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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.
The text was updated successfully, but these errors were encountered:
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.
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: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.The text was updated successfully, but these errors were encountered: