From patrick.tranvan at unil.ch Mon Aug 30 02:45:25 2021 From: patrick.tranvan at unil.ch (Patrick Tran Van) Date: Mon, 30 Aug 2021 08:45:25 +0000 Subject: [maker-devel] Fatal error in PMPI_Send Message-ID: <7bad655de17b4a1ab537e1b624c1da06@unil.ch> Hi, I have this strange error that kill my job and tthat seems to occur randomly: running est2genome search. #--------- command -------------# Widget::exonerate::est2genome: exonerate -q /tmp/maker_JZ_DUt/12/MSTRG%2E13631%2E1.for.154952409-154955259.12.fasta -t /tmp/maker_JZ_DUt/12/Tps_LRv5b_scf2.154952409-154955259.12.fasta -Q dna -T dna --model est2genome --minintron 20 --maxintron 100000 --showcigar --percent 20 > /tmp/maker_JZ_DUt/12/Tps_LRv5b_scf2.154952409-154955259.MSTRG%2E13631%2E1.e.exonerate #-------------------------------# Fatal error in PMPI_Send: Invalid count, error stack: PMPI_Send(159): MPI_Send(buf=0x7f526282e010, count=-1326766804, MPI_CHAR, dest=22, tag=9999, MPI_COMM_WORLD) failed PMPI_Send(99).: Negative count, value is -1326766804 Do you know what could be the problem ? Best, Patrick Tran Van Bioinformatician: Lab Chapuisat & Schwander Department of Ecology and Evolution University of Lausanne Lausanne - Switzerland Office 3206 -------------- next part -------------- An HTML attachment was scrubbed... URL: From mjg4792 at utexas.edu Mon Aug 9 11:53:26 2021 From: mjg4792 at utexas.edu (=?UTF-8?Q?Mar=C3=ADa_Jose_Gomez?=) Date: Mon, 09 Aug 2021 17:53:26 -0000 Subject: [maker-devel] Thread server rejected connection error when using maker Message-ID: Hi, I am currently trying to use maker through a cluster, but have encountered some problems. Every time I try to run it (even if it's to show the help page), it says the following: Thread server rejected connection: 157.253.80.17:55106 does not match allowed IP mask This happens with all the versions installed in the cluster (MPI and not MPI). I tried creating my own conda environment and installing it there, but the same thing happened. Do you have any suggestions about what to do to fix this? Running it local is not really an option, but if I were to do that, how much time do you think it would take if I have a 1.2 Gb genome and my computer has 32 Gb of ram and 12 threads? Any help would be much appreciated, Maria -------------- next part -------------- An HTML attachment was scrubbed... URL: From Martinson.John at epa.gov Wed Aug 11 11:41:36 2021 From: Martinson.John at epa.gov (Martinson, John) Date: Wed, 11 Aug 2021 17:41:36 -0000 Subject: [maker-devel] Error Message using Maker3 with EvidenceModeler Message-ID: Hi. I am trying to update some gene models with new RNA data in maker3, using EvidenceModeler, and I am encountering the error below. I have tried various adjustments to my inputs, focusing on changes to the maker_evm.ctl file, the models-to-be-updated gff file, and the new RNA input (trying it as both sequence and genome-aligned gff files). None of the many changes I've tried, other than just "turning off" EVidenceModeler entirely, has made a difference, so I thought I'd ask for some help. Any idea on what might be happening here? Thanks, John Martinson USEPA Maker Google group email johnm50_01 at yahoo.com ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ERROR: No hit source {_HMM} in maker::auto_annotator at /data/progs/maker3/maker/bin/../lib/maker/auto_annotator.pm line 2873. maker::auto_annotator::group_transcripts('ARRAY(0xe7b1788)', 'ARRAY(0x70110a0)', 'FastaSeq=HASH(0x6304360)', 'scaf101', 0, 'evm_abinit', '/data/maker/fourScafsGffBasedEvm.maker.output/fourScafsGffBas...', 'HASH(0x44634a0)') called at /data/progs/maker3/maker/bin/../lib/maker/auto_annotator.pm line 1182 maker::auto_annotator::annotate_genes('HASH(0x20f88800)', 'ARRAY(0x70110a0)', 'FastaSeq=HASH(0x6304360)', 'scaf101', 0, '/data/maker/fourScafsGffBasedEvm.maker.output/fourScafsGffBas...', 'HASH(0x44634a0)') called at /data/progs/maker3/maker/bin/../lib/Process/MpiChunk.pm line 3894 Process::MpiChunk::__ANON__() called at /data/progs/maker3/maker/bin/../lib/Error.pm line 415 eval {...