From liorglic at mail.tau.ac.il  Fri Oct  2 02:54:55 2020
From: liorglic at mail.tau.ac.il (Lior Glick)
Date: Fri, 2 Oct 2020 11:54:55 +0300
Subject: [maker-devel] MAKER failing during Augustus run
Message-ID: <CAOzMDPxivd1gxOJRuaQd6vDLMizt39qRNsAajzvO+Hhy1K--6A@mail.gmail.com>

Hello,
I am using MAKER2 with Augustus 3.2.2. I keep getting an error message when
annotating a specific contig. The relevant section of the MAKER stderr
looks like this:

Widget::augustus:
/powerapps/share/centos7/miniconda/miniconda2-4.5.4-MakerMPI/bin/augustus
--species=arabidopsis --strand=backward --UTR=off
--hintsfile=/home/tmp_liorglic/maker_zfUstg/0/265_0.10292360-10294752.arabidopsis.auto_annotator.xdef.augustus
--extrinsicCfgFile=/powerapps/share/centos7/miniconda/miniconda2-4.5.4-MakerMPI/config/extrinsic/extrinsic.MPE.cfg
/home/tmp_liorglic/maker_zfUstg/0/265_0.10292360-10294752.arabidopsis.auto_annotator.augustus.fasta
>
/home/tmp_liorglic/maker_zfUstg/0/265_0.10292360-10294752.arabidopsis.auto_annotator.augustus
#-------------------------------#
Sampling error in intron model. state=37 base=2391

/powerapps/share/centos7/miniconda/miniconda2-4.5.4-MakerMPI/bin/augustus:
ERROR
        Tried to sample from empty list.

Sampling error in intron model. state=37 base=2391

/powerapps/share/centos7/miniconda/miniconda2-4.5.4-MakerMPI/bin/augustus:
ERROR
        Tried to sample from empty list.

ERROR: Augustus failed
--> rank=NA, hostname=compute-0-301.power5
ERROR: Failed while annotating transcripts
ERROR: Chunk failed at level:1, tier_type:4
FAILED CONTIG:chunk08

ERROR: Chunk failed at level:6, tier_type:0
FAILED CONTIG:chunk08

examining contents of the fasta file and run log



--Next Contig--

Processing run.log file...
MAKER WARNING: The file
chunk.maker.output/chunk_datastore/76/17/chunk08//theVoid.chunk08/265_0.10292360-10294752.arabidopsis.auto_annotator.augustus
did not finish on the last run and must be erased


Maker is now finished!!!

I found this thread
<https://groups.google.com/g/maker-devel/c/WBD_GEvELDE> with
a similar error but slightly different augustus command. The suggestion
there was to isolate the augustus command. This sounds like good advice,
but most of the inputs to the command are stored in a temporary location
and are deleted at the end of the MAKER run. Is there any way to restore
them?
Alternatively, are there any known solutions/explanations to this error?
All I could find was this thread
<https://bioinf.uni-greifswald.de/bioinf/forum/viewtopic.php?f=4&t=150> from
the Augustus forum, but it doesn't seem to provide much help.
Would appreciate any ideas/workarounds.
Thanks!
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From carsonhh at gmail.com  Fri Oct  2 14:25:22 2020
From: carsonhh at gmail.com (Carson Holt)
Date: Fri, 2 Oct 2020 14:25:22 -0600
Subject: [maker-devel] Maker yields sequences without start and stop
 codon
In-Reply-To: <CAOXM=CUaZ3+6-YHVzm7Lc+h3fgEtX9ikD8z43Ez9Laj9jGT2DQ@mail.gmail.com>
References: <CAOXM=CUaZ3+6-YHVzm7Lc+h3fgEtX9ikD8z43Ez9Laj9jGT2DQ@mail.gmail.com>
Message-ID: <D281818D-F30A-447D-987F-F5A0434AF7A6@gmail.com>

You can set always_complete=1 for MAKER tottery and fix partial models (it walks out on both sides looking for canonical stops/starts).  Also to clean up partial models and other submission issues, try using Comparative Annotation Toolkit (CAT).  It will take MAEKR results and do all the NCBI related corrections automatically.  It makes submission so much easier.

?Carson



> On Sep 1, 2020, at 12:31 PM, Emmanuel Nnadi <eennadi at gmail.com> wrote:
> 
> I ran my annotation using ESTs from NCBI and transcriptome data and Swiss-prot data. I used SNAP trained twice after which Augustus was trained once.
> 
> I tried to submit the annotated genome to NCBI but have some problems I have not experienced before and do not know how to solve.
> 
> Some of the CDS features have invalid translations. Every CDS feature should have a valid start and stop codon, and should not have any internal stops.  The only exception is if the CDS is partial at the end of a sequence or at an intron/exon boundary.  If the CDS is partial, it must have the appropriate partial symbols.  
> 
> If a CDS feature does not have a valid translation (for example if there is a frameshift), please remove the CDS feature and annotate this with a single gene feature across the entire span.  Include a note on the gene with a brief description.  For example:
> 
> 1       200     gene
>                         gene    phoA
>                         gene_desc       alkaline phosphatase
>                         locus_tag     OBB_0001
>                         note    nonfunctional due to frameshift
> 
> [3] There are 1075 gene features that are not associated with
> any other features (CDS, rRNA, etc.) and are not labelled as
> pseudogenes or as nonfunctional genes.  Did you lose some of
> the annotation you intended to include.
> 
> Please how can this be solved?
> 
> Thanks
> 
> 
> Nnadi Nnaemeka Emmanuel,Ph.D
> Department of Microbiology,
> Faculty of Natural and Applied Science,
> Plateau State University, Bokkos, Plateau State, Nigeria.
> +2348068124819
> Publications: 
>  https://www.researchgate.net/profile/Emmanuel_Nnadi/publications <https://www.researchgate.net/profile/Emmanuel_Nnadi/publications>
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From carsonhh at gmail.com  Fri Oct  2 14:38:39 2020
From: carsonhh at gmail.com (Carson Holt)
Date: Fri, 2 Oct 2020 14:38:39 -0600
Subject: [maker-devel] maker-devel post from guerrer@uni-duesseldorf.de
 requires approval
In-Reply-To: <mailman.370.1600180681.587812.maker-devel_yandell-lab.org@yandell-lab.org>
References: <mailman.370.1600180681.587812.maker-devel_yandell-lab.org@yandell-lab.org>
Message-ID: <483B474B-052F-4148-8FAB-EB2F381BA0DF@gmail.com>

Try looking at it in a browser.  You may see that models are merging because of evidence overlap, snap or augustus does not match the evidence well (you can drop one if it performs poorly).  But visualizing things will help.  For example fungi can lose genes because of UTR overlap (there is an allow_overlap option in MAKER for that).  mRNA-seq can falsely merge into extended transcripts (results in long UTR on models and maker has correct_est_fusion for that).  Neigboring parlors can cluster into a single model (you will see same hit coordinates multiple,e times in the browser - there is a tool called DeFusion for that).  Or evidence may be sparse (should be obvious from a browser).  Assembly errors can be found when you have nice transcripts alignments that do not have working ORFs (found by dragging and dropping est2genome results in browsers like Apollo and letting it calculate ORF).


?Carson


> 
> Hello,
> 
> It appears to me that my abInitio SNAP + Augustus (trained by nexflow) results are worse than the first (est2genome and prot2genome) run. The gene number decreases by more than 6000, the opposite of what I expected.
> 
> Additionally, my abInitio rerun also has less genes than a previous SNAP reannotation.. The AED plots all look more or less the same but the number of genes lowers instead of increasing as I expected (image in annex).
> 
> I'be been running my maker+nextflow pipeline with consistently good results, this species is the exception now.
> 
> Do you have any suggestion? Should I ditch AbInitio training and use the Evidence based annotation? Or maybe just use the closest Augustus model instead of training my own?
> 
> Kind regards,
> Ricardo
> 
> 
> 
> <AEDs.png>
> 


From carsonhh at gmail.com  Fri Oct  2 14:50:35 2020
From: carsonhh at gmail.com (Carson Holt)
Date: Fri, 2 Oct 2020 14:50:35 -0600
Subject: [maker-devel] map_forward and temporary storage questions
In-Reply-To: <YTBPR01MB3839BACB6F6296B734775AA09C360@YTBPR01MB3839.CANPRD01.PROD.OUTLOOK.COM>
References: <YTBPR01MB3839BACB6F6296B734775AA09C360@YTBPR01MB3839.CANPRD01.PROD.OUTLOOK.COM>
Message-ID: <7742D4BF-2BEB-426D-9858-EC2621B5077D@gmail.com>

MAKER uses GFF3 format which is not the same as GTF.  You will need to convert your file to GFF3 format.

You can try this online tool (I haven?t used it to tell you how well it works) http://www.sequenceontology.org/cgi-bin/converter.cgi <http://www.sequenceontology.org/cgi-bin/converter.cgi> 

There are also a number of other resources available when you google "how to convert GTF to GFF3?.

?Carson


> On Sep 25, 2020, at 3:17 AM, Zoe Clarke <zoe.clarke at utoronto.ca> wrote:
> 
> Hello!
> 
> I am currently running Maker on a 2.5GB genome that has already had a list of ~8000 genes very thoroughly annotated. My hope is to find and annotate the rest of the genes using ESTs and protein homology. However, I tested Maker on a single contig of my genome (there are ~20,000 contigs) and I can't find any of the genes from my original gtf file even though I followed all of the instructions in this wiki: http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/Updating_annotations_in_light_of_new_data <http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/Updating_annotations_in_light_of_new_data> (I entered the original gff under model_gff, and used map_forward=1). I am worried this is because my gff3 file isn't formatted properly. Here are a few lines in my gff file as an example:
> --------------------------------------------
> WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  transcript      1094446 1105585 .       +       .       ID=DIMT1.1;geneID=DIMT1
> WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  exon    1094446 1094521 97.75   +       .       Parent=DIMT1.1
> WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  exon    1094874 1094947 97.75   +       .       Parent=DIMT1.1
> WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  exon    1095459 1095545 97.75   +       .       Parent=DIMT1.1
> WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  exon    1097351 1097412 97.75   +       .       Parent=DIMT1.1
> WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  exon    1097492 1097585 97.75   +       .       Parent=DIMT1.1
> WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  exon    1097670 1097719 97.75   +       .       Parent=DIMT1.1
> WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  exon    1098957 1099080 97.75   +       .       Parent=DIMT1.1
> WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  exon    1099217 1099309 97.75   +       .       Parent=DIMT1.1
> WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  exon    1100870 1100934 97.75   +       .       Parent=DIMT1.1
> WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  exon    1101967 1102030 97.75   +       .       Parent=DIMT1.1
> WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  exon    1103784 1103890 97.75   +       .       Parent=DIMT1.1
> WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  exon    1105543 1105585 97.75   +       .       Parent=DIMT1.1
> WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  CDS     1094446 1094521 .       +       0       Parent=DIMT1.1
> WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  CDS     1094874 1094947 .       +       2       Parent=DIMT1.1
> WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  CDS     1095459 1095545 .       +       0       Parent=DIMT1.1
> WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  CDS     1097351 1097412 .       +       0       Parent=DIMT1.1
> WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  CDS     1097492 1097585 .       +       1       Parent=DIMT1.1
> WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  CDS     1097670 1097719 .       +       0       Parent=DIMT1.1
> WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  CDS     1098957 1099080 .       +       1       Parent=DIMT1.1
> WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  CDS     1099217 1099309 .       +       0       Parent=DIMT1.1
> WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  CDS     1100870 1100934 .       +       0       Parent=DIMT1.1
> WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  CDS     1101967 1102030 .       +       1       Parent=DIMT1.1
> WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  CDS     1103784 1103890 .       +       0       Parent=DIMT1.1
> WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  CDS     1105543 1105582 .       +       1       Parent=DIMT1.1
> --------------------------------------
> ?This is from the contig I used as a test for maker, and I can't find DIMT1.1 in the final gff file. At first I thought it might be because "geneID" is a listed attribute, but changing this to "Name" didn't help. Do you have any ideas why these genes might not be mapping forward? If it's something I can fix in the gff file, I am hoping I can fix it and use it for the second round of Maker after I have trained Snap.
> 
> Also, do you think a better quality annotation would results from Snap trained from this curated list of ~8000 genes (that has been expertly done) or by the round 1 output of Maker?
> 
> A final question: I am having memory storage issues with Maker, as it is currently taking up ~15TB of storage with temporary files. I am running Maker on a cluster and whenever my submitted Maker job runs out of memory it fails, so I have to resubmit it about every hour, which leaves a lot of temporary folders (e.g. maker_x6V2y4) in my directory. I notice that some of these temporary files haven't been updated in days - is it okay to delete them?
> 
> Thank you so much for your help!
> Zoe
> ______________________________________
> Zoe Clarke
> PhD candidate in Computational Biology at U of T
> Lab profile: http://baderlab.org/Zoe%20Clarke <http://baderlab.org/Zoe%20Clarke>
> Personal website: https://zoe-clarke.weebly.com/ <https://zoe-clarke.weebly.com/>_______________________________________________
> maker-devel mailing list
> maker-devel at yandell-lab.org <mailto:maker-devel at yandell-lab.org>
> http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org <http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org>
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From carsonhh at gmail.com  Fri Oct  2 15:01:24 2020
From: carsonhh at gmail.com (Carson Holt)
Date: Fri, 2 Oct 2020 15:01:24 -0600
Subject: [maker-devel] MAKER failing during Augustus run
In-Reply-To: <CAOzMDPxivd1gxOJRuaQd6vDLMizt39qRNsAajzvO+Hhy1K--6A@mail.gmail.com>
References: <CAOzMDPxivd1gxOJRuaQd6vDLMizt39qRNsAajzvO+Hhy1K--6A@mail.gmail.com>
Message-ID: <8DAF41A6-5983-482C-ABA1-4F5EDC7388FA@gmail.com>

First try using Augustu v3.3.3 or the live version from GitHub (https://github.com/Gaius-Augustus/Augustus <https://github.com/Gaius-Augustus/Augustus>). You can specify the other augustus version in maker_exe.ctl.  You can use ctl+z to pause the run right when MAKER reaches the specified augustus call.  Or after trying the newer agusuts version, you can upload everything from the run to https://github.com/Gaius-Augustus/Augustus <https://github.com/Gaius-Augustus/Augustus> and I can try to extract the files for you.

Or if you are adventurous you can run in the perl debugger.

#start debugger
perl -dS maker

#continue to augustus calls
DB<1> c Widget::augustus::run

#continue to augustus failure (right before dieing)
DB<2> c 282

At this point just copy the command as files still exist

?Carson


> On Oct 2, 2020, at 2:54 AM, Lior Glick <liorglic at mail.tau.ac.il> wrote:
> 
> Hello,
> I am using MAKER2 with Augustus 3.2.2. I keep getting an error message when annotating a specific contig. The relevant section of the MAKER stderr looks like this:
> 
> Widget::augustus:
> /powerapps/share/centos7/miniconda/miniconda2-4.5.4-MakerMPI/bin/augustus --species=arabidopsis --strand=backward --UTR=off --hintsfile=/home/tmp_liorglic/maker_zfUstg/0/265_0.10292360-10294752.arabidopsis.auto_annotator.xdef.augustus --extrinsicCfgFile=/powerapps/share/centos7/miniconda/miniconda2-4.5.4-MakerMPI/config/extrinsic/extrinsic.MPE.cfg /home/tmp_liorglic/maker_zfUstg/0/265_0.10292360-10294752.arabidopsis.auto_annotator.augustus.fasta > /home/tmp_liorglic/maker_zfUstg/0/265_0.10292360-10294752.arabidopsis.auto_annotator.augustus
> #-------------------------------#
> Sampling error in intron model. state=37 base=2391
> 
> /powerapps/share/centos7/miniconda/miniconda2-4.5.4-MakerMPI/bin/augustus: ERROR
>         Tried to sample from empty list.
> 
> Sampling error in intron model. state=37 base=2391
> 
> /powerapps/share/centos7/miniconda/miniconda2-4.5.4-MakerMPI/bin/augustus: ERROR
>         Tried to sample from empty list.
> 
> ERROR: Augustus failed
> --> rank=NA, hostname=compute-0-301.power5
> ERROR: Failed while annotating transcripts
> ERROR: Chunk failed at level:1, tier_type:4
> FAILED CONTIG:chunk08
> 
> ERROR: Chunk failed at level:6, tier_type:0
> FAILED CONTIG:chunk08
> 
> examining contents of the fasta file and run log
> 
> 
> 
> --Next Contig--
> 
> Processing run.log file...
> MAKER WARNING: The file chunk.maker.output/chunk_datastore/76/17/chunk08//theVoid.chunk08/265_0.10292360-10294752.arabidopsis.auto_annotator.augustus
> did not finish on the last run and must be erased
> 
> 
> Maker is now finished!!!
> 
> I found this thread <https://groups.google.com/g/maker-devel/c/WBD_GEvELDE> with a similar error but slightly different augustus command. The suggestion there was to isolate the augustus command. This sounds like good advice, but most of the inputs to the command are stored in a temporary location and are deleted at the end of the MAKER run. Is there any way to restore them?
> Alternatively, are there any known solutions/explanations to this error? All I could find was this thread <https://bioinf.uni-greifswald.de/bioinf/forum/viewtopic.php?f=4&t=150> from the Augustus forum, but it doesn't seem to provide much help.
> Would appreciate any ideas/workarounds.
> Thanks!
> 
> _______________________________________________
> maker-devel mailing list
> maker-devel at yandell-lab.org
> http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org

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From zoe.clarke at utoronto.ca  Mon Oct  5 07:47:19 2020
From: zoe.clarke at utoronto.ca (Zoe Clarke)
Date: Mon, 5 Oct 2020 13:47:19 +0000
Subject: [maker-devel] map_forward and temporary storage questions
In-Reply-To: <7742D4BF-2BEB-426D-9858-EC2621B5077D@gmail.com>
References: <YTBPR01MB3839BACB6F6296B734775AA09C360@YTBPR01MB3839.CANPRD01.PROD.OUTLOOK.COM>,
	<7742D4BF-2BEB-426D-9858-EC2621B5077D@gmail.com>
Message-ID: <YTBPR01MB3839AFB99FE4758AAA9BBFAA9C0C0@YTBPR01MB3839.CANPRD01.PROD.OUTLOOK.COM>

Thanks Carson!

I managed to get the GFF3 file fixed and Maker is now recognizing it the way it should.

I am hoping I can also ask for your advice on functional annotation with Maker. The result of my current run will be gff and fasta files that have the original gff3 genes plus Maker's. The original gff3 file was annotated with HGNC gene symbols, so these new files are a mix of gene symbols and Maker-derived gene names. I would ideally like my final annotation to consist almost entirely of gene symbols. Is the only way to do this (after using Blastp and InterProScan to get putative homology) to undergo an additional manual curation process through something like Apollo?

Thanks again,
Zoe

______________________________________
Zoe Clarke
PhD candidate in Computational Biology at U of T
Lab profile: http://baderlab.org/Zoe%20Clarke
Personal website: https://zoe-clarke.weebly.com/
________________________________
From: Carson Holt <carsonhh at gmail.com>
Sent: October 2, 2020 4:50 PM
To: Zoe Clarke <zoe.clarke at utoronto.ca>
Cc: maker-devel at yandell-lab.org <maker-devel at yandell-lab.org>
Subject: Re: [maker-devel] map_forward and temporary storage questions

EXTERNAL EMAIL:  Treat content with extra caution.
MAKER uses GFF3 format which is not the same as GTF.  You will need to convert your file to GFF3 format.

You can try this online tool (I haven?t used it to tell you how well it works) http://www.sequenceontology.org/cgi-bin/converter.cgi

There are also a number of other resources available when you google "how to convert GTF to GFF3?.

?Carson


On Sep 25, 2020, at 3:17 AM, Zoe Clarke <zoe.clarke at utoronto.ca<mailto:zoe.clarke at utoronto.ca>> wrote:

Hello!

I am currently running Maker on a 2.5GB genome that has already had a list of ~8000 genes very thoroughly annotated. My hope is to find and annotate the rest of the genes using ESTs and protein homology. However, I tested Maker on a single contig of my genome (there are ~20,000 contigs) and I can't find any of the genes from my original gtf file even though I followed all of the instructions in this wiki: http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/Updating_annotations_in_light_of_new_data (I entered the original gff under model_gff, and used map_forward=1). I am worried this is because my gff3 file isn't formatted properly. Here are a few lines in my gff file as an example:
--------------------------------------------
WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  transcript      1094446 1105585 .       +       .       ID=DIMT1.1;geneID=DIMT1
WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  exon    1094446 1094521 97.75   +       .       Parent=DIMT1.1
WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  exon    1094874 1094947 97.75   +       .       Parent=DIMT1.1
WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  exon    1095459 1095545 97.75   +       .       Parent=DIMT1.1
WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  exon    1097351 1097412 97.75   +       .       Parent=DIMT1.1
WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  exon    1097492 1097585 97.75   +       .       Parent=DIMT1.1
WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  exon    1097670 1097719 97.75   +       .       Parent=DIMT1.1
WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  exon    1098957 1099080 97.75   +       .       Parent=DIMT1.1
WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  exon    1099217 1099309 97.75   +       .       Parent=DIMT1.1
WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  exon    1100870 1100934 97.75   +       .       Parent=DIMT1.1
WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  exon    1101967 1102030 97.75   +       .       Parent=DIMT1.1
WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  exon    1103784 1103890 97.75   +       .       Parent=DIMT1.1
WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  exon    1105543 1105585 97.75   +       .       Parent=DIMT1.1
WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  CDS     1094446 1094521 .       +       0       Parent=DIMT1.1
WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  CDS     1094874 1094947 .       +       2       Parent=DIMT1.1
WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  CDS     1095459 1095545 .       +       0       Parent=DIMT1.1
WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  CDS     1097351 1097412 .       +       0       Parent=DIMT1.1
WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  CDS     1097492 1097585 .       +       1       Parent=DIMT1.1
WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  CDS     1097670 1097719 .       +       0       Parent=DIMT1.1
WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  CDS     1098957 1099080 .       +       1       Parent=DIMT1.1
WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  CDS     1099217 1099309 .       +       0       Parent=DIMT1.1
WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  CDS     1100870 1100934 .       +       0       Parent=DIMT1.1
WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  CDS     1101967 1102030 .       +       1       Parent=DIMT1.1
WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  CDS     1103784 1103890 .       +       0       Parent=DIMT1.1
WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  CDS     1105543 1105582 .       +       1       Parent=DIMT1.1
--------------------------------------
?This is from the contig I used as a test for maker, and I can't find DIMT1.1 in the final gff file. At first I thought it might be because "geneID" is a listed attribute, but changing this to "Name" didn't help. Do you have any ideas why these genes might not be mapping forward? If it's something I can fix in the gff file, I am hoping I can fix it and use it for the second round of Maker after I have trained Snap.

Also, do you think a better quality annotation would results from Snap trained from this curated list of ~8000 genes (that has been expertly done) or by the round 1 output of Maker?

A final question: I am having memory storage issues with Maker, as it is currently taking up ~15TB of storage with temporary files. I am running Maker on a cluster and whenever my submitted Maker job runs out of memory it fails, so I have to resubmit it about every hour, which leaves a lot of temporary folders (e.g. maker_x6V2y4) in my directory. I notice that some of these temporary files haven't been updated in days - is it okay to delete them?

Thank you so much for your help!
Zoe
______________________________________
Zoe Clarke
PhD candidate in Computational Biology at U of T
Lab profile: http://baderlab.org/Zoe%20Clarke
Personal website: https://zoe-clarke.weebly.com/
_______________________________________________
maker-devel mailing list
maker-devel at yandell-lab.org<mailto:maker-devel at yandell-lab.org>
http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org

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From carsonhh at gmail.com  Thu Oct 15 19:45:45 2020
From: carsonhh at gmail.com (Carson Holt)
Date: Thu, 15 Oct 2020 19:45:45 -0600
Subject: [maker-devel] map_forward and temporary storage questions
In-Reply-To: <YTBPR01MB3839AFB99FE4758AAA9BBFAA9C0C0@YTBPR01MB3839.CANPRD01.PROD.OUTLOOK.COM>
References: <YTBPR01MB3839BACB6F6296B734775AA09C360@YTBPR01MB3839.CANPRD01.PROD.OUTLOOK.COM>
	<7742D4BF-2BEB-426D-9858-EC2621B5077D@gmail.com>
	<YTBPR01MB3839AFB99FE4758AAA9BBFAA9C0C0@YTBPR01MB3839.CANPRD01.PROD.OUTLOOK.COM>
Message-ID: <28F61590-140A-44E9-AD63-BCFAC9179391@gmail.com>

If you can create a two column file (column1 being the old ID and column2 being the new ID), you can use the map_fasta_ids and map_gff_ids to rename everything with a corresponding line in the two column file.  Make sure no ID's occur twice (in old or new), it will create issues.  The maker ID will not be lost, instead it will move to the Alias= field in the GFF3.

?Carson



> On Oct 5, 2020, at 7:47 AM, Zoe Clarke <zoe.clarke at utoronto.ca> wrote:
> 
> Thanks Carson!
> 
> I managed to get the GFF3 file fixed and Maker is now recognizing it the way it should.
> 
> I am hoping I can also ask for your advice on functional annotation with Maker. The result of my current run will be gff and fasta files that have the original gff3 genes plus Maker's. The original gff3 file was annotated with HGNC gene symbols, so these new files are a mix of gene symbols and Maker-derived gene names. I would ideally like my final annotation to consist almost entirely of gene symbols. Is the only way to do this (after using Blastp and InterProScan to get putative homology) to undergo an additional manual curation process through something like Apollo?
> 
> Thanks again,
> Zoe
> 
> ______________________________________
> Zoe Clarke
> PhD candidate in Computational Biology at U of T
> Lab profile: http://baderlab.org/Zoe%20Clarke <http://baderlab.org/Zoe%20Clarke>
> Personal website: https://zoe-clarke.weebly.com/ <https://zoe-clarke.weebly.com/>
> From: Carson Holt <carsonhh at gmail.com <mailto:carsonhh at gmail.com>>
> Sent: October 2, 2020 4:50 PM
> To: Zoe Clarke <zoe.clarke at utoronto.ca <mailto:zoe.clarke at utoronto.ca>>
> Cc: maker-devel at yandell-lab.org <mailto:maker-devel at yandell-lab.org> <maker-devel at yandell-lab.org <mailto:maker-devel at yandell-lab.org>>
> Subject: Re: [maker-devel] map_forward and temporary storage questions
>  
> EXTERNAL EMAIL:  Treat content with extra caution. 
> MAKER uses GFF3 format which is not the same as GTF.  You will need to convert your file to GFF3 format.
> 
> You can try this online tool (I haven?t used it to tell you how well it works) http://www.sequenceontology.org/cgi-bin/converter.cgi <http://www.sequenceontology.org/cgi-bin/converter.cgi> 
> 
> There are also a number of other resources available when you google "how to convert GTF to GFF3?.
> 
> ?Carson
> 
> 
>> On Sep 25, 2020, at 3:17 AM, Zoe Clarke <zoe.clarke at utoronto.ca <mailto:zoe.clarke at utoronto.ca>> wrote:
>> 
>> Hello!
>> 
>> I am currently running Maker on a 2.5GB genome that has already had a list of ~8000 genes very thoroughly annotated. My hope is to find and annotate the rest of the genes using ESTs and protein homology. However, I tested Maker on a single contig of my genome (there are ~20,000 contigs) and I can't find any of the genes from my original gtf file even though I followed all of the instructions in this wiki: http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/Updating_annotations_in_light_of_new_data <http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/Updating_annotations_in_light_of_new_data> (I entered the original gff under model_gff, and used map_forward=1). I am worried this is because my gff3 file isn't formatted properly. Here are a few lines in my gff file as an example:
>> --------------------------------------------
>> WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  transcript      1094446 1105585 .       +       .       ID=DIMT1.1;geneID=DIMT1
>> WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  exon    1094446 1094521 97.75   +       .       Parent=DIMT1.1
>> WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  exon    1094874 1094947 97.75   +       .       Parent=DIMT1.1
>> WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  exon    1095459 1095545 97.75   +       .       Parent=DIMT1.1
>> WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  exon    1097351 1097412 97.75   +       .       Parent=DIMT1.1
>> WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  exon    1097492 1097585 97.75   +       .       Parent=DIMT1.1
>> WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  exon    1097670 1097719 97.75   +       .       Parent=DIMT1.1
>> WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  exon    1098957 1099080 97.75   +       .       Parent=DIMT1.1
>> WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  exon    1099217 1099309 97.75   +       .       Parent=DIMT1.1
>> WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  exon    1100870 1100934 97.75   +       .       Parent=DIMT1.1
>> WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  exon    1101967 1102030 97.75   +       .       Parent=DIMT1.1
>> WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  exon    1103784 1103890 97.75   +       .       Parent=DIMT1.1
>> WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  exon    1105543 1105585 97.75   +       .       Parent=DIMT1.1
>> WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  CDS     1094446 1094521 .       +       0       Parent=DIMT1.1
>> WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  CDS     1094874 1094947 .       +       2       Parent=DIMT1.1
>> WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  CDS     1095459 1095545 .       +       0       Parent=DIMT1.1
>> WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  CDS     1097351 1097412 .       +       0       Parent=DIMT1.1
>> WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  CDS     1097492 1097585 .       +       1       Parent=DIMT1.1
>> WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  CDS     1097670 1097719 .       +       0       Parent=DIMT1.1
>> WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  CDS     1098957 1099080 .       +       1       Parent=DIMT1.1
>> WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  CDS     1099217 1099309 .       +       0       Parent=DIMT1.1
>> WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  CDS     1100870 1100934 .       +       0       Parent=DIMT1.1
>> WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  CDS     1101967 1102030 .       +       1       Parent=DIMT1.1
>> WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  CDS     1103784 1103890 .       +       0       Parent=DIMT1.1
>> WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  CDS     1105543 1105582 .       +       1       Parent=DIMT1.1
>> --------------------------------------
>> ?This is from the contig I used as a test for maker, and I can't find DIMT1.1 in the final gff file. At first I thought it might be because "geneID" is a listed attribute, but changing this to "Name" didn't help. Do you have any ideas why these genes might not be mapping forward? If it's something I can fix in the gff file, I am hoping I can fix it and use it for the second round of Maker after I have trained Snap.
>> 
>> Also, do you think a better quality annotation would results from Snap trained from this curated list of ~8000 genes (that has been expertly done) or by the round 1 output of Maker?
>> 
>> A final question: I am having memory storage issues with Maker, as it is currently taking up ~15TB of storage with temporary files. I am running Maker on a cluster and whenever my submitted Maker job runs out of memory it fails, so I have to resubmit it about every hour, which leaves a lot of temporary folders (e.g. maker_x6V2y4) in my directory. I notice that some of these temporary files haven't been updated in days - is it okay to delete them?
>> 
>> Thank you so much for your help!
>> Zoe
>> ______________________________________
>> Zoe Clarke
>> PhD candidate in Computational Biology at U of T
>> Lab profile: http://baderlab.org/Zoe%20Clarke <http://baderlab.org/Zoe%20Clarke>
>> Personal website: https://zoe-clarke.weebly.com/ <https://zoe-clarke.weebly.com/>_______________________________________________
>> maker-devel mailing list
>> maker-devel at yandell-lab.org <mailto:maker-devel at yandell-lab.org>
>> http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org <http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org>
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From taosheng.x at gmail.com  Sat Oct 17 00:48:06 2020
From: taosheng.x at gmail.com (Xu, taosheng)
Date: Sat, 17 Oct 2020 14:48:06 +0800
Subject: [maker-devel] Does maker support muti-processing for a single long
 fasta sequence using openMPI?
Message-ID: <CALJhmFoNOdxFb4gQ4jYP=FZqaHgZdVOhQOpPuyd5bMAeYZ8ucg@mail.gmail.com>

Dear Maker Development Team,
I wonder whether maker supports parallel processing for a single long
genome sequence?

When I submit my maker task using openMPI with multiple cpus (like, mpiexec
-n 40  maker) to annotate a single long genome sequence, always only one
maker with 4 rmblast run. The other cpus is on idle.

I want to use the maker parallel processing with openMPI to speed up a
single ultra-long genome sequence annotation.

Best regards,
Taosheng
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From carsonhh at gmail.com  Mon Oct 19 08:32:20 2020
From: carsonhh at gmail.com (Carson Holt)
Date: Mon, 19 Oct 2020 08:32:20 -0600
Subject: [maker-devel] Does maker support muti-processing for a single
 long fasta sequence using openMPI?
In-Reply-To: <CALJhmFoNOdxFb4gQ4jYP=FZqaHgZdVOhQOpPuyd5bMAeYZ8ucg@mail.gmail.com>
References: <CALJhmFoNOdxFb4gQ4jYP=FZqaHgZdVOhQOpPuyd5bMAeYZ8ucg@mail.gmail.com>
Message-ID: <AC94C4EB-A696-4830-A650-1A33EB67B281@gmail.com>

Yes. It will divide contigs into chunks the same size as the max_dna_len parameter.

?Carson

Sent from my iPhone

> On Oct 17, 2020, at 12:48 AM, Xu, taosheng <taosheng.x at gmail.com> wrote:
> 
> ?
> Dear Maker Development Team,
> I wonder whether maker supports parallel processing for a single long genome sequence?
> 
> When I submit my maker task using openMPI with multiple cpus (like, mpiexec -n 40  maker) to annotate a single long genome sequence, always only one maker with 4 rmblast run. The other cpus is on idle.
> 
> I want to use the maker parallel processing with openMPI to speed up a single ultra-long genome sequence annotation.
> 
> Best regards,
> Taosheng
> _______________________________________________
> maker-devel mailing list
> maker-devel at yandell-lab.org
> http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org


From taosheng.x at gmail.com  Tue Oct 20 10:23:25 2020
From: taosheng.x at gmail.com (Xu, taosheng)
Date: Wed, 21 Oct 2020 00:23:25 +0800
Subject: [maker-devel] Does maker support muti-processing for a single
 long fasta sequence using openMPI?
In-Reply-To: <AC94C4EB-A696-4830-A650-1A33EB67B281@gmail.com>
References: <CALJhmFoNOdxFb4gQ4jYP=FZqaHgZdVOhQOpPuyd5bMAeYZ8ucg@mail.gmail.com>
	<AC94C4EB-A696-4830-A650-1A33EB67B281@gmail.com>
Message-ID: <CALJhmFocG7D-K0gdGJ5831V=gnPp0BDrEMu138W3HV=QmKs2Ug@mail.gmail.com>

Thank you very much Carson for your timely response,
Yes I think so. The Maker MPI should support the multi-processing of an
ultra-long single sequence. But I cannot run it successfully for a single
sequence.
First I  make sure the openMPI with maker has been installed properly. It
works well for multiple DNA sequences in a parallel way.
When I submit a maker job for an ultra-long single sequence (mpiexec -mca
btl ^openib -n 40 maker -g scaffold1.fasta -fix_nucleotides, The
max_dna_len is set to 100000). It always left only one maker thread run.
The other maker threads are disappeared and show finished in the output
information. See the output information below. Please help me to check it.
Thanks for your kind help and your time.

#-----MAKER Behavior Options
max_dna_len=100000 #length for dividing up contigs into chunks
(increases/decreases memory usage)
min_contig=1 #skip genome contigs below this length (under 10kb are often
useless)

Best regards,
Taosheng



OUTPUT Information
STATUS: Processing and indexing input FASTA files...
STATUS: Setting up database for any GFF3 input...
examining contents of the fasta file and run log
A data structure will be created for you at:
/data/splitgenome/top1000/splitGenome/part1/plant.maker.output/plant_datastore

To access files for individual sequences use the datastore index:
/data/splitgenome/top1000/splitGenome/part1/plant.maker.output/plant_master_datastore_index.log

STATUS: Now running MAKER...



--Next Contig--

Processing run.log file...
examining contents of the fasta file and run log



--Next Contig--

#---------------------------------------------------------------------
Another instance of maker is processing this contig!!
SeqID: scaffold#1
Length: 73580997
#---------------------------------------------------------------------


examining contents of the fasta file and run log



--Next Contig--

#---------------------------------------------------------------------
Another instance of maker is processing this contig!!
SeqID: scaffold#1
Length: 73580997
#---------------------------------------------------------------------




Maker is now finished!!!



Start_time: 1603000030
End_time:   1603000033
Elapsed:    3
A data structure will be created for you at:
/data/splitgenome/top1000/splitGenome/part1/plant.maker.output/plant_datastore

To access files for individual sequences use the datastore index:
/data/splitgenome/top1000/splitGenome/part1/plant.maker.output/plant_master_datastore_index.log

STATUS: Now running MAKER...
MAKER WARNING: The file
plant.maker.output/plant_datastore/B5/CD/scaffold#1//theVoid.scaffold#1/28/scaffold#1.289.plant_repeatFinal%2Elib%2Empi%2E10%2E2.specific.out
did not finish on the last run and must be erased
WARNING: Multiple MAKER processes have been started in the
same directory.

STATUS: Processing and indexing input FASTA files...
examining contents of the fasta file and run log



--Next Contig--

#---------------------------------------------------------------------
Another instance of maker is processing this contig!!
SeqID: scaffold#1
Length: 73580997
#---------------------------------------------------------------------


WARNING: Multiple MAKER processes have been started in the
same directory.

STATUS: Processing and indexing input FASTA files...
STATUS: Setting up database for any GFF3 input...
STATUS: Setting up database for any GFF3 input...
A data structure will be created for you at:
/data/splitgenome/top1000/splitGenome/part1/plant.maker.output/plant_datastore

To access files for individual sequences use the datastore index:
/data/splitgenome/top1000/splitGenome/part1/plant.maker.output/plant_master_datastore_index.log

STATUS: Now running MAKER...
examining contents of the fasta file and run log



--Next Contig--

#---------------------------------------------------------------------
Another instance of maker is processing this contig!!
SeqID: scaffold#1
Length: 73580997
#---------------------------------------------------------------------




*Maker is now finished!!!*



Start_time: 1603000030
End_time:   1603000034
Elapsed:    4
#---------------------------------------------------------------------
Now starting the contig!!
SeqID: scaffold#1
Length: 73580997
#---------------------------------------------------------------------


examining contents of the fasta file and run log



--Next Contig--

#---------------------------------------------------------------------
Another instance of maker is processing this contig!!
SeqID: scaffold#1
Length: 73580997
#---------------------------------------------------------------------


examining contents of the fasta file and run log



--Next Contig--

#---------------------------------------------------------------------
Another instance of maker is processing this contig!!
SeqID: scaffold#1
Length: 73580997
#---------------------------------------------------------------------




Start_time: 1603000030
End_time:   1603000034
Elapsed:    4


*Maker is now finished!!!*

A data structure will be created for you at:
/data/splitgenome/top1000/splitGenome/part1/plant.maker.output/plant_datastore

To access files for individual sequences use the datastore index:
/data/splitgenome/top1000/splitGenome/part1/plant.maker.output/plant_master_datastore_index.log

STATUS: Now running MAKER...
examining contents of the fasta file and run log
..........

Maker is now finished!!!



Start_time: 1602920407
End_time:   1602920580
Elapsed:    173
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_VflRYH; ./maker3.01/exe/RepeatMasker/RepeatMasker
/data/splitgenome/top1000/splitGenome/part1/plant.maker.output/plant_datastore/B5/CD/scaffold#1//theVoid.scaffold#1/0/scaffold#1.0.plant_repeatFinal%2Elib%2Empi%2E10%2E0.specific
-dir
/data/splitgenome/top1000/splitGenome/part1/plant.maker.output/plant_datastore/B5/CD/scaffold#1//theVoid.scaffold#1/0
-pa 1 -lib
/data/splitgenome/top1000/splitGenome/part1/plant.maker.output/mpi_blastdb/plant_repeatFinal%2Elib.mpi.10/plant_repeatFinal%2Elib.mpi.10.0
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_VflRYH; ./maker3.01/exe/RepeatMasker/RepeatMasker
/data/splitgenome/top1000/splitGenome/part1/plant.maker.output/plant_datastore/B5/CD/scaffold#1//theVoid.scaffold#1/0/scaffold#1.0.plant_repeatFinal%2Elib%2Empi%2E10%2E1.specific
-dir
/data/splitgenome/top1000/splitGenome/part1/plant.maker.output/plant_datastore/B5/CD/scaffold#1//theVoid.scaffold#1/0
-pa 1 -lib
/data/splitgenome/top1000/splitGenome/part1/plant.maker.output/mpi_blastdb/plant_repeatFinal%2Elib.mpi.10/plant_repeatFinal%2Elib.mpi.10.1
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_VflRYH; ./maker3.01/exe/RepeatMasker/RepeatMasker
/data/splitgenome/top1000/splitGenome/part1/plant.maker.output/plant_datastore/B5/CD/scaffold#1//theVoid.scaffold#1/0/scaffold#1.0.plant_repeatFinal%2Elib%2Empi%2E10%2E2.specific
-dir
/data/splitgenome/top1000/splitGenome/part1/plant.maker.output/plant_datastore/B5/CD/scaffold#1//theVoid.scaffold#1/0
-pa 1 -lib
/data/splitgenome/top1000/splitGenome/part1/plant.maker.output/mpi_blastdb/plant_repeatFinal%2Elib.mpi.10/plant_repeatFinal%2Elib.mpi.10.2
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_VflRYH; ./maker3.01/exe/RepeatMasker/RepeatMasker
/data/splitgenome/top1000/splitGenome/part1/plant.maker.output/plant_datastore/B5/CD/scaffold#1//theVoid.scaffold#1/0/scaffold#1.0.plant_repeatFinal%2Elib%2Empi%2E10%2E3.specific
-dir
/data/splitgenome/top1000/splitGenome/part1/plant.maker.output/plant_datastore/B5/CD/scaffold#1//theVoid.scaffold#1/0
-pa 1 -lib
/data/splitgenome/top1000/splitGenome/part1/plant.maker.output/mpi_blastdb/plant_repeatFinal%2Elib.mpi.10/plant_repeatFinal%2Elib.mpi.10.3
#-------------------------------#
running  repeat masker.
#--------- command -------------#

.....

On Mon, Oct 19, 2020 at 10:32 PM Carson Holt <carsonhh at gmail.com> wrote:

> Yes. It will divide contigs into chunks the same size as the max_dna_len
> parameter.
>
> ?Carson
>
> Sent from my iPhone
>
> > On Oct 17, 2020, at 12:48 AM, Xu, taosheng <taosheng.x at gmail.com> wrote:
> >
> > ?
> > Dear Maker Development Team,
> > I wonder whether maker supports parallel processing for a single long
> genome sequence?
> >
> > When I submit my maker task using openMPI with multiple cpus (like,
> mpiexec -n 40  maker) to annotate a single long genome sequence, always
> only one maker with 4 rmblast run. The other cpus is on idle.
> >
> > I want to use the maker parallel processing with openMPI to speed up a
> single ultra-long genome sequence annotation.
> >
> > Best regards,
> > Taosheng
> > _______________________________________________
> > maker-devel mailing list
> > maker-devel at yandell-lab.org
> > http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org
>
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From zoe.clarke at utoronto.ca  Fri Oct  9 05:39:57 2020
From: zoe.clarke at utoronto.ca (Zoe Clarke)
Date: Fri, 9 Oct 2020 11:39:57 +0000
Subject: [maker-devel] Issue with single contig
Message-ID: <YTBPR01MB3839C4605F16FAA8BDA8EFFE9C080@YTBPR01MB3839.CANPRD01.PROD.OUTLOOK.COM>

Hello!

Sorry to bother you again. I am having a very specific problem with one of my contigs, and I was hoping you could help.

I can cancelled my last Maker run because one of my contigs failed around 56,000 times according to the output_rnd1_master_datastore_index.log file. It was just perpetually failing during the run with the following message:

ERROR: Chunk failed at level:0, tier_type:0open3: fork failed: Cannot allocate memory at dir/File/NFSLock.pm line 1037.

I am running Maker over multiple nodes, so I figured there might be an issue with a log file getting truncated or malformed. Looking at the files stored in the void for this contig, there are also a ton of files which I think might be causing an issue:

0                         run.log.child.112                                     WCK01_AAF20200214_F8-ctg57.118-119.raw.section       WCK01_AAF20200214_F8-ctg57.55-56.raw.section
1                         run.log.child.113                                     WCK01_AAF20200214_F8-ctg57.118.pred.raw.section      WCK01_AAF20200214_F8-ctg57.55.pred.raw.section
10                        run.log.child.114                                     WCK01_AAF20200214_F8-ctg57.118.raw.section           WCK01_AAF20200214_F8-ctg57.55.raw.section
11                        run.log.child.115                                     WCK01_AAF20200214_F8-ctg57.119-120.raw.section       WCK01_AAF20200214_F8-ctg57.56-57.raw.section
12                        run.log.child.116                                     WCK01_AAF20200214_F8-ctg57.119.pred.raw.section      WCK01_AAF20200214_F8-ctg57.56.pred.raw.section
2                         run.log.child.117                                     WCK01_AAF20200214_F8-ctg57.119.raw.section           WCK01_AAF20200214_F8-ctg57.5-6.raw.section
3                         run.log.child.118                                     WCK01_AAF20200214_F8-ctg57.11.pred.raw.section       WCK01_AAF20200214_F8-ctg57.56.raw.section
4                         run.log.child.119                                     WCK01_AAF20200214_F8-ctg57.11.raw.section            WCK01_AAF20200214_F8-ctg57.57-58.raw.section
5                         run.log.child.12                                      WCK01_AAF20200214_F8-ctg57.120-121.raw.section       WCK01_AAF20200214_F8-ctg57.57.pred.raw.section
6                         run.log.child.120                                     WCK01_AAF20200214_F8-ctg57.120.pred.raw.section      WCK01_AAF20200214_F8-ctg57.57.raw.section
7                         run.log.child.121                                     WCK01_AAF20200214_F8-ctg57.120.raw.section           WCK01_AAF20200214_F8-ctg57.58-59.raw.section
8                         run.log.child.122                                     WCK01_AAF20200214_F8-ctg57.121-122.raw.section       WCK01_AAF20200214_F8-ctg57.58.pred.raw.section
9                         run.log.child.123                                     WCK01_AAF20200214_F8-ctg57.12-13.raw.section         WCK01_AAF20200214_F8-ctg57.58.raw.section
evidence_0.gff            run.log.child.124                                     WCK01_AAF20200214_F8-ctg57.121.end.blastn.holdover   WCK01_AAF20200214_F8-ctg57.59-60.raw.section
evidence_100.gff          run.log.child.125                                     WCK01_AAF20200214_F8-ctg57.121.end.blastx.holdover   WCK01_AAF20200214_F8-ctg57.59.pred.raw.section
evidence_101.gff          run.log.child.13                                      WCK01_AAF20200214_F8-ctg57.121.pred.raw.section      WCK01_AAF20200214_F8-ctg57.59.raw.section
evidence_102.gff          run.log.child.14                                      WCK01_AAF20200214_F8-ctg57.121.raw.section           WCK01_AAF20200214_F8-ctg57.5.pred.raw.section
evidence_103.gff          run.log.child.15                                      WCK01_AAF20200214_F8-ctg57.122-123.raw.section       WCK01_AAF20200214_F8-ctg57.5.raw.section
evidence_104.gff          run.log.child.16                                      WCK01_AAF20200214_F8-ctg57.122.pred.raw.section      WCK01_AAF20200214_F8-ctg57.60-61.raw.section
evidence_105.gff          run.log.child.17                                      WCK01_AAF20200214_F8-ctg57.122.raw.section           WCK01_AAF20200214_F8-ctg57.60.pred.raw.section
evidence_106.gff          run.log.child.18                                      WCK01_AAF20200214_F8-ctg57.123-124.raw.section       WCK01_AAF20200214_F8-ctg57.60.raw.section
evidence_107.gff          run.log.child.19                                      WCK01_AAF20200214_F8-ctg57.123.pred.raw.section      WCK01_AAF20200214_F8-ctg57.61-62.raw.section
evidence_108.gff          run.log.child.2                                       WCK01_AAF20200214_F8-ctg57.123.raw.section           WCK01_AAF20200214_F8-ctg57.61.pred.raw.section
evidence_109.gff          run.log.child.20                                      WCK01_AAF20200214_F8-ctg57.124-125.raw.section       WCK01_AAF20200214_F8-ctg57.61.raw.section
evidence_10.gff           run.log.child.21                                      WCK01_AAF20200214_F8-ctg57.124.pred.raw.section      WCK01_AAF20200214_F8-ctg57.62-63.raw.section
evidence_110.gff          run.log.child.22                                      WCK01_AAF20200214_F8-ctg57.124.raw.section           WCK01_AAF20200214_F8-ctg57.62.pred.raw.section
evidence_111.gff          run.log.child.23                                      WCK01_AAF20200214_F8-ctg57.125.pred.raw.section      WCK01_AAF20200214_F8-ctg57.62.raw.section
evidence_112.gff          run.log.child.24                                      WCK01_AAF20200214_F8-ctg57.125.raw.section           WCK01_AAF20200214_F8-ctg57.63-64.raw.section
evidence_113.gff          run.log.child.25                                      WCK01_AAF20200214_F8-ctg57.12.pred.raw.section       WCK01_AAF20200214_F8-ctg57.63.pred.raw.section
evidence_114.gff          run.log.child.26                                      WCK01_AAF20200214_F8-ctg57.1-2.raw.section           WCK01_AAF20200214_F8-ctg57.63.raw.section
evidence_115.gff          run.log.child.27                                      WCK01_AAF20200214_F8-ctg57.12.raw.section            WCK01_AAF20200214_F8-ctg57.64-65.raw.section
evidence_116.gff          run.log.child.28                                      WCK01_AAF20200214_F8-ctg57.13-14.raw.section         WCK01_AAF20200214_F8-ctg57.64.pred.raw.section
evidence_116.gff.ann      run.log.child.29                                      WCK01_AAF20200214_F8-ctg57.13.pred.raw.section       WCK01_AAF20200214_F8-ctg57.64.raw.section
evidence_116.gff.def      run.log.child.3                                       WCK01_AAF20200214_F8-ctg57.13.raw.section            WCK01_AAF20200214_F8-ctg57.65-66.raw.section
evidence_116.gff.seq      run.log.child.30                                      WCK01_AAF20200214_F8-ctg57.14-15.raw.section         WCK01_AAF20200214_F8-ctg57.65.pred.raw.section
evidence_117.gff          run.log.child.31                                      WCK01_AAF20200214_F8-ctg57.14.pred.raw.section       WCK01_AAF20200214_F8-ctg57.65.raw.section
evidence_118.gff          run.log.child.32                                      WCK01_AAF20200214_F8-ctg57.14.raw.section            WCK01_AAF20200214_F8-ctg57.66-67.raw.section
evidence_119.gff          run.log.child.33                                      WCK01_AAF20200214_F8-ctg57.15-16.raw.section         WCK01_AAF20200214_F8-ctg57.66.pred.raw.section
evidence_11.gff           run.log.child.34                                      WCK01_AAF20200214_F8-ctg57.15.pred.raw.section       WCK01_AAF20200214_F8-ctg57.66.raw.section
evidence_120.gff          run.log.child.35                                      WCK01_AAF20200214_F8-ctg57.15.raw.section            WCK01_AAF20200214_F8-ctg57.67-68.raw.section
evidence_121.gff          run.log.child.36                                      WCK01_AAF20200214_F8-ctg57.16-17.raw.section         WCK01_AAF20200214_F8-ctg57.67.pred.raw.section
evidence_122.gff          run.log.child.37                                      WCK01_AAF20200214_F8-ctg57.16.pred.raw.section       WCK01_AAF20200214_F8-ctg57.6-7.raw.section
evidence_123.gff          run.log.child.38                                      WCK01_AAF20200214_F8-ctg57.16.raw.section            WCK01_AAF20200214_F8-ctg57.67.raw.section
evidence_124.gff          run.log.child.39                                      WCK01_AAF20200214_F8-ctg57.17-18.raw.section         WCK01_AAF20200214_F8-ctg57.68-69.raw.section
evidence_125.gff          run.log.child.4                                       WCK01_AAF20200214_F8-ctg57.17.pred.raw.section       WCK01_AAF20200214_F8-ctg57.68.pred.raw.section
evidence_12.gff           run.log.child.40                                      WCK01_AAF20200214_F8-ctg57.17.raw.section            WCK01_AAF20200214_F8-ctg57.68.raw.section
evidence_13.gff           run.log.child.41                                      WCK01_AAF20200214_F8-ctg57.18-19.raw.section         WCK01_AAF20200214_F8-ctg57.68.start.blastn.holdover
evidence_14.gff           run.log.child.42                                      WCK01_AAF20200214_F8-ctg57.18.pred.raw.section       WCK01_AAF20200214_F8-ctg57.68.start.blastx.holdover
evidence_15.gff           run.log.child.43                                      WCK01_AAF20200214_F8-ctg57.18.raw.section            WCK01_AAF20200214_F8-ctg57.69-70.raw.section
evidence_16.gff           run.log.child.44                                      WCK01_AAF20200214_F8-ctg57.19-20.raw.section         WCK01_AAF20200214_F8-ctg57.69.end.blastn.holdover
evidence_17.gff           run.log.child.45                                      WCK01_AAF20200214_F8-ctg57.19.pred.raw.section       WCK01_AAF20200214_F8-ctg57.69.pred.raw.section
evidence_18.gff           run.log.child.46                                      WCK01_AAF20200214_F8-ctg57.19.raw.section            WCK01_AAF20200214_F8-ctg57.69.raw.section
evidence_19.gff           run.log.child.47                                      WCK01_AAF20200214_F8-ctg57.1.pred.raw.section        WCK01_AAF20200214_F8-ctg57.6.pred.raw.section
evidence_1.gff            run.log.child.48                                      WCK01_AAF20200214_F8-ctg57.1.raw.section             WCK01_AAF20200214_F8-ctg57.6.raw.section
evidence_20.gff           run.log.child.49                                      WCK01_AAF20200214_F8-ctg57.20-21.raw.section         WCK01_AAF20200214_F8-ctg57.70-71.raw.section
evidence_21.gff           run.log.child.5                                       WCK01_AAF20200214_F8-ctg57.20.pred.raw.section       WCK01_AAF20200214_F8-ctg57.70.end.blastn.holdover
evidence_22.gff           run.log.child.50                                      WCK01_AAF20200214_F8-ctg57.20.raw.section            WCK01_AAF20200214_F8-ctg57.70.end.blastx.holdover
evidence_23.gff           run.log.child.51                                      WCK01_AAF20200214_F8-ctg57.21-22.raw.section         WCK01_AAF20200214_F8-ctg57.70.pred.raw.section
evidence_24.gff           run.log.child.52                                      WCK01_AAF20200214_F8-ctg57.21.pred.raw.section       WCK01_AAF20200214_F8-ctg57.70.raw.section
evidence_25.gff           run.log.child.53                                      WCK01_AAF20200214_F8-ctg57.21.raw.section            WCK01_AAF20200214_F8-ctg57.71-72.raw.section
evidence_25.gff.ann       run.log.child.54                                      WCK01_AAF20200214_F8-ctg57.22-23.raw.section         WCK01_AAF20200214_F8-ctg57.71.pred.raw.section
evidence_25.gff.def       run.log.child.55                                      WCK01_AAF20200214_F8-ctg57.22.pred.raw.section       WCK01_AAF20200214_F8-ctg57.71.raw.section
evidence_25.gff.seq       run.log.child.56                                      WCK01_AAF20200214_F8-ctg57.22.raw.section            WCK01_AAF20200214_F8-ctg57.72-73.raw.section
evidence_26.gff           run.log.child.57                                      WCK01_AAF20200214_F8-ctg57.23-24.raw.section         WCK01_AAF20200214_F8-ctg57.72.pred.raw.section
evidence_27.gff           run.log.child.58                                      WCK01_AAF20200214_F8-ctg57.23.pred.raw.section       WCK01_AAF20200214_F8-ctg57.72.raw.section
evidence_28.gff           run.log.child.59                                      WCK01_AAF20200214_F8-ctg57.2-3.raw.section           WCK01_AAF20200214_F8-ctg57.73-74.raw.section
evidence_29.gff           run.log.child.6                                       WCK01_AAF20200214_F8-ctg57.23.raw.section            WCK01_AAF20200214_F8-ctg57.73.pred.raw.section
evidence_2.gff            run.log.child.60                                      WCK01_AAF20200214_F8-ctg57.23.start.blastn.holdover  WCK01_AAF20200214_F8-ctg57.73.raw.section
evidence_30.gff           run.log.child.61                                      WCK01_AAF20200214_F8-ctg57.23.start.blastx.holdover  WCK01_AAF20200214_F8-ctg57.73.start.blastn.holdover
evidence_31.gff           run.log.child.62                                      WCK01_AAF20200214_F8-ctg57.24-25.raw.section         WCK01_AAF20200214_F8-ctg57.73.start.blastx.holdover
evidence_32.gff           run.log.child.63                                      WCK01_AAF20200214_F8-ctg57.24.pred.raw.section       WCK01_AAF20200214_F8-ctg57.74-75.raw.section
evidence_33.gff           run.log.child.64                                      WCK01_AAF20200214_F8-ctg57.24.raw.section            WCK01_AAF20200214_F8-ctg57.74.pred.raw.section
evidence_34.gff           run.log.child.65                                      WCK01_AAF20200214_F8-ctg57.25-26.raw.section         WCK01_AAF20200214_F8-ctg57.74.raw.section
evidence_35.gff           run.log.child.66                                      WCK01_AAF20200214_F8-ctg57.25.end.blastn.holdover    WCK01_AAF20200214_F8-ctg57.75-76.raw.section
evidence_36.gff           run.log.child.67                                      WCK01_AAF20200214_F8-ctg57.25.pred.raw.section       WCK01_AAF20200214_F8-ctg57.75.end.blastn.holdover
evidence_37.gff           run.log.child.68                                      WCK01_AAF20200214_F8-ctg57.25.raw.section            WCK01_AAF20200214_F8-ctg57.75.end.blastx.holdover
evidence_38.gff           run.log.child.69                                      WCK01_AAF20200214_F8-ctg57.26-27.raw.section         WCK01_AAF20200214_F8-ctg57.75.pred.raw.section
evidence_39.gff           run.log.child.7                                       WCK01_AAF20200214_F8-ctg57.26.pred.raw.section       WCK01_AAF20200214_F8-ctg57.75.raw.section
evidence_3.gff            run.log.child.70                                      WCK01_AAF20200214_F8-ctg57.26.raw.section            WCK01_AAF20200214_F8-ctg57.76-77.raw.section
evidence_40.gff           run.log.child.71                                      WCK01_AAF20200214_F8-ctg57.27-28.raw.section         WCK01_AAF20200214_F8-ctg57.76.pred.raw.section
evidence_41.gff           run.log.child.72                                      WCK01_AAF20200214_F8-ctg57.27.pred.raw.section       WCK01_AAF20200214_F8-ctg57.76.raw.section
evidence_42.gff           run.log.child.73                                      WCK01_AAF20200214_F8-ctg57.27.raw.section            WCK01_AAF20200214_F8-ctg57.77-78.raw.section
evidence_43.gff           run.log.child.74                                      WCK01_AAF20200214_F8-ctg57.28-29.raw.section         WCK01_AAF20200214_F8-ctg57.77.pred.raw.section
evidence_44.gff           run.log.child.75                                      WCK01_AAF20200214_F8-ctg57.28.pred.raw.section       WCK01_AAF20200214_F8-ctg57.77.raw.section
evidence_45.gff           run.log.child.76                                      WCK01_AAF20200214_F8-ctg57.28.raw.section            WCK01_AAF20200214_F8-ctg57.78-79.raw.section
evidence_46.gff           run.log.child.77                                      WCK01_AAF20200214_F8-ctg57.29-30.raw.section         WCK01_AAF20200214_F8-ctg57.78.pred.raw.section
evidence_47.gff           run.log.child.78                                      WCK01_AAF20200214_F8-ctg57.29.pred.raw.section       WCK01_AAF20200214_F8-ctg57.7-8.raw.section
evidence_48.gff           run.log.child.79                                      WCK01_AAF20200214_F8-ctg57.29.raw.section            WCK01_AAF20200214_F8-ctg57.78.raw.section
evidence_49.gff           run.log.child.8                                       WCK01_AAF20200214_F8-ctg57.2.pred.raw.section        WCK01_AAF20200214_F8-ctg57.79-80.raw.section
evidence_4.gff            run.log.child.80                                      WCK01_AAF20200214_F8-ctg57.2.raw.section             WCK01_AAF20200214_F8-ctg57.79.pred.raw.section
evidence_50.gff           run.log.child.81                                      WCK01_AAF20200214_F8-ctg57.2.start.blastn.holdover   WCK01_AAF20200214_F8-ctg57.79.raw.section
evidence_51.gff           run.log.child.82                                      WCK01_AAF20200214_F8-ctg57.2.start.blastx.holdover   WCK01_AAF20200214_F8-ctg57.7.pred.raw.section
evidence_52.gff           run.log.child.83                                      WCK01_AAF20200214_F8-ctg57.30-31.raw.section         WCK01_AAF20200214_F8-ctg57.7.raw.section
evidence_53.gff           run.log.child.84                                      WCK01_AAF20200214_F8-ctg57.30.pred.raw.section       WCK01_AAF20200214_F8-ctg57.80-81.raw.section
evidence_54.gff           run.log.child.85                                      WCK01_AAF20200214_F8-ctg57.30.raw.section            WCK01_AAF20200214_F8-ctg57.80.pred.raw.section
evidence_55.gff           run.log.child.86                                      WCK01_AAF20200214_F8-ctg57.31-32.raw.section         WCK01_AAF20200214_F8-ctg57.80.raw.section
evidence_56.gff           run.log.child.87                                      WCK01_AAF20200214_F8-ctg57.31.pred.raw.section       WCK01_AAF20200214_F8-ctg57.80.start.blastn.holdover
evidence_57.gff           run.log.child.88                                      WCK01_AAF20200214_F8-ctg57.31.raw.section            WCK01_AAF20200214_F8-ctg57.80.start.blastx.holdover
evidence_58.gff           run.log.child.89                                      WCK01_AAF20200214_F8-ctg57.32-33.raw.section         WCK01_AAF20200214_F8-ctg57.81-82.raw.section
evidence_59.gff           run.log.child.9                                       WCK01_AAF20200214_F8-ctg57.32.pred.raw.section       WCK01_AAF20200214_F8-ctg57.81.pred.raw.section
evidence_5.gff            run.log.child.90                                      WCK01_AAF20200214_F8-ctg57.32.raw.section            WCK01_AAF20200214_F8-ctg57.81.raw.section
evidence_60.gff           run.log.child.91                                      WCK01_AAF20200214_F8-ctg57.33-34.raw.section         WCK01_AAF20200214_F8-ctg57.82-83.raw.section
evidence_61.gff           run.log.child.92                                      WCK01_AAF20200214_F8-ctg57.33.pred.raw.section       WCK01_AAF20200214_F8-ctg57.82.end.blastn.holdover
evidence_62.gff           run.log.child.93                                      WCK01_AAF20200214_F8-ctg57.33.raw.section            WCK01_AAF20200214_F8-ctg57.82.end.blastx.holdover
evidence_63.gff           run.log.child.94                                      WCK01_AAF20200214_F8-ctg57.34-35.raw.section         WCK01_AAF20200214_F8-ctg57.82.pred.raw.section
evidence_64.gff           run.log.child.95                                      WCK01_AAF20200214_F8-ctg57.34.pred.raw.section       WCK01_AAF20200214_F8-ctg57.82.raw.section
evidence_65.gff           run.log.child.96                                      WCK01_AAF20200214_F8-ctg57.3-4.raw.section           WCK01_AAF20200214_F8-ctg57.83-84.raw.section
evidence_66.gff           run.log.child.97                                      WCK01_AAF20200214_F8-ctg57.34.raw.section            WCK01_AAF20200214_F8-ctg57.83.pred.raw.section
evidence_67.gff           run.log.child.98                                      WCK01_AAF20200214_F8-ctg57.35-36.raw.section         WCK01_AAF20200214_F8-ctg57.83.raw.section
evidence_68.gff           run.log.child.99                                      WCK01_AAF20200214_F8-ctg57.35.pred.raw.section       WCK01_AAF20200214_F8-ctg57.84-85.raw.section
evidence_69.gff           WCK01_AAF20200214_F8-ctg57.0-1.raw.section            WCK01_AAF20200214_F8-ctg57.35.raw.section            WCK01_AAF20200214_F8-ctg57.84.pred.raw.section
evidence_6.gff            WCK01_AAF20200214_F8-ctg57.0.pred.raw.section         WCK01_AAF20200214_F8-ctg57.36-37.raw.section         WCK01_AAF20200214_F8-ctg57.84.raw.section
evidence_70.gff           WCK01_AAF20200214_F8-ctg57.0.raw.section              WCK01_AAF20200214_F8-ctg57.36.pred.raw.section       WCK01_AAF20200214_F8-ctg57.84.start.blastn.holdover
evidence_70.gff.ann       WCK01_AAF20200214_F8-ctg57.100-101.raw.section        WCK01_AAF20200214_F8-ctg57.36.raw.section            WCK01_AAF20200214_F8-ctg57.84.start.blastx.holdover
evidence_70.gff.def       WCK01_AAF20200214_F8-ctg57.100.pred.raw.section       WCK01_AAF20200214_F8-ctg57.37-38.raw.section         WCK01_AAF20200214_F8-ctg57.85-86.raw.section
evidence_70.gff.seq       WCK01_AAF20200214_F8-ctg57.100.raw.section            WCK01_AAF20200214_F8-ctg57.37.pred.raw.section       WCK01_AAF20200214_F8-ctg57.85.pred.raw.section
evidence_71.gff           WCK01_AAF20200214_F8-ctg57.101-102.raw.section        WCK01_AAF20200214_F8-ctg57.37.raw.section            WCK01_AAF20200214_F8-ctg57.85.raw.section
evidence_72.gff           WCK01_AAF20200214_F8-ctg57.10-11.raw.section          WCK01_AAF20200214_F8-ctg57.38-39.raw.section         WCK01_AAF20200214_F8-ctg57.86-87.raw.section
evidence_73.gff           WCK01_AAF20200214_F8-ctg57.101.pred.raw.section       WCK01_AAF20200214_F8-ctg57.38.pred.raw.section       WCK01_AAF20200214_F8-ctg57.86.end.blastn.holdover
evidence_74.gff           WCK01_AAF20200214_F8-ctg57.101.raw.section            WCK01_AAF20200214_F8-ctg57.38.raw.section            WCK01_AAF20200214_F8-ctg57.86.end.blastx.holdover
evidence_75.gff           WCK01_AAF20200214_F8-ctg57.102-103.raw.section        WCK01_AAF20200214_F8-ctg57.39-40.raw.section         WCK01_AAF20200214_F8-ctg57.86.pred.raw.section
evidence_76.gff           WCK01_AAF20200214_F8-ctg57.102.end.blastn.holdover    WCK01_AAF20200214_F8-ctg57.39.pred.raw.section       WCK01_AAF20200214_F8-ctg57.86.raw.section
evidence_77.gff           WCK01_AAF20200214_F8-ctg57.102.end.blastx.holdover    WCK01_AAF20200214_F8-ctg57.39.raw.section            WCK01_AAF20200214_F8-ctg57.87-88.raw.section
evidence_78.gff           WCK01_AAF20200214_F8-ctg57.102.pred.raw.section       WCK01_AAF20200214_F8-ctg57.3.pred.raw.section        WCK01_AAF20200214_F8-ctg57.87.pred.raw.section
evidence_79.gff           WCK01_AAF20200214_F8-ctg57.102.raw.section            WCK01_AAF20200214_F8-ctg57.3.raw.section             WCK01_AAF20200214_F8-ctg57.87.raw.section
evidence_7.gff            WCK01_AAF20200214_F8-ctg57.103-104.raw.section        WCK01_AAF20200214_F8-ctg57.40-41.raw.section         WCK01_AAF20200214_F8-ctg57.88-89.raw.section
evidence_80.gff           WCK01_AAF20200214_F8-ctg57.103.pred.raw.section       WCK01_AAF20200214_F8-ctg57.40.pred.raw.section       WCK01_AAF20200214_F8-ctg57.88.pred.raw.section
evidence_81.gff           WCK01_AAF20200214_F8-ctg57.103.raw.section            WCK01_AAF20200214_F8-ctg57.40.raw.section            WCK01_AAF20200214_F8-ctg57.88.raw.section
evidence_82.gff           WCK01_AAF20200214_F8-ctg57.104-105.raw.section        WCK01_AAF20200214_F8-ctg57.41-42.raw.section         WCK01_AAF20200214_F8-ctg57.89-90.raw.section
evidence_83.gff           WCK01_AAF20200214_F8-ctg57.104.pred.raw.section       WCK01_AAF20200214_F8-ctg57.41.pred.raw.section       WCK01_AAF20200214_F8-ctg57.89.pred.raw.section
evidence_84.gff           WCK01_AAF20200214_F8-ctg57.104.raw.section            WCK01_AAF20200214_F8-ctg57.41.raw.section            WCK01_AAF20200214_F8-ctg57.8-9.raw.section
evidence_85.gff           WCK01_AAF20200214_F8-ctg57.105-106.raw.section        WCK01_AAF20200214_F8-ctg57.42-43.raw.section         WCK01_AAF20200214_F8-ctg57.89.raw.section
evidence_86.gff           WCK01_AAF20200214_F8-ctg57.105.pred.raw.section       WCK01_AAF20200214_F8-ctg57.42.pred.raw.section       WCK01_AAF20200214_F8-ctg57.8.pred.raw.section
evidence_87.gff           WCK01_AAF20200214_F8-ctg57.105.raw.section            WCK01_AAF20200214_F8-ctg57.42.raw.section            WCK01_AAF20200214_F8-ctg57.8.raw.section
evidence_88.gff           WCK01_AAF20200214_F8-ctg57.106-107.raw.section        WCK01_AAF20200214_F8-ctg57.43-44.raw.section         WCK01_AAF20200214_F8-ctg57.90-91.raw.section
evidence_89.gff           WCK01_AAF20200214_F8-ctg57.106.pred.raw.section       WCK01_AAF20200214_F8-ctg57.43.pred.raw.section       WCK01_AAF20200214_F8-ctg57.90.pred.raw.section
evidence_8.gff            WCK01_AAF20200214_F8-ctg57.106.raw.section            WCK01_AAF20200214_F8-ctg57.43.raw.section            WCK01_AAF20200214_F8-ctg57.90.raw.section
evidence_90.gff           WCK01_AAF20200214_F8-ctg57.107-108.raw.section        WCK01_AAF20200214_F8-ctg57.44-45.raw.section         WCK01_AAF20200214_F8-ctg57.9-10.raw.section
evidence_91.gff           WCK01_AAF20200214_F8-ctg57.107.pred.raw.section       WCK01_AAF20200214_F8-ctg57.44.pred.raw.section       WCK01_AAF20200214_F8-ctg57.91-92.raw.section
evidence_92.gff           WCK01_AAF20200214_F8-ctg57.107.raw.section            WCK01_AAF20200214_F8-ctg57.44.raw.section            WCK01_AAF20200214_F8-ctg57.91.pred.raw.section
evidence_93.gff           WCK01_AAF20200214_F8-ctg57.108-109.raw.section        WCK01_AAF20200214_F8-ctg57.45-46.raw.section         WCK01_AAF20200214_F8-ctg57.91.raw.section
evidence_94.gff           WCK01_AAF20200214_F8-ctg57.108.pred.raw.section       WCK01_AAF20200214_F8-ctg57.45.pred.raw.section       WCK01_AAF20200214_F8-ctg57.92-93.raw.section
evidence_95.gff           WCK01_AAF20200214_F8-ctg57.108.raw.section            WCK01_AAF20200214_F8-ctg57.4-5.raw.section           WCK01_AAF20200214_F8-ctg57.92.pred.raw.section
evidence_96.gff           WCK01_AAF20200214_F8-ctg57.109-110.raw.section        WCK01_AAF20200214_F8-ctg57.45.raw.section            WCK01_AAF20200214_F8-ctg57.92.raw.section
evidence_96.gff.ann       WCK01_AAF20200214_F8-ctg57.109.pred.raw.section       WCK01_AAF20200214_F8-ctg57.46-47.raw.section         WCK01_AAF20200214_F8-ctg57.93-94.raw.section
evidence_96.gff.def       WCK01_AAF20200214_F8-ctg57.109.raw.section            WCK01_AAF20200214_F8-ctg57.46.pred.raw.section       WCK01_AAF20200214_F8-ctg57.93.pred.raw.section
evidence_96.gff.seq       WCK01_AAF20200214_F8-ctg57.10.pred.raw.section        WCK01_AAF20200214_F8-ctg57.46.raw.section            WCK01_AAF20200214_F8-ctg57.93.raw.section
evidence_97.gff.ann       WCK01_AAF20200214_F8-ctg57.10.raw.section             WCK01_AAF20200214_F8-ctg57.47-48.raw.section         WCK01_AAF20200214_F8-ctg57.94-95.raw.section
evidence_97.gff.def       WCK01_AAF20200214_F8-ctg57.110-111.raw.section        WCK01_AAF20200214_F8-ctg57.47.pred.raw.section       WCK01_AAF20200214_F8-ctg57.94.pred.raw.section
evidence_97.gff.seq       WCK01_AAF20200214_F8-ctg57.110.pred.raw.section       WCK01_AAF20200214_F8-ctg57.47.raw.section            WCK01_AAF20200214_F8-ctg57.94.raw.section
evidence_98.gff.ann       WCK01_AAF20200214_F8-ctg57.110.raw.section            WCK01_AAF20200214_F8-ctg57.48-49.raw.section         WCK01_AAF20200214_F8-ctg57.95-96.raw.section
evidence_98.gff.def       WCK01_AAF20200214_F8-ctg57.111-112.raw.section        WCK01_AAF20200214_F8-ctg57.48.pred.raw.section       WCK01_AAF20200214_F8-ctg57.95.pred.raw.section
evidence_98.gff.seq       WCK01_AAF20200214_F8-ctg57.11-12.raw.section          WCK01_AAF20200214_F8-ctg57.48.raw.section            WCK01_AAF20200214_F8-ctg57.95.raw.section
evidence_99.gff           WCK01_AAF20200214_F8-ctg57.111.pred.raw.section       WCK01_AAF20200214_F8-ctg57.48.start.blastn.holdover  WCK01_AAF20200214_F8-ctg57.96.end.blastn.holdover
evidence_99.gff.ann       WCK01_AAF20200214_F8-ctg57.111.raw.section            WCK01_AAF20200214_F8-ctg57.48.start.blastx.holdover  WCK01_AAF20200214_F8-ctg57.96.end.blastx.holdover
evidence_99.gff.def       WCK01_AAF20200214_F8-ctg57.112-113.raw.section        WCK01_AAF20200214_F8-ctg57.49-50.raw.section         WCK01_AAF20200214_F8-ctg57.96.end.section.holdover
evidence_99.gff.seq       WCK01_AAF20200214_F8-ctg57.112.pred.raw.section       WCK01_AAF20200214_F8-ctg57.49.pred.raw.section       WCK01_AAF20200214_F8-ctg57.96.pred.raw.section
evidence_9.gff            WCK01_AAF20200214_F8-ctg57.112.raw.section            WCK01_AAF20200214_F8-ctg57.49.raw.section            WCK01_AAF20200214_F8-ctg57.96.raw.section
query.fasta               WCK01_AAF20200214_F8-ctg57.113-114.raw.section        WCK01_AAF20200214_F8-ctg57.4.pred.raw.section        WCK01_AAF20200214_F8-ctg57.96.start.blastn.holdover
query.masked.fasta        WCK01_AAF20200214_F8-ctg57.113.pred.raw.section       WCK01_AAF20200214_F8-ctg57.4.raw.section             WCK01_AAF20200214_F8-ctg57.96.start.blastx.holdover
query.masked.fasta.index  WCK01_AAF20200214_F8-ctg57.113.raw.section            WCK01_AAF20200214_F8-ctg57.50-51.raw.section         WCK01_AAF20200214_F8-ctg57.97.pred.raw.section
query.masked.gff          WCK01_AAF20200214_F8-ctg57.114-115.raw.section        WCK01_AAF20200214_F8-ctg57.50.end.blastn.holdover    WCK01_AAF20200214_F8-ctg57.98.pred.raw.section
run.log.child.0           WCK01_AAF20200214_F8-ctg57.114.pred.raw.section       WCK01_AAF20200214_F8-ctg57.50.end.blastx.holdover    WCK01_AAF20200214_F8-ctg57.98.start.blastn.holdover
run.log.child.1           WCK01_AAF20200214_F8-ctg57.114.raw.section            WCK01_AAF20200214_F8-ctg57.50.pred.raw.section       WCK01_AAF20200214_F8-ctg57.99-100.raw.section
run.log.child.10          WCK01_AAF20200214_F8-ctg57.114.start.blastn.holdover  WCK01_AAF20200214_F8-ctg57.50.raw.section            WCK01_AAF20200214_F8-ctg57.99.end.blastn.holdover
run.log.child.100         WCK01_AAF20200214_F8-ctg57.114.start.blastx.holdover  WCK01_AAF20200214_F8-ctg57.50.start.blastx.holdover  WCK01_AAF20200214_F8-ctg57.99.end.blastx.holdover
run.log.child.101         WCK01_AAF20200214_F8-ctg57.115-116.raw.section        WCK01_AAF20200214_F8-ctg57.51-52.raw.section         WCK01_AAF20200214_F8-ctg57.99.pred.raw.section
run.log.child.102         WCK01_AAF20200214_F8-ctg57.115.end.blastn.holdover    WCK01_AAF20200214_F8-ctg57.51.pred.raw.section       WCK01_AAF20200214_F8-ctg57.99.raw.section
run.log.child.103         WCK01_AAF20200214_F8-ctg57.115.pred.raw.section       WCK01_AAF20200214_F8-ctg57.51.raw.section            WCK01_AAF20200214_F8-ctg57.99.start.blastx.holdover
run.log.child.104         WCK01_AAF20200214_F8-ctg57.115.raw.section            WCK01_AAF20200214_F8-ctg57.52-53.raw.section         WCK01_AAF20200214_F8-ctg57.99.start.section.holdover
run.log.child.105         WCK01_AAF20200214_F8-ctg57.116-117.raw.section        WCK01_AAF20200214_F8-ctg57.52.pred.raw.section       WCK01_AAF20200214_F8-ctg57.9.pred.raw.section
run.log.child.106         WCK01_AAF20200214_F8-ctg57.116.pred.raw.section       WCK01_AAF20200214_F8-ctg57.52.raw.section            WCK01_AAF20200214_F8-ctg57.9.raw.section
run.log.child.107         WCK01_AAF20200214_F8-ctg57.116.raw.section            WCK01_AAF20200214_F8-ctg57.53-54.raw.section         WCK01_AAF20200214_F8-ctg57.gff.ann
run.log.child.108         WCK01_AAF20200214_F8-ctg57.117-118.raw.section        WCK01_AAF20200214_F8-ctg57.53.pred.raw.section       WCK01_AAF20200214_F8-ctg57.gff.def
run.log.child.109         WCK01_AAF20200214_F8-ctg57.117.pred.raw.section       WCK01_AAF20200214_F8-ctg57.53.raw.section            WCK01_AAF20200214_F8-ctg57.gff.seq
run.log.child.11          WCK01_AAF20200214_F8-ctg57.117.raw.section            WCK01_AAF20200214_F8-ctg57.54-55.raw.section
run.log.child.110         WCK01_AAF20200214_F8-ctg57.117.start.blastn.holdover  WCK01_AAF20200214_F8-ctg57.54.pred.raw.section
run.log.child.111         WCK01_AAF20200214_F8-ctg57.117.start.blastx.holdover  WCK01_AAF20200214_F8-ctg57.54.raw.section

I set clean_try=1 and am trying to fix this contig (it's only this one contig which is causing trouble), but I'm wondering if it's also okay to completely delete the void directory to force it to start this contig from scratch. I have already tried rerunning maker with clean_try=1 two times and now I'm getting an mpich2 error:

Fatal error in MPI_Send: Invalid count, error stack:
MPI_Send(173): MPI_Send(buf=0x2aec3d6a3010, count=-1279995089, MPI_CHAR, dest=15, tag=9999, MPI_COMM_WORLD) failed
MPI_Send(97).: Negative count, value is -1279995089

I am currently trying again with fewer MPI jobs requested, worrying that there might be a memory issue on the computer cluster I am using. My temporary directory still has lots of space, but I have ~200G RAM per node and sometimes the jobs use a ton of RAM. I don't have too many more contigs left of this run, so I just really don't want to mess anything up. Do you have any advice?

Thanks so much!
Zoe

______________________________________
Zoe Clarke
PhD candidate in Computational Biology at U of T
Lab profile: http://baderlab.org/Zoe%20Clarke
Personal website: https://zoe-clarke.weebly.com/
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From carsonhh at gmail.com  Thu Oct 22 13:31:11 2020
From: carsonhh at gmail.com (Carson Holt)
Date: Thu, 22 Oct 2020 13:31:11 -0600
Subject: [maker-devel] Issue with single contig
In-Reply-To: <YTBPR01MB3839C4605F16FAA8BDA8EFFE9C080@YTBPR01MB3839.CANPRD01.PROD.OUTLOOK.COM>
References: <YTBPR01MB3839C4605F16FAA8BDA8EFFE9C080@YTBPR01MB3839.CANPRD01.PROD.OUTLOOK.COM>
Message-ID: <7DEEBFBB-2247-413A-96F1-0EF1A8E9EE62@gmail.com>

Your datacenter may have implemented the temporary storage (?/tmp? by default) to be in memory storage. As a result, every file you store is really being stored in RAM behind the scenes.  Or you have specified TMP= in the control files to point to in memory storage.  The result is that, at some point there was not enough memory left.  You may want to ask about this and ensure that you can point to a real node based disk storage like traditional /tmp space.

?Carson



> On Oct 9, 2020, at 5:39 AM, Zoe Clarke <zoe.clarke at utoronto.ca> wrote:
> 
> Hello!
> 
> Sorry to bother you again. I am having a very specific problem with one of my contigs, and I was hoping you could help.
> 
> I can cancelled my last Maker run because one of my contigs failed around 56,000 times according to the output_rnd1_master_datastore_index.log file. It was just perpetually failing during the run with the following message:
> 
> ERROR: Chunk failed at level:0, tier_type:0open3: fork failed: Cannot allocate memory at dir/File/NFSLock.pm line 1037.
> 
> I am running Maker over multiple nodes, so I figured there might be an issue with a log file getting truncated or malformed. Looking at the files stored in the void for this contig, there are also a ton of files which I think might be causing an issue:
> 
> 0                         run.log.child.112                                     WCK01_AAF20200214_F8-ctg57.118-119.raw.section       WCK01_AAF20200214_F8-ctg57.55-56.raw.section
> 1                         run.log.child.113                                     WCK01_AAF20200214_F8-ctg57.118.pred.raw.section      WCK01_AAF20200214_F8-ctg57.55.pred.raw.section
> 10                        run.log.child.114                                     WCK01_AAF20200214_F8-ctg57.118.raw.section           WCK01_AAF20200214_F8-ctg57.55.raw.section
> 11                        run.log.child.115                                     WCK01_AAF20200214_F8-ctg57.119-120.raw.section       WCK01_AAF20200214_F8-ctg57.56-57.raw.section
> 12                        run.log.child.116                                     WCK01_AAF20200214_F8-ctg57.119.pred.raw.section      WCK01_AAF20200214_F8-ctg57.56.pred.raw.section
> 2                         run.log.child.117                                     WCK01_AAF20200214_F8-ctg57.119.raw.section           WCK01_AAF20200214_F8-ctg57.5-6.raw.section
> 3                         run.log.child.118                                     WCK01_AAF20200214_F8-ctg57.11.pred.raw.section       WCK01_AAF20200214_F8-ctg57.56.raw.section
> 4                         run.log.child.119                                     WCK01_AAF20200214_F8-ctg57.11.raw.section            WCK01_AAF20200214_F8-ctg57.57-58.raw.section
> 5                         run.log.child.12                                      WCK01_AAF20200214_F8-ctg57.120-121.raw.section       WCK01_AAF20200214_F8-ctg57.57.pred.raw.section
> 6                         run.log.child.120                                     WCK01_AAF20200214_F8-ctg57.120.pred.raw.section      WCK01_AAF20200214_F8-ctg57.57.raw.section
> 7                         run.log.child.121                                     WCK01_AAF20200214_F8-ctg57.120.raw.section           WCK01_AAF20200214_F8-ctg57.58-59.raw.section
> 8                         run.log.child.122                                     WCK01_AAF20200214_F8-ctg57.121-122.raw.section       WCK01_AAF20200214_F8-ctg57.58.pred.raw.section
> 9                         run.log.child.123                                     WCK01_AAF20200214_F8-ctg57.12-13.raw.section         WCK01_AAF20200214_F8-ctg57.58.raw.section
> evidence_0.gff            run.log.child.124                                     WCK01_AAF20200214_F8-ctg57.121.end.blastn.holdover   WCK01_AAF20200214_F8-ctg57.59-60.raw.section
> evidence_100.gff          run.log.child.125                                     WCK01_AAF20200214_F8-ctg57.121.end.blastx.holdover   WCK01_AAF20200214_F8-ctg57.59.pred.raw.section
> evidence_101.gff          run.log.child.13                                      WCK01_AAF20200214_F8-ctg57.121.pred.raw.section      WCK01_AAF20200214_F8-ctg57.59.raw.section
> evidence_102.gff          run.log.child.14                                      WCK01_AAF20200214_F8-ctg57.121.raw.section           WCK01_AAF20200214_F8-ctg57.5.pred.raw.section
> evidence_103.gff          run.log.child.15                                      WCK01_AAF20200214_F8-ctg57.122-123.raw.section       WCK01_AAF20200214_F8-ctg57.5.raw.section
> evidence_104.gff          run.log.child.16                                      WCK01_AAF20200214_F8-ctg57.122.pred.raw.section      WCK01_AAF20200214_F8-ctg57.60-61.raw.section
> evidence_105.gff          run.log.child.17                                      WCK01_AAF20200214_F8-ctg57.122.raw.section           WCK01_AAF20200214_F8-ctg57.60.pred.raw.section
> evidence_106.gff          run.log.child.18                                      WCK01_AAF20200214_F8-ctg57.123-124.raw.section       WCK01_AAF20200214_F8-ctg57.60.raw.section
> evidence_107.gff          run.log.child.19                                      WCK01_AAF20200214_F8-ctg57.123.pred.raw.section      WCK01_AAF20200214_F8-ctg57.61-62.raw.section
> evidence_108.gff          run.log.child.2                                       WCK01_AAF20200214_F8-ctg57.123.raw.section           WCK01_AAF20200214_F8-ctg57.61.pred.raw.section
> evidence_109.gff          run.log.child.20                                      WCK01_AAF20200214_F8-ctg57.124-125.raw.section       WCK01_AAF20200214_F8-ctg57.61.raw.section
> evidence_10.gff           run.log.child.21                                      WCK01_AAF20200214_F8-ctg57.124.pred.raw.section      WCK01_AAF20200214_F8-ctg57.62-63.raw.section
> evidence_110.gff          run.log.child.22                                      WCK01_AAF20200214_F8-ctg57.124.raw.section           WCK01_AAF20200214_F8-ctg57.62.pred.raw.section
> evidence_111.gff          run.log.child.23                                      WCK01_AAF20200214_F8-ctg57.125.pred.raw.section      WCK01_AAF20200214_F8-ctg57.62.raw.section
> evidence_112.gff          run.log.child.24                                      WCK01_AAF20200214_F8-ctg57.125.raw.section           WCK01_AAF20200214_F8-ctg57.63-64.raw.section
> evidence_113.gff          run.log.child.25                                      WCK01_AAF20200214_F8-ctg57.12.pred.raw.section       WCK01_AAF20200214_F8-ctg57.63.pred.raw.section
> evidence_114.gff          run.log.child.26                                      WCK01_AAF20200214_F8-ctg57.1-2.raw.section           WCK01_AAF20200214_F8-ctg57.63.raw.section
> evidence_115.gff          run.log.child.27                                      WCK01_AAF20200214_F8-ctg57.12.raw.section            WCK01_AAF20200214_F8-ctg57.64-65.raw.section
> evidence_116.gff          run.log.child.28                                      WCK01_AAF20200214_F8-ctg57.13-14.raw.section         WCK01_AAF20200214_F8-ctg57.64.pred.raw.section
> evidence_116.gff.ann      run.log.child.29                                      WCK01_AAF20200214_F8-ctg57.13.pred.raw.section       WCK01_AAF20200214_F8-ctg57.64.raw.section
> evidence_116.gff.def      run.log.child.3                                       WCK01_AAF20200214_F8-ctg57.13.raw.section            WCK01_AAF20200214_F8-ctg57.65-66.raw.section
> evidence_116.gff.seq      run.log.child.30                                      WCK01_AAF20200214_F8-ctg57.14-15.raw.section         WCK01_AAF20200214_F8-ctg57.65.pred.raw.section
> evidence_117.gff          run.log.child.31                                      WCK01_AAF20200214_F8-ctg57.14.pred.raw.section       WCK01_AAF20200214_F8-ctg57.65.raw.section
> evidence_118.gff          run.log.child.32                                      WCK01_AAF20200214_F8-ctg57.14.raw.section            WCK01_AAF20200214_F8-ctg57.66-67.raw.section
> evidence_119.gff          run.log.child.33                                      WCK01_AAF20200214_F8-ctg57.15-16.raw.section         WCK01_AAF20200214_F8-ctg57.66.pred.raw.section
> evidence_11.gff           run.log.child.34                                      WCK01_AAF20200214_F8-ctg57.15.pred.raw.section       WCK01_AAF20200214_F8-ctg57.66.raw.section
> evidence_120.gff          run.log.child.35                                      WCK01_AAF20200214_F8-ctg57.15.raw.section            WCK01_AAF20200214_F8-ctg57.67-68.raw.section
> evidence_121.gff          run.log.child.36                                      WCK01_AAF20200214_F8-ctg57.16-17.raw.section         WCK01_AAF20200214_F8-ctg57.67.pred.raw.section
> evidence_122.gff          run.log.child.37                                      WCK01_AAF20200214_F8-ctg57.16.pred.raw.section       WCK01_AAF20200214_F8-ctg57.6-7.raw.section
> evidence_123.gff          run.log.child.38                                      WCK01_AAF20200214_F8-ctg57.16.raw.section            WCK01_AAF20200214_F8-ctg57.67.raw.section
> evidence_124.gff          run.log.child.39                                      WCK01_AAF20200214_F8-ctg57.17-18.raw.section         WCK01_AAF20200214_F8-ctg57.68-69.raw.section
> evidence_125.gff          run.log.child.4                                       WCK01_AAF20200214_F8-ctg57.17.pred.raw.section       WCK01_AAF20200214_F8-ctg57.68.pred.raw.section
> evidence_12.gff           run.log.child.40                                      WCK01_AAF20200214_F8-ctg57.17.raw.section            WCK01_AAF20200214_F8-ctg57.68.raw.section
> evidence_13.gff           run.log.child.41                                      WCK01_AAF20200214_F8-ctg57.18-19.raw.section         WCK01_AAF20200214_F8-ctg57.68.start.blastn.holdover
> evidence_14.gff           run.log.child.42                                      WCK01_AAF20200214_F8-ctg57.18.pred.raw.section       WCK01_AAF20200214_F8-ctg57.68.start.blastx.holdover
> evidence_15.gff           run.log.child.43                                      WCK01_AAF20200214_F8-ctg57.18.raw.section            WCK01_AAF20200214_F8-ctg57.69-70.raw.section
> evidence_16.gff           run.log.child.44                                      WCK01_AAF20200214_F8-ctg57.19-20.raw.section         WCK01_AAF20200214_F8-ctg57.69.end.blastn.holdover
> evidence_17.gff           run.log.child.45                                      WCK01_AAF20200214_F8-ctg57.19.pred.raw.section       WCK01_AAF20200214_F8-ctg57.69.pred.raw.section
> evidence_18.gff           run.log.child.46                                      WCK01_AAF20200214_F8-ctg57.19.raw.section            WCK01_AAF20200214_F8-ctg57.69.raw.section
> evidence_19.gff           run.log.child.47                                      WCK01_AAF20200214_F8-ctg57.1.pred.raw.section        WCK01_AAF20200214_F8-ctg57.6.pred.raw.section
> evidence_1.gff            run.log.child.48                                      WCK01_AAF20200214_F8-ctg57.1.raw.section             WCK01_AAF20200214_F8-ctg57.6.raw.section
> evidence_20.gff           run.log.child.49                                      WCK01_AAF20200214_F8-ctg57.20-21.raw.section         WCK01_AAF20200214_F8-ctg57.70-71.raw.section
> evidence_21.gff           run.log.child.5                                       WCK01_AAF20200214_F8-ctg57.20.pred.raw.section       WCK01_AAF20200214_F8-ctg57.70.end.blastn.holdover
> evidence_22.gff           run.log.child.50                                      WCK01_AAF20200214_F8-ctg57.20.raw.section            WCK01_AAF20200214_F8-ctg57.70.end.blastx.holdover
> evidence_23.gff           run.log.child.51                                      WCK01_AAF20200214_F8-ctg57.21-22.raw.section         WCK01_AAF20200214_F8-ctg57.70.pred.raw.section
> evidence_24.gff           run.log.child.52                                      WCK01_AAF20200214_F8-ctg57.21.pred.raw.section       WCK01_AAF20200214_F8-ctg57.70.raw.section
> evidence_25.gff           run.log.child.53                                      WCK01_AAF20200214_F8-ctg57.21.raw.section            WCK01_AAF20200214_F8-ctg57.71-72.raw.section
> evidence_25.gff.ann       run.log.child.54                                      WCK01_AAF20200214_F8-ctg57.22-23.raw.section         WCK01_AAF20200214_F8-ctg57.71.pred.raw.section
> evidence_25.gff.def       run.log.child.55                                      WCK01_AAF20200214_F8-ctg57.22.pred.raw.section       WCK01_AAF20200214_F8-ctg57.71.raw.section
> evidence_25.gff.seq       run.log.child.56                                      WCK01_AAF20200214_F8-ctg57.22.raw.section            WCK01_AAF20200214_F8-ctg57.72-73.raw.section
> evidence_26.gff           run.log.child.57                                      WCK01_AAF20200214_F8-ctg57.23-24.raw.section         WCK01_AAF20200214_F8-ctg57.72.pred.raw.section
> evidence_27.gff           run.log.child.58                                      WCK01_AAF20200214_F8-ctg57.23.pred.raw.section       WCK01_AAF20200214_F8-ctg57.72.raw.section
> evidence_28.gff           run.log.child.59                                      WCK01_AAF20200214_F8-ctg57.2-3.raw.section           WCK01_AAF20200214_F8-ctg57.73-74.raw.section
> evidence_29.gff           run.log.child.6                                       WCK01_AAF20200214_F8-ctg57.23.raw.section            WCK01_AAF20200214_F8-ctg57.73.pred.raw.section
> evidence_2.gff            run.log.child.60                                      WCK01_AAF20200214_F8-ctg57.23.start.blastn.holdover  WCK01_AAF20200214_F8-ctg57.73.raw.section
> evidence_30.gff           run.log.child.61                                      WCK01_AAF20200214_F8-ctg57.23.start.blastx.holdover  WCK01_AAF20200214_F8-ctg57.73.start.blastn.holdover
> evidence_31.gff           run.log.child.62                                      WCK01_AAF20200214_F8-ctg57.24-25.raw.section         WCK01_AAF20200214_F8-ctg57.73.start.blastx.holdover
> evidence_32.gff           run.log.child.63                                      WCK01_AAF20200214_F8-ctg57.24.pred.raw.section       WCK01_AAF20200214_F8-ctg57.74-75.raw.section
> evidence_33.gff           run.log.child.64                                      WCK01_AAF20200214_F8-ctg57.24.raw.section            WCK01_AAF20200214_F8-ctg57.74.pred.raw.section
> evidence_34.gff           run.log.child.65                                      WCK01_AAF20200214_F8-ctg57.25-26.raw.section         WCK01_AAF20200214_F8-ctg57.74.raw.section
> evidence_35.gff           run.log.child.66                                      WCK01_AAF20200214_F8-ctg57.25.end.blastn.holdover    WCK01_AAF20200214_F8-ctg57.75-76.raw.section
> evidence_36.gff           run.log.child.67                                      WCK01_AAF20200214_F8-ctg57.25.pred.raw.section       WCK01_AAF20200214_F8-ctg57.75.end.blastn.holdover
> evidence_37.gff           run.log.child.68                                      WCK01_AAF20200214_F8-ctg57.25.raw.section            WCK01_AAF20200214_F8-ctg57.75.end.blastx.holdover
> evidence_38.gff           run.log.child.69                                      WCK01_AAF20200214_F8-ctg57.26-27.raw.section         WCK01_AAF20200214_F8-ctg57.75.pred.raw.section
> evidence_39.gff           run.log.child.7                                       WCK01_AAF20200214_F8-ctg57.26.pred.raw.section       WCK01_AAF20200214_F8-ctg57.75.raw.section
> evidence_3.gff            run.log.child.70                                      WCK01_AAF20200214_F8-ctg57.26.raw.section            WCK01_AAF20200214_F8-ctg57.76-77.raw.section
> evidence_40.gff           run.log.child.71                                      WCK01_AAF20200214_F8-ctg57.27-28.raw.section         WCK01_AAF20200214_F8-ctg57.76.pred.raw.section
> evidence_41.gff           run.log.child.72                                      WCK01_AAF20200214_F8-ctg57.27.pred.raw.section       WCK01_AAF20200214_F8-ctg57.76.raw.section
> evidence_42.gff           run.log.child.73                                      WCK01_AAF20200214_F8-ctg57.27.raw.section            WCK01_AAF20200214_F8-ctg57.77-78.raw.section
> evidence_43.gff           run.log.child.74                                      WCK01_AAF20200214_F8-ctg57.28-29.raw.section         WCK01_AAF20200214_F8-ctg57.77.pred.raw.section
> evidence_44.gff           run.log.child.75                                      WCK01_AAF20200214_F8-ctg57.28.pred.raw.section       WCK01_AAF20200214_F8-ctg57.77.raw.section
> evidence_45.gff           run.log.child.76                                      WCK01_AAF20200214_F8-ctg57.28.raw.section            WCK01_AAF20200214_F8-ctg57.78-79.raw.section
> evidence_46.gff           run.log.child.77                                      WCK01_AAF20200214_F8-ctg57.29-30.raw.section         WCK01_AAF20200214_F8-ctg57.78.pred.raw.section
> evidence_47.gff           run.log.child.78                                      WCK01_AAF20200214_F8-ctg57.29.pred.raw.section       WCK01_AAF20200214_F8-ctg57.7-8.raw.section
> evidence_48.gff           run.log.child.79                                      WCK01_AAF20200214_F8-ctg57.29.raw.section            WCK01_AAF20200214_F8-ctg57.78.raw.section
> evidence_49.gff           run.log.child.8                                       WCK01_AAF20200214_F8-ctg57.2.pred.raw.section        WCK01_AAF20200214_F8-ctg57.79-80.raw.section
> evidence_4.gff            run.log.child.80                                      WCK01_AAF20200214_F8-ctg57.2.raw.section             WCK01_AAF20200214_F8-ctg57.79.pred.raw.section
> evidence_50.gff           run.log.child.81                                      WCK01_AAF20200214_F8-ctg57.2.start.blastn.holdover   WCK01_AAF20200214_F8-ctg57.79.raw.section
> evidence_51.gff           run.log.child.82                                      WCK01_AAF20200214_F8-ctg57.2.start.blastx.holdover   WCK01_AAF20200214_F8-ctg57.7.pred.raw.section
> evidence_52.gff           run.log.child.83                                      WCK01_AAF20200214_F8-ctg57.30-31.raw.section         WCK01_AAF20200214_F8-ctg57.7.raw.section
> evidence_53.gff           run.log.child.84                                      WCK01_AAF20200214_F8-ctg57.30.pred.raw.section       WCK01_AAF20200214_F8-ctg57.80-81.raw.section
> evidence_54.gff           run.log.child.85                                      WCK01_AAF20200214_F8-ctg57.30.raw.section            WCK01_AAF20200214_F8-ctg57.80.pred.raw.section
> evidence_55.gff           run.log.child.86                                      WCK01_AAF20200214_F8-ctg57.31-32.raw.section         WCK01_AAF20200214_F8-ctg57.80.raw.section
> evidence_56.gff           run.log.child.87                                      WCK01_AAF20200214_F8-ctg57.31.pred.raw.section       WCK01_AAF20200214_F8-ctg57.80.start.blastn.holdover
> evidence_57.gff           run.log.child.88                                      WCK01_AAF20200214_F8-ctg57.31.raw.section            WCK01_AAF20200214_F8-ctg57.80.start.blastx.holdover
> evidence_58.gff           run.log.child.89                                      WCK01_AAF20200214_F8-ctg57.32-33.raw.section         WCK01_AAF20200214_F8-ctg57.81-82.raw.section
> evidence_59.gff           run.log.child.9                                       WCK01_AAF20200214_F8-ctg57.32.pred.raw.section       WCK01_AAF20200214_F8-ctg57.81.pred.raw.section
> evidence_5.gff            run.log.child.90                                      WCK01_AAF20200214_F8-ctg57.32.raw.section            WCK01_AAF20200214_F8-ctg57.81.raw.section
> evidence_60.gff           run.log.child.91                                      WCK01_AAF20200214_F8-ctg57.33-34.raw.section         WCK01_AAF20200214_F8-ctg57.82-83.raw.section
> evidence_61.gff           run.log.child.92                                      WCK01_AAF20200214_F8-ctg57.33.pred.raw.section       WCK01_AAF20200214_F8-ctg57.82.end.blastn.holdover
> evidence_62.gff           run.log.child.93                                      WCK01_AAF20200214_F8-ctg57.33.raw.section            WCK01_AAF20200214_F8-ctg57.82.end.blastx.holdover
> evidence_63.gff           run.log.child.94                                      WCK01_AAF20200214_F8-ctg57.34-35.raw.section         WCK01_AAF20200214_F8-ctg57.82.pred.raw.section
> evidence_64.gff           run.log.child.95                                      WCK01_AAF20200214_F8-ctg57.34.pred.raw.section       WCK01_AAF20200214_F8-ctg57.82.raw.section
> evidence_65.gff           run.log.child.96                                      WCK01_AAF20200214_F8-ctg57.3-4.raw.section           WCK01_AAF20200214_F8-ctg57.83-84.raw.section
> evidence_66.gff           run.log.child.97                                      WCK01_AAF20200214_F8-ctg57.34.raw.section            WCK01_AAF20200214_F8-ctg57.83.pred.raw.section
> evidence_67.gff           run.log.child.98                                      WCK01_AAF20200214_F8-ctg57.35-36.raw.section         WCK01_AAF20200214_F8-ctg57.83.raw.section
> evidence_68.gff           run.log.child.99                                      WCK01_AAF20200214_F8-ctg57.35.pred.raw.section       WCK01_AAF20200214_F8-ctg57.84-85.raw.section
> evidence_69.gff           WCK01_AAF20200214_F8-ctg57.0-1.raw.section            WCK01_AAF20200214_F8-ctg57.35.raw.section            WCK01_AAF20200214_F8-ctg57.84.pred.raw.section
> evidence_6.gff            WCK01_AAF20200214_F8-ctg57.0.pred.raw.section         WCK01_AAF20200214_F8-ctg57.36-37.raw.section         WCK01_AAF20200214_F8-ctg57.84.raw.section
> evidence_70.gff           WCK01_AAF20200214_F8-ctg57.0.raw.section              WCK01_AAF20200214_F8-ctg57.36.pred.raw.section       WCK01_AAF20200214_F8-ctg57.84.start.blastn.holdover
> evidence_70.gff.ann       WCK01_AAF20200214_F8-ctg57.100-101.raw.section        WCK01_AAF20200214_F8-ctg57.36.raw.section            WCK01_AAF20200214_F8-ctg57.84.start.blastx.holdover
> evidence_70.gff.def       WCK01_AAF20200214_F8-ctg57.100.pred.raw.section       WCK01_AAF20200214_F8-ctg57.37-38.raw.section         WCK01_AAF20200214_F8-ctg57.85-86.raw.section
> evidence_70.gff.seq       WCK01_AAF20200214_F8-ctg57.100.raw.section            WCK01_AAF20200214_F8-ctg57.37.pred.raw.section       WCK01_AAF20200214_F8-ctg57.85.pred.raw.section
> evidence_71.gff           WCK01_AAF20200214_F8-ctg57.101-102.raw.section        WCK01_AAF20200214_F8-ctg57.37.raw.section            WCK01_AAF20200214_F8-ctg57.85.raw.section
> evidence_72.gff           WCK01_AAF20200214_F8-ctg57.10-11.raw.section          WCK01_AAF20200214_F8-ctg57.38-39.raw.section         WCK01_AAF20200214_F8-ctg57.86-87.raw.section
> evidence_73.gff           WCK01_AAF20200214_F8-ctg57.101.pred.raw.section       WCK01_AAF20200214_F8-ctg57.38.pred.raw.section       WCK01_AAF20200214_F8-ctg57.86.end.blastn.holdover
> evidence_74.gff           WCK01_AAF20200214_F8-ctg57.101.raw.section            WCK01_AAF20200214_F8-ctg57.38.raw.section            WCK01_AAF20200214_F8-ctg57.86.end.blastx.holdover
> evidence_75.gff           WCK01_AAF20200214_F8-ctg57.102-103.raw.section        WCK01_AAF20200214_F8-ctg57.39-40.raw.section         WCK01_AAF20200214_F8-ctg57.86.pred.raw.section
> evidence_76.gff           WCK01_AAF20200214_F8-ctg57.102.end.blastn.holdover    WCK01_AAF20200214_F8-ctg57.39.pred.raw.section       WCK01_AAF20200214_F8-ctg57.86.raw.section
> evidence_77.gff           WCK01_AAF20200214_F8-ctg57.102.end.blastx.holdover    WCK01_AAF20200214_F8-ctg57.39.raw.section            WCK01_AAF20200214_F8-ctg57.87-88.raw.section
> evidence_78.gff           WCK01_AAF20200214_F8-ctg57.102.pred.raw.section       WCK01_AAF20200214_F8-ctg57.3.pred.raw.section        WCK01_AAF20200214_F8-ctg57.87.pred.raw.section
> evidence_79.gff           WCK01_AAF20200214_F8-ctg57.102.raw.section            WCK01_AAF20200214_F8-ctg57.3.raw.section             WCK01_AAF20200214_F8-ctg57.87.raw.section
> evidence_7.gff            WCK01_AAF20200214_F8-ctg57.103-104.raw.section        WCK01_AAF20200214_F8-ctg57.40-41.raw.section         WCK01_AAF20200214_F8-ctg57.88-89.raw.section
> evidence_80.gff           WCK01_AAF20200214_F8-ctg57.103.pred.raw.section       WCK01_AAF20200214_F8-ctg57.40.pred.raw.section       WCK01_AAF20200214_F8-ctg57.88.pred.raw.section
> evidence_81.gff           WCK01_AAF20200214_F8-ctg57.103.raw.section            WCK01_AAF20200214_F8-ctg57.40.raw.section            WCK01_AAF20200214_F8-ctg57.88.raw.section
> evidence_82.gff           WCK01_AAF20200214_F8-ctg57.104-105.raw.section        WCK01_AAF20200214_F8-ctg57.41-42.raw.section         WCK01_AAF20200214_F8-ctg57.89-90.raw.section
> evidence_83.gff           WCK01_AAF20200214_F8-ctg57.104.pred.raw.section       WCK01_AAF20200214_F8-ctg57.41.pred.raw.section       WCK01_AAF20200214_F8-ctg57.89.pred.raw.section
> evidence_84.gff           WCK01_AAF20200214_F8-ctg57.104.raw.section            WCK01_AAF20200214_F8-ctg57.41.raw.section            WCK01_AAF20200214_F8-ctg57.8-9.raw.section
> evidence_85.gff           WCK01_AAF20200214_F8-ctg57.105-106.raw.section        WCK01_AAF20200214_F8-ctg57.42-43.raw.section         WCK01_AAF20200214_F8-ctg57.89.raw.section
> evidence_86.gff           WCK01_AAF20200214_F8-ctg57.105.pred.raw.section       WCK01_AAF20200214_F8-ctg57.42.pred.raw.section       WCK01_AAF20200214_F8-ctg57.8.pred.raw.section
> evidence_87.gff           WCK01_AAF20200214_F8-ctg57.105.raw.section            WCK01_AAF20200214_F8-ctg57.42.raw.section            WCK01_AAF20200214_F8-ctg57.8.raw.section
> evidence_88.gff           WCK01_AAF20200214_F8-ctg57.106-107.raw.section        WCK01_AAF20200214_F8-ctg57.43-44.raw.section         WCK01_AAF20200214_F8-ctg57.90-91.raw.section
> evidence_89.gff           WCK01_AAF20200214_F8-ctg57.106.pred.raw.section       WCK01_AAF20200214_F8-ctg57.43.pred.raw.section       WCK01_AAF20200214_F8-ctg57.90.pred.raw.section
> evidence_8.gff            WCK01_AAF20200214_F8-ctg57.106.raw.section            WCK01_AAF20200214_F8-ctg57.43.raw.section            WCK01_AAF20200214_F8-ctg57.90.raw.section
> evidence_90.gff           WCK01_AAF20200214_F8-ctg57.107-108.raw.section        WCK01_AAF20200214_F8-ctg57.44-45.raw.section         WCK01_AAF20200214_F8-ctg57.9-10.raw.section
> evidence_91.gff           WCK01_AAF20200214_F8-ctg57.107.pred.raw.section       WCK01_AAF20200214_F8-ctg57.44.pred.raw.section       WCK01_AAF20200214_F8-ctg57.91-92.raw.section
> evidence_92.gff           WCK01_AAF20200214_F8-ctg57.107.raw.section            WCK01_AAF20200214_F8-ctg57.44.raw.section            WCK01_AAF20200214_F8-ctg57.91.pred.raw.section
> evidence_93.gff           WCK01_AAF20200214_F8-ctg57.108-109.raw.section        WCK01_AAF20200214_F8-ctg57.45-46.raw.section         WCK01_AAF20200214_F8-ctg57.91.raw.section
> evidence_94.gff           WCK01_AAF20200214_F8-ctg57.108.pred.raw.section       WCK01_AAF20200214_F8-ctg57.45.pred.raw.section       WCK01_AAF20200214_F8-ctg57.92-93.raw.section
> evidence_95.gff           WCK01_AAF20200214_F8-ctg57.108.raw.section            WCK01_AAF20200214_F8-ctg57.4-5.raw.section           WCK01_AAF20200214_F8-ctg57.92.pred.raw.section
> evidence_96.gff           WCK01_AAF20200214_F8-ctg57.109-110.raw.section        WCK01_AAF20200214_F8-ctg57.45.raw.section            WCK01_AAF20200214_F8-ctg57.92.raw.section
> evidence_96.gff.ann       WCK01_AAF20200214_F8-ctg57.109.pred.raw.section       WCK01_AAF20200214_F8-ctg57.46-47.raw.section         WCK01_AAF20200214_F8-ctg57.93-94.raw.section
> evidence_96.gff.def       WCK01_AAF20200214_F8-ctg57.109.raw.section            WCK01_AAF20200214_F8-ctg57.46.pred.raw.section       WCK01_AAF20200214_F8-ctg57.93.pred.raw.section
> evidence_96.gff.seq       WCK01_AAF20200214_F8-ctg57.10.pred.raw.section        WCK01_AAF20200214_F8-ctg57.46.raw.section            WCK01_AAF20200214_F8-ctg57.93.raw.section
> evidence_97.gff.ann       WCK01_AAF20200214_F8-ctg57.10.raw.section             WCK01_AAF20200214_F8-ctg57.47-48.raw.section         WCK01_AAF20200214_F8-ctg57.94-95.raw.section
> evidence_97.gff.def       WCK01_AAF20200214_F8-ctg57.110-111.raw.section        WCK01_AAF20200214_F8-ctg57.47.pred.raw.section       WCK01_AAF20200214_F8-ctg57.94.pred.raw.section
> evidence_97.gff.seq       WCK01_AAF20200214_F8-ctg57.110.pred.raw.section       WCK01_AAF20200214_F8-ctg57.47.raw.section            WCK01_AAF20200214_F8-ctg57.94.raw.section
> evidence_98.gff.ann       WCK01_AAF20200214_F8-ctg57.110.raw.section            WCK01_AAF20200214_F8-ctg57.48-49.raw.section         WCK01_AAF20200214_F8-ctg57.95-96.raw.section
> evidence_98.gff.def       WCK01_AAF20200214_F8-ctg57.111-112.raw.section        WCK01_AAF20200214_F8-ctg57.48.pred.raw.section       WCK01_AAF20200214_F8-ctg57.95.pred.raw.section
> evidence_98.gff.seq       WCK01_AAF20200214_F8-ctg57.11-12.raw.section          WCK01_AAF20200214_F8-ctg57.48.raw.section            WCK01_AAF20200214_F8-ctg57.95.raw.section
> evidence_99.gff           WCK01_AAF20200214_F8-ctg57.111.pred.raw.section       WCK01_AAF20200214_F8-ctg57.48.start.blastn.holdover  WCK01_AAF20200214_F8-ctg57.96.end.blastn.holdover
> evidence_99.gff.ann       WCK01_AAF20200214_F8-ctg57.111.raw.section            WCK01_AAF20200214_F8-ctg57.48.start.blastx.holdover  WCK01_AAF20200214_F8-ctg57.96.end.blastx.holdover
> evidence_99.gff.def       WCK01_AAF20200214_F8-ctg57.112-113.raw.section        WCK01_AAF20200214_F8-ctg57.49-50.raw.section         WCK01_AAF20200214_F8-ctg57.96.end.section.holdover
> evidence_99.gff.seq       WCK01_AAF20200214_F8-ctg57.112.pred.raw.section       WCK01_AAF20200214_F8-ctg57.49.pred.raw.section       WCK01_AAF20200214_F8-ctg57.96.pred.raw.section
> evidence_9.gff            WCK01_AAF20200214_F8-ctg57.112.raw.section            WCK01_AAF20200214_F8-ctg57.49.raw.section            WCK01_AAF20200214_F8-ctg57.96.raw.section
> query.fasta               WCK01_AAF20200214_F8-ctg57.113-114.raw.section        WCK01_AAF20200214_F8-ctg57.4.pred.raw.section        WCK01_AAF20200214_F8-ctg57.96.start.blastn.holdover
> query.masked.fasta        WCK01_AAF20200214_F8-ctg57.113.pred.raw.section       WCK01_AAF20200214_F8-ctg57.4.raw.section             WCK01_AAF20200214_F8-ctg57.96.start.blastx.holdover
> query.masked.fasta.index  WCK01_AAF20200214_F8-ctg57.113.raw.section            WCK01_AAF20200214_F8-ctg57.50-51.raw.section         WCK01_AAF20200214_F8-ctg57.97.pred.raw.section
> query.masked.gff          WCK01_AAF20200214_F8-ctg57.114-115.raw.section        WCK01_AAF20200214_F8-ctg57.50.end.blastn.holdover    WCK01_AAF20200214_F8-ctg57.98.pred.raw.section
> run.log.child.0           WCK01_AAF20200214_F8-ctg57.114.pred.raw.section       WCK01_AAF20200214_F8-ctg57.50.end.blastx.holdover    WCK01_AAF20200214_F8-ctg57.98.start.blastn.holdover
> run.log.child.1           WCK01_AAF20200214_F8-ctg57.114.raw.section            WCK01_AAF20200214_F8-ctg57.50.pred.raw.section       WCK01_AAF20200214_F8-ctg57.99-100.raw.section
> run.log.child.10          WCK01_AAF20200214_F8-ctg57.114.start.blastn.holdover  WCK01_AAF20200214_F8-ctg57.50.raw.section            WCK01_AAF20200214_F8-ctg57.99.end.blastn.holdover
> run.log.child.100         WCK01_AAF20200214_F8-ctg57.114.start.blastx.holdover  WCK01_AAF20200214_F8-ctg57.50.start.blastx.holdover  WCK01_AAF20200214_F8-ctg57.99.end.blastx.holdover
> run.log.child.101         WCK01_AAF20200214_F8-ctg57.115-116.raw.section        WCK01_AAF20200214_F8-ctg57.51-52.raw.section         WCK01_AAF20200214_F8-ctg57.99.pred.raw.section
> run.log.child.102         WCK01_AAF20200214_F8-ctg57.115.end.blastn.holdover    WCK01_AAF20200214_F8-ctg57.51.pred.raw.section       WCK01_AAF20200214_F8-ctg57.99.raw.section
> run.log.child.103         WCK01_AAF20200214_F8-ctg57.115.pred.raw.section       WCK01_AAF20200214_F8-ctg57.51.raw.section            WCK01_AAF20200214_F8-ctg57.99.start.blastx.holdover
> run.log.child.104         WCK01_AAF20200214_F8-ctg57.115.raw.section            WCK01_AAF20200214_F8-ctg57.52-53.raw.section         WCK01_AAF20200214_F8-ctg57.99.start.section.holdover
> run.log.child.105         WCK01_AAF20200214_F8-ctg57.116-117.raw.section        WCK01_AAF20200214_F8-ctg57.52.pred.raw.section       WCK01_AAF20200214_F8-ctg57.9.pred.raw.section
> run.log.child.106         WCK01_AAF20200214_F8-ctg57.116.pred.raw.section       WCK01_AAF20200214_F8-ctg57.52.raw.section            WCK01_AAF20200214_F8-ctg57.9.raw.section
> run.log.child.107         WCK01_AAF20200214_F8-ctg57.116.raw.section            WCK01_AAF20200214_F8-ctg57.53-54.raw.section         WCK01_AAF20200214_F8-ctg57.gff.ann
> run.log.child.108         WCK01_AAF20200214_F8-ctg57.117-118.raw.section        WCK01_AAF20200214_F8-ctg57.53.pred.raw.section       WCK01_AAF20200214_F8-ctg57.gff.def
> run.log.child.109         WCK01_AAF20200214_F8-ctg57.117.pred.raw.section       WCK01_AAF20200214_F8-ctg57.53.raw.section            WCK01_AAF20200214_F8-ctg57.gff.seq
> run.log.child.11          WCK01_AAF20200214_F8-ctg57.117.raw.section            WCK01_AAF20200214_F8-ctg57.54-55.raw.section
> run.log.child.110         WCK01_AAF20200214_F8-ctg57.117.start.blastn.holdover  WCK01_AAF20200214_F8-ctg57.54.pred.raw.section
> run.log.child.111         WCK01_AAF20200214_F8-ctg57.117.start.blastx.holdover  WCK01_AAF20200214_F8-ctg57.54.raw.section
> 
> I set clean_try=1 and am trying to fix this contig (it's only this one contig which is causing trouble), but I'm wondering if it's also okay to completely delete the void directory to force it to start this contig from scratch. I have already tried rerunning maker with clean_try=1 two times and now I'm getting an mpich2 error:
> 
> Fatal error in MPI_Send: Invalid count, error stack:
> MPI_Send(173): MPI_Send(buf=0x2aec3d6a3010, count=-1279995089, MPI_CHAR, dest=15, tag=9999, MPI_COMM_WORLD) failed
> MPI_Send(97).: Negative count, value is -1279995089
> 
> I am currently trying again with fewer MPI jobs requested, worrying that there might be a memory issue on the computer cluster I am using. My temporary directory still has lots of space, but I have ~200G RAM per node and sometimes the jobs use a ton of RAM. I don't have too many more contigs left of this run, so I just really don't want to mess anything up. Do you have any advice?
> 
> Thanks so much!
> Zoe
> 
> ______________________________________
> Zoe Clarke
> PhD candidate in Computational Biology at U of T
> Lab profile: http://baderlab.org/Zoe%20Clarke <http://baderlab.org/Zoe%20Clarke>
> Personal website: https://zoe-clarke.weebly.com/ <https://zoe-clarke.weebly.com/>_______________________________________________
> maker-devel mailing list
> maker-devel at yandell-lab.org <mailto:maker-devel at yandell-lab.org>
> http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org <http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org>
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From eennadi at gmail.com  Fri Oct 23 00:15:33 2020
From: eennadi at gmail.com (Emmanuel Nnadi)
Date: Fri, 23 Oct 2020 07:15:33 +0100
Subject: [maker-devel] Can maker be used to improve genome assembly?
Message-ID: <CAOXM=CXTCX5tyDeM29fTGi5u0qjOXT7TSCUeQrYt-PogCphvSg@mail.gmail.com>

Hi Carson,
Greetings! This is just a random question that came to my mind. Looking at
the way maker structures files and brings contigs together based on "gene"
locations. Can this be explored to improve genome assemblies? Maybe a tool
that can work from a good annotation to generating a set of improved genome
assembly based on these gene locations


Just a thought
Nnaemeka Emmanuel Nnadi,Ph.D
Department of Microbiology,
Faculty of Natural and Applied Science,
Plateau State University, Bokkos, Plateau State, Nigeria.
+2348068124819
Publications:
 https://www.researchgate.net/profile/Emmanuel_Nnadi/publications
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From carsonhh at gmail.com  Mon Oct 26 13:33:00 2020
From: carsonhh at gmail.com (Carson Holt)
Date: Mon, 26 Oct 2020 13:33:00 -0600
Subject: [maker-devel] Does maker support muti-processing for a single
 long fasta sequence using openMPI?
In-Reply-To: <CALJhmFocG7D-K0gdGJ5831V=gnPp0BDrEMu138W3HV=QmKs2Ug@mail.gmail.com>
References: <CALJhmFoNOdxFb4gQ4jYP=FZqaHgZdVOhQOpPuyd5bMAeYZ8ucg@mail.gmail.com>
	<AC94C4EB-A696-4830-A650-1A33EB67B281@gmail.com>
	<CALJhmFocG7D-K0gdGJ5831V=gnPp0BDrEMu138W3HV=QmKs2Ug@mail.gmail.com>
Message-ID: <926FDE45-F317-43CD-BF2E-A0B00FDBD9A7@gmail.com>

Your MPI processes may not be seeing each other.  So you are getting multiple maker runs all colliding.  You need to reinstall MAKER and say ?yes? to the compile for MPI question.  You may also have to reinstall OpenMPI if just reinstalling MAKER does not work.  You can test MAKER for MPI by running the following ?> mpiexec -mca btl ^openib -n 40 maker -help

If you get a single help message then everything is fine.  If you get 40 help messages, then MPI is not communicating correctly.

?Carson


> On Oct 20, 2020, at 10:23 AM, Xu, taosheng <taosheng.x at gmail.com> wrote:
> 
> Thank you very much Carson for your timely response,
> Yes I think so. The Maker MPI should support the multi-processing of an ultra-long single sequence. But I cannot run it successfully for a single sequence.
> First I  make sure the openMPI with maker has been installed properly. It works well for multiple DNA sequences in a parallel way.
> When I submit a maker job for an ultra-long single sequence (mpiexec -mca btl ^openib -n 40 maker -g scaffold1.fasta -fix_nucleotides, The max_dna_len is set to 100000). It always left only one maker thread run. The other maker threads are disappeared and show finished in the output information. See the output information below. Please help me to check it. Thanks for your kind help and your time.
> 
> #-----MAKER Behavior Options
> max_dna_len=100000 #length for dividing up contigs into chunks (increases/decreases memory usage)
> min_contig=1 #skip genome contigs below this length (under 10kb are often useless)
> 
> Best regards,
> Taosheng
> 
> 
> 
> OUTPUT Information
> STATUS: Processing and indexing input FASTA files...
> STATUS: Setting up database for any GFF3 input...
> examining contents of the fasta file and run log
> A data structure will be created for you at:
> /data/splitgenome/top1000/splitGenome/part1/plant.maker.output/plant_datastore
> 
> To access files for individual sequences use the datastore index:
> /data/splitgenome/top1000/splitGenome/part1/plant.maker.output/plant_master_datastore_index.log
> 
> STATUS: Now running MAKER...
> 
> 
> 
> --Next Contig--
> 
> Processing run.log file...
> examining contents of the fasta file and run log
> 
> 
> 
> --Next Contig--
> 
> #---------------------------------------------------------------------
> Another instance of maker is processing this contig!!
> SeqID: scaffold#1
> Length: 73580997
> #---------------------------------------------------------------------
> 
> 
> examining contents of the fasta file and run log
> 
> 
> 
> --Next Contig--
> 
> #---------------------------------------------------------------------
> Another instance of maker is processing this contig!!
> SeqID: scaffold#1
> Length: 73580997
> #---------------------------------------------------------------------
> 
> 
> 
> 
> Maker is now finished!!!
> 
> 
> 
> Start_time: 1603000030
> End_time:   1603000033
> Elapsed:    3
> A data structure will be created for you at:
> /data/splitgenome/top1000/splitGenome/part1/plant.maker.output/plant_datastore
> 
> To access files for individual sequences use the datastore index:
> /data/splitgenome/top1000/splitGenome/part1/plant.maker.output/plant_master_datastore_index.log
> 
> STATUS: Now running MAKER...
> MAKER WARNING: The file plant.maker.output/plant_datastore/B5/CD/scaffold#1//theVoid.scaffold#1/28/scaffold#1.289.plant_repeatFinal%2Elib%2Empi%2E10%2E2.specific.out
> did not finish on the last run and must be erased
> WARNING: Multiple MAKER processes have been started in the
> same directory.
> 
> STATUS: Processing and indexing input FASTA files...
> examining contents of the fasta file and run log
> 
> 
> 
> --Next Contig--
> 
> #---------------------------------------------------------------------
> Another instance of maker is processing this contig!!
> SeqID: scaffold#1
> Length: 73580997
> #---------------------------------------------------------------------
> 
> 
> WARNING: Multiple MAKER processes have been started in the
> same directory.
> 
> STATUS: Processing and indexing input FASTA files...
> STATUS: Setting up database for any GFF3 input...
> STATUS: Setting up database for any GFF3 input...
> A data structure will be created for you at:
> /data/splitgenome/top1000/splitGenome/part1/plant.maker.output/plant_datastore
> 
> To access files for individual sequences use the datastore index:
> /data/splitgenome/top1000/splitGenome/part1/plant.maker.output/plant_master_datastore_index.log
> 
> STATUS: Now running MAKER...
> examining contents of the fasta file and run log
> 
> 
> 
> --Next Contig--
> 
> #---------------------------------------------------------------------
> Another instance of maker is processing this contig!!
> SeqID: scaffold#1
> Length: 73580997
> #---------------------------------------------------------------------
> 
> 
> 
> 
> Maker is now finished!!!
> 
> 
> 
> Start_time: 1603000030
> End_time:   1603000034
> Elapsed:    4
> #---------------------------------------------------------------------
> Now starting the contig!!
> SeqID: scaffold#1
> Length: 73580997
> #---------------------------------------------------------------------
> 
> 
> examining contents of the fasta file and run log
> 
> 
> 
> --Next Contig--
> 
> #---------------------------------------------------------------------
> Another instance of maker is processing this contig!!
> SeqID: scaffold#1
> Length: 73580997
> #---------------------------------------------------------------------
> 
> 
> examining contents of the fasta file and run log
> 
> 
> 
> --Next Contig--
> 
> #---------------------------------------------------------------------
> Another instance of maker is processing this contig!!
> SeqID: scaffold#1
> Length: 73580997
> #---------------------------------------------------------------------
> 
> 
> 
> 
> Start_time: 1603000030
> End_time:   1603000034
> Elapsed:    4
> 
> 
> Maker is now finished!!!
> 
> A data structure will be created for you at:
> /data/splitgenome/top1000/splitGenome/part1/plant.maker.output/plant_datastore
> 
> To access files for individual sequences use the datastore index:
> /data/splitgenome/top1000/splitGenome/part1/plant.maker.output/plant_master_datastore_index.log
> 
> STATUS: Now running MAKER...
> examining contents of the fasta file and run log
> ..........
> 
> Maker is now finished!!!
> 
> 
> 
> Start_time: 1602920407
> End_time:   1602920580
> Elapsed:    173
> running  repeat masker.
> #--------- command -------------#
> Widget::RepeatMasker:
> cd /tmp/maker_VflRYH; ./maker3.01/exe/RepeatMasker/RepeatMasker /data/splitgenome/top1000/splitGenome/part1/plant.maker.output/plant_datastore/B5/CD/scaffold#1//theVoid.scaffold#1/0/scaffold#1.0.plant_repeatFinal%2Elib%2Empi%2E10%2E0.specific -dir /data/splitgenome/top1000/splitGenome/part1/plant.maker.output/plant_datastore/B5/CD/scaffold#1//theVoid.scaffold#1/0 -pa 1 -lib /data/splitgenome/top1000/splitGenome/part1/plant.maker.output/mpi_blastdb/plant_repeatFinal%2Elib.mpi.10/plant_repeatFinal%2Elib.mpi.10.0
> #-------------------------------#
> running  repeat masker.
> #--------- command -------------#
> Widget::RepeatMasker:
> cd /tmp/maker_VflRYH; ./maker3.01/exe/RepeatMasker/RepeatMasker /data/splitgenome/top1000/splitGenome/part1/plant.maker.output/plant_datastore/B5/CD/scaffold#1//theVoid.scaffold#1/0/scaffold#1.0.plant_repeatFinal%2Elib%2Empi%2E10%2E1.specific -dir /data/splitgenome/top1000/splitGenome/part1/plant.maker.output/plant_datastore/B5/CD/scaffold#1//theVoid.scaffold#1/0 -pa 1 -lib /data/splitgenome/top1000/splitGenome/part1/plant.maker.output/mpi_blastdb/plant_repeatFinal%2Elib.mpi.10/plant_repeatFinal%2Elib.mpi.10.1
> #-------------------------------#
> running  repeat masker.
> #--------- command -------------#
> Widget::RepeatMasker:
> cd /tmp/maker_VflRYH; ./maker3.01/exe/RepeatMasker/RepeatMasker /data/splitgenome/top1000/splitGenome/part1/plant.maker.output/plant_datastore/B5/CD/scaffold#1//theVoid.scaffold#1/0/scaffold#1.0.plant_repeatFinal%2Elib%2Empi%2E10%2E2.specific -dir /data/splitgenome/top1000/splitGenome/part1/plant.maker.output/plant_datastore/B5/CD/scaffold#1//theVoid.scaffold#1/0 -pa 1 -lib /data/splitgenome/top1000/splitGenome/part1/plant.maker.output/mpi_blastdb/plant_repeatFinal%2Elib.mpi.10/plant_repeatFinal%2Elib.mpi.10.2
> #-------------------------------#
> running  repeat masker.
> #--------- command -------------#
> Widget::RepeatMasker:
> cd /tmp/maker_VflRYH; ./maker3.01/exe/RepeatMasker/RepeatMasker /data/splitgenome/top1000/splitGenome/part1/plant.maker.output/plant_datastore/B5/CD/scaffold#1//theVoid.scaffold#1/0/scaffold#1.0.plant_repeatFinal%2Elib%2Empi%2E10%2E3.specific -dir /data/splitgenome/top1000/splitGenome/part1/plant.maker.output/plant_datastore/B5/CD/scaffold#1//theVoid.scaffold#1/0 -pa 1 -lib /data/splitgenome/top1000/splitGenome/part1/plant.maker.output/mpi_blastdb/plant_repeatFinal%2Elib.mpi.10/plant_repeatFinal%2Elib.mpi.10.3
> #-------------------------------#
> running  repeat masker.
> #--------- command -------------#
> 
> .....
> 
> On Mon, Oct 19, 2020 at 10:32 PM Carson Holt <carsonhh at gmail.com <mailto:carsonhh at gmail.com>> wrote:
> Yes. It will divide contigs into chunks the same size as the max_dna_len parameter.
> 
> ?Carson
> 
> Sent from my iPhone
> 
> > On Oct 17, 2020, at 12:48 AM, Xu, taosheng <taosheng.x at gmail.com <mailto:taosheng.x at gmail.com>> wrote:
> > 
> > ?
> > Dear Maker Development Team,
> > I wonder whether maker supports parallel processing for a single long genome sequence?
> > 
> > When I submit my maker task using openMPI with multiple cpus (like, mpiexec -n 40  maker) to annotate a single long genome sequence, always only one maker with 4 rmblast run. The other cpus is on idle.
> > 
> > I want to use the maker parallel processing with openMPI to speed up a single ultra-long genome sequence annotation.
> > 
> > Best regards,
> > Taosheng
> > _______________________________________________
> > maker-devel mailing list
> > maker-devel at yandell-lab.org <mailto:maker-devel at yandell-lab.org>
> > http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org <http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org>

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From carsonhh at gmail.com  Mon Oct 26 13:49:33 2020
From: carsonhh at gmail.com (Carson Holt)
Date: Mon, 26 Oct 2020 13:49:33 -0600
Subject: [maker-devel] Can maker be used to improve genome assembly?
In-Reply-To: <CAOXM=CXTCX5tyDeM29fTGi5u0qjOXT7TSCUeQrYt-PogCphvSg@mail.gmail.com>
References: <CAOXM=CXTCX5tyDeM29fTGi5u0qjOXT7TSCUeQrYt-PogCphvSg@mail.gmail.com>
Message-ID: <B7F4EEA8-9F57-4CF3-9EFA-7D9F9B763537@gmail.com>

We haven?t explored this.  On re-assembly projects I rarely find more than a handful of instances where a gene was obviously split across contigs in the first assembly's annotation.  More often what I find is that extra contigs tend to contain fragments of a gene that is complete on another contig in the same assembly (caused by high heterozygosity, so maternal and paternal contigs can assemble independently).

?Carson


> On Oct 23, 2020, at 12:15 AM, Emmanuel Nnadi <eennadi at gmail.com> wrote:
> 
> Hi Carson,
> Greetings! This is just a random question that came to my mind. Looking at the way maker structures files and brings contigs together based on "gene" locations. Can this be explored to improve genome assemblies? Maybe a tool that can work from a good annotation to generating a set of improved genome assembly based on these gene locations
> 
> 
> Just a thought
> Nnaemeka Emmanuel Nnadi,Ph.D
> Department of Microbiology,
> Faculty of Natural and Applied Science,
> Plateau State University, Bokkos, Plateau State, Nigeria.
> +2348068124819
> Publications: 
>  https://www.researchgate.net/profile/Emmanuel_Nnadi/publications <https://www.researchgate.net/profile/Emmanuel_Nnadi/publications>
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From daren.card at gmail.com  Thu Oct 29 10:35:57 2020
From: daren.card at gmail.com (Daren Card)
Date: Thu, 29 Oct 2020 12:35:57 -0400
Subject: [maker-devel] tblastx of alt-ESTs failing on single scaffold
Message-ID: <CACNE1p+-JynX7_vdakS0ibS3Hf-9M5K_8AxKEOmUgWzc7ScOtg@mail.gmail.com>

Hello,

I am having an issue running MAKER and am hoping to get some
troubleshooting guidance. I am running MAKER v. 2.31.10 on a Unix cluster
using a Singularity image with BLAST v. 2.9.0+ and Exonerate v. 3.3.2. I am
running MAKER with the following command options: "-fix_nucleotides
-nodatastore -RM_off". I am providing assembled transcripts from the target
species (est) and a close relative (alt-est) and proteins from several
species within the same general clade (Squamata). Gene models are being
derived from Augustus with est2genome and protein2genome turned off. I have
largely successfully run MAKER on a couple of genomes from the same
vertebrate genus, but have this lingering problem with a single scaffold
from one of the genomes. If it were pretty short, I'd just ignore it, but
it is 2 Mb, so I do not want to miss out on annotating it.

When I ran MAKER on the entire genome, it finished properly except for this
problematic scaffold. So I separated that scaffold out and tried running it
alone with otherwise the same settings. Each time, it appears I get the
same error during the 1st try when MAKER runs.

ERROR: TBLASTX does not appear to be finished in Widget::tblastx::keepers
--> rank=23, hostname=holy7c18405.rc.fas.harvard.edu
--> rank=23, hostname=holy7c18405.rc.fas.harvard.edu
--> rank=23, hostname=holy7c18405.rc.fas.harvard.edu
--> rank=23, hostname=holy7c18405.rc.fas.harvard.edu
ERROR: Failed while doing tblastx of alt-ESTs
ERROR: Chunk failed at level:4, tier_type:3
FAILED CONTIG:scaffold_77

ERROR: Chunk failed at level:4, tier_type:0
FAILED CONTIG:scaffold_77

Then MAKER keeps retrying and apparently hitting the same problem. I
checked the logs the best I can and see the following issue within
run.log.child.0 for that scaffold.

STARTED lerBou1_maker_rnd2.maker.output/lerBou1_maker_rnd2_datastore/scaffold_77/theVoid.scaffold_77/0/scaffold_77.0.lerEdw1_Trinity_combined_denovo_refguided%2Ecdhit%2Efasta.tblastx
DIED    RANK    17:4:0:0
DIED    COUNT   7

This output file noted there is not present to check, which must stem from
whatever issue there is.

I'm not sure what to do next about this issue and see no obvious
information about what the problem is besides failure of tblastx to run.
Any help that anyone can provide is greatly appreciated.

Kind regards,
Daren Card

NSF Postdoctoral Fellow
Harvard University
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From eennadi at gmail.com  Tue Oct 27 21:01:05 2020
From: eennadi at gmail.com (Emmanuel Nnadi)
Date: Wed, 28 Oct 2020 04:01:05 +0100
Subject: [maker-devel] Maker yields sequences without start and stop codon
Message-ID: <CAOXM=CU=3Y3SgOiAyDiR3Qa56KegaZE-rwEBESNKYO4cBos5uw@mail.gmail.com>

Hi Carson
I always set always_complete=1 yet I still get sequences without start and
stop codon.

Can
https://github.com/Gaius-Augustus/Augustus/blob/master/scripts/fix_in_frame_stop_codon_genes.py
be
used on the final sequence to fix start and stop codon problem?


Nnaemeka Emmanuel Nnadi,Ph.D
Department of Microbiology,
Faculty of Natural and Applied Science,
Plateau State University, Bokkos, Plateau State, Nigeria.
+2348068124819
Publications:
 https://www.researchgate.net/profile/Emmanuel_Nnadi/publications
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From liorglic at mail.tau.ac.il  Fri Oct  2 02:54:55 2020
From: liorglic at mail.tau.ac.il (Lior Glick)
Date: Fri, 2 Oct 2020 11:54:55 +0300
Subject: [maker-devel] MAKER failing during Augustus run
Message-ID: <CAOzMDPxivd1gxOJRuaQd6vDLMizt39qRNsAajzvO+Hhy1K--6A@mail.gmail.com>

Hello,
I am using MAKER2 with Augustus 3.2.2. I keep getting an error message when
annotating a specific contig. The relevant section of the MAKER stderr
looks like this:

Widget::augustus:
/powerapps/share/centos7/miniconda/miniconda2-4.5.4-MakerMPI/bin/augustus
--species=arabidopsis --strand=backward --UTR=off
--hintsfile=/home/tmp_liorglic/maker_zfUstg/0/265_0.10292360-10294752.arabidopsis.auto_annotator.xdef.augustus
--extrinsicCfgFile=/powerapps/share/centos7/miniconda/miniconda2-4.5.4-MakerMPI/config/extrinsic/extrinsic.MPE.cfg
/home/tmp_liorglic/maker_zfUstg/0/265_0.10292360-10294752.arabidopsis.auto_annotator.augustus.fasta
>
/home/tmp_liorglic/maker_zfUstg/0/265_0.10292360-10294752.arabidopsis.auto_annotator.augustus
#-------------------------------#
Sampling error in intron model. state=37 base=2391

/powerapps/share/centos7/miniconda/miniconda2-4.5.4-MakerMPI/bin/augustus:
ERROR
        Tried to sample from empty list.

Sampling error in intron model. state=37 base=2391

/powerapps/share/centos7/miniconda/miniconda2-4.5.4-MakerMPI/bin/augustus:
ERROR
        Tried to sample from empty list.

ERROR: Augustus failed
--> rank=NA, hostname=compute-0-301.power5
ERROR: Failed while annotating transcripts
ERROR: Chunk failed at level:1, tier_type:4
FAILED CONTIG:chunk08

ERROR: Chunk failed at level:6, tier_type:0
FAILED CONTIG:chunk08

examining contents of the fasta file and run log



--Next Contig--

Processing run.log file...
MAKER WARNING: The file
chunk.maker.output/chunk_datastore/76/17/chunk08//theVoid.chunk08/265_0.10292360-10294752.arabidopsis.auto_annotator.augustus
did not finish on the last run and must be erased


Maker is now finished!!!

I found this thread
<https://groups.google.com/g/maker-devel/c/WBD_GEvELDE> with
a similar error but slightly different augustus command. The suggestion
there was to isolate the augustus command. This sounds like good advice,
but most of the inputs to the command are stored in a temporary location
and are deleted at the end of the MAKER run. Is there any way to restore
them?
Alternatively, are there any known solutions/explanations to this error?
All I could find was this thread
<https://bioinf.uni-greifswald.de/bioinf/forum/viewtopic.php?f=4&t=150> from
the Augustus forum, but it doesn't seem to provide much help.
Would appreciate any ideas/workarounds.
Thanks!
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From carsonhh at gmail.com  Fri Oct  2 14:25:22 2020
From: carsonhh at gmail.com (Carson Holt)
Date: Fri, 2 Oct 2020 14:25:22 -0600
Subject: [maker-devel] Maker yields sequences without start and stop
 codon
In-Reply-To: <CAOXM=CUaZ3+6-YHVzm7Lc+h3fgEtX9ikD8z43Ez9Laj9jGT2DQ@mail.gmail.com>
References: <CAOXM=CUaZ3+6-YHVzm7Lc+h3fgEtX9ikD8z43Ez9Laj9jGT2DQ@mail.gmail.com>
Message-ID: <D281818D-F30A-447D-987F-F5A0434AF7A6@gmail.com>

You can set always_complete=1 for MAKER tottery and fix partial models (it walks out on both sides looking for canonical stops/starts).  Also to clean up partial models and other submission issues, try using Comparative Annotation Toolkit (CAT).  It will take MAEKR results and do all the NCBI related corrections automatically.  It makes submission so much easier.

?Carson



> On Sep 1, 2020, at 12:31 PM, Emmanuel Nnadi <eennadi at gmail.com> wrote:
> 
> I ran my annotation using ESTs from NCBI and transcriptome data and Swiss-prot data. I used SNAP trained twice after which Augustus was trained once.
> 
> I tried to submit the annotated genome to NCBI but have some problems I have not experienced before and do not know how to solve.
> 
> Some of the CDS features have invalid translations. Every CDS feature should have a valid start and stop codon, and should not have any internal stops.  The only exception is if the CDS is partial at the end of a sequence or at an intron/exon boundary.  If the CDS is partial, it must have the appropriate partial symbols.  
> 
> If a CDS feature does not have a valid translation (for example if there is a frameshift), please remove the CDS feature and annotate this with a single gene feature across the entire span.  Include a note on the gene with a brief description.  For example:
> 
> 1       200     gene
>                         gene    phoA
>                         gene_desc       alkaline phosphatase
>                         locus_tag     OBB_0001
>                         note    nonfunctional due to frameshift
> 
> [3] There are 1075 gene features that are not associated with
> any other features (CDS, rRNA, etc.) and are not labelled as
> pseudogenes or as nonfunctional genes.  Did you lose some of
> the annotation you intended to include.
> 
> Please how can this be solved?
> 
> Thanks
> 
> 
> Nnadi Nnaemeka Emmanuel,Ph.D
> Department of Microbiology,
> Faculty of Natural and Applied Science,
> Plateau State University, Bokkos, Plateau State, Nigeria.
> +2348068124819
> Publications: 
>  https://www.researchgate.net/profile/Emmanuel_Nnadi/publications <https://www.researchgate.net/profile/Emmanuel_Nnadi/publications>
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From carsonhh at gmail.com  Fri Oct  2 14:38:39 2020
From: carsonhh at gmail.com (Carson Holt)
Date: Fri, 2 Oct 2020 14:38:39 -0600
Subject: [maker-devel] maker-devel post from guerrer@uni-duesseldorf.de
 requires approval
In-Reply-To: <mailman.370.1600180681.587812.maker-devel_yandell-lab.org@yandell-lab.org>
References: <mailman.370.1600180681.587812.maker-devel_yandell-lab.org@yandell-lab.org>
Message-ID: <483B474B-052F-4148-8FAB-EB2F381BA0DF@gmail.com>

Try looking at it in a browser.  You may see that models are merging because of evidence overlap, snap or augustus does not match the evidence well (you can drop one if it performs poorly).  But visualizing things will help.  For example fungi can lose genes because of UTR overlap (there is an allow_overlap option in MAKER for that).  mRNA-seq can falsely merge into extended transcripts (results in long UTR on models and maker has correct_est_fusion for that).  Neigboring parlors can cluster into a single model (you will see same hit coordinates multiple,e times in the browser - there is a tool called DeFusion for that).  Or evidence may be sparse (should be obvious from a browser).  Assembly errors can be found when you have nice transcripts alignments that do not have working ORFs (found by dragging and dropping est2genome results in browsers like Apollo and letting it calculate ORF).


?Carson


> 
> Hello,
> 
> It appears to me that my abInitio SNAP + Augustus (trained by nexflow) results are worse than the first (est2genome and prot2genome) run. The gene number decreases by more than 6000, the opposite of what I expected.
> 
> Additionally, my abInitio rerun also has less genes than a previous SNAP reannotation.. The AED plots all look more or less the same but the number of genes lowers instead of increasing as I expected (image in annex).
> 
> I'be been running my maker+nextflow pipeline with consistently good results, this species is the exception now.
> 
> Do you have any suggestion? Should I ditch AbInitio training and use the Evidence based annotation? Or maybe just use the closest Augustus model instead of training my own?
> 
> Kind regards,
> Ricardo
> 
> 
> 
> <AEDs.png>
> 



From carsonhh at gmail.com  Fri Oct  2 14:50:35 2020
From: carsonhh at gmail.com (Carson Holt)
Date: Fri, 2 Oct 2020 14:50:35 -0600
Subject: [maker-devel] map_forward and temporary storage questions
In-Reply-To: <YTBPR01MB3839BACB6F6296B734775AA09C360@YTBPR01MB3839.CANPRD01.PROD.OUTLOOK.COM>
References: <YTBPR01MB3839BACB6F6296B734775AA09C360@YTBPR01MB3839.CANPRD01.PROD.OUTLOOK.COM>
Message-ID: <7742D4BF-2BEB-426D-9858-EC2621B5077D@gmail.com>

MAKER uses GFF3 format which is not the same as GTF.  You will need to convert your file to GFF3 format.

You can try this online tool (I haven?t used it to tell you how well it works) http://www.sequenceontology.org/cgi-bin/converter.cgi <http://www.sequenceontology.org/cgi-bin/converter.cgi> 

There are also a number of other resources available when you google "how to convert GTF to GFF3?.

?Carson


> On Sep 25, 2020, at 3:17 AM, Zoe Clarke <zoe.clarke at utoronto.ca> wrote:
> 
> Hello!
> 
> I am currently running Maker on a 2.5GB genome that has already had a list of ~8000 genes very thoroughly annotated. My hope is to find and annotate the rest of the genes using ESTs and protein homology. However, I tested Maker on a single contig of my genome (there are ~20,000 contigs) and I can't find any of the genes from my original gtf file even though I followed all of the instructions in this wiki: http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/Updating_annotations_in_light_of_new_data <http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/Updating_annotations_in_light_of_new_data> (I entered the original gff under model_gff, and used map_forward=1). I am worried this is because my gff3 file isn't formatted properly. Here are a few lines in my gff file as an example:
> --------------------------------------------
> WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  transcript      1094446 1105585 .       +       .       ID=DIMT1.1;geneID=DIMT1
> WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  exon    1094446 1094521 97.75   +       .       Parent=DIMT1.1
> WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  exon    1094874 1094947 97.75   +       .       Parent=DIMT1.1
> WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  exon    1095459 1095545 97.75   +       .       Parent=DIMT1.1
> WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  exon    1097351 1097412 97.75   +       .       Parent=DIMT1.1
> WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  exon    1097492 1097585 97.75   +       .       Parent=DIMT1.1
> WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  exon    1097670 1097719 97.75   +       .       Parent=DIMT1.1
> WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  exon    1098957 1099080 97.75   +       .       Parent=DIMT1.1
> WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  exon    1099217 1099309 97.75   +       .       Parent=DIMT1.1
> WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  exon    1100870 1100934 97.75   +       .       Parent=DIMT1.1
> WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  exon    1101967 1102030 97.75   +       .       Parent=DIMT1.1
> WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  exon    1103784 1103890 97.75   +       .       Parent=DIMT1.1
> WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  exon    1105543 1105585 97.75   +       .       Parent=DIMT1.1
> WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  CDS     1094446 1094521 .       +       0       Parent=DIMT1.1
> WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  CDS     1094874 1094947 .       +       2       Parent=DIMT1.1
> WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  CDS     1095459 1095545 .       +       0       Parent=DIMT1.1
> WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  CDS     1097351 1097412 .       +       0       Parent=DIMT1.1
> WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  CDS     1097492 1097585 .       +       1       Parent=DIMT1.1
> WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  CDS     1097670 1097719 .       +       0       Parent=DIMT1.1
> WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  CDS     1098957 1099080 .       +       1       Parent=DIMT1.1
> WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  CDS     1099217 1099309 .       +       0       Parent=DIMT1.1
> WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  CDS     1100870 1100934 .       +       0       Parent=DIMT1.1
> WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  CDS     1101967 1102030 .       +       1       Parent=DIMT1.1
> WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  CDS     1103784 1103890 .       +       0       Parent=DIMT1.1
> WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  CDS     1105543 1105582 .       +       1       Parent=DIMT1.1
> --------------------------------------
> ?This is from the contig I used as a test for maker, and I can't find DIMT1.1 in the final gff file. At first I thought it might be because "geneID" is a listed attribute, but changing this to "Name" didn't help. Do you have any ideas why these genes might not be mapping forward? If it's something I can fix in the gff file, I am hoping I can fix it and use it for the second round of Maker after I have trained Snap.
> 
> Also, do you think a better quality annotation would results from Snap trained from this curated list of ~8000 genes (that has been expertly done) or by the round 1 output of Maker?
> 
> A final question: I am having memory storage issues with Maker, as it is currently taking up ~15TB of storage with temporary files. I am running Maker on a cluster and whenever my submitted Maker job runs out of memory it fails, so I have to resubmit it about every hour, which leaves a lot of temporary folders (e.g. maker_x6V2y4) in my directory. I notice that some of these temporary files haven't been updated in days - is it okay to delete them?
> 
> Thank you so much for your help!
> Zoe
> ______________________________________
> Zoe Clarke
> PhD candidate in Computational Biology at U of T
> Lab profile: http://baderlab.org/Zoe%20Clarke <http://baderlab.org/Zoe%20Clarke>
> Personal website: https://zoe-clarke.weebly.com/ <https://zoe-clarke.weebly.com/>_______________________________________________
> maker-devel mailing list
> maker-devel at yandell-lab.org <mailto:maker-devel at yandell-lab.org>
> http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org <http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org>
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From carsonhh at gmail.com  Fri Oct  2 15:01:24 2020
From: carsonhh at gmail.com (Carson Holt)
Date: Fri, 2 Oct 2020 15:01:24 -0600
Subject: [maker-devel] MAKER failing during Augustus run
In-Reply-To: <CAOzMDPxivd1gxOJRuaQd6vDLMizt39qRNsAajzvO+Hhy1K--6A@mail.gmail.com>
References: <CAOzMDPxivd1gxOJRuaQd6vDLMizt39qRNsAajzvO+Hhy1K--6A@mail.gmail.com>
Message-ID: <8DAF41A6-5983-482C-ABA1-4F5EDC7388FA@gmail.com>

First try using Augustu v3.3.3 or the live version from GitHub (https://github.com/Gaius-Augustus/Augustus <https://github.com/Gaius-Augustus/Augustus>). You can specify the other augustus version in maker_exe.ctl.  You can use ctl+z to pause the run right when MAKER reaches the specified augustus call.  Or after trying the newer agusuts version, you can upload everything from the run to https://github.com/Gaius-Augustus/Augustus <https://github.com/Gaius-Augustus/Augustus> and I can try to extract the files for you.

Or if you are adventurous you can run in the perl debugger.

#start debugger
perl -dS maker

#continue to augustus calls
DB<1> c Widget::augustus::run

#continue to augustus failure (right before dieing)
DB<2> c 282

At this point just copy the command as files still exist

?Carson


> On Oct 2, 2020, at 2:54 AM, Lior Glick <liorglic at mail.tau.ac.il> wrote:
> 
> Hello,
> I am using MAKER2 with Augustus 3.2.2. I keep getting an error message when annotating a specific contig. The relevant section of the MAKER stderr looks like this:
> 
> Widget::augustus:
> /powerapps/share/centos7/miniconda/miniconda2-4.5.4-MakerMPI/bin/augustus --species=arabidopsis --strand=backward --UTR=off --hintsfile=/home/tmp_liorglic/maker_zfUstg/0/265_0.10292360-10294752.arabidopsis.auto_annotator.xdef.augustus --extrinsicCfgFile=/powerapps/share/centos7/miniconda/miniconda2-4.5.4-MakerMPI/config/extrinsic/extrinsic.MPE.cfg /home/tmp_liorglic/maker_zfUstg/0/265_0.10292360-10294752.arabidopsis.auto_annotator.augustus.fasta > /home/tmp_liorglic/maker_zfUstg/0/265_0.10292360-10294752.arabidopsis.auto_annotator.augustus
> #-------------------------------#
> Sampling error in intron model. state=37 base=2391
> 
> /powerapps/share/centos7/miniconda/miniconda2-4.5.4-MakerMPI/bin/augustus: ERROR
>         Tried to sample from empty list.
> 
> Sampling error in intron model. state=37 base=2391
> 
> /powerapps/share/centos7/miniconda/miniconda2-4.5.4-MakerMPI/bin/augustus: ERROR
>         Tried to sample from empty list.
> 
> ERROR: Augustus failed
> --> rank=NA, hostname=compute-0-301.power5
> ERROR: Failed while annotating transcripts
> ERROR: Chunk failed at level:1, tier_type:4
> FAILED CONTIG:chunk08
> 
> ERROR: Chunk failed at level:6, tier_type:0
> FAILED CONTIG:chunk08
> 
> examining contents of the fasta file and run log
> 
> 
> 
> --Next Contig--
> 
> Processing run.log file...
> MAKER WARNING: The file chunk.maker.output/chunk_datastore/76/17/chunk08//theVoid.chunk08/265_0.10292360-10294752.arabidopsis.auto_annotator.augustus
> did not finish on the last run and must be erased
> 
> 
> Maker is now finished!!!
> 
> I found this thread <https://groups.google.com/g/maker-devel/c/WBD_GEvELDE> with a similar error but slightly different augustus command. The suggestion there was to isolate the augustus command. This sounds like good advice, but most of the inputs to the command are stored in a temporary location and are deleted at the end of the MAKER run. Is there any way to restore them?
> Alternatively, are there any known solutions/explanations to this error? All I could find was this thread <https://bioinf.uni-greifswald.de/bioinf/forum/viewtopic.php?f=4&t=150> from the Augustus forum, but it doesn't seem to provide much help.
> Would appreciate any ideas/workarounds.
> Thanks!
> 
> _______________________________________________
> maker-devel mailing list
> maker-devel at yandell-lab.org
> http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org

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From zoe.clarke at utoronto.ca  Mon Oct  5 07:47:19 2020
From: zoe.clarke at utoronto.ca (Zoe Clarke)
Date: Mon, 5 Oct 2020 13:47:19 +0000
Subject: [maker-devel] map_forward and temporary storage questions
In-Reply-To: <7742D4BF-2BEB-426D-9858-EC2621B5077D@gmail.com>
References: <YTBPR01MB3839BACB6F6296B734775AA09C360@YTBPR01MB3839.CANPRD01.PROD.OUTLOOK.COM>,
	<7742D4BF-2BEB-426D-9858-EC2621B5077D@gmail.com>
Message-ID: <YTBPR01MB3839AFB99FE4758AAA9BBFAA9C0C0@YTBPR01MB3839.CANPRD01.PROD.OUTLOOK.COM>

Thanks Carson!

