRCLA_contig1645 1645 THRCLA_contig1646 1646 THRCLA_contig1647 1647 THRCLA_contig1648 1648 THRCLA_contig1649 1649 THRCLA_contig1650 1650 THRCLA_contig1651 1651 THRCLA_contig1652 1652 THRCLA_contig1653 1653 THRCLA_contig1654 1654 THRCLA_contig1655 1655 THRCLA_contig1656 1656 THRCLA_contig1657 1657 THRCLA_contig1658 1658 THRCLA_contig1659 1659 THRCLA_contig1660 1660 THRCLA_contig1661 1661 THRCLA_contig1662 1662 THRCLA_contig1663 1663 THRCLA_contig1664 1664 THRCLA_contig1665 1665 THRCLA_contig1666 1666 THRCLA_contig1667 1667 THRCLA_contig1668 1668 THRCLA_contig1669 1669 THRCLA_contig1670 1670 THRCLA_contig1671 1671 THRCLA_contig1672 1672 THRCLA_contig1673 1673 THRCLA_contig1674 1674 THRCLA_contig1675 1675 THRCLA_contig1676 1676 THRCLA_contig1677 1677 THRCLA_contig1678 1678 THRCLA_contig1679 1679 THRCLA_contig1680 1680 THRCLA_contig1681 1681 THRCLA_contig1682 1682 THRCLA_contig1683 1683 THRCLA_contig1684 1684 THRCLA_contig1685 1685 THRCLA_contig1686 1686 THRCLA_contig1687 1687 THRCLA_contig1688 1688 THRCLA_contig1689 1689 THRCLA_contig1690 1690 THRCLA_contig1691 1691 THRCLA_contig1692 1692 THRCLA_contig1693 1693 THRCLA_contig1694 1694 THRCLA_contig1695 1695 THRCLA_contig1696 1696 THRCLA_contig1697 1697 THRCLA_contig1698 1698 THRCLA_contig1699 1699 THRCLA_contig1700 1700 THRCLA_contig1701 1701 THRCLA_contig1702 1702 THRCLA_contig1703 1703 THRCLA_contig1704 1704 THRCLA_contig1705 1705 THRCLA_contig1706 1706 THRCLA_contig1707 1707 THRCLA_contig1708 1708 THRCLA_contig1709 1709 THRCLA_contig1710 1710 THRCLA_contig1711 1711 THRCLA_contig1712 1712 THRCLA_contig1713 1713 THRCLA_contig1714 1714 THRCLA_contig1715 1715 THRCLA_contig1716 1716 THRCLA_contig1717 1717 THRCLA_contig1718 1718 THRCLA_contig1719 1719 THRCLA_contig1720 1720 THRCLA_contig1721 1721 THRCLA_contig1722 1722 THRCLA_contig1723 1723 THRCLA_contig1724 1724 THRCLA_contig1725 1725 THRCLA_contig1726 1726 THRCLA_contig1727 1727 THRCLA_contig1728 1728 THRCLA_contig1729 1729 THRCLA_contig1730 1730 THRCLA_contig1731 1731 THRCLA_contig1732 1732 THRCLA_contig1733 1733 THRCLA_contig1734 1734 THRCLA_contig1735 1735 THRCLA_contig1736 1736 THRCLA_contig1737 1737 THRCLA_contig1738 1738 THRCLA_contig1739 1739 THRCLA_contig1740 1740 THRCLA_contig1741 1741 THRCLA_contig1742 1742 THRCLA_contig1743 1743 THRCLA_contig1744 1744 THRCLA_contig1745 1745 THRCLA_contig1746 1746 THRCLA_contig1747 1747 THRCLA_contig1748 1748 THRCLA_contig1749 1749 THRCLA_contig1750 1750 THRCLA_contig1751 1751 THRCLA_contig1752 1752 THRCLA_contig1753 1753 THRCLA_contig1754 1754 THRCLA_contig1755 1755 THRCLA_contig1756 1756 THRCLA_contig1757 1757 THRCLA_contig1758 1758 THRCLA_contig1759 1759 THRCLA_contig1760 1760 THRCLA_contig1761 1761 THRCLA_contig1762 1762 THRCLA_contig1763 1763 THRCLA_contig1764 1764 THRCLA_contig1765 1765 THRCLA_contig1766 1766 THRCLA_contig1767 1767 THRCLA_contig1768 1768 THRCLA_contig1769 1769 THRCLA_contig1770 1770 THRCLA_contig1771 1771 THRCLA_contig1772 1772 THRCLA_contig1773 1773 THRCLA_contig1774 1774 THRCLA_contig1775 1775 THRCLA_contig1776 1776 THRCLA_contig1777 1777 THRCLA_contig1778 1778 THRCLA_contig1779 1779 THRCLA_contig1780 1780 THRCLA_contig1781 1781 THRCLA_contig1782 1782 THRCLA_contig1783 1783 THRCLA_contig1784 1784 THRCLA_contig1785 1785 THRCLA_contig1786 1786 THRCLA_contig1787 1787 THRCLA_contig1788 1788 THRCLA_contig1789 1789 THRCLA_contig1790 1790 THRCLA_contig1791 1791 THRCLA_contig1792 1792 THRCLA_contig1793 1793 THRCLA_contig1794 1794 THRCLA_contig1795 1795 THRCLA_contig1796 1796 THRCLA_contig1797 1797 THRCLA_contig1798 1798 THRCLA_contig1799 1799 THRCLA_contig1800 1800 THRCLA_contig1801 1801 THRCLA_contig1802 1802 THRCLA_contig1803 1803 THRCLA_contig1804 1804 THRCLA_contig1805 1805 THRCLA_contig1806 1806 THRCLA_contig1807 1807 THRCLA_contig1808 1808 THRCLA_contig1809 1809 THRCLA_contig1810 1810 THRCLA_contig1811 1811 THRCLA_contig1812 1812 THRCLA_contig1813 1813 THRCLA_contig1814 1814 THRCLA_contig1815 1815 THRCLA_contig1816 1816 THRCLA_contig1817 1817 THRCLA_contig1818 1818 THRCLA_contig1819 1819 THRCLA_contig1820 1820 THRCLA_contig1821 1821 THRCLA_contig1822 1822 THRCLA_contig1823 1823 THRCLA_contig1824 1824 THRCLA_contig1825 1825 THRCLA_contig1826 1826 THRCLA_contig1827 1827 THRCLA_contig1828 1828 THRCLA_contig1829 1829 THRCLA_contig1830 1830 THRCLA_contig1831 1831 THRCLA_contig1832 1832 THRCLA_contig1833 1833 THRCLA_contig1834 1834 THRCLA_contig1835 1835 THRCLA_contig1836 1836 THRCLA_contig1837 1837 THRCLA_contig1838 1838 THRCLA_contig1839 1839 THRCLA_contig1840 1840 THRCLA_contig1841 1841 THRCLA_contig1842 1842 THRCLA_contig1843 1843 THRCLA_contig1844 1844 THRCLA_contig1845 1845 THRCLA_contig1846 1846 THRCLA_contig1847 1847 THRCLA_contig1848 1848 THRCLA_contig1849 1849 THRCLA_contig1850 1850 THRCLA_contig1851 1851 THRCLA_contig1852 1852 THRCLA_contig1853 1853 THRCLA_contig1854 1854 THRCLA_contig1855 1855 THRCLA_contig1856 1856 THRCLA_contig1857 1857 THRCLA_contig1858 1858 THRCLA_contig1859 1859 THRCLA_contig1860 1860 THRCLA_contig1861 1861 THRCLA_contig1862 1862 THRCLA_contig1863 1863 THRCLA_contig1864 1864 THRCLA_contig1865 1865 THRCLA_contig1866 1866 THRCLA_contig1867 1867 THRCLA_contig1868 1868 THRCLA_contig1869 1869 THRCLA_contig1870 1870 THRCLA_contig1871 1871 THRCLA_contig1872 1872 THRCLA_contig1873 1873 THRCLA_contig1874 1874 THRCLA_contig1875 1875 THRCLA_contig1876 1876 THRCLA_contig1877 1877 THRCLA_contig1878 1878 THRCLA_contig1879 1879 THRCLA_contig1880 1880 THRCLA_contig1881 1881 THRCLA_contig1882 1882 THRCLA_contig1883 1883 THRCLA_contig1884 1884 THRCLA_contig1885 1885 THRCLA_contig1886 1886 THRCLA_contig1887 1887 THRCLA_contig1888 1888 THRCLA_contig1889 1889 THRCLA_contig1890 1890 THRCLA_contig1891 1891 THRCLA_contig1892 1892 THRCLA_contig1893 1893 THRCLA_contig1894 1894 THRCLA_contig1895 1895 THRCLA_contig1896 1896 THRCLA_contig1897 1897 THRCLA_contig1898 1898 THRCLA_contig1899 1899 THRCLA_contig1900 1900 THRCLA_contig1901 1901 THRCLA_contig1902 1902 THRCLA_contig1903 1903 THRCLA_contig1904 1904 THRCLA_contig1905 1905 THRCLA_contig1906 1906 THRCLA_contig1907 1907 THRCLA_contig1908 1908 THRCLA_contig1909 1909 THRCLA_contig1910 1910 THRCLA_contig1911 1911 THRCLA_contig1912 1912 THRCLA_contig1913 1913 THRCLA_contig1914 1914 THRCLA_contig1915 1915 THRCLA_contig1916 1916 THRCLA_contig1917 1917 THRCLA_contig1918 1918 THRCLA_contig1919 1919 THRCLA_contig1920 1920 THRCLA_contig1921 1921 THRCLA_contig1922 1922 THRCLA_contig1923 1923 THRCLA_contig1924 1924 THRCLA_contig1925 1925 THRCLA_contig1926 1926 THRCLA_contig1927 1927 THRCLA_contig1928 1928 THRCLA_contig1929 1929 THRCLA_contig1930 1930 THRCLA_contig1931 1931 THRCLA_contig1932 1932 THRCLA_contig1933 1933 THRCLA_contig1934 1934 THRCLA_contig1935 1935 THRCLA_contig1936 1936 THRCLA_contig1937 1937 THRCLA_contig1938 1938 THRCLA_contig1939 1939 THRCLA_contig1940 1940 THRCLA_contig1941 1941 THRCLA_contig1942 1942 THRCLA_contig1943 1943 THRCLA_contig1944 1944 THRCLA_contig1945 1945 THRCLA_contig1946 1946 THRCLA_contig1947 1947 THRCLA_contig1948 1948 THRCLA_contig1949 1949 THRCLA_contig1950 1950 THRCLA_contig1951 1951 THRCLA_contig1952 1952 THRCLA_contig1953 1953 THRCLA_contig1954 1954 THRCLA_contig1955 1955 THRCLA_contig1956 1956 THRCLA_contig1957 1957 THRCLA_contig1958 1958 THRCLA_contig1959 1959 THRCLA_contig1960 1960 THRCLA_contig1961 1961 THRCLA_contig1962 1962 THRCLA_contig1963 1963 THRCLA_contig1964 1964 THRCLA_contig1965 1965 THRCLA_contig1966 1966 THRCLA_contig1967 1967 THRCLA_contig1968 1968 THRCLA_contig1969 1969 THRCLA_contig1970 1970 THRCLA_contig1971 1971 THRCLA_contig1972 1972 THRCLA_contig1973 1973 THRCLA_contig1974 1974 THRCLA_contig1975 1975 THRCLA_contig1976 1976 THRCLA_contig1977 1977 THRCLA_contig1978 1978 THRCLA_contig1979 1979 THRCLA_contig1980 1980 THRCLA_contig1981 1981 THRCLA_contig1982 1982 THRCLA_contig1983 1983 THRCLA_contig1984 1984 THRCLA_contig1985 1985 THRCLA_contig1986 1986 THRCLA_contig1987 1987 THRCLA_contig1988 1988 THRCLA_contig1989 1989 THRCLA_contig1990 1990 THRCLA_contig1991 1991 THRCLA_contig1992 1992 THRCLA_contig1993 1993 THRCLA_contig1994 1994 THRCLA_contig1995 1995 THRCLA_contig1996 1996 THRCLA_contig1997 1997 THRCLA_contig1998 1998 THRCLA_contig1999 1999 THRCLA_contig2000 2000 THRCLA_contig2001 2001 THRCLA_contig2002 2002 THRCLA_contig2003 2003 THRCLA_contig2004 2004 THRCLA_contig2005 2005 THRCLA_contig2006 2006 THRCLA_contig2007 2007 THRCLA_contig2008 2008 THRCLA_contig2009 2009 THRCLA_contig2010 2010 THRCLA_contig2011 2011 THRCLA_contig2012 2012 THRCLA_contig2013 2013 THRCLA_contig2014 2014 THRCLA_contig2015 2015 THRCLA_contig2016 2016 THRCLA_contig2017 2017 THRCLA_contig2018 2018 THRCLA_contig2019 2019 THRCLA_contig2020 2020 THRCLA_contig2021 2021 THRCLA_contig2022 2022 THRCLA_contig2023 2023 THRCLA_contig2024 2024 THRCLA_contig2025 2025 THRCLA_contig2026 2026 THRCLA_contig2027 2027 THRCLA_contig2028 2028 THRCLA_contig2029 2029 THRCLA_contig2030 2030 THRCLA_contig2031 2031 THRCLA_contig2032 2032 THRCLA_contig2033 2033 THRCLA_contig2034 2034 THRCLA_contig2035 2035 THRCLA_contig2036 2036 THRCLA_contig2037 2037 THRCLA_contig2038 2038 THRCLA_contig2039 2039 THRCLA_contig2040 2040 THRCLA_contig2041 2041 THRCLA_contig2042 2042 THRCLA_contig2043 2043 THRCLA_contig2044 2044 THRCLA_contig2045 2045 THRCLA_contig2046 2046 THRCLA_contig2047 2047 THRCLA_contig2048 2048 THRCLA_contig2049 2049 THRCLA_contig2050 2050 THRCLA_contig2051 2051 THRCLA_contig2052 2052 THRCLA_contig2053 2053 THRCLA_contig2054 2054 THRCLA_contig2055 2055 THRCLA_contig2056 2056 THRCLA_contig2057 2057 THRCLA_contig2058 2058 THRCLA_contig2059 2059 THRCLA_contig2060 2060 THRCLA_contig2061 2061 THRCLA_contig2062 2062 THRCLA_contig2063 2063 THRCLA_contig2064 2064 THRCLA_contig2065 2065 THRCLA_contig2066 2066 THRCLA_contig2067 2067 THRCLA_contig2068 2068 THRCLA_contig2069 2069 THRCLA_contig2070 2070 THRCLA_contig2071 2071 THRCLA_contig2072 2072 THRCLA_contig2073 2073 THRCLA_contig2074 2074 THRCLA_contig2075 2075 THRCLA_contig2076 2076 THRCLA_contig2077 2077 THRCLA_contig2078 2078 THRCLA_contig2079 2079 THRCLA_contig2080 2080 THRCLA_contig2081 2081 THRCLA_contig2082 2082 THRCLA_contig2083 2083 THRCLA_contig2084 2084 THRCLA_contig2085 2085 THRCLA_contig2086 2086 THRCLA_contig2087 2087 THRCLA_contig2088 2088 THRCLA_contig2089 2089 THRCLA_contig2090 2090 THRCLA_contig2091 2091 THRCLA_contig2092 2092 THRCLA_contig2093 2093 THRCLA_contig2094 2094 THRCLA_contig2095 2095 THRCLA_contig2096 2096 THRCLA_contig2097 2097 THRCLA_contig2098 2098 THRCLA_contig2099 2099 THRCLA_contig2100 2100 THRCLA_contig2101 2101 THRCLA_contig2102 2102 THRCLA_contig2103 2103 THRCLA_contig2104 2104 THRCLA_contig2105 2105 THRCLA_contig2106 2106 THRCLA_contig2107 2107 THRCLA_contig2108 2108 THRCLA_contig2109 2109 THRCLA_contig2110 2110 THRCLA_contig2111 2111 THRCLA_contig2112 2112 THRCLA_contig2113 2113 THRCLA_contig2114 2114 THRCLA_contig2115 2115 THRCLA_contig2116 2116 THRCLA_contig2117 2117 THRCLA_contig2118 2118 THRCLA_contig2119 2119 THRCLA_contig2120 2120 THRCLA_contig2121 2121 THRCLA_contig2122 2122 THRCLA_contig2123 2123 THRCLA_contig2124 2124 THRCLA_contig2125 2125 THRCLA_contig2126 2126 THRCLA_contig2127 2127 THRCLA_contig2128 2128 THRCLA_contig2129 2129 THRCLA_contig2130 2130 THRCLA_contig2131 2131 THRCLA_contig2132 2132 THRCLA_contig2133 2133 THRCLA_contig2134 2134 THRCLA_contig2135 2135 THRCLA_contig2136 2136 THRCLA_contig2137 2137 THRCLA_contig2138 2138 THRCLA_contig2139 2139 THRCLA_contig2140 2140 THRCLA_contig2141 2141 THRCLA_contig2142 2142 THRCLA_contig2143 2143 THRCLA_contig2144 2144 THRCLA_contig2145 2145 THRCLA_contig2146 2146 THRCLA_contig2147 2147 THRCLA_contig2148 2148 THRCLA_contig2149 2149 THRCLA_contig2150 2150 THRCLA_contig2151 2151 THRCLA_contig2152 2152 THRCLA_contig2153 2153 THRCLA_contig2154 2154 THRCLA_contig2155 2155 THRCLA_contig2156 2156 THRCLA_contig2157 2157 THRCLA_contig2158 2158 THRCLA_contig2159 2159 THRCLA_contig2160 2160 THRCLA_contig2161 2161 THRCLA_contig2162 2162 THRCLA_contig2163 2163 THRCLA_contig2164 2164 THRCLA_contig2165 2165 THRCLA_contig2166 2166 THRCLA_contig2167 2167 THRCLA_contig2168 2168 THRCLA_contig2169 2169 THRCLA_contig2170 2170 THRCLA_contig2171 2171 THRCLA_contig2172 2172 THRCLA_contig2173 2173 THRCLA_contig2174 2174 THRCLA_contig2175 2175 THRCLA_contig2176 2176 THRCLA_contig2177 2177 THRCLA_contig2178 2178 THRCLA_contig2179 2179 THRCLA_contig2180 2180 THRCLA_contig2181 2181 THRCLA_contig2182 2182 THRCLA_contig2183 2183 THRCLA_contig2184 2184 THRCLA_contig2185 2185 THRCLA_contig2186 2186 THRCLA_contig2187 2187 THRCLA_contig2188 2188 THRCLA_contig2189 2189 THRCLA_contig2190 2190 THRCLA_contig2191 2191 THRCLA_contig2192 2192 THRCLA_contig2193 2193 THRCLA_contig2194 2194 THRCLA_contig2195 2195 THRCLA_contig2196 2196 THRCLA_contig2197 2197 THRCLA_contig2198 2198 THRCLA_contig2199 2199 THRCLA_contig2200 2200 THRCLA_contig2201 2201 THRCLA_contig2202 2202 THRCLA_contig2203 2203 THRCLA_contig2204 2204 THRCLA_contig2205 2205 THRCLA_contig2206 2206 THRCLA_contig2207 2207 THRCLA_contig2208 2208 THRCLA_contig2209 2209 THRCLA_contig2210 2210 THRCLA_contig2211 2211 THRCLA_contig2212 2212 THRCLA_contig2213 2213 THRCLA_contig2214 2214 THRCLA_contig2215 2215 THRCLA_contig2216 2216 THRCLA_contig2217 2217 THRCLA_contig2218 2218 THRCLA_contig2219 2219 THRCLA_contig2220 2220 THRCLA_contig2221 2221 THRCLA_contig2222 2222 THRCLA_contig2223 2223 THRCLA_contig2224 2224 THRCLA_contig2225 2225 THRCLA_contig2226 2226 THRCLA_contig2227 2227 THRCLA_contig2228 2228 THRCLA_contig2229 2229 THRCLA_contig2230 2230 THRCLA_contig2231 2231 THRCLA_contig2232 2232 THRCLA_contig2233 2233 THRCLA_contig2234 2234 THRCLA_contig2235 2235 THRCLA_contig2236 2236 THRCLA_contig2237 2237 THRCLA_contig2238 2238 THRCLA_contig2239 2239 THRCLA_contig2240 2240 THRCLA_contig2241 2241 THRCLA_contig2242 2242 THRCLA_contig2243 2243 THRCLA_contig2244 2244 THRCLA_contig2245 2245 THRCLA_contig2246 2246 THRCLA_contig2247 2247 THRCLA_contig2248 2248 THRCLA_contig2249 2249 THRCLA_contig2250 2250 THRCLA_contig2251 2251 THRCLA_contig2252 2252 THRCLA_contig2253 2253 THRCLA_contig2254 2254 THRCLA_contig2255 2255 THRCLA_contig2256 2256 THRCLA_contig2257 2257 THRCLA_contig2258 2258 THRCLA_contig2259 2259 THRCLA_contig2260 2260 THRCLA_contig2261 2261 THRCLA_contig2262 2262 THRCLA_contig2263 2263 THRCLA_contig2264 2264 THRCLA_contig2265 2265 THRCLA_contig2266 2266 THRCLA_contig2267 2267 THRCLA_contig2268 2268 THRCLA_contig2269 2269 THRCLA_contig2270 2270 THRCLA_contig2271 2271 THRCLA_contig2272 2272 THRCLA_contig2273 2273 THRCLA_contig2274 2274 THRCLA_contig2275 2275 THRCLA_contig2276 2276 THRCLA_contig2277 2277 THRCLA_contig2278 2278 THRCLA_contig2279 2279 THRCLA_contig2280 2280 THRCLA_contig2281 2281 THRCLA_contig2282 2282 THRCLA_contig2283 2283 THRCLA_contig2284 2284 THRCLA_contig2285 2285 THRCLA_contig2286 2286 THRCLA_contig2287 2287 THRCLA_contig2288 2288 THRCLA_contig2289 2289 THRCLA_contig2290 2290 THRCLA_contig2291 2291 THRCLA_contig2292 2292 THRCLA_contig2293 2293 THRCLA_contig2294 2294 THRCLA_contig2295 2295 THRCLA_contig2296 2296 THRCLA_contig2297 2297 THRCLA_contig2298 2298 THRCLA_contig2299 2299 THRCLA_contig2300 2300 THRCLA_contig2301 2301 THRCLA_contig2302 2302 THRCLA_contig2303 2303 THRCLA_contig2304 2304 THRCLA_contig2305 2305 THRCLA_contig2306 2306 THRCLA_contig2307 2307 THRCLA_contig2308 2308 THRCLA_contig2309 2309 THRCLA_contig2310 2310 THRCLA_contig2311 2311 THRCLA_contig2312 2312 THRCLA_contig2313 2313 THRCLA_contig2314 2314 THRCLA_contig2315 2315 THRCLA_contig2316 2316 THRCLA_contig2317 2317 THRCLA_contig2318 2318 THRCLA_contig2319 2319 THRCLA_contig2320 2320 THRCLA_contig2321 2321 THRCLA_contig2322 2322 THRCLA_contig2323 2323 THRCLA_contig2324 2324 THRCLA_contig2325 2325 THRCLA_contig2326 2326 THRCLA_contig2327 2327 THRCLA_contig2328 2328 THRCLA_contig2329 2329 THRCLA_contig2330 2330 THRCLA_contig2331 2331 THRCLA_contig2332 2332 THRCLA_contig2333 2333 THRCLA_contig2334 2334 THRCLA_contig2335 2335 THRCLA_contig2336 2336 THRCLA_contig2337 2337 THRCLA_contig2338 2338 THRCLA_contig2339 2339 THRCLA_contig2340 2340 THRCLA_contig2341 2341 THRCLA_contig2342 2342 THRCLA_contig2343 2343 THRCLA_contig2344 2344 THRCLA_contig2345 2345 THRCLA_contig2346 2346 THRCLA_contig2347 2347 THRCLA_contig2348 2348 THRCLA_contig2349 2349 THRCLA_contig2350 2350 THRCLA_contig2351 2351 THRCLA_contig2352 2352 THRCLA_contig2353 2353 THRCLA_contig2354 2354 THRCLA_contig2355 2355 THRCLA_contig2356 2356 THRCLA_contig2357 2357 THRCLA_contig2358 2358 THRCLA_contig2359 2359 THRCLA_contig2360 2360 THRCLA_contig2361 2361 THRCLA_contig2362 2362 THRCLA_contig2363 2363 THRCLA_contig2364 2364 THRCLA_contig2365 2365 THRCLA_contig2366 2366 THRCLA_contig2367 2367 THRCLA_contig2368 2368 THRCLA_contig2369 2369 THRCLA_contig2370 2370 THRCLA_contig2371 2371 THRCLA_contig2372 2372 THRCLA_contig2373 2373 THRCLA_contig2374 2374 THRCLA_contig2375 2375 THRCLA_contig2376 2376 THRCLA_contig2377 2377 THRCLA_contig2378 2378 THRCLA_contig2379 2379 THRCLA_contig2380 2380 THRCLA_contig2381 2381 THRCLA_contig2382 2382 THRCLA_contig2383 2383 THRCLA_contig2384 2384 THRCLA_contig2385 2385 THRCLA_contig2386 2386 THRCLA_contig2387 2387 THRCLA_contig2388 2388 THRCLA_contig2389 2389 THRCLA_contig2390 2390 THRCLA_contig2391 2391 THRCLA_contig2392 2392 THRCLA_contig2393 2393 THRCLA_contig2394 2394 THRCLA_contig2395 2395 THRCLA_contig2396 2396 THRCLA_contig2397 2397 THRCLA_contig2398 2398 THRCLA_contig2399 2399 THRCLA_contig2400 2400 THRCLA_contig2401 2401 THRCLA_contig2402 2402 THRCLA_contig2403 2403 THRCLA_contig2404 2404 THRCLA_contig2405 2405 THRCLA_contig2406 2406 THRCLA_contig2407 2407 THRCLA_contig2408 2408 THRCLA_contig2409 2409 THRCLA_contig2410 2410 THRCLA_contig2411 2411 THRCLA_contig2412 2412 THRCLA_contig2413 2413 THRCLA_contig2414 2414 THRCLA_contig2415 2415 THRCLA_contig2416 2416 THRCLA_contig2417 2417 THRCLA_contig2418 2418 THRCLA_contig2419 2419 THRCLA_contig2420 2420 THRCLA_contig2421 2421 THRCLA_contig2422 2422 THRCLA_contig2423 2423 THRCLA_contig2424 2424 THRCLA_contig2425 2425 THRCLA_contig2426 2426 THRCLA_contig2427 2427 THRCLA_contig2428 2428 THRCLA_contig2429 2429 THRCLA_contig2430 2430 THRCLA_contig2431 2431 THRCLA_contig2432 2432 THRCLA_contig2433 2433 THRCLA_contig2434 2434 THRCLA_contig2435 2435 THRCLA_contig2436 2436 THRCLA_contig2437 2437 THRCLA_contig2438 2438 THRCLA_contig2439 2439 THRCLA_contig2440 2440 THRCLA_contig2441 2441 THRCLA_contig2442 2442 THRCLA_contig2443 2443 THRCLA_contig2444 2444 THRCLA_contig2445 2445 THRCLA_contig2446 2446 THRCLA_contig2447 2447 THRCLA_contig2448 2448 THRCLA_contig2449 2449 THRCLA_contig2450 2450 THRCLA_contig2451 2451 THRCLA_contig2452 2452 THRCLA_contig2453 2453 THRCLA_contig2454 2454 THRCLA_contig2455 2455 THRCLA_contig2456 2456 THRCLA_contig2457 2457 THRCLA_contig2458 2458 THRCLA_contig2459 2459 THRCLA_contig2460 2460 THRCLA_contig2461 2461 THRCLA_contig2462 2462 THRCLA_contig2463 2463 THRCLA_contig2464 2464 THRCLA_contig2465 2465 THRCLA_contig2466 2466 THRCLA_contig2467 2467 THRCLA_contig2468 2468 THRCLA_contig2469 2469 THRCLA_contig2470 2470 THRCLA_contig2471 2471 THRCLA_contig2472 2472 THRCLA_contig2473 2473 THRCLA_contig2474 2474 THRCLA_contig2475 2475 THRCLA_contig2476 2476 THRCLA_contig2477 2477 THRCLA_contig2478 2478 THRCLA_contig2479 2479 THRCLA_contig2480 2480 THRCLA_contig2481 2481 THRCLA_contig2482 2482 THRCLA_contig2483 2483 THRCLA_contig2484 2484 THRCLA_contig2485 2485 THRCLA_contig2486 2486 THRCLA_contig2487 2487 THRCLA_contig2488 2488 THRCLA_contig2489 2489 THRCLA_contig2490 2490 THRCLA_contig2491 2491 THRCLA_contig2492 2492 THRCLA_contig2493 2493 THRCLA_contig2494 2494 THRCLA_contig2495 2495 THRCLA_contig2496 2496 THRCLA_contig2497 2497 THRCLA_contig2498 2498 THRCLA_contig2499 2499 THRCLA_contig2500 2500 THRCLA_contig2501 2501 THRCLA_contig2502 2502 THRCLA_contig2503 2503 THRCLA_contig2504 2504 THRCLA_contig2505 2505 THRCLA_contig2506 2506 THRCLA_contig2507 2507 THRCLA_contig2508 2508 THRCLA_contig2509 2509 THRCLA_contig2510 2510 THRCLA_contig2511 2511 THRCLA_contig2512 2512 THRCLA_contig2513 2513 THRCLA_contig2514 2514 THRCLA_contig2515 2515 THRCLA_contig2516 2516 THRCLA_contig2517 2517 THRCLA_contig2518 2518 THRCLA_contig2519 2519 THRCLA_contig2520 2520 THRCLA_contig2521 2521 THRCLA_contig2522 2522 THRCLA_contig2523 2523 THRCLA_contig2524 2524 THRCLA_contig2525 2525 THRCLA_contig2526 2526 THRCLA_contig2527 2527 THRCLA_contig2528 2528 THRCLA_contig2529 2529 THRCLA_contig2530 2530 THRCLA_contig2531 2531 THRCLA_contig2532 2532 THRCLA_contig2533 2533 THRCLA_contig2534 2534 THRCLA_contig2535 2535 THRCLA_contig2536 2536 THRCLA_contig2537 2537 THRCLA_contig2538 2538 THRCLA_contig2539 2539 THRCLA_contig2540 2540 THRCLA_contig2541 2541 THRCLA_contig2542 2542 THRCLA_contig2543 2543 THRCLA_contig2544 2544 THRCLA_contig2545 2545 THRCLA_contig2546 2546 THRCLA_contig2547 2547 THRCLA_contig2548 2548 THRCLA_contig2549 2549 THRCLA_contig2550 2550 THRCLA_contig2551 2551 THRCLA_contig2552 2552 THRCLA_contig2553 2553 THRCLA_contig2554 2554 THRCLA_contig2555 2555 THRCLA_contig2556 2556 THRCLA_contig2557 2557 THRCLA_contig2558 2558 THRCLA_contig2559 2559 THRCLA_contig2560 2560 THRCLA_contig2561 2561 THRCLA_contig2562 2562 THRCLA_contig2563 2563 THRCLA_contig2564 2564 THRCLA_contig2565 2565 THRCLA_contig2566 2566 THRCLA_contig2567 2567 THRCLA_contig2568 2568 THRCLA_contig2569 2569 THRCLA_contig2570 2570 THRCLA_contig2571 2571 THRCLA_contig2572 2572 THRCLA_contig2573 2573 THRCLA_contig2574 2574 THRCLA_contig2575 2575 THRCLA_contig2576 2576 THRCLA_contig2577 2577 THRCLA_contig2578 2578 THRCLA_contig2579 2579 THRCLA_contig2580 2580 THRCLA_contig2581 2581 THRCLA_contig2582 2582 THRCLA_contig2583 2583 THRCLA_contig2584 2584 THRCLA_contig2585 2585 THRCLA_contig2586 2586 THRCLA_contig2587 2587 THRCLA_contig2588 2588 THRCLA_contig2589 2589 THRCLA_contig2590 2590 THRCLA_contig2591 2591 THRCLA_contig2592 2592 THRCLA_contig2593 2593 THRCLA_contig2594 2594 THRCLA_contig2595 2595 THRCLA_contig2596 2596 THRCLA_contig2597 2597 THRCLA_contig2598 2598 THRCLA_contig2599 2599 THRCLA_contig2600 2600 THRCLA_contig2601 2601 THRCLA_contig2602 2602 THRCLA_contig2603 2603 THRCLA_contig2604 2604 THRCLA_contig2605 2605 THRCLA_contig2606 2606 THRCLA_contig2607 2607 THRCLA_contig2608 2608 THRCLA_contig2609 2609 THRCLA_contig2610 2610 THRCLA_contig2611 2611 THRCLA_contig2612 2612 THRCLA_contig2613 2613 THRCLA_contig2614 2614 THRCLA_contig2615 2615 THRCLA_contig2616 2616 THRCLA_contig2617 2617 THRCLA_contig2618 2618 THRCLA_contig2619 2619 THRCLA_contig2620 2620 THRCLA_contig2621 2621 THRCLA_contig2622 2622 THRCLA_contig2623 2623 THRCLA_contig2624 2624 THRCLA_contig2625 2625 THRCLA_contig2626 2626 THRCLA_contig2627 2627 THRCLA_contig2628 2628 THRCLA_contig2629 2629 THRCLA_contig2630 2630 THRCLA_contig2631 2631 THRCLA_contig2632 2632 THRCLA_contig2633 2633 THRCLA_contig2634 2634 THRCLA_contig2635 2635 THRCLA_contig2636 2636 THRCLA_contig2637 2637 THRCLA_contig2638 2638 THRCLA_contig2639 2639 THRCLA_contig2640 2640 THRCLA_contig2641 2641 THRCLA_contig2642 2642 THRCLA_contig2643 2643 THRCLA_contig2644 2644 THRCLA_contig2645 2645 THRCLA_contig2646 2646 THRCLA_contig2647 2647 THRCLA_contig2648 2648 THRCLA_contig2649 2649 THRCLA_contig2650 2650 THRCLA_contig2651 2651 THRCLA_contig2652 2652 THRCLA_contig2653 2653 THRCLA_contig2654 2654 THRCLA_contig2655 2655 THRCLA_contig2656 2656 THRCLA_contig2657 2657 THRCLA_contig2658 2658 THRCLA_contig2659 2659 THRCLA_contig2660 2660 THRCLA_contig2661 2661 THRCLA_contig2662 2662 THRCLA_contig2663 2663 THRCLA_contig2664 2664 THRCLA_contig2665 2665 THRCLA_contig2666 2666 THRCLA_contig2667 2667 THRCLA_contig2668 2668 THRCLA_contig2669 2669 THRCLA_contig2670 2670 THRCLA_contig2671 2671 THRCLA_contig2672 2672 THRCLA_contig2673 2673 THRCLA_contig2674 2674 THRCLA_contig2675 2675 THRCLA_contig2676 2676 THRCLA_contig2677 2677 THRCLA_contig2678 2678 THRCLA_contig2679 2679 THRCLA_contig2680 2680 THRCLA_contig2681 2681 THRCLA_contig2682 2682 THRCLA_contig2683 2683 THRCLA_contig2684 2684 THRCLA_contig2685 2685 THRCLA_contig2686 2686 THRCLA_contig2687 2687 THRCLA_contig2688 2688 THRCLA_contig2689 2689 THRCLA_contig2690 2690 THRCLA_contig2691 2691 THRCLA_contig2692 2692 THRCLA_contig2693 2693 THRCLA_contig2694 2694 THRCLA_contig2695 2695 THRCLA_contig2696 2696 THRCLA_contig2697 2697 THRCLA_contig2698 2698 THRCLA_contig2699 2699 THRCLA_contig2700 2700 THRCLA_contig2701 2701 THRCLA_contig2702 2702 THRCLA_contig2703 2703 THRCLA_contig2704 2704 THRCLA_contig2705 2705 THRCLA_contig2706 2706 THRCLA_contig2707 2707 THRCLA_contig2708 2708 THRCLA_contig2709 2709 THRCLA_contig2710 2710 THRCLA_contig2711 2711 THRCLA_contig2712 2712 THRCLA_contig2713 2713 THRCLA_contig2714 2714 THRCLA_contig2715 2715 THRCLA_contig2716 2716 THRCLA_contig2717 2717 THRCLA_contig2718 2718 THRCLA_contig2719 2719 THRCLA_contig2720 2720 THRCLA_contig2721 2721 THRCLA_contig2722 2722 THRCLA_contig2723 2723 THRCLA_contig2724 2724 THRCLA_contig2725 2725 THRCLA_contig2726 2726 THRCLA_contig2727 2727 THRCLA_contig2728 2728 THRCLA_contig2729 2729 THRCLA_contig2730 2730 THRCLA_contig2731 2731 THRCLA_contig2732 2732 THRCLA_contig2733 2733 THRCLA_contig2734 2734 THRCLA_contig2735 2735 THRCLA_contig2736 2736 THRCLA_contig2737 2737 THRCLA_contig2738 2738 THRCLA_contig2739 2739 THRCLA_contig2740 2740 THRCLA_contig2741 2741 THRCLA_contig2742 2742 THRCLA_contig2743 2743 THRCLA_contig2744 2744 THRCLA_contig2745 2745 THRCLA_contig2746 2746 THRCLA_contig2747 2747 THRCLA_contig2748 2748 THRCLA_contig2749 2749 THRCLA_contig2750 2750 THRCLA_contig2751 2751 THRCLA_contig2752 2752 THRCLA_contig2753 2753 THRCLA_contig2754 2754 THRCLA_contig2755 2755 THRCLA_contig2756 2756 THRCLA_contig2757 2757 THRCLA_contig2758 2758 THRCLA_contig2759 2759 THRCLA_contig2760 2760 THRCLA_contig2761 2761 THRCLA_contig2762 2762 THRCLA_contig2763 2763 THRCLA_contig2764 2764 THRCLA_contig2765 2765 THRCLA_contig2766 2766 THRCLA_contig2767 2767 THRCLA_contig2768 2768 THRCLA_contig2769 2769 THRCLA_contig2770 2770 THRCLA_contig2771 2771 THRCLA_contig2772 2772 THRCLA_contig2773 2773 