Thread: [Mauve-users] 'genome::gnException' => "Error creating sorted mer list"
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From: sebastien l. <seb...@ir...> - 2017-02-09 13:07:21
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Hi everybody, First try with progressiveMauve, and I got this error. I'm trying to align two de novo assembly genome of Brassica napus on its reference (850 MB). It seems that something goes wrong on the first steps. ./progressiveMauve --seed-family --seed-weight 41 $REF_FASTA $ASS_PATH/aviso.fa $ASS_PATH/tower.fa > run.log 2> run.err This list makes reference to memory or version pb for this error. I launched the command on a cluster with a lot of memory. ./progressiveMauve --version progressiveMauve build date Feb 13 2015 at 05:57:13 I tried with default size for seed-weight, it didn't change the error. Any help ? Sébastien ------ run.log Storing raw sequence at /tmp/rawseq11609.000 Sequence loaded successfully. Brassica_napus_v4.1.chromosomes.fasta 850292103 base pairs. Storing raw sequence at /tmp/rawseq11609.001 Sequence loaded successfully. aviso.fa 699132284 base pairs. Storing raw sequence at /tmp/rawseq11609.002 Sequence loaded successfully. tower.fa 690335263 base pairs. Creating sorted mer list **** run.err Error creating sorted mer list terminate called after throwing an instance of 'genome::gnException' (code error 134) |
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From: Aaron D. <aar...@ut...> - 2017-02-10 01:31:53
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Hi Sébastien, It's certainly possible to align genomes of that size with progressiveMauve, but your computer will need enough RAM and disk space, and you will need some patience. I would suggest using entirely default parameters at first (--seed-family will use extra RAM & compute time), and it would be well worth ordering the contigs in your draft genomes against the reference before trying to compute a 3-way alignment. In terms of RAM you are likely to need 60-100GB available, with similar amounts of free disk space. The point at which your run failed is where it's trying to allocate a large block of RAM, so I suggest checking that first. Best, -Aaron On Thu, 2017-02-09 at 14:07 +0100, sebastien letort wrote: > Hi everybody, > > First try with progressiveMauve, and I got this error. > > I'm trying to align two de novo assembly genome of Brassica napus on > its > reference (850 MB). > It seems that something goes wrong on the first steps. > > ./progressiveMauve --seed-family --seed-weight 41 $REF_FASTA > $ASS_PATH/aviso.fa $ASS_PATH/tower.fa > run.log 2> run.err > > This list makes reference to memory or version pb for this error. > I launched the command on a cluster with a lot of memory. > > ./progressiveMauve --version > progressiveMauve build date Feb 13 2015 at 05:57:13 > > I tried with default size for seed-weight, it didn't change the > error. > > Any help ? > Sébastien > > ------ > run.log > Storing raw sequence at /tmp/rawseq11609.000 > Sequence loaded successfully. > Brassica_napus_v4.1.chromosomes.fasta 850292103 base pairs. > Storing raw sequence at /tmp/rawseq11609.001 > Sequence loaded successfully. > aviso.fa 699132284 base pairs. > Storing raw sequence at /tmp/rawseq11609.002 > Sequence loaded successfully. > tower.fa 690335263 base pairs. > Creating sorted mer list > **** > run.err > Error creating sorted mer list > terminate called after throwing an instance of 'genome::gnException' > > (code error 134) > > ------------------------------------------------------------------- > ----------- > Check out the vibrant tech community on one of the world's most > engaging tech sites, SlashDot.org! http://sdm.link/slashdot > _______________________________________________ > Mauve-users mailing list > Mau...@li... > https://lists.sourceforge.net/lists/listinfo/mauve-users > -- Aaron E. Darling, Ph.D. Associate Professor, ithree institute University of Technology Sydney Australia http://darlinglab.org twitter: @koadman UTS CRICOS Provider Code: 00099F DISCLAIMER: This email message and any accompanying attachments may contain confidential information. If you are not the intended recipient, do not read, use, disseminate, distribute or copy this message or attachments. If you have received this message in error, please notify the sender immediately and delete this message. Any views expressed in this message are those of the individual sender, except where the sender expressly, and with authority, states them to be the views of the University of Technology Sydney. Before opening any attachments, please check them for viruses and defects. Think. Green. Do. Please consider the environment before printing this email. |
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From: sebastien l. <seb...@ir...> - 2017-02-10 09:50:35
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Hi Aaron, I have 190 GB of ram and more than 1TB of disk space available. I redefined TMPDIR to have enough space here too. The program fail again, at the same stage. I only used one cultivar against its reference with default parameter. Here are the last output lines of vmstat -S M -tn 1 before the prog did end. procs -----------memory---------- ---swap-- -----io---- --system-- -----cpu------ ---timestamp--- 2 0 621 191889 33 60193 0 0 0 0 2618 198 5 0 95 0 0 2017-02-10 09:59:06 CET 2 0 621 191886 33 60196 0 0 0 0 2637 211 5 0 95 0 0 2017-02-10 09:59:07 CET 2 0 621 191882 33 60200 0 0 0 0 2595 151 5 0 95 0 0 2017-02-10 09:59:08 CET 2 0 621 191879 33 60203 0 0 0 0 2607 182 5 0 95 0 0 2017-02-10 09:59:09 CET 2 0 621 192553 33 59538 0 0 0 0 4518 1093 4 0 95 0 0 2017-02-10 09:59:10 CET besst, Sébastien Le 10/02/2017 à 02:31, Aaron Darling a écrit : > Hi Sébastien, > > It's certainly possible to align genomes of that size with > progressiveMauve, but your computer will need enough RAM and disk space, > and you will need some patience. I would suggest using entirely default > parameters at first (--seed-family will use extra RAM & compute time), > and it would be well worth ordering the contigs in your draft genomes > against the reference before trying to compute a 3-way alignment. In > terms of RAM you are likely to need 60-100GB available, with similar > amounts of free disk space. The point at which your run failed is where > it's trying to allocate a large block of RAM, so I suggest checking that > first. > > Best, > -Aaron > > > On Thu, 2017-02-09 at 14:07 +0100, sebastien letort wrote: >> Hi everybody, >> >> First try with progressiveMauve, and I got this error. >> >> I'm trying to align two de novo assembly genome of Brassica napus on its >> reference (850 MB). >> It seems that something goes wrong on the first steps. >> >> ./progressiveMauve --seed-family --seed-weight 41 $REF_FASTA >> $ASS_PATH/aviso.fa $ASS_PATH/tower.fa > run.log 2> run.err >> >> This list makes reference to memory or version pb for this error. >> I launched the command on a cluster with a lot of memory. >> >> ./progressiveMauve --version >> progressiveMauve build date Feb 13 2015 at 05:57:13 >> >> I tried with default size for seed-weight, it didn't change the error. >> >> Any help ? >> Sébastien >> >> ------ >> run.log >> Storing raw sequence at /tmp/rawseq11609.000 >> Sequence loaded successfully. >> Brassica_napus_v4.1.chromosomes.fasta 850292103 base pairs. >> Storing raw sequence at /tmp/rawseq11609.001 >> Sequence loaded successfully. >> aviso.fa 699132284 base pairs. >> Storing raw sequence at /tmp/rawseq11609.002 >> Sequence loaded successfully. >> tower.fa 690335263 base pairs. >> Creating sorted mer list >> **** >> run.err >> Error creating sorted mer list >> terminate called after throwing an instance of 'genome::gnException' >> >> (code error 134) >> >> ------------------------------------------------------------------------------ >> Check out the vibrant tech community on one of the world's most >> engaging tech sites, SlashDot.org! http://sdm.link/slashdot >> _______________________________________________ >> Mauve-users mailing list >> Mau...@li... >> <mailto:Mau...@li...> >> https://lists.sourceforge.net/lists/listinfo/mauve-users >> > -- > Aaron E. Darling, Ph.D. > Associate Professor, ithree institute > University of Technology Sydney > Australia > > http://darlinglab.org > twitter: @koadman > > > ------------------------------------------------------------------------ > UTS CRICOS Provider Code: 00099F DISCLAIMER: This email message and any > accompanying attachments may contain confidential information. If you > are not the intended recipient, do not read, use, disseminate, > distribute or copy this message or attachments. If you have received > this message in error, please notify the sender immediately and delete > this message. Any views expressed in this message are those of the > individual sender, except where the sender expressly, and with > authority, states them to be the views of the University of Technology > Sydney. Before opening any attachments, please check them for viruses > and defects. Think. Green. Do. Please consider the environment before > printing this email. > > > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, SlashDot.org! http://sdm.link/slashdot > > > > _______________________________________________ > Mauve-users mailing list > Mau...@li... > https://lists.sourceforge.net/lists/listinfo/mauve-users > |
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From: Aaron D. <aar...@ut...> - 2017-02-10 23:57:28
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Can you check whether the directory where the sequence files are located is writable by the compute node and has enough space to store the sorted seed (k-mer) list? progressiveMauve does not use TMPDIR to store those, they go in a file with the same name as the sequence file, with a .sslist extension added. They require approximately 4.25 bytes/base, so in your case around 6GB for both sequences. That seems like the most likely problem, but if that's not it then it would be helpful if you could send me the sequence files somehow (google drive? dropbox?) so I can check whether there's some kind of unexpected file format parsing problem. -Aaron On Fri, 2017-02-10 at 10:50 +0100, sebastien letort wrote: > Hi Aaron, > > I have 190 GB of ram and more than 1TB of disk space available. > I redefined TMPDIR to have enough space here too. > The program fail again, at the same stage. > > I only used one cultivar against its reference with default > parameter. > > Here are the last output lines of vmstat -S M -tn 1 before the prog > did end. > procs -----------memory---------- ---swap-- -----io---- --system-- > -----cpu------ ---timestamp--- > 2 0 621 191889 33 60193 0 0 0 0 > 2618 198 5 0 > 95 0 0 2017-02-10 09:59:06 CET > 2 0 621 191886 33 60196 0 0 0 0 > 2637 211 5 0 > 95 0 0 2017-02-10 09:59:07 CET > 2 0 621 191882 33 60200 0 0 0 0 > 2595 151 5 0 > 95 0 0 2017-02-10 09:59:08 CET > 2 0 621 191879 33 60203 0 0 0 0 > 2607 182 5 0 > 95 0 0 2017-02-10 09:59:09 CET > 2 0 621 192553 33 59538 0 0 0 0 4518 > 1093 4 0 > 95 0 0 2017-02-10 09:59:10 CET > > besst, > Sébastien > > Le 10/02/2017 à 02:31, Aaron Darling a écrit : > > > > Hi Sébastien, > > > > It's certainly possible to align genomes of that size with > > progressiveMauve, but your computer will need enough RAM and disk > > space, > > and you will need some patience. I would suggest using entirely > > default > > parameters at first (--seed-family will use extra RAM & compute > > time), > > and it would be well worth ordering the contigs in your draft > > genomes > > against the reference before trying to compute a 3-way alignment. > > In > > terms of RAM you are likely to need 60-100GB available, with > > similar > > amounts of free disk space. The point at which your run failed is > > where > > it's trying to allocate a large block of RAM, so I suggest checking > > that > > first. > > > > Best, > > -Aaron > > > > > > On Thu, 2017-02-09 at 14:07 +0100, sebastien letort wrote: > > > > > > Hi everybody, > > > > > > First try with progressiveMauve, and I got this error. > > > > > > I'm trying to align two de novo assembly genome of Brassica napus > > > on its > > > reference (850 MB). > > > It seems that something goes wrong on the first steps. > > > > > > ./progressiveMauve --seed-family --seed-weight 41 $REF_FASTA > > > $ASS_PATH/aviso.fa $ASS_PATH/tower.fa > run.log 2> run.err > > > > > > This list makes reference to memory or version pb for this error. > > > I launched the command on a cluster with a lot of memory. > > > > > > ./progressiveMauve --version > > > progressiveMauve build date Feb 13 2015 at 05:57:13 > > > > > > I tried with default size for seed-weight, it didn't change the > > > error. > > > > > > Any help ? > > > Sébastien > > > > > > ------ > > > run.log > > > Storing raw sequence at /tmp/rawseq11609.000 > > > Sequence loaded successfully. > > > Brassica_napus_v4.1.chromosomes.fasta 850292103 base pairs. > > > Storing raw sequence at /tmp/rawseq11609.001 > > > Sequence loaded successfully. > > > aviso.fa 699132284 base pairs. > > > Storing raw sequence at /tmp/rawseq11609.002 > > > Sequence loaded successfully. > > > tower.fa 690335263 base pairs. > > > Creating sorted mer list > > > **** > > > run.err > > > Error creating sorted mer list > > > terminate called after throwing an instance of > > > 'genome::gnException' > > > > > > (code error 134) > > > > > > --------------------------------------------------------------- > > > --------------- > > > Check out the vibrant tech community on one of the world's most > > > engaging tech sites, SlashDot.org! http://sdm.link/slashdot > > > _______________________________________________ > > > Mauve-users mailing list > > > Mau...@li... > > > Mau...@li...> > > > https://lists.sourceforge.net/lists/listinfo/mauve-users > > > > > -- > > Aaron E. Darling, Ph.D. > > Associate Professor, ithree institute > > University of Technology Sydney > > Australia > > > > http://darlinglab.org > > twitter: @koadman > > > > > > ----------------------------------------------------------------- > > ------- > > UTS CRICOS Provider Code: 00099F DISCLAIMER: This email message and > > any > > accompanying attachments may contain confidential information. If > > you > > are not the intended recipient, do not read, use, disseminate, > > distribute or copy this message or attachments. If you have > > received > > this message in error, please notify the sender immediately and > > delete > > this message. Any views expressed in this message are those of the > > individual sender, except where the sender expressly, and with > > authority, states them to be the views of the University of > > Technology > > Sydney. Before opening any attachments, please check them for > > viruses > > and defects. Think. Green. Do. Please consider the environment > > before > > printing this email. > > > > > > > > ----------------------------------------------------------------- > > ------------- > > Check out the vibrant tech community on one of the world's most > > engaging tech sites, SlashDot.org! http://sdm.link/slashdot > > > > > > > > _______________________________________________ > > Mauve-users mailing list > > Mau...@li... > > https://lists.sourceforge.net/lists/listinfo/mauve-users > > > ------------------------------------------------------------------- > ----------- > Check out the vibrant tech community on one of the world's most > engaging tech sites, SlashDot.org! http://sdm.link/slashdot > _______________________________________________ > Mauve-users mailing list > Mau...@li... > https://lists.sourceforge.net/lists/listinfo/mauve-users -- Aaron E. Darling, Ph.D. Associate Professor, ithree institute University of Technology Sydney Australia http://darlinglab.org twitter: @koadman UTS CRICOS Provider Code: 00099F DISCLAIMER: This email message and any accompanying attachments may contain confidential information. If you are not the intended recipient, do not read, use, disseminate, distribute or copy this message or attachments. If you have received this message in error, please notify the sender immediately and delete this message. Any views expressed in this message are those of the individual sender, except where the sender expressly, and with authority, states them to be the views of the University of Technology Sydney. Before opening any attachments, please check them for viruses and defects. Think. Green. Do. Please consider the environment before printing this email. |
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