} called at /data/progs/maker3/maker/bin/../lib/Error.pm line 407 Error::subs::try('CODE(0x123909e0)', 'HASH(0x6185338)') called at /data/progs/maker3/maker/bin/../lib/Process/MpiChunk.pm line 4277 Process::MpiChunk::_go('Process::MpiChunk=HASH(0x7310030)', 'run', 'HASH(0x5193580)', 2, 4) called at /data/progs/maker3/maker/bin/../lib/Process/MpiChunk.pm line 340 Process::MpiChunk::run('Process::MpiChunk=HASH(0x7310030)', 0) called at /data/progs/maker3/maker/bin/../lib/Process/MpiChunk.pm line 356 Process::MpiChunk::run_all('Process::MpiChunk=HASH(0x7310030)', 0) called at /data/progs/maker3/maker/bin/../lib/Process/MpiTiers.pm line 287 Process::MpiTiers::run_all('Process::MpiTiers=HASH(0x11058b50)', 0) called at /data/progs/maker3/maker/bin/../lib/Process/MpiTiers.pm line 287 Process::MpiTiers::run_all('Process::MpiTiers=HASH(0x44a4dc0)', 0) called at /data/progs/maker3/maker/bin/maker line 680 --> rank=NA, hostname=d2626ujmartins4.aa.ad.epa.gov ERROR: Failed while clustering transcripts into genes for annotations ERROR: Chunk failed at level:2, tier_type:4 FAILED CONTIG:scaf101 ERROR: Chunk failed at level:6, tier_type:0 FAILED CONTIG:scaf101 -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Mon Aug 30 12:48:51 2021 From: carsonhh at gmail.com (Carson Holt) Date: Mon, 30 Aug 2021 12:48:51 -0600 Subject: [maker-devel] Thread server rejected connection error when using maker In-Reply-To: References: Message-ID: The error you get is not a MAKER error, but rather an error with the system or cluster you are running it on. To simplify running MAKER, I suggest not installing via Conda. Rather install your own standalone copy of MAKER ?> http://yandell-lab.org/software/maker.html Use with OpenMPI, MPICH, or Intel MPI when setting it up. Do not use MVAPICH2 (it won?t work with MAKER). ?Carson > On Aug 9, 2021, at 11:53 AM, Mar?a Jose Gomez wrote: > > Hi, > > I am currently trying to use maker through a cluster, but have encountered some problems. Every time I try to run it (even if it's to show the help page), it says the following: > > Thread server rejected connection: 157.253.80.17:55106 does not match allowed IP mask > > This happens with all the versions installed in the cluster (MPI and not MPI). I tried creating my own conda environment and installing it there, but the same thing happened. > > Do you have any suggestions about what to do to fix this? Running it local is not really an option, but if I were to do that, how much time do you think it would take if I have a 1.2 Gb genome and my computer has 32 Gb of ram and 12 threads? > > Any help would be much appreciated, > > Maria > _______________________________________________ > maker-devel mailing list > maker-devel at yandell-lab.org > http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: smime.p7s Type: application/pkcs7-signature Size: 1376 bytes Desc: not available URL: From patrick.tranvan at unil.ch Mon Aug 30 02:45:25 2021 From: patrick.tranvan at unil.ch (Patrick Tran Van) Date: Mon, 30 Aug 2021 08:45:25 +0000 Subject: [maker-devel] Fatal error in PMPI_Send Message-ID: <7bad655de17b4a1ab537e1b624c1da06@unil.ch> Hi, I have this strange error that kill my job and tthat seems to occur randomly: running est2genome search. #--------- command -------------# Widget::exonerate::est2genome: exonerate -q /tmp/maker_JZ_DUt/12/MSTRG%2E13631%2E1.for.154952409-154955259.12.fasta -t /tmp/maker_JZ_DUt/12/Tps_LRv5b_scf2.154952409-154955259.12.fasta -Q dna -T dna --model est2genome --minintron 20 --maxintron 100000 --showcigar --percent 20 > /tmp/maker_JZ_DUt/12/Tps_LRv5b_scf2.154952409-154955259.MSTRG%2E13631%2E1.e.exonerate #-------------------------------# Fatal error in PMPI_Send: Invalid count, error stack: PMPI_Send(159): MPI_Send(buf=0x7f526282e010, count=-1326766804, MPI_CHAR, dest=22, tag=9999, MPI_COMM_WORLD) failed PMPI_Send(99).: Negative count, value is -1326766804 Do you know what could be the problem ? Best, Patrick Tran Van Bioinformatician: Lab Chapuisat & Schwander Department of Ecology and Evolution University of Lausanne Lausanne - Switzerland Office 3206 -------------- next part -------------- An HTML attachment was scrubbed... URL: From mjg4792 at utexas.edu Mon Aug 9 11:53:26 2021 From: mjg4792 at utexas.edu (=?UTF-8?Q?Mar=C3=ADa_Jose_Gomez?