From ggirmate at purdue.edu Wed Nov 3 10:06:07 2021 From: ggirmate at purdue.edu (Gezahegn Girma) Date: Wed, 3 Nov 2021 12:06:07 -0400 Subject: [maker-devel] Request for support on maker pipeline Message-ID: <75D943B0-2EBE-4B32-84A4-B4D48BF2EC25@purdue.edu> Hello, I am using maker for genome annotation of sorghum genotype. Maker is running and keep increasing the log file but I see the following error messages. This is to request for your kind support to resolve this issue. ========================================================= STATUS: Now running MAKER... WARNING: Cannot find >0, trying to re-index the fasta. stop here: 0 ERROR: Fasta index error at /depot/bioinfo/apps/apps/MAKER-2.31.10-nompi/bin/../lib/Process/MpiChunk.pm line 239. Process::MpiChunk::_prepare(Process::MpiChunk=HASH(0x5e83458), HASH(0x5e8f9b0), 0) called at /depot/bioinfo/apps/apps/MAKER-2.31. 10-nompi/bin/../lib/Process/MpiTiers.pm line 73 Process::MpiTiers::__ANON__() called at /depot/bioinfo/apps/apps/MAKER-2.31.10-nompi/bin/../lib/Error.pm line 415 eval {...} called at /depot/bioinfo/apps/apps/MAKER-2.31.10-nompi/bin/../lib/Error.pm line 407 Error::subs::try(CODE(0x5e89c60), HASH(0x5e8f6f8)) called at /depot/bioinfo/apps/apps/MAKER-2.31.10-nompi/bin/../lib/Process/MpiT iers.pm line 79 Process::MpiTiers::_prepare(Process::MpiTiers=HASH(0x5e902f8)) called at /depot/bioinfo/apps/apps/MAKER-2.31.10-nompi/bin/../lib/ Process/MpiTiers.pm line 56 Process::MpiTiers::new("Process::MpiTiers", HASH(0x5e89870), 0, "Process::MpiChunk") called at /group/bioinfo/apps/apps/MAKER-2.3 1.10-nompi/bin/maker line 669 --> rank=NA, hostname=bell-a105.rcac.purdue.edu ERROR: Failed in tier preparation examining contents of the fasta file and run log . . . Warning: [blastn] Query_1 1 97 18 masked CH.. : Could not calculate ungapped Karlin-Altschul parameters due to an invalid query sequence or its translation. Please verify the query sequence(s) and/or filtering options deleted:0 hits ================================================================================ Regards, Gez -------------- next part -------------- An HTML attachment was scrubbed... URL: From Fungi at uwyo.edu Wed Nov 17 14:04:47 2021 From: Fungi at uwyo.edu (Steven L. Miller) Date: Wed, 17 Nov 2021 21:04:47 +0000 Subject: [maker-devel] Continuing problems Message-ID: I just ran Maker on my 75,507 unitig database. The maker_opts.ctl file included EST Evidence in the form of a large transcript rna file from Arabidopsis thaliana (GenBank) for est=, and protein= files from Arabidopsis thaliana and a uniprot file from a closely related plant to my organism. All contigs started and finished. Looking at the SLURM output some of them ran the #Widget:: RepeatMasker only. Other contigs (e.g. tig00000004) ran 111 pages of RepeatMasker, blastx repeats, formater, running blast search, blastx, setting up GFF3 output and fast chunks, formatting database, etc. on the Arabidopsis rna file, then on the two protein files. However, when I look at the location of that particular contig ptero.unitigs_datastore/C3/F2/tig00000004/ in the _master_datastor_index.log file I get only this: .././theVoid.tig00000004/run.logtig00000004.gff.swp There is no maker.proteins.fasta or maker.transcripts.fasta file. When I look at the tig00000004.gff file, it is empty. Am I even on the right track? Thanks for any help you can provide.Sincerely,Steve MillerBotanyUniversity of Wyoming -------------- next part -------------- An HTML attachment was scrubbed... URL: From peruzzaluca at gmail.com Thu Nov 18 04:44:54 2021 From: peruzzaluca at gmail.com (Luca Peruzza) Date: Thu, 18 Nov 2021 12:44:54 +0100 Subject: [maker-devel] Maker 3 stuck at "processing chunk output" Message-ID: Dear Maker developers, I am posting here because we have a curious situation happening while using maker 3.01.03 to annotate a fish genome and we have one scaffold, which