THRCLA_contig2774 2774 THRCLA_contig2775 2775 THRCLA_contig2776 2776 THRCLA_contig2777 2777 THRCLA_contig2778 2778 THRCLA_contig2779 2779 THRCLA_contig2780 2780 THRCLA_contig2781 2781 THRCLA_contig2782 2782 THRCLA_contig2783 2783 THRCLA_contig2784 2784 THRCLA_contig2785 2785 THRCLA_contig2786 2786 THRCLA_contig2787 2787 THRCLA_contig2788 2788 THRCLA_contig2789 2789 THRCLA_contig2790 2790 THRCLA_contig2791 2791 THRCLA_contig2792 2792 THRCLA_contig2793 2793 THRCLA_contig2794 2794 THRCLA_contig2795 2795 THRCLA_contig2796 2796 THRCLA_contig2797 2797 THRCLA_contig2798 2798 THRCLA_contig2799 2799 THRCLA_contig2800 2800 THRCLA_contig2801 2801 THRCLA_contig2802 2802 THRCLA_contig2803 2803 THRCLA_contig2804 2804 THRCLA_contig2805 2805 THRCLA_contig2806 2806 THRCLA_contig2807 2807 THRCLA_contig2808 2808 THRCLA_contig2809 2809 THRCLA_contig2810 2810 THRCLA_contig2811 2811 THRCLA_contig2812 2812 THRCLA_contig2813 2813 THRCLA_contig2814 2814 THRCLA_contig2815 2815 THRCLA_contig2816 2816 THRCLA_contig2817 2817 THRCLA_contig2818 2818 THRCLA_contig2819 2819 THRCLA_contig2820 2820 THRCLA_contig2821 2821 THRCLA_contig2822 2822 THRCLA_contig2823 2823 THRCLA_contig2824 2824 THRCLA_contig2825 2825 THRCLA_contig2826 2826 THRCLA_contig2827 2827 THRCLA_contig2828 2828 THRCLA_contig2829 2829 THRCLA_contig2830 2830 THRCLA_contig2831 2831 THRCLA_contig2832 2832 THRCLA_contig2833 2833 THRCLA_contig2834 2834 THRCLA_contig2835 2835 THRCLA_contig2836 2836 THRCLA_contig2837 2837 THRCLA_contig2838 2838 THRCLA_contig2839 2839 THRCLA_contig2840 2840 THRCLA_contig2841 2841 THRCLA_contig2842 2842 THRCLA_contig2843 2843 THRCLA_contig2844 2844 THRCLA_contig2845 2845 THRCLA_contig2846 2846 THRCLA_contig2847 2847 THRCLA_contig2848 2848 THRCLA_contig2849 2849 THRCLA_contig2850 2850 THRCLA_contig2851 2851 THRCLA_contig2852 2852 THRCLA_contig2853 2853 THRCLA_contig2854 2854 THRCLA_contig2855 2855 THRCLA_contig2856 2856 THRCLA_contig2857 2857 THRCLA_contig2858 2858 THRCLA_contig2859 2859 THRCLA_contig2860 2860 THRCLA_contig2861 2861 THRCLA_contig2862 2862 THRCLA_contig2863 2863 THRCLA_contig2864 2864 THRCLA_contig2865 2865 THRCLA_contig2866 2866 THRCLA_contig2867 2867 THRCLA_contig2868 2868 THRCLA_contig2869 2869 THRCLA_contig2870 2870 THRCLA_contig2871 2871 THRCLA_contig2872 2872 THRCLA_contig2873 2873 THRCLA_contig2874 2874 THRCLA_contig2875 2875 THRCLA_contig2876 2876 THRCLA_contig2877 2877 THRCLA_contig2878 2878 THRCLA_contig2879 2879 THRCLA_contig2880 2880 THRCLA_contig2881 2881 THRCLA_contig2882 2882 THRCLA_contig2883 2883 THRCLA_contig2884 2884 THRCLA_contig2885 2885 THRCLA_contig2886 2886 THRCLA_contig2887 2887 THRCLA_contig2888 2888 THRCLA_contig2889 2889 THRCLA_contig2890 2890 THRCLA_contig2891 2891 THRCLA_contig2892 2892 THRCLA_contig2893 2893 THRCLA_contig2894 2894 THRCLA_contig2895 2895 THRCLA_contig2896 2896 THRCLA_contig2897 2897 THRCLA_contig2898 2898 THRCLA_contig2899 2899 THRCLA_contig2900 2900 THRCLA_contig2901 2901 THRCLA_contig2902 2902 THRCLA_contig2903 2903 THRCLA_contig2904 2904 THRCLA_contig2905 2905 THRCLA_contig2906 2906 THRCLA_contig2907 2907 THRCLA_contig2908 2908 THRCLA_contig2909 2909 THRCLA_contig2910 2910 THRCLA_contig2911 2911 THRCLA_contig2912 2912 THRCLA_contig2913 2913 THRCLA_contig2914 2914 THRCLA_contig2915 2915 THRCLA_contig2916 2916 THRCLA_contig2917 2917 THRCLA_contig2918 2918 THRCLA_contig2919 2919 THRCLA_contig2920 2920 THRCLA_contig2921 2921 THRCLA_contig2922 2922 THRCLA_contig2923 2923 THRCLA_contig2924 2924 THRCLA_contig2925 2925 THRCLA_contig2926 2926 THRCLA_contig2927 2927 THRCLA_contig2928 2928 THRCLA_contig2929 2929 THRCLA_contig2930 2930 THRCLA_contig2931 2931 THRCLA_contig2932 2932 THRCLA_contig2933 2933 THRCLA_contig2934 2934 THRCLA_contig2935 2935 THRCLA_contig2936 2936 THRCLA_contig2937 2937 THRCLA_contig2938 2938 THRCLA_contig2939 2939 THRCLA_contig2940 2940 THRCLA_contig2941 2941 THRCLA_contig2942 2942 THRCLA_contig2943 2943 THRCLA_contig2944 2944 THRCLA_contig2945 2945 THRCLA_contig2946 2946 THRCLA_contig2947 2947 THRCLA_contig2948 2948 THRCLA_contig2949 2949 THRCLA_contig2950 2950 THRCLA_contig2951 2951 THRCLA_contig2952 2952 THRCLA_contig2953 2953 THRCLA_contig2954 2954 THRCLA_contig2955 2955 THRCLA_contig2956 2956 THRCLA_contig2957 2957 THRCLA_contig2958 2958 THRCLA_contig2959 2959 THRCLA_contig2960 2960 THRCLA_contig2961 2961 THRCLA_contig2962 2962 THRCLA_contig2963 2963 THRCLA_contig2964 2964 THRCLA_contig2965 2965 THRCLA_contig2966 2966 THRCLA_contig2967 2967 THRCLA_contig2968 2968 THRCLA_contig2969 2969 THRCLA_contig2970 2970 THRCLA_contig2971 2971 THRCLA_contig2972 2972 THRCLA_contig2973 2973 THRCLA_contig2974 2974 THRCLA_contig2975 2975 THRCLA_contig2976 2976 THRCLA_contig2977 2977 THRCLA_contig2978 2978 THRCLA_contig2979 2979 THRCLA_contig2980 2980 THRCLA_contig2981 2981 THRCLA_contig2982 2982 THRCLA_contig2983 2983 THRCLA_contig2984 2984 THRCLA_contig2985 2985 THRCLA_contig2986 2986 THRCLA_contig2987 2987 THRCLA_contig2988 2988 THRCLA_contig2989 2989 THRCLA_contig2990 2990 THRCLA_contig2991 2991 THRCLA_contig2992 2992 THRCLA_contig2993 2993 THRCLA_contig2994 2994 THRCLA_contig2995 2995 THRCLA_contig2996 2996 THRCLA_contig2997 2997 THRCLA_contig2998 2998 THRCLA_contig2999 2999 THRCLA_contig3000 3000 THRCLA_contig3001 3001 THRCLA_contig3002 3002 THRCLA_contig3003 3003 THRCLA_contig3004 3004 THRCLA_contig3005 3005 THRCLA_contig3006 3006 THRCLA_contig3007 3007 THRCLA_contig3008 3008 THRCLA_contig3009 3009 THRCLA_contig3010 3010 THRCLA_contig3011 3011 THRCLA_contig3012 3012 THRCLA_contig3013 3013 THRCLA_contig3014 3014 THRCLA_contig3015 3015 THRCLA_contig3016 3016 THRCLA_contig3017 3017 THRCLA_contig3018 3018 THRCLA_contig3019 3019 THRCLA_contig3020 3020 THRCLA_contig3021 3021 THRCLA_contig3022 3022 THRCLA_contig3023 3023 THRCLA_contig3024 3024 THRCLA_contig3025 3025 THRCLA_contig3026 3026 THRCLA_contig3027 3027 THRCLA_contig3028 3028 THRCLA_contig3029 3029 THRCLA_contig3030 3030 THRCLA_contig3031 3031 THRCLA_contig3032 3032 THRCLA_contig3033 3033 THRCLA_contig3034 3034 THRCLA_contig3035 3035 THRCLA_contig3036 3036 THRCLA_contig3037 3037 THRCLA_contig3038 3038 THRCLA_contig3039 3039 THRCLA_contig3040 3040 THRCLA_contig3041 3041 THRCLA_contig3042 3042 THRCLA_contig3043 3043 THRCLA_contig3044 3044 THRCLA_contig3045 3045 THRCLA_contig3046 3046 THRCLA_contig3047 3047 THRCLA_contig3048 3048 THRCLA_contig3049 3049 THRCLA_contig3050 3050 THRCLA_contig3051 3051 THRCLA_contig3052 3052 THRCLA_contig3053 3053 THRCLA_contig3054 3054 THRCLA_contig3055 3055 THRCLA_contig3056 3056 THRCLA_contig3057 3057 THRCLA_contig3058 3058 THRCLA_contig3059 3059 THRCLA_contig3060 3060 THRCLA_contig3061 3061 THRCLA_contig3062 3062 THRCLA_contig3063 3063 THRCLA_contig3064 3064 THRCLA_contig3065 3065 THRCLA_contig3066 3066 THRCLA_contig3067 3067 THRCLA_contig3068 3068 THRCLA_contig3069 3069 THRCLA_contig3070 3070 THRCLA_contig3071 3071 THRCLA_contig3072 3072 THRCLA_contig3073 3073 THRCLA_contig3074 3074 THRCLA_contig3075 3075 THRCLA_contig3076 3076 THRCLA_contig3077 3077 THRCLA_contig3078 3078 THRCLA_contig3079 3079 THRCLA_contig3080 3080 THRCLA_contig3081 3081 THRCLA_contig3082 3082 THRCLA_contig3083 3083 THRCLA_contig3084 3084 THRCLA_contig3085 3085 THRCLA_contig3086 3086 THRCLA_contig3087 3087 THRCLA_contig3088 3088 THRCLA_contig3089 3089 THRCLA_contig3090 3090 THRCLA_contig3091 3091 THRCLA_contig3092 3092 THRCLA_contig3093 3093 THRCLA_contig3094 3094 THRCLA_contig3095 3095 THRCLA_contig3096 3096 THRCLA_contig3097 3097 THRCLA_contig3098 3098 THRCLA_contig3099 3099 THRCLA_contig3100 3100 THRCLA_contig3101 3101 THRCLA_contig3102 3102 THRCLA_contig3103 3103 THRCLA_contig3104 3104 THRCLA_contig3105 3105 THRCLA_contig3106 3106 THRCLA_contig3107 3107 THRCLA_contig3108 3108 THRCLA_contig3109 3109 THRCLA_contig3110 3110 THRCLA_contig3111 3111 THRCLA_contig3112 3112 THRCLA_contig3113 3113 THRCLA_contig3114 3114 THRCLA_contig3115 3115 THRCLA_contig3116 3116 THRCLA_contig3117 3117 THRCLA_contig3118 3118 THRCLA_contig3119 3119 THRCLA_contig3120 3120 THRCLA_contig3121 3121 THRCLA_contig3122 3122 THRCLA_contig3123 3123 THRCLA_contig3124 3124 THRCLA_contig3125 3125 THRCLA_contig3126 3126 THRCLA_contig3127 3127 THRCLA_contig3128 3128 THRCLA_contig3129 3129 THRCLA_contig3130 3130 THRCLA_contig3131 3131 THRCLA_contig3132 3132 THRCLA_contig3133 3133 THRCLA_contig3134 3134 THRCLA_contig3135 3135 THRCLA_contig3136 3136 THRCLA_contig3137 3137 THRCLA_contig3138 3138 THRCLA_contig3139 3139 THRCLA_contig3140 3140 THRCLA_contig3141 3141 THRCLA_contig3142 3142 THRCLA_contig3143 3143 THRCLA_contig3144 3144 THRCLA_contig3145 3145 THRCLA_contig3146 3146 THRCLA_contig3147 3147 THRCLA_contig3148 3148 THRCLA_contig3149 3149 THRCLA_contig3150 3150 THRCLA_contig3151 3151 THRCLA_contig3152 3152 THRCLA_contig3153 3153 THRCLA_contig3154 3154 THRCLA_contig3155 3155 THRCLA_contig3156 3156 THRCLA_contig3157 3157 THRCLA_contig3158 3158 THRCLA_contig3159 3159 THRCLA_contig3160 3160 THRCLA_contig3161 3161 THRCLA_contig3162 3162 THRCLA_contig3163 3163 THRCLA_contig3164 3164 THRCLA_contig3165 3165 THRCLA_contig3166 3166 THRCLA_contig3167 3167 THRCLA_contig3168 3168 THRCLA_contig3169 3169 THRCLA_contig3170 3170 THRCLA_contig3171 3171 THRCLA_contig3172 3172 THRCLA_contig3173 3173 THRCLA_contig3174 3174 THRCLA_contig3175 3175 THRCLA_contig3176 3176 THRCLA_contig3177 3177 THRCLA_contig3178 3178 THRCLA_contig3179 3179 THRCLA_contig3180 3180 THRCLA_contig3181 3181 THRCLA_contig3182 3182 THRCLA_contig3183 3183 THRCLA_contig3184 3184 THRCLA_contig3185 3185 THRCLA_contig3186 3186 THRCLA_contig3187 3187 THRCLA_contig3188 3188 THRCLA_contig3189 3189 THRCLA_contig3190 3190 THRCLA_contig3191 3191 THRCLA_contig3192 3192 THRCLA_contig3193 3193 THRCLA_contig3194 3194 THRCLA_contig3195 3195 THRCLA_contig3196 3196 THRCLA_contig3197 3197 THRCLA_contig3198 3198 THRCLA_contig3199 3199 THRCLA_contig3200 3200 THRCLA_contig3201 3201 THRCLA_contig3202 3202 THRCLA_contig3203 3203 THRCLA_contig3204 3204 THRCLA_contig3205 3205 THRCLA_contig3206 3206 THRCLA_contig3207 3207 THRCLA_contig3208 3208 THRCLA_contig3209 3209 THRCLA_contig3210 3210 THRCLA_contig3211 3211 THRCLA_contig3212 3212 THRCLA_contig3213 3213 THRCLA_contig3214 3214 THRCLA_contig3215 3215 THRCLA_contig3216 3216 THRCLA_contig3217 3217 THRCLA_contig3218 3218 THRCLA_contig3219 3219 THRCLA_contig3220 3220 THRCLA_contig3221 3221 THRCLA_contig3222 3222 THRCLA_contig3223 3223 THRCLA_contig3224 3224 THRCLA_contig3225 3225 THRCLA_contig3226 3226 THRCLA_contig3227 3227 THRCLA_contig3228 3228 THRCLA_contig3229 3229 THRCLA_contig3230 3230 THRCLA_contig3231 3231 THRCLA_contig3232 3232 THRCLA_contig3233 3233 THRCLA_contig3234 3234 THRCLA_contig3235 3235 THRCLA_contig3236 3236 THRCLA_contig3237 3237 THRCLA_contig3238 3238 THRCLA_contig3239 3239 THRCLA_contig3240 3240 THRCLA_contig3241 3241 THRCLA_contig3242 3242 THRCLA_contig3243 3243 THRCLA_contig3244 3244 THRCLA_contig3245 3245 THRCLA_contig3246 3246 THRCLA_contig3247 3247 THRCLA_contig3248 3248 THRCLA_contig3249 3249 THRCLA_contig3250 3250 THRCLA_contig3251 3251 THRCLA_contig3252 3252 THRCLA_contig3253 3253 THRCLA_contig3254 3254 THRCLA_contig3255 3255 THRCLA_contig3256 3256 THRCLA_contig3257 3257 THRCLA_contig3258 3258 THRCLA_contig3259 3259 THRCLA_contig3260 3260 THRCLA_contig3261 3261 THRCLA_contig3262 3262 THRCLA_contig3263 3263 THRCLA_contig3264 3264 THRCLA_contig3265 3265 THRCLA_contig3266 3266 THRCLA_contig3267 3267 THRCLA_contig3268 3268 THRCLA_contig3269 3269 THRCLA_contig3270 3270 THRCLA_contig3271 3271 THRCLA_contig3272 3272 THRCLA_contig3273 3273 THRCLA_contig3274 3274 THRCLA_contig3275 3275 THRCLA_contig3276 3276 THRCLA_contig3277 3277 THRCLA_contig3278 3278 THRCLA_contig3279 3279 THRCLA_contig3280 3280 THRCLA_contig3281 3281 THRCLA_contig3282 3282 THRCLA_contig3283 3283 THRCLA_contig3284 3284 THRCLA_contig3285 3285 THRCLA_contig3286 3286 THRCLA_contig3287 3287 THRCLA_contig3288 3288 THRCLA_contig3289 3289 THRCLA_contig3290 3290 THRCLA_contig3291 3291 THRCLA_contig3292 3292 THRCLA_contig3293 3293 THRCLA_contig3294 3294 THRCLA_contig3295 3295 THRCLA_contig3296 3296 THRCLA_contig3297 3297 THRCLA_contig3298 3298 THRCLA_contig3299 3299 THRCLA_contig3300 3300 THRCLA_contig3301 3301 THRCLA_contig3302 3302 THRCLA_contig3303 3303 THRCLA_contig3304 3304 THRCLA_contig3305 3305 THRCLA_contig3306 3306 THRCLA_contig3307 3307 THRCLA_contig3308 3308 THRCLA_contig3309 3309 THRCLA_contig3310 3310 THRCLA_contig3311 3311 THRCLA_contig3312 3312 THRCLA_contig3313 3313 THRCLA_contig3314 3314 THRCLA_contig3315 3315 THRCLA_contig3316 3316 THRCLA_contig3317 3317 THRCLA_contig3318 3318 THRCLA_contig3319 3319 THRCLA_contig3320 3320 THRCLA_contig3321 3321 THRCLA_contig3322 3322 THRCLA_contig3323 3323 THRCLA_contig3324 3324 THRCLA_contig3325 3325 THRCLA_contig3326 3326 THRCLA_contig3327 3327 THRCLA_contig3328 3328 THRCLA_contig3329 3329 THRCLA_contig3330 3330 THRCLA_contig3331 3331 THRCLA_contig3332 3332 THRCLA_contig3333 3333 THRCLA_contig3334 3334 THRCLA_contig3335 3335 THRCLA_contig3336 3336 THRCLA_contig3337 3337 THRCLA_contig3338 3338 THRCLA_contig3339 3339 THRCLA_contig3340 3340 THRCLA_contig3341 3341 THRCLA_contig3342 3342 THRCLA_contig3343 3343 THRCLA_contig3344 3344 THRCLA_contig3345 3345 THRCLA_contig3346 3346 THRCLA_contig3347 3347 THRCLA_contig3348 3348 THRCLA_contig3349 3349 THRCLA_contig3350 3350 THRCLA_contig3351 3351 THRCLA_contig3352 3352 THRCLA_contig3353 3353 THRCLA_contig3354 3354 THRCLA_contig3355 3355 THRCLA_contig3356 3356 THRCLA_contig3357 3357 THRCLA_contig3358 3358 THRCLA_contig3359 3359 THRCLA_contig3360 3360 THRCLA_contig3361 3361 THRCLA_contig3362 3362 THRCLA_contig3363 3363 THRCLA_contig3364 3364 THRCLA_contig3365 3365 THRCLA_contig3366 3366 THRCLA_contig3367 3367 THRCLA_contig3368 3368 THRCLA_contig3369 3369 THRCLA_contig3370 3370 THRCLA_contig3371 3371 THRCLA_contig3372 3372 THRCLA_contig3373 3373 THRCLA_contig3374 3374 THRCLA_contig3375 3375 THRCLA_contig3376 3376 THRCLA_contig3377 3377 THRCLA_contig3378 3378 THRCLA_contig3379 3379 THRCLA_contig3380 3380 THRCLA_contig3381 3381 THRCLA_contig3382 3382 THRCLA_contig3383 3383 THRCLA_contig3384 3384 THRCLA_contig3385 3385 THRCLA_contig3386 3386 THRCLA_contig3387 3387 THRCLA_contig3388 3388 THRCLA_contig3389 3389 THRCLA_contig3390 3390 THRCLA_contig3391 3391 THRCLA_contig3392 3392 THRCLA_contig3393 3393 THRCLA_contig3394 3394 THRCLA_contig3395 3395 THRCLA_contig3396 3396 THRCLA_contig3397 3397 THRCLA_contig3398 3398 THRCLA_contig3399 3399 THRCLA_contig3400 3400 THRCLA_contig3401 3401 THRCLA_contig3402 3402 THRCLA_contig3403 3403 THRCLA_contig3404 3404 THRCLA_contig3405 3405 THRCLA_contig3406 3406 THRCLA_contig3407 3407 THRCLA_contig3408 3408 THRCLA_contig3409 3409 THRCLA_contig3410 3410 THRCLA_contig3411 3411 THRCLA_contig3412 3412 THRCLA_contig3413 3413 THRCLA_contig3414 3414 THRCLA_contig3415 3415 THRCLA_contig3416 3416 THRCLA_contig3417 3417 THRCLA_contig3418 3418 THRCLA_contig3419 3419 THRCLA_contig3420 3420 THRCLA_contig3421 3421 THRCLA_contig3422 3422 THRCLA_contig3423 3423 THRCLA_contig3424 3424 THRCLA_contig3425 3425 THRCLA_contig3426 3426 THRCLA_contig3427 3427 THRCLA_contig3428 3428 THRCLA_contig3429 3429 THRCLA_contig3430 3430 THRCLA_contig3431 3431 THRCLA_contig3432 3432 THRCLA_contig3433 3433 THRCLA_contig3434 3434 THRCLA_contig3435 3435 THRCLA_contig3436 3436 THRCLA_contig3437 3437 THRCLA_contig3438 3438 THRCLA_contig3439 3439 THRCLA_contig3440 3440 THRCLA_contig3441 3441 THRCLA_contig3442 3442 THRCLA_contig3443 3443 THRCLA_contig3444 3444 THRCLA_contig3445 3445 THRCLA_contig3446 3446 THRCLA_contig3447 3447 THRCLA_contig3448 3448 THRCLA_contig3449 3449 THRCLA_contig3450 3450 THRCLA_contig3451 3451 THRCLA_contig3452 3452 THRCLA_contig3453 3453 THRCLA_contig3454 3454 THRCLA_contig3455 3455 THRCLA_contig3456 3456 THRCLA_contig3457 3457 THRCLA_contig3458 3458 THRCLA_contig3459 3459 THRCLA_contig3460 3460 THRCLA_contig3461 3461 THRCLA_contig3462 3462 THRCLA_contig3463 3463 THRCLA_contig3464 3464 THRCLA_contig3465 3465 THRCLA_contig3466 3466 THRCLA_contig3467 3467 THRCLA_contig3468 3468 THRCLA_contig3469 3469 THRCLA_contig3470 3470 THRCLA_contig3471 3471 THRCLA_contig3472 3472 THRCLA_contig3473 3473 THRCLA_contig3474 3474 THRCLA_contig3475 3475 THRCLA_contig3476 3476 THRCLA_contig3477 3477 THRCLA_contig3478 3478 THRCLA_contig3479 3479 THRCLA_contig3480 3480 THRCLA_contig3481 3481 THRCLA_contig3482 3482 THRCLA_contig3483 3483 THRCLA_contig3484 3484 THRCLA_contig3485 3485 THRCLA_contig3486 3486 THRCLA_contig3487 3487 THRCLA_contig3488 3488 THRCLA_contig3489 3489 THRCLA_contig3490 3490 THRCLA_contig3491 3491 THRCLA_contig3492 3492 THRCLA_contig3493 3493 THRCLA_contig3494 3494 THRCLA_contig3495 3495 THRCLA_contig3496 3496 THRCLA_contig3497 3497 THRCLA_contig3498 3498 THRCLA_contig3499 3499 THRCLA_contig3500 3500 THRCLA_contig3501 3501 THRCLA_contig3502 3502 THRCLA_contig3503 3503 THRCLA_contig3504 3504 THRCLA_contig3505 3505 THRCLA_contig3506 3506 THRCLA_contig3507 3507 THRCLA_contig3508 3508 THRCLA_contig3509 3509 THRCLA_contig3510 3510 THRCLA_contig3511 3511 THRCLA_contig3512 3512 THRCLA_contig3513 3513 THRCLA_contig3514 3514 THRCLA_contig3515 3515 THRCLA_contig3516 3516 THRCLA_contig3517 3517 THRCLA_contig3518 3518 THRCLA_contig3519 3519 THRCLA_contig3520 3520 THRCLA_contig3521 3521 THRCLA_contig3522 3522 THRCLA_contig3523 3523 THRCLA_contig3524 3524 THRCLA_contig3525 3525 THRCLA_contig3526 3526 THRCLA_contig3527 3527 THRCLA_contig3528 3528 THRCLA_contig3529 3529 THRCLA_contig3530 3530 THRCLA_contig3531 3531 THRCLA_contig3532 3532 THRCLA_contig3533 3533 THRCLA_contig3534 3534 THRCLA_contig3535 3535 THRCLA_contig3536 3536 THRCLA_contig3537 3537 THRCLA_contig3538 3538 THRCLA_contig3539 3539 THRCLA_contig3540 3540 THRCLA_contig3541 3541 THRCLA_contig3542 3542 THRCLA_contig3543 3543 THRCLA_contig3544 3544 THRCLA_contig3545 3545 THRCLA_contig3546 3546 THRCLA_contig3547 3547 THRCLA_contig3548 3548 THRCLA_contig3549 3549 THRCLA_contig3550 3550 THRCLA_contig3551 3551 THRCLA_contig3552 3552 THRCLA_contig3553 3553 THRCLA_contig3554 3554 THRCLA_contig3555 3555 THRCLA_contig3556 3556 THRCLA_contig3557 3557 THRCLA_contig3558 3558 THRCLA_contig3559 3559 THRCLA_contig3560 3560 THRCLA_contig3561 3561 THRCLA_contig3562 3562 THRCLA_contig3563 3563 THRCLA_contig3564 3564 THRCLA_contig3565 3565 THRCLA_contig3566 3566 THRCLA_contig3567 3567 THRCLA_contig3568 3568 THRCLA_contig3569 3569 THRCLA_contig3570 3570 THRCLA_contig3571 3571 THRCLA_contig3572 3572 THRCLA_contig3573 3573 THRCLA_contig3574 3574 THRCLA_contig3575 3575 THRCLA_contig3576 3576 THRCLA_contig3577 3577 THRCLA_contig3578 3578 THRCLA_contig3579 3579 THRCLA_contig3580 3580 THRCLA_contig3581 3581 THRCLA_contig3582 3582 THRCLA_contig3583 3583 THRCLA_contig3584 3584 THRCLA_contig3585 3585 THRCLA_contig3586 3586 THRCLA_contig3587 3587 THRCLA_contig3588 3588 THRCLA_contig3589 3589 THRCLA_contig3590 3590 THRCLA_contig3591 3591 THRCLA_contig3592 3592 THRCLA_contig3593 3593 THRCLA_contig3594 3594 THRCLA_contig3595 3595 THRCLA_contig3596 3596 THRCLA_contig3597 3597 THRCLA_contig3598 3598 THRCLA_contig3599 3599 THRCLA_contig3600 3600 THRCLA_contig3601 3601 THRCLA_contig3602 3602 THRCLA_contig3603 3603 THRCLA_contig3604 3604 THRCLA_contig3605 3605 THRCLA_contig3606 3606 THRCLA_contig3607 3607 THRCLA_contig3608 3608 THRCLA_contig3609 3609 THRCLA_contig3610 3610 THRCLA_contig3611 3611 THRCLA_contig3612 3612 THRCLA_contig3613 3613 THRCLA_contig3614 3614 THRCLA_contig3615 3615 THRCLA_contig3616 3616 THRCLA_contig3617 3617 THRCLA_contig3618 3618 THRCLA_contig3619 3619 THRCLA_contig3620 3620 THRCLA_contig3621 3621 THRCLA_contig3622 3622 THRCLA_contig3623 3623 THRCLA_contig3624 3624 THRCLA_contig3625 3625 THRCLA_contig3626 3626 THRCLA_contig3627 3627 THRCLA_contig3628 3628 THRCLA_contig3629 3629 THRCLA_contig3630 3630 THRCLA_contig3631 3631 THRCLA_contig3632 3632 THRCLA_contig3633 3633 THRCLA_contig3634 3634 THRCLA_contig3635 3635 THRCLA_contig3636 3636 THRCLA_contig3637 3637 THRCLA_contig3638 3638 THRCLA_contig3639 3639 THRCLA_contig3640 3640 THRCLA_contig3641 3641 THRCLA_contig3642 3642 THRCLA_contig3643 3643 THRCLA_contig3644 3644 THRCLA_contig3645 3645 THRCLA_contig3646 3646 THRCLA_contig3647 3647 THRCLA_contig3648 3648 THRCLA_contig3649 3649 THRCLA_contig3650 3650 THRCLA_contig3651 3651 THRCLA_contig3652 3652 THRCLA_contig3653 3653 THRCLA_contig3654 3654 THRCLA_contig3655 3655 THRCLA_contig3656 3656 THRCLA_contig3657 3657 THRCLA_contig3658 3658 THRCLA_contig3659 3659 THRCLA_contig3660 3660 THRCLA_contig3661 3661 THRCLA_contig3662 3662 THRCLA_contig3663 3663 THRCLA_contig3664 3664 THRCLA_contig3665 3665 THRCLA_contig3666 3666 THRCLA_contig3667 3667 THRCLA_contig3668 3668 THRCLA_contig3669 3669 THRCLA_contig3670 3670 THRCLA_contig3671 3671 THRCLA_contig3672 3672 THRCLA_contig3673 3673 THRCLA_contig3674 3674 THRCLA_contig3675 3675 THRCLA_contig3676 3676 THRCLA_contig3677 3677 THRCLA_contig3678 3678 THRCLA_contig3679 3679 THRCLA_contig3680 3680 THRCLA_contig3681 3681 THRCLA_contig3682 3682 THRCLA_contig3683 3683 THRCLA_contig3684 3684 THRCLA_contig3685 3685 THRCLA_contig3686 3686 THRCLA_contig3687 3687 THRCLA_contig3688 3688 THRCLA_contig3689 3689 THRCLA_contig3690 3690 THRCLA_contig3691 3691 THRCLA_contig3692 3692 THRCLA_contig3693 3693 THRCLA_contig3694 3694 THRCLA_contig3695 3695 THRCLA_contig3696 3696 THRCLA_contig3697 3697 THRCLA_contig3698 3698 THRCLA_contig3699 3699 THRCLA_contig3700 3700 THRCLA_contig3701 3701 THRCLA_contig3702 3702 THRCLA_contig3703 3703 THRCLA_contig3704 3704 THRCLA_contig3705 3705 THRCLA_contig3706 3706 THRCLA_contig3707 3707 THRCLA_contig3708 3708 THRCLA_contig3709 3709 THRCLA_contig3710 3710 THRCLA_contig3711 3711 THRCLA_contig3712 3712 THRCLA_contig3713 3713 THRCLA_contig3714 3714 THRCLA_contig3715 3715 THRCLA_contig3716 3716 THRCLA_contig3717 3717 THRCLA_contig3718 3718 THRCLA_contig3719 3719 THRCLA_contig3720 3720 THRCLA_contig3721 3721 THRCLA_contig3722 3722 THRCLA_contig3723 3723 THRCLA_contig3724 3724 THRCLA_contig3725 3725 THRCLA_contig3726 3726 THRCLA_contig3727 3727 THRCLA_contig3728 3728 THRCLA_contig3729 3729 THRCLA_contig3730 3730 THRCLA_contig3731 3731 THRCLA_contig3732 3732 THRCLA_contig3733 3733 THRCLA_contig3734 3734 THRCLA_contig3735 3735 THRCLA_contig3736 3736 THRCLA_contig3737 3737 THRCLA_contig3738 3738 THRCLA_contig3739 3739 THRCLA_contig3740 3740 THRCLA_contig3741 3741 THRCLA_contig3742 3742 THRCLA_contig3743 3743 THRCLA_contig3744 3744 THRCLA_contig3745 3745 THRCLA_contig3746 3746 THRCLA_contig3747 3747 THRCLA_contig3748 3748 THRCLA_contig3749 3749 THRCLA_contig3750 3750 THRCLA_contig3751 3751 THRCLA_contig3752 3752 THRCLA_contig3753 3753 THRCLA_contig3754 3754 THRCLA_contig3755 3755 THRCLA_contig3756 3756 THRCLA_contig3757 3757 THRCLA_contig3758 3758 THRCLA_contig3759 3759 THRCLA_contig3760 3760 THRCLA_contig3761 3761 THRCLA_contig3762 3762 THRCLA_contig3763 3763 THRCLA_contig3764 3764 THRCLA_contig3765 3765 THRCLA_contig3766 3766 THRCLA_contig3767 3767 THRCLA_contig3768 3768 THRCLA_contig3769 3769 THRCLA_contig3770 3770 THRCLA_contig3771 3771 THRCLA_contig3772 3772 THRCLA_contig3773 3773 THRCLA_contig3774 3774 THRCLA_contig3775 3775 THRCLA_contig3776 3776 THRCLA_contig3777 3777 THRCLA_contig3778 3778 THRCLA_contig3779 3779 THRCLA_contig3780 3780 THRCLA_contig3781 3781 THRCLA_contig3782 3782 THRCLA_contig3783 3783 THRCLA_contig3784 3784 THRCLA_contig3785 3785 THRCLA_contig3786 3786 THRCLA_contig3787 3787 THRCLA_contig3788 3788 THRCLA_contig3789 3789 THRCLA_contig3790 3790 THRCLA_contig3791 3791 THRCLA_contig3792 3792 THRCLA_contig3793 3793 THRCLA_contig3794 3794 THRCLA_contig3795 3795 THRCLA_contig3796 3796 THRCLA_contig3797 3797 THRCLA_contig3798 3798 THRCLA_contig3799 3799 THRCLA_contig3800 3800 THRCLA_contig3801 3801 THRCLA_contig3802 3802 THRCLA_contig3803 3803 THRCLA_contig3804 3804 THRCLA_contig3805 3805 THRCLA_contig3806 3806 THRCLA_contig3807 3807 THRCLA_contig3808 3808 THRCLA_contig3809 3809 THRCLA_contig3810 3810 THRCLA_contig3811 3811 THRCLA_contig3812 3812 THRCLA_contig3813 3813 THRCLA_contig3814 3814 THRCLA_contig3815 3815 THRCLA_contig3816 3816 THRCLA_contig3817 3817 THRCLA_contig3818 3818 THRCLA_contig3819 3819 THRCLA_contig3820 3820 THRCLA_contig3821 3821 THRCLA_contig3822 3822 THRCLA_contig3823 3823 THRCLA_contig3824 3824 THRCLA_contig3825 3825 THRCLA_contig3826 3826 THRCLA_contig3827 3827 THRCLA_contig3828 3828 THRCLA_contig3829 3829 THRCLA_contig3830 3830 THRCLA_contig3831 3831 THRCLA_contig3832 3832 THRCLA_contig3833 3833 THRCLA_contig3834 3834 THRCLA_contig3835 3835 THRCLA_contig3836 3836 THRCLA_contig3837 3837 THRCLA_contig3838 3838 THRCLA_contig3839 3839 THRCLA_contig3840 3840 THRCLA_contig3841 3841 THRCLA_contig3842 3842 THRCLA_contig3843 3843 THRCLA_contig3844 3844 THRCLA_contig3845 3845 THRCLA_contig3846 3846 THRCLA_contig3847 3847 THRCLA_contig3848 3848 THRCLA_contig3849 3849 THRCLA_contig3850 3850 THRCLA_contig3851 3851 THRCLA_contig3852 3852 THRCLA_contig3853 3853 THRCLA_contig3854 3854 THRCLA_contig3855 3855 THRCLA_contig3856 3856 THRCLA_contig3857 3857 THRCLA_contig3858 3858 THRCLA_contig3859 3859 THRCLA_contig3860 3860 THRCLA_contig3861 3861 THRCLA_contig3862 3862 THRCLA_contig3863 3863 THRCLA_contig3864 3864 THRCLA_contig3865 3865 THRCLA_contig3866 3866 THRCLA_contig3867 3867 THRCLA_contig3868 3868 THRCLA_contig3869 3869 THRCLA_contig3870 3870 THRCLA_contig3871 3871 THRCLA_contig3872 3872 THRCLA_contig3873 3873 THRCLA_contig3874 3874 THRCLA_contig3875 3875 THRCLA_contig3876 3876 THRCLA_contig3877 3877 THRCLA_contig3878 3878 THRCLA_contig3879 3879 THRCLA_contig3880 3880 THRCLA_contig3881 3881 THRCLA_contig3882 3882 THRCLA_contig3883 3883 THRCLA_contig3884 3884 THRCLA_contig3885 3885 THRCLA_contig3886 3886 THRCLA_contig3887 3887 THRCLA_contig3888 3888 THRCLA_contig3889 3889 THRCLA_contig3890 3890 THRCLA_contig3891 3891 THRCLA_contig3892 3892 THRCLA_contig3893 3893 THRCLA_contig3894 3894 THRCLA_contig3895 3895 THRCLA_contig3896 3896 THRCLA_contig3897 3897 THRCLA_contig3898 3898 THRCLA_contig3899 3899 THRCLA_contig3900 3900 THRCLA_contig3901 3901 THRCLA_contig3902 3902 