=) Date: Mon, 09 Aug 2021 17:53:26 -0000 Subject: [maker-devel] Thread server rejected connection error when using maker Message-ID: Hi, I am currently trying to use maker through a cluster, but have encountered some problems. Every time I try to run it (even if it's to show the help page), it says the following: Thread server rejected connection: 157.253.80.17:55106 does not match allowed IP mask This happens with all the versions installed in the cluster (MPI and not MPI). I tried creating my own conda environment and installing it there, but the same thing happened. Do you have any suggestions about what to do to fix this? Running it local is not really an option, but if I were to do that, how much time do you think it would take if I have a 1.2 Gb genome and my computer has 32 Gb of ram and 12 threads? Any help would be much appreciated, Maria -------------- next part -------------- An HTML attachment was scrubbed... URL: From Martinson.John at epa.gov Wed Aug 11 11:41:36 2021 From: Martinson.John at epa.gov (Martinson, John) Date: Wed, 11 Aug 2021 17:41:36 -0000 Subject: [maker-devel] Error Message using Maker3 with EvidenceModeler Message-ID: Hi. I am trying to update some gene models with new RNA data in maker3, using EvidenceModeler, and I am encountering the error below. I have tried various adjustments to my inputs, focusing on changes to the maker_evm.ctl file, the models-to-be-updated gff file, and the new RNA input (trying it as both sequence and genome-aligned gff files). None of the many changes I've tried, other than just "turning off" EVidenceModeler entirely, has made a difference, so I thought I'd ask for some help. Any idea on what might be happening here? Thanks, John Martinson USEPA Maker Google group email johnm50_01 at yahoo.com ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ERROR: No hit source {_HMM} in maker::auto_annotator at /data/progs/maker3/maker/bin/../lib/maker/auto_annotator.pm line 2873. maker::auto_annotator::group_transcripts('ARRAY(0xe7b1788)', 'ARRAY(0x70110a0)', 'FastaSeq=HASH(0x6304360)', 'scaf101', 0, 'evm_abinit', '/data/maker/fourScafsGffBasedEvm.maker.output/fourScafsGffBas...', 'HASH(0x44634a0)') called at /data/progs/maker3/maker/bin/../lib/maker/auto_annotator.pm line 1182 maker::auto_annotator::annotate_genes('HASH(0x20f88800)', 'ARRAY(0x70110a0)', 'FastaSeq=HASH(0x6304360)', 'scaf101', 0, '/data/maker/fourScafsGffBasedEvm.maker.output/fourScafsGffBas...', 'HASH(0x44634a0)') called at /data/progs/maker3/maker/bin/../lib/Process/MpiChunk.pm line 3894 Process::MpiChunk::__ANON__() called at /data/progs/maker3/maker/bin/../lib/Error.pm line 415 eval {...} called at /data/progs/maker3/maker/bin/../lib/Error.pm line 407 Error::subs::try('CODE(0x123909e0)', 'HASH(0x6185338)') called at /data/progs/maker3/maker/bin/../lib/Process/MpiChunk.pm line 4277 Process::MpiChunk::_go('Process::MpiChunk=HASH(0x7310030)', 'run', 'HASH(0x5193580)', 2, 4) called at /data/progs/maker3/maker/bin/../lib/Process/MpiChunk.pm line 340 Process::MpiChunk::run('Process::MpiChunk=HASH(0x7310030)', 0) called at /data/progs/maker3/maker/bin/../lib/Process/MpiChunk.pm line 356 Process::MpiChunk::run_all('Process::MpiChunk=HASH(0x7310030)', 0) called at /data/progs/maker3/maker/bin/../lib/Process/MpiTiers.pm line 287 Process::MpiTiers::run_all('Process::MpiTiers=HASH(0x11058b50)', 0) called at /data/progs/maker3/maker/bin/../lib/Process/MpiTiers.pm line 287 Process::MpiTiers::run_all('Process::MpiTiers=HASH(0x44a4dc0)', 0) called at /data/progs/maker3/maker/bin/maker line 680 --> rank=NA, hostname=d2626ujmartins4.aa.ad.epa.gov ERROR: Failed while clustering transcripts into genes for annotations ERROR: Chunk failed at level:2, tier_type:4 FAILED CONTIG:scaf101 ERROR: Chunk failed at level:6, tier_type:0 FAILED CONTIG:scaf101 -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Mon Aug 30 12:48:51 2021 From: carsonhh at gmail.com (Carson Holt) Date: Mon, 30 Aug 2021 12:48:51 -0600 Subject: [maker-devel] Thread server rejected connection error when using maker In-Reply-To: References: Message-ID: The error you get is not a MAKER error, but rather an error with the system or cluster you are running it on. To simplify running MAKER, I suggest not installing via Conda. Rather install your own standalone copy of MAKER ?