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Pipeline test: findscaffoldorf error #179

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shaman-narayanasamy opened this Issue Feb 9, 2015 · 4 comments

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@shaman-narayanasamy

shaman-narayanasamy commented Feb 9, 2015

Dear authors,

I installed MetAmos on our cluster and tried to run the test to make sure everything is working. Unfortunately, I received the error below at the findscaffoldorfs step:

$ ./run_pipeline_test.sh

## ... All OK here ...

Starting Task = findscaffoldorfs.FINDSCAFFOLDORFS
�[*****************************************************************
*************************ERROR***********************************
During findscaffoldorfs, the following command failed with return code -11:
>> /mnt/src_nfs1/projects/ecosystem_biology/local_tools/metAMOS-1.5rc3/Utilities/cpp/Linux-x86_64/FragGeneScan -s /mnt/src_nfs1/projects/ecosystem_biology/local_tools/metAMOS-1.5rc3/Test/test1/Scaffold/out/proba.linearize.scaffolds.final -o /mnt/src_nfs1/projects/ecosystem_biology/local_tools/metAMOS-1.5rc3/Test/test1/FindScaffoldORFS/out/proba.orfs -w 0 -t complete

*************************DETAILS***********************************
Last 10 commands run before the error (/mnt/src_nfs1/projects/ecosystem_biology/local_tools/metAMOS-1.5rc3/Test/test1/Logs/COMMANDS.log)
|2015-02-09 16:16:59| /mnt/src_nfs1/projects/ecosystem_biology/local_tools/metAMOS-1.5rc3/AMOS/Linux-x86_64/bin/Bundler -b /mnt/src_nfs1/projects/ecosystem_biology/local_tools/metAMOS-1.5rc3/Test/test1/Scaffold/in/proba.bnk
|2015-02-09 16:16:59| /mnt/src_nfs1/projects/ecosystem_biology/local_tools/metAMOS-1.5rc3/AMOS/Linux-x86_64/bin/MarkRepeats -redundancy 50  -b /mnt/src_nfs1/projects/ecosystem_biology/local_tools/metAMOS-1.5rc3/Test/test1/Scaffold/in/proba.bnk > /mnt/src_nfs1/projects/ecosystem_biology/local_tools/metAMOS-1.5rc3/Test/test1/Scaffold/in/proba.reps
|2015-02-09 16:17:00| /mnt/src_nfs1/projects/ecosystem_biology/local_tools/metAMOS-1.5rc3/AMOS/Linux-x86_64/bin/OrientContigs -minRedundancy 5 -all  -redundancy 10  -b /mnt/src_nfs1/projects/ecosystem_biology/local_tools/metAMOS-1.5rc3/Test/test1/Scaffold/in/proba.bnk -repeats /mnt/src_nfs1/projects/ecosystem_biology/local_tools/metAMOS-1.5rc3/Test/test1/Scaffold/in/proba.reps 
|2015-02-09 16:17:00| /mnt/src_nfs1/projects/ecosystem_biology/local_tools/metAMOS-1.5rc3/AMOS/Linux-x86_64/bin/bank2fasta -eid  -b /mnt/src_nfs1/projects/ecosystem_biology/local_tools/metAMOS-1.5rc3/Test/test1/Scaffold/in/proba.bnk > /mnt/src_nfs1/projects/ecosystem_biology/local_tools/metAMOS-1.5rc3/Test/test1/Scaffold/out/proba.contigs
|2015-02-09 16:17:00| /mnt/src_nfs1/projects/ecosystem_biology/local_tools/metAMOS-1.5rc3/AMOS/Linux-x86_64/bin/OutputMotifs -b /mnt/src_nfs1/projects/ecosystem_biology/local_tools/metAMOS-1.5rc3/Test/test1/Scaffold/in/proba.bnk > /mnt/src_nfs1/projects/ecosystem_biology/local_tools/metAMOS-1.5rc3/Test/test1/Scaffold/out/proba.motifs
|2015-02-09 16:17:00| /mnt/src_nfs1/projects/ecosystem_biology/local_tools/metAMOS-1.5rc3/AMOS/Linux-x86_64/bin/OutputScaffolds -b /mnt/src_nfs1/projects/ecosystem_biology/local_tools/metAMOS-1.5rc3/Test/test1/Scaffold/in/proba.bnk > /mnt/src_nfs1/projects/ecosystem_biology/local_tools/metAMOS-1.5rc3/Test/test1/Scaffold/out/proba.scaffolds.final
|2015-02-09 16:17:01| /mnt/src_nfs1/projects/ecosystem_biology/local_tools/metAMOS-1.5rc3/AMOS/Linux-x86_64/bin/Linearize -b /mnt/src_nfs1/projects/ecosystem_biology/local_tools/metAMOS-1.5rc3/Test/test1/Scaffold/in/proba.bnk
|2015-02-09 16:17:01| /mnt/src_nfs1/projects/ecosystem_biology/local_tools/metAMOS-1.5rc3/AMOS/Linux-x86_64/bin/OutputScaffolds -b /mnt/src_nfs1/projects/ecosystem_biology/local_tools/metAMOS-1.5rc3/Test/test1/Scaffold/in/proba.bnk > /mnt/src_nfs1/projects/ecosystem_biology/local_tools/metAMOS-1.5rc3/Test/test1/Scaffold/out/proba.linearize.scaffolds.final
|2015-02-09 16:17:02|# [FINDSCAFFOLDORFS]
|2015-02-09 16:17:02| /mnt/src_nfs1/projects/ecosystem_biology/local_tools/metAMOS-1.5rc3/Utilities/cpp/Linux-x86_64/FragGeneScan -s /mnt/src_nfs1/projects/ecosystem_biology/local_tools/metAMOS-1.5rc3/Test/test1/Scaffold/out/proba.linearize.scaffolds.final -o /mnt/src_nfs1/projects/ecosystem_biology/local_tools/metAMOS-1.5rc3/Test/test1/FindScaffoldORFS/out/proba.orfs -w 0 -t complete

Last 10 lines of output (/mnt/src_nfs1/projects/ecosystem_biology/local_tools/metAMOS-1.5rc3/Test/test1/Logs/FINDSCAFFOLDORFS.log)

Please veryify input data and restart MetAMOS. If the problem persists please contact the MetAMOS development team.
*************************ERROR***********************************
*****************************************************************
rm: cannot remove `/mnt/src_nfs1/projects/ecosystem_biology/local_tools/metAMOS-1.5rc3/Test/test1/Logs/findscaffoldorfs.ok': No such file or directory
Oops, MetAMOS finished with errors! see text in red above for details.

I checked in the log file mentioned at the last line of the error but it was empty... I am unable to figure it out based on the information given from this error. Any idea how to fix this?

Best,
Shaman

@shaman-narayanasamy shaman-narayanasamy changed the title from Testing pipeline findscaffoldorf error to Pipeline test: findscaffoldorf error Feb 9, 2015

@glew8

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glew8 commented Mar 19, 2015

I'm having the same issue with paired-end 2x300 MiSeq data. Did you ever figure out how to resolve this issue?

Thanks!
Gina

@skoren

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skoren commented Mar 19, 2015

This looks like an issue with the FragGeneScan binary on your system. My suggestion would be to try installing MetaGeneMark and adding it to your path. You can then tell metAMOS to use it instead of FragGeneScan.

@glew8

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glew8 commented Mar 23, 2015

Thank you!! I think this helped fix the problem.

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skoren commented Apr 8, 2015

Closing, issue was FragGeneScan incompatibility

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