THRCLA_contig3903 3903 THRCLA_contig3904 3904 THRCLA_contig3905 3905 THRCLA_contig3906 3906 THRCLA_contig3907 3907 THRCLA_contig3908 3908 THRCLA_contig3909 3909 THRCLA_contig3910 3910 THRCLA_contig3911 3911 THRCLA_contig3912 3912 THRCLA_contig3913 3913 THRCLA_contig3914 3914 THRCLA_contig3915 3915 THRCLA_contig3916 3916 THRCLA_contig3917 3917 THRCLA_contig3918 3918 THRCLA_contig3919 3919 THRCLA_contig3920 3920 THRCLA_contig3921 3921 THRCLA_contig3922 3922 THRCLA_contig3923 3923 THRCLA_contig3924 3924 THRCLA_contig3925 3925 THRCLA_contig3926 3926 THRCLA_contig3927 3927 THRCLA_contig3928 3928 THRCLA_contig3929 3929 THRCLA_contig3930 3930 THRCLA_contig3931 3931 THRCLA_contig3932 3932 THRCLA_contig3933 3933 THRCLA_contig3934 3934 THRCLA_contig3935 3935 THRCLA_contig3936 3936 THRCLA_contig3937 3937 THRCLA_contig3938 3938 THRCLA_contig3939 3939 THRCLA_contig3940 3940 THRCLA_contig3941 3941 THRCLA_contig3942 3942 THRCLA_contig3943 3943 THRCLA_contig3944 3944 THRCLA_contig3945 3945 THRCLA_contig3946 3946 THRCLA_contig3947 3947 THRCLA_contig3948 3948 THRCLA_contig3949 3949 THRCLA_contig3950 3950 THRCLA_contig3951 3951 THRCLA_contig3952 3952 THRCLA_contig3953 3953 THRCLA_contig3954 3954 THRCLA_contig3955 3955 THRCLA_contig3956 3956 THRCLA_contig3957 3957 THRCLA_contig3958 3958 THRCLA_contig3959 3959 THRCLA_contig3960 3960 THRCLA_contig3961 3961 THRCLA_contig3962 3962 THRCLA_contig3963 3963 THRCLA_contig3964 3964 THRCLA_contig3965 3965 THRCLA_contig3966 3966 THRCLA_contig3967 3967 THRCLA_contig3968 3968 THRCLA_contig3969 3969 THRCLA_contig3970 3970 THRCLA_contig3971 3971 THRCLA_contig3972 3972 THRCLA_contig3973 3973 THRCLA_contig3974 3974 THRCLA_contig3975 3975 THRCLA_contig3976 3976 THRCLA_contig3977 3977 THRCLA_contig3978 3978 THRCLA_contig3979 3979 THRCLA_contig3980 3980 THRCLA_contig3981 3981 THRCLA_contig3982 3982 THRCLA_contig3983 3983 THRCLA_contig3984 3984 THRCLA_contig3985 3985 THRCLA_contig3986 3986 THRCLA_contig3987 3987 THRCLA_contig3988 3988 THRCLA_contig3989 3989 THRCLA_contig3990 3990 THRCLA_contig3991 3991 THRCLA_contig3992 3992 THRCLA_contig3993 3993 THRCLA_contig3994 3994 THRCLA_contig3995 3995 THRCLA_contig3996 3996 THRCLA_contig3997 3997 THRCLA_contig3998 3998 THRCLA_contig3999 3999 THRCLA_contig4000 4000 THRCLA_contig4001 4001 THRCLA_contig4002 4002 THRCLA_contig4003 4003 THRCLA_contig4004 4004 THRCLA_contig4005 4005 THRCLA_contig4006 4006 THRCLA_contig4007 4007 THRCLA_contig4008 4008 THRCLA_contig4009 4009 THRCLA_contig4010 4010 THRCLA_contig4011 4011 THRCLA_contig4012 4012 THRCLA_contig4013 4013 THRCLA_contig4014 4014 THRCLA_contig4015 4015 THRCLA_contig4016 4016 THRCLA_contig4017 4017 THRCLA_contig4018 4018 THRCLA_contig4019 4019 THRCLA_contig4020 4020 THRCLA_contig4021 4021 THRCLA_contig4022 4022 THRCLA_contig4023 4023 THRCLA_contig4024 4024 THRCLA_contig4025 4025 THRCLA_contig4026 4026 THRCLA_contig4027 4027 THRCLA_contig4028 4028 THRCLA_contig4029 4029 THRCLA_contig4030 4030 THRCLA_contig4031 4031 THRCLA_contig4032 4032 THRCLA_contig4033 4033 THRCLA_contig4034 4034 THRCLA_contig4035 4035 THRCLA_contig4036 4036 THRCLA_contig4037 4037 THRCLA_contig4038 4038 THRCLA_contig4039 4039 THRCLA_contig4040 4040 THRCLA_contig4041 4041 THRCLA_contig4042 4042 THRCLA_contig4043 4043 THRCLA_contig4044 4044 THRCLA_contig4045 4045 THRCLA_contig4046 4046 THRCLA_contig4047 4047 THRCLA_contig4048 4048 THRCLA_contig4049 4049 THRCLA_contig4050 4050 THRCLA_contig4051 4051 THRCLA_contig4052 4052 THRCLA_contig4053 4053 THRCLA_contig4054 4054 THRCLA_contig4055 4055 THRCLA_contig4056 4056 THRCLA_contig4057 4057 THRCLA_contig4058 4058 THRCLA_contig4059 4059 THRCLA_contig4060 4060 THRCLA_contig4061 4061 THRCLA_contig4062 4062 THRCLA_contig4063 4063 THRCLA_contig4064 4064 THRCLA_contig4065 4065 THRCLA_contig4066 4066 THRCLA_contig4067 4067 THRCLA_contig4068 4068 THRCLA_contig4069 4069 THRCLA_contig4070 4070 THRCLA_contig4071 4071 THRCLA_contig4072 4072 THRCLA_contig4073 4073 THRCLA_contig4074 4074 THRCLA_contig4075 4075 THRCLA_contig4076 4076 THRCLA_contig4077 4077 THRCLA_contig4078 4078 THRCLA_contig4079 4079 THRCLA_contig4080 4080 THRCLA_contig4081 4081 THRCLA_contig4082 4082 THRCLA_contig4083 4083 THRCLA_contig4084 4084 THRCLA_contig4085 4085 THRCLA_contig4086 4086 THRCLA_contig4087 4087 THRCLA_contig4088 4088 THRCLA_contig4089 4089 THRCLA_contig4090 4090 THRCLA_contig4091 4091 THRCLA_contig4092 4092 THRCLA_contig4093 4093 THRCLA_contig4094 4094 THRCLA_contig4095 4095 THRCLA_contig4096 4096 THRCLA_contig4097 4097 THRCLA_contig4098 4098 THRCLA_contig4099 4099 THRCLA_contig4100 4100 THRCLA_contig4101 4101 THRCLA_contig4102 4102 THRCLA_contig4103 4103 THRCLA_contig4104 4104 THRCLA_contig4105 4105 THRCLA_contig4106 4106 THRCLA_contig4107 4107 THRCLA_contig4108 4108 THRCLA_contig4109 4109 THRCLA_contig4110 4110 THRCLA_contig4111 4111 THRCLA_contig4112 4112 THRCLA_contig4113 4113 THRCLA_contig4114 4114 THRCLA_contig4115 4115 THRCLA_contig4116 4116 THRCLA_contig4117 4117 THRCLA_contig4118 4118 THRCLA_contig4119 4119 THRCLA_contig4120 4120 THRCLA_contig4121 4121 THRCLA_contig4122 4122 THRCLA_contig4123 4123 THRCLA_contig4124 4124 THRCLA_contig4125 4125 THRCLA_contig4126 4126 THRCLA_contig4127 4127 THRCLA_contig4128 4128 THRCLA_contig4129 4129 THRCLA_contig4130 4130 THRCLA_contig4131 4131 THRCLA_contig4132 4132 THRCLA_contig4133 4133 THRCLA_contig4134 4134 THRCLA_contig4135 4135 THRCLA_contig4136 4136 THRCLA_contig4137 4137 THRCLA_contig4138 4138 THRCLA_contig4139 4139 THRCLA_contig4140 4140 THRCLA_contig4141 4141 THRCLA_contig4142 4142 THRCLA_contig4143 4143 THRCLA_contig4144 4144 THRCLA_contig4145 4145 THRCLA_contig4146 4146 THRCLA_contig4147 4147 THRCLA_contig4148 4148 THRCLA_contig4149 4149 THRCLA_contig4150 4150 THRCLA_contig4151 4151 THRCLA_contig4152 4152 THRCLA_contig4153 4153 THRCLA_contig4154 4154 THRCLA_contig4155 4155 THRCLA_contig4156 4156 THRCLA_contig4157 4157 THRCLA_contig4158 4158 THRCLA_contig4159 4159 THRCLA_contig4160 4160 THRCLA_contig4161 4161 THRCLA_contig4162 4162 THRCLA_contig4163 4163 THRCLA_contig4164 4164 THRCLA_contig4165 4165 THRCLA_contig4166 4166 THRCLA_contig4167 4167 THRCLA_contig4168 4168 THRCLA_contig4169 4169 THRCLA_contig4170 4170 THRCLA_contig4171 4171 THRCLA_contig4172 4172 THRCLA_contig4173 4173 THRCLA_contig4174 4174 THRCLA_contig4175 4175 THRCLA_contig4176 4176 THRCLA_contig4177 4177 THRCLA_contig4178 4178 THRCLA_contig4179 4179 THRCLA_contig4180 4180 THRCLA_contig4181 4181 THRCLA_contig4182 4182 THRCLA_contig4183 4183 THRCLA_contig4184 4184 THRCLA_contig4185 4185 THRCLA_contig4186 4186 THRCLA_contig4187 4187 THRCLA_contig4188 4188 THRCLA_contig4189 4189 THRCLA_contig4190 4190 THRCLA_contig4191 4191 THRCLA_contig4192 4192 THRCLA_contig4193 4193 THRCLA_contig4194 4194 THRCLA_contig4195 4195 THRCLA_contig4196 4196 THRCLA_contig4197 4197 THRCLA_contig4198 4198 THRCLA_contig4199 4199 THRCLA_contig4200 4200 THRCLA_contig4201 4201 THRCLA_contig4202 4202 THRCLA_contig4203 4203 THRCLA_contig4204 4204 THRCLA_contig4205 4205 THRCLA_contig4206 4206 THRCLA_contig4207 4207 THRCLA_contig4208 4208 THRCLA_contig4209 4209 THRCLA_contig4210 4210 THRCLA_contig4211 4211 THRCLA_contig4212 4212 THRCLA_contig4213 4213 THRCLA_contig4214 4214 THRCLA_contig4215 4215 THRCLA_contig4216 4216 THRCLA_contig4217 4217 THRCLA_contig4218 4218 THRCLA_contig4219 4219 THRCLA_contig4220 4220 THRCLA_contig4221 4221 THRCLA_contig4222 4222 THRCLA_contig4223 4223 THRCLA_contig4224 4224 THRCLA_contig4225 4225 THRCLA_contig4226 4226 THRCLA_contig4227 4227 THRCLA_contig4228 4228 THRCLA_contig4229 4229 THRCLA_contig4230 4230 THRCLA_contig4231 4231 THRCLA_contig4232 4232 THRCLA_contig4233 4233 THRCLA_contig4234 4234 THRCLA_contig4235 4235 THRCLA_contig4236 4236 THRCLA_contig4237 4237 THRCLA_contig4238 4238 THRCLA_contig4239 4239 THRCLA_contig4240 4240 THRCLA_contig4241 4241 THRCLA_contig4242 4242 THRCLA_contig4243 4243 THRCLA_contig4244 4244 THRCLA_contig4245 4245 THRCLA_contig4246 4246 THRCLA_contig4247 4247 THRCLA_contig4248 4248 THRCLA_contig4249 4249 THRCLA_contig4250 4250 THRCLA_contig4251 4251 THRCLA_contig4252 4252 THRCLA_contig4253 4253 THRCLA_contig4254 4254 THRCLA_contig4255 4255 THRCLA_contig4256 4256 THRCLA_contig4257 4257 THRCLA_contig4258 4258 THRCLA_contig4259 4259 THRCLA_contig4260 4260 THRCLA_contig4261 4261 THRCLA_contig4262 4262 THRCLA_contig4263 4263 THRCLA_contig4264 4264 THRCLA_contig4265 4265 THRCLA_contig4266 4266 THRCLA_contig4267 4267 THRCLA_contig4268 4268 THRCLA_contig4269 4269 THRCLA_contig4270 4270 THRCLA_contig4271 4271 THRCLA_contig4272 4272 THRCLA_contig4273 4273 THRCLA_contig4274 4274 THRCLA_contig4275 4275 THRCLA_contig4276 4276 THRCLA_contig4277 4277 THRCLA_contig4278 4278 THRCLA_contig4279 4279 THRCLA_contig4280 4280 THRCLA_contig4281 4281 THRCLA_contig4282 4282 THRCLA_contig4283 4283 THRCLA_contig4284 4284 THRCLA_contig4285 4285 THRCLA_contig4286 4286 THRCLA_contig4287 4287 THRCLA_contig4288 4288 THRCLA_contig4289 4289 THRCLA_contig4290 4290 THRCLA_contig4291 4291 THRCLA_contig4292 4292 THRCLA_contig4293 4293 THRCLA_contig4294 4294 THRCLA_contig4295 4295 THRCLA_contig4296 4296 THRCLA_contig4297 4297 THRCLA_contig4298 4298 THRCLA_contig4299 4299 THRCLA_contig4300 4300 THRCLA_contig4301 4301 THRCLA_contig4302 4302 THRCLA_contig4303 4303 THRCLA_contig4304 4304 THRCLA_contig4305 4305 THRCLA_contig4306 4306 THRCLA_contig4307 4307 THRCLA_contig4308 4308 THRCLA_contig4309 4309 THRCLA_contig4310 4310 THRCLA_contig4311 4311 THRCLA_contig4312 4312 THRCLA_contig4313 4313 THRCLA_contig4314 4314 THRCLA_contig4315 4315 THRCLA_contig4316 4316 THRCLA_contig4317 4317 THRCLA_contig4318 4318 THRCLA_contig4319 4319 THRCLA_contig4320 4320 THRCLA_contig4321 4321 THRCLA_contig4322 4322 THRCLA_contig4323 4323 THRCLA_contig4324 4324 THRCLA_contig4325 4325 THRCLA_contig4326 4326 THRCLA_contig4327 4327 THRCLA_contig4328 4328 THRCLA_contig4329 4329 THRCLA_contig4330 4330 THRCLA_contig4331 4331 THRCLA_contig4332 4332 THRCLA_contig4333 4333 THRCLA_contig4334 4334 THRCLA_contig4335 4335 THRCLA_contig4336 4336 THRCLA_contig4337 4337 THRCLA_contig4338 4338 THRCLA_contig4339 4339 THRCLA_contig4340 4340 THRCLA_contig4341 4341 THRCLA_contig4342 4342 THRCLA_contig4343 4343 THRCLA_contig4344 4344 THRCLA_contig4345 4345 THRCLA_contig4346 4346 THRCLA_contig4347 4347 THRCLA_contig4348 4348 THRCLA_contig4349 4349 THRCLA_contig4350 4350 THRCLA_contig4351 4351 THRCLA_contig4352 4352 THRCLA_contig4353 4353 THRCLA_contig4354 4354 THRCLA_contig4355 4355 THRCLA_contig4356 4356 THRCLA_contig4357 4357 THRCLA_contig4358 4358 THRCLA_contig4359 4359 THRCLA_contig4360 4360 THRCLA_contig4361 4361 THRCLA_contig4362 4362 THRCLA_contig4363 4363 THRCLA_contig4364 4364 THRCLA_contig4365 4365 THRCLA_contig4366 4366 THRCLA_contig4367 4367 THRCLA_contig4368 4368 THRCLA_contig4369 4369 THRCLA_contig4370 4370 THRCLA_contig4371 4371 THRCLA_contig4372 4372 THRCLA_contig4373 4373 THRCLA_contig4374 4374 THRCLA_contig4375 4375 THRCLA_contig4376 4376 THRCLA_contig4377 4377 THRCLA_contig4378 4378 THRCLA_contig4379 4379 THRCLA_contig4380 4380 THRCLA_contig4381 4381 THRCLA_contig4382 4382 THRCLA_contig4383 4383 THRCLA_contig4384 4384 THRCLA_contig4385 4385 THRCLA_contig4386 4386 THRCLA_contig4387 4387 THRCLA_contig4388 4388 THRCLA_contig4389 4389 THRCLA_contig4390 4390 THRCLA_contig4391 4391 THRCLA_contig4392 4392 THRCLA_contig4393 4393 THRCLA_contig4394 4394 THRCLA_contig4395 4395 THRCLA_contig4396 4396 THRCLA_contig4397 4397 THRCLA_contig4398 4398 THRCLA_contig4399 4399 THRCLA_contig4400 4400 THRCLA_contig4401 4401 THRCLA_contig4402 4402 THRCLA_contig4403 4403 THRCLA_contig4404 4404 THRCLA_contig4405 4405 THRCLA_contig4406 4406 THRCLA_contig4407 4407 THRCLA_contig4408 4408 THRCLA_contig4409 4409 THRCLA_contig4410 4410 THRCLA_contig4411 4411 THRCLA_contig4412 4412 THRCLA_contig4413 4413 THRCLA_contig4414 4414 THRCLA_contig4415 4415 THRCLA_contig4416 4416 THRCLA_contig4417 4417 THRCLA_contig4418 4418 THRCLA_contig4419 4419 THRCLA_contig4420 4420 THRCLA_contig4421 4421 THRCLA_contig4422 4422 THRCLA_contig4423 4423 THRCLA_contig4424 4424 THRCLA_contig4425 4425 THRCLA_contig4426 4426 THRCLA_contig4427 4427 THRCLA_contig4428 4428 THRCLA_contig4429 4429 THRCLA_contig4430 4430 THRCLA_contig4431 4431 THRCLA_contig4432 4432 THRCLA_contig4433 4433 THRCLA_contig4434 4434 THRCLA_contig4435 4435 THRCLA_contig4436 4436 THRCLA_contig4437 4437 THRCLA_contig4438 4438 THRCLA_contig4439 4439 THRCLA_contig4440 4440 THRCLA_contig4441 4441 THRCLA_contig4442 4442 THRCLA_contig4443 4443 THRCLA_contig4444 4444 THRCLA_contig4445 4445 THRCLA_contig4446 4446 THRCLA_contig4447 4447 THRCLA_contig4448 4448 THRCLA_contig4449 4449 THRCLA_contig4450 4450 THRCLA_contig4451 4451 THRCLA_contig4452 4452 THRCLA_contig4453 4453 THRCLA_contig4454 4454 THRCLA_contig4455 4455 THRCLA_contig4456 4456 THRCLA_contig4457 4457 THRCLA_contig4458 4458 THRCLA_contig4459 4459 THRCLA_contig4460 4460 THRCLA_contig4461 4461 THRCLA_contig4462 4462 THRCLA_contig4463 4463 THRCLA_contig4464 4464 THRCLA_contig4465 4465 THRCLA_contig4466 4466 THRCLA_contig4467 4467 THRCLA_contig4468 4468 THRCLA_contig4469 4469 THRCLA_contig4470 4470 THRCLA_contig4471 4471 THRCLA_contig4472 4472 THRCLA_contig4473 4473 THRCLA_contig4474 4474 THRCLA_contig4475 4475 THRCLA_contig4476 4476 THRCLA_contig4477 4477 THRCLA_contig4478 4478 THRCLA_contig4479 4479 THRCLA_contig4480 4480 THRCLA_contig4481 4481 THRCLA_contig4482 4482 THRCLA_contig4483 4483 THRCLA_contig4484 4484 THRCLA_contig4485 4485 THRCLA_contig4486 4486 THRCLA_contig4487 4487 THRCLA_contig4488 4488 THRCLA_contig4489 4489 THRCLA_contig4490 4490 THRCLA_contig4491 4491 THRCLA_contig4492 4492 THRCLA_contig4493 4493 THRCLA_contig4494 4494 THRCLA_contig4495 4495 THRCLA_contig4496 4496 THRCLA_contig4497 4497 THRCLA_contig4498 4498 THRCLA_contig4499 4499 THRCLA_contig4500 4500 THRCLA_contig4501 4501 THRCLA_contig4502 4502 THRCLA_contig4503 4503 THRCLA_contig4504 4504 THRCLA_contig4505 4505 THRCLA_contig4506 4506 THRCLA_contig4507 4507 THRCLA_contig4508 4508 THRCLA_contig4509 4509 THRCLA_contig4510 4510 THRCLA_contig4511 4511 THRCLA_contig4512 4512 THRCLA_contig4513 4513 THRCLA_contig4514 4514 THRCLA_contig4515 4515 THRCLA_contig4516 4516 THRCLA_contig4517 4517 THRCLA_contig4518 4518 THRCLA_contig4519 4519 THRCLA_contig4520 4520 THRCLA_contig4521 4521 THRCLA_contig4522 4522 THRCLA_contig4523 4523 THRCLA_contig4524 4524 THRCLA_contig4525 4525 THRCLA_contig4526 4526 THRCLA_contig4527 4527 THRCLA_contig4528 4528 THRCLA_contig4529 4529 THRCLA_contig4530 4530 THRCLA_contig4531 4531 THRCLA_contig4532 4532 THRCLA_contig4533 4533 THRCLA_contig4534 4534 THRCLA_contig4535 4535 THRCLA_contig4536 4536 THRCLA_contig4537 4537 THRCLA_contig4538 4538 THRCLA_contig4539 4539 THRCLA_contig4540 4540 THRCLA_contig4541 4541 THRCLA_contig4542 4542 THRCLA_contig4543 4543 THRCLA_contig4544 4544 THRCLA_contig4545 4545 THRCLA_contig4546 4546 THRCLA_contig4547 4547 THRCLA_contig4548 4548 THRCLA_contig4549 4549 THRCLA_contig4550 4550 THRCLA_contig4551 4551 THRCLA_contig4552 4552 THRCLA_contig4553 4553 THRCLA_contig4554 4554 THRCLA_contig4555 4555 THRCLA_contig4556 4556 THRCLA_contig4557 4557 THRCLA_contig4558 4558 THRCLA_contig4559 4559 THRCLA_contig4560 4560 THRCLA_contig4561 4561 THRCLA_contig4562 4562 THRCLA_contig4563 4563 THRCLA_contig4564 4564 THRCLA_contig4565 4565 THRCLA_contig4566 4566 THRCLA_contig4567 4567 THRCLA_contig4568 4568 THRCLA_contig4569 4569 THRCLA_contig4570 4570 THRCLA_contig4571 4571 THRCLA_contig4572 4572 THRCLA_contig4573 4573 THRCLA_contig4574 4574 THRCLA_contig4575 4575 THRCLA_contig4576 4576 THRCLA_contig4577 4577 THRCLA_contig4578 4578 THRCLA_contig4579 4579 THRCLA_contig4580 4580 THRCLA_contig4581 4581 THRCLA_contig4582 4582 THRCLA_contig4583 4583 THRCLA_contig4584 4584 THRCLA_contig4585 4585 THRCLA_contig4586 4586 THRCLA_contig4587 4587 THRCLA_contig4588 4588 THRCLA_contig4589 4589 THRCLA_contig4590 4590 THRCLA_contig4591 4591 THRCLA_contig4592 4592 THRCLA_contig4593 4593 THRCLA_contig4594 4594 THRCLA_contig4595 4595 THRCLA_contig4596 4596 THRCLA_contig4597 4597 THRCLA_contig4598 4598 THRCLA_contig4599 4599 THRCLA_contig4600 4600 THRCLA_contig4601 4601 THRCLA_contig4602 4602 THRCLA_contig4603 4603 THRCLA_contig4604 4604 THRCLA_contig4605 4605 THRCLA_contig4606 4606 THRCLA_contig4607 4607 THRCLA_contig4608 4608 THRCLA_contig4609 4609 THRCLA_contig4610 4610 THRCLA_contig4611 4611 THRCLA_contig4612 4612 THRCLA_contig4613 4613 THRCLA_contig4614 4614 THRCLA_contig4615 4615 THRCLA_contig4616 4616 THRCLA_contig4617 4617 THRCLA_contig4618 4618 THRCLA_contig4619 4619 THRCLA_contig4620 4620 THRCLA_contig4621 4621 THRCLA_contig4622 4622 THRCLA_contig4623 4623 THRCLA_contig4624 4624 THRCLA_contig4625 4625 THRCLA_contig4626 4626 THRCLA_contig4627 4627 THRCLA_contig4628 4628 THRCLA_contig4629 4629 THRCLA_contig4630 4630 THRCLA_contig4631 4631 THRCLA_contig4632 4632 THRCLA_contig4633 4633 THRCLA_contig4634 4634 THRCLA_contig4635 4635 THRCLA_contig4636 4636 THRCLA_contig4637 4637 THRCLA_contig4638 4638 THRCLA_contig4639 4639 THRCLA_contig4640 4640 THRCLA_contig4641 4641 THRCLA_contig4642 4642 THRCLA_contig4643 4643 THRCLA_contig4644 4644 THRCLA_contig4645 4645 THRCLA_contig4646 4646 THRCLA_contig4647 4647 THRCLA_contig4648 4648 THRCLA_contig4649 4649 THRCLA_contig4650 4650 THRCLA_contig4651 4651 THRCLA_contig4652 4652 THRCLA_contig4653 4653 THRCLA_contig4654 4654 THRCLA_contig4655 4655 THRCLA_contig4656 4656 THRCLA_contig4657 4657 THRCLA_contig4658 4658 THRCLA_contig4659 4659 THRCLA_contig4660 4660 THRCLA_contig4661 4661 THRCLA_contig4662 4662 THRCLA_contig4663 4663 THRCLA_contig4664 4664 THRCLA_contig4665 4665 THRCLA_contig4666 4666 THRCLA_contig4667 4667 THRCLA_contig4668 4668 THRCLA_contig4669 4669 THRCLA_contig4670 4670 THRCLA_contig4671 4671 THRCLA_contig4672 4672 THRCLA_contig4673 4673 THRCLA_contig4674 4674 THRCLA_contig4675 4675 THRCLA_contig4676 4676 THRCLA_contig4677 4677 THRCLA_contig4678 4678 THRCLA_contig4679 4679 THRCLA_contig4680 4680 THRCLA_contig4681 4681 THRCLA_contig4682 4682 THRCLA_contig4683 4683 THRCLA_contig4684 4684 THRCLA_contig4685 4685 THRCLA_contig4686 4686 THRCLA_contig4687 4687 THRCLA_contig4688 4688 THRCLA_contig4689 4689 THRCLA_contig4690 4690 THRCLA_contig4691 4691 THRCLA_contig4692 4692 THRCLA_contig4693 4693 THRCLA_contig4694 4694 THRCLA_contig4695 4695 THRCLA_contig4696 4696 THRCLA_contig4697 4697 THRCLA_contig4698 4698 THRCLA_contig4699 4699 THRCLA_contig4700 4700 THRCLA_contig4701 4701 THRCLA_contig4702 4702 THRCLA_contig4703 4703 THRCLA_contig4704 4704 THRCLA_contig4705 4705 THRCLA_contig4706 4706 THRCLA_contig4707 4707 THRCLA_contig4708 4708 THRCLA_contig4709 4709 THRCLA_contig4710 4710 THRCLA_contig4711 4711 THRCLA_contig4712 4712 THRCLA_contig4713 4713 THRCLA_contig4714 4714 THRCLA_contig4715 4715 THRCLA_contig4716 4716 THRCLA_contig4717 4717 THRCLA_contig4718 4718 THRCLA_contig4719 4719 THRCLA_contig4720 4720 THRCLA_contig4721 4721 THRCLA_contig4722 4722 THRCLA_contig4723 4723 THRCLA_contig4724 4724 THRCLA_contig4725 4725 THRCLA_contig4726 4726 THRCLA_contig4727 4727 THRCLA_contig4728 4728 THRCLA_contig4729 4729 THRCLA_contig4730 4730 THRCLA_contig4731 4731 THRCLA_contig4732 4732 THRCLA_contig4733 4733 THRCLA_contig4734 4734 THRCLA_contig4735 4735 THRCLA_contig4736 4736 THRCLA_contig4737 4737 THRCLA_contig4738 4738 THRCLA_contig4739 4739 THRCLA_contig4740 4740 THRCLA_contig4741 4741 THRCLA_contig4742 4742 THRCLA_contig4743 4743 THRCLA_contig4744 4744 THRCLA_contig4745 4745 THRCLA_contig4746 4746 THRCLA_contig4747 4747 THRCLA_contig4748 4748 THRCLA_contig4749 4749 THRCLA_contig4750 4750 THRCLA_contig4751 4751 THRCLA_contig4752 4752 THRCLA_contig4753 4753 THRCLA_contig4754 4754 THRCLA_contig4755 4755 THRCLA_contig4756 4756 THRCLA_contig4757 4757 THRCLA_contig4758 4758 THRCLA_contig4759 4759 THRCLA_contig4760 4760 THRCLA_contig4761 4761 THRCLA_contig4762 4762 THRCLA_contig4763 4763 THRCLA_contig4764 4764 THRCLA_contig4765 4765 THRCLA_contig4766 4766 THRCLA_contig4767 4767 THRCLA_contig4768 4768 THRCLA_contig4769 4769 THRCLA_contig4770 4770 THRCLA_contig4771 4771 THRCLA_contig4772 4772 THRCLA_contig4773 4773 THRCLA_contig4774 4774 THRCLA_contig4775 4775 THRCLA_contig4776 4776 THRCLA_contig4777 4777 THRCLA_contig4778 4778 THRCLA_contig4779 4779 THRCLA_contig4780 4780 THRCLA_contig4781 4781 THRCLA_contig4782 4782 THRCLA_contig4783 4783 THRCLA_contig4784 4784 THRCLA_contig4785 4785 THRCLA_contig4786 4786 THRCLA_contig4787 4787 THRCLA_contig4788 4788 THRCLA_contig4789 4789 THRCLA_contig4790 4790 THRCLA_contig4791 4791 THRCLA_contig4792 4792 THRCLA_contig4793 4793 THRCLA_contig4794 4794 THRCLA_contig4795 4795 THRCLA_contig4796 4796 THRCLA_contig4797 4797 THRCLA_contig4798 4798 THRCLA_contig4799 4799 THRCLA_contig4800 4800 THRCLA_contig4801 4801 THRCLA_contig4802 4802 THRCLA_contig4803 4803 THRCLA_contig4804 4804 THRCLA_contig4805 4805 THRCLA_contig4806 4806 THRCLA_contig4807 4807 THRCLA_contig4808 4808 THRCLA_contig4809 4809 THRCLA_contig4810 4810 THRCLA_contig4811 4811 THRCLA_contig4812 4812 THRCLA_contig4813 4813 THRCLA_contig4814 4814 THRCLA_contig4815 4815 THRCLA_contig4816 4816 THRCLA_contig4817 4817 THRCLA_contig4818 4818 THRCLA_contig4819 4819 THRCLA_contig4820 4820 THRCLA_contig4821 4821 THRCLA_contig4822 4822 THRCLA_contig4823 4823 THRCLA_contig4824 4824 THRCLA_contig4825 4825 THRCLA_contig4826 4826 THRCLA_contig4827 4827 THRCLA_contig4828 4828 THRCLA_contig4829 4829 THRCLA_contig4830 4830 THRCLA_contig4831 4831 THRCLA_contig4832 4832 THRCLA_contig4833 4833 THRCLA_contig4834 4834 THRCLA_contig4835 4835 THRCLA_contig4836 4836 THRCLA_contig4837 4837 THRCLA_contig4838 4838 THRCLA_contig4839 4839 THRCLA_contig4840 4840 THRCLA_contig4841 4841 THRCLA_contig4842 4842 THRCLA_contig4843 4843 THRCLA_contig4844 4844 THRCLA_contig4845 4845 THRCLA_contig4846 4846 THRCLA_contig4847 4847 THRCLA_contig4848 4848 THRCLA_contig4849 4849 THRCLA_contig4850 4850 THRCLA_contig4851 4851 THRCLA_contig4852 4852 THRCLA_contig4853 4853 THRCLA_contig4854 4854 THRCLA_contig4855 4855 THRCLA_contig4856 4856 THRCLA_contig4857 4857 THRCLA_contig4858 4858 THRCLA_contig4859 4859 THRCLA_contig4860 4860 THRCLA_contig4861 4861 THRCLA_contig4862 4862 THRCLA_contig4863 4863 THRCLA_contig4864 4864 THRCLA_contig4865 4865 THRCLA_contig4866 4866 THRCLA_contig4867 4867 THRCLA_contig4868 4868 THRCLA_contig4869 4869 THRCLA_contig4870 4870 THRCLA_contig4871 4871 THRCLA_contig4872 4872 THRCLA_contig4873 4873 THRCLA_contig4874 4874 THRCLA_contig4875 4875 THRCLA_contig4876 4876 THRCLA_contig4877 4877 THRCLA_contig4878 4878 THRCLA_contig4879 4879 THRCLA_contig4880 4880 THRCLA_contig4881 4881 THRCLA_contig4882 4882 THRCLA_contig4883 4883 THRCLA_contig4884 4884 THRCLA_contig4885 4885 THRCLA_contig4886 4886 THRCLA_contig4887 4887 THRCLA_contig4888 4888 THRCLA_contig4889 4889 THRCLA_contig4890 4890 THRCLA_contig4891 4891 THRCLA_contig4892 4892 THRCLA_contig4893 4893 THRCLA_contig4894 4894 THRCLA_contig4895 4895 THRCLA_contig4896 4896 THRCLA_contig4897 4897 THRCLA_contig4898 4898 THRCLA_contig4899 4899 THRCLA_contig4900 4900 THRCLA_contig4901 4901 THRCLA_contig4902 4902 THRCLA_contig4903 4903 THRCLA_contig4904 4904 THRCLA_contig4905 4905 THRCLA_contig4906 4906 THRCLA_contig4907 4907 THRCLA_contig4908 4908 THRCLA_contig4909 4909 THRCLA_contig4910 4910 THRCLA_contig4911 4911 THRCLA_contig4912 4912 THRCLA_contig4913 4913 THRCLA_contig4914 4914 THRCLA_contig4915 4915 THRCLA_contig4916 4916 THRCLA_contig4917 4917 THRCLA_contig4918 4918 THRCLA_contig4919 4919 THRCLA_contig4920 4920 THRCLA_contig4921 4921 THRCLA_contig4922 4922 THRCLA_contig4923 4923 THRCLA_contig4924 4924 THRCLA_contig4925 4925 THRCLA_contig4926 4926 THRCLA_contig4927 4927 THRCLA_contig4928 4928 THRCLA_contig4929 4929 THRCLA_contig4930 4930 THRCLA_contig4931 4931 THRCLA_contig4932 4932 THRCLA_contig4933 4933 THRCLA_contig4934 4934 THRCLA_contig4935 4935 THRCLA_contig4936 4936 THRCLA_contig4937 4937 THRCLA_contig4938 4938 THRCLA_contig4939 4939 THRCLA_contig4940 4940 THRCLA_contig4941 4941 THRCLA_contig4942 4942 THRCLA_contig4943 4943 THRCLA_contig4944 4944 THRCLA_contig4945 4945 THRCLA_contig4946 4946 THRCLA_contig4947 4947 THRCLA_contig4948 4948 THRCLA_contig4949 4949 THRCLA_contig4950 4950 THRCLA_contig4951 4951 THRCLA_contig4952 4952 THRCLA_contig4953 4953 THRCLA_contig4954 4954 THRCLA_contig4955 4955 THRCLA_contig4956 4956 THRCLA_contig4957 4957 THRCLA_contig4958 4958 THRCLA_contig4959 4959 THRCLA_contig4960 4960 THRCLA_contig4961 4961 THRCLA_contig4962 4962 THRCLA_contig4963 4963 THRCLA_contig4964 4964 THRCLA_contig4965 4965 THRCLA_contig4966 4966 THRCLA_contig4967 4967 THRCLA_contig4968 4968 THRCLA_contig4969 4969 THRCLA_contig4970 4970 THRCLA_contig4971 4971 THRCLA_contig4972 4972 THRCLA_contig4973 4973 THRCLA_contig4974 4974 THRCLA_contig4975 4975 THRCLA_contig4976 4976 THRCLA_contig4977 4977 THRCLA_contig4978 4978 THRCLA_contig4979 4979 THRCLA_contig4980 4980 THRCLA_contig4981 4981 THRCLA_contig4982 4982 THRCLA_contig4983 4983 THRCLA_contig4984 4984 THRCLA_contig4985 4985 THRCLA_contig4986 4986 THRCLA_contig4987 4987 THRCLA_contig4988 4988 THRCLA_contig4989 4989 THRCLA_contig4990 4990 THRCLA_contig4991 4991 THRCLA_contig4992 4992 THRCLA_contig4993 4993 THRCLA_contig4994 4994 THRCLA_contig4995 4995 THRCLA_contig4996 4996 THRCLA_contig4997 4997 THRCLA_contig4998 4998 THRCLA_contig4999 4999 THRCLA_contig5000 5000 THRCLA_contig5001 5001 THRCLA_contig5002 5002 THRCLA_contig5003 5003 THRCLA_contig5004 5004 THRCLA_contig5005 5005 THRCLA_contig5006 5006 THRCLA_contig5007 5007 THRCLA_contig5008 5008 THRCLA_contig5009 5009 THRCLA_contig5010 5010 THRCLA_contig5011 5011 THRCLA_contig5012 5012 THRCLA_contig5013 5013 THRCLA_contig5014 5014 THRCLA_contig5015 5015 THRCLA_contig5016 5016 THRCLA_contig5017 5017 THRCLA_contig5018 5018 THRCLA_contig5019 5019 THRCLA_contig5020 5020 THRCLA_contig5021 5021 THRCLA_contig5022 5022 THRCLA_contig5023 5023 THRCLA_contig5024 5024 THRCLA_contig5025 5025 THRCLA_contig5026 5026 THRCLA_contig5027 5027 THRCLA_contig5028 5028 THRCLA_contig5029 5029 THRCLA_contig5030 5030 THRCLA_contig5031 5031 