> http://yandell-lab.org/software/maker.html Use with OpenMPI, MPICH, or Intel MPI when setting it up. Do not use MVAPICH2 (it won?t work with MAKER). ?Carson > On Aug 9, 2021, at 11:53 AM, Mar?a Jose Gomez wrote: > > Hi, > > I am currently trying to use maker through a cluster, but have encountered some problems. Every time I try to run it (even if it's to show the help page), it says the following: > > Thread server rejected connection: 157.253.80.17:55106 does not match allowed IP mask > > This happens with all the versions installed in the cluster (MPI and not MPI). I tried creating my own conda environment and installing it there, but the same thing happened. > > Do you have any suggestions about what to do to fix this? Running it local is not really an option, but if I were to do that, how much time do you think it would take if I have a 1.2 Gb genome and my computer has 32 Gb of ram and 12 threads? > > Any help would be much appreciated, > > Maria > _______________________________________________ > maker-devel mailing list > maker-devel at yandell-lab.org > http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: smime.p7s Type: application/pkcs7-signature Size: 1376 bytes Desc: not available URL: From patrick.tranvan at unil.ch Mon Aug 30 02:45:25 2021 From: patrick.tranvan at unil.ch (Patrick Tran Van) Date: Mon, 30 Aug 2021 08:45:25 +0000 Subject: [maker-devel] Fatal error in PMPI_Send Message-ID: <7bad655de17b4a1ab537e1b624c1da06@unil.ch> Hi, I have this strange error that kill my job and tthat seems to occur randomly: running est2genome search. #--------- command -------------# Widget::exonerate::est2genome: exonerate -q /tmp/maker_JZ_DUt/12/MSTRG%2E13631%2E1.for.154952409-154955259.12.fasta -t /tmp/maker_JZ_DUt/12/Tps_LRv5b_scf2.154952409-154955259.12.fasta -Q dna -T dna --model est2genome --minintron 20 --maxintron 100000 --showcigar --percent 20 > /tmp/maker_JZ_DUt/12/Tps_LRv5b_scf2.154952409-154955259.MSTRG%2E13631%2E1.e.exonerate #-------------------------------# Fatal error in PMPI_Send: Invalid count, error stack: PMPI_Send(159): MPI_Send(buf=0x7f526282e010, count=-1326766804, MPI_CHAR, dest=22, tag=9999, MPI_COMM_WORLD) failed PMPI_Send(99).: Negative count, value is -1326766804 Do you know what could be the problem ? Best, Patrick Tran Van Bioinformatician: Lab Chapuisat & Schwander Department of Ecology and Evolution University of Lausanne Lausanne - Switzerland Office 3206 -------------- next part -------------- An HTML attachment was scrubbed... URL: From mjg4792 at utexas.edu Mon Aug 9 11:53:26 2021 From: mjg4792 at utexas.edu (=?UTF-8?Q?Mar=C3=ADa_Jose_Gomez?=) Date: Mon, 09 Aug 2021 17:53:26 -0000 Subject: [maker-devel] Thread server rejected connection error when using maker Message-ID: Hi, I am currently trying to use maker through a cluster, but have encountered some problems. Every time I try to run it (even if it's to show the help page), it says the following: Thread server rejected connection: 157.253.80.17:55106 does not match allowed IP mask This happens with all the versions installed in the cluster (MPI and not MPI). I tried creating my own conda environment and installing it there, but the same thing happened. Do you have any suggestions about what to do to fix this? Running it local is not really an option, but if I were to do that, how much time do you think it would take if I have a 1.2 Gb genome and my computer has 32 Gb of ram and 12 threads? Any help would be much appreciated, Maria -------------- next part -------------- An HTML attachment was scrubbed... URL: From Martinson.John at epa.gov Wed Aug 11 11:41:36 2021 From: Martinson.John at epa.gov (Martinson, John) Date: Wed, 11 Aug 2021 17:41:36 -0000 Subject: [maker-devel] Error Message using Maker3 with EvidenceModeler Message-ID: Hi. I am trying to update some gene models with new RNA data in maker3, using EvidenceModeler, and I am encountering the error below. I have tried various adjustments to my