Thread: [Mauve-users] Fwd: Mauve Errors
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From: femi a. e. <phe...@gm...> - 2017-05-29 14:40:34
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Hi everyone,what must I do to solved this mauve error problem.
trying path /home/bioifworkstation1/Desktop/mauve_snapshot_2015-
02-13/linux-x64/progressiveMauve
Running alignment.
Executing
/home/bioifworkstation1/Desktop/mauve_snapshot_2015-02-13/linux-x64/
progressiveMauve
--output=/media/bioifworkstation1/Bioinf2drive/Mauve/NewMauve1/
Mauvetest1
--output-guide-tree=/media/bioifworkstation1/
Bioinf2drive/Mauve/NewMauve1/Mauvetest1.guide_tree
--backbone-output=/media/bioifworkstation1/Bioinf2drive/Mauve/NewMauve1/
Mauvetest1.backbone
/home/bioifworkstation1/Desktop/HR_fasta
/home/bioifworkstation1/Desktop/WR_fasta
/home/bioifworkstation1/Desktop/BR_fasta
Storing raw sequence at /tmp/rawseq10955.000
Sequence loaded successfully.
/home/bioifworkstation1/Desktop/HR_fasta 2366941834 <(236)%20694-1834> base
pairs.
Storing raw sequence at /tmp/rawseq10955.001
Sequence loaded successfully.
/home/bioifworkstation1/Desktop/WR_fasta 2464350348 <(246)%20435-0348> base
pairs.
Storing raw sequence at /tmp/rawseq10955.002
Sequence loaded successfully.
/home/bioifworkstation1/Desktop/BR_fasta 2331675994 base pairs.
Using weight 21 mers for initial seeds
Creating sorted mer list
Create time was: 4762 seconds.
Creating sorted mer list
Create time was: 5723 seconds.
Creating sorted mer list
Create time was: 4674 seconds.
0%..2%..3%..4%..5%..6%..7%..8%..9%..10%..
11%..12%..13%..14%..15%..16%..17%..18%..19%..20%..
21%..22%..23%..24%..25%..26%..27%..28%..29%..30%..
31%..32%..33%..34%..35%..36%..37%..38%..39%..40%..
41%..42%..43%..44%..45%..46%..47%..48%..49%..50%..
51%..52%..53%..54%..55%..56%..57%..58%..59%..60%..
61%..62%..63%..64%..65%..66%..67%..68%..69%..70%..
71%..72%..73%..74%..75%..76%..77%..78%..79%..80%..
81%..82%..83%..84%..85%..86%..87%..88%..89%..90%..
91%..92%..93%..94%..95%..96%..97%..98%..99%..100%..
done.
using default bp penalty: 218071
using default bp estimate min score: 654212
Starting with 92379629 multi-matches
Computing genome content distance matrix...
Genome conservation distance matrix:
0 0.677953 0.682706
0.677953 0 0.152984
0.682706 0.152984 0
Writing guide tree to /media/bioifworkstation1/Bioinf2drive/Mauve/NewMauve1/
Mauvetest1.guide_tree
reading tree...
initializing alignment tree...
Constructing seed occurrence lists for repeat detection
Calculating pairwise breakpoint distances
Pair 0, 1 has 23118547 initial LCBs
Using scaled bp penalty: 7037.1
terminate called after throwing an instance of 'std::bad_alloc'
what(): std::bad_alloc
Exited with error code: 134
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From: Aaron D. <aar...@ut...> - 2017-05-30 02:28:37
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Hi Femi, The error std::bad_alloc occurs in C++ programs when there is not enough RAM in the machine to satisfy a memory allocation request. I notice you are attempting an alignment of three genomes each around 2.3GB in size. It is likely that progressiveMauve will need a machine with several hundred GB of RAM in order to do that, possibly more. Best, -Aaron On Mon, 2017-05-29 at 16:40 +0200, femi abiodun elegbeleye wrote: > > Hi everyone,what must I do to solved this mauve error problem. > > > > trying path /home/bioifworkstation1/Desktop/mauve_snapshot_2015-02- > 13/linux-x64/progressiveMauve > Running alignment. > Executing > /home/bioifworkstation1/Desktop/mauve_snapshot_2015-02-13/linux- > x64/progressiveMauve > -- > output=/media/bioifworkstation1/Bioinf2drive/Mauve/NewMauve1/Mauvetes > t1 > --output-guide- > tree=/media/bioifworkstation1/Bioinf2drive/Mauve/NewMauve1/Mauvetest1 > .guide_tree > --backbone- > output=/media/bioifworkstation1/Bioinf2drive/Mauve/NewMauve1/Mauvetes > t1.backbone > /home/bioifworkstation1/Desktop/HR_fasta > /home/bioifworkstation1/Desktop/WR_fasta > /home/bioifworkstation1/Desktop/BR_fasta > Storing raw sequence at /tmp/rawseq10955.000 > Sequence loaded successfully. > /home/bioifworkstation1/Desktop/HR_fasta 2366941834 base pairs. > Storing raw sequence at /tmp/rawseq10955.001 > Sequence loaded successfully. > /home/bioifworkstation1/Desktop/WR_fasta 2464350348 base pairs. > Storing raw sequence at /tmp/rawseq10955.002 > Sequence loaded successfully. > /home/bioifworkstation1/Desktop/BR_fasta 2331675994 base pairs. > Using weight 21 mers for initial seeds > Creating sorted mer list > Create time was: 4762 seconds. > Creating sorted mer list > Create time was: 5723 seconds. > Creating sorted mer list > Create time was: 4674 seconds. > 0%..2%..3%..4%..5%..6%..7%..8%..9%..10%.. > 11%..12%..13%..14%..15%..16%..17%..18%..19%..20%.. > 21%..22%..23%..24%..25%..26%..27%..28%..29%..30%.. > 31%..32%..33%..34%..35%..36%..37%..38%..39%..40%.. > 41%..42%..43%..44%..45%..46%..47%..48%..49%..50%.. > 51%..52%..53%..54%..55%..56%..57%..58%..59%..60%.. > 61%..62%..63%..64%..65%..66%..67%..68%..69%..70%.. > 71%..72%..73%..74%..75%..76%..77%..78%..79%..80%.. > 81%..82%..83%..84%..85%..86%..87%..88%..89%..90%.. > 91%..92%..93%..94%..95%..96%..97%..98%..99%..100%.. > done. > using default bp penalty: 218071 > using default bp estimate min score: 654212 > Starting with 92379629 multi-matches > Computing genome content distance matrix... > > > Genome conservation distance matrix: > 0 0.677953 0.682706 > 0.677953 0 0.152984 > 0.682706 0.152984 0 > > Writing guide tree to > /media/bioifworkstation1/Bioinf2drive/Mauve/NewMauve1/Mauvetest1.guid > e_tree > reading tree... > initializing alignment tree... > Constructing seed occurrence lists for repeat detection > Calculating pairwise breakpoint distances > Pair 0, 1 has 23118547 initial LCBs > Using scaled bp penalty: 7037.1 > terminate called after throwing an instance of 'std::bad_alloc' > what(): std::bad_alloc > Exited with error code: 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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