THRCLA_contig5032 5032 THRCLA_contig5033 5033 THRCLA_contig5034 5034 THRCLA_contig5035 5035 THRCLA_contig5036 5036 THRCLA_contig5037 5037 THRCLA_contig5038 5038 THRCLA_contig5039 5039 THRCLA_contig5040 5040 THRCLA_contig5041 5041 THRCLA_contig5042 5042 THRCLA_contig5043 5043 THRCLA_contig5044 5044 THRCLA_contig5045 5045 THRCLA_contig5046 5046 THRCLA_contig5047 5047 THRCLA_contig5048 5048 THRCLA_contig5049 5049 THRCLA_contig5050 5050 THRCLA_contig5051 5051 THRCLA_contig5052 5052 THRCLA_contig5053 5053 THRCLA_contig5054 5054 THRCLA_contig5055 5055 THRCLA_contig5056 5056 THRCLA_contig5057 5057 THRCLA_contig5058 5058 THRCLA_contig5059 5059 THRCLA_contig5060 5060 THRCLA_contig5061 5061 THRCLA_contig5062 5062 THRCLA_contig5063 5063 THRCLA_contig5064 5064 THRCLA_contig5065 5065 THRCLA_contig5066 5066 THRCLA_contig5067 5067 THRCLA_contig5068 5068 THRCLA_contig5069 5069 THRCLA_contig5070 5070 THRCLA_contig5071 5071 THRCLA_contig5072 5072 THRCLA_contig5073 5073 THRCLA_contig5074 5074 THRCLA_contig5075 5075 THRCLA_contig5076 5076 THRCLA_contig5077 5077 THRCLA_contig5078 5078 THRCLA_contig5079 5079 THRCLA_contig5080 5080 THRCLA_contig5081 5081 THRCLA_contig5082 5082 THRCLA_contig5083 5083 THRCLA_contig5084 5084 THRCLA_contig5085 5085 THRCLA_contig5086 5086 THRCLA_contig5087 5087 THRCLA_contig5088 5088 THRCLA_contig5089 5089 THRCLA_contig5090 5090 THRCLA_contig5091 5091 THRCLA_contig5092 5092 THRCLA_contig5093 5093 THRCLA_contig5094 5094 THRCLA_contig5095 5095 THRCLA_contig5096 5096 THRCLA_contig5097 5097 THRCLA_contig5098 5098 THRCLA_contig5099 5099 THRCLA_contig5100 5100 THRCLA_contig5101 5101 THRCLA_contig5102 5102 THRCLA_contig5103 5103 THRCLA_contig5104 5104 THRCLA_contig5105 5105 THRCLA_contig5106 5106 THRCLA_contig5107 5107 THRCLA_contig5108 5108 THRCLA_contig5109 5109 THRCLA_contig5110 5110 THRCLA_contig5111 5111 THRCLA_contig5112 5112 THRCLA_contig5113 5113 THRCLA_contig5114 5114 THRCLA_contig5115 5115 THRCLA_contig5116 5116 THRCLA_contig5117 5117 THRCLA_contig5118 5118 THRCLA_contig5119 5119 THRCLA_contig5120 5120 THRCLA_contig5121 5121 THRCLA_contig5122 5122 THRCLA_contig5123 5123 THRCLA_contig5124 5124 THRCLA_contig5125 5125 THRCLA_contig5126 5126 THRCLA_contig5127 5127 THRCLA_contig5128 5128 THRCLA_contig5129 5129 THRCLA_contig5130 5130 THRCLA_contig5131 5131 THRCLA_contig5132 5132 THRCLA_contig5133 5133 THRCLA_contig5134 5134 THRCLA_contig5135 5135 THRCLA_contig5136 5136 THRCLA_contig5137 5137 THRCLA_contig5138 5138 THRCLA_contig5139 5139 THRCLA_contig5140 5140 THRCLA_contig5141 5141 THRCLA_contig5142 5142 THRCLA_contig5143 5143 THRCLA_contig5144 5144 THRCLA_contig5145 5145 THRCLA_contig5146 5146 THRCLA_contig5147 5147 THRCLA_contig5148 5148 THRCLA_contig5149 5149 THRCLA_contig5150 5150 THRCLA_contig5151 5151 THRCLA_contig5152 5152 THRCLA_contig5153 5153 THRCLA_contig5154 5154 THRCLA_contig5155 5155 THRCLA_contig5156 5156 THRCLA_contig5157 5157 THRCLA_contig5158 5158 THRCLA_contig5159 5159 THRCLA_contig5160 5160 THRCLA_contig5161 5161 THRCLA_contig5162 5162 THRCLA_contig5163 5163 THRCLA_contig5164 5164 THRCLA_contig5165 5165 THRCLA_contig5166 5166 THRCLA_contig5167 5167 THRCLA_contig5168 5168 THRCLA_contig5169 5169 THRCLA_contig5170 5170 THRCLA_contig5171 5171 THRCLA_contig5172 5172 THRCLA_contig5173 5173 THRCLA_contig5174 5174 THRCLA_contig5175 5175 THRCLA_contig5176 5176 THRCLA_contig5177 5177 THRCLA_contig5178 5178 THRCLA_contig5179 5179 THRCLA_contig5180 5180 THRCLA_contig5181 5181 THRCLA_contig5182 5182 THRCLA_contig5183 5183 THRCLA_contig5184 5184 THRCLA_contig5185 5185 THRCLA_contig5186 5186 THRCLA_contig5187 5187 THRCLA_contig5188 5188 THRCLA_contig5189 5189 THRCLA_contig5190 5190 THRCLA_contig5191 5191 THRCLA_contig5192 5192 THRCLA_contig5193 5193 THRCLA_contig5194 5194 THRCLA_contig5195 5195 THRCLA_contig5196 5196 THRCLA_contig5197 5197 THRCLA_contig5198 5198 THRCLA_contig5199 5199 THRCLA_contig5200 5200 THRCLA_contig5201 5201 THRCLA_contig5202 5202 THRCLA_contig5203 5203 THRCLA_contig5204 5204 THRCLA_contig5205 5205 THRCLA_contig5206 5206 THRCLA_contig5207 5207 THRCLA_contig5208 5208 THRCLA_contig5209 5209 THRCLA_contig5210 5210 THRCLA_contig5211 5211 THRCLA_contig5212 5212 THRCLA_contig5213 5213 THRCLA_contig5214 5214 THRCLA_contig5215 5215 THRCLA_contig5216 5216 THRCLA_contig5217 5217 THRCLA_contig5218 5218 THRCLA_contig5219 5219 THRCLA_contig5220 5220 THRCLA_contig5221 5221 THRCLA_contig5222 5222 THRCLA_contig5223 5223 THRCLA_contig5224 5224 THRCLA_contig5225 5225 THRCLA_contig5226 5226 THRCLA_contig5227 5227 THRCLA_contig5228 5228 THRCLA_contig5229 5229 THRCLA_contig5230 5230 THRCLA_contig5231 5231 THRCLA_contig5232 5232 THRCLA_contig5233 5233 THRCLA_contig5234 5234 THRCLA_contig5235 5235 THRCLA_contig5236 5236 THRCLA_contig5237 5237 THRCLA_contig5238 5238 THRCLA_contig5239 5239 THRCLA_contig5240 5240 THRCLA_contig5241 5241 THRCLA_contig5242 5242 THRCLA_contig5243 5243 THRCLA_contig5244 5244 THRCLA_contig5245 5245 THRCLA_contig5246 5246 THRCLA_contig5247 5247 THRCLA_contig5248 5248 THRCLA_contig5249 5249 THRCLA_contig5250 5250 THRCLA_contig5251 5251 THRCLA_contig5252 5252 THRCLA_contig5253 5253 THRCLA_contig5254 5254 THRCLA_contig5255 5255 THRCLA_contig5256 5256 THRCLA_contig5257 5257 THRCLA_contig5258 5258 THRCLA_contig5259 5259 THRCLA_contig5260 5260 THRCLA_contig5261 5261 THRCLA_contig5262 5262 THRCLA_contig5263 5263 THRCLA_contig5264 5264 THRCLA_contig5265 5265 THRCLA_contig5266 5266 THRCLA_contig5267 5267 THRCLA_contig5268 5268 THRCLA_contig5269 5269 THRCLA_contig5270 5270 THRCLA_contig5271 5271 THRCLA_contig5272 5272 THRCLA_contig5273 5273 THRCLA_contig5274 5274 THRCLA_contig5275 5275 THRCLA_contig5276 5276 THRCLA_contig5277 5277 THRCLA_contig5278 5278 THRCLA_contig5279 5279 THRCLA_contig5280 5280 THRCLA_contig5281 5281 THRCLA_contig5282 5282 THRCLA_contig5283 5283 THRCLA_contig5284 5284 THRCLA_contig5285 5285 THRCLA_contig5286 5286 THRCLA_contig5287 5287 THRCLA_contig5288 5288 THRCLA_contig5289 5289 THRCLA_contig5290 5290 THRCLA_contig5291 5291 THRCLA_contig5292 5292 THRCLA_contig5293 5293 THRCLA_contig5294 5294 THRCLA_contig5295 5295 THRCLA_contig5296 5296 THRCLA_contig5297 5297 THRCLA_contig5298 5298 THRCLA_contig5299 5299 THRCLA_contig5300 5300 THRCLA_contig5301 5301 THRCLA_contig5302 5302 THRCLA_contig5303 5303 THRCLA_contig5304 5304 THRCLA_contig5305 5305 THRCLA_contig5306 5306 THRCLA_contig5307 5307 THRCLA_contig5308 5308 THRCLA_contig5309 5309 THRCLA_contig5310 5310 THRCLA_contig5311 5311 THRCLA_contig5312 5312 THRCLA_contig5313 5313 THRCLA_contig5314 5314 THRCLA_contig5315 5315 THRCLA_contig5316 5316 THRCLA_contig5317 5317 THRCLA_contig5318 5318 THRCLA_contig5319 5319 THRCLA_contig5320 5320 THRCLA_contig5321 5321 THRCLA_contig5322 5322 THRCLA_contig5323 5323 THRCLA_contig5324 5324 THRCLA_contig5325 5325 THRCLA_contig5326 5326 THRCLA_contig5327 5327 THRCLA_contig5328 5328 THRCLA_contig5329 5329 THRCLA_contig5330 5330 THRCLA_contig5331 5331 THRCLA_contig5332 5332 THRCLA_contig5333 5333 THRCLA_contig5334 5334 THRCLA_contig5335 5335 THRCLA_contig5336 5336 THRCLA_contig5337 5337 THRCLA_contig5338 5338 From ianmisner at my.uri.edu Tue Sep 25 06:31:23 2012 From: ianmisner at my.uri.edu (Ian Misner) Date: Tue, 25 Sep 2012 08:31:23 -0400 Subject: [maker-devel] Problem with maker_map_ids Message-ID: <0FCB8ACD-35A0-4ED8-BAE2-02C2621E3F65@my.uri.edu> Hello, I'm trying to create human friendly ids and I'm getting an error when I use the -sort_file option. Without the sort file it runs fine just not numbered from the first contig. I have had some programers at our cluster look at the script and they attempted a fix but it did not work. They mentioned the script was "buggy" so this might be part of the problem. I've attached the error as well as the sort file. I can send more files if necessary. Thanks for you time. Cheers Ian $ maker_map_ids --prefix THRCLA_ --justify 5 --sort_order 34112_sort.txt 34112_3June11Ass.gff > 34112_3June11Ass_named.txt Can't use string ("34112_sort.txt") as a HASH ref while "strict refs" in use at /gpfs/runtime/opt/maker/2.10/maker/bin/maker_map_ids line 311, <$IN> line 499186. -------------- next part -------------- THRCLA_contig1 1 THRCLA_contig2 2 THRCLA_contig3 3 THRCLA_contig4 4 THRCLA_contig5 5 THRCLA_contig6 6 THRCLA_contig7 7 THRCLA_contig8 8 THRCLA_contig9 9 THRCLA_contig10 10 THRCLA_contig11 11 THRCLA_contig12 12 THRCLA_contig13 13 THRCLA_contig14 14 THRCLA_contig15 15 THRCLA_contig16 16 THRCLA_contig17 17 THRCLA_contig18 18 THRCLA_contig19 19 THRCLA_contig20 20 THRCLA_contig21 21 THRCLA_contig22 22 THRCLA_contig23 23 THRCLA_contig24 24 THRCLA_contig25 25 THRCLA_contig26 26 THRCLA_contig27 27 THRCLA_contig28 28 THRCLA_contig29 29 THRCLA_contig30 30 THRCLA_contig31 31 THRCLA_contig32 32 THRCLA_contig33 33 THRCLA_contig34 34 THRCLA_contig35 35 THRCLA_contig36 36 THRCLA_contig37 37 THRCLA_contig38 38 THRCLA_contig39 39 THRCLA_contig40 40 THRCLA_contig41 41 THRCLA_contig42 42 THRCLA_contig43 43 THRCLA_contig44 44 THRCLA_contig45 45 THRCLA_contig46 46 THRCLA_contig47 47 THRCLA_contig48 48 THRCLA_contig49 49 THRCLA_contig50 50 THRCLA_contig51 51 THRCLA_contig52 52 THRCLA_contig53 53 THRCLA_contig54 54 THRCLA_contig55 55 THRCLA_contig56 56 THRCLA_contig57 57 THRCLA_contig58 58 THRCLA_contig59 59 THRCLA_contig60 60 THRCLA_contig61 61 THRCLA_contig62 62 THRCLA_contig63 63 THRCLA_contig64 64 THRCLA_contig65 65 THRCLA_contig66 66 THRCLA_contig67 67 THRCLA_contig68 68 THRCLA_contig69 69 THRCLA_contig70 70 THRCLA_contig71 71 THRCLA_contig72 72 THRCLA_contig73 73 THRCLA_contig74 74 THRCLA_contig75 75 THRCLA_contig76 76 THRCLA_contig77 77 THRCLA_contig78 78 THRCLA_contig79 79 THRCLA_contig80 80 THRCLA_contig81 81 THRCLA_contig82 82 THRCLA_contig83 83 THRCLA_contig84 84 THRCLA_contig85 85 THRCLA_contig86 86 THRCLA_contig87 87 THRCLA_contig88 88 THRCLA_contig89 89 THRCLA_contig90 90 THRCLA_contig91 91 THRCLA_contig92 92 THRCLA_contig93 93 THRCLA_contig94 94 THRCLA_contig95 95 THRCLA_contig96 96 THRCLA_contig97 97 THRCLA_contig98 98 THRCLA_contig99 99 THRCLA_contig100 100 THRCLA_contig101 101 THRCLA_contig102 102 THRCLA_contig103 103 THRCLA_contig104 104 THRCLA_contig105 105 THRCLA_contig106 106 THRCLA_contig107 107 THRCLA_contig108 108 THRCLA_contig109 109 THRCLA_contig110 110 THRCLA_contig111 111 THRCLA_contig112 112 THRCLA_contig113 113 THRCLA_contig114 114 THRCLA_contig115 115 THRCLA_contig116 116 THRCLA_contig117 117 THRCLA_contig118 118 THRCLA_contig119 119 THRCLA_contig120 120 THRCLA_contig121 121 THRCLA_contig122 122 THRCLA_contig123 123 THRCLA_contig124 124 THRCLA_contig125 125 THRCLA_contig126 126 THRCLA_contig127 127 THRCLA_contig128 128 THRCLA_contig129 129 THRCLA_contig130 130 THRCLA_contig131 131 THRCLA_contig132 132 THRCLA_contig133 133 THRCLA_contig134 134 THRCLA_contig135 135 THRCLA_contig136 136 THRCLA_contig137 137 THRCLA_contig138 138 THRCLA_contig139 139 THRCLA_contig140 140 THRCLA_contig141 141 THRCLA_contig142 142 THRCLA_contig143 143 THRCLA_contig144 144 THRCLA_contig145 145 THRCLA_contig146 146 THRCLA_contig147 147 THRCLA_contig148 148 THRCLA_contig149 149 THRCLA_contig150 150 THRCLA_contig151 151 THRCLA_contig152 152 THRCLA_contig153 153 THRCLA_contig154 154 THRCLA_contig155 155 THRCLA_contig156 156 THRCLA_contig157 157 THRCLA_contig158 158 THRCLA_contig159 159 THRCLA_contig160 160 THRCLA_contig161 161 THRCLA_contig162 162 THRCLA_contig163 163 THRCLA_contig164 164 THRCLA_contig165 165 THRCLA_contig166 166 THRCLA_contig167 167 THRCLA_contig168 168 THRCLA_contig169 169 THRCLA_contig170 170 THRCLA_contig171 171 THRCLA_contig172 172 THRCLA_contig173 173 THRCLA_contig174 174 THRCLA_contig175 175 THRCLA_contig176 176 THRCLA_contig177 177 THRCLA_contig178 178 THRCLA_contig179 179 THRCLA_contig180 180 THRCLA_contig181 181 THRCLA_contig182 182 THRCLA_contig183 183 THRCLA_contig184 184 THRCLA_contig185 185 THRCLA_contig186 186 THRCLA_contig187 187 THRCLA_contig188 188 THRCLA_contig189 189 THRCLA_contig190 190 THRCLA_contig191 191 THRCLA_contig192 192 THRCLA_contig193 193 THRCLA_contig194 194 THRCLA_contig195 195 THRCLA_contig196 196 THRCLA_contig197 197 THRCLA_contig198 198 THRCLA_contig199 199 THRCLA_contig200 200 THRCLA_contig201 201 THRCLA_contig202 202 THRCLA_contig203 203 THRCLA_contig204 204 THRCLA_contig205 205 THRCLA_contig206 206 THRCLA_contig207 207 THRCLA_contig208 208 THRCLA_contig209 209 THRCLA_contig210 210 THRCLA_contig211 211 THRCLA_contig212 212 THRCLA_contig213 213 THRCLA_contig214 214 THRCLA_contig215 215 THRCLA_contig216 216 THRCLA_contig217 217 THRCLA_contig218 218 THRCLA_contig219 219 THRCLA_contig220 220 THRCLA_contig221 221 THRCLA_contig222 222 THRCLA_contig223 223 THRCLA_contig224 224 THRCLA_contig225 225 THRCLA_contig226 226 THRCLA_contig227 227 THRCLA_contig228 228 THRCLA_contig229 229 THRCLA_contig230 230 THRCLA_contig231 231 THRCLA_contig232 232 THRCLA_contig233 233 THRCLA_contig234 234 THRCLA_contig235 235 THRCLA_contig236 236 THRCLA_contig237 237 THRCLA_contig238 238 THRCLA_contig239 239 THRCLA_contig240 240 THRCLA_contig241 241 THRCLA_contig242 242 THRCLA_contig243 243 THRCLA_contig244 244 THRCLA_contig245 245 THRCLA_contig246 246 THRCLA_contig247 247 THRCLA_contig248 248 THRCLA_contig249 249 THRCLA_contig250 250 THRCLA_contig251 251 THRCLA_contig252 252 THRCLA_contig253 253 THRCLA_contig254 254 THRCLA_contig255 255 THRCLA_contig256 256 THRCLA_contig257 257 THRCLA_contig258 258 THRCLA_contig259 259 THRCLA_contig260 260 THRCLA_contig261 261 THRCLA_contig262 262 THRCLA_contig263 263 THRCLA_contig264 264 THRCLA_contig265 265 THRCLA_contig266 266 THRCLA_contig267 267 THRCLA_contig268 268 THRCLA_contig269 269 THRCLA_contig270 270 THRCLA_contig271 271 THRCLA_contig272 272 THRCLA_contig273 273 THRCLA_contig274 274 THRCLA_contig275 275 THRCLA_contig276 276 THRCLA_contig277 277 THRCLA_contig278 278 THRCLA_contig279 279 THRCLA_contig280 280 THRCLA_contig281 281 THRCLA_contig282 282 THRCLA_contig283 283 THRCLA_contig284 284 THRCLA_contig285 285 THRCLA_contig286 286 THRCLA_contig287 287 THRCLA_contig288 288 THRCLA_contig289 289 THRCLA_contig290 290 THRCLA_contig291 291 THRCLA_contig292 292 THRCLA_contig293 293 THRCLA_contig294 294 THRCLA_contig295 295 THRCLA_contig296 296 THRCLA_contig297 297 THRCLA_contig298 298 THRCLA_contig299 299 THRCLA_contig300 300 THRCLA_contig301 301 THRCLA_contig302 302 THRCLA_contig303 303 THRCLA_contig304 304 THRCLA_contig305 305 THRCLA_contig306 306 THRCLA_contig307 307 THRCLA_contig308 308 THRCLA_contig309 309 THRCLA_contig310 310 THRCLA_contig311 311 THRCLA_contig312 312 THRCLA_contig313 313 THRCLA_contig314 314 THRCLA_contig315 315 THRCLA_contig316 316 THRCLA_contig317 317 THRCLA_contig318 318 THRCLA_contig319 319 THRCLA_contig320 320 THRCLA_contig321 321 THRCLA_contig322 322 THRCLA_contig323 323 THRCLA_contig324 324 THRCLA_contig325 325 THRCLA_contig326 326 THRCLA_contig327 327 THRCLA_contig328 328 THRCLA_contig329 329 THRCLA_contig330 330 THRCLA_contig331 331 THRCLA_contig332 332 THRCLA_contig333 333 THRCLA_contig334 334 THRCLA_contig335 335 THRCLA_contig336 336 THRCLA_contig337 337 THRCLA_contig338 338 THRCLA_contig339 339 THRCLA_contig340 340 THRCLA_contig341 341 THRCLA_contig342 342 THRCLA_contig343 343 THRCLA_contig344 344 THRCLA_contig345 345 THRCLA_contig346 346 THRCLA_contig347 347 THRCLA_contig348 348 THRCLA_contig349 349 THRCLA_contig350 350 THRCLA_contig351 351 THRCLA_contig352 352 THRCLA_contig353 353 THRCLA_contig354 354 THRCLA_contig355 355 THRCLA_contig356 356 THRCLA_contig357 357 THRCLA_contig358 358 THRCLA_contig359 359 THRCLA_contig360 360 THRCLA_contig361 361 THRCLA_contig362 362 THRCLA_contig363 363 THRCLA_contig364 364 THRCLA_contig365 365 THRCLA_contig366 366 THRCLA_contig367 367 THRCLA_contig368 368 THRCLA_contig369 369 THRCLA_contig370 370 THRCLA_contig371 371 THRCLA_contig372 372 THRCLA_contig373 373 THRCLA_contig374 374 THRCLA_contig375 375 THRCLA_contig376 376 THRCLA_contig377 377 THRCLA_contig378 378 THRCLA_contig379 379 THRCLA_contig380 380 THRCLA_contig381 381 THRCLA_contig382 382 THRCLA_contig383 383 THRCLA_contig384 384 THRCLA_contig385 385 THRCLA_contig386 386 THRCLA_contig387 387 THRCLA_contig388 388 THRCLA_contig389 389 THRCLA_contig390 390 THRCLA_contig391 391 THRCLA_contig392 392 THRCLA_contig393 393 THRCLA_contig394 394 THRCLA_contig395 395 THRCLA_contig396 396 THRCLA_contig397 397 THRCLA_contig398 398 THRCLA_contig399 399 THRCLA_contig400 400 THRCLA_contig401 401 THRCLA_contig402 402 THRCLA_contig403 403 THRCLA_contig404 404 THRCLA_contig405 405 THRCLA_contig406 406 THRCLA_contig407 407 THRCLA_contig408 408 THRCLA_contig409 409 THRCLA_contig410 410 THRCLA_contig411 411 THRCLA_contig412 412 THRCLA_contig413 413 THRCLA_contig414 414 THRCLA_contig415 415 THRCLA_contig416 416 THRCLA_contig417 417 THRCLA_contig418 418 THRCLA_contig419 419 THRCLA_contig420 420 THRCLA_contig421 421 THRCLA_contig422 422 THRCLA_contig423 423 THRCLA_contig424 424 THRCLA_contig425 425 THRCLA_contig426 426 THRCLA_contig427 427 THRCLA_contig428 428 THRCLA_contig429 429 THRCLA_contig430 430 THRCLA_contig431 431 THRCLA_contig432 432 THRCLA_contig433 433 THRCLA_contig434 434 THRCLA_contig435 435 THRCLA_contig436 436 THRCLA_contig437 437 THRCLA_contig438 438 THRCLA_contig439 439 THRCLA_contig440 440 THRCLA_contig441 441 THRCLA_contig442 442 THRCLA_contig443 443 THRCLA_contig444 444 THRCLA_contig445 445 THRCLA_contig446 446 THRCLA_contig447 447 THRCLA_contig448 448 THRCLA_contig449 449 THRCLA_contig450 450 THRCLA_contig451 451 THRCLA_contig452 452 THRCLA_contig453 453 THRCLA_contig454 454 THRCLA_contig455 455 THRCLA_contig456 456 THRCLA_contig457 457 THRCLA_contig458 458 THRCLA_contig459 459 THRCLA_contig460 460 THRCLA_contig461 461 THRCLA_contig462 462 THRCLA_contig463 463 THRCLA_contig464 464 THRCLA_contig465 465 THRCLA_contig466 466 THRCLA_contig467 467 THRCLA_contig468 468 THRCLA_contig469 469 THRCLA_contig470 470 THRCLA_contig471 471 THRCLA_contig472 472 THRCLA_contig473 473 THRCLA_contig474 474 THRCLA_contig475 475 THRCLA_contig476 476 THRCLA_contig477 477 THRCLA_contig478 478 THRCLA_contig479 479 THRCLA_contig480 480 THRCLA_contig481 481 THRCLA_contig482 482 THRCLA_contig483 483 THRCLA_contig484 484 THRCLA_contig485 485 THRCLA_contig486 486 THRCLA_contig487 487 THRCLA_contig488 488 THRCLA_contig489 489 THRCLA_contig490 490 THRCLA_contig491 491 THRCLA_contig492 492 THRCLA_contig493 493 THRCLA_contig494 494 THRCLA_contig495 495 THRCLA_contig496 496 THRCLA_contig497 497 THRCLA_contig498 498 THRCLA_contig499 499 THRCLA_contig500 500 THRCLA_contig501 501 THRCLA_contig502 502 THRCLA_contig503 503 THRCLA_contig504 504 THRCLA_contig505 505 THRCLA_contig506 506 THRCLA_contig507 507 THRCLA_contig508 508 THRCLA_contig509 509 THRCLA_contig510 510 THRCLA_contig511 511 THRCLA_contig512 512 THRCLA_contig513 513 THRCLA_contig514 514 THRCLA_contig515 515 THRCLA_contig516 516 THRCLA_contig517 517 THRCLA_contig518 518 THRCLA_contig519 519 THRCLA_contig520 520 THRCLA_contig521 521 THRCLA_contig522 522 THRCLA_contig523 523 THRCLA_contig524 524 THRCLA_contig525 525 THRCLA_contig526 526 THRCLA_contig527 527 THRCLA_contig528 528 THRCLA_contig529 529 THRCLA_contig530 530 THRCLA_contig531 531 THRCLA_contig532 532 THRCLA_contig533 533 THRCLA_contig534 534 THRCLA_contig535 535 THRCLA_contig536 536 THRCLA_contig537 537 THRCLA_contig538 538 THRCLA_contig539 539 THRCLA_contig540 540 THRCLA_contig541 541 THRCLA_contig542 542 THRCLA_contig543 543 THRCLA_contig544 544 THRCLA_contig545 545 THRCLA_contig546 546 THRCLA_contig547 547 THRCLA_contig548 548 THRCLA_contig549 549 THRCLA_contig550 550 THRCLA_contig551 551 THRCLA_contig552 552 THRCLA_contig553 553 THRCLA_contig554 554 THRCLA_contig555 555 THRCLA_contig556 556 THRCLA_contig557 557 THRCLA_contig558 558 THRCLA_contig559 559 THRCLA_contig560 560 THRCLA_contig561 561 THRCLA_contig562 562 THRCLA_contig563 563 THRCLA_contig564 564 THRCLA_contig565 565 THRCLA_contig566 566 THRCLA_contig567 567 THRCLA_contig568 568 THRCLA_contig569 569 THRCLA_contig570 570 THRCLA_contig571 571 THRCLA_contig572 572 THRCLA_contig573 573 THRCLA_contig574 574 THRCLA_contig575 575 THRCLA_contig576 576 THRCLA_contig577 577 THRCLA_contig578 578 THRCLA_contig579 579 THRCLA_contig580 580 THRCLA_contig581 581 THRCLA_contig582 582 THRCLA_contig583 583 THRCLA_contig584 584 THRCLA_contig585 585 THRCLA_contig586 586 THRCLA_contig587 587 THRCLA_contig588 588 THRCLA_contig589 589 THRCLA_contig590 590 THRCLA_contig591 591 THRCLA_contig592 592 THRCLA_contig593 593 THRCLA_contig594 594 THRCLA_contig595 595 THRCLA_contig596 596 THRCLA_contig597 597 THRCLA_contig598 598 THRCLA_contig599 599 THRCLA_contig600 600 THRCLA_contig601 601 THRCLA_contig602 602 THRCLA_contig603 603 THRCLA_contig604 604 THRCLA_contig605 605 THRCLA_contig606 606 THRCLA_contig607 607 THRCLA_contig608 608 THRCLA_contig609 609 THRCLA_contig610 610 THRCLA_contig611 611 THRCLA_contig612 612 THRCLA_contig613 613 THRCLA_contig614 614 THRCLA_contig615 615 THRCLA_contig616 616 THRCLA_contig617 617 THRCLA_contig618 618 THRCLA_contig619 619 THRCLA_contig620 620 THRCLA_contig621 621 THRCLA_contig622 622 THRCLA_contig623 623 THRCLA_contig624 624 THRCLA_contig625 625 THRCLA_contig626 626 THRCLA_contig627 627 THRCLA_contig628 628 THRCLA_contig629 629 THRCLA_contig630 630 THRCLA_contig631 631 THRCLA_contig632 632 THRCLA_contig633 633 THRCLA_contig634 634 THRCLA_contig635 635 THRCLA_contig636 636 THRCLA_contig637 637 THRCLA_contig638 638 THRCLA_contig639 639 THRCLA_contig640 640 THRCLA_contig641 641 THRCLA_contig642 642 THRCLA_contig643 643 THRCLA_contig644 644 THRCLA_contig645 645 THRCLA_contig646 646 THRCLA_contig647 647 THRCLA_contig648 648 THRCLA_contig649 649 THRCLA_contig650 650 THRCLA_contig651 651 THRCLA_contig652 652 THRCLA_contig653 653 THRCLA_contig654 654 THRCLA_contig655 655 THRCLA_contig656 656 THRCLA_contig657 657 THRCLA_contig658 658 THRCLA_contig659 659 THRCLA_contig660 660 THRCLA_contig661 661 THRCLA_contig662 662 THRCLA_contig663 663 THRCLA_contig664 664 THRCLA_contig665 665 THRCLA_contig666 666 THRCLA_contig667 667 THRCLA_contig668 668 THRCLA_contig669 669 THRCLA_contig670 670 THRCLA_contig671 671 THRCLA_contig672 672 THRCLA_contig673 673 THRCLA_contig674 674 THRCLA_contig675 675 THRCLA_contig676 676 THRCLA_contig677 677 THRCLA_contig678 678 THRCLA_contig679 679 THRCLA_contig680 680 THRCLA_contig681 681 THRCLA_contig682 682 THRCLA_contig683 683 THRCLA_contig684 684 THRCLA_contig685 685 THRCLA_contig686 686 THRCLA_contig687 687 THRCLA_contig688 688 THRCLA_contig689 689 THRCLA_contig690 690 THRCLA_contig691 691 THRCLA_contig692 692 THRCLA_contig693 693 THRCLA_contig694 694 THRCLA_contig695 695 THRCLA_contig696 696 THRCLA_contig697 697 THRCLA_contig698 698 THRCLA_contig699 699 THRCLA_contig700 700 THRCLA_contig701 701 THRCLA_contig702 702 THRCLA_contig703 703 THRCLA_contig704 704 THRCLA_contig705 705 THRCLA_contig706 706 THRCLA_contig707 707 THRCLA_contig708 708 THRCLA_contig709 709 THRCLA_contig710 710 THRCLA_contig711 711 THRCLA_contig712 712 THRCLA_contig713 713 THRCLA_contig714 714 THRCLA_contig715 715 THRCLA_contig716 716 THRCLA_contig717 717 THRCLA_contig718 718 THRCLA_contig719 719 THRCLA_contig720 720 THRCLA_contig721 721 THRCLA_contig722 722 THRCLA_contig723 723 THRCLA_contig724 724 THRCLA_contig725 725 THRCLA_contig726 726 THRCLA_contig727 727 THRCLA_contig728 728 THRCLA_contig729 729 THRCLA_contig730 730 THRCLA_contig731 731 THRCLA_contig732 732 THRCLA_contig733 733 THRCLA_contig734 734 THRCLA_contig735 735 THRCLA_contig736 736 THRCLA_contig737 737 THRCLA_contig738 738 THRCLA_contig739 739 THRCLA_contig740 740 THRCLA_contig741 741 THRCLA_contig742 742 THRCLA_contig743 743 THRCLA_contig744 744 THRCLA_contig745 745 THRCLA_contig746 746 THRCLA_contig747 747 THRCLA_contig748 748 THRCLA_contig749 749 THRCLA_contig750 750 THRCLA_contig751 751 THRCLA_contig752 752 THRCLA_contig753 753 THRCLA_contig754 754 THRCLA_contig755 755 THRCLA_contig756 756 THRCLA_contig757 757 THRCLA_contig758 758 THRCLA_contig759 759 THRCLA_contig760 760 THRCLA_contig761 761 THRCLA_contig762 762 THRCLA_contig763 763 THRCLA_contig764 764 THRCLA_contig765 765 THRCLA_contig766 766 THRCLA_contig767 767 THRCLA_contig768 768 THRCLA_contig769 769 THRCLA_contig770 770 THRCLA_contig771 771 THRCLA_contig772 772 THRCLA_contig773 773 THRCLA_contig774 774 THRCLA_contig775 775 THRCLA_contig776 776 THRCLA_contig777 777 THRCLA_contig778 778 THRCLA_contig779 779 THRCLA_contig780 780 THRCLA_contig781 781 THRCLA_contig782 782 THRCLA_contig783 783 THRCLA_contig784 784 THRCLA_contig785 785 THRCLA_contig786 786 THRCLA_contig787 787 THRCLA_contig788 788 THRCLA_contig789 789 THRCLA_contig790 790 THRCLA_contig791 791 THRCLA_contig792 792 THRCLA_contig793 793 THRCLA_contig794 794 THRCLA_contig795 795 THRCLA_contig796 796 THRCLA_contig797 797 THRCLA_contig798 798 THRCLA_contig799 799 THRCLA_contig800 800 THRCLA_contig801 801 THRCLA_contig802 802 THRCLA_contig803 803 THRCLA_contig804 804 THRCLA_contig805 805 THRCLA_contig806 806 THRCLA_contig807 807 THRCLA_contig808 808 THRCLA_contig809 809 THRCLA_contig810 810 THRCLA_contig811 811 THRCLA_contig812 812 THRCLA_contig813 813 THRCLA_contig814 814 THRCLA_contig815 815 THRCLA_contig816 816 THRCLA_contig817 817 THRCLA_contig818 818 THRCLA_contig819 819 THRCLA_contig820 820 THRCLA_contig821 821 THRCLA_contig822 822 THRCLA_contig823 823 THRCLA_contig824 824 THRCLA_contig825 825 THRCLA_contig826 826 THRCLA_contig827 827 THRCLA_contig828 828 THRCLA_contig829 829 THRCLA_contig830 830 THRCLA_contig831 831 THRCLA_contig832 832 THRCLA_contig833 833 THRCLA_contig834 834 THRCLA_contig835 835 THRCLA_contig836 836 THRCLA_contig837 837 THRCLA_contig838 838 THRCLA_contig839 839 THRCLA_contig840 840 THRCLA_contig841 841 THRCLA_contig842 842 THRCLA_contig843 843 THRCLA_contig844 844 THRCLA_contig845 845 THRCLA_contig846 846 THRCLA_contig847 847 THRCLA_contig848 848 THRCLA_contig849 849 THRCLA_contig850 850 THRCLA_contig851 851 THRCLA_contig852 852 THRCLA_contig853 853 THRCLA_contig854 854 THRCLA_contig855 855 THRCLA_contig856 856 THRCLA_contig857 857 THRCLA_contig858 858 THRCLA_contig859 859 THRCLA_contig860 860 THRCLA_contig861 