inputs, focusing on changes to the maker_evm.ctl file, the models-to-be-updated gff file, and the new RNA input (trying it as both sequence and genome-aligned gff files). None of the many changes I've tried, other than just "turning off" EVidenceModeler entirely, has made a difference, so I thought I'd ask for some help. Any idea on what might be happening here? Thanks, John Martinson USEPA Maker Google group email johnm50_01 at yahoo.com ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ERROR: No hit source {_HMM} in maker::auto_annotator at /data/progs/maker3/maker/bin/../lib/maker/auto_annotator.pm line 2873. maker::auto_annotator::group_transcripts('ARRAY(0xe7b1788)', 'ARRAY(0x70110a0)', 'FastaSeq=HASH(0x6304360)', 'scaf101', 0, 'evm_abinit', '/data/maker/fourScafsGffBasedEvm.maker.output/fourScafsGffBas...', 'HASH(0x44634a0)') called at /data/progs/maker3/maker/bin/../lib/maker/auto_annotator.pm line 1182 maker::auto_annotator::annotate_genes('HASH(0x20f88800)', 'ARRAY(0x70110a0)', 'FastaSeq=HASH(0x6304360)', 'scaf101', 0, '/data/maker/fourScafsGffBasedEvm.maker.output/fourScafsGffBas...', 'HASH(0x44634a0)') called at /data/progs/maker3/maker/bin/../lib/Process/MpiChunk.pm line 3894 Process::MpiChunk::__ANON__() called at /data/progs/maker3/maker/bin/../lib/Error.pm line 415 eval {...} called at /data/progs/maker3/maker/bin/../lib/Error.pm line 407 Error::subs::try('CODE(0x123909e0)', 'HASH(0x6185338)') called at /data/progs/maker3/maker/bin/../lib/Process/MpiChunk.pm line 4277 Process::MpiChunk::_go('Process::MpiChunk=HASH(0x7310030)', 'run', 'HASH(0x5193580)', 2, 4) called at /data/progs/maker3/maker/bin/../lib/Process/MpiChunk.pm line 340 Process::MpiChunk::run('Process::MpiChunk=HASH(0x7310030)', 0) called at /data/progs/maker3/maker/bin/../lib/Process/MpiChunk.pm line 356 Process::MpiChunk::run_all('Process::MpiChunk=HASH(0x7310030)', 0) called at /data/progs/maker3/maker/bin/../lib/Process/MpiTiers.pm line 287 Process::MpiTiers::run_all('Process::MpiTiers=HASH(0x11058b50)', 0) called at /data/progs/maker3/maker/bin/../lib/Process/MpiTiers.pm line 287 Process::MpiTiers::run_all('Process::MpiTiers=HASH(0x44a4dc0)', 0) called at /data/progs/maker3/maker/bin/maker line 680 --> rank=NA, hostname=d2626ujmartins4.aa.ad.epa.gov ERROR: Failed while clustering transcripts into genes for annotations ERROR: Chunk failed at level:2, tier_type:4 FAILED CONTIG:scaf101 ERROR: Chunk failed at level:6, tier_type:0 FAILED CONTIG:scaf101 -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Mon Aug 30 12:48:51 2021 From: carsonhh at gmail.com (Carson Holt) Date: Mon, 30 Aug 2021 12:48:51 -0600 Subject: [maker-devel] Thread server rejected connection error when using maker In-Reply-To: References: Message-ID: The error you get is not a MAKER error, but rather an error with the system or cluster you are running it on. To simplify running MAKER, I suggest not installing via Conda. Rather install your own standalone copy of MAKER ?> http://yandell-lab.org/software/maker.html Use with OpenMPI, MPICH, or Intel MPI when setting it up. Do not use MVAPICH2 (it won?t work with MAKER). ?Carson > On Aug 9, 2021, at 11:53 AM, Mar?a Jose Gomez wrote: > > Hi, > > I am currently trying to use maker through a cluster, but have encountered some problems. Every time I try to run it (even if it's to show the help page), it says the following: > > Thread server rejected connection: 157.253.80.17:55106 does not match allowed IP mask > > This happens with all the versions installed in the cluster (MPI and not MPI). I tried creating my own conda environment and installing it there, but the same thing happened. > > Do you have any suggestions about what to do to fix this? Running it local is not really an option, but if I were to do that, how much time do you think it would take if I have a 1.2 Gb genome and my computer has 32 Gb of ram and 12 threads? > > Any help would be much appreciated, > > Maria > _______________________________________________ > maker-devel mailing list > maker-devel at yandell-lab.org > http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... 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