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 >> Mauve-users@lists.sourceforge.net >> <mailto:Mauve-users@lists.sourceforge.net> >> 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 > Mauve-users@lists.sourceforge.net > 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 Mauve-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/mauve-users
