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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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metAMOS failed with return code -9 #239

Closed osnattirosh closed 8 years ago

osnattirosh commented 8 years ago

Hi, The error seem to occur in the annotation step. this is from the job log: Job = [[1085_notbac3.1.fastq, 1085_notbac3.2.fastq] -> preprocess.success] completed Completed Task = preprocess.Preprocess Job = [preprocess.success -> *.run] completed Completed Task = assemble.SplitAssemblers Job = [soapdenovo.55.run -> soapdenovo.55.asm.contig] completed Completed Task = assemble.Assemble Job = [[soapdenovo.55.asm.contig] -> [assemble.ok]] completed Completed Task = assemble.CheckAsmResults Uptodate Task = assemble.SplitMappers Job = [soapdenovo.55.asm.contig -> soapdenovo.55.contig.cvg] completed Completed Task = mapreads.MapReads Job = [[soapdenovo.55.contig.cvg] -> [mapreads.ok]] completed Completed Task = mapreads.CheckMapResults Uptodate Task = mapreads.SplitForORFs Job = [soapdenovo.55.contig.cvg -> soapdenovo.55.faa] completed Completed Task = findorfs.FindORFS Job = [[soapdenovo.55.faa] -> [validate.ok]] completed Completed Task = validate.Validate Job = [proba.fna -> proba.repeats] completed Completed Task = findreps.FindRepeats Starting Task = preprocess.PREPROCESS Starting Task = assemble.ASSEMBLE Starting Task = mapreads.MAPREADS Starting Task = findorfs.FINDORFS Starting Task = validate.VALIDATE Starting Task = findrepeats.FINDREPEATS Starting Task = annotate.ANNOTATE rm: cannot remove `/data/tirosho/metAMOS5/Logs/annotate.ok': No such file or directory Error: parallel annotation job 0 failed

Oops, MetAMOS finished with errors! see text in red above for details.

****ERROR****** During annotate, the following command failed with return code -9:

python /spin1/sys2/usrlocal/apps/metAMOS/metAMOS-1.5rc3/Utilities/python/NB-BL.py /data/tirosho/metAMOS5/Annotate/out/proba.ctg_1.nb_results.txt /data/tirosho/metAMOS5/Annotate/out/proba.ctg_1.bl_results.txt /data/tirosho/metAMOS5/Annotate/out/proba.ctg_1.intermediate.epsilon-nb_results.txt

****DETAILS****** Last 10 commands run before the error (/data/tirosho/metAMOS5/Logs/COMMANDS.log) |2016-02-23 21:05:56| unlink /data/tirosho/metAMOS5/Annotate/out/proba.hits |2016-02-23 21:05:57| rm -f /data/tirosho/metAMOS5/Annotate/out/.hits |2016-02-23 21:05:58| rm -f /data/tirosho/metAMOS5/Annotate/out/.epsilon-nb_results.txt |2016-02-23 21:05:58| rm -f /data/tirosho/metAMOS5/Annotate/out/*.phymm.out |2016-02-23 21:06:08| ln -s /spin1/sys2/usrlocal/apps/metAMOS/metAMOS-1.5rc3/Utilities/models |2016-02-23 21:06:08| ln -s /spin1/sys2/usrlocal/apps/metAMOS/metAMOS-1.5rc3/Utilities/models/taxonomy.txt |2016-02-23 21:21:00| /spin1/sys2/usrlocal/apps/metAMOS/metAMOS-1.5rc3/Utilities/cpp/Linux-x86_64/nb-classify -q /data/tirosho/metAMOS5/Annotate/in/proba.asm.contig_part1.fa -m /spin1/sys2/usrlocal/apps/metAMOS/metAMOS-1.5rc3/Utilities/models/models.txt -r /data/tirosho/metAMOS5/Annotate/out/proba.ctg_1.nb_results.txt -e proba.ctg_1 |2016-02-23 21:21:01| ln -s /spin1/sys2/usrlocal/apps/metAMOS/metAMOS-1.5rc3/Utilities/DB//blast_data blast_data |2016-02-24 03:49:11| /spin1/sys2/usrlocal/apps/metAMOS/metAMOS-1.5rc3/Utilities/cpp/Linux-x86_64/blastn -query /data/tirosho/metAMOS5/Annotate/in/proba.asm.contig_part1.fa -out /data/tirosho/metAMOS5/Annotate/out/proba.ctg_1.bl_results.txt -db /spin1/sys2/usrlocal/apps/metAMOS/metAMOS-1.5rc3/Utilities/DB//blast_data/BacteriaAndArchaeaGenomesDB -evalue 10 -outfmt 7 -task blastn -num_threads 16 |2016-02-24 03:51:20| python /spin1/sys2/usrlocal/apps/metAMOS/metAMOS-1.5rc3/Utilities/python/NB-BL.py /data/tirosho/metAMOS5/Annotate/out/proba.ctg_1.nb_results.txt /data/tirosho/metAMOS5/Annotate/out/proba.ctg_1.bl_results.txt /data/tirosho/metAMOS5/Annotate/out/proba.ctg_1.intermediate.epsilon-nb_results.txt

Last 10 lines of output (/data/tirosho/metAMOS5/Logs/ANNOTATE.log) Applying models to query sequences: 0 200 400 600 800 1000 1200 1400 1600 1800 2000 Writing out classification results.

Batch #7 Calculating n-mers in query fragment: .... Applying models to query sequences: 0 200 400 600 800 1000 1200 1400 1600 1800 2000 Writing out classification results.

Building results file: ....... Done.

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

Other error in thread 0, quitting

I get this with another set of data. is it a memory issue? thanks!

skoren commented 8 years ago

This looks like an FCP bug, have you tried using kraken instead as the classifier?

osnattirosh commented 8 years ago

not yet, I'll give it a try. thanks!

skoren commented 8 years ago

Closed, inactivity