is ~30.4 M bases that is problematic. We perform 3 rounds of annotation (as suggested by the maker wikis available). The first round uses EST and protein evidence to generate gene models (--> we set est2genome=1 and protein2genome=1) and we do not use gene predictors. This round always complete successfully. In the second and third round we use the results from the previous run to train SNAP and Augustus, plus we use gmhmm and we set runEVM=1 (and of course we set est2genome=0 and protein2genome=0). These rounds never finish. Maker is stuck forever as shown in Screen1.png and keeps using a substantial amount of CPUs (as seen in Screen2.png), which I honestly do not think is normal at that final stage of the program run (?!?). We have noticed that if we enter the "theVOid" folder, the log file of the contig has this error (Screen3.png). The "curious" thing is that we have 18 other scaffolds that are between 10 and 27.6 M bases in length and maker is always able to correctly annotate them. Could you help us solving this issue? I could send you the fasta file and the est and protein gff with the evidences and the gene predictor input files if need be so you could try to replicate the error yourself (just let me know where I can upload the relevant files). -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Screen2.png Type: image/png Size: 259168 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Screen1.png Type: image/png Size: 67301 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Screen3.png Type: image/png Size: 271528 bytes Desc: not available URL: From prometheus07.06 at gmail.com Sun Nov 28 21:21:18 2021 From: prometheus07.06 at gmail.com (zc y) Date: Mon, 29 Nov 2021 04:21:18 -0000 Subject: [maker-devel] cds error Message-ID: Dear Maker developers, I found a CDS error in my rice project. I ran the maker (3.01.03) and it finished without error in master_datastore_index.log. But when I use gffread to translate the protein from maker gff, I found that almost all of proteins are not start with 'M' and many stop codons in it. In fact, I checked the protein file (Chr12.maker.proteins.fasta) provided by the maker, it is correct. I used the same parameter and evidence in another rice, it don't have the problem. What should I do? thanks, [image: QQ??20211129121755.png][image: QQ??20211129121917.png] -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: QQ??20211129121755.png Type: image/png Size: 211768 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: QQ??20211129121917.png Type: image/png Size: 202235 bytes Desc: not available URL: From ggirmate at purdue.edu Wed Nov 3 10:06:07 2021 From: ggirmate at purdue.edu (Gezahegn Girma) Date: Wed, 3 Nov 2021 12:06:07 -0400 Subject: [maker-devel] Request for support on maker pipeline Message-ID: <75D943B0-2EBE-4B32-84A4-B4D48BF2EC25@purdue.edu> Hello, I am using maker for genome annotation of sorghum genotype. Maker is running and keep increasing the log file but I see the following error messages. This is to request for your kind support to resolve this issue. ========================================================= STATUS: Now running MAKER... WARNING: Cannot find >0, trying to re-index the fasta. stop here: 0 ERROR: Fasta index error at /depot/bioinfo/apps/apps/MAKER-2.31.10-nompi/bin/../lib/Process/MpiChunk.pm line 239. Process::MpiChunk::_prepare(Process::MpiChunk=HASH(0x5e83458), HASH(0x5e8f9b0), 0) called at /depot/bioinfo/apps/apps/MAKER-2.31. 10-nompi/bin/../lib/Process/MpiTiers.pm line 73 Process::MpiTiers::__ANON__() called at /depot/bioinfo/apps/apps/MAKER-2.31.10-nompi/bin/../lib/Error.pm line 415 eval {...} called at /depot/bioinfo/apps/apps/MAKER-2.31.10-nompi/bin/../lib/Error.pm line 407 Error::subs::try(CODE(0x5e89c60), HASH(0x5e8f6f8)) called at /depot/bioinfo/apps/apps/MAKER-2.31.10-nompi/bin/../lib/Process/MpiT iers.pm line 79 Process::MpiTiers::_prepare(Process::MpiTiers=HASH(0x5e902f8)) called at /depot/bioinfo/apps/apps/MAKER-2.31.10-nompi/bin/../lib/ Process/MpiTiers.pm line 56 Process::MpiTiers::new("Process::MpiTiers", HASH(0x5e89870), 0, "Process::MpiChunk") called at /group/bioinfo/apps/apps/MAKER-2.3 1.10-nompi/bin/maker line 669 --> rank=NA, hostname=bell-a105.rcac.purdue.edu ERROR: Failed in tier preparation examining contents of the fasta file and run log . . . Warning: [blastn] Query_1 1 97 18 masked CH.. : Could not calculate ungapped Karlin-Altschul parameters due to an invalid query sequence or its translation. Please verify the query sequence(s) and/or filtering options deleted:0 hits ================================================================================ Regards, Gez -------------- next part -------------- An HTML attachment was scrubbed... URL: From Fungi at uwyo.edu Wed Nov 17 14:04:47 2021 From: Fungi at uwyo.edu (Steven L. Miller) Date: Wed, 17 Nov 2021 21:04:47 +0000 Subject: [maker-devel] Continuing problems Message-ID: I just ran Maker on my 75,507 unitig database. The maker_opts.ctl file included EST Evidence in the form of a large transcript rna file from Arabidopsis thaliana (GenBank) for est=, and protein= files from Arabidopsis thaliana and a uniprot file from a closely related plant to my organism. All contigs started and finished. Looking at the SLURM output some of them ran the #Widget:: RepeatMasker only. Other contigs (e.g. tig00000004) ran 111 pages of RepeatMasker, blastx repeats, formater, running blast search, blastx, setting up GFF3 output and fast chunks, formatting database, etc. on the Arabidopsis rna file, then on the two protein files. However, when I look at the location of that particular contig ptero.unitigs_datastore/C3/F2/tig00000004/ in the _master_datastor_index.log file I get only this: .././theVoid.tig00000004/run.logtig00000004.gff.swp There is no maker.proteins.fasta or maker.transcripts.fasta file. When I look at the tig00000004.gff file, it is empty. Am I even on the right track? Thanks for any help you can provide.Sincerely,Steve MillerBotanyUniversity of Wyoming -------------- next part -------------- An HTML attachment was scrubbed... URL: From peruzzaluca at gmail.com Thu Nov 18 04:44:54 2021 From: peruzzaluca at gmail.com (Luca Peruzza) Date: Thu, 18 Nov 2021 12:44:54 +0100 Subject: [maker-devel] Maker 3 stuck at "processing chunk output" Message-ID: Dear Maker developers, I am posting here because we have a curious situation happening while using maker 3.01.03 to annotate a fish genome and we have one scaffold, which is ~30.4 M bases that is problematic. We perform 3 rounds of annotation (as suggested by the maker wikis available). The first round uses EST and protein evidence to generate gene models (--> we set est2genome=1 and protein2genome=1) and we do not use gene predictors. This round always complete successfully. In the second and third round we use the results from the previous run to train SNAP and Augustus, plus we use gmhmm and we set runEVM=1 (and of course we set est2genome=0 and protein2genome=0). These rounds never finish. Maker is stuck forever as shown in Screen1.png and keeps using a substantial amount of CPUs (as seen in Screen2.png), which I honestly do not think is normal at that final stage of the program run (?!?). We have noticed that if we enter the "theVOid" folder, the log file of the contig has this error (Screen3.png). The "curious" thing is that we have 18 other scaffolds that are between 10 and 27.6 M bases in length and maker is always able to correctly annotate them. Could you help us solving this issue? I could send you the fasta file and the est and protein gff with the evidences and the gene predictor input files if need be so you could try to replicate the error yourself (just let me know where I can upload the relevant