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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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running error about abundance #84

Closed jjjscuedu closed 11 years ago

jjjscuedu commented 11 years ago

Dear all,

When I try to run metAMOS on test data like this:

[jjin01@tll-rv2 MetaAMOS]$ /data/apps/metAMOS/./runPipeline -a soap -c fcp -g fraggenescan -p 15 -d test1 -k 55 -t -f Assemble,MapReads,FindORFS,FindScaffoldORFS ERROR: easy-install.pth file missing, likely means something went wrong with psutil/pysam install. Disabling psutil and pysam..

rm: cannot remove `/home/jjin01/project/test/MetaAMOS/test1/Logs/*.started': No such file or directory Starting Task = runpipeline.RUNPIPELINE Starting metAMOS pipeline Warning: Newbler is not found, some functionality will not be available Warning: MetaGeneMark is not found, some functionality will not be available Warning: Phymm is not found, some functionality will not be available Starting Task = classify.CLASSIFY

Tasks which will be run:

Task = preprocess.Preprocess Task = assemble.Assemble Task = mapreads.MapReads Task = findorfs.FindORFS 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: Time and Date: 2013-07-31 Working directory: /home/jjin01/project/test/MetaAMOS/test1 Prefix: proba K-Mer: 55 Threads: 15 Taxonomic level: class Verbose: False Steps to skip: FindRepeats Steps to force: Assemble, MapReads, FindORFS, FindScaffoldORFS

Step-specific configuration: [abundance] MetaPhyler /data/apps/metAMOS/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.

[fannotate] BLAST /data/apps/metAMOS/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 /data/apps/metAMOS/AMOS/Linux-x86_64/bin Koren S, Treangen TJ, Pop M. Bambus 2: scaffolding metagenomes. Bioinformatics 27(21): 2964-2971 2011.

[findorfs] FragGeneScan /data/apps/metAMOS/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.

[mapreads] Bowtie /data/apps/metAMOS/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.

[assemble] SOAPdenovo /data/apps/metAMOS/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.

[classify] FCP,Naive Bayesian Classifier /data/apps/metAMOS/Utilities/cpp/Linux-x86_64 Macdonald NJ, Parks DH, Beiko RG. Rapid identification of high-confidence taxonomic assignments for metagenomic data. Nucleic Acids Res. 2012 Apr 24.

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

Starting Task = preprocess.PREPROCESS Job = [[carsonella_pe_filt.fna] -> preprocess.success] completed Completed Task = preprocess.Preprocess Starting Task = assemble.ASSEMBLE Job = [preprocess.success -> [assemble.ok]] completed Completed Task = assemble.Assemble Starting Task = mapreads.MAPREADS Job = [proba.asm.contig -> mapreads.success] completed Completed Task = mapreads.MapReads Starting Task = findorfs.FINDORFS Job = [proba.asm.contig -> proba.faa] completed Completed Task = findorfs.FindORFS Starting Task = findrepeats.FINDREPEATS Job = [proba.fna -> proba.repeats] completed Completed Task = findreps.FindRepeats Starting Task = annotate.ANNOTATE The size of the contigs is 160787 per thread 10000000

Warning: unmapped/unaligned sequences will not be annotated! Job = [proba.faa -> proba.hits] completed Completed Task = annotate.Annotate Starting Task = functionalannotation.FUNCTIONALANNOTATION Loading EC names... Importing /home/jjin01/project/test/MetaAMOS/test1/FunctionalAnnotation/out/krona.ec.input... Writing ec.krona.html...

Job  = [proba.faa -> [blast.out, krona.ec.input]] completed

Completed Task = fannotate.FunctionalAnnotation Warning: cannot retain bank, it does not exist yet

Starting Task = scaffold.SCAFFOLD Job = [[proba.asm.contig] -> proba.scaffolds.final] completed Completed Task = scaffold.Scaffold no. of seqs: 3

Starting Task = findscaffoldorfs.FINDSCAFFOLDORFS Job = [proba.linearize.scaffolds.final -> proba.scaffolds.orfs] completed Completed Task = findscforfs.FindScaffoldORFS Starting Task = propagate.PROPAGATE Job = [proba.annots -> propagate.ok] completed Completed Task = propagate.Propagate Starting Task = abundance.ABUNDANCE [91m***** ****ERROR****** During abundance, the following command failed with return code 2:

/data/apps/metAMOS/Utilities/cpp/Linux-x86_64/formatdb -p T -i /data/apps/metAMOS/Utilities/DB/markers.pfasta

****DETAILS****** Last 10 commands run before the error (/home/jjin01/project/test/MetaAMOS/test1/Logs/COMMANDS.log) |2013-07-31 22:56:19| /data/apps/metAMOS/AMOS/Linux-x86_64/bin/OutputScaffolds -b /home/jjin01/project/test/MetaAMOS/test1/Scaffold/in/proba.bnk > /home/jjin01/project/test/MetaAMOS/test1/Scaffold/out/proba.linearize.scaffolds.final |2013-07-31 22:56:24|# [FINDSCAFFOLDORFS] |2013-07-31 22:56:24| cp /home/jjin01/project/test/MetaAMOS/test1/FindScaffoldORFS/out/proba.orfs.ffn /home/jjin01/project/test/MetaAMOS/test1/FindScaffoldORFS/out/proba.fna |2013-07-31 22:56:24| cp /home/jjin01/project/test/MetaAMOS/test1/FindScaffoldORFS/out/proba.orfs.faa /home/jjin01/project/test/MetaAMOS/test1/FindScaffoldORFS/out/proba.faa |2013-07-31 22:56:26|# [PROPAGATE] |2013-07-31 22:56:26| ln /home/jjin01/project/test/MetaAMOS/test1/Annotate/out/proba.annots /home/jjin01/project/test/MetaAMOS/test1/Propagate/in/proba.annots |2013-07-31 22:56:26| cat /home/jjin01/project/test/MetaAMOS/test1/Propagate/in/proba.annots | grep -v "\"" | grep -v contigID |sed s/utg//g |sed s/ctg//g > /home/jjin01/project/test/MetaAMOS/test1/Propagate/in/proba.clusters |2013-07-31 22:56:26| /data/apps/metAMOS/AMOS/Linux-x86_64/bin/FilterEdgesByCluster -b /home/jjin01/project/test/MetaAMOS/test1/Scaffold/in/proba.bnk -clusters /home/jjin01/project/test/MetaAMOS/test1/Propagate/in/proba.clusters -noRemoveEdges > /home/jjin01/project/test/MetaAMOS/test1/Propagate/out/proba.clusters |2013-07-31 22:56:28|# [ABUNDANCE] |2013-07-31 22:56:28| /data/apps/metAMOS/Utilities/cpp/Linux-x86_64/formatdb -p T -i /data/apps/metAMOS/Utilities/DB/markers.pfasta

Last 10 lines of output (/home/jjin01/project/test/MetaAMOS/test1/Logs/ABUNDANCE.log)

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

rm: cannot remove `/home/jjin01/project/test/MetaAMOS/test1/Logs/abundance.ok': No such file or directory ruffus.ruffus_exceptions.RethrownJobError:

Can anyone give me some suggestions?

Thanks!

Jingjing

skoren commented 11 years ago

This is likely a permissions issue. The formatdb call is trying to write to the MetaAMOS/Utilities/DB folder. The fix for this is committed so doing a git pull should fix it.