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marbl / metAMOS

A metagenomic and isolate assembly and analysis pipeline built with AMOS
http://marbl.github.io/metAMOS
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SCAFFOLD segfaults with code 139 in v1.5 fb #115

Closed chevrm closed 10 years ago

chevrm commented 10 years ago

With runPipeline command: ./runPipeline -a soap,metaidba,metavelvet -b -t -q -u -d dir

scaffold segfaults with 139 error below:

****ERROR****** During scaffold, the following command failed with return code 139:

/tmp/_MEIPgFGGi/AMOS/Linux-x86_64/bin/OutputScaffolds -b /media/user/data/workspace/metAMOS_v1.5rc1_binary/dir/Scaffold/in/proba.bnk > /media/user/data/workspace/metAMOS_v1.5rc1_binary/dir/Scaffold/out/proba.scaffolds.final ****DETAILS****** Last 10 commands run before the error (/media/user/data/workspace/metAMOS_v1.5rc1_binary/dir/Logs/COMMANDS.log) |2014-02-23 14:37:57| /tmp/_MEIPgFGGi/AMOS/Linux-x86_64/bin/toAmos_new -c /media/user/data/workspace/metAMOS_v1.5rc1_binary/dir/Assemble/out/proba.asm.tigr -b /media/user/data/workspace/metAMOS_v1.5rc1_binary/dir/Scaffold/in/proba.bnk |2014-02-23 14:38:06| /tmp/_MEIPgFGGi/AMOS/Linux-x86_64/bin/asmQC -b /media/user/data/workspace/metAMOS_v1.5rc1_binary/dir/Scaffold/in/proba.bnk -scaff -recompute -update -numsd 2 |2014-02-23 14:38:06| perl /tmp/_MEIPgFGGi/AMOS/Linux-x86_64/bin/bank-unlock /media/user/data/workspace/metAMOS_v1.5rc1_binary/dir/Scaffold/in/proba.bnk |2014-02-23 14:38:12| /tmp/_MEIPgFGGi/AMOS/Linux-x86_64/bin/clk -b /media/user/data/workspace/metAMOS_v1.5rc1_binary/dir/Scaffold/in/proba.bnk |2014-02-23 14:38:13| /tmp/_MEIPgFGGi/AMOS/Linux-x86_64/bin/Bundler -b /media/user/data/workspace/metAMOS_v1.5rc1_binary/dir/Scaffold/in/proba.bnk |2014-02-23 14:38:13| /tmp/_MEIPgFGGi/AMOS/Linux-x86_64/bin/MarkRepeats -redundancy 50 -b /media/user/data/workspace/metAMOS_v1.5rc1_binary/dir/Scaffold/in/proba.bnk > /media/user/data/workspace/metAMOS_v1.5rc1_binary/dir/Scaffold/in/proba.reps |2014-02-23 14:38:17| /tmp/_MEIPgFGGi/AMOS/Linux-x86_64/bin/OrientContigs -minRedundancy 5 -all -redundancy 10 -b /media/user/data/workspace/metAMOS_v1.5rc1_binary/dir/Scaffold/in/proba.bnk -repeats /media/user/data/workspace/metAMOS_v1.5rc1_binary/dir/Scaffold/in/proba.reps |2014-02-23 14:38:17| /tmp/_MEIPgFGGi/AMOS/Linux-x86_64/bin/bank2fasta -eid -b /media/user/data/workspace/metAMOS_v1.5rc1_binary/dir/Scaffold/in/proba.bnk > /media/user/data/workspace/metAMOS_v1.5rc1_binary/dir/Scaffold/out/proba.contigs |2014-02-23 14:38:18| /tmp/_MEIPgFGGi/AMOS/Linux-x86_64/bin/OutputMotifs -b /media/user/data/workspace/metAMOS_v1.5rc1_binary/dir/Scaffold/in/proba.bnk > /media/user/data/workspace/metAMOS_v1.5rc1_binary/dir/Scaffold/out/proba.motifs |2014-02-23 14:54:13| /tmp/_MEIPgFGGi/AMOS/Linux-x86_64/bin/OutputScaffolds -b /media/user/data/workspace/metAMOS_v1.5rc1_binary/dir/Scaffold/in/proba.bnk > /media/user/data/workspace/metAMOS_v1.5rc1_binary/dir/Scaffold/out/proba.scaffolds.final

Last 10 lines of output (/media/user/data/workspace/metAMOS_v1.5rc1_binary/dir/Logs/SCAFFOLD.log) PROCESSING SCAFFOLD 514 PROCESSING CONTIG 954 PROCESSING SCAFFOLD 515 PROCESSING CONTIG 955 PROCESSING SCAFFOLD 516 PROCESSING CONTIG 956 END COMPRESSION ITERATION #4 UPDATED: 0 DONE COMPRESSION Finished! Had 466 Good links and 98 bad ones. /bin/bash: line 1: 3180 Segmentation fault /tmp/_MEIPgFGGi/AMOS/Linux-x86_64/bin/OutputScaffolds -b /media/user/data/workspace/metAMOS_v1.5rc1_binary/dir/Scaffold/in/proba.bnk > /media/user/data/workspace/metAMOS_v1.5rc1_binary/dir/Scaffold/out/proba.scaffolds.final

Please veryify input data and restart MetAMOS. If the problem persists please contact the MetAMOS development team. ****ERROR******

rm: cannot remove ‘/media/user/data/workspace/metAMOS_v1.5rc1_binary/dir/Logs/scaffold.ok’: No such file or directory

This is with the miniDB, if that is relevant. Let me know if I should upload other logs to be more helpful.

skoren commented 10 years ago

Hi,

This looks like a bug in Bambus 2. Are you able to share the data (or a subset) so we can reproduce the error here? In the meantime, if you enable isolate mode (initPipeline -W iMetAMOS or -I parameter to runPipeline), metAMOS will skip Bambus 2 and rely on the scaffolds from your selected assemblers.

skoren commented 10 years ago

Should be fixed in RC2, reopen if not.