files). -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Screen2.png Type: image/png Size: 259168 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Screen1.png Type: image/png Size: 67301 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Screen3.png Type: image/png Size: 271528 bytes Desc: not available URL: From prometheus07.06 at gmail.com Sun Nov 28 21:21:18 2021 From: prometheus07.06 at gmail.com (zc y) Date: Mon, 29 Nov 2021 04:21:18 -0000 Subject: [maker-devel] cds error Message-ID: Dear Maker developers, I found a CDS error in my rice project. I ran the maker (3.01.03) and it finished without error in master_datastore_index.log. But when I use gffread to translate the protein from maker gff, I found that almost all of proteins are not start with 'M' and many stop codons in it. In fact, I checked the protein file (Chr12.maker.proteins.fasta) provided by the maker, it is correct. I used the same parameter and evidence in another rice, it don't have the problem. What should I do? thanks, [image: QQ??20211129121755.png][image: QQ??20211129121917.png] -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: QQ??20211129121755.png Type: image/png Size: 211768 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: QQ??20211129121917.png Type: image/png Size: 202235 bytes Desc: not available URL: From ggirmate at purdue.edu Wed Nov 3 10:06:07 2021 From: ggirmate at purdue.edu (Gezahegn Girma) Date: Wed, 3 Nov 2021 12:06:07 -0400 Subject: [maker-devel] Request for support on maker pipeline Message-ID: <75D943B0-2EBE-4B32-84A4-B4D48BF2EC25@purdue.edu> Hello, I am using maker for genome annotation of sorghum genotype. Maker is running and keep increasing the log file but I see the following error messages. This is to request for your kind support to resolve this issue. ========================================================= STATUS: Now running MAKER... WARNING: Cannot find >0, trying to re-index the fasta. stop here: 0 ERROR: Fasta index error at /depot/bioinfo/apps/apps/MAKER-2.31.10-nompi/bin/../lib/Process/MpiChunk.pm line 239. Process::MpiChunk::_prepare(Process::MpiChunk=HASH(0x5e83458), HASH(0x5e8f9b0), 0) called at /depot/bioinfo/apps/apps/MAKER-2.31. 10-nompi/bin/../lib/Process/MpiTiers.pm line 73 Process::MpiTiers::__ANON__() called at /depot/bioinfo/apps/apps/MAKER-2.31.10-nompi/bin/../lib/Error.pm line 415 eval {...} called at /depot/bioinfo/apps/apps/MAKER-2.31.10-nompi/bin/../lib/Error.pm line 407 Error::subs::try(CODE(0x5e89c60), HASH(0x5e8f6f8)) called at /depot/bioinfo/apps/apps/MAKER-2.31.10-nompi/bin/../lib/Process/MpiT iers.pm line 79 Process::MpiTiers::_prepare(Process::MpiTiers=HASH(0x5e902f8)) called at /depot/bioinfo/apps/apps/MAKER-2.31.10-nompi/bin/../lib/ Process/MpiTiers.pm line 56 Process::MpiTiers::new("Process::MpiTiers", HASH(0x5e89870), 0, "Process::MpiChunk") called at /group/bioinfo/apps/apps/MAKER-2.3 1.10-nompi/bin/maker line 669 --> rank=NA, hostname=bell-a105.rcac.purdue.edu ERROR: Failed in tier preparation examining contents of the fasta file and run log . . . Warning: [blastn] Query_1 1 97 18 masked CH.. : Could not calculate ungapped Karlin-Altschul parameters due to an invalid query sequence or its translation. Please verify the query sequence(s) and/or filtering options deleted:0 hits ================================================================================ Regards, Gez -------------- next part -------------- An HTML attachment was scrubbed... URL: From Fungi at uwyo.edu Wed Nov 17 14:04:47 2021 From: Fungi at uwyo.edu (Steven L. Miller) Date: Wed, 17 Nov 2021 21:04:47 +0000 Subject: [maker-devel] Continuing problems Message-ID: I just ran Maker on my 75,507 unitig database. The maker_opts.ctl file included EST Evidence in the form of a large transcript rna file from Arabidopsis thaliana (GenBank) for est=, and protein= files from Arabidopsis thaliana and a uniprot file from a closely related