I managed to get the GFF3 file fixed and Maker is now recognizing it the way it should.

I am hoping I can also ask for your advice on functional annotation with Maker. The result of my current run will be gff and fasta files that have the original gff3 genes plus Maker's. The original gff3 file was annotated with HGNC gene symbols, so these new files are a mix of gene symbols and Maker-derived gene names. I would ideally like my final annotation to consist almost entirely of gene symbols. Is the only way to do this (after using Blastp and InterProScan to get putative homology) to undergo an additional manual curation process through something like Apollo?

Thanks again,
Zoe

______________________________________
Zoe Clarke
PhD candidate in Computational Biology at U of T
Lab profile: http://baderlab.org/Zoe%20Clarke
Personal website: https://zoe-clarke.weebly.com/
________________________________
From: Carson Holt <carsonhh at gmail.com>
Sent: October 2, 2020 4:50 PM
To: Zoe Clarke <zoe.clarke at utoronto.ca>
Cc: maker-devel at yandell-lab.org <maker-devel at yandell-lab.org>
Subject: Re: [maker-devel] map_forward and temporary storage questions

EXTERNAL EMAIL:  Treat content with extra caution.
MAKER uses GFF3 format which is not the same as GTF.  You will need to convert your file to GFF3 format.

You can try this online tool (I haven?t used it to tell you how well it works) http://www.sequenceontology.org/cgi-bin/converter.cgi

There are also a number of other resources available when you google "how to convert GTF to GFF3?.

?Carson


On Sep 25, 2020, at 3:17 AM, Zoe Clarke <zoe.clarke at utoronto.ca<mailto:zoe.clarke at utoronto.ca>> wrote:

Hello!

I am currently running Maker on a 2.5GB genome that has already had a list of ~8000 genes very thoroughly annotated. My hope is to find and annotate the rest of the genes using ESTs and protein homology. However, I tested Maker on a single contig of my genome (there are ~20,000 contigs) and I can't find any of the genes from my original gtf file even though I followed all of the instructions in this wiki: http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/Updating_annotations_in_light_of_new_data (I entered the original gff under model_gff, and used map_forward=1). I am worried this is because my gff3 file isn't formatted properly. Here are a few lines in my gff file as an example:
--------------------------------------------
WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  transcript      1094446 1105585 .       +       .       ID=DIMT1.1;geneID=DIMT1
WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  exon    1094446 1094521 97.75   +       .       Parent=DIMT1.1
WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  exon    1094874 1094947 97.75   +       .       Parent=DIMT1.1
WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  exon    1095459 1095545 97.75   +       .       Parent=DIMT1.1
WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  exon    1097351 1097412 97.75   +       .       Parent=DIMT1.1
WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  exon    1097492 1097585 97.75   +       .       Parent=DIMT1.1
WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  exon    1097670 1097719 97.75   +       .       Parent=DIMT1.1
WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  exon    1098957 1099080 97.75   +       .       Parent=DIMT1.1
WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  exon    1099217 1099309 97.75   +       .       Parent=DIMT1.1
WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  exon    1100870 1100934 97.75   +       .       Parent=DIMT1.1
WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  exon    1101967 1102030 97.75   +       .       Parent=DIMT1.1
WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  exon    1103784 1103890 97.75   +       .       Parent=DIMT1.1
WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  exon    1105543 1105585 97.75   +       .       Parent=DIMT1.1
WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  CDS     1094446 1094521 .       +       0       Parent=DIMT1.1
WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  CDS     1094874 1094947 .       +       2       Parent=DIMT1.1
WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  CDS     1095459 1095545 .       +       0       Parent=DIMT1.1
WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  CDS     1097351 1097412 .       +       0       Parent=DIMT1.1
WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  CDS     1097492 1097585 .       +       1       Parent=DIMT1.1
WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  CDS     1097670 1097719 .       +       0       Parent=DIMT1.1
WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  CDS     1098957 1099080 .       +       1       Parent=DIMT1.1
WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  CDS     1099217 1099309 .       +       0       Parent=DIMT1.1
WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  CDS     1100870 1100934 .       +       0       Parent=DIMT1.1
WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  CDS     1101967 1102030 .       +       1       Parent=DIMT1.1
WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  CDS     1103784 1103890 .       +       0       Parent=DIMT1.1
WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  CDS     1105543 1105582 .       +       1       Parent=DIMT1.1
--------------------------------------
?This is from the contig I used as a test for maker, and I can't find DIMT1.1 in the final gff file. At first I thought it might be because "geneID" is a listed attribute, but changing this to "Name" didn't help. Do you have any ideas why these genes might not be mapping forward? If it's something I can fix in the gff file, I am hoping I can fix it and use it for the second round of Maker after I have trained Snap.

Also, do you think a better quality annotation would results from Snap trained from this curated list of ~8000 genes (that has been expertly done) or by the round 1 output of Maker?

A final question: I am having memory storage issues with Maker, as it is currently taking up ~15TB of storage with temporary files. I am running Maker on a cluster and whenever my submitted Maker job runs out of memory it fails, so I have to resubmit it about every hour, which leaves a lot of temporary folders (e.g. maker_x6V2y4) in my directory. I notice that some of these temporary files haven't been updated in days - is it okay to delete them?

Thank you so much for your help!
Zoe
______________________________________
Zoe Clarke
PhD candidate in Computational Biology at U of T
Lab profile: http://baderlab.org/Zoe%20Clarke
Personal website: https://zoe-clarke.weebly.com/
_______________________________________________
maker-devel mailing list
maker-devel at yandell-lab.org<mailto:maker-devel at yandell-lab.org>
http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org

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From carsonhh at gmail.com  Thu Oct 15 19:45:45 2020
From: carsonhh at gmail.com (Carson Holt)
Date: Thu, 15 Oct 2020 19:45:45 -0600
Subject: [maker-devel] map_forward and temporary storage questions
In-Reply-To: <YTBPR01MB3839AFB99FE4758AAA9BBFAA9C0C0@YTBPR01MB3839.CANPRD01.PROD.OUTLOOK.COM>
References: <YTBPR01MB3839BACB6F6296B734775AA09C360@YTBPR01MB3839.CANPRD01.PROD.OUTLOOK.COM>
	<7742D4BF-2BEB-426D-9858-EC2621B5077D@gmail.com>
	<YTBPR01MB3839AFB99FE4758AAA9BBFAA9C0C0@YTBPR01MB3839.CANPRD01.PROD.OUTLOOK.COM>
Message-ID: <28F61590-140A-44E9-AD63-BCFAC9179391@gmail.com>

If you can create a two column file (column1 being the old ID and column2 being the new ID), you can use the map_fasta_ids and map_gff_ids to rename everything with a corresponding line in the two column file.  Make sure no ID's occur twice (in old or new), it will create issues.  The maker ID will not be lost, instead it will move to the Alias= field in the GFF3.

?Carson



> On Oct 5, 2020, at 7:47 AM, Zoe Clarke <zoe.clarke at utoronto.ca> wrote:
> 
> Thanks Carson!
> 
> I managed to get the GFF3 file fixed and Maker is now recognizing it the way it should.
> 
> I am hoping I can also ask for your advice on functional annotation with Maker. The result of my current run will be gff and fasta files that have the original gff3 genes plus Maker's. The original gff3 file was annotated with HGNC gene symbols, so these new files are a mix of gene symbols and Maker-derived gene names. I would ideally like my final annotation to consist almost entirely of gene symbols. Is the only way to do this (after using Blastp and InterProScan to get putative homology) to undergo an additional manual curation process through something like Apollo?
> 
> Thanks again,
> Zoe
> 
> ______________________________________
> Zoe Clarke
> PhD candidate in Computational Biology at U of T
> Lab profile: http://baderlab.org/Zoe%20Clarke <http://baderlab.org/Zoe%20Clarke>
> Personal website: https://zoe-clarke.weebly.com/ <https://zoe-clarke.weebly.com/>
> From: Carson Holt <carsonhh at gmail.com <mailto:carsonhh at gmail.com>>
> Sent: October 2, 2020 4:50 PM
> To: Zoe Clarke <zoe.clarke at utoronto.ca <mailto:zoe.clarke at utoronto.ca>>
> Cc: maker-devel at yandell-lab.org <mailto:maker-devel at yandell-lab.org> <maker-devel at yandell-lab.org <mailto:maker-devel at yandell-lab.org>>
> Subject: Re: [maker-devel] map_forward and temporary storage questions
>  
> EXTERNAL EMAIL:  Treat content with extra caution. 
> MAKER uses GFF3 format which is not the same as GTF.  You will need to convert your file to GFF3 format.
> 
> You can try this online tool (I haven?t used it to tell you how well it works) http://www.sequenceontology.org/cgi-bin/converter.cgi <http://www.sequenceontology.org/cgi-bin/converter.cgi> 
> 
> There are also a number of other resources available when you google "how to convert GTF to GFF3?.
> 
> ?Carson
> 
> 
>> On Sep 25, 2020, at 3:17 AM, Zoe Clarke <zoe.clarke at utoronto.ca <mailto:zoe.clarke at utoronto.ca>> wrote:
>> 
>> Hello!
>> 
>> I am currently running Maker on a 2.5GB genome that has already had a list of ~8000 genes very thoroughly annotated. My hope is to find and annotate the rest of the genes using ESTs and protein homology. However, I tested Maker on a single contig of my genome (there are ~20,000 contigs) and I can't find any of the genes from my original gtf file even though I followed all of the instructions in this wiki: http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/Updating_annotations_in_light_of_new_data <http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/Updating_annotations_in_light_of_new_data> (I entered the original gff under model_gff, and used map_forward=1). I am worried this is because my gff3 file isn't formatted properly. Here are a few lines in my gff file as an example:
>> --------------------------------------------
>> WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  transcript      1094446 1105585 .       +       .       ID=DIMT1.1;geneID=DIMT1
>> WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  exon    1094446 1094521 97.75   +       .       Parent=DIMT1.1
>> WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  exon    1094874 1094947 97.75   +       .       Parent=DIMT1.1
>> WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  exon    1095459 1095545 97.75   +       .       Parent=DIMT1.1
>> WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  exon    1097351 1097412 97.75   +       .       Parent=DIMT1.1
>> WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  exon    1097492 1097585 97.75   +       .       Parent=DIMT1.1
>> WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  exon    1097670 1097719 97.75   +       .       Parent=DIMT1.1
>> WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  exon    1098957 1099080 97.75   +       .       Parent=DIMT1.1
>> WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  exon    1099217 1099309 97.75   +       .       Parent=DIMT1.1
>> WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  exon    1100870 1100934 97.75   +       .       Parent=DIMT1.1
>> WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  exon    1101967 1102030 97.75   +       .       Parent=DIMT1.1
>> WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  exon    1103784 1103890 97.75   +       .       Parent=DIMT1.1
>> WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  exon    1105543 1105585 97.75   +       .       Parent=DIMT1.1
>> WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  CDS     1094446 1094521 .       +       0       Parent=DIMT1.1
>> WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  CDS     1094874 1094947 .       +       2       Parent=DIMT1.1
>> WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  CDS     1095459 1095545 .       +       0       Parent=DIMT1.1
>> WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  CDS     1097351 1097412 .       +       0       Parent=DIMT1.1
>> WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  CDS     1097492 1097585 .       +       1       Parent=DIMT1.1
>> WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  CDS     1097670 1097719 .       +       0       Parent=DIMT1.1
>> WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  CDS     1098957 1099080 .       +       1       Parent=DIMT1.1
>> WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  CDS     1099217 1099309 .       +       0       Parent=DIMT1.1
>> WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  CDS     1100870 1100934 .       +       0       Parent=DIMT1.1
>> WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  CDS     1101967 1102030 .       +       1       Parent=DIMT1.1
>> WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  CDS     1103784 1103890 .       +       0       Parent=DIMT1.1
>> WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  CDS     1105543 1105582 .       +       1       Parent=DIMT1.1
>> --------------------------------------
>> ?This is from the contig I used as a test for maker, and I can't find DIMT1.1 in the final gff file. At first I thought it might be because "geneID" is a listed attribute, but changing this to "Name" didn't help. Do you have any ideas why these genes might not be mapping forward? If it's something I can fix in the gff file, I am hoping I can fix it and use it for the second round of Maker after I have trained Snap.
>> 
>> Also, do you think a better quality annotation would results from Snap trained from this curated list of ~8000 genes (that has been expertly done) or by the round 1 output of Maker?
>> 
>> A final question: I am having memory storage issues with Maker, as it is currently taking up ~15TB of storage with temporary files. I am running Maker on a cluster and whenever my submitted Maker job runs out of memory it fails, so I have to resubmit it about every hour, which leaves a lot of temporary folders (e.g. maker_x6V2y4) in my directory. I notice that some of these temporary files haven't been updated in days - is it okay to delete them?
>> 
>> Thank you so much for your help!
>> Zoe
>> ______________________________________
>> Zoe Clarke
>> PhD candidate in Computational Biology at U of T
>> Lab profile: http://baderlab.org/Zoe%20Clarke <http://baderlab.org/Zoe%20Clarke>
>> Personal website: https://zoe-clarke.weebly.com/ <https://zoe-clarke.weebly.com/>_______________________________________________
>> maker-devel mailing list
>> maker-devel at yandell-lab.org <mailto:maker-devel at yandell-lab.org>
>> http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org <http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org>
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From taosheng.x at gmail.com  Sat Oct 17 00:48:06 2020
From: taosheng.x at gmail.com (Xu, taosheng)
Date: Sat, 17 Oct 2020 14:48:06 +0800
Subject: [maker-devel] Does maker support muti-processing for a single long
 fasta sequence using openMPI?
Message-ID: <CALJhmFoNOdxFb4gQ4jYP=FZqaHgZdVOhQOpPuyd5bMAeYZ8ucg@mail.gmail.com>

Dear Maker Development Team,
I wonder whether maker supports parallel processing for a single long
genome sequence?

When I submit my maker task using openMPI with multiple cpus (like, mpiexec
-n 40  maker) to annotate a single long genome sequence, always only one
maker with 4 rmblast run. The other cpus is on idle.

I want to use the maker parallel processing with openMPI to speed up a
single ultra-long genome sequence annotation.

Best regards,
Taosheng
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From carsonhh at gmail.com  Mon Oct 19 08:32:20 2020
From: carsonhh at gmail.com (Carson Holt)
Date: Mon, 19 Oct 2020 08:32:20 -0600
Subject: [maker-devel] Does maker support muti-processing for a single
 long fasta sequence using openMPI?
In-Reply-To: <CALJhmFoNOdxFb4gQ4jYP=FZqaHgZdVOhQOpPuyd5bMAeYZ8ucg@mail.gmail.com>
References: <CALJhmFoNOdxFb4gQ4jYP=FZqaHgZdVOhQOpPuyd5bMAeYZ8ucg@mail.gmail.com>
Message-ID: <AC94C4EB-A696-4830-A650-1A33EB67B281@gmail.com>

Yes. It will divide contigs into chunks the same size as the max_dna_len parameter.

?Carson

Sent from my iPhone

> On Oct 17, 2020, at 12:48 AM, Xu, taosheng <taosheng.x at gmail.com> wrote:
> 
> ?
> Dear Maker Development Team,
> I wonder whether maker supports parallel processing for a single long genome sequence?
> 
> When I submit my maker task using openMPI with multiple cpus (like, mpiexec -n 40  maker) to annotate a single long genome sequence, always only one maker with 4 rmblast run. The other cpus is on idle.
> 
> I want to use the maker parallel processing with openMPI to speed up a single ultra-long genome sequence annotation.
> 
> Best regards,
> Taosheng
> _______________________________________________
> maker-devel mailing list
> maker-devel at yandell-lab.org
> http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org



From taosheng.x at gmail.com  Tue Oct 20 10:23:25 2020
From: taosheng.x at gmail.com (Xu, taosheng)
Date: Wed, 21 Oct 2020 00:23:25 +0800
Subject: [maker-devel] Does maker support muti-processing for a single
 long fasta sequence using openMPI?
In-Reply-To: <AC94C4EB-A696-4830-A650-1A33EB67B281@gmail.com>
References: <CALJhmFoNOdxFb4gQ4jYP=FZqaHgZdVOhQOpPuyd5bMAeYZ8ucg@mail.gmail.com>
	<AC94C4EB-A696-4830-A650-1A33EB67B281@gmail.com>
Message-ID: <CALJhmFocG7D-K0gdGJ5831V=gnPp0BDrEMu138W3HV=QmKs2Ug@mail.gmail.com>

Thank you very much Carson for your timely response,
Yes I think so. The Maker MPI should support the multi-processing of an
ultra-long single sequence. But I cannot run it successfully for a single
sequence.
First I  make sure the openMPI with maker has been installed properly. It
works well for multiple DNA sequences in a parallel way.
When I submit a maker job for an ultra-long single sequence (mpiexec -mca
btl ^openib -n 40 maker -g scaffold1.fasta -fix_nucleotides, The
max_dna_len is set to 100000). It always left only one maker thread run.
The other maker threads are disappeared and show finished in the output
information. See the output information below. Please help me to check it.
Thanks for your kind help and your time.

#-----MAKER Behavior Options
max_dna_len=100000 #length for dividing up contigs into chunks
(increases/decreases memory usage)
min_contig=1 #skip genome contigs below this length (under 10kb are often
useless)

Best regards,
Taosheng



OUTPUT Information
STATUS: Processing and indexing input FASTA files...
STATUS: Setting up database for any GFF3 input...
examining contents of the fasta file and run log
A data structure will be created for you at:
/data/splitgenome/top1000/splitGenome/part1/plant.maker.output/plant_datastore

To access files for individual sequences use the datastore index:
/data/splitgenome/top1000/splitGenome/part1/plant.maker.output/plant_master_datastore_index.log

STATUS: Now running MAKER...



--Next Contig--

Processing run.log file...
examining contents of the fasta file and run log



--Next Contig--

#---------------------------------------------------------------------
Another instance of maker is processing this contig!!
SeqID: scaffold#1
Length: 73580997
#---------------------------------------------------------------------


examining contents of the fasta file and run log



--Next Contig--

#---------------------------------------------------------------------
Another instance of maker is processing this contig!!
SeqID: scaffold#1
Length: 73580997
#---------------------------------------------------------------------




Maker is now finished!!!



Start_time: 1603000030
End_time:   1603000033
Elapsed:    3
A data structure will be created for you at:
/data/splitgenome/top1000/splitGenome/part1/plant.maker.output/plant_datastore

To access files for individual sequences use the datastore index:
/data/splitgenome/top1000/splitGenome/part1/plant.maker.output/plant_master_datastore_index.log

STATUS: Now running MAKER...
MAKER WARNING: The file
plant.maker.output/plant_datastore/B5/CD/scaffold#1//theVoid.scaffold#1/28/scaffold#1.289.plant_repeatFinal%2Elib%2Empi%2E10%2E2.specific.out
did not finish on the last run and must be erased
WARNING: Multiple MAKER processes have been started in the
same directory.

STATUS: Processing and indexing input FASTA files...
examining contents of the fasta file and run log



--Next Contig--

#---------------------------------------------------------------------
Another instance of maker is processing this contig!!
SeqID: scaffold#1
Length: 73580997
#---------------------------------------------------------------------


WARNING: Multiple MAKER processes have been started in the
same directory.

STATUS: Processing and indexing input FASTA files...
STATUS: Setting up database for any GFF3 input...
STATUS: Setting up database for any GFF3 input...
A data structure will be created for you at:
/data/splitgenome/top1000/splitGenome/part1/plant.maker.output/plant_datastore

To access files for individual sequences use the datastore index:
/data/splitgenome/top1000/splitGenome/part1/plant.maker.output/plant_master_datastore_index.log

STATUS: Now running MAKER...
examining contents of the fasta file and run log



--Next Contig--

#---------------------------------------------------------------------
Another instance of maker is processing this contig!!
SeqID: scaffold#1
Length: 73580997
#---------------------------------------------------------------------




*Maker is now finished!!!*



Start_time: 1603000030
End_time:   1603000034
Elapsed:    4
#---------------------------------------------------------------------
Now starting the contig!!
SeqID: scaffold#1
Length: 73580997
#---------------------------------------------------------------------


examining contents of the fasta file and run log



--Next Contig--

#---------------------------------------------------------------------
Another instance of maker is processing this contig!!
SeqID: scaffold#1
Length: 73580997
#---------------------------------------------------------------------


examining contents of the fasta file and run log



--Next Contig--

#---------------------------------------------------------------------
Another instance of maker is processing this contig!!
SeqID: scaffold#1
Length: 73580997
#---------------------------------------------------------------------




Start_time: 1603000030
End_time:   1603000034
Elapsed:    4


*Maker is now finished!!!*

A data structure will be created for you at:
/data/splitgenome/top1000/splitGenome/part1/plant.maker.output/plant_datastore

To access files for individual sequences use the datastore index:
/data/splitgenome/top1000/splitGenome/part1/plant.maker.output/plant_master_datastore_index.log

STATUS: Now running MAKER...
examining contents of the fasta file and run log
..........

Maker is now finished!!!



Start_time: 1602920407
End_time:   1602920580
Elapsed:    173
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_VflRYH; ./maker3.01/exe/RepeatMasker/RepeatMasker
/data/splitgenome/top1000/splitGenome/part1/plant.maker.output/plant_datastore/B5/CD/scaffold#1//theVoid.scaffold#1/0/scaffold#1.0.plant_repeatFinal%2Elib%2Empi%2E10%2E0.specific
-dir
/data/splitgenome/top1000/splitGenome/part1/plant.maker.output/plant_datastore/B5/CD/scaffold#1//theVoid.scaffold#1/0
-pa 1 -lib
/data/splitgenome/top1000/splitGenome/part1/plant.maker.output/mpi_blastdb/plant_repeatFinal%2Elib.mpi.10/plant_repeatFinal%2Elib.mpi.10.0
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_VflRYH; ./maker3.01/exe/RepeatMasker/RepeatMasker
/data/splitgenome/top1000/splitGenome/part1/plant.maker.output/plant_datastore/B5/CD/scaffold#1//theVoid.scaffold#1/0/scaffold#1.0.plant_repeatFinal%2Elib%2Empi%2E10%2E1.specific
-dir
/data/splitgenome/top1000/splitGenome/part1/plant.maker.output/plant_datastore/B5/CD/scaffold#1//theVoid.scaffold#1/0
-pa 1 -lib
/data/splitgenome/top1000/splitGenome/part1/plant.maker.output/mpi_blastdb/plant_repeatFinal%2Elib.mpi.10/plant_repeatFinal%2Elib.mpi.10.1
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_VflRYH; ./maker3.01/exe/RepeatMasker/RepeatMasker
/data/splitgenome/top1000/splitGenome/part1/plant.maker.output/plant_datastore/B5/CD/scaffold#1//theVoid.scaffold#1/0/scaffold#1.0.plant_repeatFinal%2Elib%2Empi%2E10%2E2.specific
-dir
/data/splitgenome/top1000/splitGenome/part1/plant.maker.output/plant_datastore/B5/CD/scaffold#1//theVoid.scaffold#1/0
-pa 1 -lib
/data/splitgenome/top1000/splitGenome/part1/plant.maker.output/mpi_blastdb/plant_repeatFinal%2Elib.mpi.10/plant_repeatFinal%2Elib.mpi.10.2
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_VflRYH; ./maker3.01/exe/RepeatMasker/RepeatMasker
/data/splitgenome/top1000/splitGenome/part1/plant.maker.output/plant_datastore/B5/CD/scaffold#1//theVoid.scaffold#1/0/scaffold#1.0.plant_repeatFinal%2Elib%2Empi%2E10%2E3.specific
-dir
/data/splitgenome/top1000/splitGenome/part1/plant.maker.output/plant_datastore/B5/CD/scaffold#1//theVoid.scaffold#1/0
-pa 1 -lib
/data/splitgenome/top1000/splitGenome/part1/plant.maker.output/mpi_blastdb/plant_repeatFinal%2Elib.mpi.10/plant_repeatFinal%2Elib.mpi.10.3
#-------------------------------#
running  repeat masker.
#--------- command -------------#

.....

On Mon, Oct 19, 2020 at 10:32 PM Carson Holt <carsonhh at gmail.com> wrote:

> Yes. It will divide contigs into chunks the same size as the max_dna_len
> parameter.
>
> ?Carson
>
> Sent from my iPhone
>
> > On Oct 17, 2020, at 12:48 AM, Xu, taosheng <taosheng.x at gmail.com> wrote:
> >
> > ?
> > Dear Maker Development Team,
> > I wonder whether maker supports parallel processing for a single long
> genome sequence?
> >
> > When I submit my maker task using openMPI with multiple cpus (like,
> mpiexec -n 40  maker) to annotate a single long genome sequence, always
> only one maker with 4 rmblast run. The other cpus is on idle.
> >
> > I want to use the maker parallel processing with openMPI to speed up a
> single ultra-long genome sequence annotation.
> >
> > Best regards,
> > Taosheng
> > _______________________________________________
> > maker-devel mailing list
> > maker-devel at yandell-lab.org
> > http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org
>
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From zoe.clarke at utoronto.ca  Fri Oct  9 05:39:57 2020
From: zoe.clarke at utoronto.ca (Zoe Clarke)
Date: Fri, 9 Oct 2020 11:39:57 +0000
Subject: [maker-devel] Issue with single contig
Message-ID: <YTBPR01MB3839C4605F16FAA8BDA8EFFE9C080@YTBPR01MB3839.CANPRD01.PROD.OUTLOOK.COM>

Hello!

Sorry to bother you again. I am having a very specific problem with one of my contigs, and I was hoping you could help.

I can cancelled my last Maker run because one of my contigs failed around 56,000 times according to the output_rnd1_master_datastore_index.log file. It was just perpetually failing during the run with the following message:

ERROR: Chunk failed at level:0, tier_type:0open3: fork failed: Cannot allocate memory at dir/File/NFSLock.pm line 1037.

I am running Maker over multiple nodes, so I figured there might be an issue with a log file getting truncated or malformed. Looking at the files stored in the void for this contig, there are also a ton of files which I think might be causing an issue:

0                         run.log.child.112                                     WCK01_AAF20200214_F8-ctg57.118-119.raw.section       WCK01_AAF20200214_F8-ctg57.55-56.raw.section
1                         run.log.child.113                                     WCK01_AAF20200214_F8-ctg57.118.pred.raw.section      WCK01_AAF20200214_F8-ctg57.55.pred.raw.section
10                        run.log.child.114                                     WCK01_AAF20200214_F8-ctg57.118.raw.section           WCK01_AAF20200214_F8-ctg57.55.raw.section
11                        run.log.child.115                                     WCK01_AAF20200214_F8-ctg57.119-120.raw.section       WCK01_AAF20200214_F8-ctg57.56-57.raw.section
12                        run.log.child.116                                     WCK01_AAF20200214_F8-ctg57.119.pred.raw.section      WCK01_AAF20200214_F8-ctg57.56.pred.raw.section
2                         run.log.child.117                                     WCK01_AAF20200214_F8-ctg57.119.raw.section           WCK01_AAF20200214_F8-ctg57.5-6.raw.section
3                         run.log.child.118                                     WCK01_AAF20200214_F8-ctg57.11.pred.raw.section       WCK01_AAF20200214_F8-ctg57.56.raw.section
4                         run.log.child.119                                     WCK01_AAF20200214_F8-ctg57.11.raw.section            WCK01_AAF20200214_F8-ctg57.57-58.raw.section
5                         run.log.child.12                                      WCK01_AAF20200214_F8-ctg57.120-121.raw.section       WCK01_AAF20200214_F8-ctg57.57.pred.raw.section
6                         run.log.child.120                                     WCK01_AAF20200214_F8-ctg57.120.pred.raw.section      WCK01_AAF20200214_F8-ctg57.57.raw.section
7                         run.log.child.121                                     WCK01_AAF20200214_F8-ctg57.120.raw.section           WCK01_AAF20200214_F8-ctg57.58-59.raw.section
8                         run.log.child.122                                     WCK01_AAF20200214_F8-ctg57.121-122.raw.section       WCK01_AAF20200214_F8-ctg57.58.pred.raw.section
9                         run.log.child.123                                     WCK01_AAF20200214_F8-ctg57.12-13.raw.section         WCK01_AAF20200214_F8-ctg57.58.raw.section
evidence_0.gff            run.log.child.124                                     WCK01_AAF20200214_F8-ctg57.121.end.blastn.holdover   WCK01_AAF20200214_F8-ctg57.59-60.raw.section
evidence_100.gff          run.log.child.125                                     WCK01_AAF20200214_F8-ctg57.121.end.blastx.holdover   WCK01_AAF20200214_F8-ctg57.59.pred.raw.section
evidence_101.gff          run.log.child.13                                      WCK01_AAF20200214_F8-ctg57.121.pred.raw.section      WCK01_AAF20200214_F8-ctg57.59.raw.section
evidence_102.gff          run.log.child.14                                      WCK01_AAF20200214_F8-ctg57.121.raw.section           WCK01_AAF20200214_F8-ctg57.5.pred.raw.section
evidence_103.gff          run.log.child.15                                      WCK01_AAF20200214_F8-ctg57.122-123.raw.section       WCK01_AAF20200214_F8-ctg57.5.raw.section
evidence_104.gff          run.log.child.16                                      WCK01_AAF20200214_F8-ctg57.122.pred.raw.section      WCK01_AAF20200214_F8-ctg57.60-61.raw.section
evidence_105.gff          run.log.child.17                                      WCK01_AAF20200214_F8-ctg57.122.raw.section           WCK01_AAF20200214_F8-ctg57.60.pred.raw.section
evidence_106.gff          run.log.child.18                                      WCK01_AAF20200214_F8-ctg57.123-124.raw.section       WCK01_AAF20200214_F8-ctg57.60.raw.section
evidence_107.gff          run.log.child.19                                      WCK01_AAF20200214_F8-ctg57.123.pred.raw.section      WCK01_AAF20200214_F8-ctg57.61-62.raw.section
evidence_108.gff          run.log.child.2                                       WCK01_AAF20200214_F8-ctg57.123.raw.section           WCK01_AAF20200214_F8-ctg57.61.pred.raw.section
evidence_109.gff          run.log.child.20                                      WCK01_AAF20200214_F8-ctg57.124-125.raw.section       WCK01_AAF20200214_F8-ctg57.61.raw.section
evidence_10.gff           run.log.child.21                                      WCK01_AAF20200214_F8-ctg57.124.pred.raw.section      WCK01_AAF20200214_F8-ctg57.62-63.raw.section
evidence_110.gff          run.log.child.22                                      WCK01_AAF20200214_F8-ctg57.124.raw.section           WCK01_AAF20200214_F8-ctg57.62.pred.raw.section
evidence_111.gff          run.log.child.23                                      WCK01_AAF20200214_F8-ctg57.125.pred.raw.section      WCK01_AAF20200214_F8-ctg57.62.raw.section
evidence_112.gff          run.log.child.24                                      WCK01_AAF20200214_F8-ctg57.125.raw.section           WCK01_AAF20200214_F8-ctg57.63-64.raw.section
evidence_113.gff          run.log.child.25                                      WCK01_AAF20200214_F8-ctg57.12.pred.raw.section       WCK01_AAF20200214_F8-ctg57.63.pred.raw.section
evidence_114.gff          run.log.child.26                                      WCK01_AAF20200214_F8-ctg57.1-2.raw.section           WCK01_AAF20200214_F8-ctg57.63.raw.section
evidence_115.gff          run.log.child.27                                      WCK01_AAF20200214_F8-ctg57.12.raw.section            WCK01_AAF20200214_F8-ctg57.64-65.raw.section
evidence_116.gff          run.log.child.28                                      WCK01_AAF20200214_F8-ctg57.13-14.raw.section         WCK01_AAF20200214_F8-ctg57.64.pred.raw.section
evidence_116.gff.ann      run.log.child.29                                      WCK01_AAF20200214_F8-ctg57.13.pred.raw.section       WCK01_AAF20200214_F8-ctg57.64.raw.section
evidence_116.gff.def      run.log.child.3                                       WCK01_AAF20200214_F8-ctg57.13.raw.section            WCK01_AAF20200214_F8-ctg57.65-66.raw.section
evidence_116.gff.seq      run.log.child.30                                      WCK01_AAF20200214_F8-ctg57.14-15.raw.section         WCK01_AAF20200214_F8-ctg57.65.pred.raw.section
evidence_117.gff          run.log.child.31                                      WCK01_AAF20200214_F8-ctg57.14.pred.raw.section       WCK01_AAF20200214_F8-ctg57.65.raw.section
evidence_118.gff          run.log.child.32                                      WCK01_AAF20200214_F8-ctg57.14.raw.section            WCK01_AAF20200214_F8-ctg57.66-67.raw.section
evidence_119.gff          run.log.child.33                                      WCK01_AAF20200214_F8-ctg57.15-16.raw.section         WCK01_AAF20200214_F8-ctg57.66.pred.raw.section
evidence_11.gff           run.log.child.34                                      WCK01_AAF20200214_F8-ctg57.15.pred.raw.section       WCK01_AAF20200214_F8-ctg57.66.raw.section
evidence_120.gff          run.log.child.35                                      WCK01_AAF20200214_F8-ctg57.15.raw.section            WCK01_AAF20200214_F8-ctg57.67-68.raw.section
evidence_121.gff          run.log.child.36                                      WCK01_AAF20200214_F8-ctg57.16-17.raw.section         WCK01_AAF20200214_F8-ctg57.67.pred.raw.section
evidence_122.gff          run.log.child.37                                      WCK01_AAF20200214_F8-ctg57.16.pred.raw.section       WCK01_AAF20200214_F8-ctg57.6-7.raw.section
evidence_123.gff          run.log.child.38                                      WCK01_AAF20200214_F8-ctg57.16.raw.section            WCK01_AAF20200214_F8-ctg57.67.raw.section
evidence_124.gff          run.log.child.39                                      WCK01_AAF20200214_F8-ctg57.17-18.raw.section         WCK01_AAF20200214_F8-ctg57.68-69.raw.section
evidence_125.gff          run.log.child.4                                       WCK01_AAF20200214_F8-ctg57.17.pred.raw.section       WCK01_AAF20200214_F8-ctg57.68.pred.raw.section
evidence_12.gff           run.log.child.40                                      WCK01_AAF20200214_F8-ctg57.17.raw.section            WCK01_AAF20200214_F8-ctg57.68.raw.section
evidence_13.gff           run.log.child.41                                      WCK01_AAF20200214_F8-ctg57.18-19.raw.section         WCK01_AAF20200214_F8-ctg57.68.start.blastn.holdover
evidence_14.gff           run.log.child.42                                      WCK01_AAF20200214_F8-ctg57.18.pred.raw.section       WCK01_AAF20200214_F8-ctg57.68.start.blastx.holdover
evidence_15.gff           run.log.child.43                                      WCK01_AAF20200214_F8-ctg57.18.raw.section            WCK01_AAF20200214_F8-ctg57.69-70.raw.section
evidence_16.gff           run.log.child.44                                      WCK01_AAF20200214_F8-ctg57.19-20.raw.section         WCK01_AAF20200214_F8-ctg57.69.end.blastn.holdover
evidence_17.gff           run.log.child.45                                      WCK01_AAF20200214_F8-ctg57.19.pred.raw.section       WCK01_AAF20200214_F8-ctg57.69.pred.raw.section
evidence_18.gff           run.log.child.46                                      WCK01_AAF20200214_F8-ctg57.19.raw.section            WCK01_AAF20200214_F8-ctg57.69.raw.section
evidence_19.gff           run.log.child.47                                      WCK01_AAF20200214_F8-ctg57.1.pred.raw.section        WCK01_AAF20200214_F8-ctg57.6.pred.raw.section
evidence_1.gff            run.log.child.48                                      WCK01_AAF20200214_F8-ctg57.1.raw.section             WCK01_AAF20200214_F8-ctg57.6.raw.section
evidence_20.gff           run.log.child.49                                      WCK01_AAF20200214_F8-ctg57.20-21.raw.section         WCK01_AAF20200214_F8-ctg57.70-71.raw.section
evidence_21.gff           run.log.child.5                                       WCK01_AAF20200214_F8-ctg57.20.pred.raw.section       WCK01_AAF20200214_F8-ctg57.70.end.blastn.holdover
evidence_22.gff           run.log.child.50                                      WCK01_AAF20200214_F8-ctg57.20.raw.section            WCK01_AAF20200214_F8-ctg57.70.end.blastx.holdover
evidence_23.gff           run.log.child.51                                      WCK01_AAF20200214_F8-ctg57.21-22.raw.section         WCK01_AAF20200214_F8-ctg57.70.pred.raw.section
evidence_24.gff           run.log.child.52                                      WCK01_AAF20200214_F8-ctg57.21.pred.raw.section       WCK01_AAF20200214_F8-ctg57.70.raw.section
evidence_25.gff           run.log.child.53                                      WCK01_AAF20200214_F8-ctg57.21.raw.section            WCK01_AAF20200214_F8-ctg57.71-72.raw.section
evidence_25.gff.ann       run.log.child.54                                      WCK01_AAF20200214_F8-ctg57.22-23.raw.section         WCK01_AAF20200214_F8-ctg57.71.pred.raw.section
evidence_25.gff.def       run.log.child.55                                      WCK01_AAF20200214_F8-ctg57.22.pred.raw.section       WCK01_AAF20200214_F8-ctg57.71.raw.section
evidence_25.gff.seq       run.log.child.56                                      WCK01_AAF20200214_F8-ctg57.22.raw.section            WCK01_AAF20200214_F8-ctg57.72-73.raw.section
evidence_26.gff           run.log.child.57                                      WCK01_AAF20200214_F8-ctg57.23-24.raw.section         WCK01_AAF20200214_F8-ctg57.72.pred.raw.section
evidence_27.gff           run.log.child.58                                      WCK01_AAF20200214_F8-ctg57.23.pred.raw.section       WCK01_AAF20200214_F8-ctg57.72.raw.section
evidence_28.gff           run.log.child.59                                      WCK01_AAF20200214_F8-ctg57.2-3.raw.section           WCK01_AAF20200214_F8-ctg57.73-74.raw.section
evidence_29.gff           run.log.child.6                                       WCK01_AAF20200214_F8-ctg57.23.raw.section            WCK01_AAF20200214_F8-ctg57.73.pred.raw.section
evidence_2.gff            run.log.child.60                                      WCK01_AAF20200214_F8-ctg57.23.start.blastn.holdover  WCK01_AAF20200214_F8-ctg57.73.raw.section
evidence_30.gff           run.log.child.61                                      WCK01_AAF20200214_F8-ctg57.23.start.blastx.holdover  WCK01_AAF20200214_F8-ctg57.73.start.blastn.holdover
evidence_31.gff           run.log.child.62                                      WCK01_AAF20200214_F8-ctg57.24-25.raw.section         WCK01_AAF20200214_F8-ctg57.73.start.blastx.holdover
evidence_32.gff           run.log.child.63                                      WCK01_AAF20200214_F8-ctg57.24.pred.raw.section       WCK01_AAF20200214_F8-ctg57.74-75.raw.section
evidence_33.gff           run.log.child.64                                      WCK01_AAF20200214_F8-ctg57.24.raw.section            WCK01_AAF20200214_F8-ctg57.74.pred.raw.section
evidence_34.gff           run.log.child.65                                      WCK01_AAF20200214_F8-ctg57.25-26.raw.section         WCK01_AAF20200214_F8-ctg57.74.raw.section
evidence_35.gff           run.log.child.66                                      WCK01_AAF20200214_F8-ctg57.25.end.blastn.holdover    WCK01_AAF20200214_F8-ctg57.75-76.raw.section
evidence_36.gff           run.log.child.67                                      WCK01_AAF20200214_F8-ctg57.25.pred.raw.section       WCK01_AAF20200214_F8-ctg57.75.end.blastn.holdover
evidence_37.gff           run.log.child.68                                      WCK01_AAF20200214_F8-ctg57.25.raw.section            WCK01_AAF20200214_F8-ctg57.75.end.blastx.holdover
evidence_38.gff           run.log.child.69                                      WCK01_AAF20200214_F8-ctg57.26-27.raw.section         WCK01_AAF20200214_F8-ctg57.75.pred.raw.section
evidence_39.gff           run.log.child.7                                       WCK01_AAF20200214_F8-ctg57.26.pred.raw.section       WCK01_AAF20200214_F8-ctg57.75.raw.section
evidence_3.gff            run.log.child.70                                      WCK01_AAF20200214_F8-ctg57.26.raw.section            WCK01_AAF20200214_F8-ctg57.76-77.raw.section
evidence_40.gff           run.log.child.71                                      WCK01_AAF20200214_F8-ctg57.27-28.raw.section         WCK01_AAF20200214_F8-ctg57.76.pred.raw.section
evidence_41.gff           run.log.child.72                                      WCK01_AAF20200214_F8-ctg57.27.pred.raw.section       WCK01_AAF20200214_F8-ctg57.76.raw.section
evidence_42.gff           run.log.child.73                                      WCK01_AAF20200214_F8-ctg57.27.raw.section            WCK01_AAF20200214_F8-ctg57.77-78.raw.section
evidence_43.gff           run.log.child.74                                      WCK01_AAF20200214_F8-ctg57.28-29.raw.section         WCK01_AAF20200214_F8-ctg57.77.pred.raw.section
evidence_44.gff           run.log.child.75                                      WCK01_AAF20200214_F8-ctg57.28.pred.raw.section       WCK01_AAF20200214_F8-ctg57.77.raw.section
evidence_45.gff           run.log.child.76                                      WCK01_AAF20200214_F8-ctg57.28.raw.section            WCK01_AAF20200214_F8-ctg57.78-79.raw.section
evidence_46.gff           run.log.child.77                                      WCK01_AAF20200214_F8-ctg57.29-30.raw.section         WCK01_AAF20200214_F8-ctg57.78.pred.raw.section
evidence_47.gff           run.log.child.78                                      WCK01_AAF20200214_F8-ctg57.29.pred.raw.section       WCK01_AAF20200214_F8-ctg57.7-8.raw.section
evidence_48.gff           run.log.child.79                                      WCK01_AAF20200214_F8-ctg57.29.raw.section            WCK01_AAF20200214_F8-ctg57.78.raw.section
evidence_49.gff           run.log.child.8                                       WCK01_AAF20200214_F8-ctg57.2.pred.raw.section        WCK01_AAF20200214_F8-ctg57.79-80.raw.section
evidence_4.gff            run.log.child.80                                      WCK01_AAF20200214_F8-ctg57.2.raw.section             WCK01_AAF20200214_F8-ctg57.79.pred.raw.section
evidence_50.gff           run.log.child.81                                      WCK01_AAF20200214_F8-ctg57.2.start.blastn.holdover   WCK01_AAF20200214_F8-ctg57.79.raw.section
evidence_51.gff           run.log.child.82                                      WCK01_AAF20200214_F8-ctg57.2.start.blastx.holdover   WCK01_AAF20200214_F8-ctg57.7.pred.raw.section
evidence_52.gff           run.log.child.83                                      WCK01_AAF20200214_F8-ctg57.30-31.raw.section         WCK01_AAF20200214_F8-ctg57.7.raw.section
evidence_53.gff           run.log.child.84                                      WCK01_AAF20200214_F8-ctg57.30.pred.raw.section       WCK01_AAF20200214_F8-ctg57.80-81.raw.section
evidence_54.gff           run.log.child.85                                      WCK01_AAF20200214_F8-ctg57.30.raw.section            WCK01_AAF20200214_F8-ctg57.80.pred.raw.section
evidence_55.gff           run.log.child.86                                      WCK01_AAF20200214_F8-ctg57.31-32.raw.section         WCK01_AAF20200214_F8-ctg57.80.raw.section
evidence_56.gff           run.log.child.87                                      WCK01_AAF20200214_F8-ctg57.31.pred.raw.section       WCK01_AAF20200214_F8-ctg57.80.start.blastn.holdover
evidence_57.gff           run.log.child.88                                      WCK01_AAF20200214_F8-ctg57.31.raw.section            WCK01_AAF20200214_F8-ctg57.80.start.blastx.holdover
evidence_58.gff           run.log.child.89                                      WCK01_AAF20200214_F8-ctg57.32-33.raw.section         WCK01_AAF20200214_F8-ctg57.81-82.raw.section
evidence_59.gff           run.log.child.9                                       WCK01_AAF20200214_F8-ctg57.32.pred.raw.section       WCK01_AAF20200214_F8-ctg57.81.pred.raw.section
evidence_5.gff            run.log.child.90                                      WCK01_AAF20200214_F8-ctg57.32.raw.section            WCK01_AAF20200214_F8-ctg57.81.raw.section
evidence_60.gff           run.log.child.91                                      WCK01_AAF20200214_F8-ctg57.33-34.raw.section         WCK01_AAF20200214_F8-ctg57.82-83.raw.section
evidence_61.gff           run.log.child.92                                      WCK01_AAF20200214_F8-ctg57.33.pred.raw.section       WCK01_AAF20200214_F8-ctg57.82.end.blastn.holdover
evidence_62.gff           run.log.child.93                                      WCK01_AAF20200214_F8-ctg57.33.raw.section            WCK01_AAF20200214_F8-ctg57.82.end.blastx.holdover
evidence_63.gff           run.log.child.94                                      WCK01_AAF20200214_F8-ctg57.34-35.raw.section         WCK01_AAF20200214_F8-ctg57.82.pred.raw.section
evidence_64.gff           run.log.child.95                                      WCK01_AAF20200214_F8-ctg57.34.pred.raw.section       WCK01_AAF20200214_F8-ctg57.82.raw.section
evidence_65.gff           run.log.child.96                                      WCK01_AAF20200214_F8-ctg57.3-4.raw.section           WCK01_AAF20200214_F8-ctg57.83-84.raw.section
evidence_66.gff           run.log.child.97                                      WCK01_AAF20200214_F8-ctg57.34.raw.section            WCK01_AAF20200214_F8-ctg57.83.pred.raw.section
evidence_67.gff           run.log.child.98                                      WCK01_AAF20200214_F8-ctg57.35-36.raw.section         WCK01_AAF20200214_F8-ctg57.83.raw.section
evidence_68.gff           run.log.child.99                                      WCK01_AAF20200214_F8-ctg57.35.pred.raw.section       WCK01_AAF20200214_F8-ctg57.84-85.raw.section
evidence_69.gff           WCK01_AAF20200214_F8-ctg57.0-1.raw.section            WCK01_AAF20200214_F8-ctg57.35.raw.section            WCK01_AAF20200214_F8-ctg57.84.pred.raw.section
evidence_6.gff            WCK01_AAF20200214_F8-ctg57.0.pred.raw.section         WCK01_AAF20200214_F8-ctg57.36-37.raw.section         WCK01_AAF20200214_F8-ctg57.84.raw.section
evidence_70.gff           WCK01_AAF20200214_F8-ctg57.0.raw.section              WCK01_AAF20200214_F8-ctg57.36.pred.raw.section       WCK01_AAF20200214_F8-ctg57.84.start.blastn.holdover
evidence_70.gff.ann       WCK01_AAF20200214_F8-ctg57.100-101.raw.section        WCK01_AAF20200214_F8-ctg57.36.raw.section            WCK01_AAF20200214_F8-ctg57.84.start.blastx.holdover
evidence_70.gff.def       WCK01_AAF20200214_F8-ctg57.100.pred.raw.section       WCK01_AAF20200214_F8-ctg57.37-38.raw.section         WCK01_AAF20200214_F8-ctg57.85-86.raw.section
evidence_70.gff.seq       WCK01_AAF20200214_F8-ctg57.100.raw.section            WCK01_AAF20200214_F8-ctg57.37.pred.raw.section       WCK01_AAF20200214_F8-ctg57.85.pred.raw.section
evidence_71.gff           WCK01_AAF20200214_F8-ctg57.101-102.raw.section        WCK01_AAF20200214_F8-ctg57.37.raw.section            WCK01_AAF20200214_F8-ctg57.85.raw.section
evidence_72.gff           WCK01_AAF20200214_F8-ctg57.10-11.raw.section          WCK01_AAF20200214_F8-ctg57.38-39.raw.section         WCK01_AAF20200214_F8-ctg57.86-87.raw.section
evidence_73.gff           WCK01_AAF20200214_F8-ctg57.101.pred.raw.section       WCK01_AAF20200214_F8-ctg57.38.pred.raw.section       WCK01_AAF20200214_F8-ctg57.86.end.blastn.holdover
evidence_74.gff           WCK01_AAF20200214_F8-ctg57.101.raw.section            WCK01_AAF20200214_F8-ctg57.38.raw.section            WCK01_AAF20200214_F8-ctg57.86.end.blastx.holdover
evidence_75.gff           WCK01_AAF20200214_F8-ctg57.102-103.raw.section        WCK01_AAF20200214_F8-ctg57.39-40.raw.section         WCK01_AAF20200214_F8-ctg57.86.pred.raw.section
evidence_76.gff           WCK01_AAF20200214_F8-ctg57.102.end.blastn.holdover    WCK01_AAF20200214_F8-ctg57.39.pred.raw.section       WCK01_AAF20200214_F8-ctg57.86.raw.section
evidence_77.gff           WCK01_AAF20200214_F8-ctg57.102.end.blastx.holdover    WCK01_AAF20200214_F8-ctg57.39.raw.section            WCK01_AAF20200214_F8-ctg57.87-88.raw.section
evidence_78.gff           WCK01_AAF20200214_F8-ctg57.102.pred.raw.section       WCK01_AAF20200214_F8-ctg57.3.pred.raw.section        WCK01_AAF20200214_F8-ctg57.87.pred.raw.section
evidence_79.gff           WCK01_AAF20200214_F8-ctg57.102.raw.section            WCK01_AAF20200214_F8-ctg57.3.raw.section             WCK01_AAF20200214_F8-ctg57.87.raw.section
evidence_7.gff            WCK01_AAF20200214_F8-ctg57.103-104.raw.section        WCK01_AAF20200214_F8-ctg57.40-41.raw.section         WCK01_AAF20200214_F8-ctg57.88-89.raw.section
evidence_80.gff           WCK01_AAF20200214_F8-ctg57.103.pred.raw.section       WCK01_AAF20200214_F8-ctg57.40.pred.raw.section       WCK01_AAF20200214_F8-ctg57.88.pred.raw.section
evidence_81.gff           WCK01_AAF20200214_F8-ctg57.103.raw.section            WCK01_AAF20200214_F8-ctg57.40.raw.section            WCK01_AAF20200214_F8-ctg57.88.raw.section
evidence_82.gff           WCK01_AAF20200214_F8-ctg57.104-105.raw.section        WCK01_AAF20200214_F8-ctg57.41-42.raw.section         WCK01_AAF20200214_F8-ctg57.89-90.raw.section
evidence_83.gff           WCK01_AAF20200214_F8-ctg57.104.pred.raw.section       WCK01_AAF20200214_F8-ctg57.41.pred.raw.section       WCK01_AAF20200214_F8-ctg57.89.pred.raw.section
evidence_84.gff           WCK01_AAF20200214_F8-ctg57.104.raw.section            WCK01_AAF20200214_F8-ctg57.41.raw.section            WCK01_AAF20200214_F8-ctg57.8-9.raw.section
evidence_85.gff           WCK01_AAF20200214_F8-ctg57.105-106.raw.section        WCK01_AAF20200214_F8-ctg57.42-43.raw.section         WCK01_AAF20200214_F8-ctg57.89.raw.section
evidence_86.gff           WCK01_AAF20200214_F8-ctg57.105.pred.raw.section       WCK01_AAF20200214_F8-ctg57.42.pred.raw.section       WCK01_AAF20200214_F8-ctg57.8.pred.raw.section
evidence_87.gff           WCK01_AAF20200214_F8-ctg57.105.raw.section            WCK01_AAF20200214_F8-ctg57.42.raw.section            WCK01_AAF20200214_F8-ctg57.8.raw.section
evidence_88.gff           WCK01_AAF20200214_F8-ctg57.106-107.raw.section        WCK01_AAF20200214_F8-ctg57.43-44.raw.section         WCK01_AAF20200214_F8-ctg57.90-91.raw.section
evidence_89.gff           WCK01_AAF20200214_F8-ctg57.106.pred.raw.section       WCK01_AAF20200214_F8-ctg57.43.pred.raw.section       WCK01_AAF20200214_F8-ctg57.90.pred.raw.section
evidence_8.gff            WCK01_AAF20200214_F8-ctg57.106.raw.section            WCK01_AAF20200214_F8-ctg57.43.raw.section            WCK01_AAF20200214_F8-ctg57.90.raw.section
evidence_90.gff           WCK01_AAF20200214_F8-ctg57.107-108.raw.section        WCK01_AAF20200214_F8-ctg57.44-45.raw.section         WCK01_AAF20200214_F8-ctg57.9-10.raw.section
evidence_91.gff           WCK01_AAF20200214_F8-ctg57.107.pred.raw.section       WCK01_AAF20200214_F8-ctg57.44.pred.raw.section       WCK01_AAF20200214_F8-ctg57.91-92.raw.section
evidence_92.gff           WCK01_AAF20200214_F8-ctg57.107.raw.section            WCK01_AAF20200214_F8-ctg57.44.raw.section            WCK01_AAF20200214_F8-ctg57.91.pred.raw.section
evidence_93.gff           WCK01_AAF20200214_F8-ctg57.108-109.raw.section        WCK01_AAF20200214_F8-ctg57.45-46.raw.section         WCK01_AAF20200214_F8-ctg57.91.raw.section
evidence_94.gff           WCK01_AAF20200214_F8-ctg57.108.pred.raw.section       WCK01_AAF20200214_F8-ctg57.45.pred.raw.section       WCK01_AAF20200214_F8-ctg57.92-93.raw.section
evidence_95.gff           WCK01_AAF20200214_F8-ctg57.108.raw.section            WCK01_AAF20200214_F8-ctg57.4-5.raw.section           WCK01_AAF20200214_F8-ctg57.92.pred.raw.section
evidence_96.gff           WCK01_AAF20200214_F8-ctg57.109-110.raw.section        WCK01_AAF20200214_F8-ctg57.45.raw.section            WCK01_AAF20200214_F8-ctg57.92.raw.section
evidence_96.gff.ann       WCK01_AAF20200214_F8-ctg57.109.pred.raw.section       WCK01_AAF20200214_F8-ctg57.46-47.raw.section         WCK01_AAF20200214_F8-ctg57.93-94.raw.section
evidence_96.gff.def       WCK01_AAF20200214_F8-ctg57.109.raw.section            WCK01_AAF20200214_F8-ctg57.46.pred.raw.section       WCK01_AAF20200214_F8-ctg57.93.pred.raw.section
evidence_96.gff.seq       WCK01_AAF20200214_F8-ctg57.10.pred.raw.section        WCK01_AAF20200214_F8-ctg57.46.raw.section            WCK01_AAF20200214_F8-ctg57.93.raw.section
evidence_97.gff.ann       WCK01_AAF20200214_F8-ctg57.10.raw.section             WCK01_AAF20200214_F8-ctg57.47-48.raw.section         WCK01_AAF20200214_F8-ctg57.94-95.raw.section
evidence_97.gff.def       WCK01_AAF20200214_F8-ctg57.110-111.raw.section        WCK01_AAF20200214_F8-ctg57.47.pred.raw.section       WCK01_AAF20200214_F8-ctg57.94.pred.raw.section
evidence_97.gff.seq       WCK01_AAF20200214_F8-ctg57.110.pred.raw.section       WCK01_AAF20200214_F8-ctg57.47.raw.section            WCK01_AAF20200214_F8-ctg57.94.raw.section
evidence_98.gff.ann       WCK01_AAF20200214_F8-ctg57.110.raw.section            WCK01_AAF20200214_F8-ctg57.48-49.raw.section         WCK01_AAF20200214_F8-ctg57.95-96.raw.section
evidence_98.gff.def       WCK01_AAF20200214_F8-ctg57.111-112.raw.section        WCK01_AAF20200214_F8-ctg57.48.pred.raw.section       WCK01_AAF20200214_F8-ctg57.95.pred.raw.section
evidence_98.gff.seq       WCK01_AAF20200214_F8-ctg57.11-12.raw.section          WCK01_AAF20200214_F8-ctg57.48.raw.section            WCK01_AAF20200214_F8-ctg57.95.raw.section
evidence_99.gff           WCK01_AAF20200214_F8-ctg57.111.pred.raw.section       WCK01_AAF20200214_F8-ctg57.48.start.blastn.holdover  WCK01_AAF20200214_F8-ctg57.96.end.blastn.holdover
evidence_99.gff.ann       WCK01_AAF20200214_F8-ctg57.111.raw.section            WCK01_AAF20200214_F8-ctg57.48.start.blastx.holdover  WCK01_AAF20200214_F8-ctg57.96.end.blastx.holdover
evidence_99.gff.def       WCK01_AAF20200214_F8-ctg57.112-113.raw.section        WCK01_AAF20200214_F8-ctg57.49-50.raw.section         WCK01_AAF20200214_F8-ctg57.96.end.section.holdover
evidence_99.gff.seq       WCK01_AAF20200214_F8-ctg57.112.pred.raw.section       WCK01_AAF20200214_F8-ctg57.49.pred.raw.section       WCK01_AAF20200214_F8-ctg57.96.pred.raw.section
evidence_9.gff            WCK01_AAF20200214_F8-ctg57.112.raw.section            WCK01_AAF20200214_F8-ctg57.49.raw.section            WCK01_AAF20200214_F8-ctg57.96.raw.section
query.fasta               WCK01_AAF20200214_F8-ctg57.113-114.raw.section        WCK01_AAF20200214_F8-ctg57.4.pred.raw.section        WCK01_AAF20200214_F8-ctg57.96.start.blastn.holdover
query.masked.fasta        WCK01_AAF20200214_F8-ctg57.113.pred.raw.section       WCK01_AAF20200214_F8-ctg57.4.raw.section             WCK01_AAF20200214_F8-ctg57.96.start.blastx.holdover
query.masked.fasta.index  WCK01_AAF20200214_F8-ctg57.113.raw.section            WCK01_AAF20200214_F8-ctg57.50-51.raw.section         WCK01_AAF20200214_F8-ctg57.97.pred.raw.section
query.masked.gff          WCK01_AAF20200214_F8-ctg57.114-115.raw.section        WCK01_AAF20200214_F8-ctg57.50.end.blastn.holdover    WCK01_AAF20200214_F8-ctg57.98.pred.raw.section
run.log.child.0           WCK01_AAF20200214_F8-ctg57.114.pred.raw.section       WCK01_AAF20200214_F8-ctg57.50.end.blastx.holdover    WCK01_AAF20200214_F8-ctg57.98.start.blastn.holdover
run.log.child.1           WCK01_AAF20200214_F8-ctg57.114.raw.section            WCK01_AAF20200214_F8-ctg57.50.pred.raw.section       WCK01_AAF20200214_F8-ctg57.99-100.raw.section
run.log.child.10          WCK01_AAF20200214_F8-ctg57.114.start.blastn.holdover  WCK01_AAF20200214_F8-ctg57.50.raw.section            WCK01_AAF20200214_F8-ctg57.99.end.blastn.holdover
run.log.child.100         WCK01_AAF20200214_F8-ctg57.114.start.blastx.holdover  WCK01_AAF20200214_F8-ctg57.50.start.blastx.holdover  WCK01_AAF20200214_F8-ctg57.99.end.blastx.holdover
run.log.child.101         WCK01_AAF20200214_F8-ctg57.115-116.raw.section        WCK01_AAF20200214_F8-ctg57.51-52.raw.section         WCK01_AAF20200214_F8-ctg57.99.pred.raw.section
run.log.child.102         WCK01_AAF20200214_F8-ctg57.115.end.blastn.holdover    WCK01_AAF20200214_F8-ctg57.51.pred.raw.section       WCK01_AAF20200214_F8-ctg57.99.raw.section
run.log.child.103         WCK01_AAF20200214_F8-ctg57.115.pred.raw.section       WCK01_AAF20200214_F8-ctg57.51.raw.section            WCK01_AAF20200214_F8-ctg57.99.start.blastx.holdover
run.log.child.104         WCK01_AAF20200214_F8-ctg57.115.raw.section            WCK01_AAF20200214_F8-ctg57.52-53.raw.section         WCK01_AAF20200214_F8-ctg57.99.start.section.holdover
run.log.child.105         WCK01_AAF20200214_F8-ctg57.116-117.raw.section        WCK01_AAF20200214_F8-ctg57.52.pred.raw.section       WCK01_AAF20200214_F8-ctg57.9.pred.raw.section
run.log.child.106         WCK01_AAF20200214_F8-ctg57.116.pred.raw.section       WCK01_AAF20200214_F8-ctg57.52.raw.section            WCK01_AAF20200214_F8-ctg57.9.raw.section
run.log.child.107         WCK01_AAF20200214_F8-ctg57.116.raw.section            WCK01_AAF20200214_F8-ctg57.53-54.raw.section         WCK01_AAF20200214_F8-ctg57.gff.ann
run.log.child.108         WCK01_AAF20200214_F8-ctg57.117-118.raw.section        WCK01_AAF20200214_F8-ctg57.53.pred.raw.section       WCK01_AAF20200214_F8-ctg57.gff.def
run.log.child.109         WCK01_AAF20200214_F8-ctg57.117.pred.raw.section       WCK01_AAF20200214_F8-ctg57.53.raw.section            WCK01_AAF20200214_F8-ctg57.gff.seq
run.log.child.11          WCK01_AAF20200214_F8-ctg57.117.raw.section            WCK01_AAF20200214_F8-ctg57.54-55.raw.section
run.log.child.110         WCK01_AAF20200214_F8-ctg57.117.start.blastn.holdover  WCK01_AAF20200214_F8-ctg57.54.pred.raw.section
run.log.child.111         WCK01_AAF20200214_F8-ctg57.117.start.blastx.holdover  WCK01_AAF20200214_F8-ctg57.54.raw.section

I set clean_try=1 and am trying to fix this contig (it's only this one contig which is causing trouble), but I'm wondering if it's also okay to completely delete the void directory to force it to start this contig from scratch. I have already tried rerunning maker with clean_try=1 two times and now I'm getting an mpich2 error:

Fatal error in MPI_Send: Invalid count, error stack:
MPI_Send(173): MPI_Send(buf=0x2aec3d6a3010, count=-1279995089, MPI_CHAR, dest=15, tag=9999, MPI_COMM_WORLD) failed
MPI_Send(97).: Negative count, value is -1279995089

I am currently trying again with fewer MPI jobs requested, worrying that there might be a memory issue on the computer cluster I am using. My temporary directory still has lots of space, but I have ~200G RAM per node and sometimes the jobs use a ton of RAM. I don't have too many more contigs left of this run, so I just really don't want to mess anything up. Do you have any advice?

Thanks so much!
Zoe

______________________________________
Zoe Clarke
PhD candidate in Computational Biology at U of T
Lab profile: http://baderlab.org/Zoe%20Clarke
Personal website: https://zoe-clarke.weebly.com/
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From carsonhh at gmail.com  Thu Oct 22 13:31:11 2020
From: carsonhh at gmail.com (Carson Holt)
Date: Thu, 22 Oct 2020 13:31:11 -0600
Subject: [maker-devel] Issue with single contig
In-Reply-To: <YTBPR01MB3839C4605F16FAA8BDA8EFFE9C080@YTBPR01MB3839.CANPRD01.PROD.OUTLOOK.COM>
References: <YTBPR01MB3839C4605F16FAA8BDA8EFFE9C080@YTBPR01MB3839.CANPRD01.PROD.OUTLOOK.COM>
Message-ID: <7DEEBFBB-2247-413A-96F1-0EF1A8E9EE62@gmail.com>

Your datacenter may have implemented the temporary storage (?/tmp? by default) to be in memory storage. As a result, every file you store is really being stored in RAM behind the scenes.  Or you have specified TMP= in the control files to point to in memory storage.  The result is that, at some point there was not enough memory left.  You may want to ask about this and ensure that you can point to a real node based disk storage like traditional /tmp space.

?Carson



> On Oct 9, 2020, at 5:39 AM, Zoe Clarke <zoe.clarke at utoronto.ca> wrote:
> 
> Hello!
> 
> Sorry to bother you again. I am having a very specific problem with one of my contigs, and I was hoping you could help.
> 
> I can cancelled my last Maker run because one of my contigs failed around 56,000 times according to the output_rnd1_master_datastore_index.log file. It was just perpetually failing during the run with the following message:
> 
> ERROR: Chunk failed at level:0, tier_type:0open3: fork failed: Cannot allocate memory at dir/File/NFSLock.pm line 1037.
> 
> I am running Maker over multiple nodes, so I figured there might be an issue with a log file getting truncated or malformed. Looking at the files stored in the void for this contig, there are also a ton of files which I think might be causing an issue:
> 
> 0                         run.log.child.112                                     WCK01_AAF20200214_F8-ctg57.118-119.raw.section       WCK01_AAF20200214_F8-ctg57.55-56.raw.section
> 1                         run.log.child.113                                     WCK01_AAF20200214_F8-ctg57.118.pred.raw.section      WCK01_AAF20200214_F8-ctg57.55.pred.raw.section
> 10                        run.log.child.114                                     WCK01_AAF20200214_F8-ctg57.118.raw.section           WCK01_AAF20200214_F8-ctg57.55.raw.section
> 11                        run.log.child.115                                     WCK01_AAF20200214_F8-ctg57.119-120.raw.section       WCK01_AAF20200214_F8-ctg57.56-57.raw.section
> 12                        run.log.child.116                                     WCK01_AAF20200214_F8-ctg57.119.pred.raw.section      WCK01_AAF20200214_F8-ctg57.56.pred.raw.section
> 2                         run.log.child.117                                     WCK01_AAF20200214_F8-ctg57.119.raw.section           WCK01_AAF20200214_F8-ctg57.5-6.raw.section
> 3                         run.log.child.118                                     WCK01_AAF20200214_F8-ctg57.11.pred.raw.section       WCK01_AAF20200214_F8-ctg57.56.raw.section
> 4                         run.log.child.119                                     WCK01_AAF20200214_F8-ctg57.11.raw.section            WCK01_AAF20200214_F8-ctg57.57-58.raw.section
> 5                         run.log.child.12                                      WCK01_AAF20200214_F8-ctg57.120-121.raw.section       WCK01_AAF20200214_F8-ctg57.57.pred.raw.section
> 6                         run.log.child.120                                     WCK01_AAF20200214_F8-ctg57.120.pred.raw.section      WCK01_AAF20200214_F8-ctg57.57.raw.section
> 7                         run.log.child.121                                     WCK01_AAF20200214_F8-ctg57.120.raw.section           WCK01_AAF20200214_F8-ctg57.58-59.raw.section
> 8                         run.log.child.122                                     WCK01_AAF20200214_F8-ctg57.121-122.raw.section       WCK01_AAF20200214_F8-ctg57.58.pred.raw.section
> 9                         run.log.child.123                                     WCK01_AAF20200214_F8-ctg57.12-13.raw.section         WCK01_AAF20200214_F8-ctg57.58.raw.section
> evidence_0.gff            run.log.child.124                                     WCK01_AAF20200214_F8-ctg57.121.end.blastn.holdover   WCK01_AAF20200214_F8-ctg57.59-60.raw.section
> evidence_100.gff          run.log.child.125                                     WCK01_AAF20200214_F8-ctg57.121.end.blastx.holdover   WCK01_AAF20200214_F8-ctg57.59.pred.raw.section
> evidence_101.gff          run.log.child.13                                      WCK01_AAF20200214_F8-ctg57.121.pred.raw.section      WCK01_AAF20200214_F8-ctg57.59.raw.section
> evidence_102.gff          run.log.child.14                                      WCK01_AAF20200214_F8-ctg57.121.raw.section           WCK01_AAF20200214_F8-ctg57.5.pred.raw.section
> evidence_103.gff          run.log.child.15                                      WCK01_AAF20200214_F8-ctg57.122-123.raw.section       WCK01_AAF20200214_F8-ctg57.5.raw.section
> evidence_104.gff          run.log.child.16                                      WCK01_AAF20200214_F8-ctg57.122.pred.raw.section      WCK01_AAF20200214_F8-ctg57.60-61.raw.section
> evidence_105.gff          run.log.child.17                                      WCK01_AAF20200214_F8-ctg57.122.raw.section           WCK01_AAF20200214_F8-ctg57.60.pred.raw.section
> evidence_106.gff          run.log.child.18                                      WCK01_AAF20200214_F8-ctg57.123-124.raw.section       WCK01_AAF20200214_F8-ctg57.60.raw.section
> evidence_107.gff          run.log.child.19                                      WCK01_AAF20200214_F8-ctg57.123.pred.raw.section      WCK01_AAF20200214_F8-ctg57.61-62.raw.section
> evidence_108.gff          run.log.child.2                                       WCK01_AAF20200214_F8-ctg57.123.raw.section           WCK01_AAF20200214_F8-ctg57.61.pred.raw.section
> evidence_109.gff          run.log.child.20                                      WCK01_AAF20200214_F8-ctg57.124-125.raw.section       WCK01_AAF20200214_F8-ctg57.61.raw.section
> evidence_10.gff           run.log.child.21                                      WCK01_AAF20200214_F8-ctg57.124.pred.raw.section      WCK01_AAF20200214_F8-ctg57.62-63.raw.section
> evidence_110.gff          run.log.child.22                                      WCK01_AAF20200214_F8-ctg57.124.raw.section           WCK01_AAF20200214_F8-ctg57.62.pred.raw.section
> evidence_111.gff          run.log.child.23                                      WCK01_AAF20200214_F8-ctg57.125.pred.raw.section      WCK01_AAF20200214_F8-ctg57.62.raw.section
> evidence_112.gff          run.log.child.24                                      WCK01_AAF20200214_F8-ctg57.125.raw.section           WCK01_AAF20200214_F8-ctg57.63-64.raw.section
> evidence_113.gff          run.log.child.25                                      WCK01_AAF20200214_F8-ctg57.12.pred.raw.section       WCK01_AAF20200214_F8-ctg57.63.pred.raw.section
> evidence_114.gff          run.log.child.26                                      WCK01_AAF20200214_F8-ctg57.1-2.raw.section           WCK01_AAF20200214_F8-ctg57.63.raw.section
> evidence_115.gff          run.log.child.27                                      WCK01_AAF20200214_F8-ctg57.12.raw.section            WCK01_AAF20200214_F8-ctg57.64-65.raw.section
> evidence_116.gff          run.log.child.28                                      WCK01_AAF20200214_F8-ctg57.13-14.raw.section         WCK01_AAF20200214_F8-ctg57.64.pred.raw.section
> evidence_116.gff.ann      run.log.child.29                                      WCK01_AAF20200214_F8-ctg57.13.pred.raw.section       WCK01_AAF20200214_F8-ctg57.64.raw.section
> evidence_116.gff.def      run.log.child.3                                       WCK01_AAF20200214_F8-ctg57.13.raw.section            WCK01_AAF20200214_F8-ctg57.65-66.raw.section
> evidence_116.gff.seq      run.log.child.30                                      WCK01_AAF20200214_F8-ctg57.14-15.raw.section         WCK01_AAF20200214_F8-ctg57.65.pred.raw.section
> evidence_117.gff          run.log.child.31                                      WCK01_AAF20200214_F8-ctg57.14.pred.raw.section       WCK01_AAF20200214_F8-ctg57.65.raw.section
> evidence_118.gff          run.log.child.32                                      WCK01_AAF20200214_F8-ctg57.14.raw.section            WCK01_AAF20200214_F8-ctg57.66-67.raw.section
> evidence_119.gff          run.log.child.33                                      WCK01_AAF20200214_F8-ctg57.15-16.raw.section         WCK01_AAF20200214_F8-ctg57.66.pred.raw.section
> evidence_11.gff           run.log.child.34                                      WCK01_AAF20200214_F8-ctg57.15.pred.raw.section       WCK01_AAF20200214_F8-ctg57.66.raw.section
> evidence_120.gff          run.log.child.35                                      WCK01_AAF20200214_F8-ctg57.15.raw.section            WCK01_AAF20200214_F8-ctg57.67-68.raw.section
> evidence_121.gff          run.log.child.36                                      WCK01_AAF20200214_F8-ctg57.16-17.raw.section         WCK01_AAF20200214_F8-ctg57.67.pred.raw.section
> evidence_122.gff          run.log.child.37                                      WCK01_AAF20200214_F8-ctg57.16.pred.raw.section       WCK01_AAF20200214_F8-ctg57.6-7.raw.section
> evidence_123.gff          run.log.child.38                                      WCK01_AAF20200214_F8-ctg57.16.raw.section            WCK01_AAF20200214_F8-ctg57.67.raw.section
> evidence_124.gff          run.log.child.39                                      WCK01_AAF20200214_F8-ctg57.17-18.raw.section         WCK01_AAF20200214_F8-ctg57.68-69.raw.section
> evidence_125.gff          run.log.child.4                                       WCK01_AAF20200214_F8-ctg57.17.pred.raw.section       WCK01_AAF20200214_F8-ctg57.68.pred.raw.section
> evidence_12.gff           run.log.child.40                                      WCK01_AAF20200214_F8-ctg57.17.raw.section            WCK01_AAF20200214_F8-ctg57.68.raw.section
> evidence_13.gff           run.log.child.41                                      WCK01_AAF20200214_F8-ctg57.18-19.raw.section         WCK01_AAF20200214_F8-ctg57.68.start.blastn.holdover
> evidence_14.gff           run.log.child.42                                      WCK01_AAF20200214_F8-ctg57.18.pred.raw.section       WCK01_AAF20200214_F8-ctg57.68.start.blastx.holdover
> evidence_15.gff           run.log.child.43                                      WCK01_AAF20200214_F8-ctg57.18.raw.section            WCK01_AAF20200214_F8-ctg57.69-70.raw.section
> evidence_16.gff           run.log.child.44                                      WCK01_AAF20200214_F8-ctg57.19-20.raw.section         WCK01_AAF20200214_F8-ctg57.69.end.blastn.holdover
> evidence_17.gff           run.log.child.45                                      WCK01_AAF20200214_F8-ctg57.19.pred.raw.section       WCK01_AAF20200214_F8-ctg57.69.pred.raw.section
> evidence_18.gff           run.log.child.46                                      WCK01_AAF20200214_F8-ctg57.19.raw.section            WCK01_AAF20200214_F8-ctg57.69.raw.section
> evidence_19.gff           run.log.child.47                                      WCK01_AAF20200214_F8-ctg57.1.pred.raw.section        WCK01_AAF20200214_F8-ctg57.6.pred.raw.section
> evidence_1.gff            run.log.child.48                                      WCK01_AAF20200214_F8-ctg57.1.raw.section             WCK01_AAF20200214_F8-ctg57.6.raw.section
> evidence_20.gff           run.log.child.49                                      WCK01_AAF20200214_F8-ctg57.20-21.raw.section         WCK01_AAF20200214_F8-ctg57.70-71.raw.section
> evidence_21.gff           run.log.child.5                                       WCK01_AAF20200214_F8-ctg57.20.pred.raw.section       WCK01_AAF20200214_F8-ctg57.70.end.blastn.holdover
> evidence_22.gff           run.log.child.50                                      WCK01_AAF20200214_F8-ctg57.20.raw.section            WCK01_AAF20200214_F8-ctg57.70.end.blastx.holdover
> evidence_23.gff           run.log.child.51                                      WCK01_AAF20200214_F8-ctg57.21-22.raw.section         WCK01_AAF20200214_F8-ctg57.70.pred.raw.section
> evidence_24.gff           run.log.child.52                                      WCK01_AAF20200214_F8-ctg57.21.pred.raw.section       WCK01_AAF20200214_F8-ctg57.70.raw.section
> evidence_25.gff           run.log.child.53                                      WCK01_AAF20200214_F8-ctg57.21.raw.section            WCK01_AAF20200214_F8-ctg57.71-72.raw.section
> evidence_25.gff.ann       run.log.child.54                                      WCK01_AAF20200214_F8-ctg57.22-23.raw.section         WCK01_AAF20200214_F8-ctg57.71.pred.raw.section
> evidence_25.gff.def       run.log.child.55                                      WCK01_AAF20200214_F8-ctg57.22.pred.raw.section       WCK01_AAF20200214_F8-ctg57.71.raw.section
> evidence_25.gff.seq       run.log.child.56                                      WCK01_AAF20200214_F8-ctg57.22.raw.section            WCK01_AAF20200214_F8-ctg57.72-73.raw.section
> evidence_26.gff           run.log.child.57                                      WCK01_AAF20200214_F8-ctg57.23-24.raw.section         WCK01_AAF20200214_F8-ctg57.72.pred.raw.section
> evidence_27.gff           run.log.child.58                                      WCK01_AAF20200214_F8-ctg57.23.pred.raw.section       WCK01_AAF20200214_F8-ctg57.72.raw.section
> evidence_28.gff           run.log.child.59                                      WCK01_AAF20200214_F8-ctg57.2-3.raw.section           WCK01_AAF20200214_F8-ctg57.73-74.raw.section
> evidence_29.gff           run.log.child.6                                       WCK01_AAF20200214_F8-ctg57.23.raw.section            WCK01_AAF20200214_F8-ctg57.73.pred.raw.section
> evidence_2.gff            run.log.child.60                                      WCK01_AAF20200214_F8-ctg57.23.start.blastn.holdover  WCK01_AAF20200214_F8-ctg57.73.raw.section
> evidence_30.gff           run.log.child.61                                      WCK01_AAF20200214_F8-ctg57.23.start.blastx.holdover  WCK01_AAF20200214_F8-ctg57.73.start.blastn.holdover
> evidence_31.gff           run.log.child.62                                      WCK01_AAF20200214_F8-ctg57.24-25.raw.section         WCK01_AAF20200214_F8-ctg57.73.start.blastx.holdover
> evidence_32.gff           run.log.child.63                                      WCK01_AAF20200214_F8-ctg57.24.pred.raw.section       WCK01_AAF20200214_F8-ctg57.74-75.raw.section
> evidence_33.gff           run.log.child.64                                      WCK01_AAF20200214_F8-ctg57.24.raw.section            WCK01_AAF20200214_F8-ctg57.74.pred.raw.section
> evidence_34.gff           run.log.child.65                                      WCK01_AAF20200214_F8-ctg57.25-26.raw.section         WCK01_AAF20200214_F8-ctg57.74.raw.section
> evidence_35.gff           run.log.child.66                                      WCK01_AAF20200214_F8-ctg57.25.end.blastn.holdover    WCK01_AAF20200214_F8-ctg57.75-76.raw.section
> evidence_36.gff           run.log.child.67                                      WCK01_AAF20200214_F8-ctg57.25.pred.raw.section       WCK01_AAF20200214_F8-ctg57.75.end.blastn.holdover
> evidence_37.gff           run.log.child.68                                      WCK01_AAF20200214_F8-ctg57.25.raw.section            WCK01_AAF20200214_F8-ctg57.75.end.blastx.holdover
> evidence_38.gff           run.log.child.69                                      WCK01_AAF20200214_F8-ctg57.26-27.raw.section         WCK01_AAF20200214_F8-ctg57.75.pred.raw.section
> evidence_39.gff           run.log.child.7                                       WCK01_AAF20200214_F8-ctg57.26.pred.raw.section       WCK01_AAF20200214_F8-ctg57.75.raw.section
> evidence_3.gff            run.log.child.70                                      WCK01_AAF20200214_F8-ctg57.26.raw.section            WCK01_AAF20200214_F8-ctg57.76-77.raw.section
> evidence_40.gff           run.log.child.71                                      WCK01_AAF20200214_F8-ctg57.27-28.raw.section         WCK01_AAF20200214_F8-ctg57.76.pred.raw.section
> evidence_41.gff           run.log.child.72                                      WCK01_AAF20200214_F8-ctg57.27.pred.raw.section       WCK01_AAF20200214_F8-ctg57.76.raw.section
> evidence_42.gff           run.log.child.73                                      WCK01_AAF20200214_F8-ctg57.27.raw.section            WCK01_AAF20200214_F8-ctg57.77-78.raw.section
> evidence_43.gff           run.log.child.74                                      WCK01_AAF20200214_F8-ctg57.28-29.raw.section         WCK01_AAF20200214_F8-ctg57.77.pred.raw.section
> evidence_44.gff           run.log.child.75                                      WCK01_AAF20200214_F8-ctg57.28.pred.raw.section       WCK01_AAF20200214_F8-ctg57.77.raw.section
> evidence_45.gff           run.log.child.76                                      WCK01_AAF20200214_F8-ctg57.28.raw.section            WCK01_AAF20200214_F8-ctg57.78-79.raw.section
> evidence_46.gff           run.log.child.77                                      WCK01_AAF20200214_F8-ctg57.29-30.raw.section         WCK01_AAF20200214_F8-ctg57.78.pred.raw.section
> evidence_47.gff           run.log.child.78                                      WCK01_AAF20200214_F8-ctg57.29.pred.raw.section       WCK01_AAF20200214_F8-ctg57.7-8.raw.section
> evidence_48.gff           run.log.child.79                                      WCK01_AAF20200214_F8-ctg57.29.raw.section            WCK01_AAF20200214_F8-ctg57.78.raw.section
> evidence_49.gff           run.log.child.8                                       WCK01_AAF20200214_F8-ctg57.2.pred.raw.section        WCK01_AAF20200214_F8-ctg57.79-80.raw.section
> evidence_4.gff            run.log.child.80                                      WCK01_AAF20200214_F8-ctg57.2.raw.section             WCK01_AAF20200214_F8-ctg57.79.pred.raw.section
> evidence_50.gff           run.log.child.81                                      WCK01_AAF20200214_F8-ctg57.2.start.blastn.holdover   WCK01_AAF20200214_F8-ctg57.79.raw.section
> evidence_51.gff           run.log.child.82                                      WCK01_AAF20200214_F8-ctg57.2.start.blastx.holdover   WCK01_AAF20200214_F8-ctg57.7.pred.raw.section
> evidence_52.gff           run.log.child.83                                      WCK01_AAF20200214_F8-ctg57.30-31.raw.section         WCK01_AAF20200214_F8-ctg57.7.raw.section
> evidence_53.gff           run.log.child.84                                      WCK01_AAF20200214_F8-ctg57.30.pred.raw.section       WCK01_AAF20200214_F8-ctg57.80-81.raw.section
> evidence_54.gff           run.log.child.85                                      WCK01_AAF20200214_F8-ctg57.30.raw.section            WCK01_AAF20200214_F8-ctg57.80.pred.raw.section
> evidence_55.gff           run.log.child.86                                      WCK01_AAF20200214_F8-ctg57.31-32.raw.section         WCK01_AAF20200214_F8-ctg57.80.raw.section
> evidence_56.gff           run.log.child.87                                      WCK01_AAF20200214_F8-ctg57.31.pred.raw.section       WCK01_AAF20200214_F8-ctg57.80.start.blastn.holdover
> evidence_57.gff           run.log.child.88                                      WCK01_AAF20200214_F8-ctg57.31.raw.section            WCK01_AAF20200214_F8-ctg57.80.start.blastx.holdover
> evidence_58.gff           run.log.child.89                                      WCK01_AAF20200214_F8-ctg57.32-33.raw.section         WCK01_AAF20200214_F8-ctg57.81-82.raw.section
> evidence_59.gff           run.log.child.9                                       WCK01_AAF20200214_F8-ctg57.32.pred.raw.section       WCK01_AAF20200214_F8-ctg57.81.pred.raw.section
> evidence_5.gff            run.log.child.90                                      WCK01_AAF20200214_F8-ctg57.32.raw.section            WCK01_AAF20200214_F8-ctg57.81.raw.section
> evidence_60.gff           run.log.child.91                                      WCK01_AAF20200214_F8-ctg57.33-34.raw.section         WCK01_AAF20200214_F8-ctg57.82-83.raw.section
> evidence_61.gff           run.log.child.92                                      WCK01_AAF20200214_F8-ctg57.33.pred.raw.section       WCK01_AAF20200214_F8-ctg57.82.end.blastn.holdover
> evidence_62.gff           run.log.child.93                                      WCK01_AAF20200214_F8-ctg57.33.raw.section            WCK01_AAF20200214_F8-ctg57.82.end.blastx.holdover
> evidence_63.gff           run.log.child.94                                      WCK01_AAF20200214_F8-ctg57.34-35.raw.section         WCK01_AAF20200214_F8-ctg57.82.pred.raw.section
> evidence_64.gff           run.log.child.95                                      WCK01_AAF20200214_F8-ctg57.34.pred.raw.section       WCK01_AAF20200214_F8-ctg57.82.raw.section
> evidence_65.gff           run.log.child.96                                      WCK01_AAF20200214_F8-ctg57.3-4.raw.section           WCK01_AAF20200214_F8-ctg57.83-84.raw.section
> evidence_66.gff           run.log.child.97                                      WCK01_AAF20200214_F8-ctg57.34.raw.section            WCK01_AAF20200214_F8-ctg57.83.pred.raw.section
> evidence_67.gff           run.log.child.98                                      WCK01_AAF20200214_F8-ctg57.35-36.raw.section         WCK01_AAF20200214_F8-ctg57.83.raw.section
> evidence_68.gff           run.log.child.99                                      WCK01_AAF20200214_F8-ctg57.35.pred.raw.section       WCK01_AAF20200214_F8-ctg57.84-85.raw.section
> evidence_69.gff           WCK01_AAF20200214_F8-ctg57.0-1.raw.section            WCK01_AAF20200214_F8-ctg57.35.raw.section            WCK01_AAF20200214_F8-ctg57.84.pred.raw.section
> evidence_6.gff            WCK01_AAF20200214_F8-ctg57.0.pred.raw.section         WCK01_AAF20200214_F8-ctg57.36-37.raw.section         WCK01_AAF20200214_F8-ctg57.84.raw.section
> evidence_70.gff           WCK01_AAF20200214_F8-ctg57.0.raw.section              WCK01_AAF20200214_F8-ctg57.36.pred.raw.section       WCK01_AAF20200214_F8-ctg57.84.start.blastn.holdover
> evidence_70.gff.ann       WCK01_AAF20200214_F8-ctg57.100-101.raw.section        WCK01_AAF20200214_F8-ctg57.36.raw.section            WCK01_AAF20200214_F8-ctg57.84.start.blastx.holdover
> evidence_70.gff.def       WCK01_AAF20200214_F8-ctg57.100.pred.raw.section       WCK01_AAF20200214_F8-ctg57.37-38.raw.section         WCK01_AAF20200214_F8-ctg57.85-86.raw.section
> evidence_70.gff.seq       WCK01_AAF20200214_F8-ctg57.100.raw.section            WCK01_AAF20200214_F8-ctg57.37.pred.raw.section       WCK01_AAF20200214_F8-ctg57.85.pred.raw.section
> evidence_71.gff           WCK01_AAF20200214_F8-ctg57.101-102.raw.section        WCK01_AAF20200214_F8-ctg57.37.raw.section            WCK01_AAF20200214_F8-ctg57.85.raw.section
> evidence_72.gff           WCK01_AAF20200214_F8-ctg57.10-11.raw.section          WCK01_AAF20200214_F8-ctg57.38-39.raw.section         WCK01_AAF20200214_F8-ctg57.86-87.raw.section
> evidence_73.gff           WCK01_AAF20200214_F8-ctg57.101.pred.raw.section       WCK01_AAF20200214_F8-ctg57.38.pred.raw.section       WCK01_AAF20200214_F8-ctg57.86.end.blastn.holdover
> evidence_74.gff           WCK01_AAF20200214_F8-ctg57.101.raw.section            WCK01_AAF20200214_F8-ctg57.38.raw.section            WCK01_AAF20200214_F8-ctg57.86.end.blastx.holdover
> evidence_75.gff           WCK01_AAF20200214_F8-ctg57.102-103.raw.section        WCK01_AAF20200214_F8-ctg57.39-40.raw.section         WCK01_AAF20200214_F8-ctg57.86.pred.raw.section
> evidence_76.gff           WCK01_AAF20200214_F8-ctg57.102.end.blastn.holdover    WCK01_AAF20200214_F8-ctg57.39.pred.raw.section       WCK01_AAF20200214_F8-ctg57.86.raw.section
> evidence_77.gff           WCK01_AAF20200214_F8-ctg57.102.end.blastx.holdover    WCK01_AAF20200214_F8-ctg57.39.raw.section            WCK01_AAF20200214_F8-ctg57.87-88.raw.section
> evidence_78.gff           WCK01_AAF20200214_F8-ctg57.102.pred.raw.section       WCK01_AAF20200214_F8-ctg57.3.pred.raw.section        WCK01_AAF20200214_F8-ctg57.87.pred.raw.section
> evidence_79.gff           WCK01_AAF20200214_F8-ctg57.102.raw.section            WCK01_AAF20200214_F8-ctg57.3.raw.section             WCK01_AAF20200214_F8-ctg57.87.raw.section
> evidence_7.gff            WCK01_AAF20200214_F8-ctg57.103-104.raw.section        WCK01_AAF20200214_F8-ctg57.40-41.raw.section         WCK01_AAF20200214_F8-ctg57.88-89.raw.section
> evidence_80.gff           WCK01_AAF20200214_F8-ctg57.103.pred.raw.section       WCK01_AAF20200214_F8-ctg57.40.pred.raw.section       WCK01_AAF20200214_F8-ctg57.88.pred.raw.section
> evidence_81.gff           WCK01_AAF20200214_F8-ctg57.103.raw.section            WCK01_AAF20200214_F8-ctg57.40.raw.section            WCK01_AAF20200214_F8-ctg57.88.raw.section
> evidence_82.gff           WCK01_AAF20200214_F8-ctg57.104-105.raw.section        WCK01_AAF20200214_F8-ctg57.41-42.raw.section         WCK01_AAF20200214_F8-ctg57.89-90.raw.section
> evidence_83.gff           WCK01_AAF20200214_F8-ctg57.104.pred.raw.section       WCK01_AAF20200214_F8-ctg57.41.pred.raw.section       WCK01_AAF20200214_F8-ctg57.89.pred.raw.section
> evidence_84.gff           WCK01_AAF20200214_F8-ctg57.104.raw.section            WCK01_AAF20200214_F8-ctg57.41.raw.section            WCK01_AAF20200214_F8-ctg57.8-9.raw.section
> evidence_85.gff           WCK01_AAF20200214_F8-ctg57.105-106.raw.section        WCK01_AAF20200214_F8-ctg57.42-43.raw.section         WCK01_AAF20200214_F8-ctg57.89.raw.section
> evidence_86.gff           WCK01_AAF20200214_F8-ctg57.105.pred.raw.section       WCK01_AAF20200214_F8-ctg57.42.pred.raw.section       WCK01_AAF20200214_F8-ctg57.8.pred.raw.section
> evidence_87.gff           WCK01_AAF20200214_F8-ctg57.105.raw.section            WCK01_AAF20200214_F8-ctg57.42.raw.section            WCK01_AAF20200214_F8-ctg57.8.raw.section
> evidence_88.gff           WCK01_AAF20200214_F8-ctg57.106-107.raw.section        WCK01_AAF20200214_F8-ctg57.43-44.raw.section         WCK01_AAF20200214_F8-ctg57.90-91.raw.section
> evidence_89.gff           WCK01_AAF20200214_F8-ctg57.106.pred.raw.section       WCK01_AAF20200214_F8-ctg57.43.pred.raw.section       WCK01_AAF20200214_F8-ctg57.90.pred.raw.section
> evidence_8.gff            WCK01_AAF20200214_F8-ctg57.106.raw.section            WCK01_AAF20200214_F8-ctg57.43.raw.section            WCK01_AAF20200214_F8-ctg57.90.raw.section
> evidence_90.gff           WCK01_AAF20200214_F8-ctg57.107-108.raw.section        WCK01_AAF20200214_F8-ctg57.44-45.raw.section         WCK01_AAF20200214_F8-ctg57.9-10.raw.section
> evidence_91.gff           WCK01_AAF20200214_F8-ctg57.107.pred.raw.section       WCK01_AAF20200214_F8-ctg57.44.pred.raw.section       WCK01_AAF20200214_F8-ctg57.91-92.raw.section
> evidence_92.gff           WCK01_AAF20200214_F8-ctg57.107.raw.section            WCK01_AAF20200214_F8-ctg57.44.raw.section            WCK01_AAF20200214_F8-ctg57.91.pred.raw.section
> evidence_93.gff           WCK01_AAF20200214_F8-ctg57.108-109.raw.section        WCK01_AAF20200214_F8-ctg57.45-46.raw.section         WCK01_AAF20200214_F8-ctg57.91.raw.section
> evidence_94.gff           WCK01_AAF20200214_F8-ctg57.108.pred.raw.section       WCK01_AAF20200214_F8-ctg57.45.pred.raw.section       WCK01_AAF20200214_F8-ctg57.92-93.raw.section
> evidence_95.gff           WCK01_AAF20200214_F8-ctg57.108.raw.section            WCK01_AAF20200214_F8-ctg57.4-5.raw.section           WCK01_AAF20200214_F8-ctg57.92.pred.raw.section
> evidence_96.gff           WCK01_AAF20200214_F8-ctg57.109-110.raw.section        WCK01_AAF20200214_F8-ctg57.45.raw.section            WCK01_AAF20200214_F8-ctg57.92.raw.section
> evidence_96.gff.ann       WCK01_AAF20200214_F8-ctg57.109.pred.raw.section       WCK01_AAF20200214_F8-ctg57.46-47.raw.section         WCK01_AAF20200214_F8-ctg57.93-94.raw.section
> evidence_96.gff.def       WCK01_AAF20200214_F8-ctg57.109.raw.section            WCK01_AAF20200214_F8-ctg57.46.pred.raw.section       WCK01_AAF20200214_F8-ctg57.93.pred.raw.section
> evidence_96.gff.seq       WCK01_AAF20200214_F8-ctg57.10.pred.raw.section        WCK01_AAF20200214_F8-ctg57.46.raw.section            WCK01_AAF20200214_F8-ctg57.93.raw.section
> evidence_97.gff.ann       WCK01_AAF20200214_F8-ctg57.10.raw.section             WCK01_AAF20200214_F8-ctg57.47-48.raw.section         WCK01_AAF20200214_F8-ctg57.94-95.raw.section
> evidence_97.gff.def       WCK01_AAF20200214_F8-ctg57.110-111.raw.section        WCK01_AAF20200214_F8-ctg57.47.pred.raw.section       WCK01_AAF20200214_F8-ctg57.94.pred.raw.section
> evidence_97.gff.seq       WCK01_AAF20200214_F8-ctg57.110.pred.raw.section       WCK01_AAF20200214_F8-ctg57.47.raw.section            WCK01_AAF20200214_F8-ctg57.94.raw.section
> evidence_98.gff.ann       WCK01_AAF20200214_F8-ctg57.110.raw.section            WCK01_AAF20200214_F8-ctg57.48-49.raw.section         WCK01_AAF20200214_F8-ctg57.95-96.raw.section
> evidence_98.gff.def       WCK01_AAF20200214_F8-ctg57.111-112.raw.section        WCK01_AAF20200214_F8-ctg57.48.pred.raw.section       WCK01_AAF20200214_F8-ctg57.95.pred.raw.section
> evidence_98.gff.seq       WCK01_AAF20200214_F8-ctg57.11-12.raw.section          WCK01_AAF20200214_F8-ctg57.48.raw.section            WCK01_AAF20200214_F8-ctg57.95.raw.section
> evidence_99.gff           WCK01_AAF20200214_F8-ctg57.111.pred.raw.section       WCK01_AAF20200214_F8-ctg57.48.start.blastn.holdover  WCK01_AAF20200214_F8-ctg57.96.end.blastn.holdover
> evidence_99.gff.ann       WCK01_AAF20200214_F8-ctg57.111.raw.section            WCK01_AAF20200214_F8-ctg57.48.start.blastx.holdover  WCK01_AAF20200214_F8-ctg57.96.end.blastx.holdover
> evidence_99.gff.def       WCK01_AAF20200214_F8-ctg57.112-113.raw.section        WCK01_AAF20200214_F8-ctg57.49-50.raw.section         WCK01_AAF20200214_F8-ctg57.96.end.section.holdover
> evidence_99.gff.seq       WCK01_AAF20200214_F8-ctg57.112.pred.raw.section       WCK01_AAF20200214_F8-ctg57.49.pred.raw.section       WCK01_AAF20200214_F8-ctg57.96.pred.raw.section
> evidence_9.gff            WCK01_AAF20200214_F8-ctg57.112.raw.section            WCK01_AAF20200214_F8-ctg57.49.raw.section            WCK01_AAF20200214_F8-ctg57.96.raw.section
> query.fasta               WCK01_AAF20200214_F8-ctg57.113-114.raw.section        WCK01_AAF20200214_F8-ctg57.4.pred.raw.section        WCK01_AAF20200214_F8-ctg57.96.start.blastn.holdover
> query.masked.fasta        WCK01_AAF20200214_F8-ctg57.113.pred.raw.section       WCK01_AAF20200214_F8-ctg57.4.raw.section             WCK01_AAF20200214_F8-ctg57.96.start.blastx.holdover
> query.masked.fasta.index  WCK01_AAF20200214_F8-ctg57.113.raw.section            WCK01_AAF20200214_F8-ctg57.50-51.raw.section         WCK01_AAF20200214_F8-ctg57.97.pred.raw.section
> query.masked.gff          WCK01_AAF20200214_F8-ctg57.114-115.raw.section        WCK01_AAF20200214_F8-ctg57.50.end.blastn.holdover    WCK01_AAF20200214_F8-ctg57.98.pred.raw.section
> run.log.child.0           WCK01_AAF20200214_F8-ctg57.114.pred.raw.section       WCK01_AAF20200214_F8-ctg57.50.end.blastx.holdover    WCK01_AAF20200214_F8-ctg57.98.start.blastn.holdover
> run.log.child.1           WCK01_AAF20200214_F8-ctg57.114.raw.section            WCK01_AAF20200214_F8-ctg57.50.pred.raw.section       WCK01_AAF20200214_F8-ctg57.99-100.raw.section
> run.log.child.10          WCK01_AAF20200214_F8-ctg57.114.start.blastn.holdover  WCK01_AAF20200214_F8-ctg57.50.raw.section            WCK01_AAF20200214_F8-ctg57.99.end.blastn.holdover
> run.log.child.100         WCK01_AAF20200214_F8-ctg57.114.start.blastx.holdover  WCK01_AAF20200214_F8-ctg57.50.start.blastx.holdover  WCK01_AAF20200214_F8-ctg57.99.end.blastx.holdover
> run.log.child.101         WCK01_AAF20200214_F8-ctg57.115-116.raw.section        WCK01_AAF20200214_F8-ctg57.51-52.raw.section         WCK01_AAF20200214_F8-ctg57.99.pred.raw.section
> run.log.child.102         WCK01_AAF20200214_F8-ctg57.115.end.blastn.holdover    WCK01_AAF20200214_F8-ctg57.51.pred.raw.section       WCK01_AAF20200214_F8-ctg57.99.raw.section
> run.log.child.103         WCK01_AAF20200214_F8-ctg57.115.pred.raw.section       WCK01_AAF20200214_F8-ctg57.51.raw.section            WCK01_AAF20200214_F8-ctg57.99.start.blastx.holdover
> run.log.child.104         WCK01_AAF20200214_F8-ctg57.115.raw.section            WCK01_AAF20200214_F8-ctg57.52-53.raw.section         WCK01_AAF20200214_F8-ctg57.99.start.section.holdover
> run.log.child.105         WCK01_AAF20200214_F8-ctg57.116-117.raw.section        WCK01_AAF20200214_F8-ctg57.52.pred.raw.section       WCK01_AAF20200214_F8-ctg57.9.pred.raw.section
> run.log.child.106         WCK01_AAF20200214_F8-ctg57.116.pred.raw.section       WCK01_AAF20200214_F8-ctg57.52.raw.section            WCK01_AAF20200214_F8-ctg57.9.raw.section
> run.log.child.107         WCK01_AAF20200214_F8-ctg57.116.raw.section            WCK01_AAF20200214_F8-ctg57.53-54.raw.section         WCK01_AAF20200214_F8-ctg57.gff.ann
> run.log.child.108         WCK01_AAF20200214_F8-ctg57.117-118.raw.section        WCK01_AAF20200214_F8-ctg57.53.pred.raw.section       WCK01_AAF20200214_F8-ctg57.gff.def
> run.log.child.109         WCK01_AAF20200214_F8-ctg57.117.pred.raw.section       WCK01_AAF20200214_F8-ctg57.53.raw.section            WCK01_AAF20200214_F8-ctg57.gff.seq
> run.log.child.11          WCK01_AAF20200214_F8-ctg57.117.raw.section            WCK01_AAF20200214_F8-ctg57.54-55.raw.section
> run.log.child.110         WCK01_AAF20200214_F8-ctg57.117.start.blastn.holdover  WCK01_AAF20200214_F8-ctg57.54.pred.raw.section
> run.log.child.111         WCK01_AAF20200214_F8-ctg57.117.start.blastx.holdover  WCK01_AAF20200214_F8-ctg57.54.raw.section
> 
> I set clean_try=1 and am trying to fix this contig (it's only this one contig which is causing trouble), but I'm wondering if it's also okay to completely delete the void directory to force it to start this contig from scratch. I have already tried rerunning maker with clean_try=1 two times and now I'm getting an mpich2 error:
> 
> Fatal error in MPI_Send: Invalid count, error stack:
> MPI_Send(173): MPI_Send(buf=0x2aec3d6a3010, count=-1279995089, MPI_CHAR, dest=15, tag=9999, MPI_COMM_WORLD) failed
> MPI_Send(97).: Negative count, value is -1279995089
> 
> I am currently trying again with fewer MPI jobs requested, worrying that there might be a memory issue on the computer cluster I am using. My temporary directory still has lots of space, but I have ~200G RAM per node and sometimes the jobs use a ton of RAM. I don't have too many more contigs left of this run, so I just really don't want to mess anything up. Do you have any advice?
> 
> Thanks so much!
> Zoe
> 
> ______________________________________
> Zoe Clarke
> PhD candidate in Computational Biology at U of T
> Lab profile: http://baderlab.org/Zoe%20Clarke <http://baderlab.org/Zoe%20Clarke>
> Personal website: https://zoe-clarke.weebly.com/ <https://zoe-clarke.weebly.com/>_______________________________________________
> maker-devel mailing list
> maker-devel at yandell-lab.org <mailto:maker-devel at yandell-lab.org>
> http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org <http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org>
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From eennadi at gmail.com  Fri Oct 23 00:15:33 2020
From: eennadi at gmail.com (Emmanuel Nnadi)
Date: Fri, 23 Oct 2020 07:15:33 +0100
Subject: [maker-devel] Can maker be used to improve genome assembly?
Message-ID: <CAOXM=CXTCX5tyDeM29fTGi5u0qjOXT7TSCUeQrYt-PogCphvSg@mail.gmail.com>

Hi Carson,
Greetings! This is just a random question that came to my mind. Looking at
the way maker structures files and brings contigs together based on "gene"
locations. Can this be explored to improve genome assemblies? Maybe a tool
that can work from a good annotation to generating a set of improved genome
assembly based on these gene locations


Just a thought
Nnaemeka Emmanuel Nnadi,Ph.D
Department of Microbiology,
Faculty of Natural and Applied Science,
Plateau State University, Bokkos, Plateau State, Nigeria.
+2348068124819
Publications:
 https://www.researchgate.net/profile/Emmanuel_Nnadi/publications
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From carsonhh at gmail.com  Mon Oct 26 13:33:00 2020
From: carsonhh at gmail.com (Carson Holt)
Date: Mon, 26 Oct 2020 13:33:00 -0600
Subject: [maker-devel] Does maker support muti-processing for a single
 long fasta sequence using openMPI?
In-Reply-To: <CALJhmFocG7D-K0gdGJ5831V=gnPp0BDrEMu138W3HV=QmKs2Ug@mail.gmail.com>
References: <CALJhmFoNOdxFb4gQ4jYP=FZqaHgZdVOhQOpPuyd5bMAeYZ8ucg@mail.gmail.com>
	<AC94C4EB-A696-4830-A650-1A33EB67B281@gmail.com>
	<CALJhmFocG7D-K0gdGJ5831V=gnPp0BDrEMu138W3HV=QmKs2Ug@mail.gmail.com>
Message-ID: <926FDE45-F317-43CD-BF2E-A0B00FDBD9A7@gmail.com>

Your MPI processes may not be seeing each other.  So you are getting multiple maker runs all colliding.  You need to reinstall MAKER and say ?yes? to the compile for MPI question.  You may also have to reinstall OpenMPI if just reinstalling MAKER does not work.  You can test MAKER for MPI by running the following ?> mpiexec -mca btl ^openib -n 40 maker -help

If you get a single help message then everything is fine.  If you get 40 help messages, then MPI is not communicating correctly.

?Carson


> On Oct 20, 2020, at 10:23 AM, Xu, taosheng <taosheng.x at gmail.com> wrote:
> 
> Thank you very much Carson for your timely response,
> Yes I think so. The Maker MPI should support the multi-processing of an ultra-long single sequence. But I cannot run it successfully for a single sequence.
> First I  make sure the openMPI with maker has been installed properly. It works well for multiple DNA sequences in a parallel way.
> When I submit a maker job for an ultra-long single sequence (mpiexec -mca btl ^openib -n 40 maker -g scaffold1.fasta -fix_nucleotides, The max_dna_len is set to 100000). It always left only one maker thread run. The other maker threads are disappeared and show finished in the output information. See the output information below. Please help me to check it. Thanks for your kind help and your time.
> 
> #-----MAKER Behavior Options
> max_dna_len=100000 #length for dividing up contigs into chunks (increases/decreases memory usage)
> min_contig=1 #skip genome contigs below this length (under 10kb are often useless)
> 
> Best regards,
> Taosheng
> 
> 
> 
> OUTPUT Information
> STATUS: Processing and indexing input FASTA files...
> STATUS: Setting up database for any GFF3 input...
> examining contents of the fasta file and run log
> A data structure will be created for you at:
> /data/splitgenome/top1000/splitGenome/part1/plant.maker.output/plant_datastore
> 
> To access files for individual sequences use the datastore index:
> /data/splitgenome/top1000/splitGenome/part1/plant.maker.output/plant_master_datastore_index.log
> 
> STATUS: Now running MAKER...
> 
> 
> 
> --Next Contig--
> 
> Processing run.log file...
> examining contents of the fasta file and run log
> 
> 
> 
> --Next Contig--
> 
> #---------------------------------------------------------------------
> Another instance of maker is processing this contig!!
> SeqID: scaffold#1
> Length: 73580997
> #---------------------------------------------------------------------
> 
> 
> examining contents of the fasta file and run log
> 
> 
> 
> --Next Contig--
> 
> #---------------------------------------------------------------------
> Another instance of maker is processing this contig!!
> SeqID: scaffold#1
> Length: 73580997
> #---------------------------------------------------------------------
> 
> 
> 
> 
> Maker is now finished!!!
> 
> 
> 
> Start_time: 1603000030
> End_time:   1603000033
> Elapsed:    3
> A data structure will be created for you at:
> /data/splitgenome/top1000/splitGenome/part1/plant.maker.output/plant_datastore
> 
> To access files for individual sequences use the datastore index:
> /data/splitgenome/top1000/splitGenome/part1/plant.maker.output/plant_master_datastore_index.log
> 
> STATUS: Now running MAKER...
> MAKER WARNING: The file plant.maker.output/plant_datastore/B5/CD/scaffold#1//theVoid.scaffold#1/28/scaffold#1.289.plant_repeatFinal%2Elib%2Empi%2E10%2E2.specific.out
> did not finish on the last run and must be erased
> WARNING: Multiple MAKER processes have been started in the
> same directory.
> 
> STATUS: Processing and indexing input FASTA files...
> examining contents of the fasta file and run log
> 
> 
> 
> --Next Contig--
> 
> #---------------------------------------------------------------------
> Another instance of maker is processing this contig!!
> SeqID: scaffold#1
> Length: 73580997
> #---------------------------------------------------------------------
> 
> 
> WARNING: Multiple MAKER processes have been started in the
> same directory.
> 
> STATUS: Processing and indexing input FASTA files...
> STATUS: Setting up database for any GFF3 input...
> STATUS: Setting up database for any GFF3 input...
> A data structure will be created for you at:
> /data/splitgenome/top1000/splitGenome/part1/plant.maker.output/plant_datastore
> 
> To access files for individual sequences use the datastore index:
> /data/splitgenome/top1000/splitGenome/part1/plant.maker.output/plant_master_datastore_index.log
> 
> STATUS: Now running MAKER...
> examining contents of the fasta file and run log
> 
> 
> 
> --Next Contig--
> 
> #---------------------------------------------------------------------
> Another instance of maker is processing this contig!!
> SeqID: scaffold#1
> Length: 73580997
> #---------------------------------------------------------------------
> 
> 
> 
> 
> Maker is now finished!!!
> 
> 
> 
> Start_time: 1603000030
> End_time:   1603000034
> Elapsed:    4
> #---------------------------------------------------------------------
> Now starting the contig!!
> SeqID: scaffold#1
> Length: 73580997
> #---------------------------------------------------------------------
> 
> 
> examining contents of the fasta file and run log
> 
> 
> 
> --Next Contig--
> 
> #---------------------------------------------------------------------
> Another instance of maker is processing this contig!!
> SeqID: scaffold#1
> Length: 73580997
> #---------------------------------------------------------------------
> 
> 
> examining contents of the fasta file and run log
> 
> 
> 
> --Next Contig--
> 
> #---------------------------------------------------------------------
> Another instance of maker is processing this contig!!
> SeqID: scaffold#1
> Length: 73580997
> #---------------------------------------------------------------------
> 
> 
> 
> 
> Start_time: 1603000030
> End_time:   1603000034
> Elapsed:    4
> 
> 
> Maker is now finished!!!
> 
> A data structure will be created for you at:
> /data/splitgenome/top1000/splitGenome/part1/plant.maker.output/plant_datastore
> 
> To access files for individual sequences use the datastore index:
> /data/splitgenome/top1000/splitGenome/part1/plant.maker.output/plant_master_datastore_index.log
> 
> STATUS: Now running MAKER...
> examining contents of the fasta file and run log
> ..........
> 
> Maker is now finished!!!
> 
> 
> 
> Start_time: 1602920407
> End_time:   1602920580
> Elapsed:    173
> running  repeat masker.
> #--------- command -------------#
> Widget::RepeatMasker:
> cd /tmp/maker_VflRYH; ./maker3.01/exe/RepeatMasker/RepeatMasker /data/splitgenome/top1000/splitGenome/part1/plant.maker.output/plant_datastore/B5/CD/scaffold#1//theVoid.scaffold#1/0/scaffold#1.0.plant_repeatFinal%2Elib%2Empi%2E10%2E0.specific -dir /data/splitgenome/top1000/splitGenome/part1/plant.maker.output/plant_datastore/B5/CD/scaffold#1//theVoid.scaffold#1/0 -pa 1 -lib /data/splitgenome/top1000/splitGenome/part1/plant.maker.output/mpi_blastdb/plant_repeatFinal%2Elib.mpi.10/plant_repeatFinal%2Elib.mpi.10.0
> #-------------------------------#
> running  repeat masker.
> #--------- command -------------#
> Widget::RepeatMasker:
> cd /tmp/maker_VflRYH; ./maker3.01/exe/RepeatMasker/RepeatMasker /data/splitgenome/top1000/splitGenome/part1/plant.maker.output/plant_datastore/B5/CD/scaffold#1//theVoid.scaffold#1/0/scaffold#1.0.plant_repeatFinal%2Elib%2Empi%2E10%2E1.specific -dir /data/splitgenome/top1000/splitGenome/part1/plant.maker.output/plant_datastore/B5/CD/scaffold#1//theVoid.scaffold#1/0 -pa 1 -lib /data/splitgenome/top1000/splitGenome/part1/plant.maker.output/mpi_blastdb/plant_repeatFinal%2Elib.mpi.10/plant_repeatFinal%2Elib.mpi.10.1
> #-------------------------------#
> running  repeat masker.
> #--------- command -------------#
> Widget::RepeatMasker:
> cd /tmp/maker_VflRYH; ./maker3.01/exe/RepeatMasker/RepeatMasker /data/splitgenome/top1000/splitGenome/part1/plant.maker.output/plant_datastore/B5/CD/scaffold#1//theVoid.scaffold#1/0/scaffold#1.0.plant_repeatFinal%2Elib%2Empi%2E10%2E2.specific -dir /data/splitgenome/top1000/splitGenome/part1/plant.maker.output/plant_datastore/B5/CD/scaffold#1//theVoid.scaffold#1/0 -pa 1 -lib /data/splitgenome/top1000/splitGenome/part1/plant.maker.output/mpi_blastdb/plant_repeatFinal%2Elib.mpi.10/plant_repeatFinal%2Elib.mpi.10.2
> #-------------------------------#
> running  repeat masker.
> #--------- command -------------#
> Widget::RepeatMasker:
> cd /tmp/maker_VflRYH; ./maker3.01/exe/RepeatMasker/RepeatMasker /data/splitgenome/top1000/splitGenome/part1/plant.maker.output/plant_datastore/B5/CD/scaffold#1//theVoid.scaffold#1/0/scaffold#1.0.plant_repeatFinal%2Elib%2Empi%2E10%2E3.specific -dir /data/splitgenome/top1000/splitGenome/part1/plant.maker.output/plant_datastore/B5/CD/scaffold#1//theVoid.scaffold#1/0 -pa 1 -lib /data/splitgenome/top1000/splitGenome/part1/plant.maker.output/mpi_blastdb/plant_repeatFinal%2Elib.mpi.10/plant_repeatFinal%2Elib.mpi.10.3
> #-------------------------------#
> running  repeat masker.
> #--------- command -------------#
> 
> .....
> 
> On Mon, Oct 19, 2020 at 10:32 PM Carson Holt <carsonhh at gmail.com <mailto:carsonhh at gmail.com>> wrote:
> Yes. It will divide contigs into chunks the same size as the max_dna_len parameter.
> 
> ?Carson
> 
> Sent from my iPhone
> 
> > On Oct 17, 2020, at 12:48 AM, Xu, taosheng <taosheng.x at gmail.com <mailto:taosheng.x at gmail.com>> wrote:
> > 
> > ?
> > Dear Maker Development Team,
> > I wonder whether maker supports parallel processing for a single long genome sequence?
> > 
> > When I submit my maker task using openMPI with multiple cpus (like, mpiexec -n 40  maker) to annotate a single long genome sequence, always only one maker with 4 rmblast run. The other cpus is on idle.
> > 
> > I want to use the maker parallel processing with openMPI to speed up a single ultra-long genome sequence annotation.
> > 
> > Best regards,
> > Taosheng
> > _______________________________________________
> > maker-devel mailing list
> > maker-devel at yandell-lab.org <mailto:maker-devel at yandell-lab.org>
> > http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org <http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org>

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From carsonhh at gmail.com  Mon Oct 26 13:49:33 2020
From: carsonhh at gmail.com (Carson Holt)
Date: Mon, 26 Oct 2020 13:49:33 -0600
Subject: [maker-devel] Can maker be used to improve genome assembly?
In-Reply-To: <CAOXM=CXTCX5tyDeM29fTGi5u0qjOXT7TSCUeQrYt-PogCphvSg@mail.gmail.com>
References: <CAOXM=CXTCX5tyDeM29fTGi5u0qjOXT7TSCUeQrYt-PogCphvSg@mail.gmail.com>
Message-ID: <B7F4EEA8-9F57-4CF3-9EFA-7D9F9B763537@gmail.com>

We haven?t explored this.  On re-assembly projects I rarely find more than a handful of instances where a gene was obviously split across contigs in the first assembly's annotation.  More often what I find is that extra contigs tend to contain fragments of a gene that is complete on another contig in the same assembly (caused by high heterozygosity, so maternal and paternal contigs can assemble independently).

?Carson


> On Oct 23, 2020, at 12:15 AM, Emmanuel Nnadi <eennadi at gmail.com> wrote:
> 
> Hi Carson,
> Greetings! This is just a random question that came to my mind. Looking at the way maker structures files and brings contigs together based on "gene" locations. Can this be explored to improve genome assemblies? Maybe a tool that can work from a good annotation to generating a set of improved genome assembly based on these gene locations
> 
> 
> Just a thought
> Nnaemeka Emmanuel Nnadi,Ph.D
> Department of Microbiology,
> Faculty of Natural and Applied Science,
> Plateau State University, Bokkos, Plateau State, Nigeria.
> +2348068124819
> Publications: 
>  https://www.researchgate.net/profile/Emmanuel_Nnadi/publications <https://www.researchgate.net/profile/Emmanuel_Nnadi/publications>
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From daren.card at gmail.com  Thu Oct 29 10:35:57 2020
From: daren.card at gmail.com (Daren Card)
Date: Thu, 29 Oct 2020 12:35:57 -0400
Subject: [maker-devel] tblastx of alt-ESTs failing on single scaffold
Message-ID: <CACNE1p+-JynX7_vdakS0ibS3Hf-9M5K_8AxKEOmUgWzc7ScOtg@mail.gmail.com>

Hello,

I am having an issue running MAKER and am hoping to get some
troubleshooting guidance. I am running MAKER v. 2.31.10 on a Unix cluster
using a Singularity image with BLAST v. 2.9.0+ and Exonerate v. 3.3.2. I am
running MAKER with the following command options: "-fix_nucleotides
-nodatastore -RM_off". I am providing assembled transcripts from the target
species (est) and a close relative (alt-est) and proteins from several
species within the same general clade (Squamata). Gene models are being
derived from Augustus with est2genome and protein2genome turned off. I have
largely successfully run MAKER on a couple of genomes from the same
vertebrate genus, but have this lingering problem with a single scaffold
from one of the genomes. If it were pretty short, I'd just ignore it, but
it is 2 Mb, so I do not want to miss out on annotating it.

When I ran MAKER on the entire genome, it finished properly except for this
problematic scaffold. So I separated that scaffold out and tried running it
alone with otherwise the same settings. Each time, it appears I get the
same error during the 1st try when MAKER runs.

ERROR: TBLASTX does not appear to be finished in Widget::tblastx::keepers
--> rank=23, hostname=holy7c18405.rc.fas.harvard.edu
--> rank=23, hostname=holy7c18405.rc.fas.harvard.edu
--> rank=23, hostname=holy7c18405.rc.fas.harvard.edu
--> rank=23, hostname=holy7c18405.rc.fas.harvard.edu
ERROR: Failed while doing tblastx of alt-ESTs
ERROR: Chunk failed at level:4, tier_type:3
FAILED CONTIG:scaffold_77

ERROR: Chunk failed at level:4, tier_type:0
FAILED CONTIG:scaffold_77

Then MAKER keeps retrying and apparently hitting the same problem. I
checked the logs the best I can and see the following issue within
run.log.child.0 for that scaffold.

STARTED lerBou1_maker_rnd2.maker.output/lerBou1_maker_rnd2_datastore/scaffold_77/theVoid.scaffold_77/0/scaffold_77.0.lerEdw1_Trinity_combined_denovo_refguided%2Ecdhit%2Efasta.tblastx
DIED    RANK    17:4:0:0
DIED    COUNT   7

This output file noted there is not present to check, which must stem from
whatever issue there is.

I'm not sure what to do next about this issue and see no obvious
information about what the problem is besides failure of tblastx to run.
Any help that anyone can provide is greatly appreciated.

Kind regards,
Daren Card

NSF Postdoctoral Fellow
Harvard University
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From eennadi at gmail.com  Tue Oct 27 21:01:05 2020
From: eennadi at gmail.com (Emmanuel Nnadi)
Date: Wed, 28 Oct 2020 04:01:05 +0100
Subject: [maker-devel] Maker yields sequences without start and stop codon
Message-ID: <CAOXM=CU=3Y3SgOiAyDiR3Qa56KegaZE-rwEBESNKYO4cBos5uw@mail.gmail.com>

Hi Carson
I always set always_complete=1 yet I still get sequences without start and
stop codon.

Can
https://github.com/Gaius-Augustus/Augustus/blob/master/scripts/fix_in_frame_stop_codon_genes.py
be
used on the final sequence to fix start and stop codon problem?


Nnaemeka Emmanuel Nnadi,Ph.D
Department of Microbiology,
Faculty of Natural and Applied Science,
Plateau State University, Bokkos, Plateau State, Nigeria.
+2348068124819
Publications:
 https://www.researchgate.net/profile/Emmanuel_Nnadi/publications
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From liorglic at mail.tau.ac.il  Fri Oct  2 02:54:55 2020
From: liorglic at mail.tau.ac.il (Lior Glick)
Date: Fri, 2 Oct 2020 11:54:55 +0300
Subject: [maker-devel] MAKER failing during Augustus run
Message-ID: <CAOzMDPxivd1gxOJRuaQd6vDLMizt39qRNsAajzvO+Hhy1K--6A@mail.gmail.com>

Hello,
I am using MAKER2 with Augustus 3.2.2. I keep getting an error message when
annotating a specific contig. The relevant section of the MAKER stderr
looks like this:

Widget::augustus:
/powerapps/share/centos7/miniconda/miniconda2-4.5.4-MakerMPI/bin/augustus
--species=arabidopsis --strand=backward --UTR=off
--hintsfile=/home/tmp_liorglic/maker_zfUstg/0/265_0.10292360-10294752.arabidopsis.auto_annotator.xdef.augustus
--extrinsicCfgFile=/powerapps/share/centos7/miniconda/miniconda2-4.5.4-MakerMPI/config/extrinsic/extrinsic.MPE.cfg
/home/tmp_liorglic/maker_zfUstg/0/265_0.10292360-10294752.arabidopsis.auto_annotator.augustus.fasta
>
/home/tmp_liorglic/maker_zfUstg/0/265_0.10292360-10294752.arabidopsis.auto_annotator.augustus
#-------------------------------#
Sampling error in intron model. state=37 base=2391

/powerapps/share/centos7/miniconda/miniconda2-4.5.4-MakerMPI/bin/augustus:
ERROR
        Tried to sample from empty list.

Sampling error in intron model. state=37 base=2391

/powerapps/share/centos7/miniconda/miniconda2-4.5.4-MakerMPI/bin/augustus:
ERROR
        Tried to sample from empty list.

ERROR: Augustus failed
--> rank=NA, hostname=compute-0-301.power5
ERROR: Failed while annotating transcripts
ERROR: Chunk failed at level:1, tier_type:4
FAILED CONTIG:chunk08

ERROR: Chunk failed at level:6, tier_type:0
FAILED CONTIG:chunk08

examining contents of the fasta file and run log



--Next Contig--

Processing run.log file...
MAKER WARNING: The file
chunk.maker.output/chunk_datastore/76/17/chunk08//theVoid.chunk08/265_0.10292360-10294752.arabidopsis.auto_annotator.augustus
did not finish on the last run and must be erased


Maker is now finished!!!

I found this thread
<https://groups.google.com/g/maker-devel/c/WBD_GEvELDE> with
a similar error but slightly different augustus command. The suggestion
there was to isolate the augustus command. This sounds like good advice,
but most of the inputs to the command are stored in a temporary location
and are deleted at the end of the MAKER run. Is there any way to restore
them?
Alternatively, are there any known solutions/explanations to this error?
All I could find was this thread
<https://bioinf.uni-greifswald.de/bioinf/forum/viewtopic.php?f=4&t=150> from
the Augustus forum, but it doesn't seem to provide much help.
Would appreciate any ideas/workarounds.
Thanks!
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From carsonhh at gmail.com  Fri Oct  2 14:25:22 2020
From: carsonhh at gmail.com (Carson Holt)
Date: Fri, 2 Oct 2020 14:25:22 -0600
Subject: [maker-devel] Maker yields sequences without start and stop
 codon
In-Reply-To: <CAOXM=CUaZ3+6-YHVzm7Lc+h3fgEtX9ikD8z43Ez9Laj9jGT2DQ@mail.gmail.com>
References: <CAOXM=CUaZ3+6-YHVzm7Lc+h3fgEtX9ikD8z43Ez9Laj9jGT2DQ@mail.gmail.com>
Message-ID: <D281818D-F30A-447D-987F-F5A0434AF7A6@gmail.com>

You can set always_complete=1 for MAKER tottery and fix partial models (it walks out on both sides looking for canonical stops/starts).  Also to clean up partial models and other submission issues, try using Comparative Annotation Toolkit (CAT).  It will take MAEKR results and do all the NCBI related corrections automatically.  It makes submission so much easier.

?Carson



> On Sep 1, 2020, at 12:31 PM, Emmanuel Nnadi <eennadi at gmail.com> wrote:
> 
> I ran my annotation using ESTs from NCBI and transcriptome data and Swiss-prot data. I used SNAP trained twice after which Augustus was trained once.
> 
> I tried to submit the annotated genome to NCBI but have some problems I have not experienced before and do not know how to solve.
> 
> Some of the CDS features have invalid translations. Every CDS feature should have a valid start and stop codon, and should not have any internal stops.  The only exception is if the CDS is partial at the end of a sequence or at an intron/exon boundary.  If the CDS is partial, it must have the appropriate partial symbols.  
> 
> If a CDS feature does not have a valid translation (for example if there is a frameshift), please remove the CDS feature and annotate this with a single gene feature across the entire span.  Include a note on the gene with a brief description.  For example:
> 
> 1       200     gene
>                         gene    phoA
>                         gene_desc       alkaline phosphatase
>                         locus_tag     OBB_0001
>                         note    nonfunctional due to frameshift
> 
> [3] There are 1075 gene features that are not associated with
> any other features (CDS, rRNA, etc.) and are not labelled as
> pseudogenes or as nonfunctional genes.  Did you lose some of
> the annotation you intended to include.
> 
> Please how can this be solved?
> 
> Thanks
> 
> 
> Nnadi Nnaemeka Emmanuel,Ph.D
> Department of Microbiology,
> Faculty of Natural and Applied Science,
> Plateau State University, Bokkos, Plateau State, Nigeria.
> +2348068124819
> Publications: 
>  https://www.researchgate.net/profile/Emmanuel_Nnadi/publications <https://www.researchgate.net/profile/Emmanuel_Nnadi/publications>
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From carsonhh at gmail.com  Fri Oct  2 14:38:39 2020
From: carsonhh at gmail.com (Carson Holt)
Date: Fri, 2 Oct 2020 14:38:39 -0600
Subject: [maker-devel] maker-devel post from guerrer@uni-duesseldorf.de
 requires approval
In-Reply-To: <mailman.370.1600180681.587812.maker-devel_yandell-lab.org@yandell-lab.org>
References: <mailman.370.1600180681.587812.maker-devel_yandell-lab.org@yandell-lab.org>
Message-ID: <483B474B-052F-4148-8FAB-EB2F381BA0DF@gmail.com>

Try looking at it in a browser.  You may see that models are merging because of evidence overlap, snap or augustus does not match the evidence well (you can drop one if it performs poorly).  But visualizing things will help.  For example fungi can lose genes because of UTR overlap (there is an allow_overlap option in MAKER for that).  mRNA-seq can falsely merge into extended transcripts (results in long UTR on models and maker has correct_est_fusion for that).  Neigboring parlors can cluster into a single model (you will see same hit coordinates multiple,e times in the browser - there is a tool called DeFusion for that).  Or evidence may be sparse (should be obvious from a browser).  Assembly errors can be found when you have nice transcripts alignments that do not have working ORFs (found by dragging and dropping est2genome results in browsers like Apollo and letting it calculate ORF).


?Carson


> 
> Hello,
> 
> It appears to me that my abInitio SNAP + Augustus (trained by nexflow) results are worse than the first (est2genome and prot2genome) run. The gene number decreases by more than 6000, the opposite of what I expected.
> 
> Additionally, my abInitio rerun also has less genes than a previous SNAP reannotation.. The AED plots all look more or less the same but the number of genes lowers instead of increasing as I expected (image in annex).
> 
> I'be been running my maker+nextflow pipeline with consistently good results, this species is the exception now.
> 
> Do you have any suggestion? Should I ditch AbInitio training and use the Evidence based annotation? Or maybe just use the closest Augustus model instead of training my own?
> 
> Kind regards,
> Ricardo
> 
> 
> 
> <AEDs.png>
> 



From carsonhh at gmail.com  Fri Oct  2 14:50:35 2020
From: carsonhh at gmail.com (Carson Holt)
Date: Fri, 2 Oct 2020 14:50:35 -0600
Subject: [maker-devel] map_forward and temporary storage questions
In-Reply-To: <YTBPR01MB3839BACB6F6296B734775AA09C360@YTBPR01MB3839.CANPRD01.PROD.OUTLOOK.COM>
References: <YTBPR01MB3839BACB6F6296B734775AA09C360@YTBPR01MB3839.CANPRD01.PROD.OUTLOOK.COM>
Message-ID: <7742D4BF-2BEB-426D-9858-EC2621B5077D@gmail.com>

MAKER uses GFF3 format which is not the same as GTF.  You will need to convert your file to GFF3 format.

You can try this online tool (I haven?t used it to tell you how well it works) http://www.sequenceontology.org/cgi-bin/converter.cgi <http://www.sequenceontology.org/cgi-bin/converter.cgi> 

There are also a number of other resources available when you google "how to convert GTF to GFF3?.

?Carson


> On Sep 25, 2020, at 3:17 AM, Zoe Clarke <zoe.clarke at utoronto.ca> wrote:
> 
> Hello!
> 
> I am currently running Maker on a 2.5GB genome that has already had a list of ~8000 genes very thoroughly annotated. My hope is to find and annotate the rest of the genes using ESTs and protein homology. However, I tested Maker on a single contig of my genome (there are ~20,000 contigs) and I can't find any of the genes from my original gtf file even though I followed all of the instructions in this wiki: http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/Updating_annotations_in_light_of_new_data <http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/Updating_annotations_in_light_of_new_data> (I entered the original gff under model_gff, and used map_forward=1). I am worried this is because my gff3 file isn't formatted properly. Here are a few lines in my gff file as an example:
> --------------------------------------------
> WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  transcript      1094446 1105585 .       +       .       ID=DIMT1.1;geneID=DIMT1
> WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  exon    1094446 1094521 97.75   +       .       Parent=DIMT1.1
> WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  exon    1094874 1094947 97.75   +       .       Parent=DIMT1.1
> WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  exon    1095459 1095545 97.75   +       .       Parent=DIMT1.1
> WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  exon    1097351 1097412 97.75   +       .       Parent=DIMT1.1
> WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  exon    1097492 1097585 97.75   +       .       Parent=DIMT1.1
> WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  exon    1097670 1097719 97.75   +       .       Parent=DIMT1.1
> WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  exon    1098957 1099080 97.75   +       .       Parent=DIMT1.1
> WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  exon    1099217 1099309 97.75   +       .       Parent=DIMT1.1
> WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  exon    1100870 1100934 97.75   +       .       Parent=DIMT1.1
> WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  exon    1101967 1102030 97.75   +       .       Parent=DIMT1.1
> WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  exon    1103784 1103890 97.75   +       .       Parent=DIMT1.1
> WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  exon    1105543 1105585 97.75   +       .       Parent=DIMT1.1
> WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  CDS     1094446 1094521 .       +       0       Parent=DIMT1.1
> WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  CDS     1094874 1094947 .       +       2       Parent=DIMT1.1
> WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  CDS     1095459 1095545 .       +       0       Parent=DIMT1.1
> WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  CDS     1097351 1097412 .       +       0       Parent=DIMT1.1
> WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  CDS     1097492 1097585 .       +       1       Parent=DIMT1.1
> WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  CDS     1097670 1097719 .       +       0       Parent=DIMT1.1
> WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  CDS     1098957 1099080 .       +       1       Parent=DIMT1.1
> WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  CDS     1099217 1099309 .       +       0       Parent=DIMT1.1
> WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  CDS     1100870 1100934 .       +       0       Parent=DIMT1.1
> WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  CDS     1101967 1102030 .       +       1       Parent=DIMT1.1
> WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  CDS     1103784 1103890 .       +       0       Parent=DIMT1.1
> WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  CDS     1105543 1105582 .       +       1       Parent=DIMT1.1
> --------------------------------------
> ?This is from the contig I used as a test for maker, and I can't find DIMT1.1 in the final gff file. At first I thought it might be because "geneID" is a listed attribute, but changing this to "Name" didn't help. Do you have any ideas why these genes might not be mapping forward? If it's something I can fix in the gff file, I am hoping I can fix it and use it for the second round of Maker after I have trained Snap.
> 
> Also, do you think a better quality annotation would results from Snap trained from this curated list of ~8000 genes (that has been expertly done) or by the round 1 output of Maker?
> 
> A final question: I am having memory storage issues with Maker, as it is currently taking up ~15TB of storage with temporary files. I am running Maker on a cluster and whenever my submitted Maker job runs out of memory it fails, so I have to resubmit it about every hour, which leaves a lot of temporary folders (e.g. maker_x6V2y4) in my directory. I notice that some of these temporary files haven't been updated in days - is it okay to delete them?
> 
> Thank you so much for your help!
> Zoe
> ______________________________________
> Zoe Clarke
> PhD candidate in Computational Biology at U of T
> Lab profile: http://baderlab.org/Zoe%20Clarke <http://baderlab.org/Zoe%20Clarke>
> Personal website: https://zoe-clarke.weebly.com/ <https://zoe-clarke.weebly.com/>_______________________________________________
> maker-devel mailing list
> maker-devel at yandell-lab.org <mailto:maker-devel at yandell-lab.org>
> http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org <http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org>
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From carsonhh at gmail.com  Fri Oct  2 15:01:24 2020
From: carsonhh at gmail.com (Carson Holt)
Date: Fri, 2 Oct 2020 15:01:24 -0600
Subject: [maker-devel] MAKER failing during Augustus run
In-Reply-To: <CAOzMDPxivd1gxOJRuaQd6vDLMizt39qRNsAajzvO+Hhy1K--6A@mail.gmail.com>
References: <CAOzMDPxivd1gxOJRuaQd6vDLMizt39qRNsAajzvO+Hhy1K--6A@mail.gmail.com>
Message-ID: <8DAF41A6-5983-482C-ABA1-4F5EDC7388FA@gmail.com>

First try using Augustu v3.3.3 or the live version from GitHub (https://github.com/Gaius-Augustus/Augustus <https://github.com/Gaius-Augustus/Augustus>). You can specify the other augustus version in maker_exe.ctl.  You can use ctl+z to pause the run right when MAKER reaches the specified augustus call.  Or after trying the newer agusuts version, you can upload everything from the run to https://github.com/Gaius-Augustus/Augustus <https://github.com/Gaius-Augustus/Augustus> and I can try to extract the files for you.

Or if you are adventurous you can run in the perl debugger.

#start debugger
perl -dS maker

#continue to augustus calls
DB<1> c Widget::augustus::run

#continue to augustus failure (right before dieing)
DB<2> c 282

At this point just copy the command as files still exist

?Carson


> On Oct 2, 2020, at 2:54 AM, Lior Glick <liorglic at mail.tau.ac.il> wrote:
> 
> Hello,
> I am using MAKER2 with Augustus 3.2.2. I keep getting an error message when annotating a specific contig. The relevant section of the MAKER stderr looks like this:
> 
> Widget::augustus:
> /powerapps/share/centos7/miniconda/miniconda2-4.5.4-MakerMPI/bin/augustus --species=arabidopsis --strand=backward --UTR=off --hintsfile=/home/tmp_liorglic/maker_zfUstg/0/265_0.10292360-10294752.arabidopsis.auto_annotator.xdef.augustus --extrinsicCfgFile=/powerapps/share/centos7/miniconda/miniconda2-4.5.4-MakerMPI/config/extrinsic/extrinsic.MPE.cfg /home/tmp_liorglic/maker_zfUstg/0/265_0.10292360-10294752.arabidopsis.auto_annotator.augustus.fasta > /home/tmp_liorglic/maker_zfUstg/0/265_0.10292360-10294752.arabidopsis.auto_annotator.augustus
> #-------------------------------#
> Sampling error in intron model. state=37 base=2391
> 
> /powerapps/share/centos7/miniconda/miniconda2-4.5.4-MakerMPI/bin/augustus: ERROR
>         Tried to sample from empty list.
> 
> Sampling error in intron model. state=37 base=2391
> 
> /powerapps/share/centos7/miniconda/miniconda2-4.5.4-MakerMPI/bin/augustus: ERROR
>         Tried to sample from empty list.
> 
> ERROR: Augustus failed
> --> rank=NA, hostname=compute-0-301.power5
> ERROR: Failed while annotating transcripts
> ERROR: Chunk failed at level:1, tier_type:4
> FAILED CONTIG:chunk08
> 
> ERROR: Chunk failed at level:6, tier_type:0
> FAILED CONTIG:chunk08
> 
> examining contents of the fasta file and run log
> 
> 
> 
> --Next Contig--
> 
> Processing run.log file...
> MAKER WARNING: The file chunk.maker.output/chunk_datastore/76/17/chunk08//theVoid.chunk08/265_0.10292360-10294752.arabidopsis.auto_annotator.augustus
> did not finish on the last run and must be erased
> 
> 
> Maker is now finished!!!
> 
> I found this thread <https://groups.google.com/g/maker-devel/c/WBD_GEvELDE> with a similar error but slightly different augustus command. The suggestion there was to isolate the augustus command. This sounds like good advice, but most of the inputs to the command are stored in a temporary location and are deleted at the end of the MAKER run. Is there any way to restore them?
> Alternatively, are there any known solutions/explanations to this error? All I could find was this thread <https://bioinf.uni-greifswald.de/bioinf/forum/viewtopic.php?f=4&t=150> from the Augustus forum, but it doesn't seem to provide much help.
> Would appreciate any ideas/workarounds.
> Thanks!
> 
> _______________________________________________
> maker-devel mailing list
> maker-devel at yandell-lab.org
> http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org

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From zoe.clarke at utoronto.ca  Mon Oct  5 07:47:19 2020
From: zoe.clarke at utoronto.ca (Zoe Clarke)
Date: Mon, 5 Oct 2020 13:47:19 +0000
Subject: [maker-devel] map_forward and temporary storage questions
In-Reply-To: <7742D4BF-2BEB-426D-9858-EC2621B5077D@gmail.com>
References: <YTBPR01MB3839BACB6F6296B734775AA09C360@YTBPR01MB3839.CANPRD01.PROD.OUTLOOK.COM>,
	<7742D4BF-2BEB-426D-9858-EC2621B5077D@gmail.com>
Message-ID: <YTBPR01MB3839AFB99FE4758AAA9BBFAA9C0C0@YTBPR01MB3839.CANPRD01.PROD.OUTLOOK.COM>

Thanks Carson!

I managed to get the GFF3 file fixed and Maker is now recognizing it the way it should.

I am hoping I can also ask for your advice on functional annotation with Maker. The result of my current run will be gff and fasta files that have the original gff3 genes plus Maker's. The original gff3 file was annotated with HGNC gene symbols, so these new files are a mix of gene symbols and Maker-derived gene names. I would ideally like my final annotation to consist almost entirely of gene symbols. Is the only way to do this (after using Blastp and InterProScan to get putative homology) to undergo an additional manual curation process through something like Apollo?

Thanks again,
Zoe

______________________________________
Zoe Clarke
PhD candidate in Computational Biology at U of T
Lab profile: http://baderlab.org/Zoe%20Clarke
Personal website: https://zoe-clarke.weebly.com/
________________________________
From: Carson Holt <carsonhh at gmail.com>
Sent: October 2, 2020 4:50 PM
To: Zoe Clarke <zoe.clarke at utoronto.ca>
Cc: maker-devel at yandell-lab.org <maker-devel at yandell-lab.org>
Subject: Re: [maker-devel] map_forward and temporary storage questions

EXTERNAL EMAIL:  Treat content with extra caution.
MAKER uses GFF3 format which is not the same as GTF.  You will need to convert your file to GFF3 format.

You can try this online tool (I haven?t used it to tell you how well it works) http://www.sequenceontology.org/cgi-bin/converter.cgi

There are also a number of other resources available when you google "how to convert GTF to GFF3?.

?Carson


On Sep 25, 2020, at 3:17 AM, Zoe Clarke <zoe.clarke at utoronto.ca<mailto:zoe.clarke at utoronto.ca>> wrote:

Hello!

I am currently running Maker on a 2.5GB genome that has already had a list of ~8000 genes very thoroughly annotated. My hope is to find and annotate the rest of the genes using ESTs and protein homology. However, I tested Maker on a single contig of my genome (there are ~20,000 contigs) and I can't find any of the genes from my original gtf file even though I followed all of the instructions in this wiki: http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/Updating_annotations_in_light_of_new_data (I entered the original gff under model_gff, and used map_forward=1). I am worried this is because my gff3 file isn't formatted properly. Here are a few lines in my gff file as an example:
--------------------------------------------
WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  transcript      1094446 1105585 .       +       .       ID=DIMT1.1;geneID=DIMT1
WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  exon    1094446 1094521 97.75   +       .       Parent=DIMT1.1
WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  exon    1094874 1094947 97.75   +       .       Parent=DIMT1.1
WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  exon    1095459 1095545 97.75   +       .       Parent=DIMT1.1
WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  exon    1097351 1097412 97.75   +       .       Parent=DIMT1.1
WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  exon    1097492 1097585 97.75   +       .       Parent=DIMT1.1
WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  exon    1097670 1097719 97.75   +       .       Parent=DIMT1.1
WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  exon    1098957 1099080 97.75   +       .       Parent=DIMT1.1
WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  exon    1099217 1099309 97.75   +       .       Parent=DIMT1.1
WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  exon    1100870 1100934 97.75   +       .       Parent=DIMT1.1
WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  exon    1101967 1102030 97.75   +       .       Parent=DIMT1.1
WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  exon    1103784 1103890 97.75   +       .       Parent=DIMT1.1
WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  exon    1105543 1105585 97.75   +       .       Parent=DIMT1.1
WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  CDS     1094446 1094521 .       +       0       Parent=DIMT1.1
WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  CDS     1094874 1094947 .       +       2       Parent=DIMT1.1
WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  CDS     1095459 1095545 .       +       0       Parent=DIMT1.1
WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  CDS     1097351 1097412 .       +       0       Parent=DIMT1.1
WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  CDS     1097492 1097585 .       +       1       Parent=DIMT1.1
WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  CDS     1097670 1097719 .       +       0       Parent=DIMT1.1
WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  CDS     1098957 1099080 .       +       1       Parent=DIMT1.1
WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  CDS     1099217 1099309 .       +       0       Parent=DIMT1.1
WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  CDS     1100870 1100934 .       +       0       Parent=DIMT1.1
WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  CDS     1101967 1102030 .       +       1       Parent=DIMT1.1
WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  CDS     1103784 1103890 .       +       0       Parent=DIMT1.1
WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  CDS     1105543 1105582 .       +       1       Parent=DIMT1.1
--------------------------------------
?This is from the contig I used as a test for maker, and I can't find DIMT1.1 in the final gff file. At first I thought it might be because "geneID" is a listed attribute, but changing this to "Name" didn't help. Do you have any ideas why these genes might not be mapping forward? If it's something I can fix in the gff file, I am hoping I can fix it and use it for the second round of Maker after I have trained Snap.

Also, do you think a better quality annotation would results from Snap trained from this curated list of ~8000 genes (that has been expertly done) or by the round 1 output of Maker?

A final question: I am having memory storage issues with Maker, as it is currently taking up ~15TB of storage with temporary files. I am running Maker on a cluster and whenever my submitted Maker job runs out of memory it fails, so I have to resubmit it about every hour, which leaves a lot of temporary folders (e.g. maker_x6V2y4) in my directory. I notice that some of these temporary files haven't been updated in days - is it okay to delete them?

Thank you so much for your help!
Zoe
______________________________________
Zoe Clarke
PhD candidate in Computational Biology at U of T
Lab profile: http://baderlab.org/Zoe%20Clarke
Personal website: https://zoe-clarke.weebly.com/
_______________________________________________
maker-devel mailing list
maker-devel at yandell-lab.org<mailto:maker-devel at yandell-lab.org>
http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org

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From carsonhh at gmail.com  Thu Oct 15 19:45:45 2020
From: carsonhh at gmail.com (Carson Holt)
Date: Thu, 15 Oct 2020 19:45:45 -0600
Subject: [maker-devel] map_forward and temporary storage questions
In-Reply-To: <YTBPR01MB3839AFB99FE4758AAA9BBFAA9C0C0@YTBPR01MB3839.CANPRD01.PROD.OUTLOOK.COM>
References: <YTBPR01MB3839BACB6F6296B734775AA09C360@YTBPR01MB3839.CANPRD01.PROD.OUTLOOK.COM>
	<7742D4BF-2BEB-426D-9858-EC2621B5077D@gmail.com>
	<YTBPR01MB3839AFB99FE4758AAA9BBFAA9C0C0@YTBPR01MB3839.CANPRD01.PROD.OUTLOOK.COM>
Message-ID: <28F61590-140A-44E9-AD63-BCFAC9179391@gmail.com>

If you can create a two column file (column1 being the old ID and column2 being the new ID), you can use the map_fasta_ids and map_gff_ids to rename everything with a corresponding line in the two column file.  Make sure no ID's occur twice (in old or new), it will create issues.  The maker ID will not be lost, instead it will move to the Alias= field in the GFF3.

?Carson



> On Oct 5, 2020, at 7:47 AM, Zoe Clarke <zoe.clarke at utoronto.ca> wrote:
> 
> Thanks Carson!
> 
> I managed to get the GFF3 file fixed and Maker is now recognizing it the way it should.
> 
> I am hoping I can also ask for your advice on functional annotation with Maker. The result of my current run will be gff and fasta files that have the original gff3 genes plus Maker's. The original gff3 file was annotated with HGNC gene symbols, so these new files are a mix of gene symbols and Maker-derived gene names. I would ideally like my final annotation to consist almost entirely of gene symbols. Is the only way to do this (after using Blastp and InterProScan to get putative homology) to undergo an additional manual curation process through something like Apollo?
> 
> Thanks again,
> Zoe
> 
> ______________________________________
> Zoe Clarke
> PhD candidate in Computational Biology at U of T
> Lab profile: http://baderlab.org/Zoe%20Clarke <http://baderlab.org/Zoe%20Clarke>
> Personal website: https://zoe-clarke.weebly.com/ <https://zoe-clarke.weebly.com/>
> From: Carson Holt <carsonhh at gmail.com <mailto:carsonhh at gmail.com>>
> Sent: October 2, 2020 4:50 PM
> To: Zoe Clarke <zoe.clarke at utoronto.ca <mailto:zoe.clarke at utoronto.ca>>
> Cc: maker-devel at yandell-lab.org <mailto:maker-devel at yandell-lab.org> <maker-devel at yandell-lab.org <mailto:maker-devel at yandell-lab.org>>
> Subject: Re: [maker-devel] map_forward and temporary storage questions
>  
> EXTERNAL EMAIL:  Treat content with extra caution. 
> MAKER uses GFF3 format which is not the same as GTF.  You will need to convert your file to GFF3 format.
> 
> You can try this online tool (I haven?t used it to tell you how well it works) http://www.sequenceontology.org/cgi-bin/converter.cgi <http://www.sequenceontology.org/cgi-bin/converter.cgi> 
> 
> There are also a number of other resources available when you google "how to convert GTF to GFF3?.
> 
> ?Carson
> 
> 
>> On Sep 25, 2020, at 3:17 AM, Zoe Clarke <zoe.clarke at utoronto.ca <mailto:zoe.clarke at utoronto.ca>> wrote:
>> 
>> Hello!
>> 
>> I am currently running Maker on a 2.5GB genome that has already had a list of ~8000 genes very thoroughly annotated. My hope is to find and annotate the rest of the genes using ESTs and protein homology. However, I tested Maker on a single contig of my genome (there are ~20,000 contigs) and I can't find any of the genes from my original gtf file even though I followed all of the instructions in this wiki: http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/Updating_annotations_in_light_of_new_data <http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/Updating_annotations_in_light_of_new_data> (I entered the original gff under model_gff, and used map_forward=1). I am worried this is because my gff3 file isn't formatted properly. Here are a few lines in my gff file as an example:
>> --------------------------------------------
>> WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  transcript      1094446 1105585 .       +       .       ID=DIMT1.1;geneID=DIMT1
>> WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  exon    1094446 1094521 97.75   +       .       Parent=DIMT1.1
>> WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  exon    1094874 1094947 97.75   +       .       Parent=DIMT1.1
>> WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  exon    1095459 1095545 97.75   +       .       Parent=DIMT1.1
>> WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  exon    1097351 1097412 97.75   +       .       Parent=DIMT1.1
>> WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  exon    1097492 1097585 97.75   +       .       Parent=DIMT1.1
>> WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  exon    1097670 1097719 97.75   +       .       Parent=DIMT1.1
>> WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  exon    1098957 1099080 97.75   +       .       Parent=DIMT1.1
>> WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  exon    1099217 1099309 97.75   +       .       Parent=DIMT1.1
>> WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  exon    1100870 1100934 97.75   +       .       Parent=DIMT1.1
>> WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  exon    1101967 1102030 97.75   +       .       Parent=DIMT1.1
>> WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  exon    1103784 1103890 97.75   +       .       Parent=DIMT1.1
>> WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  exon    1105543 1105585 97.75   +       .       Parent=DIMT1.1
>> WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  CDS     1094446 1094521 .       +       0       Parent=DIMT1.1
>> WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  CDS     1094874 1094947 .       +       2       Parent=DIMT1.1
>> WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  CDS     1095459 1095545 .       +       0       Parent=DIMT1.1
>> WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  CDS     1097351 1097412 .       +       0       Parent=DIMT1.1
>> WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  CDS     1097492 1097585 .       +       1       Parent=DIMT1.1
>> WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  CDS     1097670 1097719 .       +       0       Parent=DIMT1.1
>> WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  CDS     1098957 1099080 .       +       1       Parent=DIMT1.1
>> WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  CDS     1099217 1099309 .       +       0       Parent=DIMT1.1
>> WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  CDS     1100870 1100934 .       +       0       Parent=DIMT1.1
>> WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  CDS     1101967 1102030 .       +       1       Parent=DIMT1.1
>> WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  CDS     1103784 1103890 .       +       0       Parent=DIMT1.1
>> WCK01_AAF20200214_F8-ctg36      ovaltine_v0.13  CDS     1105543 1105582 .       +       1       Parent=DIMT1.1
>> --------------------------------------
>> ?This is from the contig I used as a test for maker, and I can't find DIMT1.1 in the final gff file. At first I thought it might be because "geneID" is a listed attribute, but changing this to "Name" didn't help. Do you have any ideas why these genes might not be mapping forward? If it's something I can fix in the gff file, I am hoping I can fix it and use it for the second round of Maker after I have trained Snap.
>> 
>> Also, do you think a better quality annotation would results from Snap trained from this curated list of ~8000 genes (that has been expertly done) or by the round 1 output of Maker?
>> 
>> A final question: I am having memory storage issues with Maker, as it is currently taking up ~15TB of storage with temporary files. I am running Maker on a cluster and whenever my submitted Maker job runs out of memory it fails, so I have to resubmit it about every hour, which leaves a lot of temporary folders (e.g. maker_x6V2y4) in my directory. I notice that some of these temporary files haven't been updated in days - is it okay to delete them?
>> 
>> Thank you so much for your help!
>> Zoe
>> ______________________________________
>> Zoe Clarke
>> PhD candidate in Computational Biology at U of T
>> Lab profile: http://baderlab.org/Zoe%20Clarke <http://baderlab.org/Zoe%20Clarke>
>> Personal website: https://zoe-clarke.weebly.com/ <https://zoe-clarke.weebly.com/>_______________________________________________
>> maker-devel mailing list
>> maker-devel at yandell-lab.org <mailto:maker-devel at yandell-lab.org>
>> http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org <http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org>
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From taosheng.x at gmail.com  Sat Oct 17 00:48:06 2020
From: taosheng.x at gmail.com (Xu, taosheng)
Date: Sat, 17 Oct 2020 14:48:06 +0800
Subject: [maker-devel] Does maker support muti-processing for a single long
 fasta sequence using openMPI?
Message-ID: <CALJhmFoNOdxFb4gQ4jYP=FZqaHgZdVOhQOpPuyd5bMAeYZ8ucg@mail.gmail.com>

Dear Maker Development Team,
I wonder whether maker supports parallel processing for a single long
genome sequence?

When I submit my maker task using openMPI with multiple cpus (like, mpiexec
-n 40  maker) to annotate a single long genome sequence, always only one
maker with 4 rmblast run. The other cpus is on idle.

I want to use the maker parallel processing with openMPI to speed up a
single ultra-long genome sequence annotation.

Best regards,
Taosheng
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From carsonhh at gmail.com  Mon Oct 19 08:32:20 2020
From: carsonhh at gmail.com (Carson Holt)
Date: Mon, 19 Oct 2020 08:32:20 -0600
Subject: [maker-devel] Does maker support muti-processing for a single
 long fasta sequence using openMPI?
In-Reply-To: <CALJhmFoNOdxFb4gQ4jYP=FZqaHgZdVOhQOpPuyd5bMAeYZ8ucg@mail.gmail.com>
References: <CALJhmFoNOdxFb4gQ4jYP=FZqaHgZdVOhQOpPuyd5bMAeYZ8ucg@mail.gmail.com>
Message-ID: <AC94C4EB-A696-4830-A650-1A33EB67B281@gmail.com>

Yes. It will divide contigs into chunks the same size as the max_dna_len parameter.

?Carson

Sent from my iPhone

> On Oct 17, 2020, at 12:48 AM, Xu, taosheng <taosheng.x at gmail.com> wrote:
> 
> ?
> Dear Maker Development Team,
> I wonder whether maker supports parallel processing for a single long genome sequence?
> 
> When I submit my maker task using openMPI with multiple cpus (like, mpiexec -n 40  maker) to annotate a single long genome sequence, always only one maker with 4 rmblast run. The other cpus is on idle.
> 
> I want to use the maker parallel processing with openMPI to speed up a single ultra-long genome sequence annotation.
> 
> Best regards,
> Taosheng
> _______________________________________________
> maker-devel mailing list
> maker-devel at yandell-lab.org
> http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org



From taosheng.x at gmail.com  Tue Oct 20 10:23:25 2020
From: taosheng.x at gmail.com (Xu, taosheng)
Date: Wed, 21 Oct 2020 00:23:25 +0800
Subject: [maker-devel] Does maker support muti-processing for a single
 long fasta sequence using openMPI?
In-Reply-To: <AC94C4EB-A696-4830-A650-1A33EB67B281@gmail.com>
References: <CALJhmFoNOdxFb4gQ4jYP=FZqaHgZdVOhQOpPuyd5bMAeYZ8ucg@mail.gmail.com>
	<AC94C4EB-A696-4830-A650-1A33EB67B281@gmail.com>
Message-ID: <CALJhmFocG7D-K0gdGJ5831V=gnPp0BDrEMu138W3HV=QmKs2Ug@mail.gmail.com>

Thank you very much Carson for your timely response,
Yes I think so. The Maker MPI should support the multi-processing of an
ultra-long single sequence. But I cannot run it successfully for a single
sequence.
First I  make sure the openMPI with maker has been installed properly. It
works well for multiple DNA sequences in a parallel way.
When I submit a maker job for an ultra-long single sequence (mpiexec -mca
btl ^openib -n 40 maker -g scaffold1.fasta -fix_nucleotides, The
max_dna_len is set to 100000). It always left only one maker thread run.
The other maker threads are disappeared and show finished in the output
information. See the output information below. Please help me to check it.
Thanks for your kind help and your time.

#-----MAKER Behavior Options
max_dna_len=100000 #length for dividing up contigs into chunks
(increases/decreases memory usage)
min_contig=1 #skip genome contigs below this length (under 10kb are often
useless)

Best regards,
Taosheng



OUTPUT Information
STATUS: Processing and indexing input FASTA files...
STATUS: Setting up database for any GFF3 input...
examining contents of the fasta file and run log
A data structure will be created for you at:
/data/splitgenome/top1000/splitGenome/part1/plant.maker.output/plant_datastore

To access files for individual sequences use the datastore index:
/data/splitgenome/top1000/splitGenome/part1/plant.maker.output/plant_master_datastore_index.log

STATUS: Now running MAKER...



--Next Contig--

Processing run.log file...
examining contents of the fasta file and run log



--Next Contig--

#---------------------------------------------------------------------
Another instance of maker is processing this contig!!
SeqID: scaffold#1
Length: 73580997
#---------------------------------------------------------------------


examining contents of the fasta file and run log



--Next Contig--

#---------------------------------------------------------------------
Another instance of maker is processing this contig!!
SeqID: scaffold#1
Length: 73580997
#---------------------------------------------------------------------




Maker is now finished!!!



Start_time: 1603000030
End_time:   1603000033
Elapsed:    3
A data structure will be created for you at:
/data/splitgenome/top1000/splitGenome/part1/plant.maker.output/plant_datastore

To access files for individual sequences use the datastore index:
/data/splitgenome/top1000/splitGenome/part1/plant.maker.output/plant_master_datastore_index.log

STATUS: Now running MAKER...
MAKER WARNING: The file
plant.maker.output/plant_datastore/B5/CD/scaffold#1//theVoid.scaffold#1/28/scaffold#1.289.plant_repeatFinal%2Elib%2Empi%2E10%2E2.specific.out
did not finish on the last run and must be erased
WARNING: Multiple MAKER processes have been started in the
same directory.

STATUS: Processing and indexing input FASTA files...
examining contents of the fasta file and run log



--Next Contig--

#---------------------------------------------------------------------
Another instance of maker is processing this contig!!
SeqID: scaffold#1
Length: 73580997
#---------------------------------------------------------------------


WARNING: Multiple MAKER processes have been started in the
same directory.

STATUS: Processing and indexing input FASTA files...
STATUS: Setting up database for any GFF3 input...
STATUS: Setting up database for any GFF3 input...
A data structure will be created for you at:
/data/splitgenome/top1000/splitGenome/part1/plant.maker.output/plant_datastore

To access files for individual sequences use the datastore index:
/data/splitgenome/top1000/splitGenome/part1/plant.maker.output/plant_master_datastore_index.log

STATUS: Now running MAKER...
examining contents of the fasta file and run log



--Next Contig--

#---------------------------------------------------------------------
Another instance of maker is processing this contig!!
SeqID: scaffold#1
Length: 73580997
#---------------------------------------------------------------------




*Maker is now finished!!!*



Start_time: 1603000030
End_time:   1603000034
Elapsed:    4
#---------------------------------------------------------------------
Now starting the contig!!
SeqID: scaffold#1
Length: 73580997
#---------------------------------------------------------------------


examining contents of the fasta file and run log



--Next Contig--

#---------------------------------------------------------------------
Another instance of maker is processing this contig!!
SeqID: scaffold#1
Length: 73580997
#---------------------------------------------------------------------


examining contents of the fasta file and run log



--Next Contig--

#---------------------------------------------------------------------
Another instance of maker is processing this contig!!
SeqID: scaffold#1
Length: 73580997
#---------------------------------------------------------------------




Start_time: 1603000030
End_time:   1603000034
Elapsed:    4


*Maker is now finished!!!*

A data structure will be created for you at:
/data/splitgenome/top1000/splitGenome/part1/plant.maker.output/plant_datastore

To access files for individual sequences use the datastore index:
/data/splitgenome/top1000/splitGenome/part1/plant.maker.output/plant_master_datastore_index.log

STATUS: Now running MAKER...
examining contents of the fasta file and run log
..........

Maker is now finished!!!



Start_time: 1602920407
End_time:   1602920580
Elapsed:    173
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_VflRYH; ./maker3.01/exe/RepeatMasker/RepeatMasker
/data/splitgenome/top1000/splitGenome/part1/plant.maker.output/plant_datastore/B5/CD/scaffold#1//theVoid.scaffold#1/0/scaffold#1.0.plant_repeatFinal%2Elib%2Empi%2E10%2E0.specific
-dir
/data/splitgenome/top1000/splitGenome/part1/plant.maker.output/plant_datastore/B5/CD/scaffold#1//theVoid.scaffold#1/0
-pa 1 -lib
/data/splitgenome/top1000/splitGenome/part1/plant.maker.output/mpi_blastdb/plant_repeatFinal%2Elib.mpi.10/plant_repeatFinal%2Elib.mpi.10.0
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_VflRYH; ./maker3.01/exe/RepeatMasker/RepeatMasker
/data/splitgenome/top1000/splitGenome/part1/plant.maker.output/plant_datastore/B5/CD/scaffold#1//theVoid.scaffold#1/0/scaffold#1.0.plant_repeatFinal%2Elib%2Empi%2E10%2E1.specific
-dir
/data/splitgenome/top1000/splitGenome/part1/plant.maker.output/plant_datastore/B5/CD/scaffold#1//theVoid.scaffold#1/0
-pa 1 -lib
/data/splitgenome/top1000/splitGenome/part1/plant.maker.output/mpi_blastdb/plant_repeatFinal%2Elib.mpi.10/plant_repeatFinal%2Elib.mpi.10.1
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_VflRYH; ./maker3.01/exe/RepeatMasker/RepeatMasker
/data/splitgenome/top1000/splitGenome/part1/plant.maker.output/plant_datastore/B5/CD/scaffold#1//theVoid.scaffold#1/0/scaffold#1.0.plant_repeatFinal%2Elib%2Empi%2E10%2E2.specific
-dir
/data/splitgenome/top1000/splitGenome/part1/plant.maker.output/plant_datastore/B5/CD/scaffold#1//theVoid.scaffold#1/0
-pa 1 -lib
/data/splitgenome/top1000/splitGenome/part1/plant.maker.output/mpi_blastdb/plant_repeatFinal%2Elib.mpi.10/plant_repeatFinal%2Elib.mpi.10.2
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_VflRYH; ./maker3.01/exe/RepeatMasker/RepeatMasker
/data/splitgenome/top1000/splitGenome/part1/plant.maker.output/plant_datastore/B5/CD/scaffold#1//theVoid.scaffold#1/0/scaffold#1.0.plant_repeatFinal%2Elib%2Empi%2E10%2E3.specific
-dir
/data/splitgenome/top1000/splitGenome/part1/plant.maker.output/plant_datastore/B5/CD/scaffold#1//theVoid.scaffold#1/0
-pa 1 -lib
/data/splitgenome/top1000/splitGenome/part1/plant.maker.output/mpi_blastdb/plant_repeatFinal%2Elib.mpi.10/plant_repeatFinal%2Elib.mpi.10.3
#-------------------------------#
running  repeat masker.
#--------- command -------------#

.....

On Mon, Oct 19, 2020 at 10:32 PM Carson Holt <carsonhh at gmail.com> wrote:

> Yes. It will divide contigs into chunks the same size as the max_dna_len
> parameter.
>
> ?Carson
>
> Sent from my iPhone
>
> > On Oct 17, 2020, at 12:48 AM, Xu, taosheng <taosheng.x at gmail.com> wrote:
> >
> > ?
> > Dear Maker Development Team,
> > I wonder whether maker supports parallel processing for a single long
> genome sequence?
> >
> > When I submit my maker task using openMPI with multiple cpus (like,
> mpiexec -n 40  maker) to annotate a single long genome sequence, always
> only one maker with 4 rmblast run. The other cpus is on idle.
> >
> > I want to use the maker parallel processing with openMPI to speed up a
> single ultra-long genome sequence annotation.
> >
> > Best regards,
> > Taosheng
> > _______________________________________________
> > maker-devel mailing list
> > maker-devel at yandell-lab.org
> > http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org
>
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From zoe.clarke at utoronto.ca  Fri Oct  9 05:39:57 2020
From: zoe.clarke at utoronto.ca (Zoe Clarke)
Date: Fri, 9 Oct 2020 11:39:57 +0000
Subject: [maker-devel] Issue with single contig
Message-ID: <YTBPR01MB3839C4605F16FAA8BDA8EFFE9C080@YTBPR01MB3839.CANPRD01.PROD.OUTLOOK.COM>

Hello!

Sorry to bother you again. I am having a very specific problem with one of my contigs, and I was hoping you could help.

I can cancelled my last Maker run because one of my contigs failed around 56,000 times according to the output_rnd1_master_datastore_index.log file. It was just perpetually failing during the run with the following message:

ERROR: Chunk failed at level:0, tier_type:0open3: fork failed: Cannot allocate memory at dir/File/NFSLock.pm line 1037.

I am running Maker over multiple nodes, so I figured there might be an issue with a log file getting truncated or malformed. Looking at the files stored in the void for this contig, there are also a ton of files which I think might be causing an issue:

0                         run.log.child.112                                     WCK01_AAF20200214_F8-ctg57.118-119.raw.section       WCK01_AAF20200214_F8-ctg57.55-56.raw.section
1                         run.log.child.113                                     WCK01_AAF20200214_F8-ctg57.118.pred.raw.section      WCK01_AAF20200214_F8-ctg57.55.pred.raw.section
10                        run.log.child.114                                     WCK01_AAF20200214_F8-ctg57.118.raw.section           WCK01_AAF20200214_F8-ctg57.55.raw.section
11                        run.log.child.115                                     WCK01_AAF20200214_F8-ctg57.119-120.raw.section       WCK01_AAF20200214_F8-ctg57.56-57.raw.section
12                        run.log.child.116                                     WCK01_AAF20200214_F8-ctg57.119.pred.raw.section      WCK01_AAF20200214_F8-ctg57.56.pred.raw.section
2                         run.log.child.117                                     WCK01_AAF20200214_F8-ctg57.119.raw.section           WCK01_AAF20200214_F8-ctg57.5-6.raw.section
3                         run.log.child.118                                     WCK01_AAF20200214_F8-ctg57.11.pred.raw.section       WCK01_AAF20200214_F8-ctg57.56.raw.section
4                         run.log.child.119                                     WCK01_AAF20200214_F8-ctg57.11.raw.section            WCK01_AAF20200214_F8-ctg57.57-58.raw.section
5                         run.log.child.12                                      WCK01_AAF20200214_F8-ctg57.120-121.raw.section       WCK01_AAF20200214_F8-ctg57.57.pred.raw.section
6                         run.log.child.120                                     WCK01_AAF20200214_F8-ctg57.120.pred.raw.section      WCK01_AAF20200214_F8-ctg57.57.raw.section
7                         run.log.child.121                                     WCK01_AAF20200214_F8-ctg57.120.raw.section           WCK01_AAF20200214_F8-ctg57.58-59.raw.section
8                         run.log.child.122                                     WCK01_AAF20200214_F8-ctg57.121-122.raw.section       WCK01_AAF20200214_F8-ctg57.58.pred.raw.section
9                         run.log.child.123                                     WCK01_AAF20200214_F8-ctg57.12-13.raw.section         WCK01_AAF20200214_F8-ctg57.58.raw.section
evidence_0.gff            run.log.child.124                                     WCK01_AAF20200214_F8-ctg57.121.end.blastn.holdover   WCK01_AAF20200214_F8-ctg57.59-60.raw.section
evidence_100.gff          run.log.child.125                                     WCK01_AAF20200214_F8-ctg57.121.end.blastx.holdover   WCK01_AAF20200214_F8-ctg57.59.pred.raw.section
evidence_101.gff          run.log.child.13                                      WCK01_AAF20200214_F8-ctg57.121.pred.raw.section      WCK01_AAF20200214_F8-ctg57.59.raw.section
evidence_102.gff          run.log.child.14                                      WCK01_AAF20200214_F8-ctg57.121.raw.section           WCK01_AAF20200214_F8-ctg57.5.pred.raw.section
evidence_103.gff          run.log.child.15                                      WCK01_AAF20200214_F8-ctg57.122-123.raw.section       WCK01_AAF20200214_F8-ctg57.5.raw.section
evidence_104.gff          run.log.child.16                                      WCK01_AAF20200214_F8-ctg57.122.pred.raw.section      WCK01_AAF20200214_F8-ctg57.60-61.raw.section
evidence_105.gff          run.log.child.17                                      WCK01_AAF20200214_F8-ctg57.122.raw.section           WCK01_AAF20200214_F8-ctg57.60.pred.raw.section
evidence_106.gff          run.log.child.18                                      WCK01_AAF20200214_F8-ctg57.123-124.raw.section       WCK01_AAF20200214_F8-ctg57.60.raw.section
evidence_107.gff          run.log.child.19                                      WCK01_AAF20200214_F8-ctg57.123.pred.raw.section      WCK01_AAF20200214_F8-ctg57.61-62.raw.section
evidence_108.gff          run.log.child.2                                       WCK01_AAF20200214_F8-ctg57.123.raw.section           WCK01_AAF20200214_F8-ctg57.61.pred.raw.section
evidence_109.gff          run.log.child.20                                      WCK01_AAF20200214_F8-ctg57.124-125.raw.section       WCK01_AAF20200214_F8-ctg57.61.raw.section
evidence_10.gff           run.log.child.21                                      WCK01_AAF20200214_F8-ctg57.124.pred.raw.section      WCK01_AAF20200214_F8-ctg57.62-63.raw.section
evidence_110.gff          run.log.child.22                                      WCK01_AAF20200214_F8-ctg57.124.raw.section           WCK01_AAF20200214_F8-ctg57.62.pred.raw.section
evidence_111.gff          run.log.child.23                                      WCK01_AAF20200214_F8-ctg57.125.pred.raw.section      WCK01_AAF20200214_F8-ctg57.62.raw.section
evidence_112.gff          run.log.child.24                                      WCK01_AAF20200214_F8-ctg57.125.raw.section           WCK01_AAF20200214_F8-ctg57.63-64.raw.section
evidence_113.gff          run.log.child.25                                      WCK01_AAF20200214_F8-ctg57.12.pred.raw.section       WCK01_AAF20200214_F8-ctg57.63.pred.raw.section
evidence_114.gff          run.log.child.26                                      WCK01_AAF20200214_F8-ctg57.1-2.raw.section           WCK01_AAF20200214_F8-ctg57.63.raw.section
evidence_115.gff          run.log.child.27                                      WCK01_AAF20200214_F8-ctg57.12.raw.section            WCK01_AAF20200214_F8-ctg57.64-65.raw.section
evidence_116.gff          run.log.child.28                                      WCK01_AAF20200214_F8-ctg57.13-14.raw.section         WCK01_AAF20200214_F8-ctg57.64.pred.raw.section
evidence_116.gff.ann      run.log.child.29                                      WCK01_AAF20200214_F8-ctg57.13.pred.raw.section       WCK01_AAF20200214_F8-ctg57.64.raw.section
evidence_116.gff.def      run.log.child.3                                       WCK01_AAF20200214_F8-ctg57.13.raw.section            WCK01_AAF20200214_F8-ctg57.65-66.raw.section
evidence_116.gff.seq      run.log.child.30                                      WCK01_AAF20200214_F8-ctg57.14-15.raw.section         WCK01_AAF20200214_F8-ctg57.65.pred.raw.section
evidence_117.gff          run.log.child.31                                      WCK01_AAF20200214_F8-ctg57.14.pred.raw.section       WCK01_AAF20200214_F8-ctg57.65.raw.section
evidence_118.gff          run.log.child.32                                      WCK01_AAF20200214_F8-ctg57.14.raw.section            WCK01_AAF20200214_F8-ctg57.66-67.raw.section
evidence_119.gff          run.log.child.33                                      WCK01_AAF20200214_F8-ctg57.15-16.raw.section         WCK01_AAF20200214_F8-ctg57.66.pred.raw.section
evidence_11.gff           run.log.child.34                                      WCK01_AAF20200214_F8-ctg57.15.pred.raw.section       WCK01_AAF20200214_F8-ctg57.66.raw.section
evidence_120.gff          run.log.child.35                                      WCK01_AAF20200214_F8-ctg57.15.raw.section            WCK01_AAF20200214_F8-ctg57.67-68.raw.section
evidence_121.gff          run.log.child.36                                      WCK01_AAF20200214_F8-ctg57.16-17.raw.section         WCK01_AAF20200214_F8-ctg57.67.pred.raw.section
evidence_122.gff          run.log.child.37                                      WCK01_AAF20200214_F8-ctg57.16.pred.raw.section       WCK01_AAF20200214_F8-ctg57.6-7.raw.section
evidence_123.gff          run.log.child.38                                      WCK01_AAF20200214_F8-ctg57.16.raw.section            WCK01_AAF20200214_F8-ctg57.67.raw.section
evidence_124.gff          run.log.child.39                                      WCK01_AAF20200214_F8-ctg57.17-18.raw.section         WCK01_AAF20200214_F8-ctg57.68-69.raw.section
evidence_125.gff          run.log.child.4                                       WCK01_AAF20200214_F8-ctg57.17.pred.raw.section       WCK01_AAF20200214_F8-ctg57.68.pred.raw.section
evidence_12.gff           run.log.child.40                                      WCK01_AAF20200214_F8-ctg57.17.raw.section            WCK01_AAF20200214_F8-ctg57.68.raw.section
evidence_13.gff           run.log.child.41                                      WCK01_AAF20200214_F8-ctg57.18-19.raw.section         WCK01_AAF20200214_F8-ctg57.68.start.blastn.holdover
evidence_14.gff           run.log.child.42                                      WCK01_AAF20200214_F8-ctg57.18.pred.raw.section       WCK01_AAF20200214_F8-ctg57.68.start.blastx.holdover
evidence_15.gff           run.log.child.43                                      WCK01_AAF20200214_F8-ctg57.18.raw.section            WCK01_AAF20200214_F8-ctg57.69-70.raw.section
evidence_16.gff           run.log.child.44                                      WCK01_AAF20200214_F8-ctg57.19-20.raw.section         WCK01_AAF20200214_F8-ctg57.69.end.blastn.holdover
evidence_17.gff           run.log.child.45                                      WCK01_AAF20200214_F8-ctg57.19.pred.raw.section       WCK01_AAF20200214_F8-ctg57.69.pred.raw.section
evidence_18.gff           run.log.child.46                                      WCK01_AAF20200214_F8-ctg57.19.raw.section            WCK01_AAF20200214_F8-ctg57.69.raw.section
evidence_19.gff           run.log.child.47                                      WCK01_AAF20200214_F8-ctg57.1.pred.raw.section        WCK01_AAF20200214_F8-ctg57.6.pred.raw.section
evidence_1.gff            run.log.child.48                                      WCK01_AAF20200214_F8-ctg57.1.raw.section             WCK01_AAF20200214_F8-ctg57.6.raw.section
evidence_20.gff           run.log.child.49                                      WCK01_AAF20200214_F8-ctg57.20-21.raw.section         WCK01_AAF20200214_F8-ctg57.70-71.raw.section
evidence_21.gff           run.log.child.5                                       WCK01_AAF20200214_F8-ctg57.20.pred.raw.section       WCK01_AAF20200214_F8-ctg57.70.end.blastn.holdover
evidence_22.gff           run.log.child.50                                      WCK01_AAF20200214_F8-ctg57.20.raw.section            WCK01_AAF20200214_F8-ctg57.70.end.blastx.holdover
evidence_23.gff           run.log.child.51                                      WCK01_AAF20200214_F8-ctg57.21-22.raw.section         WCK01_AAF20200214_F8-ctg57.70.pred.raw.section
evidence_24.gff           run.log.child.52                                      WCK01_AAF20200214_F8-ctg57.21.pred.raw.section       WCK01_AAF20200214_F8-ctg57.70.raw.section
evidence_25.gff           run.log.child.53                                      WCK01_AAF20200214_F8-ctg57.21.raw.section            WCK01_AAF20200214_F8-ctg57.71-72.raw.section
evidence_25.gff.ann       run.log.child.54                                      WCK01_AAF20200214_F8-ctg57.22-23.raw.section         WCK01_AAF20200214_F8-ctg57.71.pred.raw.section
evidence_25.gff.def       run.log.child.55                                      WCK01_AAF20200214_F8-ctg57.22.pred.raw.section       WCK01_AAF20200214_F8-ctg57.71.raw.section
evidence_25.gff.seq       run.log.child.56                                      WCK01_AAF20200214_F8-ctg57.22.raw.section            WCK01_AAF20200214_F8-ctg57.72-73.raw.section
evidence_26.gff           run.log.child.57                                      WCK01_AAF20200214_F8-ctg57.23-24.raw.section         WCK01_AAF20200214_F8-ctg57.72.pred.raw.section
evidence_27.gff           run.log.child.58                                      WCK01_AAF20200214_F8-ctg57.23.pred.raw.section       WCK01_AAF20200214_F8-ctg57.72.raw.section
evidence_28.gff           run.log.child.59                                      WCK01_AAF20200214_F8-ctg57.2-3.raw.section           WCK01_AAF20200214_F8-ctg57.73-74.raw.section
evidence_29.gff           run.log.child.6                                       WCK01_AAF20200214_F8-ctg57.23.raw.section            WCK01_AAF20200214_F8-ctg57.73.pred.raw.section
evidence_2.gff            run.log.child.60                                      WCK01_AAF20200214_F8-ctg57.23.start.blastn.holdover  WCK01_AAF20200214_F8-ctg57.73.raw.section
evidence_30.gff           run.log.child.61                                      WCK01_AAF20200214_F8-ctg57.23.start.blastx.holdover  WCK01_AAF20200214_F8-ctg57.73.start.blastn.holdover
evidence_31.gff           run.log.child.62                                      WCK01_AAF20200214_F8-ctg57.24-25.raw.section         WCK01_AAF20200214_F8-ctg57.73.start.blastx.holdover
evidence_32.gff           run.log.child.63                                      WCK01_AAF20200214_F8-ctg57.24.pred.raw.section       WCK01_AAF20200214_F8-ctg57.74-75.raw.section
evidence_33.gff           run.log.child.64                                      WCK01_AAF20200214_F8-ctg57.24.raw.section            WCK01_AAF20200214_F8-ctg57.74.pred.raw.section
evidence_34.gff           run.log.child.65                                      WCK01_AAF20200214_F8-ctg57.25-26.raw.section         WCK01_AAF20200214_F8-ctg57.74.raw.section
evidence_35.gff           run.log.child.66                                      WCK01_AAF20200214_F8-ctg57.25.end.blastn.holdover    WCK01_AAF20200214_F8-ctg57.75-76.raw.section
evidence_36.gff           run.log.child.67                                      WCK01_AAF20200214_F8-ctg57.25.pred.raw.section       WCK01_AAF20200214_F8-ctg57.75.end.blastn.holdover
evidence_37.gff           run.log.child.68                                      WCK01_AAF20200214_F8-ctg57.25.raw.section            WCK01_AAF20200214_F8-ctg57.75.end.blastx.holdover
evidence_38.gff           run.log.child.69                                      WCK01_AAF20200214_F8-ctg57.26-27.raw.section         WCK01_AAF20200214_F8-ctg57.75.pred.raw.section
evidence_39.gff           run.log.child.7                                       WCK01_AAF20200214_F8-ctg57.26.pred.raw.section       WCK01_AAF20200214_F8-ctg57.75.raw.section
evidence_3.gff            run.log.child.70                                      WCK01_AAF20200214_F8-ctg57.26.raw.section            WCK01_AAF20200214_F8-ctg57.76-77.raw.section
evidence_40.gff           run.log.child.71                                      WCK01_AAF20200214_F8-ctg57.27-28.raw.section         WCK01_AAF20200214_F8-ctg57.76.pred.raw.section
evidence_41.gff           run.log.child.72                                      WCK01_AAF20200214_F8-ctg57.27.pred.raw.section       WCK01_AAF20200214_F8-ctg57.76.raw.section
evidence_42.gff           run.log.child.73                                      WCK01_AAF20200214_F8-ctg57.27.raw.section            WCK01_AAF20200214_F8-ctg57.77-78.raw.section
evidence_43.gff           run.log.child.74                                      WCK01_AAF20200214_F8-ctg57.28-29.raw.section         WCK01_AAF20200214_F8-ctg57.77.pred.raw.section
evidence_44.gff           run.log.child.75                                      WCK01_AAF20200214_F8-ctg57.28.pred.raw.section       WCK01_AAF20200214_F8-ctg57.77.raw.section
evidence_45.gff           run.log.child.76                                      WCK01_AAF20200214_F8-ctg57.28.raw.section            WCK01_AAF20200214_F8-ctg57.78-79.raw.section
evidence_46.gff           run.log.child.77                                      WCK01_AAF20200214_F8-ctg57.29-30.raw.section         WCK01_AAF20200214_F8-ctg57.78.pred.raw.section
evidence_47.gff           run.log.child.78                                      WCK01_AAF20200214_F8-ctg57.29.pred.raw.section       WCK01_AAF20200214_F8-ctg57.7-8.raw.section
evidence_48.gff           run.log.child.79                                      WCK01_AAF20200214_F8-ctg57.29.raw.section            WCK01_AAF20200214_F8-ctg57.78.raw.section
evidence_49.gff           run.log.child.8                                       WCK01_AAF20200214_F8-ctg57.2.pred.raw.section        WCK01_AAF20200214_F8-ctg57.79-80.raw.section
evidence_4.gff            run.log.child.80                                      WCK01_AAF20200214_F8-ctg57.2.raw.section             WCK01_AAF20200214_F8-ctg57.79.pred.raw.section
evidence_50.gff           run.log.child.81                                      WCK01_AAF20200214_F8-ctg57.2.start.blastn.holdover   WCK01_AAF20200214_F8-ctg57.79.raw.section
evidence_51.gff           run.log.child.82                                      WCK01_AAF20200214_F8-ctg57.2.start.blastx.holdover   WCK01_AAF20200214_F8-ctg57.7.pred.raw.section
evidence_52.gff           run.log.child.83                                      WCK01_AAF20200214_F8-ctg57.30-31.raw.section         WCK01_AAF20200214_F8-ctg57.7.raw.section
evidence_53.gff           run.log.child.84                                      WCK01_AAF20200214_F8-ctg57.30.pred.raw.section       WCK01_AAF20200214_F8-ctg57.80-81.raw.section
evidence_54.gff           run.log.child.85                                      WCK01_AAF20200214_F8-ctg57.30.raw.section            WCK01_AAF20200214_F8-ctg57.80.pred.raw.section
evidence_55.gff           run.log.child.86                                      WCK01_AAF20200214_F8-ctg57.31-32.raw.section         WCK01_AAF20200214_F8-ctg57.80.raw.section
evidence_56.gff           run.log.child.87                                      WCK01_AAF20200214_F8-ctg57.31.pred.raw.section       WCK01_AAF20200214_F8-ctg57.80.start.blastn.holdover
evidence_57.gff           run.log.child.88                                      WCK01_AAF20200214_F8-ctg57.31.raw.section            WCK01_AAF20200214_F8-ctg57.80.start.blastx.holdover
evidence_58.gff           run.log.child.89                                      WCK01_AAF20200214_F8-ctg57.32-33.raw.section         WCK01_AAF20200214_F8-ctg57.81-82.raw.section
evidence_59.gff           run.log.child.9                                       WCK01_AAF20200214_F8-ctg57.32.pred.raw.section       WCK01_AAF20200214_F8-ctg57.81.pred.raw.section
evidence_5.gff            run.log.child.90                                      WCK01_AAF20200214_F8-ctg57.32.raw.section            WCK01_AAF20200214_F8-ctg57.81.raw.section
evidence_60.gff           run.log.child.91                                      WCK01_AAF20200214_F8-ctg57.33-34.raw.section         WCK01_AAF20200214_F8-ctg57.82-83.raw.section
evidence_61.gff           run.log.child.92                                      WCK01_AAF20200214_F8-ctg57.33.pred.raw.section       WCK01_AAF20200214_F8-ctg57.82.end.blastn.holdover
evidence_62.gff           run.log.child.93                                      WCK01_AAF20200214_F8-ctg57.33.raw.section            WCK01_AAF20200214_F8-ctg57.82.end.blastx.holdover
evidence_63.gff           run.log.child.94                                      WCK01_AAF20200214_F8-ctg57.34-35.raw.section         WCK01_AAF20200214_F8-ctg57.82.pred.raw.section
evidence_64.gff           run.log.child.95                                      WCK01_AAF20200214_F8-ctg57.34.pred.raw.section       WCK01_AAF20200214_F8-ctg57.82.raw.section
evidence_65.gff           run.log.child.96                                      WCK01_AAF20200214_F8-ctg57.3-4.raw.section           WCK01_AAF20200214_F8-ctg57.83-84.raw.section
evidence_66.gff           run.log.child.97                                      WCK01_AAF20200214_F8-ctg57.34.raw.section            WCK01_AAF20200214_F8-ctg57.83.pred.raw.section
evidence_67.gff           run.log.child.98                                      WCK01_AAF20200214_F8-ctg57.35-36.raw.section         WCK01_AAF20200214_F8-ctg57.83.raw.section
evidence_68.gff           run.log.child.99                                      WCK01_AAF20200214_F8-ctg57.35.pred.raw.section       WCK01_AAF20200214_F8-ctg57.84-85.raw.section
evidence_69.gff           WCK01_AAF20200214_F8-ctg57.0-1.raw.section            WCK01_AAF20200214_F8-ctg57.35.raw.section            WCK01_AAF20200214_F8-ctg57.84.pred.raw.section
evidence_6.gff            WCK01_AAF20200214_F8-ctg57.0.pred.raw.section         WCK01_AAF20200214_F8-ctg57.36-37.raw.section         WCK01_AAF20200214_F8-ctg57.84.raw.section
evidence_70.gff           WCK01_AAF20200214_F8-ctg57.0.raw.section              WCK01_AAF20200214_F8-ctg57.36.pred.raw.section       WCK01_AAF20200214_F8-ctg57.84.start.blastn.holdover
evidence_70.gff.ann       WCK01_AAF20200214_F8-ctg57.100-101.raw.section        WCK01_AAF20200214_F8-ctg57.36.raw.section            WCK01_AAF20200214_F8-ctg57.84.start.blastx.holdover
evidence_70.gff.def       WCK01_AAF20200214_F8-ctg57.100.pred.raw.section       WCK01_AAF20200214_F8-ctg57.37-38.raw.section         WCK01_AAF20200214_F8-ctg57.85-86.raw.section
evidence_70.gff.seq       WCK01_AAF20200214_F8-ctg57.100.raw.section            WCK01_AAF20200214_F8-ctg57.37.pred.raw.section       WCK01_AAF20200214_F8-ctg57.85.pred.raw.section
evidence_71.gff           WCK01_AAF20200214_F8-ctg57.101-102.raw.section        WCK01_AAF20200214_F8-ctg57.37.raw.section            WCK01_AAF20200214_F8-ctg57.85.raw.section
evidence_72.gff           WCK01_AAF20200214_F8-ctg57.10-11.raw.section          WCK01_AAF20200214_F8-ctg57.38-39.raw.section         WCK01_AAF20200214_F8-ctg57.86-87.raw.section
evidence_73.gff           WCK01_AAF20200214_F8-ctg57.101.pred.raw.section       WCK01_AAF20200214_F8-ctg57.38.pred.raw.section       WCK01_AAF20200214_F8-ctg57.86.end.blastn.holdover
evidence_74.gff           WCK01_AAF20200214_F8-ctg57.101.raw.section            WCK01_AAF20200214_F8-ctg57.38.raw.section            WCK01_AAF20200214_F8-ctg57.86.end.blastx.holdover
evidence_75.gff           WCK01_AAF20200214_F8-ctg57.102-103.raw.section        WCK01_AAF20200214_F8-ctg57.39-40.raw.section         WCK01_AAF20200214_F8-ctg57.86.pred.raw.section
evidence_76.gff           WCK01_AAF20200214_F8-ctg57.102.end.blastn.holdover    WCK01_AAF20200214_F8-ctg57.39.pred.raw.section       WCK01_AAF20200214_F8-ctg57.86.raw.section
evidence_77.gff           WCK01_AAF20200214_F8-ctg57.102.end.blastx.holdover    WCK01_AAF20200214_F8-ctg57.39.raw.section            WCK01_AAF20200214_F8-ctg57.87-88.raw.section
evidence_78.gff           WCK01_AAF20200214_F8-ctg57.102.pred.raw.section       WCK01_AAF20200214_F8-ctg57.3.pred.raw.section        WCK01_AAF20200214_F8-ctg57.87.pred.raw.section
evidence_79.gff           WCK01_AAF20200214_F8-ctg57.102.raw.section            WCK01_AAF20200214_F8-ctg57.3.raw.section             WCK01_AAF20200214_F8-ctg57.87.raw.section
evidence_7.gff            WCK01_AAF20200214_F8-ctg57.103-104.raw.section        WCK01_AAF20200214_F8-ctg57.40-41.raw.section         WCK01_AAF20200214_F8-ctg57.88-89.raw.section
evidence_80.gff           WCK01_AAF20200214_F8-ctg57.103.pred.raw.section       WCK01_AAF20200214_F8-ctg57.40.pred.raw.section       WCK01_AAF20200214_F8-ctg57.88.pred.raw.section
evidence_81.gff           WCK01_AAF20200214_F8-ctg57.103.raw.section            WCK01_AAF20200214_F8-ctg57.40.raw.section            WCK01_AAF20200214_F8-ctg57.88.raw.section
evidence_82.gff           WCK01_AAF20200214_F8-ctg57.104-105.raw.section        WCK01_AAF20200214_F8-ctg57.41-42.raw.section         WCK01_AAF20200214_F8-ctg57.89-90.raw.section
evidence_83.gff           WCK01_AAF20200214_F8-ctg57.104.pred.raw.section       WCK01_AAF20200214_F8-ctg57.41.pred.raw.section       WCK01_AAF20200214_F8-ctg57.89.pred.raw.section
evidence_84.gff           WCK01_AAF20200214_F8-ctg57.104.raw.section            WCK01_AAF20200214_F8-ctg57.41.raw.section            WCK01_AAF20200214_F8-ctg57.8-9.raw.section
evidence_85.gff           WCK01_AAF20200214_F8-ctg57.105-106.raw.section        WCK01_AAF20200214_F8-ctg57.42-43.raw.section         WCK01_AAF20200214_F8-ctg57.89.raw.section
evidence_86.gff           WCK01_AAF20200214_F8-ctg57.105.pred.raw.section       WCK01_AAF20200214_F8-ctg57.42.pred.raw.section       WCK01_AAF20200214_F8-ctg57.8.pred.raw.section
evidence_87.gff           WCK01_AAF20200214_F8-ctg57.105.raw.section            WCK01_AAF20200214_F8-ctg57.42.raw.section            WCK01_AAF20200214_F8-ctg57.8.raw.section
evidence_88.gff           WCK01_AAF20200214_F8-ctg57.106-107.raw.section        WCK01_AAF20200214_F8-ctg57.43-44.raw.section         WCK01_AAF20200214_F8-ctg57.90-91.raw.section
evidence_89.gff           WCK01_AAF20200214_F8-ctg57.106.pred.raw.section       WCK01_AAF20200214_F8-ctg57.43.pred.raw.section       WCK01_AAF20200214_F8-ctg57.90.pred.raw.section
evidence_8.gff            WCK01_AAF20200214_F8-ctg57.106.raw.section            WCK01_AAF20200214_F8-ctg57.43.raw.section            WCK01_AAF20200214_F8-ctg57.90.raw.section
evidence_90.gff           WCK01_AAF20200214_F8-ctg57.107-108.raw.section        WCK01_AAF20200214_F8-ctg57.44-45.raw.section         WCK01_AAF20200214_F8-ctg57.9-10.raw.section
evidence_91.gff           WCK01_AAF20200214_F8-ctg57.107.pred.raw.section       WCK01_AAF20200214_F8-ctg57.44.pred.raw.section       WCK01_AAF20200214_F8-ctg57.91-92.raw.section
evidence_92.gff           WCK01_AAF20200214_F8-ctg57.107.raw.section            WCK01_AAF20200214_F8-ctg57.44.raw.section            WCK01_AAF20200214_F8-ctg57.91.pred.raw.section
evidence_93.gff           WCK01_AAF20200214_F8-ctg57.108-109.raw.section        WCK01_AAF20200214_F8-ctg57.45-46.raw.section         WCK01_AAF20200214_F8-ctg57.91.raw.section
evidence_94.gff           WCK01_AAF20200214_F8-ctg57.108.pred.raw.section       WCK01_AAF20200214_F8-ctg57.45.pred.raw.section       WCK01_AAF20200214_F8-ctg57.92-93.raw.section
evidence_95.gff           WCK01_AAF20200214_F8-ctg57.108.raw.section            WCK01_AAF20200214_F8-ctg57.4-5.raw.section           WCK01_AAF20200214_F8-ctg57.92.pred.raw.section
evidence_96.gff           WCK01_AAF20200214_F8-ctg57.109-110.raw.section        WCK01_AAF20200214_F8-ctg57.45.raw.section            WCK01_AAF20200214_F8-ctg57.92.raw.section
evidence_96.gff.ann       WCK01_AAF20200214_F8-ctg57.109.pred.raw.section       WCK01_AAF20200214_F8-ctg57.46-47.raw.section         WCK01_AAF20200214_F8-ctg57.93-94.raw.section
evidence_96.gff.def       WCK01_AAF20200214_F8-ctg57.109.raw.section            WCK01_AAF20200214_F8-ctg57.46.pred.raw.section       WCK01_AAF20200214_F8-ctg57.93.pred.raw.section
evidence_96.gff.seq       WCK01_AAF20200214_F8-ctg57.10.pred.raw.section        WCK01_AAF20200214_F8-ctg57.46.raw.section            WCK01_AAF20200214_F8-ctg57.93.raw.section
evidence_97.gff.ann       WCK01_AAF20200214_F8-ctg57.10.raw.section             WCK01_AAF20200214_F8-ctg57.47-48.raw.section         WCK01_AAF20200214_F8-ctg57.94-95.raw.section
evidence_97.gff.def       WCK01_AAF20200214_F8-ctg57.110-111.raw.section        WCK01_AAF20200214_F8-ctg57.47.pred.raw.section       WCK01_AAF20200214_F8-ctg57.94.pred.raw.section
evidence_97.gff.seq       WCK01_AAF20200214_F8-ctg57.110.pred.raw.section       WCK01_AAF20200214_F8-ctg57.47.raw.section            WCK01_AAF20200214_F8-ctg57.94.raw.section
evidence_98.gff.ann       WCK01_AAF20200214_F8-ctg57.110.raw.section            WCK01_AAF20200214_F8-ctg57.48-49.raw.section         WCK01_AAF20200214_F8-ctg57.95-96.raw.section
evidence_98.gff.def       WCK01_AAF20200214_F8-ctg57.111-112.raw.section        WCK01_AAF20200214_F8-ctg57.48.pred.raw.section       WCK01_AAF20200214_F8-ctg57.95.pred.raw.section
evidence_98.gff.seq       WCK01_AAF20200214_F8-ctg57.11-12.raw.section          WCK01_AAF20200214_F8-ctg57.48.raw.section            WCK01_AAF20200214_F8-ctg57.95.raw.section
evidence_99.gff           WCK01_AAF20200214_F8-ctg57.111.pred.raw.section       WCK01_AAF20200214_F8-ctg57.48.start.blastn.holdover  WCK01_AAF20200214_F8-ctg57.96.end.blastn.holdover
evidence_99.gff.ann       WCK01_AAF20200214_F8-ctg57.111.raw.section            WCK01_AAF20200214_F8-ctg57.48.start.blastx.holdover  WCK01_AAF20200214_F8-ctg57.96.end.blastx.holdover
evidence_99.gff.def       WCK01_AAF20200214_F8-ctg57.112-113.raw.section        WCK01_AAF20200214_F8-ctg57.49-50.raw.section         WCK01_AAF20200214_F8-ctg57.96.end.section.holdover
evidence_99.gff.seq       WCK01_AAF20200214_F8-ctg57.112.pred.raw.section       WCK01_AAF20200214_F8-ctg57.49.pred.raw.section       WCK01_AAF20200214_F8-ctg57.96.pred.raw.section
evidence_9.gff            WCK01_AAF20200214_F8-ctg57.112.raw.section            WCK01_AAF20200214_F8-ctg57.49.raw.section            WCK01_AAF20200214_F8-ctg57.96.raw.section
query.fasta               WCK01_AAF20200214_F8-ctg57.113-114.raw.section        WCK01_AAF20200214_F8-ctg57.4.pred.raw.section        WCK01_AAF20200214_F8-ctg57.96.start.blastn.holdover
query.masked.fasta        WCK01_AAF20200214_F8-ctg57.113.pred.raw.section       WCK01_AAF20200214_F8-ctg57.4.raw.section             WCK01_AAF20200214_F8-ctg57.96.start.blastx.holdover
query.masked.fasta.index  WCK01_AAF20200214_F8-ctg57.113.raw.section            WCK01_AAF20200214_F8-ctg57.50-51.raw.section         WCK01_AAF20200214_F8-ctg57.97.pred.raw.section
query.masked.gff          WCK01_AAF20200214_F8-ctg57.114-115.raw.section        WCK01_AAF20200214_F8-ctg57.50.end.blastn.holdover    WCK01_AAF20200214_F8-ctg57.98.pred.raw.section
run.log.child.0           WCK01_AAF20200214_F8-ctg57.114.pred.raw.section       WCK01_AAF20200214_F8-ctg57.50.end.blastx.holdover    WCK01_AAF20200214_F8-ctg57.98.start.blastn.holdover
run.log.child.1           WCK01_AAF20200214_F8-ctg57.114.raw.section            WCK01_AAF20200214_F8-ctg57.50.pred.raw.section       WCK01_AAF20200214_F8-ctg57.99-100.raw.section
run.log.child.10          WCK01_AAF20200214_F8-ctg57.114.start.blastn.holdover  WCK01_AAF20200214_F8-ctg57.50.raw.section            WCK01_AAF20200214_F8-ctg57.99.end.blastn.holdover
run.log.child.100         WCK01_AAF20200214_F8-ctg57.114.start.blastx.holdover  WCK01_AAF20200214_F8-ctg57.50.start.blastx.holdover  WCK01_AAF20200214_F8-ctg57.99.end.blastx.holdover
run.log.child.101         WCK01_AAF20200214_F8-ctg57.115-116.raw.section        WCK01_AAF20200214_F8-ctg57.51-52.raw.section         WCK01_AAF20200214_F8-ctg57.99.pred.raw.section
run.log.child.102         WCK01_AAF20200214_F8-ctg57.115.end.blastn.holdover    WCK01_AAF20200214_F8-ctg57.51.pred.raw.section       WCK01_AAF20200214_F8-ctg57.99.raw.section
run.log.child.103         WCK01_AAF20200214_F8-ctg57.115.pred.raw.section       WCK01_AAF20200214_F8-ctg57.51.raw.section            WCK01_AAF20200214_F8-ctg57.99.start.blastx.holdover
run.log.child.104         WCK01_AAF20200214_F8-ctg57.115.raw.section            WCK01_AAF20200214_F8-ctg57.52-53.raw.section         WCK01_AAF20200214_F8-ctg57.99.start.section.holdover
run.log.child.105         WCK01_AAF20200214_F8-ctg57.116-117.raw.section        WCK01_AAF20200214_F8-ctg57.52.pred.raw.section       WCK01_AAF20200214_F8-ctg57.9.pred.raw.section
run.log.child.106         WCK01_AAF20200214_F8-ctg57.116.pred.raw.section       WCK01_AAF20200214_F8-ctg57.52.raw.section            WCK01_AAF20200214_F8-ctg57.9.raw.section
run.log.child.107         WCK01_AAF20200214_F8-ctg57.116.raw.section            WCK01_AAF20200214_F8-ctg57.53-54.raw.section         WCK01_AAF20200214_F8-ctg57.gff.ann
run.log.child.108         WCK01_AAF20200214_F8-ctg57.117-118.raw.section        WCK01_AAF20200214_F8-ctg57.53.pred.raw.section       WCK01_AAF20200214_F8-ctg57.gff.def
run.log.child.109         WCK01_AAF20200214_F8-ctg57.117.pred.raw.section       WCK01_AAF20200214_F8-ctg57.53.raw.section            WCK01_AAF20200214_F8-ctg57.gff.seq
run.log.child.11          WCK01_AAF20200214_F8-ctg57.117.raw.section            WCK01_AAF20200214_F8-ctg57.54-55.raw.section
run.log.child.110         WCK01_AAF20200214_F8-ctg57.117.start.blastn.holdover  WCK01_AAF20200214_F8-ctg57.54.pred.raw.section
run.log.child.111         WCK01_AAF20200214_F8-ctg57.117.start.blastx.holdover  WCK01_AAF20200214_F8-ctg57.54.raw.section

I set clean_try=1 and am trying to fix this contig (it's only this one contig which is causing trouble), but I'm wondering if it's also okay to completely delete the void directory to force it to start this contig from scratch. I have already tried rerunning maker with clean_try=1 two times and now I'm getting an mpich2 error:

Fatal error in MPI_Send: Invalid count, error stack:
MPI_Send(173): MPI_Send(buf=0x2aec3d6a3010, count=-1279995089, MPI_CHAR, dest=15, tag=9999, MPI_COMM_WORLD) failed
MPI_Send(97).: Negative count, value is -1279995089

I am currently trying again with fewer MPI jobs requested, worrying that there might be a memory issue on the computer cluster I am using. My temporary directory still has lots of space, but I have ~200G RAM per node and sometimes the jobs use a ton of RAM. I don't have too many more contigs left of this run, so I just really don't want to mess anything up. Do you have any advice?

Thanks so much!
Zoe

______________________________________
Zoe Clarke
PhD candidate in Computational Biology at U of T
Lab profile: http://baderlab.org/Zoe%20Clarke
Personal website: https://zoe-clarke.weebly.com/
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From carsonhh at gmail.com  Thu Oct 22 13:31:11 2020
From: carsonhh at gmail.com (Carson Holt)
Date: Thu, 22 Oct 2020 13:31:11 -0600
Subject: [maker-devel] Issue with single contig
In-Reply-To: <YTBPR01MB3839C4605F16FAA8BDA8EFFE9C080@YTBPR01MB3839.CANPRD01.PROD.OUTLOOK.COM>
References: <YTBPR01MB3839C4605F16FAA8BDA8EFFE9C080@YTBPR01MB3839.CANPRD01.PROD.OUTLOOK.COM>
Message-ID: <7DEEBFBB-2247-413A-96F1-0EF1A8E9EE62@gmail.com>

Your datacenter may have implemented the temporary storage (?/tmp? by default) to be in memory storage. As a result, every file you store is really being stored in RAM behind the scenes.  Or you have specified TMP= in the control files to point to in memory storage.  The result is that, at some point there was not enough memory left.  You may want to ask about this and ensure that you can point to a real node based disk storage like traditional /tmp space.

?Carson



> On Oct 9, 2020, at 5:39 AM, Zoe Clarke <zoe.clarke at utoronto.ca> wrote:
> 
> Hello!
> 
> Sorry to bother you again. I am having a very specific problem with one of my contigs, and I was hoping you could help.
> 
> I can cancelled my last Maker run because one of my contigs failed around 56,000 times according to the output_rnd1_master_datastore_index.log file. It was just perpetually failing during the run with the following message:
> 
> ERROR: Chunk failed at level:0, tier_type:0open3: fork failed: Cannot allocate memory at dir/File/NFSLock.pm line 1037.
> 
> I am running Maker over multiple nodes, so I figured there might be an issue with a log file getting truncated or malformed. Looking at the files stored in the void for this contig, there are also a ton of files which I think might be causing an issue:
> 
> 0                         run.log.child.112                                     WCK01_AAF20200214_F8-ctg57.118-119.raw.section       WCK01_AAF20200214_F8-ctg57.55-56.raw.section
> 1                         run.log.child.113                                     WCK01_AAF20200214_F8-ctg57.118.pred.raw.section      WCK01_AAF20200214_F8-ctg57.55.pred.raw.section
> 10                        run.log.child.114                                     WCK01_AAF20200214_F8-ctg57.118.raw.section           WCK01_AAF20200214_F8-ctg57.55.raw.section
> 11                        run.log.child.115                                     WCK01_AAF20200214_F8-ctg57.119-120.raw.section       WCK01_AAF20200214_F8-ctg57.56-57.raw.section
> 12                        run.log.child.116                                     WCK01_AAF20200214_F8-ctg57.119.pred.raw.section      WCK01_AAF20200214_F8-ctg57.56.pred.raw.section
> 2                         run.log.child.117                                     WCK01_AAF20200214_F8-ctg57.119.raw.section           WCK01_AAF20200214_F8-ctg57.5-6.raw.section
> 3                         run.log.child.118                                     WCK01_AAF20200214_F8-ctg57.11.pred.raw.section       WCK01_AAF20200214_F8-ctg57.56.raw.section
> 4                         run.log.child.119                                     WCK01_AAF20200214_F8-ctg57.11.raw.section            WCK01_AAF20200214_F8-ctg57.57-58.raw.section
> 5                         run.log.child.12                                      WCK01_AAF20200214_F8-ctg57.120-121.raw.section       WCK01_AAF20200214_F8-ctg57.57.pred.raw.section
> 6                         run.log.child.120                                     WCK01_AAF20200214_F8-ctg57.120.pred.raw.section      WCK01_AAF20200214_F8-ctg57.57.raw.section
> 7                         run.log.child.121                                     WCK01_AAF20200214_F8-ctg57.120.raw.section           WCK01_AAF20200214_F8-ctg57.58-59.raw.section
> 8                         run.log.child.122                                     WCK01_AAF20200214_F8-ctg57.121-122.raw.section       WCK01_AAF20200214_F8-ctg57.58.pred.raw.section
> 9                         run.log.child.123                                     WCK01_AAF20200214_F8-ctg57.12-13.raw.section         WCK01_AAF20200214_F8-ctg57.58.raw.section
> evidence_0.gff            run.log.child.124                                     WCK01_AAF20200214_F8-ctg57.121.end.blastn.holdover   WCK01_AAF20200214_F8-ctg57.59-60.raw.section
> evidence_100.gff          run.log.child.125                                     WCK01_AAF20200214_F8-ctg57.121.end.blastx.holdover   WCK01_AAF20200214_F8-ctg57.59.pred.raw.section
> evidence_101.gff          run.log.child.13                                      WCK01_AAF20200214_F8-ctg57.121.pred.raw.section      WCK01_AAF20200214_F8-ctg57.59.raw.section
> evidence_102.gff          run.log.child.14                                      WCK01_AAF20200214_F8-ctg57.121.raw.section           WCK01_AAF20200214_F8-ctg57.5.pred.raw.section
> evidence_103.gff          run.log.child.15                                      WCK01_AAF20200214_F8-ctg57.122-123.raw.section       WCK01_AAF20200214_F8-ctg57.5.raw.section
> evidence_104.gff          run.log.child.16                                      WCK01_AAF20200214_F8-ctg57.122.pred.raw.section      WCK01_AAF20200214_F8-ctg57.60-61.raw.section
> evidence_105.gff          run.log.child.17                                      WCK01_AAF20200214_F8-ctg57.122.raw.section           WCK01_AAF20200214_F8-ctg57.60.pred.raw.section
> evidence_106.gff          run.log.child.18                                      WCK01_AAF20200214_F8-ctg57.123-124.raw.section       WCK01_AAF20200214_F8-ctg57.60.raw.section
> evidence_107.gff          run.log.child.19                                      WCK01_AAF20200214_F8-ctg57.123.pred.raw.section      WCK01_AAF20200214_F8-ctg57.61-62.raw.section
> evidence_108.gff          run.log.child.2                                       WCK01_AAF20200214_F8-ctg57.123.raw.section           WCK01_AAF20200214_F8-ctg57.61.pred.raw.section
> evidence_109.gff          run.log.child.20                                      WCK01_AAF20200214_F8-ctg57.124-125.raw.section       WCK01_AAF20200214_F8-ctg57.61.raw.section
> evidence_10.gff           run.log.child.21                                      WCK01_AAF20200214_F8-ctg57.124.pred.raw.section      WCK01_AAF20200214_F8-ctg57.62-63.raw.section
> evidence_110.gff          run.log.child.22                                      WCK01_AAF20200214_F8-ctg57.124.raw.section           WCK01_AAF20200214_F8-ctg57.62.pred.raw.section
> evidence_111.gff          run.log.child.23                                      WCK01_AAF20200214_F8-ctg57.125.pred.raw.section      WCK01_AAF20200214_F8-ctg57.62.raw.section
> evidence_112.gff          run.log.child.24                                      WCK01_AAF20200214_F8-ctg57.125.raw.section           WCK01_AAF20200214_F8-ctg57.63-64.raw.section
> evidence_113.gff          run.log.child.25                                      WCK01_AAF20200214_F8-ctg57.12.pred.raw.section       WCK01_AAF20200214_F8-ctg57.63.pred.raw.section
> evidence_114.gff          run.log.child.26                                      WCK01_AAF20200214_F8-ctg57.1-2.raw.section           WCK01_AAF20200214_F8-ctg57.63.raw.section
> evidence_115.gff          run.log.child.27                                      WCK01_AAF20200214_F8-ctg57.12.raw.section            WCK01_AAF20200214_F8-ctg57.64-65.raw.section
> evidence_116.gff          run.log.child.28                                      WCK01_AAF20200214_F8-ctg57.13-14.raw.section         WCK01_AAF20200214_F8-ctg57.64.pred.raw.section
> evidence_116.gff.ann      run.log.child.29                                      WCK01_AAF20200214_F8-ctg57.13.pred.raw.section       WCK01_AAF20200214_F8-ctg57.64.raw.section
> evidence_116.gff.def      run.log.child.3                                       WCK01_AAF20200214_F8-ctg57.13.raw.section            WCK01_AAF20200214_F8-ctg57.65-66.raw.section
> evidence_116.gff.seq      run.log.child.30                                      WCK01_AAF20200214_F8-ctg57.14-15.raw.section         WCK01_AAF20200214_F8-ctg57.65.pred.raw.section
> evidence_117.gff          run.log.child.31                                      WCK01_AAF20200214_F8-ctg57.14.pred.raw.section       WCK01_AAF20200214_F8-ctg57.65.raw.section
> evidence_118.gff          run.log.child.32                                      WCK01_AAF20200214_F8-ctg57.14.raw.section            WCK01_AAF20200214_F8-ctg57.66-67.raw.section
> evidence_119.gff          run.log.child.33                                      WCK01_AAF20200214_F8-ctg57.15-16.raw.section         WCK01_AAF20200214_F8-ctg57.66.pred.raw.section
> evidence_11.gff           run.log.child.34                                      WCK01_AAF20200214_F8-ctg57.15.pred.raw.section       WCK01_AAF20200214_F8-ctg57.66.raw.section
> evidence_120.gff          run.log.child.35                                      WCK01_AAF20200214_F8-ctg57.15.raw.section            WCK01_AAF20200214_F8-ctg57.67-68.raw.section
> evidence_121.gff          run.log.child.36                                      WCK01_AAF20200214_F8-ctg57.16-17.raw.section         WCK01_AAF20200214_F8-ctg57.67.pred.raw.section
> evidence_122.gff          run.log.child.37                                      WCK01_AAF20200214_F8-ctg57.16.pred.raw.section       WCK01_AAF20200214_F8-ctg57.6-7.raw.section
> evidence_123.gff          run.log.child.38                                      WCK01_AAF20200214_F8-ctg57.16.raw.section            WCK01_AAF20200214_F8-ctg57.67.raw.section
> evidence_124.gff          run.log.child.39                                      WCK01_AAF20200214_F8-ctg57.17-18.raw.section         WCK01_AAF20200214_F8-ctg57.68-69.raw.section
> evidence_125.gff          run.log.child.4                                       WCK01_AAF20200214_F8-ctg57.17.pred.raw.section       WCK01_AAF20200214_F8-ctg57.68.pred.raw.section
> evidence_12.gff           run.log.child.40                                      WCK01_AAF20200214_F8-ctg57.17.raw.section            WCK01_AAF20200214_F8-ctg57.68.raw.section
> evidence_13.gff           run.log.child.41                                      WCK01_AAF20200214_F8-ctg57.18-19.raw.section         WCK01_AAF20200214_F8-ctg57.68.start.blastn.holdover
> evidence_14.gff           run.log.child.42                                      WCK01_AAF20200214_F8-ctg57.18.pred.raw.section       WCK01_AAF20200214_F8-ctg57.68.start.blastx.holdover
> evidence_15.gff           run.log.child.43                                      WCK01_AAF20200214_F8-ctg57.18.raw.section            WCK01_AAF20200214_F8-ctg57.69-70.raw.section
> evidence_16.gff           run.log.child.44                                      WCK01_AAF20200214_F8-ctg57.19-20.raw.section         WCK01_AAF20200214_F8-ctg57.69.end.blastn.holdover
> evidence_17.gff           run.log.child.45                                      WCK01_AAF20200214_F8-ctg57.19.pred.raw.section       WCK01_AAF20200214_F8-ctg57.69.pred.raw.section
> evidence_18.gff           run.log.child.46                                      WCK01_AAF20200214_F8-ctg57.19.raw.section            WCK01_AAF20200214_F8-ctg57.69.raw.section
> evidence_19.gff           run.log.child.47                                      WCK01_AAF20200214_F8-ctg57.1.pred.raw.section        WCK01_AAF20200214_F8-ctg57.6.pred.raw.section
> evidence_1.gff            run.log.child.48                                      WCK01_AAF20200214_F8-ctg57.1.raw.section             WCK01_AAF20200214_F8-ctg57.6.raw.section
> evidence_20.gff           run.log.child.49                                      WCK01_AAF20200214_F8-ctg57.20-21.raw.section         WCK01_AAF20200214_F8-ctg57.70-71.raw.section
> evidence_21.gff           run.log.child.5                                       WCK01_AAF20200214_F8-ctg57.20.pred.raw.section       WCK01_AAF20200214_F8-ctg57.70.end.blastn.holdover
> evidence_22.gff           run.log.child.50                                      WCK01_AAF20200214_F8-ctg57.20.raw.section            WCK01_AAF20200214_F8-ctg57.70.end.blastx.holdover
> evidence_23.gff           run.log.child.51                                      WCK01_AAF20200214_F8-ctg57.21-22.raw.section         WCK01_AAF20200214_F8-ctg57.70.pred.raw.section
> evidence_24.gff           run.log.child.52                                      WCK01_AAF20200214_F8-ctg57.21.pred.raw.section       WCK01_AAF20200214_F8-ctg57.70.raw.section
> evidence_25.gff           run.log.child.53                                      WCK01_AAF20200214_F8-ctg57.21.raw.section            WCK01_AAF20200214_F8-ctg57.71-72.raw.section
> evidence_25.gff.ann       run.log.child.54                                      WCK01_AAF20200214_F8-ctg57.22-23.raw.section         WCK01_AAF20200214_F8-ctg57.71.pred.raw.section
> evidence_25.gff.def       run.log.child.55                                      WCK01_AAF20200214_F8-ctg57.22.pred.raw.section       WCK01_AAF20200214_F8-ctg57.71.raw.section
> evidence_25.gff.seq       run.log.child.56                                      WCK01_AAF20200214_F8-ctg57.22.raw.section            WCK01_AAF20200214_F8-ctg57.72-73.raw.section
> evidence_26.gff           run.log.child.57                                      WCK01_AAF20200214_F8-ctg57.23-24.raw.section         WCK01_AAF20200214_F8-ctg57.72.pred.raw.section
> evidence_27.gff           run.log.child.58                                      WCK01_AAF20200214_F8-ctg57.23.pred.raw.section       WCK01_AAF20200214_F8-ctg57.72.raw.section
> evidence_28.gff           run.log.child.59                                      WCK01_AAF20200214_F8-ctg57.2-3.raw.section           WCK01_AAF20200214_F8-ctg57.73-74.raw.section
> evidence_29.gff           run.log.child.6                                       WCK01_AAF20200214_F8-ctg57.23.raw.section            WCK01_AAF20200214_F8-ctg57.73.pred.raw.section
> evidence_2.gff            run.log.child.60                                      WCK01_AAF20200214_F8-ctg57.23.start.blastn.holdover  WCK01_AAF20200214_F8-ctg57.73.raw.section
> evidence_30.gff           run.log.child.61                                      WCK01_AAF20200214_F8-ctg57.23.start.blastx.holdover  WCK01_AAF20200214_F8-ctg57.73.start.blastn.holdover
> evidence_31.gff           run.log.child.62                                      WCK01_AAF20200214_F8-ctg57.24-25.raw.section         WCK01_AAF20200214_F8-ctg57.73.start.blastx.holdover
> evidence_32.gff           run.log.child.63                                      WCK01_AAF20200214_F8-ctg57.24.pred.raw.section       WCK01_AAF20200214_F8-ctg57.74-75.raw.section
> evidence_33.gff           run.log.child.64                                      WCK01_AAF20200214_F8-ctg57.24.raw.section            WCK01_AAF20200214_F8-ctg57.74.pred.raw.section
> evidence_34.gff           run.log.child.65                                      WCK01_AAF20200214_F8-ctg57.25-26.raw.section         WCK01_AAF20200214_F8-ctg57.74.raw.section
> evidence_35.gff           run.log.child.66                                      WCK01_AAF20200214_F8-ctg57.25.end.blastn.holdover    WCK01_AAF20200214_F8-ctg57.75-76.raw.section
> evidence_36.gff           run.log.child.67                                      WCK01_AAF20200214_F8-ctg57.25.pred.raw.section       WCK01_AAF20200214_F8-ctg57.75.end.blastn.holdover
> evidence_37.gff           run.log.child.68                                      WCK01_AAF20200214_F8-ctg57.25.raw.section            WCK01_AAF20200214_F8-ctg57.75.end.blastx.holdover
> evidence_38.gff           run.log.child.69                                      WCK01_AAF20200214_F8-ctg57.26-27.raw.section         WCK01_AAF20200214_F8-ctg57.75.pred.raw.section
> evidence_39.gff           run.log.child.7                                       WCK01_AAF20200214_F8-ctg57.26.pred.raw.section       WCK01_AAF20200214_F8-ctg57.75.raw.section
> evidence_3.gff            run.log.child.70                                      WCK01_AAF20200214_F8-ctg57.26.raw.section            WCK01_AAF20200214_F8-ctg57.76-77.raw.section
> evidence_40.gff           run.log.child.71                                      WCK01_AAF20200214_F8-ctg57.27-28.raw.section         WCK01_AAF20200214_F8-ctg57.76.pred.raw.section
> evidence_41.gff           run.log.child.72                                      WCK01_AAF20200214_F8-ctg57.27.pred.raw.section       WCK01_AAF20200214_F8-ctg57.76.raw.section
> evidence_42.gff           run.log.child.73                                      WCK01_AAF20200214_F8-ctg57.27.raw.section            WCK01_AAF20200214_F8-ctg57.77-78.raw.section
> evidence_43.gff           run.log.child.74                                      WCK01_AAF20200214_F8-ctg57.28-29.raw.section         WCK01_AAF20200214_F8-ctg57.77.pred.raw.section
> evidence_44.gff           run.log.child.75                                      WCK01_AAF20200214_F8-ctg57.28.pred.raw.section       WCK01_AAF20200214_F8-ctg57.77.raw.section
> evidence_45.gff           run.log.child.76                                      WCK01_AAF20200214_F8-ctg57.28.raw.section            WCK01_AAF20200214_F8-ctg57.78-79.raw.section
> evidence_46.gff           run.log.child.77                                      WCK01_AAF20200214_F8-ctg57.29-30.raw.section         WCK01_AAF20200214_F8-ctg57.78.pred.raw.section
> evidence_47.gff           run.log.child.78                                      WCK01_AAF20200214_F8-ctg57.29.pred.raw.section       WCK01_AAF20200214_F8-ctg57.7-8.raw.section
> evidence_48.gff           run.log.child.79                                      WCK01_AAF20200214_F8-ctg57.29.raw.section            WCK01_AAF20200214_F8-ctg57.78.raw.section
> evidence_49.gff           run.log.child.8                                       WCK01_AAF20200214_F8-ctg57.2.pred.raw.section        WCK01_AAF20200214_F8-ctg57.79-80.raw.section
> evidence_4.gff            run.log.child.80                                      WCK01_AAF20200214_F8-ctg57.2.raw.section             WCK01_AAF20200214_F8-ctg57.79.pred.raw.section
> evidence_50.gff           run.log.child.81                                      WCK01_AAF20200214_F8-ctg57.2.start.blastn.holdover   WCK01_AAF20200214_F8-ctg57.79.raw.section
> evidence_51.gff           run.log.child.82                                      WCK01_AAF20200214_F8-ctg57.2.start.blastx.holdover   WCK01_AAF20200214_F8-ctg57.7.pred.raw.section
> evidence_52.gff           run.log.child.83                                      WCK01_AAF20200214_F8-ctg57.30-31.raw.section         WCK01_AAF20200214_F8-ctg57.7.raw.section
> evidence_53.gff           run.log.child.84                                      WCK01_AAF20200214_F8-ctg57.30.pred.raw.section       WCK01_AAF20200214_F8-ctg57.80-81.raw.section
> evidence_54.gff           run.log.child.85                                      WCK01_AAF20200214_F8-ctg57.30.raw.section            WCK01_AAF20200214_F8-ctg57.80.pred.raw.section
> evidence_55.gff           run.log.child.86                                      WCK01_AAF20200214_F8-ctg57.31-32.raw.section         WCK01_AAF20200214_F8-ctg57.80.raw.section
> evidence_56.gff           run.log.child.87                                      WCK01_AAF20200214_F8-ctg57.31.pred.raw.section       WCK01_AAF20200214_F8-ctg57.80.start.blastn.holdover
> evidence_57.gff           run.log.child.88                                      WCK01_AAF20200214_F8-ctg57.31.raw.section            WCK01_AAF20200214_F8-ctg57.80.start.blastx.holdover
> evidence_58.gff           run.log.child.89                                      WCK01_AAF20200214_F8-ctg57.32-33.raw.section         WCK01_AAF20200214_F8-ctg57.81-82.raw.section
> evidence_59.gff           run.log.child.9                                       WCK01_AAF20200214_F8-ctg57.32.pred.raw.section       WCK01_AAF20200214_F8-ctg57.81.pred.raw.section
> evidence_5.gff            run.log.child.90                                      WCK01_AAF20200214_F8-ctg57.32.raw.section            WCK01_AAF20200214_F8-ctg57.81.raw.section
> evidence_60.gff           run.log.child.91                                      WCK01_AAF20200214_F8-ctg57.33-34.raw.section         WCK01_AAF20200214_F8-ctg57.82-83.raw.section
> evidence_61.gff           run.log.child.92                                      WCK01_AAF20200214_F8-ctg57.33.pred.raw.section       WCK01_AAF20200214_F8-ctg57.82.end.blastn.holdover
> evidence_62.gff           run.log.child.93                                      WCK01_AAF20200214_F8-ctg57.33.raw.section            WCK01_AAF20200214_F8-ctg57.82.end.blastx.holdover
> evidence_63.gff           run.log.child.94                                      WCK01_AAF20200214_F8-ctg57.34-35.raw.section         WCK01_AAF20200214_F8-ctg57.82.pred.raw.section
> evidence_64.gff           run.log.child.95                                      WCK01_AAF20200214_F8-ctg57.34.pred.raw.section       WCK01_AAF20200214_F8-ctg57.82.raw.section
> evidence_65.gff           run.log.child.96                                      WCK01_AAF20200214_F8-ctg57.3-4.raw.section           WCK01_AAF20200214_F8-ctg57.83-84.raw.section
> evidence_66.gff           run.log.child.97                                      WCK01_AAF20200214_F8-ctg57.34.raw.section            WCK01_AAF20200214_F8-ctg57.83.pred.raw.section
> evidence_67.gff           run.log.child.98                                      WCK01_AAF20200214_F8-ctg57.35-36.raw.section         WCK01_AAF20200214_F8-ctg57.83.raw.section
> evidence_68.gff           run.log.child.99                                      WCK01_AAF20200214_F8-ctg57.35.pred.raw.section       WCK01_AAF20200214_F8-ctg57.84-85.raw.section
> evidence_69.gff           WCK01_AAF20200214_F8-ctg57.0-1.raw.section            WCK01_AAF20200214_F8-ctg57.35.raw.section            WCK01_AAF20200214_F8-ctg57.84.pred.raw.section
> evidence_6.gff            WCK01_AAF20200214_F8-ctg57.0.pred.raw.section         WCK01_AAF20200214_F8-ctg57.36-37.raw.section         WCK01_AAF20200214_F8-ctg57.84.raw.section
> evidence_70.gff           WCK01_AAF20200214_F8-ctg57.0.raw.section              WCK01_AAF20200214_F8-ctg57.36.pred.raw.section       WCK01_AAF20200214_F8-ctg57.84.start.blastn.holdover
> evidence_70.gff.ann       WCK01_AAF20200214_F8-ctg57.100-101.raw.section        WCK01_AAF20200214_F8-ctg57.36.raw.section            WCK01_AAF20200214_F8-ctg57.84.start.blastx.holdover
> evidence_70.gff.def       WCK01_AAF20200214_F8-ctg57.100.pred.raw.section       WCK01_AAF20200214_F8-ctg57.37-38.raw.section         WCK01_AAF20200214_F8-ctg57.85-86.raw.section
> evidence_70.gff.seq       WCK01_AAF20200214_F8-ctg57.100.raw.section            WCK01_AAF20200214_F8-ctg57.37.pred.raw.section       WCK01_AAF20200214_F8-ctg57.85.pred.raw.section
> evidence_71.gff           WCK01_AAF20200214_F8-ctg57.101-102.raw.section        WCK01_AAF20200214_F8-ctg57.37.raw.section            WCK01_AAF20200214_F8-ctg57.85.raw.section
> evidence_72.gff           WCK01_AAF20200214_F8-ctg57.10-11.raw.section          WCK01_AAF20200214_F8-ctg57.38-39.raw.section         WCK01_AAF20200214_F8-ctg57.86-87.raw.section
> evidence_73.gff           WCK01_AAF20200214_F8-ctg57.101.pred.raw.section       WCK01_AAF20200214_F8-ctg57.38.pred.raw.section       WCK01_AAF20200214_F8-ctg57.86.end.blastn.holdover
> evidence_74.gff           WCK01_AAF20200214_F8-ctg57.101.raw.section            WCK01_AAF20200214_F8-ctg57.38.raw.section            WCK01_AAF20200214_F8-ctg57.86.end.blastx.holdover
> evidence_75.gff           WCK01_AAF20200214_F8-ctg57.102-103.raw.section        WCK01_AAF20200214_F8-ctg57.39-40.raw.section         WCK01_AAF20200214_F8-ctg57.86.pred.raw.section
> evidence_76.gff           WCK01_AAF20200214_F8-ctg57.102.end.blastn.holdover    WCK01_AAF20200214_F8-ctg57.39.pred.raw.section       WCK01_AAF20200214_F8-ctg57.86.raw.section
> evidence_77.gff           WCK01_AAF20200214_F8-ctg57.102.end.blastx.holdover    WCK01_AAF20200214_F8-ctg57.39.raw.section            WCK01_AAF20200214_F8-ctg57.87-88.raw.section
> evidence_78.gff           WCK01_AAF20200214_F8-ctg57.102.pred.raw.section       WCK01_AAF20200214_F8-ctg57.3.pred.raw.section        WCK01_AAF20200214_F8-ctg57.87.pred.raw.section
> evidence_79.gff           WCK01_AAF20200214_F8-ctg57.102.raw.section            WCK01_AAF20200214_F8-ctg57.3.raw.section             WCK01_AAF20200214_F8-ctg57.87.raw.section
> evidence_7.gff            WCK01_AAF20200214_F8-ctg57.103-104.raw.section        WCK01_AAF20200214_F8-ctg57.40-41.raw.section         WCK01_AAF20200214_F8-ctg57.88-89.raw.section
> evidence_80.gff           WCK01_AAF20200214_F8-ctg57.103.pred.raw.section       WCK01_AAF20200214_F8-ctg57.40.pred.raw.section       WCK01_AAF20200214_F8-ctg57.88.pred.raw.section
> evidence_81.gff           WCK01_AAF20200214_F8-ctg57.103.raw.section            WCK01_AAF20200214_F8-ctg57.40.raw.section            WCK01_AAF20200214_F8-ctg57.88.raw.section
> evidence_82.gff           WCK01_AAF20200214_F8-ctg57.104-105.raw.section        WCK01_AAF20200214_F8-ctg57.41-42.raw.section         WCK01_AAF20200214_F8-ctg57.89-90.raw.section
> evidence_83.gff           WCK01_AAF20200214_F8-ctg57.104.pred.raw.section       WCK01_AAF20200214_F8-ctg57.41.pred.raw.section       WCK01_AAF20200214_F8-ctg57.89.pred.raw.section
> evidence_84.gff           WCK01_AAF20200214_F8-ctg57.104.raw.section            WCK01_AAF20200214_F8-ctg57.41.raw.section            WCK01_AAF20200214_F8-ctg57.8-9.raw.section
> evidence_85.gff           WCK01_AAF20200214_F8-ctg57.105-106.raw.section        WCK01_AAF20200214_F8-ctg57.42-43.raw.section         WCK01_AAF20200214_F8-ctg57.89.raw.section
> evidence_86.gff           WCK01_AAF20200214_F8-ctg57.105.pred.raw.section       WCK01_AAF20200214_F8-ctg57.42.pred.raw.section       WCK01_AAF20200214_F8-ctg57.8.pred.raw.section
> evidence_87.gff           WCK01_AAF20200214_F8-ctg57.105.raw.section            WCK01_AAF20200214_F8-ctg57.42.raw.section            WCK01_AAF20200214_F8-ctg57.8.raw.section
> evidence_88.gff           WCK01_AAF20200214_F8-ctg57.106-107.raw.section        WCK01_AAF20200214_F8-ctg57.43-44.raw.section         WCK01_AAF20200214_F8-ctg57.90-91.raw.section
> evidence_89.gff           WCK01_AAF20200214_F8-ctg57.106.pred.raw.section       WCK01_AAF20200214_F8-ctg57.43.pred.raw.section       WCK01_AAF20200214_F8-ctg57.90.pred.raw.section
> evidence_8.gff            WCK01_AAF20200214_F8-ctg57.106.raw.section            WCK01_AAF20200214_F8-ctg57.43.raw.section            WCK01_AAF20200214_F8-ctg57.90.raw.section
> evidence_90.gff           WCK01_AAF20200214_F8-ctg57.107-108.raw.section        WCK01_AAF20200214_F8-ctg57.44-45.raw.section         WCK01_AAF20200214_F8-ctg57.9-10.raw.section
> evidence_91.gff           WCK01_AAF20200214_F8-ctg57.107.pred.raw.section       WCK01_AAF20200214_F8-ctg57.44.pred.raw.section       WCK01_AAF20200214_F8-ctg57.91-92.raw.section
> evidence_92.gff           WCK01_AAF20200214_F8-ctg57.107.raw.section            WCK01_AAF20200214_F8-ctg57.44.raw.section            WCK01_AAF20200214_F8-ctg57.91.pred.raw.section
> evidence_93.gff           WCK01_AAF20200214_F8-ctg57.108-109.raw.section        WCK01_AAF20200214_F8-ctg57.45-46.raw.section         WCK01_AAF20200214_F8-ctg57.91.raw.section
> evidence_94.gff           WCK01_AAF20200214_F8-ctg57.108.pred.raw.section       WCK01_AAF20200214_F8-ctg57.45.pred.raw.section       WCK01_AAF20200214_F8-ctg57.92-93.raw.section
> evidence_95.gff           WCK01_AAF20200214_F8-ctg57.108.raw.section            WCK01_AAF20200214_F8-ctg57.4-5.raw.section           WCK01_AAF20200214_F8-ctg57.92.pred.raw.section
> evidence_96.gff           WCK01_AAF20200214_F8-ctg57.109-110.raw.section        WCK01_AAF20200214_F8-ctg57.45.raw.section            WCK01_AAF20200214_F8-ctg57.92.raw.section
> evidence_96.gff.ann       WCK01_AAF20200214_F8-ctg57.109.pred.raw.section       WCK01_AAF20200214_F8-ctg57.46-47.raw.section         WCK01_AAF20200214_F8-ctg57.93-94.raw.section
> evidence_96.gff.def       WCK01_AAF20200214_F8-ctg57.109.raw.section            WCK01_AAF20200214_F8-ctg57.46.pred.raw.section       WCK01_AAF20200214_F8-ctg57.93.pred.raw.section
> evidence_96.gff.seq       WCK01_AAF20200214_F8-ctg57.10.pred.raw.section        WCK01_AAF20200214_F8-ctg57.46.raw.section            WCK01_AAF20200214_F8-ctg57.93.raw.section
> evidence_97.gff.ann       WCK01_AAF20200214_F8-ctg57.10.raw.section             WCK01_AAF20200214_F8-ctg57.47-48.raw.section         WCK01_AAF20200214_F8-ctg57.94-95.raw.section
> evidence_97.gff.def       WCK01_AAF20200214_F8-ctg57.110-111.raw.section        WCK01_AAF20200214_F8-ctg57.47.pred.raw.section       WCK01_AAF20200214_F8-ctg57.94.pred.raw.section
> evidence_97.gff.seq       WCK01_AAF20200214_F8-ctg57.110.pred.raw.section       WCK01_AAF20200214_F8-ctg57.47.raw.section            WCK01_AAF20200214_F8-ctg57.94.raw.section
> evidence_98.gff.ann       WCK01_AAF20200214_F8-ctg57.110.raw.section            WCK01_AAF20200214_F8-ctg57.48-49.raw.section         WCK01_AAF20200214_F8-ctg57.95-96.raw.section
> evidence_98.gff.def       WCK01_AAF20200214_F8-ctg57.111-112.raw.section        WCK01_AAF20200214_F8-ctg57.48.pred.raw.section       WCK01_AAF20200214_F8-ctg57.95.pred.raw.section
> evidence_98.gff.seq       WCK01_AAF20200214_F8-ctg57.11-12.raw.section          WCK01_AAF20200214_F8-ctg57.48.raw.section            WCK01_AAF20200214_F8-ctg57.95.raw.section
> evidence_99.gff           WCK01_AAF20200214_F8-ctg57.111.pred.raw.section       WCK01_AAF20200214_F8-ctg57.48.start.blastn.holdover  WCK01_AAF20200214_F8-ctg57.96.end.blastn.holdover
> evidence_99.gff.ann       WCK01_AAF20200214_F8-ctg57.111.raw.section            WCK01_AAF20200214_F8-ctg57.48.start.blastx.holdover  WCK01_AAF20200214_F8-ctg57.96.end.blastx.holdover
> evidence_99.gff.def       WCK01_AAF20200214_F8-ctg57.112-113.raw.section        WCK01_AAF20200214_F8-ctg57.49-50.raw.section         WCK01_AAF20200214_F8-ctg57.96.end.section.holdover
> evidence_99.gff.seq       WCK01_AAF20200214_F8-ctg57.112.pred.raw.section       WCK01_AAF20200214_F8-ctg57.49.pred.raw.section       WCK01_AAF20200214_F8-ctg57.96.pred.raw.section
> evidence_9.gff            WCK01_AAF20200214_F8-ctg57.112.raw.section            WCK01_AAF20200214_F8-ctg57.49.raw.section            WCK01_AAF20200214_F8-ctg57.96.raw.section
> query.fasta               WCK01_AAF20200214_F8-ctg57.113-114.raw.section        WCK01_AAF20200214_F8-ctg57.4.pred.raw.section        WCK01_AAF20200214_F8-ctg57.96.start.blastn.holdover
> query.masked.fasta        WCK01_AAF20200214_F8-ctg57.113.pred.raw.section       WCK01_AAF20200214_F8-ctg57.4.raw.section             WCK01_AAF20200214_F8-ctg57.96.start.blastx.holdover
> query.masked.fasta.index  WCK01_AAF20200214_F8-ctg57.113.raw.section            WCK01_AAF20200214_F8-ctg57.50-51.raw.section         WCK01_AAF20200214_F8-ctg57.97.pred.raw.section
> query.masked.gff          WCK01_AAF20200214_F8-ctg57.114-115.raw.section        WCK01_AAF20200214_F8-ctg57.50.end.blastn.holdover    WCK01_AAF20200214_F8-ctg57.98.pred.raw.section
> run.log.child.0           WCK01_AAF20200214_F8-ctg57.114.pred.raw.section       WCK01_AAF20200214_F8-ctg57.50.end.blastx.holdover    WCK01_AAF20200214_F8-ctg57.98.start.blastn.holdover
> run.log.child.1           WCK01_AAF20200214_F8-ctg57.114.raw.section            WCK01_AAF20200214_F8-ctg57.50.pred.raw.section       WCK01_AAF20200214_F8-ctg57.99-100.raw.section
> run.log.child.10          WCK01_AAF20200214_F8-ctg57.114.start.blastn.holdover  WCK01_AAF20200214_F8-ctg57.50.raw.section            WCK01_AAF20200214_F8-ctg57.99.end.blastn.holdover
> run.log.child.100         WCK01_AAF20200214_F8-ctg57.114.start.blastx.holdover  WCK01_AAF20200214_F8-ctg57.50.start.blastx.holdover  WCK01_AAF20200214_F8-ctg57.99.end.blastx.holdover
> run.log.child.101         WCK01_AAF20200214_F8-ctg57.115-116.raw.section        WCK01_AAF20200214_F8-ctg57.51-52.raw.section         WCK01_AAF20200214_F8-ctg57.99.pred.raw.section
> run.log.child.102         WCK01_AAF20200214_F8-ctg57.115.end.blastn.holdover    WCK01_AAF20200214_F8-ctg57.51.pred.raw.section       WCK01_AAF20200214_F8-ctg57.99.raw.section
> run.log.child.103         WCK01_AAF20200214_F8-ctg57.115.pred.raw.section       WCK01_AAF20200214_F8-ctg57.51.raw.section            WCK01_AAF20200214_F8-ctg57.99.start.blastx.holdover
> run.log.child.104         WCK01_AAF20200214_F8-ctg57.115.raw.section            WCK01_AAF20200214_F8-ctg57.52-53.raw.section         WCK01_AAF20200214_F8-ctg57.99.start.section.holdover
> run.log.child.105         WCK01_AAF20200214_F8-ctg57.116-117.raw.section        WCK01_AAF20200214_F8-ctg57.52.pred.raw.section       WCK01_AAF20200214_F8-ctg57.9.pred.raw.section
> run.log.child.106         WCK01_AAF20200214_F8-ctg57.116.pred.raw.section       WCK01_AAF20200214_F8-ctg57.52.raw.section            WCK01_AAF20200214_F8-ctg57.9.raw.section
> run.log.child.107         WCK01_AAF20200214_F8-ctg57.116.raw.section            WCK01_AAF20200214_F8-ctg57.53-54.raw.section         WCK01_AAF20200214_F8-ctg57.gff.ann
> run.log.child.108         WCK01_AAF20200214_F8-ctg57.117-118.raw.section        WCK01_AAF20200214_F8-ctg57.53.pred.raw.section       WCK01_AAF20200214_F8-ctg57.gff.def
> run.log.child.109         WCK01_AAF20200214_F8-ctg57.117.pred.raw.section       WCK01_AAF20200214_F8-ctg57.53.raw.section            WCK01_AAF20200214_F8-ctg57.gff.seq
> run.log.child.11          WCK01_AAF20200214_F8-ctg57.117.raw.section            WCK01_AAF20200214_F8-ctg57.54-55.raw.section
> run.log.child.110         WCK01_AAF20200214_F8-ctg57.117.start.blastn.holdover  WCK01_AAF20200214_F8-ctg57.54.pred.raw.section
> run.log.child.111         WCK01_AAF20200214_F8-ctg57.117.start.blastx.holdover  WCK01_AAF20200214_F8-ctg57.54.raw.section
> 
> I set clean_try=1 and am trying to fix this contig (it's only this one contig which is causing trouble), but I'm wondering if it's also okay to completely delete the void directory to force it to start this contig from scratch. I have already tried rerunning maker with clean_try=1 two times and now I'm getting an mpich2 error:
> 
> Fatal error in MPI_Send: Invalid count, error stack:
> MPI_Send(173): MPI_Send(buf=0x2aec3d6a3010, count=-1279995089, MPI_CHAR, dest=15, tag=9999, MPI_COMM_WORLD) failed
> MPI_Send(97).: Negative count, value is -1279995089
> 
> I am currently trying again with fewer MPI jobs requested, worrying that there might be a memory issue on the computer cluster I am using. My temporary directory still has lots of space, but I have ~200G RAM per node and sometimes the jobs use a ton of RAM. I don't have too many more contigs left of this run, so I just really don't want to mess anything up. Do you have any advice?
> 
> Thanks so much!
> Zoe
> 
> ______________________________________
> Zoe Clarke
> PhD candidate in Computational Biology at U of T
> Lab profile: http://baderlab.org/Zoe%20Clarke <http://baderlab.org/Zoe%20Clarke>
> Personal website: https://zoe-clarke.weebly.com/ <https://zoe-clarke.weebly.com/>_______________________________________________
> maker-devel mailing list
> maker-devel at yandell-lab.org <mailto:maker-devel at yandell-lab.org>
> http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org <http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org>
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From eennadi at gmail.com  Fri Oct 23 00:15:33 2020
From: eennadi at gmail.com (Emmanuel Nnadi)
Date: Fri, 23 Oct 2020 07:15:33 +0100
Subject: [maker-devel] Can maker be used to improve genome assembly?
Message-ID: <CAOXM=CXTCX5tyDeM29fTGi5u0qjOXT7TSCUeQrYt-PogCphvSg@mail.gmail.com>

Hi Carson,
Greetings! This is just a random question that came to my mind. Looking at
the way maker structures files and brings contigs together based on "gene"
locations. Can this be explored to improve genome assemblies? Maybe a tool
that can work from a good annotation to generating a set of improved genome
assembly based on these gene locations


Just a thought
Nnaemeka Emmanuel Nnadi,Ph.D
Department of Microbiology,
Faculty of Natural and Applied Science,
Plateau State University, Bokkos, Plateau State, Nigeria.
+2348068124819
Publications:
 https://www.researchgate.net/profile/Emmanuel_Nnadi/publications
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From carsonhh at gmail.com  Mon Oct 26 13:33:00 2020
From: carsonhh at gmail.com (Carson Holt)
Date: Mon, 26 Oct 2020 13:33:00 -0600
Subject: [maker-devel] Does maker support muti-processing for a single
 long fasta sequence using openMPI?
In-Reply-To: <CALJhmFocG7D-K0gdGJ5831V=gnPp0BDrEMu138W3HV=QmKs2Ug@mail.gmail.com>
References: <CALJhmFoNOdxFb4gQ4jYP=FZqaHgZdVOhQOpPuyd5bMAeYZ8ucg@mail.gmail.com>
	<AC94C4EB-A696-4830-A650-1A33EB67B281@gmail.com>
	<CALJhmFocG7D-K0gdGJ5831V=gnPp0BDrEMu138W3HV=QmKs2Ug@mail.gmail.com>
Message-ID: <926FDE45-F317-43CD-BF2E-A0B00FDBD9A7@gmail.com>

Your MPI processes may not be seeing each other.  So you are getting multiple maker runs all colliding.  You need to reinstall MAKER and say ?yes? to the compile for MPI question.  You may also have to reinstall OpenMPI if just reinstalling MAKER does not work.  You can test MAKER for MPI by running the following ?> mpiexec -mca btl ^openib -n 40 maker -help

If you get a single help message then everything is fine.  If you get 40 help messages, then MPI is not communicating correctly.

?Carson


> On Oct 20, 2020, at 10:23 AM, Xu, taosheng <taosheng.x at gmail.com> wrote:
> 
> Thank you very much Carson for your timely response,
> Yes I think so. The Maker MPI should support the multi-processing of an ultra-long single sequence. But I cannot run it successfully for a single sequence.
> First I  make sure the openMPI with maker has been installed properly. It works well for multiple DNA sequences in a parallel way.
> When I submit a maker job for an ultra-long single sequence (mpiexec -mca btl ^openib -n 40 maker -g scaffold1.fasta -fix_nucleotides, The max_dna_len is set to 100000). It always left only one maker thread run. The other maker threads are disappeared and show finished in the output information. See the output information below. Please help me to check it. Thanks for your kind help and your time.
> 
> #-----MAKER Behavior Options
> max_dna_len=100000 #length for dividing up contigs into chunks (increases/decreases memory usage)
> min_contig=1 #skip genome contigs below this length (under 10kb are often useless)
> 
> Best regards,
> Taosheng
> 
> 
> 
> OUTPUT Information
> STATUS: Processing and indexing input FASTA files...
> STATUS: Setting up database for any GFF3 input...
> examining contents of the fasta file and run log
> A data structure will be created for you at:
> /data/splitgenome/top1000/splitGenome/part1/plant.maker.output/plant_datastore
> 
> To access files for individual sequences use the datastore index:
> /data/splitgenome/top1000/splitGenome/part1/plant.maker.output/plant_master_datastore_index.log
> 
> STATUS: Now running MAKER...
> 
> 
> 
> --Next Contig--
> 
> Processing run.log file...
> examining contents of the fasta file and run log
> 
> 
> 
> --Next Contig--
> 
> #---------------------------------------------------------------------
> Another instance of maker is processing this contig!!
> SeqID: scaffold#1
> Length: 73580997
> #---------------------------------------------------------------------
> 
> 
> examining contents of the fasta file and run log
> 
> 
> 
> --Next Contig--
> 
> #---------------------------------------------------------------------
> Another instance of maker is processing this contig!!
> SeqID: scaffold#1
> Length: 73580997
> #---------------------------------------------------------------------
> 
> 
> 
> 
> Maker is now finished!!!
> 
> 
> 
> Start_time: 1603000030
> End_time:   1603000033
> Elapsed:    3
> A data structure will be created for you at:
> /data/splitgenome/top1000/splitGenome/part1/plant.maker.output/plant_datastore
> 
> To access files for individual sequences use the datastore index:
> /data/splitgenome/top1000/splitGenome/part1/plant.maker.output/plant_master_datastore_index.log
> 
> STATUS: Now running MAKER...
> MAKER WARNING: The file plant.maker.output/plant_datastore/B5/CD/scaffold#1//theVoid.scaffold#1/28/scaffold#1.289.plant_repeatFinal%2Elib%2Empi%2E10%2E2.specific.out
> did not finish on the last run and must be erased
> WARNING: Multiple MAKER processes have been started in the
> same directory.
> 
> STATUS: Processing and indexing input FASTA files...
> examining contents of the fasta file and run log
> 
> 
> 
> --Next Contig--
> 
> #---------------------------------------------------------------------
> Another instance of maker is processing this contig!!
> SeqID: scaffold#1
> Length: 73580997
> #---------------------------------------------------------------------
> 
> 
> WARNING: Multiple MAKER processes have been started in the
> same directory.
> 
> STATUS: Processing and indexing input FASTA files...
> STATUS: Setting up database for any GFF3 input...
> STATUS: Setting up database for any GFF3 input...
> A data structure will be created for you at:
> /data/splitgenome/top1000/splitGenome/part1/plant.maker.output/plant_datastore
> 
> To access files for individual sequences use the datastore index:
> /data/splitgenome/top1000/splitGenome/part1/plant.maker.output/plant_master_datastore_index.log
> 
> STATUS: Now running MAKER...
> examining contents of the fasta file and run log
> 
> 
> 
> --Next Contig--
> 
> #---------------------------------------------------------------------
> Another instance of maker is processing this contig!!
> SeqID: scaffold#1
> Length: 73580997
> #---------------------------------------------------------------------
> 
> 
> 
> 
> Maker is now finished!!!
> 
> 
> 
> Start_time: 1603000030
> End_time:   1603000034
> Elapsed:    4
> #---------------------------------------------------------------------
> Now starting the contig!!
> SeqID: scaffold#1
> Length: 73580997
> #---------------------------------------------------------------------
> 
> 
> examining contents of the fasta file and run log
> 
> 
> 
> --Next Contig--
> 
> #---------------------------------------------------------------------
> Another instance of maker is processing this contig!!
> SeqID: scaffold#1
> Length: 73580997
> #---------------------------------------------------------------------
> 
> 
> examining contents of the fasta file and run log
> 
> 
> 
> --Next Contig--
> 
> #---------------------------------------------------------------------
> Another instance of maker is processing this contig!!
> SeqID: scaffold#1
> Length: 73580997
> #---------------------------------------------------------------------
> 
> 
> 
> 
> Start_time: 1603000030
> End_time:   1603000034
> Elapsed:    4
> 
> 
> Maker is now finished!!!
> 
> A data structure will be created for you at:
> /data/splitgenome/top1000/splitGenome/part1/plant.maker.output/plant_datastore
> 
> To access files for individual sequences use the datastore index:
> /data/splitgenome/top1000/splitGenome/part1/plant.maker.output/plant_master_datastore_index.log
> 
> STATUS: Now running MAKER...
> examining contents of the fasta file and run log
> ..........
> 
> Maker is now finished!!!
> 
> 
> 
> Start_time: 1602920407
> End_time:   1602920580
> Elapsed:    173
> running  repeat masker.
> #--------- command -------------#
> Widget::RepeatMasker:
> cd /tmp/maker_VflRYH; ./maker3.01/exe/RepeatMasker/RepeatMasker /data/splitgenome/top1000/splitGenome/part1/plant.maker.output/plant_datastore/B5/CD/scaffold#1//theVoid.scaffold#1/0/scaffold#1.0.plant_repeatFinal%2Elib%2Empi%2E10%2E0.specific -dir /data/splitgenome/top1000/splitGenome/part1/plant.maker.output/plant_datastore/B5/CD/scaffold#1//theVoid.scaffold#1/0 -pa 1 -lib /data/splitgenome/top1000/splitGenome/part1/plant.maker.output/mpi_blastdb/plant_repeatFinal%2Elib.mpi.10/plant_repeatFinal%2Elib.mpi.10.0
> #-------------------------------#
> running  repeat masker.
> #--------- command -------------#
> Widget::RepeatMasker:
> cd /tmp/maker_VflRYH; ./maker3.01/exe/RepeatMasker/RepeatMasker /data/splitgenome/top1000/splitGenome/part1/plant.maker.output/plant_datastore/B5/CD/scaffold#1//theVoid.scaffold#1/0/scaffold#1.0.plant_repeatFinal%2Elib%2Empi%2E10%2E1.specific -dir /data/splitgenome/top1000/splitGenome/part1/plant.maker.output/plant_datastore/B5/CD/scaffold#1//theVoid.scaffold#1/0 -pa 1 -lib /data/splitgenome/top1000/splitGenome/part1/plant.maker.output/mpi_blastdb/plant_repeatFinal%2Elib.mpi.10/plant_repeatFinal%2Elib.mpi.10.1
> #-------------------------------#
> running  repeat masker.
> #--------- command -------------#
> Widget::RepeatMasker:
> cd /tmp/maker_VflRYH; ./maker3.01/exe/RepeatMasker/RepeatMasker /data/splitgenome/top1000/splitGenome/part1/plant.maker.output/plant_datastore/B5/CD/scaffold#1//theVoid.scaffold#1/0/scaffold#1.0.plant_repeatFinal%2Elib%2Empi%2E10%2E2.specific -dir /data/splitgenome/top1000/splitGenome/part1/plant.maker.output/plant_datastore/B5/CD/scaffold#1//theVoid.scaffold#1/0 -pa 1 -lib /data/splitgenome/top1000/splitGenome/part1/plant.maker.output/mpi_blastdb/plant_repeatFinal%2Elib.mpi.10/plant_repeatFinal%2Elib.mpi.10.2
> #-------------------------------#
> running  repeat masker.
> #--------- command -------------#
> Widget::RepeatMasker:
> cd /tmp/maker_VflRYH; ./maker3.01/exe/RepeatMasker/RepeatMasker /data/splitgenome/top1000/splitGenome/part1/plant.maker.output/plant_datastore/B5/CD/scaffold#1//theVoid.scaffold#1/0/scaffold#1.0.plant_repeatFinal%2Elib%2Empi%2E10%2E3.specific -dir /data/splitgenome/top1000/splitGenome/part1/plant.maker.output/plant_datastore/B5/CD/scaffold#1//theVoid.scaffold#1/0 -pa 1 -lib /data/splitgenome/top1000/splitGenome/part1/plant.maker.output/mpi_blastdb/plant_repeatFinal%2Elib.mpi.10/plant_repeatFinal%2Elib.mpi.10.3
> #-------------------------------#
> running  repeat masker.
> #--------- command -------------#
> 
> .....
> 
> On Mon, Oct 19, 2020 at 10:32 PM Carson Holt <carsonhh at gmail.com <mailto:carsonhh at gmail.com>> wrote:
> Yes. It will divide contigs into chunks the same size as the max_dna_len parameter.
> 
> ?Carson
> 
> Sent from my iPhone
> 
> > On Oct 17, 2020, at 12:48 AM, Xu, taosheng <taosheng.x at gmail.com <mailto:taosheng.x at gmail.com>> wrote:
> > 
> > ?
> > Dear Maker Development Team,
> > I wonder whether maker supports parallel processing for a single long genome sequence?
> > 
> > When I submit my maker task using openMPI with multiple cpus (like, mpiexec -n 40  maker) to annotate a single long genome sequence, always only one maker with 4 rmblast run. The other cpus is on idle.
> > 
> > I want to use the maker parallel processing with openMPI to speed up a single ultra-long genome sequence annotation.
> > 
> > Best regards,
> > Taosheng
> > _______________________________________________
> > maker-devel mailing list
> > maker-devel at yandell-lab.org <mailto:maker-devel at yandell-lab.org>
> > http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org <http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org>

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From carsonhh at gmail.com  Mon Oct 26 13:49:33 2020
From: carsonhh at gmail.com (Carson Holt)
Date: Mon, 26 Oct 2020 13:49:33 -0600
Subject: [maker-devel] Can maker be used to improve genome assembly?
In-Reply-To: <CAOXM=CXTCX5tyDeM29fTGi5u0qjOXT7TSCUeQrYt-PogCphvSg@mail.gmail.com>
References: <CAOXM=CXTCX5tyDeM29fTGi5u0qjOXT7TSCUeQrYt-PogCphvSg@mail.gmail.com>
Message-ID: <B7F4EEA8-9F57-4CF3-9EFA-7D9F9B763537@gmail.com>

We haven?t explored this.  On re-assembly projects I rarely find more than a handful of instances where a gene was obviously split across contigs in the first assembly's annotation.  More often what I find is that extra contigs tend to contain fragments of a gene that is complete on another contig in the same assembly (caused by high heterozygosity, so maternal and paternal contigs can assemble independently).

?Carson


> On Oct 23, 2020, at 12:15 AM, Emmanuel Nnadi <eennadi at gmail.com> wrote:
> 
> Hi Carson,
> Greetings! This is just a random question that came to my mind. Looking at the way maker structures files and brings contigs together based on "gene" locations. Can this be explored to improve genome assemblies? Maybe a tool that can work from a good annotation to generating a set of improved genome assembly based on these gene locations
> 
> 
> Just a thought
> Nnaemeka Emmanuel Nnadi,Ph.D
> Department of Microbiology,
> Faculty of Natural and Applied Science,
> Plateau State University, Bokkos, Plateau State, Nigeria.
> +2348068124819
> Publications: 
>  https://www.researchgate.net/profile/Emmanuel_Nnadi/publications <https://www.researchgate.net/profile/Emmanuel_Nnadi/publications>
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From daren.card at gmail.com  Thu Oct 29 10:35:57 2020
From: daren.card at gmail.com (Daren Card)
Date: Thu, 29 Oct 2020 12:35:57 -0400
Subject: [maker-devel] tblastx of alt-ESTs failing on single scaffold
Message-ID: <CACNE1p+-JynX7_vdakS0ibS3Hf-9M5K_8AxKEOmUgWzc7ScOtg@mail.gmail.com>

Hello,

I am having an issue running MAKER and am hoping to get some
troubleshooting guidance. I am running MAKER v. 2.31.10 on a Unix cluster
using a Singularity image with BLAST v. 2.9.0+ and Exonerate v. 3.3.2. I am
running MAKER with the following command options: "-fix_nucleotides
-nodatastore -RM_off". I am providing assembled transcripts from the target
species (est) and a close relative (alt-est) and proteins from several
species within the same general clade (Squamata). Gene models are being
derived from Augustus with est2genome and protein2genome turned off. I have
largely successfully run MAKER on a couple of genomes from the same
vertebrate genus, but have this lingering problem with a single scaffold
from one of the genomes. If it were pretty short, I'd just ignore it, but
it is 2 Mb, so I do not want to miss out on annotating it.

When I ran MAKER on the entire genome, it finished properly except for this
problematic scaffold. So I separated that scaffold out and tried running it
alone with otherwise the same settings. Each time, it appears I get the
same error during the 1st try when MAKER runs.

ERROR: TBLASTX does not appear to be finished in Widget::tblastx::keepers
--> rank=23, hostname=holy7c18405.rc.fas.harvard.edu
--> rank=23, hostname=holy7c18405.rc.fas.harvard.edu
--> rank=23, hostname=holy7c18405.rc.fas.harvard.edu
--> rank=23, hostname=holy7c18405.rc.fas.harvard.edu
ERROR: Failed while doing tblastx of alt-ESTs
ERROR: Chunk failed at level:4, tier_type:3
FAILED CONTIG:scaffold_77

ERROR: Chunk failed at level:4, tier_type:0
FAILED CONTIG:scaffold_77

Then MAKER keeps retrying and apparently hitting the same problem. I
checked the logs the best I can and see the following issue within
run.log.child.0 for that scaffold.

STARTED lerBou1_maker_rnd2.maker.output/lerBou1_maker_rnd2_datastore/scaffold_77/theVoid.scaffold_77/0/scaffold_77.0.lerEdw1_Trinity_combined_denovo_refguided%2Ecdhit%2Efasta.tblastx
DIED    RANK    17:4:0:0
DIED    COUNT   7

This output file noted there is not present to check, which must stem from
whatever issue there is.

I'm not sure what to do next about this issue and see no obvious
information about what the problem is besides failure of tblastx to run.
Any help that anyone can provide is greatly appreciated.

Kind regards,
Daren Card

NSF Postdoctoral Fellow
Harvard University
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From eennadi at gmail.com  Tue Oct 27 21:01:05 2020
From: eennadi at gmail.com (Emmanuel Nnadi)
Date: Wed, 28 Oct 2020 04:01:05 +0100
Subject: [maker-devel] Maker yields sequences without start and stop codon
Message-ID: <CAOXM=CU=3Y3SgOiAyDiR3Qa56KegaZE-rwEBESNKYO4cBos5uw@mail.gmail.com>

Hi Carson
I always set always_complete=1 yet I still get sequences without start and
stop codon.

Can
https://github.com/Gaius-Augustus/Augustus/blob/master/scripts/fix_in_frame_stop_codon_genes.py
be
used on the final sequence to fix start and stop codon problem?


Nnaemeka Emmanuel Nnadi,Ph.D
Department of Microbiology,
Faculty of Natural and Applied Science,
Plateau State University, Bokkos, Plateau State, Nigeria.
+2348068124819
Publications:
 https://www.researchgate.net/profile/Emmanuel_Nnadi/publications
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