Re: [Mauve-users] 'genome::gnException' => "Error creating sorted mer list"
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koadman
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. |