plant to my organism. All contigs started and finished. Looking at the SLURM output some of them ran the #Widget:: RepeatMasker only. Other contigs (e.g. tig00000004) ran 111 pages of RepeatMasker, blastx repeats, formater, running blast search, blastx, setting up GFF3 output and fast chunks, formatting database, etc. on the Arabidopsis rna file, then on the two protein files. However, when I look at the location of that particular contig ptero.unitigs_datastore/C3/F2/tig00000004/ in the _master_datastor_index.log file I get only this: .././theVoid.tig00000004/run.logtig00000004.gff.swp There is no maker.proteins.fasta or maker.transcripts.fasta file. When I look at the tig00000004.gff file, it is empty. Am I even on the right track? Thanks for any help you can provide.Sincerely,Steve MillerBotanyUniversity of Wyoming -------------- next part -------------- An HTML attachment was scrubbed... URL: From peruzzaluca at gmail.com Thu Nov 18 04:44:54 2021 From: peruzzaluca at gmail.com (Luca Peruzza) Date: Thu, 18 Nov 2021 12:44:54 +0100 Subject: [maker-devel] Maker 3 stuck at "processing chunk output" Message-ID: Dear Maker developers, I am posting here because we have a curious situation happening while using maker 3.01.03 to annotate a fish genome and we have one scaffold, which is ~30.4 M bases that is problematic. We perform 3 rounds of annotation (as suggested by the maker wikis available). The first round uses EST and protein evidence to generate gene models (--> we set est2genome=1 and protein2genome=1) and we do not use gene predictors. This round always complete successfully. In the second and third round we use the results from the previous run to train SNAP and Augustus, plus we use gmhmm and we set runEVM=1 (and of course we set est2genome=0 and protein2genome=0). These rounds never finish. Maker is stuck forever as shown in Screen1.png and keeps using a substantial amount of CPUs (as seen in Screen2.png), which I honestly do not think is normal at that final stage of the program run (?!?). We have noticed that if we enter the "theVOid" folder, the log file of the contig has this error (Screen3.png). The "curious" thing is that we have 18 other scaffolds that are between 10 and 27.6 M bases in length and maker is always able to correctly annotate them. Could you help us solving this issue? I could send you the fasta file and the est and protein gff with the evidences and the gene predictor input files if need be so you could try to replicate the error yourself (just let me know where I can upload the relevant files). -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Screen2.png Type: image/png Size: 259168 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Screen1.png Type: image/png Size: 67301 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Screen3.png Type: image/png Size: 271528 bytes Desc: not available URL: From prometheus07.06 at gmail.com Sun Nov 28 21:21:18 2021 From: prometheus07.06 at gmail.com (zc y) Date: Mon, 29 Nov 2021 04:21:18 -0000 Subject: [maker-devel] cds error Message-ID: Dear Maker developers, I found a CDS error in my rice project. I ran the maker (3.01.03) and it finished without error in master_datastore_index.log. But when I use gffread to translate the protein from maker gff, I found that almost all of proteins are not start with 'M' and many stop codons in it. In fact, I checked the protein file (Chr12.maker.proteins.fasta) provided by the maker, it is correct. I used the same parameter and evidence in another rice, it don't have the problem. What should I do? thanks, [image: QQ??20211129121755.png][image: QQ??20211129121917.png] -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: QQ??20211129121755.png Type: image/png Size: 211768 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: QQ??20211129121917.png Type: image/png Size: 202235 bytes Desc: not available URL: