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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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Error when running run_pipeline_test.sh (FragGeneScan, exit code -11) #270

Open jwestrob opened 7 years ago

jwestrob commented 7 years ago

Hello! I'm trying to install MetAMOS on my system, but having a bit of trouble. I've run the following commands, which completed without incident:

python INSTALL.py core python INSTALL.py optional

However, when I execute run_pipeline_test.sh, I get the following error:

*****************************************************************
*************************ERROR***********************************
During findscaffoldorfs, the following command failed with return code -11:
>> /pylon2/mc562pp/jwestrob/metAMOS-1.5rc3/Utilities/cpp/Linux-x86_64/FragGeneScan -s /pylon2/mc562pp/jwestrob/metAMOS-1.5rc3/Test/test1/Scaffold/out/proba.linearize.scaffolds.final -o /pylon2/mc562pp/jwestrob/metAMOS-1.5rc3/Test/test1/FindScaffoldORFS/out/proba.orfs -w 0 -t complete

Is there something I'm doing incorrectly? I've checked that all dependencies for MetAMOS are met and I've tried multiple times to do a clean install.

I attach my full output of run_pipeline_test.sh for inspection should you need it. I sincerely apologize if there's something that I've overlooked- I don't mean to waste your time. Thank you very much for your time and for putting together this software- I believe it will be very useful for me! I look forward to using it.

Warning: Celera Assembler is not found, some functionality will not be available
Warning: BLASR is not found, some functionality will not be available
Warning: Newbler is not found, some functionality will not be available
Warning: MetaGeneMark is not found, some functionality will not be available
Warning: Prokka is not found, some functionality will not be available
Warning: SignalP+ is not found, some functionality will not be available
Warning: PHmmer is not found, some functionality will not be available
Warning: EA-UTILS is not found, some functionality will not be available
Warning: KmerGenie is not found, some functionality will not be available
Warning: ALE is not found, some functionality will not be available
Warning: CGAL is not found, some functionality will not be available
Warning: REAPR is not found, some functionality will not be available
Warning: FRCbam is not found, some functionality will not be available
Warning: FreeBayes is not found, some functionality will not be available
Warning: QUAST is not found, some functionality will not be available
Project dir /pylon2/mc562pp/jwestrob/metAMOS-1.5rc3/Test/test1 successfully created!
Use runPipeline.py to start Pipeline
[Steps to be skipped]:  set(['FunctionalAnnotation', 'FindRepeats'])
Starting Task = runpipeline.RUNPIPELINE
Starting metAMOS pipeline
Warning: Celera Assembler is not found, some functionality will not be available
Warning: BLASR is not found, some functionality will not be available
Warning: Newbler is not found, some functionality will not be available
Warning: MetaGeneMark is not found, some functionality will not be available
Warning: Prokka is not found, some functionality will not be available
Warning: SignalP+ is not found, some functionality will not be available
Warning: PHmmer is not found, some functionality will not be available
Warning: EA-UTILS is not found, some functionality will not be available
Warning: KmerGenie is not found, some functionality will not be available
Warning: ALE is not found, some functionality will not be available
Warning: CGAL is not found, some functionality will not be available
Warning: REAPR is not found, some functionality will not be available
Warning: FRCbam is not found, some functionality will not be available
Warning: FreeBayes is not found, some functionality will not be available
Warning: QUAST is not found, some functionality will not be available
[Available RAM: 110 GB]
    *ok
[Available CPUs: 28]
    *ok

________________________________________
Tasks which will be run:

Task = preprocess.Preprocess
Task = assemble.SplitAssemblers
Task = assemble.Assemble
Task = assemble.CheckAsmResults
Task = assemble.SplitMappers
Task = mapreads.MapReads
Task = mapreads.CheckMapResults
Task = mapreads.SplitForORFs
Task = findorfs.FindORFS
Task = validate.Validate
Task = findreps.FindRepeats
Task = annotate.Annotate
Task = fannotate.FunctionalAnnotation
Task = scaffold.Scaffold
Task = findscforfs.FindScaffoldORFS
Task = abundance.Abundance
Task = propagate.Propagate
Task = classify.Classify
Task = postprocess.Postprocess
________________________________________
metAMOS configuration summary:
metAMOS Version:    v1.5rc3 "Praline Brownie"  workflows: core,optional
Time and Date:      2017-10-25
Working directory:  /pylon2/mc562pp/jwestrob/metAMOS-1.5rc3/Test/test1
Prefix:         proba
K-Mer:          55
Threads:        15
Taxonomic level:    class
Verbose:        False
Steps to skip:      MultiAlign, FunctionalAnnotation, FindRepeats
Steps to force:     Abundance, FindORFS, Annotate, Propagate, MapReads, Assemble, FindScaffoldORFS, Classify

[citation]
MetAMOS
    Treangen, TJ ⇔  Koren, S, Sommer, DD, Liu, B, Astrovskaya, I, Ondov, B, Darling AE, Phillippy AM, Pop, M. MetAMOS: a modular and open source metagenomic assembly and analysis pipeline. Genome biology, 14(1), R2, 2013.

Step-specific configuration:
[abundance]
MetaPhyler
    /pylon2/mc562pp/jwestrob/metAMOS-1.5rc3/Utilities/cpp/Linux-x86_64
    Liu B, Gibbons T, Ghodsi M, Treangen T, Pop M. Accurate and fast estimation of taxonomic profiles from metagenomic shotgun sequences. BMC Genomics. 2011;12 Suppl 2:S4. Epub 2011 Jul 27.

[multialign]
M-GCAT
    /pylon2/mc562pp/jwestrob/metAMOS-1.5rc3/Utilities/cpp/Linux-x86_64
    Treangen TJ, Messeguer X. M-GCAT: interactively and efficiently constructing large-scale multiple genome comparison frameworks in closely related species. BMC Bioinformatics, 2006.

[fannotate]
BLAST
    /pylon2/mc562pp/jwestrob/metAMOS-1.5rc3/Utilities/cpp/Linux-x86_64
    Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990 Oct 5;215(3):403-10.

[scaffold]
Bambus 2
    /pylon2/mc562pp/jwestrob/metAMOS-1.5rc3/AMOS/Linux-x86_64/bin
    Koren S, Treangen TJ, Pop M. Bambus 2: scaffolding metagenomes. Bioinformatics 27(21): 2964-2971 2011.

[findorfs]
FragGeneScan
    /pylon2/mc562pp/jwestrob/metAMOS-1.5rc3/Utilities/cpp/Linux-x86_64
    Rho M, Tang H, Ye Y: FragGeneScan: predicting genes in short and error-prone reads. Nucleic Acids Research 2010, 38:e191-e191.

[annotate]
Kraken
    /pylon2/mc562pp/jwestrob/metAMOS-1.5rc3/Utilities/cpp/Linux-x86_64/kraken/bin
    Wood DE, Salzberg SL: Kraken: ultrafast metagenomic sequence classification using exact alignments. Genome Biology 2014, 15:R46.

[assemble]
SOAPdenovo
    /pylon2/mc562pp/jwestrob/metAMOS-1.5rc3/Utilities/cpp/Linux-x86_64
    Li Y, Hu Y, Bolund L, Wang J: State of the art de novo assembly of human genomes from massively parallel sequencing data.Human genomics 2010, 4:271-277.

[mapreads]
Bowtie
    /pylon2/mc562pp/jwestrob/metAMOS-1.5rc3/Utilities/cpp/Linux-x86_64
    Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 2009;10(3):R25. Epub 2009 Mar 4.

[preprocess]
metAMOS built-in filtering
    N/A

[validate]
LAP
    /pylon2/mc562pp/jwestrob/metAMOS-1.5rc3/LAP
    Ghodsi M, Hill CM, Astrovskaya I, Lin H, Sommer DD, Koren S, Pop M. De novo likelihood-based measures for comparing genome assemblies. BMC research notes 6:334, 2013.

[other]
Krona
    /pylon2/mc562pp/jwestrob/metAMOS-1.5rc3/KronaTools/bin
    Ondov BD, Bergman NH, Phillippy AM. Interactive metagenomic visualization in a Web browser. BMC Bioinformatics. 2011 Sep 30;12:385.

    Job  = [[carsonella_pe_filt.fna] -> 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
    Job  = [proba.faa -> proba.hits] completed
Completed Task = annotate.Annotate
    Job  = [proba.faa -> [blast.out, krona.ec.input]] completed
Completed Task = fannotate.FunctionalAnnotation
    Job  = [[proba.asm.contig] -> scaffold.ok] completed
Completed Task = scaffold.Scaffold
rm: cannot remove ‘/pylon2/mc562pp/jwestrob/metAMOS-1.5rc3/Test/test1/Logs/findscaffoldorfs.ok’: No such file or directory
Starting Task = functionalannotation.FUNCTIONALANNOTATION
Starting Task = scaffold.SCAFFOLD
Starting Task = findscaffoldorfs.FINDSCAFFOLDORFS
[*****************************************************************
*************************ERROR***********************************
During findscaffoldorfs, the following command failed with return code -11:
>> /pylon2/mc562pp/jwestrob/metAMOS-1.5rc3/Utilities/cpp/Linux-x86_64/FragGeneScan -s /pylon2/mc562pp/jwestrob/metAMOS-1.5rc3/Test/test1/Scaffold/out/proba.linearize.scaffolds.final -o /pylon2/mc562pp/jwestrob/metAMOS-1.5rc3/Test/test1/FindScaffoldORFS/out/proba.orfs -w 0 -t complete

*************************DETAILS***********************************
Last 10 commands run before the error (/pylon2/mc562pp/jwestrob/metAMOS-1.5rc3/Test/test1/Logs/COMMANDS.log)
|2017-10-25 20:13:23| /pylon2/mc562pp/jwestrob/metAMOS-1.5rc3/AMOS/Linux-x86_64/bin/Bundler -b /pylon2/mc562pp/jwestrob/metAMOS-1.5rc3/Test/test1/Scaffold/in/proba.bnk
|2017-10-25 20:13:23| /pylon2/mc562pp/jwestrob/metAMOS-1.5rc3/AMOS/Linux-x86_64/bin/MarkRepeats -redundancy 50  -b /pylon2/mc562pp/jwestrob/metAMOS-1.5rc3/Test/test1/Scaffold/in/proba.bnk > /pylon2/mc562pp/jwestrob/metAMOS-1.5rc3/Test/test1/Scaffold/in/proba.reps
|2017-10-25 20:13:27| /pylon2/mc562pp/jwestrob/metAMOS-1.5rc3/AMOS/Linux-x86_64/bin/OrientContigs -minRedundancy 5 -all  -redundancy 10  -b /pylon2/mc562pp/jwestrob/metAMOS-1.5rc3/Test/test1/Scaffold/in/proba.bnk -repeats /pylon2/mc562pp/jwestrob/metAMOS-1.5rc3/Test/test1/Scaffold/in/proba.reps 
|2017-10-25 20:13:27| /pylon2/mc562pp/jwestrob/metAMOS-1.5rc3/AMOS/Linux-x86_64/bin/bank2fasta -eid  -b /pylon2/mc562pp/jwestrob/metAMOS-1.5rc3/Test/test1/Scaffold/in/proba.bnk > /pylon2/mc562pp/jwestrob/metAMOS-1.5rc3/Test/test1/Scaffold/out/proba.contigs
|2017-10-25 20:13:28| /pylon2/mc562pp/jwestrob/metAMOS-1.5rc3/AMOS/Linux-x86_64/bin/OutputMotifs -b /pylon2/mc562pp/jwestrob/metAMOS-1.5rc3/Test/test1/Scaffold/in/proba.bnk > /pylon2/mc562pp/jwestrob/metAMOS-1.5rc3/Test/test1/Scaffold/out/proba.motifs
|2017-10-25 20:13:28| /pylon2/mc562pp/jwestrob/metAMOS-1.5rc3/AMOS/Linux-x86_64/bin/OutputScaffolds -b /pylon2/mc562pp/jwestrob/metAMOS-1.5rc3/Test/test1/Scaffold/in/proba.bnk > /pylon2/mc562pp/jwestrob/metAMOS-1.5rc3/Test/test1/Scaffold/out/proba.scaffolds.final
|2017-10-25 20:13:28| /pylon2/mc562pp/jwestrob/metAMOS-1.5rc3/AMOS/Linux-x86_64/bin/Linearize -b /pylon2/mc562pp/jwestrob/metAMOS-1.5rc3/Test/test1/Scaffold/in/proba.bnk
|2017-10-25 20:13:29| /pylon2/mc562pp/jwestrob/metAMOS-1.5rc3/AMOS/Linux-x86_64/bin/OutputScaffolds -b /pylon2/mc562pp/jwestrob/metAMOS-1.5rc3/Test/test1/Scaffold/in/proba.bnk > /pylon2/mc562pp/jwestrob/metAMOS-1.5rc3/Test/test1/Scaffold/out/proba.linearize.scaffolds.final
|2017-10-25 20:13:30|# [FINDSCAFFOLDORFS]
|2017-10-25 20:13:30| /pylon2/mc562pp/jwestrob/metAMOS-1.5rc3/Utilities/cpp/Linux-x86_64/FragGeneScan -s /pylon2/mc562pp/jwestrob/metAMOS-1.5rc3/Test/test1/Scaffold/out/proba.linearize.scaffolds.final -o /pylon2/mc562pp/jwestrob/metAMOS-1.5rc3/Test/test1/FindScaffoldORFS/out/proba.orfs -w 0 -t complete

Last 10 lines of output (/pylon2/mc562pp/jwestrob/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***********************************
*****************************************************************
Oops, MetAMOS finished with errors! see text in red above for details.
skoren commented 7 years ago

That looks like an error in fraggenescan. I would suggest trying to install the latest version and replace the binary distributed with metAMOS to see if it fixes the issue. Also, confirm the `test1/Scaffold/out/proba.linearize.scaffolds.final file isn't empty.