861 THRCLA_contig862 862 THRCLA_contig863 863 THRCLA_contig864 864 THRCLA_contig865 865 THRCLA_contig866 866 THRCLA_contig867 867 THRCLA_contig868 868 THRCLA_contig869 869 THRCLA_contig870 870 THRCLA_contig871 871 THRCLA_contig872 872 THRCLA_contig873 873 THRCLA_contig874 874 THRCLA_contig875 875 THRCLA_contig876 876 THRCLA_contig877 877 THRCLA_contig878 878 THRCLA_contig879 879 THRCLA_contig880 880 THRCLA_contig881 881 THRCLA_contig882 882 THRCLA_contig883 883 THRCLA_contig884 884 THRCLA_contig885 885 THRCLA_contig886 886 THRCLA_contig887 887 THRCLA_contig888 888 THRCLA_contig889 889 THRCLA_contig890 890 THRCLA_contig891 891 THRCLA_contig892 892 THRCLA_contig893 893 THRCLA_contig894 894 THRCLA_contig895 895 THRCLA_contig896 896 THRCLA_contig897 897 THRCLA_contig898 898 THRCLA_contig899 899 THRCLA_contig900 900 THRCLA_contig901 901 THRCLA_contig902 902 THRCLA_contig903 903 THRCLA_contig904 904 THRCLA_contig905 905 THRCLA_contig906 906 THRCLA_contig907 907 THRCLA_contig908 908 THRCLA_contig909 909 THRCLA_contig910 910 THRCLA_contig911 911 THRCLA_contig912 912 THRCLA_contig913 913 THRCLA_contig914 914 THRCLA_contig915 915 THRCLA_contig916 916 THRCLA_contig917 917 THRCLA_contig918 918 THRCLA_contig919 919 THRCLA_contig920 920 THRCLA_contig921 921 THRCLA_contig922 922 THRCLA_contig923 923 THRCLA_contig924 924 THRCLA_contig925 925 THRCLA_contig926 926 THRCLA_contig927 927 THRCLA_contig928 928 THRCLA_contig929 929 THRCLA_contig930 930 THRCLA_contig931 931 THRCLA_contig932 932 THRCLA_contig933 933 THRCLA_contig934 934 THRCLA_contig935 935 THRCLA_contig936 936 THRCLA_contig937 937 THRCLA_contig938 938 THRCLA_contig939 939 THRCLA_contig940 940 THRCLA_contig941 941 THRCLA_contig942 942 THRCLA_contig943 943 THRCLA_contig944 944 THRCLA_contig945 945 THRCLA_contig946 946 THRCLA_contig947 947 THRCLA_contig948 948 THRCLA_contig949 949 THRCLA_contig950 950 THRCLA_contig951 951 THRCLA_contig952 952 THRCLA_contig953 953 THRCLA_contig954 954 THRCLA_contig955 955 THRCLA_contig956 956 THRCLA_contig957 957 THRCLA_contig958 958 THRCLA_contig959 959 THRCLA_contig960 960 THRCLA_contig961 961 THRCLA_contig962 962 THRCLA_contig963 963 THRCLA_contig964 964 THRCLA_contig965 965 THRCLA_contig966 966 THRCLA_contig967 967 THRCLA_contig968 968 THRCLA_contig969 969 THRCLA_contig970 970 THRCLA_contig971 971 THRCLA_contig972 972 THRCLA_contig973 973 THRCLA_contig974 974 THRCLA_contig975 975 THRCLA_contig976 976 THRCLA_contig977 977 THRCLA_contig978 978 THRCLA_contig979 979 THRCLA_contig980 980 THRCLA_contig981 981 THRCLA_contig982 982 THRCLA_contig983 983 THRCLA_contig984 984 THRCLA_contig985 985 THRCLA_contig986 986 THRCLA_contig987 987 THRCLA_contig988 988 THRCLA_contig989 989 THRCLA_contig990 990 THRCLA_contig991 991 THRCLA_contig992 992 THRCLA_contig993 993 THRCLA_contig994 994 THRCLA_contig995 995 THRCLA_contig996 996 THRCLA_contig997 997 THRCLA_contig998 998 THRCLA_contig999 999 THRCLA_contig1000 1000 THRCLA_contig1001 1001 THRCLA_contig1002 1002 THRCLA_contig1003 1003 THRCLA_contig1004 1004 THRCLA_contig1005 1005 THRCLA_contig1006 1006 THRCLA_contig1007 1007 THRCLA_contig1008 1008 THRCLA_contig1009 1009 THRCLA_contig1010 1010 THRCLA_contig1011 1011 THRCLA_contig1012 1012 THRCLA_contig1013 1013 THRCLA_contig1014 1014 THRCLA_contig1015 1015 THRCLA_contig1016 1016 THRCLA_contig1017 1017 THRCLA_contig1018 1018 THRCLA_contig1019 1019 THRCLA_contig1020 1020 THRCLA_contig1021 1021 THRCLA_contig1022 1022 THRCLA_contig1023 1023 THRCLA_contig1024 1024 THRCLA_contig1025 1025 THRCLA_contig1026 1026 THRCLA_contig1027 1027 THRCLA_contig1028 1028 THRCLA_contig1029 1029 THRCLA_contig1030 1030 THRCLA_contig1031 1031 THRCLA_contig1032 1032 THRCLA_contig1033 1033 THRCLA_contig1034 1034 THRCLA_contig1035 1035 THRCLA_contig1036 1036 THRCLA_contig1037 1037 THRCLA_contig1038 1038 THRCLA_contig1039 1039 THRCLA_contig1040 1040 THRCLA_contig1041 1041 THRCLA_contig1042 1042 THRCLA_contig1043 1043 THRCLA_contig1044 1044 THRCLA_contig1045 1045 THRCLA_contig1046 1046 THRCLA_contig1047 1047 THRCLA_contig1048 1048 THRCLA_contig1049 1049 THRCLA_contig1050 1050 THRCLA_contig1051 1051 THRCLA_contig1052 1052 THRCLA_contig1053 1053 THRCLA_contig1054 1054 THRCLA_contig1055 1055 THRCLA_contig1056 1056 THRCLA_contig1057 1057 THRCLA_contig1058 1058 THRCLA_contig1059 1059 THRCLA_contig1060 1060 THRCLA_contig1061 1061 THRCLA_contig1062 1062 THRCLA_contig1063 1063 THRCLA_contig1064 1064 THRCLA_contig1065 1065 THRCLA_contig1066 1066 THRCLA_contig1067 1067 THRCLA_contig1068 1068 THRCLA_contig1069 1069 THRCLA_contig1070 1070 THRCLA_contig1071 1071 THRCLA_contig1072 1072 THRCLA_contig1073 1073 THRCLA_contig1074 1074 THRCLA_contig1075 1075 THRCLA_contig1076 1076 THRCLA_contig1077 1077 THRCLA_contig1078 1078 THRCLA_contig1079 1079 THRCLA_contig1080 1080 THRCLA_contig1081 1081 THRCLA_contig1082 1082 THRCLA_contig1083 1083 THRCLA_contig1084 1084 THRCLA_contig1085 1085 THRCLA_contig1086 1086 THRCLA_contig1087 1087 THRCLA_contig1088 1088 THRCLA_contig1089 1089 THRCLA_contig1090 1090 THRCLA_contig1091 1091 THRCLA_contig1092 1092 THRCLA_contig1093 1093 THRCLA_contig1094 1094 THRCLA_contig1095 1095 THRCLA_contig1096 1096 THRCLA_contig1097 1097 THRCLA_contig1098 1098 THRCLA_contig1099 1099 THRCLA_contig1100 1100 THRCLA_contig1101 1101 THRCLA_contig1102 1102 THRCLA_contig1103 1103 THRCLA_contig1104 1104 THRCLA_contig1105 1105 THRCLA_contig1106 1106 THRCLA_contig1107 1107 THRCLA_contig1108 1108 THRCLA_contig1109 1109 THRCLA_contig1110 1110 THRCLA_contig1111 1111 THRCLA_contig1112 1112 THRCLA_contig1113 1113 THRCLA_contig1114 1114 THRCLA_contig1115 1115 THRCLA_contig1116 1116 THRCLA_contig1117 1117 THRCLA_contig1118 1118 THRCLA_contig1119 1119 THRCLA_contig1120 1120 THRCLA_contig1121 1121 THRCLA_contig1122 1122 THRCLA_contig1123 1123 THRCLA_contig1124 1124 THRCLA_contig1125 1125 THRCLA_contig1126 1126 THRCLA_contig1127 1127 THRCLA_contig1128 1128 THRCLA_contig1129 1129 THRCLA_contig1130 1130 THRCLA_contig1131 1131 THRCLA_contig1132 1132 THRCLA_contig1133 1133 THRCLA_contig1134 1134 THRCLA_contig1135 1135 THRCLA_contig1136 1136 THRCLA_contig1137 1137 THRCLA_contig1138 1138 THRCLA_contig1139 1139 THRCLA_contig1140 1140 THRCLA_contig1141 1141 THRCLA_contig1142 1142 THRCLA_contig1143 1143 THRCLA_contig1144 1144 THRCLA_contig1145 1145 THRCLA_contig1146 1146 THRCLA_contig1147 1147 THRCLA_contig1148 1148 THRCLA_contig1149 1149 THRCLA_contig1150 1150 THRCLA_contig1151 1151 THRCLA_contig1152 1152 THRCLA_contig1153 1153 THRCLA_contig1154 1154 THRCLA_contig1155 1155 THRCLA_contig1156 1156 THRCLA_contig1157 1157 THRCLA_contig1158 1158 THRCLA_contig1159 1159 THRCLA_contig1160 1160 THRCLA_contig1161 1161 THRCLA_contig1162 1162 THRCLA_contig1163 1163 THRCLA_contig1164 1164 THRCLA_contig1165 1165 THRCLA_contig1166 1166 THRCLA_contig1167 1167 THRCLA_contig1168 1168 THRCLA_contig1169 1169 THRCLA_contig1170 1170 THRCLA_contig1171 1171 THRCLA_contig1172 1172 THRCLA_contig1173 1173 THRCLA_contig1174 1174 THRCLA_contig1175 1175 THRCLA_contig1176 1176 THRCLA_contig1177 1177 THRCLA_contig1178 1178 THRCLA_contig1179 1179 THRCLA_contig1180 1180 THRCLA_contig1181 1181 THRCLA_contig1182 1182 THRCLA_contig1183 1183 THRCLA_contig1184 1184 THRCLA_contig1185 1185 THRCLA_contig1186 1186 THRCLA_contig1187 1187 THRCLA_contig1188 1188 THRCLA_contig1189 1189 THRCLA_contig1190 1190 THRCLA_contig1191 1191 THRCLA_contig1192 1192 THRCLA_contig1193 1193 THRCLA_contig1194 1194 THRCLA_contig1195 1195 THRCLA_contig1196 1196 THRCLA_contig1197 1197 THRCLA_contig1198 1198 THRCLA_contig1199 1199 THRCLA_contig1200 1200 THRCLA_contig1201 1201 THRCLA_contig1202 1202 THRCLA_contig1203 1203 THRCLA_contig1204 1204 THRCLA_contig1205 1205 THRCLA_contig1206 1206 THRCLA_contig1207 1207 THRCLA_contig1208 1208 THRCLA_contig1209 1209 THRCLA_contig1210 1210 THRCLA_contig1211 1211 THRCLA_contig1212 1212 THRCLA_contig1213 1213 THRCLA_contig1214 1214 THRCLA_contig1215 1215 THRCLA_contig1216 1216 THRCLA_contig1217 1217 THRCLA_contig1218 1218 THRCLA_contig1219 1219 THRCLA_contig1220 1220 THRCLA_contig1221 1221 THRCLA_contig1222 1222 THRCLA_contig1223 1223 THRCLA_contig1224 1224 THRCLA_contig1225 1225 THRCLA_contig1226 1226 THRCLA_contig1227 1227 THRCLA_contig1228 1228 THRCLA_contig1229 1229 THRCLA_contig1230 1230 THRCLA_contig1231 1231 THRCLA_contig1232 1232 THRCLA_contig1233 1233 THRCLA_contig1234 1234 THRCLA_contig1235 1235 THRCLA_contig1236 1236 THRCLA_contig1237 1237 THRCLA_contig1238 1238 THRCLA_contig1239 1239 THRCLA_contig1240 1240 THRCLA_contig1241 1241 THRCLA_contig1242 1242 THRCLA_contig1243 1243 THRCLA_contig1244 1244 THRCLA_contig1245 1245 THRCLA_contig1246 1246 THRCLA_contig1247 1247 THRCLA_contig1248 1248 THRCLA_contig1249 1249 THRCLA_contig1250 1250 THRCLA_contig1251 1251 THRCLA_contig1252 1252 THRCLA_contig1253 1253 THRCLA_contig1254 1254 THRCLA_contig1255 1255 THRCLA_contig1256 1256 THRCLA_contig1257 1257 THRCLA_contig1258 1258 THRCLA_contig1259 1259 THRCLA_contig1260 1260 THRCLA_contig1261 1261 THRCLA_contig1262 1262 THRCLA_contig1263 1263 THRCLA_contig1264 1264 THRCLA_contig1265 1265 THRCLA_contig1266 1266 THRCLA_contig1267 1267 THRCLA_contig1268 1268 THRCLA_contig1269 1269 THRCLA_contig1270 1270 THRCLA_contig1271 1271 THRCLA_contig1272 1272 THRCLA_contig1273 1273 THRCLA_contig1274 1274 THRCLA_contig1275 1275 THRCLA_contig1276 1276 THRCLA_contig1277 1277 THRCLA_contig1278 1278 THRCLA_contig1279 1279 THRCLA_contig1280 1280 THRCLA_contig1281 1281 THRCLA_contig1282 1282 THRCLA_contig1283 1283 THRCLA_contig1284 1284 THRCLA_contig1285 1285 THRCLA_contig1286 1286 THRCLA_contig1287 1287 THRCLA_contig1288 1288 THRCLA_contig1289 1289 THRCLA_contig1290 1290 THRCLA_contig1291 1291 THRCLA_contig1292 1292 THRCLA_contig1293 1293 THRCLA_contig1294 1294 THRCLA_contig1295 1295 THRCLA_contig1296 1296 THRCLA_contig1297 1297 THRCLA_contig1298 1298 THRCLA_contig1299 1299 THRCLA_contig1300 1300 THRCLA_contig1301 1301 THRCLA_contig1302 1302 THRCLA_contig1303 1303 THRCLA_contig1304 1304 THRCLA_contig1305 1305 THRCLA_contig1306 1306 THRCLA_contig1307 1307 THRCLA_contig1308 1308 THRCLA_contig1309 1309 THRCLA_contig1310 1310 THRCLA_contig1311 1311 THRCLA_contig1312 1312 THRCLA_contig1313 1313 THRCLA_contig1314 1314 THRCLA_contig1315 1315 THRCLA_contig1316 1316 THRCLA_contig1317 1317 THRCLA_contig1318 1318 THRCLA_contig1319 1319 THRCLA_contig1320 1320 THRCLA_contig1321 1321 THRCLA_contig1322 1322 THRCLA_contig1323 1323 THRCLA_contig1324 1324 THRCLA_contig1325 1325 THRCLA_contig1326 1326 THRCLA_contig1327 1327 THRCLA_contig1328 1328 THRCLA_contig1329 1329 THRCLA_contig1330 1330 THRCLA_contig1331 1331 THRCLA_contig1332 1332 THRCLA_contig1333 1333 THRCLA_contig1334 1334 THRCLA_contig1335 1335 THRCLA_contig1336 1336 THRCLA_contig1337 1337 THRCLA_contig1338 1338 THRCLA_contig1339 1339 THRCLA_contig1340 1340 THRCLA_contig1341 1341 THRCLA_contig1342 1342 THRCLA_contig1343 1343 THRCLA_contig1344 1344 THRCLA_contig1345 1345 THRCLA_contig1346 1346 THRCLA_contig1347 1347 THRCLA_contig1348 1348 THRCLA_contig1349 1349 THRCLA_contig1350 1350 THRCLA_contig1351 1351 THRCLA_contig1352 1352 THRCLA_contig1353 1353 THRCLA_contig1354 1354 THRCLA_contig1355 1355 THRCLA_contig1356 1356 THRCLA_contig1357 1357 THRCLA_contig1358 1358 THRCLA_contig1359 1359 THRCLA_contig1360 1360 THRCLA_contig1361 1361 THRCLA_contig1362 1362 THRCLA_contig1363 1363 THRCLA_contig1364 1364 THRCLA_contig1365 1365 THRCLA_contig1366 1366 THRCLA_contig1367 1367 THRCLA_contig1368 1368 THRCLA_contig1369 1369 THRCLA_contig1370 1370 THRCLA_contig1371 1371 THRCLA_contig1372 1372 THRCLA_contig1373 1373 THRCLA_contig1374 1374 THRCLA_contig1375 1375 THRCLA_contig1376 1376 THRCLA_contig1377 1377 THRCLA_contig1378 1378 THRCLA_contig1379 1379 THRCLA_contig1380 1380 THRCLA_contig1381 1381 THRCLA_contig1382 1382 THRCLA_contig1383 1383 THRCLA_contig1384 1384 THRCLA_contig1385 1385 THRCLA_contig1386 1386 THRCLA_contig1387 1387 THRCLA_contig1388 1388 THRCLA_contig1389 1389 THRCLA_contig1390 1390 THRCLA_contig1391 1391 THRCLA_contig1392 1392 THRCLA_contig1393 1393 THRCLA_contig1394 1394 THRCLA_contig1395 1395 THRCLA_contig1396 1396 THRCLA_contig1397 1397 THRCLA_contig1398 1398 THRCLA_contig1399 1399 THRCLA_contig1400 1400 THRCLA_contig1401 1401 THRCLA_contig1402 1402 THRCLA_contig1403 1403 THRCLA_contig1404 1404 THRCLA_contig1405 1405 THRCLA_contig1406 1406 THRCLA_contig1407 1407 THRCLA_contig1408 1408 THRCLA_contig1409 1409 THRCLA_contig1410 1410 THRCLA_contig1411 1411 THRCLA_contig1412 1412 THRCLA_contig1413 1413 THRCLA_contig1414 1414 THRCLA_contig1415 1415 THRCLA_contig1416 1416 THRCLA_contig1417 1417 THRCLA_contig1418 1418 THRCLA_contig1419 1419 THRCLA_contig1420 1420 THRCLA_contig1421 1421 THRCLA_contig1422 1422 THRCLA_contig1423 1423 THRCLA_contig1424 1424 THRCLA_contig1425 1425 THRCLA_contig1426 1426 THRCLA_contig1427 1427 THRCLA_contig1428 1428 THRCLA_contig1429 1429 THRCLA_contig1430 1430 THRCLA_contig1431 1431 THRCLA_contig1432 1432 THRCLA_contig1433 1433 THRCLA_contig1434 1434 THRCLA_contig1435 1435 THRCLA_contig1436 1436 THRCLA_contig1437 1437 THRCLA_contig1438 1438 THRCLA_contig1439 1439 THRCLA_contig1440 1440 THRCLA_contig1441 1441 THRCLA_contig1442 1442 THRCLA_contig1443 1443 THRCLA_contig1444 1444 THRCLA_contig1445 1445 THRCLA_contig1446 1446 THRCLA_contig1447 1447 THRCLA_contig1448 1448 THRCLA_contig1449 1449 THRCLA_contig1450 1450 THRCLA_contig1451 1451 THRCLA_contig1452 1452 THRCLA_contig1453 1453 THRCLA_contig1454 1454 THRCLA_contig1455 1455 THRCLA_contig1456 1456 THRCLA_contig1457 1457 THRCLA_contig1458 1458 THRCLA_contig1459 1459 THRCLA_contig1460 1460 THRCLA_contig1461 1461 THRCLA_contig1462 1462 THRCLA_contig1463 1463 THRCLA_contig1464 1464 THRCLA_contig1465 1465 THRCLA_contig1466 1466 THRCLA_contig1467 1467 THRCLA_contig1468 1468 THRCLA_contig1469 1469 THRCLA_contig1470 1470 THRCLA_contig1471 1471 THRCLA_contig1472 1472 THRCLA_contig1473 1473 THRCLA_contig1474 1474 THRCLA_contig1475 1475 THRCLA_contig1476 1476 THRCLA_contig1477 1477 THRCLA_contig1478 1478 THRCLA_contig1479 1479 THRCLA_contig1480 1480 THRCLA_contig1481 1481 THRCLA_contig1482 1482 THRCLA_contig1483 1483 THRCLA_contig1484 1484 THRCLA_contig1485 1485 THRCLA_contig1486 1486 THRCLA_contig1487 1487 THRCLA_contig1488 1488 THRCLA_contig1489 1489 THRCLA_contig1490 1490 THRCLA_contig1491 1491 THRCLA_contig1492 1492 THRCLA_contig1493 1493 THRCLA_contig1494 1494 THRCLA_contig1495 1495 THRCLA_contig1496 1496 THRCLA_contig1497 1497 THRCLA_contig1498 1498 THRCLA_contig1499 1499 THRCLA_contig1500 1500 THRCLA_contig1501 1501 THRCLA_contig1502 1502 THRCLA_contig1503 1503 THRCLA_contig1504 1504 THRCLA_contig1505 1505 THRCLA_contig1506 1506 THRCLA_contig1507 1507 THRCLA_contig1508 1508 THRCLA_contig1509 1509 THRCLA_contig1510 1510 THRCLA_contig1511 1511 THRCLA_contig1512 1512 THRCLA_contig1513 1513 THRCLA_contig1514 1514 THRCLA_contig1515 1515 THRCLA_contig1516 1516 THRCLA_contig1517 1517 THRCLA_contig1518 1518 THRCLA_contig1519 1519 THRCLA_contig1520 1520 THRCLA_contig1521 1521 THRCLA_contig1522 1522 THRCLA_contig1523 1523 THRCLA_contig1524 1524 THRCLA_contig1525 1525 THRCLA_contig1526 1526 THRCLA_contig1527 1527 THRCLA_contig1528 1528 THRCLA_contig1529 1529 THRCLA_contig1530 1530 THRCLA_contig1531 1531 THRCLA_contig1532 1532 THRCLA_contig1533 1533 THRCLA_contig1534 1534 THRCLA_contig1535 1535 THRCLA_contig1536 1536 THRCLA_contig1537 1537 THRCLA_contig1538 1538 THRCLA_contig1539 1539 THRCLA_contig1540 1540 THRCLA_contig1541 1541 THRCLA_contig1542 1542 THRCLA_contig1543 1543 THRCLA_contig1544 1544 THRCLA_contig1545 1545 THRCLA_contig1546 1546 THRCLA_contig1547 1547 THRCLA_contig1548 1548 THRCLA_contig1549 1549 THRCLA_contig1550 1550 THRCLA_contig1551 1551 THRCLA_contig1552 1552 THRCLA_contig1553 1553 THRCLA_contig1554 1554 THRCLA_contig1555 1555 THRCLA_contig1556 1556 THRCLA_contig1557 1557 THRCLA_contig1558 1558 THRCLA_contig1559 1559 THRCLA_contig1560 1560 THRCLA_contig1561 1561 THRCLA_contig1562 1562 THRCLA_contig1563 1563 THRCLA_contig1564 1564 THRCLA_contig1565 1565 THRCLA_contig1566 1566 THRCLA_contig1567 1567 THRCLA_contig1568 1568 THRCLA_contig1569 1569 THRCLA_contig1570 1570 THRCLA_contig1571 1571 THRCLA_contig1572 1572 THRCLA_contig1573 1573 THRCLA_contig1574 1574 THRCLA_contig1575 1575 THRCLA_contig1576 1576 THRCLA_contig1577 1577 THRCLA_contig1578 1578 THRCLA_contig1579 1579 THRCLA_contig1580 1580 THRCLA_contig1581 1581 THRCLA_contig1582 1582 THRCLA_contig1583 1583 THRCLA_contig1584 1584 THRCLA_contig1585 1585 THRCLA_contig1586 1586 THRCLA_contig1587 1587 THRCLA_contig1588 1588 THRCLA_contig1589 1589 THRCLA_contig1590 1590 THRCLA_contig1591 1591 THRCLA_contig1592 1592 THRCLA_contig1593 1593 THRCLA_contig1594 1594 THRCLA_contig1595 1595 THRCLA_contig1596 1596 THRCLA_contig1597 1597 THRCLA_contig1598 1598 THRCLA_contig1599 1599 THRCLA_contig1600 1600 THRCLA_contig1601 1601 THRCLA_contig1602 1602 THRCLA_contig1603 1603 THRCLA_contig1604 1604 THRCLA_contig1605 1605 THRCLA_contig1606 1606 THRCLA_contig1607 1607 THRCLA_contig1608 1608 THRCLA_contig1609 1609 THRCLA_contig1610 1610 THRCLA_contig1611 1611 THRCLA_contig1612 1612 THRCLA_contig1613 1613 THRCLA_contig1614 1614 THRCLA_contig1615 1615 THRCLA_contig1616 1616 THRCLA_contig1617 1617 THRCLA_contig1618 1618 THRCLA_contig1619 1619 THRCLA_contig1620 1620 THRCLA_contig1621 1621 THRCLA_contig1622 1622 THRCLA_contig1623 1623 THRCLA_contig1624 1624 THRCLA_contig1625 1625 THRCLA_contig1626 1626 THRCLA_contig1627 1627 THRCLA_contig1628 1628 THRCLA_contig1629 1629 THRCLA_contig1630 1630 THRCLA_contig1631 1631 THRCLA_contig1632 1632 THRCLA_contig1633 1633 THRCLA_contig1634 1634 THRCLA_contig1635 1635 THRCLA_contig1636 1636 THRCLA_contig1637 1637 THRCLA_contig1638 1638 THRCLA_contig1639 1639 THRCLA_contig1640 1640 THRCLA_contig1641 1641 THRCLA_contig1642 1642 THRCLA_contig1643 1643 THRCLA_contig1644 1644 THRCLA_contig1645 1645 THRCLA_contig1646 1646 THRCLA_contig1647 1647 THRCLA_contig1648 1648 THRCLA_contig1649 1649 THRCLA_contig1650 1650 THRCLA_contig1651 1651 THRCLA_contig1652 1652 THRCLA_contig1653 1653 THRCLA_contig1654 1654 THRCLA_contig1655 1655 THRCLA_contig1656 1656 THRCLA_contig1657 1657 THRCLA_contig1658 1658 THRCLA_contig1659 1659 THRCLA_contig1660 1660 THRCLA_contig1661 1661 THRCLA_contig1662 1662 THRCLA_contig1663 1663 THRCLA_contig1664 1664 THRCLA_contig1665 1665 THRCLA_contig1666 1666 THRCLA_contig1667 1667 THRCLA_contig1668 1668 THRCLA_contig1669 1669 THRCLA_contig1670 1670 THRCLA_contig1671 1671 THRCLA_contig1672 1672 THRCLA_contig1673 1673 THRCLA_contig1674 1674 THRCLA_contig1675 1675 THRCLA_contig1676 1676 THRCLA_contig1677 1677 THRCLA_contig1678 1678 THRCLA_contig1679 1679 THRCLA_contig1680 1680 THRCLA_contig1681 1681 THRCLA_contig1682 1682 THRCLA_contig1683 1683 THRCLA_contig1684 1684 THRCLA_contig1685 1685 THRCLA_contig1686 1686 THRCLA_contig1687 1687 THRCLA_contig1688 1688 THRCLA_contig1689 1689 THRCLA_contig1690 1690 THRCLA_contig1691 1691 THRCLA_contig1692 1692 THRCLA_contig1693 1693 THRCLA_contig1694 1694 THRCLA_contig1695 1695 THRCLA_contig1696 1696 THRCLA_contig1697 1697 THRCLA_contig1698 1698 THRCLA_contig1699 1699 THRCLA_contig1700 1700 THRCLA_contig1701 1701 THRCLA_contig1702 1702 THRCLA_contig1703 1703 THRCLA_contig1704 1704 THRCLA_contig1705 1705 THRCLA_contig1706 1706 THRCLA_contig1707 1707 THRCLA_contig1708 1708 THRCLA_contig1709 1709 THRCLA_contig1710 1710 THRCLA_contig1711 1711 THRCLA_contig1712 1712 THRCLA_contig1713 1713 THRCLA_contig1714 1714 THRCLA_contig1715 1715 THRCLA_contig1716 1716 THRCLA_contig1717 1717 THRCLA_contig1718 1718 THRCLA_contig1719 1719 THRCLA_contig1720 1720 THRCLA_contig1721 1721 THRCLA_contig1722 1722 THRCLA_contig1723 1723 THRCLA_contig1724 1724 THRCLA_contig1725 1725 THRCLA_contig1726 1726 THRCLA_contig1727 1727 THRCLA_contig1728 1728 THRCLA_contig1729 1729 THRCLA_contig1730 1730 THRCLA_contig1731 1731 THRCLA_contig1732 1732 THRCLA_contig1733 1733 THRCLA_contig1734 1734 THRCLA_contig1735 1735 THRCLA_contig1736 1736 THRCLA_contig1737 1737 THRCLA_contig1738 1738 THRCLA_contig1739 1739 THRCLA_contig1740 1740 THRCLA_contig1741 1741 THRCLA_contig1742 1742 THRCLA_contig1743 1743 THRCLA_contig1744 1744 THRCLA_contig1745 1745 THRCLA_contig1746 1746 THRCLA_contig1747 1747 THRCLA_contig1748 1748 THRCLA_contig1749 1749 THRCLA_contig1750 1750 THRCLA_contig1751 1751 THRCLA_contig1752 1752 THRCLA_contig1753 1753 THRCLA_contig1754 1754 THRCLA_contig1755 1755 THRCLA_contig1756 1756 THRCLA_contig1757 1757 THRCLA_contig1758 1758 THRCLA_contig1759 1759 THRCLA_contig1760 1760 THRCLA_contig1761 1761 THRCLA_contig1762 1762 THRCLA_contig1763 1763 THRCLA_contig1764 1764 THRCLA_contig1765 1765 THRCLA_contig1766 1766 THRCLA_contig1767 1767 THRCLA_contig1768 1768 THRCLA_contig1769 1769 THRCLA_contig1770 1770 THRCLA_contig1771 1771 THRCLA_contig1772 1772 THRCLA_contig1773 1773 THRCLA_contig1774 1774 THRCLA_contig1775 1775 THRCLA_contig1776 1776 THRCLA_contig1777 1777 THRCLA_contig1778 1778 THRCLA_contig1779 1779 THRCLA_contig1780 1780 THRCLA_contig1781 1781 THRCLA_contig1782 1782 THRCLA_contig1783 1783 THRCLA_contig1784 1784 THRCLA_contig1785 1785 THRCLA_contig1786 1786 THRCLA_contig1787 1787 THRCLA_contig1788 1788 THRCLA_contig1789 1789 THRCLA_contig1790 1790 THRCLA_contig1791 1791 THRCLA_contig1792 1792 THRCLA_contig1793 1793 THRCLA_contig1794 1794 THRCLA_contig1795 1795 THRCLA_contig1796 1796 THRCLA_contig1797 1797 THRCLA_contig1798 1798 THRCLA_contig1799 1799 THRCLA_contig1800 1800 THRCLA_contig1801 1801 THRCLA_contig1802 1802 THRCLA_contig1803 1803 THRCLA_contig1804 1804 THRCLA_contig1805 1805 THRCLA_contig1806 1806 THRCLA_contig1807 1807 THRCLA_contig1808 1808 THRCLA_contig1809 1809 THRCLA_contig1810 1810 THRCLA_contig1811 1811 THRCLA_contig1812 1812 THRCLA_contig1813 1813 THRCLA_contig1814 1814 THRCLA_contig1815 1815 THRCLA_contig1816 1816 THRCLA_contig1817 1817 THRCLA_contig1818 1818 THRCLA_contig1819 1819 THRCLA_contig1820 1820 THRCLA_contig1821 1821 THRCLA_contig1822 1822 THRCLA_contig1823 1823 THRCLA_contig1824 1824 THRCLA_contig1825 1825 THRCLA_contig1826 1826 THRCLA_contig1827 1827 THRCLA_contig1828 1828 THRCLA_contig1829 1829 THRCLA_contig1830 1830 THRCLA_contig1831 1831 THRCLA_contig1832 1832 THRCLA_contig1833 1833 THRCLA_contig1834 1834 THRCLA_contig1835 1835 THRCLA_contig1836 1836 THRCLA_contig1837 1837 THRCLA_contig1838 1838 THRCLA_contig1839 1839 THRCLA_contig1840 1840 THRCLA_contig1841 1841 THRCLA_contig1842 1842 THRCLA_contig1843 1843 THRCLA_contig1844 1844 THRCLA_contig1845 1845 THRCLA_contig1846 1846 THRCLA_contig1847 1847 THRCLA_contig1848 1848 THRCLA_contig1849 1849 THRCLA_contig1850 1850 THRCLA_contig1851 1851 THRCLA_contig1852 1852 THRCLA_contig1853 1853 THRCLA_contig1854 1854 THRCLA_contig1855 1855 THRCLA_contig1856 1856 THRCLA_contig1857 1857 THRCLA_contig1858 1858 THRCLA_contig1859 1859 THRCLA_contig1860 1860 THRCLA_contig1861 1861 THRCLA_contig1862 1862 THRCLA_contig1863 1863 THRCLA_contig1864 1864 THRCLA_contig1865 1865 THRCLA_contig1866 1866 THRCLA_contig1867 1867 THRCLA_contig1868 1868 THRCLA_contig1869 1869 THRCLA_contig1870 1870 THRCLA_contig1871 1871 THRCLA_contig1872 1872 THRCLA_contig1873 1873 THRCLA_contig1874 1874 THRCLA_contig1875 1875 THRCLA_contig1876 1876 THRCLA_contig1877 1877 THRCLA_contig1878 1878 THRCLA_contig1879 1879 THRCLA_contig1880 1880 THRCLA_contig1881 1881 THRCLA_contig1882 1882 THRCLA_contig1883 1883 THRCLA_contig1884 1884 THRCLA_contig1885 1885 THRCLA_contig1886 1886 THRCLA_contig1887 1887 THRCLA_contig1888 1888 THRCLA_contig1889 1889 THRCLA_contig1890 1890 THRCLA_contig1891 1891 THRCLA_contig1892 1892 THRCLA_contig1893 1893 THRCLA_contig1894 1894 THRCLA_contig1895 1895 THRCLA_contig1896 1896 THRCLA_contig1897 1897 THRCLA_contig1898 1898 THRCLA_contig1899 1899 THRCLA_contig1900 1900 THRCLA_contig1901 1901 THRCLA_contig1902 1902 THRCLA_contig1903 1903 THRCLA_contig1904 1904 THRCLA_contig1905 1905 THRCLA_contig1906 1906 THRCLA_contig1907 1907 THRCLA_contig1908 1908 THRCLA_contig1909 1909 THRCLA_contig1910 1910 THRCLA_contig1911 1911 THRCLA_contig1912 1912 THRCLA_contig1913 1913 THRCLA_contig1914 1914 THRCLA_contig1915 1915 THRCLA_contig1916 1916 THRCLA_contig1917 1917 THRCLA_contig1918 1918 THRCLA_contig1919 1919 THRCLA_contig1920 1920 THRCLA_contig1921 1921 THRCLA_contig1922 1922 THRCLA_contig1923 1923 THRCLA_contig1924 1924 THRCLA_contig1925 1925 THRCLA_contig1926 1926 THRCLA_contig1927 1927 THRCLA_contig1928 1928 THRCLA_contig1929 1929 THRCLA_contig1930 1930 THRCLA_contig1931 1931 THRCLA_contig1932 1932 THRCLA_contig1933 1933 THRCLA_contig1934 1934 THRCLA_contig1935 1935 THRCLA_contig1936 1936 THRCLA_contig1937 1937 THRCLA_contig1938 1938 THRCLA_contig1939 1939 THRCLA_contig1940 1940 THRCLA_contig1941 1941 THRCLA_contig1942 1942 THRCLA_contig1943 1943 THRCLA_contig1944 1944 THRCLA_contig1945 1945 THRCLA_contig1946 1946 THRCLA_contig1947 1947 THRCLA_contig1948 1948 THRCLA_contig1949 1949 THRCLA_contig1950 1950 THRCLA_contig1951 1951 THRCLA_contig1952 1952 THRCLA_contig1953 1953 THRCLA_contig1954 1954 THRCLA_contig1955 1955 THRCLA_contig1956 1956 THRCLA_contig1957 1957 THRCLA_contig1958 1958 THRCLA_contig1959 1959 THRCLA_contig1960 1960 THRCLA_contig1961 1961 THRCLA_contig1962 1962 THRCLA_contig1963 1963 THRCLA_contig1964 1964 THRCLA_contig1965 1965 THRCLA_contig1966 1966 THRCLA_contig1967 1967 THRCLA_contig1968 1968 THRCLA_contig1969 1969 THRCLA_contig1970 1970 THRCLA_contig1971 1971 THRCLA_contig1972 1972 THRCLA_contig1973 1973 THRCLA_contig1974 1974 THRCLA_contig1975 1975 THRCLA_contig1976 1976 THRCLA_contig1977 1977 THRCLA_contig1978 1978 THRCLA_contig1979 1979 THRCLA_contig1980 1980 THRCLA_contig1981 1981 THRCLA_contig1982 1982 THRCLA_contig1983 1983 THRCLA_contig1984 1984 THRCLA_contig1985 1985 THRCLA_contig1986 1986 THRCLA_contig1987 1987 THRCLA_contig1988 1988 THRCLA_contig1989 1989 THRCLA_contig1990 1990 THRCLA_contig1991 1991 THRCLA_contig1992 1992 THRCLA_contig1993 1993 THRCLA_contig1994 1994 THRCLA_contig1995 1995 THRCLA_contig1996 1996 THRCLA_contig1997 1997 THRCLA_contig1998 1998 THRCLA_contig1999 1999 THRCLA_contig2000 2000 THRCLA_contig2001 2001 THRCLA_contig2002 2002 THRCLA_contig2003 2003 THRCLA_contig2004 2004 THRCLA_contig2005 2005 THRCLA_contig2006 2006 THRCLA_contig2007 2007 THRCLA_contig2008 2008 THRCLA_contig2009 2009 THRCLA_contig2010 2010 THRCLA_contig2011 2011 THRCLA_contig2012 2012 THRCLA_contig2013 2013 THRCLA_contig2014 2014 THRCLA_contig2015 2015 THRCLA_contig2016 2016 THRCLA_contig2017 2017 THRCLA_contig2018 2018 THRCLA_contig2019 2019 THRCLA_contig2020 2020 THRCLA_contig2021 2021 THRCLA_contig2022 2022 THRCLA_contig2023 2023 THRCLA_contig2024 2024 THRCLA_contig2025 2025 THRCLA_contig2026 2026 THRCLA_contig2027 2027 THRCLA_contig2028 2028 THRCLA_contig2029 2029 THRCLA_contig2030 2030 THRCLA_contig2031 2031 THRCLA_contig2032 2032 THRCLA_contig2033 2033 THRCLA_contig2034 2034 THRCLA_contig2035 2035 THRCLA_contig2036 2036 THRCLA_contig2037 2037 THRCLA_contig2038 2038 THRCLA_contig2039 2039 THRCLA_contig2040 2040 THRCLA_contig2041 2041 THRCLA_contig2042 2042 THRCLA_contig2043 2043 THRCLA_contig2044 2044 THRCLA_contig2045 2045 THRCLA_contig2046 2046 THRCLA_contig2047 2047 THRCLA_contig2048 2048 THRCLA_contig2049 2049 THRCLA_contig2050 2050 THRCLA_contig2051 2051 THRCLA_contig2052 2052 THRCLA_contig2053 2053 THRCLA_contig2054 2054 THRCLA_contig2055 2055 THRCLA_contig2056 2056 THRCLA_contig2057 2057 THRCLA_contig2058 2058 THRCLA_contig2059 2059 THRCLA_contig2060 2060 THRCLA_contig2061 2061 THRCLA_contig2062 2062 THRCLA_contig2063 2063 THRCLA_contig2064 2064 THRCLA_contig2065 2065 THRCLA_contig2066 2066 THRCLA_contig2067 2067 THRCLA_contig2068 2068 THRCLA_contig2069 2069 THRCLA_contig2070 2070 THRCLA_contig2071 2071 THRCLA_contig2072 2072 THRCLA_contig2073 2073 THRCLA_contig2074 2074 THRCLA_contig2075 2075 THRCLA_contig2076 2076 THRCLA_contig2077 2077 THRCLA_contig2078 2078 THRCLA_contig2079 2079 THRCLA_contig2080 2080 THRCLA_contig2081 2081 THRCLA_contig2082 2082 THRCLA_contig2083 2083 THRCLA_contig2084 2084 THRCLA_contig2085 2085 THRCLA_contig2086 2086 THRCLA_contig2087 2087 THRCLA_contig2088 2088 THRCLA_contig2089 2089 THRCLA_contig2090 2090 THRCLA_contig2091 2091 THRCLA_contig2092 2092 THRCLA_contig2093 2093 THRCLA_contig2094 2094 THRCLA_contig2095 2095 THRCLA_contig2096 2096 THRCLA_contig2097 2097 THRCLA_contig2098 2098 THRCLA_contig2099 2099 THRCLA_contig2100 2100 THRCLA_contig2101 2101 THRCLA_contig2102 2102 THRCLA_contig2103 2103 THRCLA_contig2104 2104 THRCLA_contig2105 2105 THRCLA_contig2106 2106 THRCLA_contig2107 2107 THRCLA_contig2108 2108 THRCLA_contig2109 2109 THRCLA_contig2110 2110 THRCLA_contig2111 2111 THRCLA_contig2112 2112 THRCLA_contig2113 2113 THRCLA_contig2114 2114 THRCLA_contig2115 2115 THRCLA_contig2116 2116 THRCLA_contig2117 2117 THRCLA_contig2118 2118 THRCLA_contig2119 2119 THRCLA_contig2120 2120 THRCLA_contig2121 2121 THRCLA_contig2122 2122 THRCLA_contig2123 2123 THRCLA_contig2124 2124 THRCLA_contig2125 2125 THRCLA_contig2126 2126 THRCLA_contig2127 2127 THRCLA_contig2128 2128 THRCLA_contig2129 2129 THRCLA_contig2130 2130 THRCLA_contig2131 2131 THRCLA_contig2132 2132 THRCLA_contig2133 2133 THRCLA_contig2134 2134 THRCLA_contig2135 2135 THRCLA_contig2136 2136 THRCLA_contig2137 2137 THRCLA_contig2138 2138 THRCLA_contig2139 2139 THRCLA_contig2140 2140 THRCLA_contig2141 2141 THRCLA_contig2142 2142 THRCLA_contig2143 2143 THRCLA_contig2144 2144 THRCLA_contig2145 2145 THRCLA_contig2146 2146 THRCLA_contig2147 2147 THRCLA_contig2148 2148 THRCLA_contig2149 2149 THRCLA_contig2150 2150 THRCLA_contig2151 2151 THRCLA_contig2152 2152 THRCLA_contig2153 2153 THRCLA_contig2154 2154 THRCLA_contig2155 2155 THRCLA_contig2156 2156 THRCLA_contig2157 2157 THRCLA_contig2158 2158 THRCLA_contig2159 2159 THRCLA_contig2160 2160 THRCLA_contig2161 2161 THRCLA_contig2162 2162 THRCLA_contig2163 2163 THRCLA_contig2164 2164 THRCLA_contig2165 2165 THRCLA_contig2166 2166 THRCLA_contig2167 2167 THRCLA_contig2168 2168 THRCLA_contig2169 2169 THRCLA_contig2170 2170 THRCLA_contig2171 2171 THRCLA_contig2172 2172 THRCLA_contig2173 2173 THRCLA_contig2174 2174 THRCLA_contig2175 2175 THRCLA_contig2176 2176 THRCLA_contig2177 2177 THRCLA_contig2178 2178 THRCLA_contig2179 2179 THRCLA_contig2180 2180 THRCLA_contig2181 2181 THRCLA_contig2182 2182 THRCLA_contig2183 2183 THRCLA_contig2184 2184 THRCLA_contig2185 2185 THRCLA_contig2186 2186 THRCLA_contig2187 2187 THRCLA_contig2188 2188 THRCLA_contig2189 2189 THRCLA_contig2190 2190 THRCLA_contig2191 2191 THRCLA_contig2192 2192 THRCLA_contig2193 2193 THRCLA_contig2194 2194 THRCLA_contig2195 2195 THRCLA_contig2196 2196 THRCLA_contig2197 2197 THRCLA_contig2198 2198 THRCLA_contig2199 2199 THRCLA_contig2200 2200 THRCLA_contig2201 2201 THRCLA_contig2202 2202 THRCLA_contig2203 2203 THRCLA_contig2204 2204 THRCLA_contig2205 2205 THRCLA_contig2206 2206 THRCLA_contig2207 2207 THRCLA_contig2208 2208 THRCLA_contig2209 2209 THRCLA_contig2210 2210 THRCLA_contig2211 2211 THRCLA_contig2212 2212 THRCLA_contig2213 2213 THRCLA_contig2214 2214 THRCLA_contig2215 2215 THRCLA_contig2216 2216 THRCLA_contig2217 2217 THRCLA_contig2218 2218 THRCLA_contig2219 2219 THRCLA_contig2220 2220 THRCLA_contig2221 2221 THRCLA_contig2222 2222 THRCLA_contig2223 2223 THRCLA_contig2224 2224 THRCLA_contig2225 2225 THRCLA_contig2226 2226 THRCLA_contig2227 2227 THRCLA_contig2228 2228 THRCLA_contig2229 2229 THRCLA_contig2230 2230 THRCLA_contig2231 2231 THRCLA_contig2232 2232 THRCLA_contig2233 2233 THRCLA_contig2234 2234 THRCLA_contig2235 2235 THRCLA_contig2236 2236 THRCLA_contig2237 2237 THRCLA_contig2238 2238 THRCLA_contig2239 2239 THRCLA_contig2240 2240 THRCLA_contig2241 2241 THRCLA_contig2242 2242 THRCLA_contig2243 2243 THRCLA_contig2244 2244 THRCLA_contig2245 2245 THRCLA_contig2246 2246 THRCLA_contig2247 2247 THRCLA_contig2248 2248 THRCLA_contig2249 2249 THRCLA_contig2250 2250 THRCLA_contig2251 2251 THRCLA_contig2252 2252 THRCLA_contig2253 2253 THRCLA_contig2254 2254 THRCLA_contig2255 2255 THRCLA_contig2256 2256 THRCLA_contig2257 2257 THRCLA_contig2258 2258 THRCLA_contig2259 2259 THRCLA_contig2260 2260 THRCLA_contig2261 2261 THRCLA_contig2262 2262 THRCLA_contig2263 2263 THRCLA_contig2264 2264 THRCLA_contig2265 2265 THRCLA_contig2266 2266 THRCLA_contig2267 2267 THRCLA_contig2268 2268 THRCLA_contig2269 2269 THRCLA_contig2270 2270 THRCLA_contig2271 2271 THRCLA_contig2272 2272 THRCLA_contig2273 2273 THRCLA_contig2274 2274 THRCLA_contig2275 2275 THRCLA_contig2276 2276 THRCLA_contig2277 2277 THRCLA_contig2278 2278 THRCLA_contig2279 2279 THRCLA_contig2280 2280 THRCLA_contig2281 2281 THRCLA_contig2282 2282 THRCLA_contig2283 2283 THRCLA_contig2284 2284 THRCLA_contig2285 2285 THRCLA_contig2286 2286 THRCLA_contig2287 2287 THRCLA_contig2288 2288 THRCLA_contig2289 2289 THRCLA_contig2290 2290 THRCLA_contig2291 2291 THRCLA_contig2292 2292 THRCLA_contig2293 2293 THRCLA_contig2294 2294 THRCLA_contig2295 2295 THRCLA_contig2296 2296 THRCLA_contig2297 2297 THRCLA_contig2298 2298 THRCLA_contig2299 2299 THRCLA_contig2300 2300 THRCLA_contig2301 2301 THRCLA_contig2302 2302 THRCLA_contig2303 2303 THRCLA_contig2304 2304 THRCLA_contig2305 2305 THRCLA_contig2306 2306 THRCLA_contig2307 2307 THRCLA_contig2308 2308 THRCLA_contig2309 2309 THRCLA_contig2310 2310 THRCLA_contig2311 2311 THRCLA_contig2312 2312 THRCLA_contig2313 2313 THRCLA_contig2314 2314 THRCLA_contig2315 2315 THRCLA_contig2316 2316 THRCLA_contig2317 2317 THRCLA_contig2318 2318 THRCLA_contig2319 2319 THRCLA_contig2320 2320 THRCLA_contig2321 2321 THRCLA_contig2322 2322 THRCLA_contig2323 2323 THRCLA_contig2324 2324 THRCLA_contig2325 2325 THRCLA_contig2326 2326 THRCLA_contig2327 2327 THRCLA_contig2328 2328 THRCLA_contig2329 2329 THRCLA_contig2330 2330 THRCLA_contig2331 2331 THRCLA_contig2332 2332 THRCLA_contig2333 2333 THRCLA_contig2334 2334 THRCLA_contig2335 2335 THRCLA_contig2336 2336 THRCLA_contig2337 2337 THRCLA_contig2338 2338 THRCLA_contig2339 2339 THRCLA_contig2340 2340 THRCLA_contig2341 2341 THRCLA_contig2342 2342 THRCLA_contig2343 2343 THRCLA_contig2344 2344 THRCLA_contig2345 2345 THRCLA_contig2346 2346 THRCLA_contig2347 2347 THRCLA_contig2348 2348 THRCLA_contig2349 2349 THRCLA_contig2350 2350 THRCLA_contig2351 2351 THRCLA_contig2352 2352 THRCLA_contig2353 2353 THRCLA_contig2354 2354 THRCLA_contig2355 2355 THRCLA_contig2356 2356 THRCLA_contig2357 2357 THRCLA_contig2358 2358 THRCLA_contig2359 2359 THRCLA_contig2360 2360 THRCLA_contig2361 2361 THRCLA_contig2362 2362 THRCLA_contig2363 2363 THRCLA_contig2364 2364 THRCLA_contig2365 2365 THRCLA_contig2366 2366 THRCLA_contig2367 2367 THRCLA_contig2368 2368 THRCLA_contig2369 2369 THRCLA_contig2370 2370 THRCLA_contig2371 2371 THRCLA_contig2372 2372 THRCLA_contig2373 2373 THRCLA_contig2374 2374 THRCLA_contig2375 2375 THRCLA_contig2376 2376 THRCLA_contig2377 2377 THRCLA_contig2378 2378 THRCLA_contig2379 2379 THRCLA_contig2380 2380 THRCLA_contig2381 2381 THRCLA_contig2382 2382 THRCLA_contig2383 2383 THRCLA_contig2384 2384 THRCLA_contig2385 2385 THRCLA_contig2386 2386 THRCLA_contig2387 2387 THRCLA_contig2388 2388 THRCLA_contig2389 2389 THRCLA_contig2390 2390 THRCLA_contig2391 2391 THRCLA_contig2392 2392 THRCLA_contig2393 2393 THRCLA_contig2394 2394 THRCLA_contig2395 2395 THRCLA_contig2396 2396 THRCLA_contig2397 2397 THRCLA_contig2398 2398 THRCLA_contig2399 2399 THRCLA_contig2400 2400 THRCLA_contig2401 2401 THRCLA_contig2402 2402 THRCLA_contig2403 2403 THRCLA_contig2404 2404 THRCLA_contig2405 2405 THRCLA_contig2406 2406 THRCLA_contig2407 2407 THRCLA_contig2408 2408 THRCLA_contig2409 2409 THRCLA_contig2410 2410 THRCLA_contig2411 2411 THRCLA_contig2412 2412 THRCLA_contig2413 2413 THRCLA_contig2414 2414 THRCLA_contig2415 2415 THRCLA_contig2416 2416 THRCLA_contig2417 2417 THRCLA_contig2418 2418 THRCLA_contig2419 2419 THRCLA_contig2420 2420 THRCLA_contig2421 2421 THRCLA_contig2422 2422 THRCLA_contig2423 2423 THRCLA_contig2424 2424 THRCLA_contig2425 2425 THRCLA_contig2426 2426 THRCLA_contig2427 2427 THRCLA_contig2428 2428 THRCLA_contig2429 2429 THRCLA_contig2430 2430 THRCLA_contig2431 2431 THRCLA_contig2432 2432 THRCLA_contig2433 2433 THRCLA_contig2434 2434 THRCLA_contig2435 2435 THRCLA_contig2436 2436 THRCLA_contig2437 2437 THRCLA_contig2438 2438 THRCLA_contig2439 2439 THRCLA_contig2440 2440 THRCLA_contig2441 2441 THRCLA_contig2442 2442 THRCLA_contig2443 2443 THRCLA_contig2444 2444 THRCLA_contig2445 2445 THRCLA_contig2446 2446 THRCLA_contig2447 2447 THRCLA_contig2448 2448 THRCLA_contig2449 2449 THRCLA_contig2450 2450 THRCLA_contig2451 2451 THRCLA_contig2452 2452 THRCLA_contig2453 2453 THRCLA_contig2454 2454 THRCLA_contig2455 2455 THRCLA_contig2456 2456 THRCLA_contig2457 2457 THRCLA_contig2458 2458 THRCLA_contig2459 2459 THRCLA_contig2460 2460 THRCLA_contig2461 2461 THRCLA_contig2462 2462 THRCLA_contig2463 2463 THRCLA_contig2464 2464 THRCLA_contig2465 2465 THRCLA_contig2466 2466 THRCLA_contig2467 2467 THRCLA_contig2468 2468 THRCLA_contig2469 2469 THRCLA_contig2470 2470 THRCLA_contig2471 2471 THRCLA_contig2472 2472 THRCLA_contig2473 2473 THRCLA_contig2474 2474 THRCLA_contig2475 2475 THRCLA_contig2476 2476 THRCLA_contig2477 2477 THRCLA_contig2478 2478 THRCLA_contig2479 2479 THRCLA_contig2480 2480 THRCLA_contig2481 2481 THRCLA_contig2482 2482 THRCLA_contig2483 2483 THRCLA_contig2484 2484 THRCLA_contig2485 2485 THRCLA_contig2486 2486 THRCLA_contig2487 2487 THRCLA_contig2488 2488 THRCLA_contig2489 2489 THRCLA_contig2490 2490 THRCLA_contig2491 2491 THRCLA_contig2492 2492 THRCLA_contig2493 2493 THRCLA_contig2494 2494 THRCLA_contig2495 2495 THRCLA_contig2496 2496 THRCLA_contig2497 2497 THRCLA_contig2498 2498 THRCLA_contig2499 2499 THRCLA_contig2500 2500 THRCLA_contig2501 2501 THRCLA_contig2502 2502 THRCLA_contig2503 2503 THRCLA_contig2504 2504 THRCLA_contig2505 2505 THRCLA_contig2506 2506 THRCLA_contig2507 2507 THRCLA_contig2508 2508 THRCLA_contig2509 2509 THRCLA_contig2510 2510 THRCLA_contig2511 2511 THRCLA_contig2512 2512 THRCLA_contig2513 2513 THRCLA_contig2514 2514 THRCLA_contig2515 2515 THRCLA_contig2516 2516 THRCLA_contig2517 2517 THRCLA_contig2518 2518 THRCLA_contig2519 2519 THRCLA_contig2520 2520 THRCLA_contig2521 2521 THRCLA_contig2522 2522 THRCLA_contig2523 2523 THRCLA_contig2524 2524 THRCLA_contig2525 2525 THRCLA_contig2526 2526 THRCLA_contig2527 2527 THRCLA_contig2528 2528 THRCLA_contig2529 2529 THRCLA_contig2530 2530 THRCLA_contig2531 2531 THRCLA_contig2532 2532 THRCLA_contig2533 2533 THRCLA_contig2534 2534 THRCLA_contig2535 2535 THRCLA_contig2536 2536 THRCLA_contig2537 2537 THRCLA_contig2538 2538 THRCLA_contig2539 2539 THRCLA_contig2540 2540 THRCLA_contig2541 2541 THRCLA_contig2542 2542 THRCLA_contig2543 2543 THRCLA_contig2544 2544 THRCLA_contig2545 2545 THRCLA_contig2546 2546 THRCLA_contig2547 2547 THRCLA_contig2548 2548 THRCLA_contig2549 2549 THRCLA_contig2550 2550 THRCLA_contig2551 2551 THRCLA_contig2552 2552 THRCLA_contig2553 2553 THRCLA_contig2554 2554 THRCLA_contig2555 2555 THRCLA_contig2556 2556 THRCLA_contig2557 2557 THRCLA_contig2558 2558 THRCLA_contig2559 2559 THRCLA_contig2560 2560 THRCLA_contig2561 2561 THRCLA_contig2562 2562 THRCLA_contig2563 2563 THRCLA_contig2564 2564 THRCLA_contig2565 2565 THRCLA_contig2566 2566 THRCLA_contig2567 2567 THRCLA_contig2568 2568 THRCLA_contig2569 2569 THRCLA_contig2570 2570 THRCLA_contig2571 2571 THRCLA_contig2572 2572 THRCLA_contig2573 2573 THRCLA_contig2574 2574 THRCLA_contig2575 2575 THRCLA_contig2576 2576 THRCLA_contig2577 2577 THRCLA_contig2578 2578 THRCLA_contig2579 2579 THRCLA_contig2580 2580 THRCLA_contig2581 2581 THRCLA_contig2582 2582 THRCLA_contig2583 2583 THRCLA_contig2584 2584 THRCLA_contig2585 2585 THRCLA_contig2586 2586 THRCLA_contig2587 2587 THRCLA_contig2588 2588 THRCLA_contig2589 2589 THRCLA_contig2590 2590 THRCLA_contig2591 2591 THRCLA_contig2592 2592 THRCLA_contig2593 2593 THRCLA_contig2594 2594 THRCLA_contig2595 2595 THRCLA_contig2596 2596 THRCLA_contig2597 2597 THRCLA_contig2598 2598 THRCLA_contig2599 2599 THRCLA_contig2600 2600 THRCLA_contig2601 2601 THRCLA_contig2602 2602 THRCLA_contig2603 2603 THRCLA_contig2604 2604 THRCLA_contig2605 2605 THRCLA_contig2606 2606 THRCLA_contig2607 2607 THRCLA_contig2608 2608 THRCLA_contig2609 2609 THRCLA_contig2610 2610 THRCLA_contig2611 2611 THRCLA_contig2612 2612 THRCLA_contig2613 2613 THRCLA_contig2614 2614 THRCLA_contig2615 2615 THRCLA_contig2616 2616 THRCLA_contig2617 2617 THRCLA_contig2618 2618 THRCLA_contig2619 2619 THRCLA_contig2620 2620 THRCLA_contig2621 2621 THRCLA_contig2622 2622 THRCLA_contig2623 2623 THRCLA_contig2624 2624 THRCLA_contig2625 2625 THRCLA_contig2626 2626 THRCLA_contig2627 2627 THRCLA_contig2628 2628 THRCLA_contig2629 2629 THRCLA_contig2630 2630 THRCLA_contig2631 2631 THRCLA_contig2632 2632 THRCLA_contig2633 2633 THRCLA_contig2634 2634 THRCLA_contig2635 2635 THRCLA_contig2636 2636 THRCLA_contig2637 2637 THRCLA_contig2638 2638 THRCLA_contig2639 2639 THRCLA_contig2640 2640 THRCLA_contig2641 2641 THRCLA_contig2642 2642 THRCLA_contig2643 2643 THRCLA_contig2644 2644 THRCLA_contig2645 2645 THRCLA_contig2646 2646 THRCLA_contig2647 2647 THRCLA_contig2648 2648 THRCLA_contig2649 2649 THRCLA_contig2650 2650 THRCLA_contig2651 2651 THRCLA_contig2652 2652 THRCLA_contig2653 2653 THRCLA_contig2654 2654 THRCLA_contig2655 2655 THRCLA_contig2656 2656 THRCLA_contig2657 2657 THRCLA_contig2658 2658 THRCLA_contig2659 2659 THRCLA_contig2660 2660 THRCLA_contig2661 2661 THRCLA_contig2662 2662 THRCLA_contig2663 2663 THRCLA_contig2664 2664 THRCLA_contig2665 2665 THRCLA_contig2666 2666 THRCLA_contig2667 2667 THRCLA_contig2668 2668 THRCLA_contig2669 2669 THRCLA_contig2670 2670 THRCLA_contig2671 2671 THRCLA_contig2672 2672 THRCLA_contig2673 2673 THRCLA_contig2674 2674 THRCLA_contig2675 2675 THRCLA_contig2676 2676 THRCLA_contig2677 2677 THRCLA_contig2678 2678 THRCLA_contig2679 2679 THRCLA_contig2680 2680 THRCLA_contig2681 2681 THRCLA_contig2682 2682 THRCLA_contig2683 2683 THRCLA_contig2684 2684 THRCLA_contig2685 2685 THRCLA_contig2686 2686 THRCLA_contig2687 2687 THRCLA_contig2688 2688 THRCLA_contig2689 2689 THRCLA_contig2690 2690 THRCLA_contig2691 2691 THRCLA_contig2692 2692 THRCLA_contig2693 2693 THRCLA_contig2694 2694 THRCLA_contig2695 2695 THRCLA_contig2696 2696 THRCLA_contig2697 2697 THRCLA_contig2698 2698 THRCLA_contig2699 2699 THRCLA_contig2700 2700 THRCLA_contig2701 2701 THRCLA_contig2702 2702 THRCLA_contig2703 2703 THRCLA_contig2704 2704 THRCLA_contig2705 2705 THRCLA_contig2706 2706 THRCLA_contig2707 2707 THRCLA_contig2708 2708 THRCLA_contig2709 2709 THRCLA_contig2710 2710 THRCLA_contig2711 2711 THRCLA_contig2712 2712 THRCLA_contig2713 2713 THRCLA_contig2714 2714 THRCLA_contig2715 2715 THRCLA_contig2716 2716 THRCLA_contig2717 2717 THRCLA_contig2718 2718 THRCLA_contig2719 2719 THRCLA_contig2720 2720 THRCLA_contig2721 2721 THRCLA_contig2722 2722 THRCLA_contig2723 2723 THRCLA_contig2724 2724 THRCLA_contig2725 2725 THRCLA_contig2726 2726 THRCLA_contig2727 2727 THRCLA_contig2728 2728 THRCLA_contig2729 2729 THRCLA_contig2730 2730 THRCLA_contig2731 2731 THRCLA_contig2732 2732 THRCLA_contig2733 2733 THRCLA_contig2734 2734 THRCLA_contig2735 2735 THRCLA_contig2736 2736 THRCLA_contig2737 2737 THRCLA_contig2738 2738 THRCLA_contig2739 2739 THRCLA_contig2740 2740 THRCLA_contig2741 2741 THRCLA_contig2742 2742 THRCLA_contig2743 2743 THRCLA_contig2744 2744 THRCLA_contig2745 2745 THRCLA_contig2746 2746 THRCLA_contig2747 2747 THRCLA_contig2748 2748 THRCLA_contig2749 2749 THRCLA_contig2750 2750 THRCLA_contig2751 2751 THRCLA_contig2752 2752 THRCLA_contig2753 2753 THRCLA_contig2754 2754 THRCLA_contig2755 2755 THRCLA_contig2756 2756 THRCLA_contig2757 2757 THRCLA_contig2758 2758 THRCLA_contig2759 2759 THRCLA_contig2760 2760 THRCLA_contig2761 2761 THRCLA_contig2762 2762 THRCLA_contig2763 2763 THRCLA_contig2764 2764 THRCLA_contig2765 2765 THRCLA_contig2766 2766 THRCLA_contig2767 2767 THRCLA_contig2768 2768 THRCLA_contig2769 2769 THRCLA_contig2770 2770 THRCLA_contig2771 2771 THRCLA_contig2772 2772 THRCLA_contig2773 2773 THRCLA_contig2774 2774 THRCLA_contig2775 2775 THRCLA_contig2776 2776 THRCLA_contig2777 2777 THRCLA_contig2778 2778 THRCLA_contig2779 2779 THRCLA_contig2780 2780 THRCLA_contig2781 2781 THRCLA_contig2782 2782 THRCLA_contig2783 2783 THRCLA_contig2784 2784 THRCLA_contig2785 2785 THRCLA_contig2786 2786 THRCLA_contig2787 2787 THRCLA_contig2788 2788 THRCLA_contig2789 2789 THRCLA_contig2790 2790 THRCLA_contig2791 2791 THRCLA_contig2792 2792 THRCLA_contig2793 2793 THRCLA_contig2794 2794 THRCLA_contig2795 2795 THRCLA_contig2796 2796 THRCLA_contig2797 2797 THRCLA_contig2798 2798 THRCLA_contig2799 2799 THRCLA_contig2800 2800 THRCLA_contig2801 2801 THRCLA_contig2802 2802 THRCLA_contig2803 2803 THRCLA_contig2804 2804 THRCLA_contig2805 2805 THRCLA_contig2806 2806 THRCLA_contig2807 2807 THRCLA_contig2808 2808 THRCLA_contig2809 2809 THRCLA_contig2810 2810 THRCLA_contig2811 2811 THRCLA_contig2812 2812 THRCLA_contig2813 2813 THRCLA_contig2814 2814 THRCLA_contig2815 2815 THRCLA_contig2816 2816 THRCLA_contig2817 2817 THRCLA_contig2818 2818 THRCLA_contig2819 2819 THRCLA_contig2820 2820 THRCLA_contig2821 2821 THRCLA_contig2822 2822 THRCLA_contig2823 2823 THRCLA_contig2824 2824 THRCLA_contig2825 2825 THRCLA_contig2826 2826 THRCLA_contig2827 2827 THRCLA_contig2828 2828 THRCLA_contig2829 2829 THRCLA_contig2830 2830 THRCLA_contig2831 2831 THRCLA_contig2832 2832 THRCLA_contig2833 2833 THRCLA_contig2834 2834 THRCLA_contig2835 2835 THRCLA_contig2836 2836 THRCLA_contig2837 2837 THRCLA_contig2838 2838 THRCLA_contig2839 2839 THRCLA_contig2840 2840 THRCLA_contig2841 2841 THRCLA_contig2842 2842 THRCLA_contig2843 2843 THRCLA_contig2844 2844 THRCLA_contig2845 2845 THRCLA_contig2846 2846 THRCLA_contig2847 2847 THRCLA_contig2848 2848 THRCLA_contig2849 2849 THRCLA_contig2850 2850 THRCLA_contig2851 2851 THRCLA_contig2852 2852 THRCLA_contig2853 2853 THRCLA_contig2854 2854 THRCLA_contig2855 2855 THRCLA_contig2856 2856 THRCLA_contig2857 2857 THRCLA_contig2858 2858 THRCLA_contig2859 2859 THRCLA_contig2860 2860 THRCLA_contig2861 2861 THRCLA_contig2862 2862 THRCLA_contig2863 2863 THRCLA_contig2864 2864 THRCLA_contig2865 2865 THRCLA_contig2866 2866 THRCLA_contig2867 2867 THRCLA_contig2868 2868 THRCLA_contig2869 2869 THRCLA_contig2870 2870 THRCLA_contig2871 2871 THRCLA_contig2872 2872 THRCLA_contig2873 2873 THRCLA_contig2874 2874 THRCLA_contig2875 2875 THRCLA_contig2876 2876 THRCLA_contig2877 2877 THRCLA_contig2878 2878 THRCLA_contig2879 2879 THRCLA_contig2880 2880 THRCLA_contig2881 2881 THRCLA_contig2882 2882 THRCLA_contig2883 2883 THRCLA_contig2884 2884 THRCLA_contig2885 2885 THRCLA_contig2886 2886 THRCLA_contig2887 2887 THRCLA_contig2888 2888 THRCLA_contig2889 2889 THRCLA_contig2890 2890 THRCLA_contig2891 2891 THRCLA_contig2892 2892 THRCLA_contig2893 2893 THRCLA_contig2894 2894 THRCLA_contig2895 2895 THRCLA_contig2896 2896 THRCLA_contig2897 2897 THRCLA_contig2898 2898 THRCLA_contig2899 2899 THRCLA_contig2900 2900 THRCLA_contig2901 2901 THRCLA_contig2902 2902 THRCLA_contig2903 2903 THRCLA_contig2904 2904 THRCLA_contig2905 2905 THRCLA_contig2906 2906 THRCLA_contig2907 2907 THRCLA_contig2908 2908 THRCLA_contig2909 2909 THRCLA_contig2910 2910 THRCLA_contig2911 2911 THRCLA_contig2912 2912 THRCLA_contig2913 2913 THRCLA_contig2914 2914 THRCLA_contig2915 2915 THRCLA_contig2916 2916 THRCLA_contig2917 2917 THRCLA_contig2918 2918 THRCLA_contig2919 2919 THRCLA_contig2920 2920 THRCLA_contig2921 2921 THRCLA_contig2922 2922 THRCLA_contig2923 2923 THRCLA_contig2924 2924 THRCLA_contig2925 2925 THRCLA_contig2926 2926 THRCLA_contig2927 2927 THRCLA_contig2928 2928 THRCLA_contig2929 2929 THRCLA_contig2930 2930 THRCLA_contig2931 2931 THRCLA_contig2932 2932 THRCLA_contig2933 2933 THRCLA_contig2934 2934 THRCLA_contig2935 2935 THRCLA_contig2936 2936 THRCLA_contig2937 2937 THRCLA_contig2938 2938 THRCLA_contig2939 2939 THRCLA_contig2940 2940 THRCLA_contig2941 2941 THRCLA_contig2942 2942 THRCLA_contig2943 2943 THRCLA_contig2944 2944 THRCLA_contig2945 2945 THRCLA_contig2946 2946 THRCLA_contig2947 2947 THRCLA_contig2948 2948 THRCLA_contig2949 2949 THRCLA_contig2950 2950 THRCLA_contig2951 2951 THRCLA_contig2952 2952 THRCLA_contig2953 2953 THRCLA_contig2954 2954 THRCLA_contig2955 2955 THRCLA_contig2956 2956 THRCLA_contig2957 2957 THRCLA_contig2958 2958 THRCLA_contig2959 2959 THRCLA_contig2960 2960 THRCLA_contig2961 2961 THRCLA_contig2962 2962 THRCLA_contig2963 2963 THRCLA_contig2964 2964 THRCLA_contig2965 2965 THRCLA_contig2966 2966 THRCLA_contig2967 2967 THRCLA_contig2968 2968 THRCLA_contig2969 2969 THRCLA_contig2970 2970 THRCLA_contig2971 2971 THRCLA_contig2972 2972 THRCLA_contig2973 2973 THRCLA_contig2974 2974 THRCLA_contig2975 2975 THRCLA_contig2976 2976 THRCLA_contig2977 2977 THRCLA_contig2978 2978 THRCLA_contig2979 2979 THRCLA_contig2980 2980 THRCLA_contig2981 2981 THRCLA_contig2982 2982 THRCLA_contig2983 2983 THRCLA_contig2984 2984 THRCLA_contig2985 2985 THRCLA_contig2986 2986 THRCLA_contig2987 2987 THRCLA_contig2988 2988 THRCLA_contig2989 2989 THRCLA_contig2990 2990 THRCLA_contig2991 2991 THRCLA_contig2992 2992 THRCLA_contig2993 2993 THRCLA_contig2994 2994 THRCLA_contig2995 2995 THRCLA_contig2996 2996 THRCLA_contig2997 2997 THRCLA_contig2998 2998 THRCLA_contig2999 2999 THRCLA_contig3000 3000 THRCLA_contig3001 3001 THRCLA_contig3002 3002 THRCLA_contig3003 3003 THRCLA_contig3004 3004 THRCLA_contig3005 3005 THRCLA_contig3006 3006 THRCLA_contig3007 3007 THRCLA_contig3008 3008 THRCLA_contig3009 3009 THRCLA_contig3010 3010 THRCLA_contig3011 3011 THRCLA_contig3012 3012 THRCLA_contig3013 3013 THRCLA_contig3014 3014 THRCLA_contig3015 3015 THRCLA_contig3016 3016 THRCLA_contig3017 3017 THRCLA_contig3018 3018 THRCLA_contig3019 3019 THRCLA_contig3020 3020 THRCLA_contig3021 3021 THRCLA_contig3022 3022 THRCLA_contig3023 3023 THRCLA_contig3024 3024 THRCLA_contig3025 3025 THRCLA_contig3026 3026 THRCLA_contig3027 3027 THRCLA_contig3028 3028 THRCLA_contig3029 3029 THRCLA_contig3030 3030 THRCLA_contig3031 3031 THRCLA_contig3032 3032 THRCLA_contig3033 3033 THRCLA_contig3034 3034 THRCLA_contig3035 3035 THRCLA_contig3036 3036 THRCLA_contig3037 3037 THRCLA_contig3038 3038 THRCLA_contig3039 3039 THRCLA_contig3040 3040 THRCLA_contig3041 3041 THRCLA_contig3042 3042 THRCLA_contig3043 3043 THRCLA_contig3044 3044 THRCLA_contig3045 3045 THRCLA_contig3046 3046 THRCLA_contig3047 3047 THRCLA_contig3048 3048 THRCLA_contig3049 3049 THRCLA_contig3050 3050 THRCLA_contig3051 3051 THRCLA_contig3052 3052 THRCLA_contig3053 3053 THRCLA_contig3054 3054 THRCLA_contig3055 3055 THRCLA_contig3056 3056 THRCLA_contig3057 3057 THRCLA_contig3058 3058 THRCLA_contig3059 3059 THRCLA_contig3060 3060 THRCLA_contig3061 3061 THRCLA_contig3062 3062 THRCLA_contig3063 3063 THRCLA_contig3064 3064 THRCLA_contig3065 3065 THRCLA_contig3066 3066 THRCLA_contig3067 3067 THRCLA_contig3068 3068 THRCLA_contig3069 3069 THRCLA_contig3070 3070 THRCLA_contig3071 3071 THRCLA_contig3072 3072 THRCLA_contig3073 3073 THRCLA_contig3074 3074 THRCLA_contig3075 3075 THRCLA_contig3076 3076 THRCLA_contig3077 3077 THRCLA_contig3078 3078 THRCLA_contig3079 3079 THRCLA_contig3080 3080 THRCLA_contig3081 3081 THRCLA_contig3082 3082 THRCLA_contig3083 3083 THRCLA_contig3084 3084 THRCLA_contig3085 3085 THRCLA_contig3086 3086 THRCLA_contig3087 3087 THRCLA_contig3088 3088 THRCLA_contig3089 3089 THRCLA_contig3090 3090 THRCLA_contig3091 3091 THRCLA_contig3092 3092 THRCLA_contig3093 3093 THRCLA_contig3094 3094 THRCLA_contig3095 3095 THRCLA_contig3096 3096 THRCLA_contig3097 3097 THRCLA_contig3098 3098 THRCLA_contig3099 3099 THRCLA_contig3100 3100 THRCLA_contig3101 3101 THRCLA_contig3102 3102 THRCLA_contig3103 3103 THRCLA_contig3104 3104 THRCLA_contig3105 3105 THRCLA_contig3106 3106 THRCLA_contig3107 3107 THRCLA_contig3108 3108 THRCLA_contig3109 3109 THRCLA_contig3110 3110 THRCLA_contig3111 3111 THRCLA_contig3112 3112 THRCLA_contig3113 3113 THRCLA_contig3114 3114 THRCLA_contig3115 3115 THRCLA_contig3116 3116 THRCLA_contig3117 3117 THRCLA_contig3118 3118 THRCLA_contig3119 3119 THRCLA_contig3120 3120 THRCLA_contig3121 3121 THRCLA_contig3122 3122 THRCLA_contig3123 3123 THRCLA_contig3124 3124 THRCLA_contig3125 3125 THRCLA_contig3126 3126 THRCLA_contig3127 3127 THRCLA_contig3128 3128 THRCLA_contig3129 3129 THRCLA_contig3130 3130 THRCLA_contig3131 3131 