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
> 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
