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cancerit / BRASS

Breakpoints via assembly - Identifies breaks and attempts to assemble rearrangements in whole genome sequencing data.
GNU Affero General Public License v3.0
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Help needed, velvet jobs being killed due to exonerate error #53

Closed Hbm3085 closed 4 years ago

Hbm3085 commented 7 years ago

Hi,

I am stuck at assembly step where exonerate is being invoked and iterations are terminating with the error shown below:

Aligning with --model affine:local for vertices: 3 at /opt/apps/bioinformatics/brass/5.3.3_threaded/lib/perl5/Bio/Brass/VelvetGraph.pm line 189. exonerate --verbose 0 --showalignment no --showvulgar no --showcigar no --querytype dna --targettype dna --ryo %qas*Q %qab %qae %qS\n%tas*T %tab %tae %tS %ti\n** %qi %s\n --query /tmp/brassAssembly_IoE7e1/tmpHFkCrf/247-6cjOsk/65/brassAssExonerateHPtSjls.fa --target /tmp/brassAssembly_IoE7e1/tmpHFkCrf/247-6cjOsk/65/brassAssExonerateRef8lFNBiA.fa --percent 80 --model affine:local Bio::Brass::Alignment::_run_exonerate(): Exonerate error: itteration: 1 (of 5), error code: 139, msg: at /opt/apps/bioinformatics/brass/5.3.3_threaded/lib/perl5/Bio/Brass/Alignment.pm line 384. Bio::Brass::Alignment::_run_exonerate(): Exonerate error: itteration: 2 (of 5), error code: 139, msg: at /opt/apps/bioinformatics/brass/5.3.3_threaded/lib/perl5/Bio/Brass/Alignment.pm line 384. Bio::Brass::Alignment::_run_exonerate(): Exonerate error: itteration: 3 (of 5), error code: 139, msg: at /opt/apps/bioinformatics/brass/5.3.3_threaded/lib/perl5/Bio/Brass/Alignment.pm line 384. Bio::Brass::Alignment::_run_exonerate(): Exonerate error: itteration: 4 (of 5), error code: 139, msg: at /opt/apps/bioinformatics/brass/5.3.3_threaded/lib/perl5/Bio/Brass/Alignment.pm line 384. Bio::Brass::Alignment::_run_exonerate(): Exonerate error: killed at itteration: 5 (of 5), error code: 139, msg: at /opt/apps/bioinformatics/brass/5.3.3_threaded/lib/perl5/Bio/Brass/Alignment.pm line 384. 2.52user 1.52system 0:24.18elapsed 16%CPU (0avgtext+0avgdata 132268maxresident)k 0inputs+31032outputs (0major+116882minor)pagefaults 0swaps

Complete error file attached. Sanger_CGP_Brass_Implement_assemble.3.err.txt

Any ideas/suggestions as to what is happening would be greatly appreciated! Thanks!

keiranmraine commented 7 years ago

Can you confirm that the version of exonerate installed by setup.sh is the one in use and no other modifications were made?

For example the following two command should point to the same 'bin' location, based on your command I'd expect /opt/apps/bioinformatics/brass/5.3.3_threaded/bin

which brass.pl
which exonerate
Hbm3085 commented 7 years ago

Thanks for your reply. Please see the output of the two commands below which both point to the same bin location /opt/apps/bioinformatics/brass/5.3.3_threaded/bin/brass.pl /opt/apps/bioinformatics/brass/5.3.3_threaded/bin/exonerate

Should I check anything else? Thanks!

keiranmraine commented 4 years ago

We recommend using the docker image either directly of via singularity. Should you be able to reproduce this we can investigate further.

Sorry it's been so long, this has been a low priority as we have not had any other reports of this problem.