THRCLA_contig3132 3132 THRCLA_contig3133 3133 THRCLA_contig3134 3134 THRCLA_contig3135 3135 THRCLA_contig3136 3136 THRCLA_contig3137 3137 THRCLA_contig3138 3138 THRCLA_contig3139 3139 THRCLA_contig3140 3140 THRCLA_contig3141 3141 THRCLA_contig3142 3142 THRCLA_contig3143 3143 THRCLA_contig3144 3144 THRCLA_contig3145 3145 THRCLA_contig3146 3146 THRCLA_contig3147 3147 THRCLA_contig3148 3148 THRCLA_contig3149 3149 THRCLA_contig3150 3150 THRCLA_contig3151 3151 THRCLA_contig3152 3152 THRCLA_contig3153 3153 THRCLA_contig3154 3154 THRCLA_contig3155 3155 THRCLA_contig3156 3156 THRCLA_contig3157 3157 THRCLA_contig3158 3158 THRCLA_contig3159 3159 THRCLA_contig3160 3160 THRCLA_contig3161 3161 THRCLA_contig3162 3162 THRCLA_contig3163 3163 THRCLA_contig3164 3164 THRCLA_contig3165 3165 THRCLA_contig3166 3166 THRCLA_contig3167 3167 THRCLA_contig3168 3168 THRCLA_contig3169 3169 THRCLA_contig3170 3170 THRCLA_contig3171 3171 THRCLA_contig3172 3172 THRCLA_contig3173 3173 THRCLA_contig3174 3174 THRCLA_contig3175 3175 THRCLA_contig3176 3176 THRCLA_contig3177 3177 THRCLA_contig3178 3178 THRCLA_contig3179 3179 THRCLA_contig3180 3180 THRCLA_contig3181 3181 THRCLA_contig3182 3182 THRCLA_contig3183 3183 THRCLA_contig3184 3184 THRCLA_contig3185 3185 THRCLA_contig3186 3186 THRCLA_contig3187 3187 THRCLA_contig3188 3188 THRCLA_contig3189 3189 THRCLA_contig3190 3190 THRCLA_contig3191 3191 THRCLA_contig3192 3192 THRCLA_contig3193 3193 THRCLA_contig3194 3194 THRCLA_contig3195 3195 THRCLA_contig3196 3196 THRCLA_contig3197 3197 THRCLA_contig3198 3198 THRCLA_contig3199 3199 THRCLA_contig3200 3200 THRCLA_contig3201 3201 THRCLA_contig3202 3202 THRCLA_contig3203 3203 THRCLA_contig3204 3204 THRCLA_contig3205 3205 THRCLA_contig3206 3206 THRCLA_contig3207 3207 THRCLA_contig3208 3208 THRCLA_contig3209 3209 THRCLA_contig3210 3210 THRCLA_contig3211 3211 THRCLA_contig3212 3212 THRCLA_contig3213 3213 THRCLA_contig3214 3214 THRCLA_contig3215 3215 THRCLA_contig3216 3216 THRCLA_contig3217 3217 THRCLA_contig3218 3218 THRCLA_contig3219 3219 THRCLA_contig3220 3220 THRCLA_contig3221 3221 THRCLA_contig3222 3222 THRCLA_contig3223 3223 THRCLA_contig3224 3224 THRCLA_contig3225 3225 THRCLA_contig3226 3226 THRCLA_contig3227 3227 THRCLA_contig3228 3228 THRCLA_contig3229 3229 THRCLA_contig3230 3230 THRCLA_contig3231 3231 THRCLA_contig3232 3232 THRCLA_contig3233 3233 THRCLA_contig3234 3234 THRCLA_contig3235 3235 THRCLA_contig3236 3236 THRCLA_contig3237 3237 THRCLA_contig3238 3238 THRCLA_contig3239 3239 THRCLA_contig3240 3240 THRCLA_contig3241 3241 THRCLA_contig3242 3242 THRCLA_contig3243 3243 THRCLA_contig3244 3244 THRCLA_contig3245 3245 THRCLA_contig3246 3246 THRCLA_contig3247 3247 THRCLA_contig3248 3248 THRCLA_contig3249 3249 THRCLA_contig3250 3250 THRCLA_contig3251 3251 THRCLA_contig3252 3252 THRCLA_contig3253 3253 THRCLA_contig3254 3254 THRCLA_contig3255 3255 THRCLA_contig3256 3256 THRCLA_contig3257 3257 THRCLA_contig3258 3258 THRCLA_contig3259 3259 THRCLA_contig3260 3260 THRCLA_contig3261 3261 THRCLA_contig3262 3262 THRCLA_contig3263 3263 THRCLA_contig3264 3264 THRCLA_contig3265 3265 THRCLA_contig3266 3266 THRCLA_contig3267 3267 THRCLA_contig3268 3268 THRCLA_contig3269 3269 THRCLA_contig3270 3270 THRCLA_contig3271 3271 THRCLA_contig3272 3272 THRCLA_contig3273 3273 THRCLA_contig3274 3274 THRCLA_contig3275 3275 THRCLA_contig3276 3276 THRCLA_contig3277 3277 THRCLA_contig3278 3278 THRCLA_contig3279 3279 THRCLA_contig3280 3280 THRCLA_contig3281 3281 THRCLA_contig3282 3282 THRCLA_contig3283 3283 THRCLA_contig3284 3284 THRCLA_contig3285 3285 THRCLA_contig3286 3286 THRCLA_contig3287 3287 THRCLA_contig3288 3288 THRCLA_contig3289 3289 THRCLA_contig3290 3290 THRCLA_contig3291 3291 THRCLA_contig3292 3292 THRCLA_contig3293 3293 THRCLA_contig3294 3294 THRCLA_contig3295 3295 THRCLA_contig3296 3296 THRCLA_contig3297 3297 THRCLA_contig3298 3298 THRCLA_contig3299 3299 THRCLA_contig3300 3300 THRCLA_contig3301 3301 THRCLA_contig3302 3302 THRCLA_contig3303 3303 THRCLA_contig3304 3304 THRCLA_contig3305 3305 THRCLA_contig3306 3306 THRCLA_contig3307 3307 THRCLA_contig3308 3308 THRCLA_contig3309 3309 THRCLA_contig3310 3310 THRCLA_contig3311 3311 THRCLA_contig3312 3312 THRCLA_contig3313 3313 THRCLA_contig3314 3314 THRCLA_contig3315 3315 THRCLA_contig3316 3316 THRCLA_contig3317 3317 THRCLA_contig3318 3318 THRCLA_contig3319 3319 THRCLA_contig3320 3320 THRCLA_contig3321 3321 THRCLA_contig3322 3322 THRCLA_contig3323 3323 THRCLA_contig3324 3324 THRCLA_contig3325 3325 THRCLA_contig3326 3326 THRCLA_contig3327 3327 THRCLA_contig3328 3328 THRCLA_contig3329 3329 THRCLA_contig3330 3330 THRCLA_contig3331 3331 THRCLA_contig3332 3332 THRCLA_contig3333 3333 THRCLA_contig3334 3334 THRCLA_contig3335 3335 THRCLA_contig3336 3336 THRCLA_contig3337 3337 THRCLA_contig3338 3338 THRCLA_contig3339 3339 THRCLA_contig3340 3340 THRCLA_contig3341 3341 THRCLA_contig3342 3342 THRCLA_contig3343 3343 THRCLA_contig3344 3344 THRCLA_contig3345 3345 THRCLA_contig3346 3346 THRCLA_contig3347 3347 THRCLA_contig3348 3348 THRCLA_contig3349 3349 THRCLA_contig3350 3350 THRCLA_contig3351 3351 THRCLA_contig3352 3352 THRCLA_contig3353 3353 THRCLA_contig3354 3354 THRCLA_contig3355 3355 THRCLA_contig3356 3356 THRCLA_contig3357 3357 THRCLA_contig3358 3358 THRCLA_contig3359 3359 THRCLA_contig3360 3360 THRCLA_contig3361 3361 THRCLA_contig3362 3362 THRCLA_contig3363 3363 THRCLA_contig3364 3364 THRCLA_contig3365 3365 THRCLA_contig3366 3366 THRCLA_contig3367 3367 THRCLA_contig3368 3368 THRCLA_contig3369 3369 THRCLA_contig3370 3370 THRCLA_contig3371 3371 THRCLA_contig3372 3372 THRCLA_contig3373 3373 THRCLA_contig3374 3374 THRCLA_contig3375 3375 THRCLA_contig3376 3376 THRCLA_contig3377 3377 THRCLA_contig3378 3378 THRCLA_contig3379 3379 THRCLA_contig3380 3380 THRCLA_contig3381 3381 THRCLA_contig3382 3382 THRCLA_contig3383 3383 THRCLA_contig3384 3384 THRCLA_contig3385 3385 THRCLA_contig3386 3386 THRCLA_contig3387 3387 THRCLA_contig3388 3388 THRCLA_contig3389 3389 THRCLA_contig3390 3390 THRCLA_contig3391 3391 THRCLA_contig3392 3392 THRCLA_contig3393 3393 THRCLA_contig3394 3394 THRCLA_contig3395 3395 THRCLA_contig3396 3396 THRCLA_contig3397 3397 THRCLA_contig3398 3398 THRCLA_contig3399 3399 THRCLA_contig3400 3400 THRCLA_contig3401 3401 THRCLA_contig3402 3402 THRCLA_contig3403 3403 THRCLA_contig3404 3404 THRCLA_contig3405 3405 THRCLA_contig3406 3406 THRCLA_contig3407 3407 THRCLA_contig3408 3408 THRCLA_contig3409 3409 THRCLA_contig3410 3410 THRCLA_contig3411 3411 THRCLA_contig3412 3412 THRCLA_contig3413 3413 THRCLA_contig3414 3414 THRCLA_contig3415 3415 THRCLA_contig3416 3416 THRCLA_contig3417 3417 THRCLA_contig3418 3418 THRCLA_contig3419 3419 THRCLA_contig3420 3420 THRCLA_contig3421 3421 THRCLA_contig3422 3422 THRCLA_contig3423 3423 THRCLA_contig3424 3424 THRCLA_contig3425 3425 THRCLA_contig3426 3426 THRCLA_contig3427 3427 THRCLA_contig3428 3428 THRCLA_contig3429 3429 THRCLA_contig3430 3430 THRCLA_contig3431 3431 THRCLA_contig3432 3432 THRCLA_contig3433 3433 THRCLA_contig3434 3434 THRCLA_contig3435 3435 THRCLA_contig3436 3436 THRCLA_contig3437 3437 THRCLA_contig3438 3438 THRCLA_contig3439 3439 THRCLA_contig3440 3440 THRCLA_contig3441 3441 THRCLA_contig3442 3442 THRCLA_contig3443 3443 THRCLA_contig3444 3444 THRCLA_contig3445 3445 THRCLA_contig3446 3446 THRCLA_contig3447 3447 THRCLA_contig3448 3448 THRCLA_contig3449 3449 THRCLA_contig3450 3450 THRCLA_contig3451 3451 THRCLA_contig3452 3452 THRCLA_contig3453 3453 THRCLA_contig3454 3454 THRCLA_contig3455 3455 THRCLA_contig3456 3456 THRCLA_contig3457 3457 THRCLA_contig3458 3458 THRCLA_contig3459 3459 THRCLA_contig3460 3460 THRCLA_contig3461 3461 THRCLA_contig3462 3462 THRCLA_contig3463 3463 THRCLA_contig3464 3464 THRCLA_contig3465 3465 THRCLA_contig3466 3466 THRCLA_contig3467 3467 THRCLA_contig3468 3468 THRCLA_contig3469 3469 THRCLA_contig3470 3470 THRCLA_contig3471 3471 THRCLA_contig3472 3472 THRCLA_contig3473 3473 THRCLA_contig3474 3474 THRCLA_contig3475 3475 THRCLA_contig3476 3476 THRCLA_contig3477 3477 THRCLA_contig3478 3478 THRCLA_contig3479 3479 THRCLA_contig3480 3480 THRCLA_contig3481 3481 THRCLA_contig3482 3482 THRCLA_contig3483 3483 THRCLA_contig3484 3484 THRCLA_contig3485 3485 THRCLA_contig3486 3486 THRCLA_contig3487 3487 THRCLA_contig3488 3488 THRCLA_contig3489 3489 THRCLA_contig3490 3490 THRCLA_contig3491 3491 THRCLA_contig3492 3492 THRCLA_contig3493 3493 THRCLA_contig3494 3494 THRCLA_contig3495 3495 THRCLA_contig3496 3496 THRCLA_contig3497 3497 THRCLA_contig3498 3498 THRCLA_contig3499 3499 THRCLA_contig3500 3500 THRCLA_contig3501 3501 THRCLA_contig3502 3502 THRCLA_contig3503 3503 THRCLA_contig3504 3504 THRCLA_contig3505 3505 THRCLA_contig3506 3506 THRCLA_contig3507 3507 THRCLA_contig3508 3508 THRCLA_contig3509 3509 THRCLA_contig3510 3510 THRCLA_contig3511 3511 THRCLA_contig3512 3512 THRCLA_contig3513 3513 THRCLA_contig3514 3514 THRCLA_contig3515 3515 THRCLA_contig3516 3516 THRCLA_contig3517 3517 THRCLA_contig3518 3518 THRCLA_contig3519 3519 THRCLA_contig3520 3520 THRCLA_contig3521 3521 THRCLA_contig3522 3522 THRCLA_contig3523 3523 THRCLA_contig3524 3524 THRCLA_contig3525 3525 THRCLA_contig3526 3526 THRCLA_contig3527 3527 THRCLA_contig3528 3528 THRCLA_contig3529 3529 THRCLA_contig3530 3530 THRCLA_contig3531 3531 THRCLA_contig3532 3532 THRCLA_contig3533 3533 THRCLA_contig3534 3534 THRCLA_contig3535 3535 THRCLA_contig3536 3536 THRCLA_contig3537 3537 THRCLA_contig3538 3538 THRCLA_contig3539 3539 THRCLA_contig3540 3540 THRCLA_contig3541 3541 THRCLA_contig3542 3542 THRCLA_contig3543 3543 THRCLA_contig3544 3544 THRCLA_contig3545 3545 THRCLA_contig3546 3546 THRCLA_contig3547 3547 THRCLA_contig3548 3548 THRCLA_contig3549 3549 THRCLA_contig3550 3550 THRCLA_contig3551 3551 THRCLA_contig3552 3552 THRCLA_contig3553 3553 THRCLA_contig3554 3554 THRCLA_contig3555 3555 THRCLA_contig3556 3556 THRCLA_contig3557 3557 THRCLA_contig3558 3558 THRCLA_contig3559 3559 THRCLA_contig3560 3560 THRCLA_contig3561 3561 THRCLA_contig3562 3562 THRCLA_contig3563 3563 THRCLA_contig3564 3564 THRCLA_contig3565 3565 THRCLA_contig3566 3566 THRCLA_contig3567 3567 THRCLA_contig3568 3568 THRCLA_contig3569 3569 THRCLA_contig3570 3570 THRCLA_contig3571 3571 THRCLA_contig3572 3572 THRCLA_contig3573 3573 THRCLA_contig3574 3574 THRCLA_contig3575 3575 THRCLA_contig3576 3576 THRCLA_contig3577 3577 THRCLA_contig3578 3578 THRCLA_contig3579 3579 THRCLA_contig3580 3580 THRCLA_contig3581 3581 THRCLA_contig3582 3582 THRCLA_contig3583 3583 THRCLA_contig3584 3584 THRCLA_contig3585 3585 THRCLA_contig3586 3586 THRCLA_contig3587 3587 THRCLA_contig3588 3588 THRCLA_contig3589 3589 THRCLA_contig3590 3590 THRCLA_contig3591 3591 THRCLA_contig3592 3592 THRCLA_contig3593 3593 THRCLA_contig3594 3594 THRCLA_contig3595 3595 THRCLA_contig3596 3596 THRCLA_contig3597 3597 THRCLA_contig3598 3598 THRCLA_contig3599 3599 THRCLA_contig3600 3600 THRCLA_contig3601 3601 THRCLA_contig3602 3602 THRCLA_contig3603 3603 THRCLA_contig3604 3604 THRCLA_contig3605 3605 THRCLA_contig3606 3606 THRCLA_contig3607 3607 THRCLA_contig3608 3608 THRCLA_contig3609 3609 THRCLA_contig3610 3610 THRCLA_contig3611 3611 THRCLA_contig3612 3612 THRCLA_contig3613 3613 THRCLA_contig3614 3614 THRCLA_contig3615 3615 THRCLA_contig3616 3616 THRCLA_contig3617 3617 THRCLA_contig3618 3618 THRCLA_contig3619 3619 THRCLA_contig3620 3620 THRCLA_contig3621 3621 THRCLA_contig3622 3622 THRCLA_contig3623 3623 THRCLA_contig3624 3624 THRCLA_contig3625 3625 THRCLA_contig3626 3626 THRCLA_contig3627 3627 THRCLA_contig3628 3628 THRCLA_contig3629 3629 THRCLA_contig3630 3630 THRCLA_contig3631 3631 THRCLA_contig3632 3632 THRCLA_contig3633 3633 THRCLA_contig3634 3634 THRCLA_contig3635 3635 THRCLA_contig3636 3636 THRCLA_contig3637 3637 THRCLA_contig3638 3638 THRCLA_contig3639 3639 THRCLA_contig3640 3640 THRCLA_contig3641 3641 THRCLA_contig3642 3642 THRCLA_contig3643 3643 THRCLA_contig3644 3644 THRCLA_contig3645 3645 THRCLA_contig3646 3646 THRCLA_contig3647 3647 THRCLA_contig3648 3648 THRCLA_contig3649 3649 THRCLA_contig3650 3650 THRCLA_contig3651 3651 THRCLA_contig3652 3652 THRCLA_contig3653 3653 THRCLA_contig3654 3654 THRCLA_contig3655 3655 THRCLA_contig3656 3656 THRCLA_contig3657 3657 THRCLA_contig3658 3658 THRCLA_contig3659 3659 THRCLA_contig3660 3660 THRCLA_contig3661 3661 THRCLA_contig3662 3662 THRCLA_contig3663 3663 THRCLA_contig3664 3664 THRCLA_contig3665 3665 THRCLA_contig3666 3666 THRCLA_contig3667 3667 THRCLA_contig3668 3668 THRCLA_contig3669 3669 THRCLA_contig3670 3670 THRCLA_contig3671 3671 THRCLA_contig3672 3672 THRCLA_contig3673 3673 THRCLA_contig3674 3674 THRCLA_contig3675 3675 THRCLA_contig3676 3676 THRCLA_contig3677 3677 THRCLA_contig3678 3678 THRCLA_contig3679 3679 THRCLA_contig3680 3680 THRCLA_contig3681 3681 THRCLA_contig3682 3682 THRCLA_contig3683 3683 THRCLA_contig3684 3684 THRCLA_contig3685 3685 THRCLA_contig3686 3686 THRCLA_contig3687 3687 THRCLA_contig3688 3688 THRCLA_contig3689 3689 THRCLA_contig3690 3690 THRCLA_contig3691 3691 THRCLA_contig3692 3692 THRCLA_contig3693 3693 THRCLA_contig3694 3694 THRCLA_contig3695 3695 THRCLA_contig3696 3696 THRCLA_contig3697 3697 THRCLA_contig3698 3698 THRCLA_contig3699 3699 THRCLA_contig3700 3700 THRCLA_contig3701 3701 THRCLA_contig3702 3702 THRCLA_contig3703 3703 THRCLA_contig3704 3704 THRCLA_contig3705 3705 THRCLA_contig3706 3706 THRCLA_contig3707 3707 THRCLA_contig3708 3708 THRCLA_contig3709 3709 THRCLA_contig3710 3710 THRCLA_contig3711 3711 THRCLA_contig3712 3712 THRCLA_contig3713 3713 THRCLA_contig3714 3714 THRCLA_contig3715 3715 THRCLA_contig3716 3716 THRCLA_contig3717 3717 THRCLA_contig3718 3718 THRCLA_contig3719 3719 THRCLA_contig3720 3720 THRCLA_contig3721 3721 THRCLA_contig3722 3722 THRCLA_contig3723 3723 THRCLA_contig3724 3724 THRCLA_contig3725 3725 THRCLA_contig3726 3726 THRCLA_contig3727 3727 THRCLA_contig3728 3728 THRCLA_contig3729 3729 THRCLA_contig3730 3730 THRCLA_contig3731 3731 THRCLA_contig3732 3732 THRCLA_contig3733 3733 THRCLA_contig3734 3734 THRCLA_contig3735 3735 THRCLA_contig3736 3736 THRCLA_contig3737 3737 THRCLA_contig3738 3738 THRCLA_contig3739 3739 THRCLA_contig3740 3740 THRCLA_contig3741 3741 THRCLA_contig3742 3742 THRCLA_contig3743 3743 THRCLA_contig3744 3744 THRCLA_contig3745 3745 THRCLA_contig3746 3746 THRCLA_contig3747 3747 THRCLA_contig3748 3748 THRCLA_contig3749 3749 THRCLA_contig3750 3750 THRCLA_contig3751 3751 THRCLA_contig3752 3752 THRCLA_contig3753 3753 THRCLA_contig3754 3754 THRCLA_contig3755 3755 THRCLA_contig3756 3756 THRCLA_contig3757 3757 THRCLA_contig3758 3758 THRCLA_contig3759 3759 THRCLA_contig3760 3760 THRCLA_contig3761 3761 THRCLA_contig3762 3762 THRCLA_contig3763 3763 THRCLA_contig3764 3764 THRCLA_contig3765 3765 THRCLA_contig3766 3766 THRCLA_contig3767 3767 THRCLA_contig3768 3768 THRCLA_contig3769 3769 THRCLA_contig3770 3770 THRCLA_contig3771 3771 THRCLA_contig3772 3772 THRCLA_contig3773 3773 THRCLA_contig3774 3774 THRCLA_contig3775 3775 THRCLA_contig3776 3776 THRCLA_contig3777 3777 THRCLA_contig3778 3778 THRCLA_contig3779 3779 THRCLA_contig3780 3780 THRCLA_contig3781 3781 THRCLA_contig3782 3782 THRCLA_contig3783 3783 THRCLA_contig3784 3784 THRCLA_contig3785 3785 THRCLA_contig3786 3786 THRCLA_contig3787 3787 THRCLA_contig3788 3788 THRCLA_contig3789 3789 THRCLA_contig3790 3790 THRCLA_contig3791 3791 THRCLA_contig3792 3792 THRCLA_contig3793 3793 THRCLA_contig3794 3794 THRCLA_contig3795 3795 THRCLA_contig3796 3796 THRCLA_contig3797 3797 THRCLA_contig3798 3798 THRCLA_contig3799 3799 THRCLA_contig3800 3800 THRCLA_contig3801 3801 THRCLA_contig3802 3802 THRCLA_contig3803 3803 THRCLA_contig3804 3804 THRCLA_contig3805 3805 THRCLA_contig3806 3806 THRCLA_contig3807 3807 THRCLA_contig3808 3808 THRCLA_contig3809 3809 THRCLA_contig3810 3810 THRCLA_contig3811 3811 THRCLA_contig3812 3812 THRCLA_contig3813 3813 THRCLA_contig3814 3814 THRCLA_contig3815 3815 THRCLA_contig3816 3816 THRCLA_contig3817 3817 THRCLA_contig3818 3818 THRCLA_contig3819 3819 THRCLA_contig3820 3820 THRCLA_contig3821 3821 THRCLA_contig3822 3822 THRCLA_contig3823 3823 THRCLA_contig3824 3824 THRCLA_contig3825 3825 THRCLA_contig3826 3826 THRCLA_contig3827 3827 THRCLA_contig3828 3828 THRCLA_contig3829 3829 THRCLA_contig3830 3830 THRCLA_contig3831 3831 THRCLA_contig3832 3832 THRCLA_contig3833 3833 THRCLA_contig3834 3834 THRCLA_contig3835 3835 THRCLA_contig3836 3836 THRCLA_contig3837 3837 THRCLA_contig3838 3838 THRCLA_contig3839 3839 THRCLA_contig3840 3840 THRCLA_contig3841 3841 THRCLA_contig3842 3842 THRCLA_contig3843 3843 THRCLA_contig3844 3844 THRCLA_contig3845 3845 THRCLA_contig3846 3846 THRCLA_contig3847 3847 THRCLA_contig3848 3848 THRCLA_contig3849 3849 THRCLA_contig3850 3850 THRCLA_contig3851 3851 THRCLA_contig3852 3852 THRCLA_contig3853 3853 THRCLA_contig3854 3854 THRCLA_contig3855 3855 THRCLA_contig3856 3856 THRCLA_contig3857 3857 THRCLA_contig3858 3858 THRCLA_contig3859 3859 THRCLA_contig3860 3860 THRCLA_contig3861 3861 THRCLA_contig3862 3862 THRCLA_contig3863 3863 THRCLA_contig3864 3864 THRCLA_contig3865 3865 THRCLA_contig3866 3866 THRCLA_contig3867 3867 THRCLA_contig3868 3868 THRCLA_contig3869 3869 THRCLA_contig3870 3870 THRCLA_contig3871 3871 THRCLA_contig3872 3872 THRCLA_contig3873 3873 THRCLA_contig3874 3874 THRCLA_contig3875 3875 THRCLA_contig3876 3876 THRCLA_contig3877 3877 THRCLA_contig3878 3878 THRCLA_contig3879 3879 THRCLA_contig3880 3880 THRCLA_contig3881 3881 THRCLA_contig3882 3882 THRCLA_contig3883 3883 THRCLA_contig3884 3884 THRCLA_contig3885 3885 THRCLA_contig3886 3886 THRCLA_contig3887 3887 THRCLA_contig3888 3888 THRCLA_contig3889 3889 THRCLA_contig3890 3890 THRCLA_contig3891 3891 THRCLA_contig3892 3892 THRCLA_contig3893 3893 THRCLA_contig3894 3894 THRCLA_contig3895 3895 THRCLA_contig3896 3896 THRCLA_contig3897 3897 THRCLA_contig3898 3898 THRCLA_contig3899 3899 THRCLA_contig3900 3900 THRCLA_contig3901 3901 THRCLA_contig3902 3902 THRCLA_contig3903 3903 THRCLA_contig3904 3904 THRCLA_contig3905 3905 THRCLA_contig3906 3906 THRCLA_contig3907 3907 THRCLA_contig3908 3908 THRCLA_contig3909 3909 THRCLA_contig3910 3910 THRCLA_contig3911 3911 THRCLA_contig3912 3912 THRCLA_contig3913 3913 THRCLA_contig3914 3914 THRCLA_contig3915 3915 THRCLA_contig3916 3916 THRCLA_contig3917 3917 THRCLA_contig3918 3918 THRCLA_contig3919 3919 THRCLA_contig3920 3920 THRCLA_contig3921 3921 THRCLA_contig3922 3922 THRCLA_contig3923 3923 THRCLA_contig3924 3924 THRCLA_contig3925 3925 THRCLA_contig3926 3926 THRCLA_contig3927 3927 THRCLA_contig3928 3928 THRCLA_contig3929 3929 THRCLA_contig3930 3930 THRCLA_contig3931 3931 THRCLA_contig3932 3932 THRCLA_contig3933 3933 THRCLA_contig3934 3934 THRCLA_contig3935 3935 THRCLA_contig3936 3936 THRCLA_contig3937 3937 THRCLA_contig3938 3938 THRCLA_contig3939 3939 THRCLA_contig3940 3940 THRCLA_contig3941 3941 THRCLA_contig3942 3942 THRCLA_contig3943 3943 THRCLA_contig3944 3944 THRCLA_contig3945 3945 THRCLA_contig3946 3946 THRCLA_contig3947 3947 THRCLA_contig3948 3948 THRCLA_contig3949 3949 THRCLA_contig3950 3950 THRCLA_contig3951 3951 THRCLA_contig3952 3952 THRCLA_contig3953 3953 THRCLA_contig3954 3954 THRCLA_contig3955 3955 THRCLA_contig3956 3956 THRCLA_contig3957 3957 THRCLA_contig3958 3958 THRCLA_contig3959 3959 THRCLA_contig3960 3960 THRCLA_contig3961 3961 THRCLA_contig3962 3962 THRCLA_contig3963 3963 THRCLA_contig3964 3964 THRCLA_contig3965 3965 THRCLA_contig3966 3966 THRCLA_contig3967 3967 THRCLA_contig3968 3968 THRCLA_contig3969 3969 THRCLA_contig3970 3970 THRCLA_contig3971 3971 THRCLA_contig3972 3972 THRCLA_contig3973 3973 THRCLA_contig3974 3974 THRCLA_contig3975 3975 THRCLA_contig3976 3976 THRCLA_contig3977 3977 THRCLA_contig3978 3978 THRCLA_contig3979 3979 THRCLA_contig3980 3980 THRCLA_contig3981 3981 THRCLA_contig3982 3982 THRCLA_contig3983 3983 THRCLA_contig3984 3984 THRCLA_contig3985 3985 THRCLA_contig3986 3986 THRCLA_contig3987 3987 THRCLA_contig3988 3988 THRCLA_contig3989 3989 THRCLA_contig3990 3990 THRCLA_contig3991 3991 THRCLA_contig3992 3992 THRCLA_contig3993 3993 THRCLA_contig3994 3994 THRCLA_contig3995 3995 THRCLA_contig3996 3996 THRCLA_contig3997 3997 THRCLA_contig3998 3998 THRCLA_contig3999 3999 THRCLA_contig4000 4000 THRCLA_contig4001 4001 THRCLA_contig4002 4002 THRCLA_contig4003 4003 THRCLA_contig4004 4004 THRCLA_contig4005 4005 THRCLA_contig4006 4006 THRCLA_contig4007 4007 THRCLA_contig4008 4008 THRCLA_contig4009 4009 THRCLA_contig4010 4010 THRCLA_contig4011 4011 THRCLA_contig4012 4012 THRCLA_contig4013 4013 THRCLA_contig4014 4014 THRCLA_contig4015 4015 THRCLA_contig4016 4016 THRCLA_contig4017 4017 THRCLA_contig4018 4018 THRCLA_contig4019 4019 THRCLA_contig4020 4020 THRCLA_contig4021 4021 THRCLA_contig4022 4022 THRCLA_contig4023 4023 THRCLA_contig4024 4024 THRCLA_contig4025 4025 THRCLA_contig4026 4026 THRCLA_contig4027 4027 THRCLA_contig4028 4028 THRCLA_contig4029 4029 THRCLA_contig4030 4030 THRCLA_contig4031 4031 THRCLA_contig4032 4032 THRCLA_contig4033 4033 THRCLA_contig4034 4034 THRCLA_contig4035 4035 THRCLA_contig4036 4036 THRCLA_contig4037 4037 THRCLA_contig4038 4038 THRCLA_contig4039 4039 THRCLA_contig4040 4040 THRCLA_contig4041 4041 THRCLA_contig4042 4042 THRCLA_contig4043 4043 THRCLA_contig4044 4044 THRCLA_contig4045 4045 THRCLA_contig4046 4046 THRCLA_contig4047 4047 THRCLA_contig4048 4048 THRCLA_contig4049 4049 THRCLA_contig4050 4050 THRCLA_contig4051 4051 THRCLA_contig4052 4052 THRCLA_contig4053 4053 THRCLA_contig4054 4054 THRCLA_contig4055 4055 THRCLA_contig4056 4056 THRCLA_contig4057 4057 THRCLA_contig4058 4058 THRCLA_contig4059 4059 THRCLA_contig4060 4060 THRCLA_contig4061 4061 THRCLA_contig4062 4062 THRCLA_contig4063 4063 THRCLA_contig4064 4064 THRCLA_contig4065 4065 THRCLA_contig4066 4066 THRCLA_contig4067 4067 THRCLA_contig4068 4068 THRCLA_contig4069 4069 THRCLA_contig4070 4070 THRCLA_contig4071 4071 THRCLA_contig4072 4072 THRCLA_contig4073 4073 THRCLA_contig4074 4074 THRCLA_contig4075 4075 THRCLA_contig4076 4076 THRCLA_contig4077 4077 THRCLA_contig4078 4078 THRCLA_contig4079 4079 THRCLA_contig4080 4080 THRCLA_contig4081 4081 THRCLA_contig4082 4082 THRCLA_contig4083 4083 THRCLA_contig4084 4084 THRCLA_contig4085 4085 THRCLA_contig4086 4086 THRCLA_contig4087 4087 THRCLA_contig4088 4088 THRCLA_contig4089 4089 THRCLA_contig4090 4090 THRCLA_contig4091 4091 THRCLA_contig4092 4092 THRCLA_contig4093 4093 THRCLA_contig4094 4094 THRCLA_contig4095 4095 THRCLA_contig4096 4096 THRCLA_contig4097 4097 THRCLA_contig4098 4098 THRCLA_contig4099 4099 THRCLA_contig4100 4100 THRCLA_contig4101 4101 THRCLA_contig4102 4102 THRCLA_contig4103 4103 THRCLA_contig4104 4104 THRCLA_contig4105 4105 THRCLA_contig4106 4106 THRCLA_contig4107 4107 THRCLA_contig4108 4108 THRCLA_contig4109 4109 THRCLA_contig4110 4110 THRCLA_contig4111 4111 THRCLA_contig4112 4112 THRCLA_contig4113 4113 THRCLA_contig4114 4114 THRCLA_contig4115 4115 THRCLA_contig4116 4116 THRCLA_contig4117 4117 THRCLA_contig4118 4118 THRCLA_contig4119 4119 THRCLA_contig4120 4120 THRCLA_contig4121 4121 THRCLA_contig4122 4122 THRCLA_contig4123 4123 THRCLA_contig4124 4124 THRCLA_contig4125 4125 THRCLA_contig4126 4126 THRCLA_contig4127 4127 THRCLA_contig4128 4128 THRCLA_contig4129 4129 THRCLA_contig4130 4130 THRCLA_contig4131 4131 THRCLA_contig4132 4132 THRCLA_contig4133 4133 THRCLA_contig4134 4134 THRCLA_contig4135 4135 THRCLA_contig4136 4136 THRCLA_contig4137 4137 THRCLA_contig4138 4138 THRCLA_contig4139 4139 THRCLA_contig4140 4140 THRCLA_contig4141 4141 THRCLA_contig4142 4142 THRCLA_contig4143 4143 THRCLA_contig4144 4144 THRCLA_contig4145 4145 THRCLA_contig4146 4146 THRCLA_contig4147 4147 THRCLA_contig4148 4148 THRCLA_contig4149 4149 THRCLA_contig4150 4150 THRCLA_contig4151 4151 THRCLA_contig4152 4152 THRCLA_contig4153 4153 THRCLA_contig4154 4154 THRCLA_contig4155 4155 THRCLA_contig4156 4156 THRCLA_contig4157 4157 THRCLA_contig4158 4158 THRCLA_contig4159 4159 THRCLA_contig4160 4160 THRCLA_contig4161 4161 THRCLA_contig4162 4162 THRCLA_contig4163 4163 THRCLA_contig4164 4164 THRCLA_contig4165 4165 THRCLA_contig4166 4166 THRCLA_contig4167 4167 THRCLA_contig4168 4168 THRCLA_contig4169 4169 THRCLA_contig4170 4170 THRCLA_contig4171 4171 THRCLA_contig4172 4172 THRCLA_contig4173 4173 THRCLA_contig4174 4174 THRCLA_contig4175 4175 THRCLA_contig4176 4176 THRCLA_contig4177 4177 THRCLA_contig4178 4178 THRCLA_contig4179 4179 THRCLA_contig4180 4180 THRCLA_contig4181 4181 THRCLA_contig4182 4182 THRCLA_contig4183 4183 THRCLA_contig4184 4184 THRCLA_contig4185 4185 THRCLA_contig4186 4186 THRCLA_contig4187 4187 THRCLA_contig4188 4188 THRCLA_contig4189 4189 THRCLA_contig4190 4190 THRCLA_contig4191 4191 THRCLA_contig4192 4192 THRCLA_contig4193 4193 THRCLA_contig4194 4194 THRCLA_contig4195 4195 THRCLA_contig4196 4196 THRCLA_contig4197 4197 THRCLA_contig4198 4198 THRCLA_contig4199 4199 THRCLA_contig4200 4200 THRCLA_contig4201 4201 THRCLA_contig4202 4202 THRCLA_contig4203 4203 THRCLA_contig4204 4204 THRCLA_contig4205 4205 THRCLA_contig4206 4206 THRCLA_contig4207 4207 THRCLA_contig4208 4208 THRCLA_contig4209 4209 THRCLA_contig4210 4210 THRCLA_contig4211 4211 THRCLA_contig4212 4212 THRCLA_contig4213 4213 THRCLA_contig4214 4214 THRCLA_contig4215 4215 THRCLA_contig4216 4216 THRCLA_contig4217 4217 THRCLA_contig4218 4218 THRCLA_contig4219 4219 THRCLA_contig4220 4220 THRCLA_contig4221 4221 THRCLA_contig4222 4222 THRCLA_contig4223 4223 THRCLA_contig4224 4224 THRCLA_contig4225 4225 THRCLA_contig4226 4226 THRCLA_contig4227 4227 THRCLA_contig4228 4228 THRCLA_contig4229 4229 THRCLA_contig4230 4230 THRCLA_contig4231 4231 THRCLA_contig4232 4232 THRCLA_contig4233 4233 THRCLA_contig4234 4234 THRCLA_contig4235 4235 THRCLA_contig4236 4236 THRCLA_contig4237 4237 THRCLA_contig4238 4238 THRCLA_contig4239 4239 THRCLA_contig4240 4240 THRCLA_contig4241 4241 THRCLA_contig4242 4242 THRCLA_contig4243 4243 THRCLA_contig4244 4244 THRCLA_contig4245 4245 THRCLA_contig4246 4246 THRCLA_contig4247 4247 THRCLA_contig4248 4248 THRCLA_contig4249 4249 THRCLA_contig4250 4250 THRCLA_contig4251 4251 THRCLA_contig4252 4252 THRCLA_contig4253 4253 THRCLA_contig4254 4254 THRCLA_contig4255 4255 THRCLA_contig4256 4256 THRCLA_contig4257 4257 THRCLA_contig4258 4258 THRCLA_contig4259 4259 THRCLA_contig4260 4260 THRCLA_contig4261 4261 THRCLA_contig4262 4262 THRCLA_contig4263 4263 THRCLA_contig4264 4264 THRCLA_contig4265 4265 THRCLA_contig4266 4266 THRCLA_contig4267 4267 THRCLA_contig4268 4268 THRCLA_contig4269 4269 THRCLA_contig4270 4270 THRCLA_contig4271 4271 THRCLA_contig4272 4272 THRCLA_contig4273 4273 THRCLA_contig4274 4274 THRCLA_contig4275 4275 THRCLA_contig4276 4276 THRCLA_contig4277 4277 THRCLA_contig4278 4278 THRCLA_contig4279 4279 THRCLA_contig4280 4280 THRCLA_contig4281 4281 THRCLA_contig4282 4282 THRCLA_contig4283 4283 THRCLA_contig4284 4284 THRCLA_contig4285 4285 THRCLA_contig4286 4286 THRCLA_contig4287 4287 THRCLA_contig4288 4288 THRCLA_contig4289 4289 THRCLA_contig4290 4290 THRCLA_contig4291 4291 THRCLA_contig4292 4292 THRCLA_contig4293 4293 THRCLA_contig4294 4294 THRCLA_contig4295 4295 THRCLA_contig4296 4296 THRCLA_contig4297 4297 THRCLA_contig4298 4298 THRCLA_contig4299 4299 THRCLA_contig4300 4300 THRCLA_contig4301 4301 THRCLA_contig4302 4302 THRCLA_contig4303 4303 THRCLA_contig4304 4304 THRCLA_contig4305 4305 THRCLA_contig4306 4306 THRCLA_contig4307 4307 THRCLA_contig4308 4308 THRCLA_contig4309 4309 THRCLA_contig4310 4310 THRCLA_contig4311 4311 THRCLA_contig4312 4312 THRCLA_contig4313 4313 THRCLA_contig4314 4314 THRCLA_contig4315 4315 THRCLA_contig4316 4316 THRCLA_contig4317 4317 THRCLA_contig4318 4318 THRCLA_contig4319 4319 THRCLA_contig4320 4320 THRCLA_contig4321 4321 THRCLA_contig4322 4322 THRCLA_contig4323 4323 THRCLA_contig4324 4324 THRCLA_contig4325 4325 THRCLA_contig4326 4326 THRCLA_contig4327 4327 THRCLA_contig4328 4328 THRCLA_contig4329 4329 THRCLA_contig4330 4330 THRCLA_contig4331 4331 THRCLA_contig4332 4332 THRCLA_contig4333 4333 THRCLA_contig4334 4334 THRCLA_contig4335 4335 THRCLA_contig4336 4336 THRCLA_contig4337 4337 THRCLA_contig4338 4338 THRCLA_contig4339 4339 THRCLA_contig4340 4340 THRCLA_contig4341 4341 THRCLA_contig4342 4342 THRCLA_contig4343 4343 THRCLA_contig4344 4344 THRCLA_contig4345 4345 THRCLA_contig4346 4346 THRCLA_contig4347 4347 THRCLA_contig4348 4348 THRCLA_contig4349 4349 THRCLA_contig4350 4350 THRCLA_contig4351 4351 THRCLA_contig4352 4352 THRCLA_contig4353 4353 THRCLA_contig4354 4354 THRCLA_contig4355 4355 THRCLA_contig4356 4356 THRCLA_contig4357 4357 THRCLA_contig4358 4358 THRCLA_contig4359 4359 THRCLA_contig4360 4360 THRCLA_contig4361 4361 THRCLA_contig4362 4362 THRCLA_contig4363 4363 THRCLA_contig4364 4364 THRCLA_contig4365 4365 THRCLA_contig4366 4366 THRCLA_contig4367 4367 THRCLA_contig4368 4368 THRCLA_contig4369 4369 THRCLA_contig4370 4370 THRCLA_contig4371 4371 THRCLA_contig4372 4372 THRCLA_contig4373 4373 THRCLA_contig4374 4374 THRCLA_contig4375 4375 THRCLA_contig4376 4376 THRCLA_contig4377 4377 THRCLA_contig4378 4378 THRCLA_contig4379 4379 THRCLA_contig4380 4380 THRCLA_contig4381 4381 THRCLA_contig4382 4382 THRCLA_contig4383 4383 THRCLA_contig4384 4384 THRCLA_contig4385 4385 THRCLA_contig4386 4386 THRCLA_contig4387 4387 THRCLA_contig4388 4388 THRCLA_contig4389 4389 THRCLA_contig4390 4390 THRCLA_contig4391 4391 THRCLA_contig4392 4392 THRCLA_contig4393 4393 THRCLA_contig4394 4394 THRCLA_contig4395 4395 THRCLA_contig4396 4396 THRCLA_contig4397 4397 THRCLA_contig4398 4398 THRCLA_contig4399 4399 THRCLA_contig4400 4400 THRCLA_contig4401 4401 THRCLA_contig4402 4402 THRCLA_contig4403 4403 THRCLA_contig4404 4404 THRCLA_contig4405 4405 THRCLA_contig4406 4406 THRCLA_contig4407 4407 THRCLA_contig4408 4408 THRCLA_contig4409 4409 THRCLA_contig4410 4410 THRCLA_contig4411 4411 THRCLA_contig4412 4412 THRCLA_contig4413 4413 THRCLA_contig4414 4414 THRCLA_contig4415 4415 THRCLA_contig4416 4416 THRCLA_contig4417 4417 THRCLA_contig4418 4418 THRCLA_contig4419 4419 THRCLA_contig4420 4420 THRCLA_contig4421 4421 THRCLA_contig4422 4422 THRCLA_contig4423 4423 THRCLA_contig4424 4424 THRCLA_contig4425 4425 THRCLA_contig4426 4426 THRCLA_contig4427 4427 THRCLA_contig4428 4428 THRCLA_contig4429 4429 THRCLA_contig4430 4430 THRCLA_contig4431 4431 THRCLA_contig4432 4432 THRCLA_contig4433 4433 THRCLA_contig4434 4434 THRCLA_contig4435 4435 THRCLA_contig4436 4436 THRCLA_contig4437 4437 THRCLA_contig4438 4438 THRCLA_contig4439 4439 THRCLA_contig4440 4440 THRCLA_contig4441 4441 THRCLA_contig4442 4442 THRCLA_contig4443 4443 THRCLA_contig4444 4444 THRCLA_contig4445 4445 THRCLA_contig4446 4446 THRCLA_contig4447 4447 THRCLA_contig4448 4448 THRCLA_contig4449 4449 THRCLA_contig4450 4450 THRCLA_contig4451 4451 THRCLA_contig4452 4452 THRCLA_contig4453 4453 THRCLA_contig4454 4454 THRCLA_contig4455 4455 THRCLA_contig4456 4456 THRCLA_contig4457 4457 THRCLA_contig4458 4458 THRCLA_contig4459 4459 THRCLA_contig4460 4460 THRCLA_contig4461 4461 THRCLA_contig4462 4462 THRCLA_contig4463 4463 THRCLA_contig4464 4464 THRCLA_contig4465 4465 THRCLA_contig4466 4466 THRCLA_contig4467 4467 THRCLA_contig4468 4468 THRCLA_contig4469 4469 THRCLA_contig4470 4470 THRCLA_contig4471 4471 THRCLA_contig4472 4472 THRCLA_contig4473 4473 THRCLA_contig4474 4474 THRCLA_contig4475 4475 THRCLA_contig4476 4476 THRCLA_contig4477 4477 THRCLA_contig4478 4478 THRCLA_contig4479 4479 THRCLA_contig4480 4480 THRCLA_contig4481 4481 THRCLA_contig4482 4482 THRCLA_contig4483 4483 THRCLA_contig4484 4484 THRCLA_contig4485 4485 THRCLA_contig4486 4486 THRCLA_contig4487 4487 THRCLA_contig4488 4488 THRCLA_contig4489 4489 THRCLA_contig4490 4490 THRCLA_contig4491 4491 THRCLA_contig4492 4492 THRCLA_contig4493 4493 THRCLA_contig4494 4494 THRCLA_contig4495 4495 THRCLA_contig4496 4496 THRCLA_contig4497 4497 THRCLA_contig4498 4498 THRCLA_contig4499 4499 THRCLA_contig4500 4500 THRCLA_contig4501 4501 THRCLA_contig4502 4502 THRCLA_contig4503 4503 THRCLA_contig4504 4504 THRCLA_contig4505 4505 THRCLA_contig4506 4506 THRCLA_contig4507 4507 THRCLA_contig4508 4508 THRCLA_contig4509 4509 THRCLA_contig4510 4510 THRCLA_contig4511 4511 THRCLA_contig4512 4512 THRCLA_contig4513 4513 THRCLA_contig4514 4514 THRCLA_contig4515 4515 THRCLA_contig4516 4516 THRCLA_contig4517 4517 THRCLA_contig4518 4518 THRCLA_contig4519 4519 THRCLA_contig4520 4520 THRCLA_contig4521 4521 THRCLA_contig4522 4522 THRCLA_contig4523 4523 THRCLA_contig4524 4524 THRCLA_contig4525 4525 THRCLA_contig4526 4526 THRCLA_contig4527 4527 THRCLA_contig4528 4528 THRCLA_contig4529 4529 THRCLA_contig4530 4530 THRCLA_contig4531 4531 THRCLA_contig4532 4532 THRCLA_contig4533 4533 THRCLA_contig4534 4534 THRCLA_contig4535 4535 THRCLA_contig4536 4536 THRCLA_contig4537 4537 THRCLA_contig4538 4538 THRCLA_contig4539 4539 THRCLA_contig4540 4540 THRCLA_contig4541 4541 THRCLA_contig4542 4542 THRCLA_contig4543 4543 THRCLA_contig4544 4544 THRCLA_contig4545 4545 THRCLA_contig4546 4546 THRCLA_contig4547 4547 THRCLA_contig4548 4548 THRCLA_contig4549 4549 THRCLA_contig4550 4550 THRCLA_contig4551 4551 THRCLA_contig4552 4552 THRCLA_contig4553 4553 THRCLA_contig4554 4554 THRCLA_contig4555 4555 THRCLA_contig4556 4556 THRCLA_contig4557 4557 THRCLA_contig4558 4558 THRCLA_contig4559 4559 THRCLA_contig4560 4560 THRCLA_contig4561 4561 THRCLA_contig4562 4562 THRCLA_contig4563 4563 THRCLA_contig4564 4564 THRCLA_contig4565 4565 THRCLA_contig4566 4566 THRCLA_contig4567 4567 THRCLA_contig4568 4568 THRCLA_contig4569 4569 THRCLA_contig4570 4570 THRCLA_contig4571 4571 THRCLA_contig4572 4572 THRCLA_contig4573 4573 THRCLA_contig4574 4574 THRCLA_contig4575 4575 THRCLA_contig4576 4576 THRCLA_contig4577 4577 THRCLA_contig4578 4578 THRCLA_contig4579 4579 THRCLA_contig4580 4580 THRCLA_contig4581 4581 THRCLA_contig4582 4582 THRCLA_contig4583 4583 THRCLA_contig4584 4584 THRCLA_contig4585 4585 THRCLA_contig4586 4586 THRCLA_contig4587 4587 THRCLA_contig4588 4588 THRCLA_contig4589 4589 THRCLA_contig4590 4590 THRCLA_contig4591 4591 THRCLA_contig4592 4592 THRCLA_contig4593 4593 THRCLA_contig4594 4594 THRCLA_contig4595 4595 THRCLA_contig4596 4596 THRCLA_contig4597 4597 THRCLA_contig4598 4598 THRCLA_contig4599 4599 THRCLA_contig4600 4600 THRCLA_contig4601 4601 THRCLA_contig4602 4602 THRCLA_contig4603 4603 THRCLA_contig4604 4604 THRCLA_contig4605 4605 THRCLA_contig4606 4606 THRCLA_contig4607 4607 THRCLA_contig4608 4608 THRCLA_contig4609 4609 THRCLA_contig4610 4610 THRCLA_contig4611 4611 THRCLA_contig4612 4612 THRCLA_contig4613 4613 THRCLA_contig4614 4614 THRCLA_contig4615 4615 THRCLA_contig4616 4616 THRCLA_contig4617 4617 THRCLA_contig4618 4618 THRCLA_contig4619 4619 THRCLA_contig4620 4620 THRCLA_contig4621 4621 THRCLA_contig4622 4622 THRCLA_contig4623 4623 THRCLA_contig4624 4624 THRCLA_contig4625 4625 THRCLA_contig4626 4626 THRCLA_contig4627 4627 THRCLA_contig4628 4628 THRCLA_contig4629 4629 THRCLA_contig4630 4630 THRCLA_contig4631 4631 THRCLA_contig4632 4632 THRCLA_contig4633 4633 THRCLA_contig4634 4634 THRCLA_contig4635 4635 THRCLA_contig4636 4636 THRCLA_contig4637 4637 THRCLA_contig4638 4638 THRCLA_contig4639 4639 THRCLA_contig4640 4640 THRCLA_contig4641 4641 THRCLA_contig4642 4642 THRCLA_contig4643 4643 THRCLA_contig4644 4644 THRCLA_contig4645 4645 THRCLA_contig4646 4646 THRCLA_contig4647 4647 THRCLA_contig4648 4648 THRCLA_contig4649 4649 THRCLA_contig4650 4650 THRCLA_contig4651 4651 THRCLA_contig4652 4652 THRCLA_contig4653 4653 THRCLA_contig4654 4654 THRCLA_contig4655 4655 THRCLA_contig4656 4656 THRCLA_contig4657 4657 THRCLA_contig4658 4658 THRCLA_contig4659 4659 THRCLA_contig4660 4660 THRCLA_contig4661 4661 THRCLA_contig4662 4662 THRCLA_contig4663 4663 THRCLA_contig4664 4664 THRCLA_contig4665 4665 THRCLA_contig4666 4666 THRCLA_contig4667 4667 THRCLA_contig4668 4668 THRCLA_contig4669 4669 THRCLA_contig4670 4670 THRCLA_contig4671 4671 THRCLA_contig4672 4672 THRCLA_contig4673 4673 THRCLA_contig4674 4674 THRCLA_contig4675 4675 THRCLA_contig4676 4676 THRCLA_contig4677 4677 THRCLA_contig4678 4678 THRCLA_contig4679 4679 THRCLA_contig4680 4680 THRCLA_contig4681 4681 THRCLA_contig4682 4682 THRCLA_contig4683 4683 THRCLA_contig4684 4684 THRCLA_contig4685 4685 THRCLA_contig4686 4686 THRCLA_contig4687 4687 THRCLA_contig4688 4688 THRCLA_contig4689 4689 THRCLA_contig4690 4690 THRCLA_contig4691 4691 THRCLA_contig4692 4692 THRCLA_contig4693 4693 THRCLA_contig4694 4694 THRCLA_contig4695 4695 THRCLA_contig4696 4696 THRCLA_contig4697 4697 THRCLA_contig4698 4698 THRCLA_contig4699 4699 THRCLA_contig4700 4700 THRCLA_contig4701 4701 THRCLA_contig4702 4702 THRCLA_contig4703 4703 THRCLA_contig4704 4704 THRCLA_contig4705 4705 THRCLA_contig4706 4706 THRCLA_contig4707 4707 THRCLA_contig4708 4708 THRCLA_contig4709 4709 THRCLA_contig4710 4710 THRCLA_contig4711 4711 THRCLA_contig4712 4712 THRCLA_contig4713 4713 THRCLA_contig4714 4714 THRCLA_contig4715 4715 THRCLA_contig4716 4716 THRCLA_contig4717 4717 THRCLA_contig4718 4718 THRCLA_contig4719 4719 THRCLA_contig4720 4720 THRCLA_contig4721 4721 THRCLA_contig4722 4722 THRCLA_contig4723 4723 THRCLA_contig4724 4724 THRCLA_contig4725 4725 THRCLA_contig4726 4726 THRCLA_contig4727 4727 THRCLA_contig4728 4728 THRCLA_contig4729 4729 THRCLA_contig4730 4730 THRCLA_contig4731 4731 THRCLA_contig4732 4732 THRCLA_contig4733 4733 THRCLA_contig4734 4734 THRCLA_contig4735 4735 THRCLA_contig4736 4736 THRCLA_contig4737 4737 THRCLA_contig4738 4738 THRCLA_contig4739 4739 THRCLA_contig4740 4740 THRCLA_contig4741 4741 THRCLA_contig4742 4742 THRCLA_contig4743 4743 THRCLA_contig4744 4744 THRCLA_contig4745 4745 THRCLA_contig4746 4746 THRCLA_contig4747 4747 THRCLA_contig4748 4748 THRCLA_contig4749 4749 THRCLA_contig4750 4750 THRCLA_contig4751 4751 THRCLA_contig4752 4752 THRCLA_contig4753 4753 THRCLA_contig4754 4754 THRCLA_contig4755 4755 THRCLA_contig4756 4756 THRCLA_contig4757 4757 THRCLA_contig4758 4758 THRCLA_contig4759 4759 THRCLA_contig4760 4760 THRCLA_contig4761 4761 THRCLA_contig4762 4762 THRCLA_contig4763 4763 THRCLA_contig4764 4764 THRCLA_contig4765 4765 THRCLA_contig4766 4766 THRCLA_contig4767 4767 THRCLA_contig4768 4768 THRCLA_contig4769 4769 THRCLA_contig4770 4770 THRCLA_contig4771 4771 THRCLA_contig4772 4772 THRCLA_contig4773 4773 THRCLA_contig4774 4774 THRCLA_contig4775 4775 THRCLA_contig4776 4776 THRCLA_contig4777 4777 THRCLA_contig4778 4778 THRCLA_contig4779 4779 THRCLA_contig4780 4780 THRCLA_contig4781 4781 THRCLA_contig4782 4782 THRCLA_contig4783 4783 THRCLA_contig4784 4784 THRCLA_contig4785 4785 THRCLA_contig4786 4786 THRCLA_contig4787 4787 THRCLA_contig4788 4788 THRCLA_contig4789 4789 THRCLA_contig4790 4790 THRCLA_contig4791 4791 THRCLA_contig4792 4792 THRCLA_contig4793 4793 THRCLA_contig4794 4794 THRCLA_contig4795 4795 THRCLA_contig4796 4796 THRCLA_contig4797 4797 THRCLA_contig4798 4798 THRCLA_contig4799 4799 THRCLA_contig4800 4800 THRCLA_contig4801 4801 THRCLA_contig4802 4802 THRCLA_contig4803 4803 THRCLA_contig4804 4804 THRCLA_contig4805 4805 THRCLA_contig4806 4806 THRCLA_contig4807 4807 THRCLA_contig4808 4808 THRCLA_contig4809 4809 THRCLA_contig4810 4810 THRCLA_contig4811 4811 THRCLA_contig4812 4812 THRCLA_contig4813 4813 THRCLA_contig4814 4814 THRCLA_contig4815 4815 THRCLA_contig4816 4816 THRCLA_contig4817 4817 THRCLA_contig4818 4818 THRCLA_contig4819 4819 THRCLA_contig4820 4820 THRCLA_contig4821 4821 THRCLA_contig4822 4822 THRCLA_contig4823 4823 THRCLA_contig4824 4824 THRCLA_contig4825 4825 THRCLA_contig4826 4826 THRCLA_contig4827 4827 THRCLA_contig4828 4828 THRCLA_contig4829 4829 THRCLA_contig4830 4830 THRCLA_contig4831 4831 THRCLA_contig4832 4832 THRCLA_contig4833 4833 THRCLA_contig4834 4834 THRCLA_contig4835 4835 THRCLA_contig4836 4836 THRCLA_contig4837 4837 THRCLA_contig4838 4838 THRCLA_contig4839 4839 THRCLA_contig4840 4840 THRCLA_contig4841 4841 THRCLA_contig4842 4842 THRCLA_contig4843 4843 THRCLA_contig4844 4844 THRCLA_contig4845 4845 THRCLA_contig4846 4846 THRCLA_contig4847 4847 THRCLA_contig4848 4848 THRCLA_contig4849 4849 THRCLA_contig4850 4850 THRCLA_contig4851 4851 THRCLA_contig4852 4852 THRCLA_contig4853 4853 THRCLA_contig4854 4854 THRCLA_contig4855 4855 THRCLA_contig4856 4856 THRCLA_contig4857 4857 THRCLA_contig4858 4858 THRCLA_contig4859 4859 THRCLA_contig4860 4860 THRCLA_contig4861 4861 THRCLA_contig4862 4862 THRCLA_contig4863 4863 THRCLA_contig4864 4864 THRCLA_contig4865 4865 THRCLA_contig4866 4866 THRCLA_contig4867 4867 THRCLA_contig4868 4868 THRCLA_contig4869 4869 THRCLA_contig4870 4870 THRCLA_contig4871 4871 THRCLA_contig4872 4872 THRCLA_contig4873 4873 THRCLA_contig4874 4874 THRCLA_contig4875 4875 THRCLA_contig4876 4876 THRCLA_contig4877 4877 THRCLA_contig4878 4878 THRCLA_contig4879 4879 THRCLA_contig4880 4880 THRCLA_contig4881 4881 THRCLA_contig4882 4882 THRCLA_contig4883 4883 THRCLA_contig4884 4884 THRCLA_contig4885 4885 THRCLA_contig4886 4886 THRCLA_contig4887 4887 THRCLA_contig4888 4888 THRCLA_contig4889 4889 THRCLA_contig4890 4890 THRCLA_contig4891 4891 THRCLA_contig4892 4892 THRCLA_contig4893 4893 THRCLA_contig4894 4894 THRCLA_contig4895 4895 THRCLA_contig4896 4896 THRCLA_contig4897 4897 THRCLA_contig4898 4898 THRCLA_contig4899 4899 THRCLA_contig4900 4900 THRCLA_contig4901 4901 THRCLA_contig4902 4902 THRCLA_contig4903 4903 THRCLA_contig4904 4904 THRCLA_contig4905 4905 THRCLA_contig4906 4906 THRCLA_contig4907 4907 THRCLA_contig4908 4908 THRCLA_contig4909 4909 THRCLA_contig4910 4910 THRCLA_contig4911 4911 THRCLA_contig4912 4912 THRCLA_contig4913 4913 THRCLA_contig4914 4914 THRCLA_contig4915 4915 THRCLA_contig4916 4916 THRCLA_contig4917 4917 THRCLA_contig4918 4918 THRCLA_contig4919 4919 THRCLA_contig4920 4920 THRCLA_contig4921 4921 THRCLA_contig4922 4922 THRCLA_contig4923 4923 THRCLA_contig4924 4924 THRCLA_contig4925 4925 THRCLA_contig4926 4926 THRCLA_contig4927 4927 THRCLA_contig4928 4928 THRCLA_contig4929 4929 THRCLA_contig4930 4930 THRCLA_contig4931 4931 THRCLA_contig4932 4932 THRCLA_contig4933 4933 THRCLA_contig4934 4934 THRCLA_contig4935 4935 THRCLA_contig4936 4936 THRCLA_contig4937 4937 THRCLA_contig4938 4938 THRCLA_contig4939 4939 THRCLA_contig4940 4940 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THRCLA_contig5285 5285 THRCLA_contig5286 5286 THRCLA_contig5287 5287 THRCLA_contig5288 5288 THRCLA_contig5289 5289 THRCLA_contig5290 5290 THRCLA_contig5291 5291 THRCLA_contig5292 5292 THRCLA_contig5293 5293 THRCLA_contig5294 5294 THRCLA_contig5295 5295 THRCLA_contig5296 5296 THRCLA_contig5297 5297 THRCLA_contig5298 5298 THRCLA_contig5299 5299 THRCLA_contig5300 5300 THRCLA_contig5301 5301 THRCLA_contig5302 5302 THRCLA_contig5303 5303 THRCLA_contig5304 5304 THRCLA_contig5305 5305 THRCLA_contig5306 5306 THRCLA_contig5307 5307 THRCLA_contig5308 5308 THRCLA_contig5309 5309 THRCLA_contig5310 5310 THRCLA_contig5311 5311 THRCLA_contig5312 5312 THRCLA_contig5313 5313 THRCLA_contig5314 5314 THRCLA_contig5315 5315 THRCLA_contig5316 5316 THRCLA_contig5317 5317 THRCLA_contig5318 5318 THRCLA_contig5319 5319 THRCLA_contig5320 5320 THRCLA_contig5321 5321 THRCLA_contig5322 5322 THRCLA_contig5323 5323 THRCLA_contig5324 5324 THRCLA_contig5325 5325 THRCLA_contig5326 5326 THRCLA_contig5327 5327 THRCLA_contig5328 5328 THRCLA_contig5329 5329 THRCLA_contig5330 5330 THRCLA_contig5331 5331 THRCLA_contig5332 5332 THRCLA_contig5333 5333 THRCLA_contig5334 5334 THRCLA_contig5335 5335 THRCLA_contig5336 5336 THRCLA_contig5337 5337 THRCLA_contig5338 5338 From carsonhh at gmail.com Tue Sep 25 06:44:02 2012 From: carsonhh at gmail.com (Carson Holt) Date: Tue, 25 Sep 2012 08:44:02 -0400 Subject: [maker-devel] Problem with maker_map_ids In-Reply-To: <0FCB8ACD-35A0-4ED8-BAE2-02C2621E3F65@my.uri.edu> Message-ID: Could you also provide 34112_3June11Ass.gff? Thanks, Carson On 12-09-25 8:31 AM, "Ian Misner" wrote: >Hello, > >I'm trying to create human friendly ids and I'm getting an error when I >use the -sort_file option. Without the sort file it runs fine just not >numbered from the first contig. I have had some programers at our cluster >look at the script and they attempted a fix but it did not work. They >mentioned the script was "buggy" so this might be part of the problem. >I've attached the error as well as the sort file. I can send more files >if necessary. Thanks for you time. > >Cheers >Ian > >$ maker_map_ids --prefix THRCLA_ --justify 5 --sort_order 34112_sort.txt >34112_3June11Ass.gff > 34112_3June11Ass_named.txt >Can't use string ("34112_sort.txt") as a HASH ref while "strict refs" in >use at /gpfs/runtime/opt/maker/2.10/maker/bin/maker_map_ids line 311, ><$IN> line 499186._______________________________________________ >maker-devel mailing list >maker-devel at box290.bluehost.com >http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org From carsonhh at gmail.com Tue Sep 25 07:01:31 2012 From: carsonhh at gmail.com (Carson Holt) Date: Tue, 25 Sep 2012 09:01:31 -0400 Subject: [maker-devel] Problem with maker_map_ids In-Reply-To: Message-ID: While you are sending me the GFF3 file also try the sort order file attached. I found a number of illegal meta character contaminating the file. Sometimes those can be introduced by text editors or sometimes e-mail clients. In case it wasn't the e-mail client I'm sending you this fixed version. Also I see you are using maker_map_ids from version 2.10. Try the 2.26 version. They are different. Thanks, Carson On 12-09-25 8:44 AM, "Carson Holt" wrote: >Could you also provide 34112_3June11Ass.gff? > >Thanks, >Carson > > >On 12-09-25 8:31 AM, "Ian Misner" wrote: > >>Hello, >> >>I'm trying to create human friendly ids and I'm getting an error when I >>use the -sort_file option. Without the sort file it runs fine just not >>numbered from the first contig. I have had some programers at our >>cluster >>look at the script and they attempted a fix but it did not work. They >>mentioned the script was "buggy" so this might be part of the problem. >>I've attached the error as well as the sort file. I can send more files >>if necessary. Thanks for you time. >> >>Cheers >>Ian >> >>$ maker_map_ids --prefix THRCLA_ --justify 5 --sort_order 34112_sort.txt >>34112_3June11Ass.gff > 34112_3June11Ass_named.txt >>Can't use string ("34112_sort.txt") as a HASH ref while "strict refs" in >>use at /gpfs/runtime/opt/maker/2.10/maker/bin/maker_map_ids line 311, >><$IN> line 499186._______________________________________________ >>maker-devel mailing list >>maker-devel at box290.bluehost.com >>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org -------------- next part -------------- A non-text attachment was scrubbed... Name: 34112_sort.txt.gz Type: application/x-gzip Size: 27598 bytes Desc: not available URL: From carsonhh at gmail.com Tue Sep 25 07:13:54 2012 From: carsonhh at gmail.com (Carson Holt) Date: Tue, 25 Sep 2012 09:13:54 -0400 Subject: [maker-devel] Problem with maker_map_ids In-Reply-To: Message-ID: Thanks for the GFF3 file. The meta character came across in the GFF3 as well, so I think it's safe to assume they are being introduced by the e-mail client used to add the attachment (so ignore the last file I sent). I've attached the fixed maker_map_ids. Thanks, Carson On 12-09-25 9:01 AM, "Carson Holt" wrote: >While you are sending me the GFF3 file also try the sort order file >attached. I found a number of illegal meta character contaminating the >file. Sometimes those can be introduced by text editors or sometimes >e-mail clients. In case it wasn't the e-mail client I'm sending you this >fixed version. > >Also I see you are using maker_map_ids from version 2.10. Try the 2.26 >version. They are different. > >Thanks, >Carson > > >On 12-09-25 8:44 AM, "Carson Holt" wrote: > >>Could you also provide 34112_3June11Ass.gff? >> >>Thanks, >>Carson >> >> >>On 12-09-25 8:31 AM, "Ian Misner" wrote: >> >>>Hello, >>> >>>I'm trying to create human friendly ids and I'm getting an error when I >>>use the -sort_file option. Without the sort file it runs fine just not >>>numbered from the first contig. I have had some programers at our >>>cluster >>>look at the script and they attempted a fix but it did not work. They >>>mentioned the script was "buggy" so this might be part of the problem. >>>I've attached the error as well as the sort file. I can send more files >>>if necessary. Thanks for you time. >>> >>>Cheers >>>Ian >>> >>>$ maker_map_ids --prefix THRCLA_ --justify 5 --sort_order >>>34112_sort.txt >>>34112_3June11Ass.gff > 34112_3June11Ass_named.txt >>>Can't use string ("34112_sort.txt") as a HASH ref while "strict refs" >>>in >>>use at /gpfs/runtime/opt/maker/2.10/maker/bin/maker_map_ids line 311, >>><$IN> line 499186._______________________________________________ >>>maker-devel mailing list >>>maker-devel at box290.bluehost.com >>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org -------------- next part -------------- A non-text attachment was scrubbed... Name: maker_map_ids.gz Type: application/x-gzip Size: 3216 bytes Desc: not available URL: From fourie.joubert at up.ac.za Thu Sep 27 08:37:53 2012 From: fourie.joubert at up.ac.za (Fourie Joubert) Date: Thu, 27 Sep 2012 16:37:53 +0200 Subject: [maker-devel] Problem with maker2chado Message-ID: <506464C1.40103@up.ac.za> Hi I am trying to load a maker gff file into chado using maker2chado, but I am seeing the following type of error: Can't locate object method "value" via package "NODE_1002_length_51300_cov_98.972473" (perhaps you forgot to load "NODE_1002_length_51300_cov_98.972473"?) at /usr/local/bin/gmod_bulk_load_gff3.pl line 722, line 2. Any advice would be sincerely appreciated! Best regards! Fourie -- -------------- Prof Fourie Joubert Bioinformatics and Computational Biology Unit Department of Biochemistry University of Pretoria fourie.joubert at up.ac.za http://www.bi.up.ac.za Tel. +27-12-420-5825 Fax. +27-12-420-5800 ------------------------------------------------------------------------- This message and attachments are subject to a disclaimer. Please refer to www.it.up.ac.za/documentation/governance/disclaimer/ for full details. From carsonhh at gmail.com Thu Sep 27 10:27:14 2012 From: carsonhh at gmail.com (Carson Holt) Date: Thu, 27 Sep 2012 12:27:14 -0400 Subject: [maker-devel] Problem with maker2chado In-Reply-To: <506464C1.40103@up.ac.za> Message-ID: The error is being thrown by /usr/local/bin/gmod_bulk_load_gff3.pl It is called by MAKER and is part of the chado install. Try getting the latest version of chado from the SVN repository and then reinstalling it. Command to use --> svn co https://gmod.svn.sourceforge.net/svnroot/gmod/schema/trunk chado --Carson On 12-09-27 10:37 AM, "Fourie Joubert" wrote: >Hi > >I am trying to load a maker gff file into chado using maker2chado, but I >am seeing the following type of error: > >Can't locate object method "value" via package >"NODE_1002_length_51300_cov_98.972473" (perhaps you forgot to load >"NODE_1002_length_51300_cov_98.972473"?) at >/usr/local/bin/gmod_bulk_load_gff3.pl line 722, line 2. > >Any advice would be sincerely appreciated! > >Best regards! > >Fourie > >-- >-------------- >Prof Fourie Joubert >Bioinformatics and Computational Biology Unit >Department of Biochemistry >University of Pretoria >fourie.joubert at up.ac.za >http://www.bi.up.ac.za >Tel. +27-12-420-5825 >Fax. +27-12-420-5800 > >------------------------------------------------------------------------- >This message and attachments are subject to a disclaimer. Please refer >to www.it.up.ac.za/documentation/governance/disclaimer/ for full details. > > >_______________________________________________ >maker-devel mailing list >maker-devel at box290.bluehost.com >http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org From mike.thon at gmail.com Sun Sep 30 23:53:23 2012 From: mike.thon at gmail.com (Michael Thon) Date: Mon, 1 Oct 2012 07:53:23 +0200 Subject: [maker-devel] model_gff question Message-ID: Under what circumstances will maker not include a gene model from the model_gff file in its final output? It was my understanding from this post: https://groups.google.com/d/topic/maker-devel/Y5jSdZ1Olcc/discussion That maker will keep or replace models in model_gff and never remove them. I'm reannotating a fungal genome and in model_gff I'm providing the gene models originally made by the sequencing center. I have 12006 models in the file I specify in model_gff but maker's final annotation has only 10727 models in it. -Mike -------------- next part -------------- An HTML attachment was scrubbed... URL: