Error: ./run_test.sh failed in classify step

[danbacastro]

Hi,

I getting the following error probably in the classify step:

Starting Task = classify.CLASSIFY *\ metAMOS running command: perl -I /home/bioinfo/programas/metAMOS-1.5rc1/AMOS/Linux-x86_64/lib /home/bioinfo/programas/metAMOS-1.5rc1/Utilities/perl/statistics.pl /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/proba.scf.fa > /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/html/asmstats.out

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

How can I solve this?

Thanks

[skoren]

Hi,

This looks like an error due to missing Statistics::Descriptive. There should be Statistics directory in your /home/bioinfo/programas/metAMOS-1.5rc1/AMOS/Linux-x86_64/lib folder. If not, you can try removing the AMOS directory and re-running INSTALL.py to re-downloaded the latest version of AMOS which includes the necessary library. Let us know if after this your /home/bioinfo/programas/metAMOS-1.5rc1/AMOS/Linux-x86_64/lib directory still does not have a Statistics subdirectory.

[danbacastro]

Hello,

I removed AMOS directory and reinstalled with the INSTALL.py, but the error continues. I do have the Statistics subdirectory with Descreptive.pm there.

Any other try?

Thanks

[skoren]

Could you run the command by hand: perl -I /home/bioinfo/programas/metAMOS-1.5rc1/AMOS/Linux-x86_64/lib /home/bioinfo/programas/metAMOS-1.5rc1/Utilities/perl/statistics.pl /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/proba.scf.fa and post any output it returns?

[danbacastro]

It returns:

bioinfo@bioinfo:~/programas/metAMOS-1.5rc1/Test$ perl -I /home/bioinfo/programas/metAMOS-1.5rc1/AMOS/Linux-x86_64/lib /home/bioinfo/programas/metAMOS-1.5rc1/Utilities/perl/statistics.pl /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/proba.scf.fa

File Number Total Size Min Size Max Size Average Size Median Size N50 Size @ 1Mbp Number @ 1Mbp Size @ 2Mbp Number @ 2Mbp Size @ 4Mbp Number @ 4Mbp Size @ 10Mbp Number @ 10Mbp /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/proba.scf.fa 1 159701 159701 159701 159701.00 159701 159701

It seems that output is correct...

[skoren]

Thanks, yes it looks like this command is not the issue but something else is causing your error. Could you post your COMMAND.log, CLASSIFY.log, and POSTPROCESS.log file from the test1/Logs/ directory as well as the full output from runPipeline?

[danbacastro]

Command line: bioinfo@bioinfo:~/programas/metAMOS-1.5rc1/Test$ ./run_test.sh Project dir /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1 successfully created! Use runPipeline.py to start Pipeline

Starting Task = runpipeline.RUNPIPELINE *\ metAMOS running command: touch /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Preprocess/out/lib1.seq

** metAMOS running command: rm /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/.contig.cvg

*\ metAMOS running command: rm /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Logs/mapreads.ok

*\ metAMOS running command: rm /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Logs/propagate.ok

*\ metAMOS running command: touch /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Annotate/out/proba.annots

*\ metAMOS running command: touch /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Scaffold/out/proba.linearize.scaffolds.final

*\ metAMOS running command: touch /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/proba.faa

*\ metAMOS running command: rm /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Abundance/out/proba.taxprof.pct.txt

*\ metAMOS running command: rm /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Annotate/out/proba.hits

** metAMOS running command: rm /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/.faa

** metAMOS running command: rm /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/.fna

** metAMOS running command: rm /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/.faa

** metAMOS running command: rm /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/.fna

*\ metAMOS running command: rm /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Logs/assemble.ok

** metAMOS running command: rm /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/.asm.contig

*\ metAMOS running command: rm /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Logs/classify.ok

Starting metAMOS pipeline Found pysam in /home/bioinfo/.local/lib/python2.7/site-packages/pysam-0.6-py2.7-linux-x86_64.egg/pysam/init.pyc Found psutil in /home/bioinfo/.local/lib/python2.7/site-packages/psutil-0.6.1-py2.7-linux-x86_64.egg/psutil/init.pyc 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: metaphylerClassify is not found, some functionality will not be available Warning: PHmmer is not found, some functionality will not be available Warning: PhyloSift was not found, 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: R package 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 Warning: MPI is not available, some functionality may not be available [Available RAM: 31 GB] [ There is 31 GB of RAM currently available on this machine, suggested minimum of 32 GB [ Enabling low MEM mode, might slow down some steps in pipeline [ If more RAM is available than what is listed above, please close down other programs and restart runPipeline [Available CPUs: 8] 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

---

Warning: Graphviz is not found, some functionality will not be available metAMOS configuration summary: metAMOS Version: v1.5rc1 "Praline Brownie" workflows: core Time and Date: 2014-03-01 Working directory: /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1 Prefix: proba K-Mer: 55 Threads: 15 Taxonomic level: class Verbose: True 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

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 /home/bioinfo/programas/metAMOS-1.5rc1/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 /home/bioinfo/programas/metAMOS-1.5rc1/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 /home/bioinfo/programas/metAMOS-1.5rc1/AMOS/Linux-x86_64/bin Koren S, Treangen TJ, Pop M. Bambus 2: scaffolding metagenomes. Bioinformatics 27(21): 2964-2971 2011.

[findorfs] FragGeneScan /home/bioinfo/programas/metAMOS-1.5rc1/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 /home/bioinfo/programas/metAMOS-1.5rc1/Utilities/cpp/Linux-x86_64/kraken/bin Wood DE, Salzberg SL. Rapid phylogenetic sequence classification through repeated exact alignment. In preparation.

[assemble] SOAPdenovo /home/bioinfo/programas/metAMOS-1.5rc1/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 /home/bioinfo/programas/metAMOS-1.5rc1/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 /home/bioinfo/programas/metAMOS-1.5rc1/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 /home/bioinfo/programas/metAMOS-1.5rc1/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 *\ metAMOS running command: java -cp /home/bioinfo/programas/metAMOS-1.5rc1/Utilities/java:.:. outputDefaultQuality /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Preprocess/in/carsonella_pe_filt.fna > /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Preprocess/in/carsonella_pe_filt.fna.qual

*\ metAMOS running command: rm /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Preprocess/out/all.seq.mates

*\ metAMOS running command: cp /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Preprocess/out/carsonella_pe_filt.fna /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Preprocess/out/lib1.seq

*\ metAMOS running command: cp /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Preprocess/out/carsonella_pe_filt.fna.qual /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Preprocess/out/lib1.seq.qual

*\ metAMOS running command: which python

*\ metAMOS running command: echo $PYTHONPATH

*\ metAMOS running command: perl /home/bioinfo/programas/metAMOS-1.5rc1/Utilities/perl/split_fasta.pl /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Preprocess/out/lib1.seq /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Preprocess/out/lib1.1.fasta /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Preprocess/out/lib1.2.fasta

*\ metAMOS running command: perl /home/bioinfo/programas/metAMOS-1.5rc1/Utilities/perl/split_fasta.pl /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Preprocess/out/lib1.seq.qual /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Preprocess/out/lib1.1.fasta.qual /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Preprocess/out/lib1.2.fasta.qual

*\ metAMOS running command: ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Preprocess/out/lib1.seq /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Preprocess/out/lib1.fasta

*\ metAMOS running command: java -cp /home/bioinfo/programas/metAMOS-1.5rc1/Utilities/java:. convertFastaAndQualToFastq /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Preprocess/out/lib1.seq /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Preprocess/out/lib1.seq.qual > /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Preprocess/out/lib1.fastq

*\ metAMOS running command: java -cp /home/bioinfo/programas/metAMOS-1.5rc1/Utilities/java:. convertFastaAndQualToFastq /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Preprocess/out/lib1.1.fasta /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Preprocess/out/lib1.1.fasta.qual > /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Preprocess/out/lib1.1.fastq

*\ metAMOS running command: java -cp /home/bioinfo/programas/metAMOS-1.5rc1/Utilities/java:. convertFastaAndQualToFastq /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Preprocess/out/lib1.2.fasta /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Preprocess/out/lib1.2.fasta.qual > /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Preprocess/out/lib1.2.fastq

*\ metAMOS running command: touch /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Preprocess/out/preprocess.success

Job  = [[carsonella_pe_filt.fna] -> preprocess.success] completed

Completed Task = preprocess.Preprocess Starting Task = assemble.ASSEMBLE *\ metAMOS running command: touch /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/soapdenovo.55.run

Job  = [preprocess.success -> *.run] completed

Completed Task = assemble.SplitAssemblers *\ metAMOS running command: cat /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/soapconfig.txt |grep -v max_rd_len > /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/soap2config.txt

*\ metAMOS running command: /home/bioinfo/programas/metAMOS-1.5rc1/Utilities/cpp/Linux-x86_64/SOAPdenovo-63mer pregraph -p 15 -K 55 -R -D -s /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/soapconfig.txt -o /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/soapdenovo.55.asm

*\ metAMOS running command: /home/bioinfo/programas/metAMOS-1.5rc1/Utilities/cpp/Linux-x86_64/SOAPdenovo-63mer contig -g /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/soapdenovo.55.asm -R -M 3

Job  = [soapdenovo.55.run -> soapdenovo.55.asm.contig] completed

Completed Task = assemble.Assemble *\ metAMOS running command: mv /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/soapdenovo.55.asm.contig /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/soapdenovo.55.asm.contigWIUPAC.fa

*\ metAMOS running command: java -cp /home/bioinfo/programas/metAMOS-1.5rc1/Utilities/java:. RemoveIUPAC /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/soapdenovo.55.asm.contigWIUPAC.fa >/home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/soapdenovo.55.asm.contig

*\ metAMOS running command: rm /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/soapdenovo.55.run

*\ metAMOS running command: touch /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/assemble.success

Job  = [[soapdenovo.55.asm.contig] -> [assemble.ok]] completed

Completed Task = assemble.CheckAsmResults Uptodate Task = assemble.SplitMappers *\ metAMOS running command: rm -f /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/soapdenovo.55.contigdict

Starting Task = mapreads.MAPREADS *\ metAMOS running command: /home/bioinfo/programas/metAMOS-1.5rc1/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/soapdenovo.55.asm.contig /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/soapdenovo.55.IDX

*\ metAMOS running command: /home/bioinfo/programas/metAMOS-1.5rc1/Utilities/cpp/Linux-x86_64/bowtie -p 15 -f -l 25 -e 140 --best --strata -m 10 -k 1 --un /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/soapdenovo.55.lib1.unaligned.fasta /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/soapdenovo.55.IDX /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Preprocess/out/lib1.seq > /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/lib1.bout

*\ metAMOS running command: cat /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/soapdenovo.55.lib1.mappedmates >> /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/soapdenovo.55.lib1.hdr

*\ metAMOS running command: cp /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/soapdenovo.55.lib1.hdr /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/soapdenovo.55.lib1.mappedmates

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 Starting Task = findorfs.FINDORFS *\ metAMOS running command: unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/in/soapdenovo.55.asm.contig

*\ metAMOS running command: ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/soapdenovo.55.asm.contig /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/in/soapdenovo.55.asm.contig

*\ metAMOS running command: /home/bioinfo/programas/metAMOS-1.5rc1/Utilities/cpp/Linux-x86_64/FragGeneScan -s /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/in/soapdenovo.55.asm.contig -o /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/soapdenovo.55.orfs -w 0 -t complete

*\ metAMOS running command: mv /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/soapdenovo.55.orfs.ffn /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/soapdenovo.55.ctg.fna

*\ metAMOS running command: mv /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/soapdenovo.55.orfs.faa /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/soapdenovo.55.ctg.faa

*\ metAMOS running command: mv /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/soapdenovo.55.gene.cvg /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/soapdenovo.55.ctg.gene.cvg

*\ metAMOS running command: mv /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/soapdenovo.55.gene.map /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/soapdenovo.55.ctg.gene.map

*\ metAMOS running command: rm -r /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/soapdenovo.55.fna

** metAMOS running command: cat /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/soapdenovo.55.fna > /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/soapdenovo.55.fna

*\ metAMOS running command: rm -r /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/soapdenovo.55.fna.bnk

*\ metAMOS running command: /home/bioinfo/programas/metAMOS-1.5rc1/AMOS/Linux-x86_64/bin/toAmos_new -s /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/soapdenovo.55.fna -b /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/soapdenovo.55.fna.bnk

*\ metAMOS running command: rm -r /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/soapdenovo.55.faa

** metAMOS running command: cat /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/soapdenovo.55.faa > /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/soapdenovo.55.faa

*\ metAMOS running command: rm -r /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/soapdenovo.55.faa.bnk

*\ metAMOS running command: /home/bioinfo/programas/metAMOS-1.5rc1/AMOS/Linux-x86_64/bin/toAmos_new -s /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/soapdenovo.55.faa -b /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/soapdenovo.55.faa.bnk

*\ metAMOS running command: rm -r /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/soapdenovo.55.gene.cvg

** metAMOS running command: cat /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/soapdenovo.55.gene.cvg > /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/soapdenovo.55.gene.cvg

*\ metAMOS running command: rm -r /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/soapdenovo.55.gene.map

** metAMOS running command: cat /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/soapdenovo.55.gene.map > /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/soapdenovo.55.gene.map

*\ metAMOS running command: ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/soapdenovo.55.faa /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/soapdenovo.55.faa

*\ metAMOS running command: ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/soapdenovo.55.fna /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/soapdenovo.55.fna

Job  = [soapdenovo.55.contig.cvg -> soapdenovo.55.faa] completed

Completed Task = findorfs.FindORFS Starting Task = validate.VALIDATE *\ metAMOS running command: touch /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Logs/validate.skip

*\ metAMOS running command: unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/proba.asm.contig

*\ metAMOS running command: ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/soapdenovo.55.asm.contig /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/proba.asm.contig

*\ metAMOS running command: unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/proba.linearize.scaffolds.final

*\ metAMOS running command: ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/soapdenovo.55.asm.contig /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/proba.linearize.scaffolds.final

*\ metAMOS running command: unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/proba.asm.tigr

*\ metAMOS running command: ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/soapdenovo.55.asm.tigr /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/proba.asm.tigr

*\ metAMOS running command: unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/proba.contig.cnt

*\ metAMOS running command: ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/soapdenovo.55.contig.cnt /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/proba.contig.cnt

*\ metAMOS running command: unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/proba.contig.cvg

*\ metAMOS running command: ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/soapdenovo.55.contig.cvg /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/proba.contig.cvg

*\ metAMOS running command: unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/proba.afg

*\ metAMOS running command: rm /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Logs/findorfs.ok

*\ metAMOS running command: unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/in/proba.asm.contig

*\ metAMOS running command: ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/proba.asm.contig /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/in/proba.asm.contig

*\ metAMOS running command: /home/bioinfo/programas/metAMOS-1.5rc1/Utilities/cpp/Linux-x86_64/FragGeneScan -s /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/in/proba.asm.contig -o /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/proba.orfs -w 0 -t complete

*\ metAMOS running command: mv /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/proba.orfs.ffn /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/proba.ctg.fna

*\ metAMOS running command: mv /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/proba.orfs.faa /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/proba.ctg.faa

*\ metAMOS running command: mv /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/proba.gene.cvg /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/proba.ctg.gene.cvg

*\ metAMOS running command: mv /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/proba.gene.map /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/proba.ctg.gene.map

*\ metAMOS running command: rm -r /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/proba.fna

** metAMOS running command: cat /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/proba.fna > /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/proba.fna

*\ metAMOS running command: rm -r /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/proba.fna.bnk

*\ metAMOS running command: /home/bioinfo/programas/metAMOS-1.5rc1/AMOS/Linux-x86_64/bin/toAmos_new -s /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/proba.fna -b /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/proba.fna.bnk

*\ metAMOS running command: rm -r /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/proba.faa

** metAMOS running command: cat /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/proba.faa > /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/proba.faa

*\ metAMOS running command: rm -r /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/proba.faa.bnk

*\ metAMOS running command: /home/bioinfo/programas/metAMOS-1.5rc1/AMOS/Linux-x86_64/bin/toAmos_new -s /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/proba.faa -b /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/proba.faa.bnk

*\ metAMOS running command: rm -r /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/proba.gene.cvg

** metAMOS running command: cat /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/proba.gene.cvg > /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/proba.gene.cvg

*\ metAMOS running command: rm -r /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/proba.gene.map

** metAMOS running command: cat /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/proba.gene.map > /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/proba.gene.map

*\ metAMOS running command: ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/proba.faa /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/proba.faa

*\ metAMOS running command: ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/proba.fna /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/proba.fna

*\ metAMOS running command: touch /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Logs/findorfs.ok

*\ metAMOS running command: unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/proba.faa

*\ metAMOS running command: ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/proba.faa /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/proba.faa

*\ metAMOS running command: unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindRepeats/in/proba.fna

*\ metAMOS running command: ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/proba.fna /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindRepeats/in/proba.fna

*\ metAMOS running command: unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindRepeats/in/proba.faa

*\ metAMOS running command: ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/proba.faa /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindRepeats/in/proba.faa

*\ metAMOS running command: unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Annotate/in/proba.fna

*\ metAMOS running command: ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/proba.fna /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Annotate/in/proba.fna

*\ metAMOS running command: unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Annotate/in/proba.faa

*\ metAMOS running command: ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/proba.faa /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Annotate/in/proba.faa

*\ metAMOS running command: unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/proba.lib1.badmates

*\ metAMOS running command: ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/soapdenovo.55.lib1.badmates /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/proba.lib1.badmates

*\ metAMOS running command: unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/proba.lib1.hdr

*\ metAMOS running command: ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/soapdenovo.55.lib1.hdr /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/proba.lib1.hdr

*\ metAMOS running command: unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/proba.lib1.mappedmates

*\ metAMOS running command: ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/soapdenovo.55.lib1.mappedmates /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/proba.lib1.mappedmates

*\ metAMOS running command: unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/proba.lib1.mates_in_diff_contigs

*\ metAMOS running command: ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/soapdenovo.55.lib1.mates_in_diff_contigs /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/proba.lib1.mates_in_diff_contigs

*\ metAMOS running command: unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/proba.lib1contig.reads

*\ metAMOS running command: ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/soapdenovo.55.lib1contig.reads /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/proba.lib1contig.reads

*\ metAMOS running command: unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/lib1.unaligned.fasta

*\ metAMOS running command: ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/soapdenovo.55.lib1.unaligned.fasta /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/lib1.unaligned.fasta

*\ metAMOS running command: unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/lib1.unaligned.fastq

Job  = [[soapdenovo.55.faa] -> [validate.ok]] completed

Completed Task = validate.Validate Starting Task = findrepeats.FINDREPEATS *\ metAMOS running command: touch /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Logs/findrepeats.skip

Job  = [proba.fna -> proba.repeats] completed

Completed Task = findreps.FindRepeats Starting Task = annotate.ANNOTATE *\ metAMOS running command: touch /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Annotate/out/proba.annots

*\ metAMOS running command: unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Annotate/in/proba.asm.contig

*\ metAMOS running command: ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/proba.asm.contig /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Annotate/in/proba.asm.contig

*\ metAMOS running command: unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Annotate/out/proba.hits

** metAMOS running command: rm -f /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Annotate/out/.hits

** metAMOS running command: rm -f /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Annotate/out/.epsilon-nb_results.txt

** metAMOS running command: rm -f /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Annotate/out/.phymm.out

*\ metAMOS running command: /home/bioinfo/programas/metAMOS-1.5rc1/Utilities/cpp/Linux-x86_64/kraken/bin/kraken --threads 15 -db /home/bioinfo/programas/metAMOS-1.5rc1/Utilities/DB//kraken --output /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Annotate/out/proba.hits /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Annotate/in/proba.asm.contig --preload

*\ metAMOS running command: perl /home/bioinfo/programas/metAMOS-1.5rc1/Utilities/perl/ImportKraken.pl -c -i -f /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Annotate/in/proba.asm.contig /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Annotate/out/proba.hits:/home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/proba.contig.cnt:class

*\ metAMOS running command: unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/in/proba.hits

*\ metAMOS running command: unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/proba.hits

*\ metAMOS running command: ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Annotate/out/proba.hits /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/in/proba.hits

*\ metAMOS running command: ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Annotate/out/proba.hits /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/proba.hits

Job  = [proba.faa -> proba.hits] completed

Completed Task = annotate.Annotate Starting Task = functionalannotation.FUNCTIONALANNOTATION *\ metAMOS running command: touch /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Logs/functionalannotation.skip

*\ metAMOS running command: touch /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FunctionalAnnotation/out/blast.out

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

Completed Task = fannotate.FunctionalAnnotation Starting Task = scaffold.SCAFFOLD *\ metAMOS running command: rm -rf /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Scaffold/in/proba.bnk

*\ metAMOS running command: /home/bioinfo/programas/metAMOS-1.5rc1/AMOS/Linux-x86_64/bin/toAmos_new -s /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Preprocess/out/lib1.seq -m /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/proba.lib1.mappedmates -b /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Scaffold/in/proba.bnk

*\ metAMOS running command: /home/bioinfo/programas/metAMOS-1.5rc1/AMOS/Linux-x86_64/bin/toAmos_new -c /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/proba.asm.tigr -b /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Scaffold/in/proba.bnk

*\ metAMOS running command: /home/bioinfo/programas/metAMOS-1.5rc1/AMOS/Linux-x86_64/bin/asmQC -b /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Scaffold/in/proba.bnk -scaff -recompute -update -numsd 2

*\ metAMOS running command: perl /home/bioinfo/programas/metAMOS-1.5rc1/AMOS/Linux-x86_64/bin/bank-unlock /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Scaffold/in/proba.bnk

*\ metAMOS running command: /home/bioinfo/programas/metAMOS-1.5rc1/AMOS/Linux-x86_64/bin/clk -b /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Scaffold/in/proba.bnk

*\ metAMOS running command: /home/bioinfo/programas/metAMOS-1.5rc1/AMOS/Linux-x86_64/bin/Bundler -b /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Scaffold/in/proba.bnk

*\ metAMOS running command: /home/bioinfo/programas/metAMOS-1.5rc1/AMOS/Linux-x86_64/bin/MarkRepeats -redundancy 50 -b /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Scaffold/in/proba.bnk > /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Scaffold/in/proba.reps

*\ metAMOS running command: /home/bioinfo/programas/metAMOS-1.5rc1/AMOS/Linux-x86_64/bin/OrientContigs -minRedundancy 5 -all -redundancy 10 -b /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Scaffold/in/proba.bnk -repeats /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Scaffold/in/proba.reps

*\ metAMOS running command: /home/bioinfo/programas/metAMOS-1.5rc1/AMOS/Linux-x86_64/bin/bank2fasta -eid -b /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Scaffold/in/proba.bnk > /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Scaffold/out/proba.contigs

*\ metAMOS running command: /home/bioinfo/programas/metAMOS-1.5rc1/AMOS/Linux-x86_64/bin/OutputMotifs -b /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Scaffold/in/proba.bnk > /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Scaffold/out/proba.motifs

*\ metAMOS running command: /home/bioinfo/programas/metAMOS-1.5rc1/AMOS/Linux-x86_64/bin/OutputResults -b /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Scaffold/in/proba.bnk -p /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Scaffold/out/proba

*\ metAMOS running command: /home/bioinfo/programas/metAMOS-1.5rc1/AMOS/Linux-x86_64/bin/OutputScaffolds -b /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Scaffold/in/proba.bnk > /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Scaffold/out/proba.scaffolds.final

*\ metAMOS running command: /home/bioinfo/programas/metAMOS-1.5rc1/AMOS/Linux-x86_64/bin/Linearize -b /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Scaffold/in/proba.bnk

*\ metAMOS running command: /home/bioinfo/programas/metAMOS-1.5rc1/AMOS/Linux-x86_64/bin/OutputResults -b /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Scaffold/in/proba.bnk -p /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Scaffold/out/proba.linearize

*\ metAMOS running command: /home/bioinfo/programas/metAMOS-1.5rc1/AMOS/Linux-x86_64/bin/OutputScaffolds -b /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Scaffold/in/proba.bnk > /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Scaffold/out/proba.linearize.scaffolds.final

Job  = [[proba.asm.contig] -> scaffold.ok] completed

Completed Task = scaffold.Scaffold Starting Task = findscaffoldorfs.FINDSCAFFOLDORFS *\ metAMOS running command: /home/bioinfo/programas/metAMOS-1.5rc1/Utilities/cpp/Linux-x86_64/FragGeneScan -s /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Scaffold/out/proba.linearize.scaffolds.final -o /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindScaffoldORFS/out/proba.orfs -w 0 -t complete

*\ metAMOS running command: cp /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindScaffoldORFS/out/proba.orfs.ffn /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindScaffoldORFS/out/proba.fna

*\ metAMOS running command: cp /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindScaffoldORFS/out/proba.orfs.faa /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindScaffoldORFS/out/proba.faa

Job  = [proba.linearize.scaffolds.final -> proba.fna] completed

Completed Task = findscforfs.FindScaffoldORFS Starting Task = abundance.ABUNDANCE *\ metAMOS running command: ln -s /home/bioinfo/programas/metAMOS-1.5rc1/Utilities/DB//markers.pfasta /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Abundance/out/markers.pfasta

*\ metAMOS running command: /home/bioinfo/programas/metAMOS-1.5rc1/Utilities/cpp/Linux-x86_64/formatdb -p T -i /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Abundance/out/markers.pfasta

*\ metAMOS running command: /home/bioinfo/programas/metAMOS-1.5rc1/Utilities/cpp/Linux-x86_64/blastall -p blastp -i /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/proba.faa -d /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Abundance/out/markers.pfasta -m 8 -b 10 -v 10 -a 15 -o /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Abundance/out/proba.blastp

*\ metAMOS running command: perl /home/bioinfo/programas/metAMOS-1.5rc1/Utilities/perl/metaphyler_contigs.pl /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Abundance/out/proba.blastp proba /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/proba.gene.cvg /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Abundance/out /home/bioinfo/programas/metAMOS-1.5rc1/Utilities

*\ metAMOS running command: perl /home/bioinfo/programas/metAMOS-1.5rc1/Utilities/perl/ImportMetaPhyler.pl -c -v -i -p /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Abundance/out/proba.taxprof.pct.txt:class

Job  = [proba.asm.contig -> proba.taxprof.pct.txt] completed

Completed Task = abundance.Abundance Starting Task = propagate.PROPAGATE *\ metAMOS running command: ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Annotate/out/proba.annots /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Propagate/in/proba.annots

*\ metAMOS running command: cat /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Propagate/in/proba.annots | grep -v "\"" | grep -v contigID |sed s/utg//g |sed s/ctg//g > /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Propagate/in/proba.clusters

*\ metAMOS running command: /home/bioinfo/programas/metAMOS-1.5rc1/AMOS/Linux-x86_64/bin/FilterEdgesByCluster -b /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Scaffold/in/proba.bnk -clusters /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Propagate/in/proba.clusters -noRemoveEdges > /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Propagate/out/proba.clusters

Job  = [proba.annots -> propagate.ok] completed

Completed Task = propagate.Propagate Job = [proba.clusters -> classify.ok] completed Completed Task = classify.Classify Starting Task = postprocess.POSTPROCESS *\ metAMOS running command: unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/annotate.krona.html

*\ metAMOS running command: ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Annotate/out/report.krona.html /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/annotate.krona.html

*\ metAMOS running command: unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/abundance.krona.html

*\ metAMOS running command: ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Abundance/out/report.krona.html /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/abundance.krona.html

*\ metAMOS running command: unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/class.classified

*\ metAMOS running command: ln -s /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Classify/out /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/class.classified

*\ metAMOS running command: unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/asm.scores

*\ metAMOS running command: ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Validate/out/proba.lap /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/asm.scores

*\ metAMOS running command: unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/best.asm

*\ metAMOS running command: ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Validate/out/proba.asm.selected /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/best.asm

*\ metAMOS running command: unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/class.original.annots

*\ metAMOS running command: ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Annotate/out/proba.annots /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/class.original.annots

*\ metAMOS running command: unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/class.original.reads.annots

*\ metAMOS running command: ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Annotate/out/proba.reads.annots /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/class.original.reads.annots

*\ metAMOS running command: unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/class.propagated.annots

*\ metAMOS running command: unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/class.propagated.reads.annots

*\ metAMOS running command: cp /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Abundance/out/proba.classify.txt /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/.

*\ metAMOS running command: cp /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Scaffold/out/proba.linearize.scaffolds.final /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/proba.scf.fa

*\ metAMOS running command: cp /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Scaffold/out/proba.contigs /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/proba.ctg.fa

*\ metAMOS running command: cp /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Scaffold/out/proba.motifs /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/proba.motifs.fa

*\ metAMOS running command: ln -s /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Scaffold/in/proba.bnk /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/

*\ metAMOS running command: ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/proba.fna /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/proba.orf.fna

*\ metAMOS running command: ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/proba.faa /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/proba.orf.faa

*\ metAMOS running command: ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindScaffoldORFS/out/proba.fna /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/proba.scf.orf.fna

*\ metAMOS running command: ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindScaffoldORFS/out/proba.faa /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/proba.scf.orf.faa

*\ metAMOS running command: unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/proba.lib1.contig.reads

*\ metAMOS running command: ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/proba.lib1contig.reads /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/proba.lib1.contig.reads

*\ metAMOS running command: unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/proba.lib1.unaligned.fasta

*\ metAMOS running command: ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/lib1.unaligned.fasta /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/proba.lib1.unaligned.fasta

*\ metAMOS running command: unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/proba.ctg.cnt

*\ metAMOS running command: ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/proba.contig.cnt /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/proba.ctg.cnt

*\ metAMOS running command: unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/proba.ctg.cvg

*\ metAMOS running command: ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/proba.contig.cvg /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/proba.ctg.cvg

*\ metAMOS running command: unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/html

*\ metAMOS running command: mkdir /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/html

*\ metAMOS running command: unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/html/class.classified

*\ metAMOS running command: ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/class.classified /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/html/class.classified

*\ metAMOS running command: unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/html/Annotate.html

*\ metAMOS running command: ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/annotate.krona.html /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/html/Annotate.html

*\ metAMOS running command: unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/html/Abundance.html

*\ metAMOS running command: ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/abundance.krona.html /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/html/Abundance.html

*\ metAMOS running command: touch /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/ref.name

** metAMOS running command: mv /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Preprocess/out/.fastqc /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/html

*\ metAMOS running command: unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/html/propagate.in.clusters

*\ metAMOS running command: ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Propagate/in/proba.clusters /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/html/propagate.in.clusters

*\ metAMOS running command: unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/html/propagate.out.clusters

*\ metAMOS running command: ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Propagate/out/proba.clusters /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/html/propagate.out.clusters

*\ metAMOS running command: unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/html/FunctionalAnnotation.html

*\ metAMOS running command: ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FunctionalAnnotation/out/ec.krona.html /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/html/FunctionalAnnotation.html

Starting Task = classify.CLASSIFY *\ metAMOS running command: perl -I /home/bioinfo/programas/metAMOS-1.5rc1/AMOS/Linux-x86_64/lib /home/bioinfo/programas/metAMOS-1.5rc1/Utilities/perl/statistics.pl /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/proba.scf.fa > /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/html/asmstats.out Oops, MetAMOS finished with errors! see text in red above for details.

[danbacastro]

COMMAND.log: |2014-03-01 15:03:47|# [RUNPIPELINE] |2014-03-01 15:03:47| touch /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Preprocess/out/lib1.seq |2014-03-01 15:03:47| rm /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/.contig.cvg |2014-03-01 15:03:47| rm /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Logs/mapreads.ok |2014-03-01 15:03:47| rm /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Logs/propagate.ok |2014-03-01 15:03:47| touch /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Annotate/out/proba.annots |2014-03-01 15:03:47| touch /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Scaffold/out/proba.linearize.scaffolds.final |2014-03-01 15:03:47| touch /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/proba.faa |2014-03-01 15:03:47| rm /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Abundance/out/proba.taxprof.pct.txt |2014-03-01 15:03:47| rm /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Annotate/out/proba.hits |2014-03-01 15:03:47| rm /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/.faa |2014-03-01 15:03:47| rm /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/.fna |2014-03-01 15:03:47| rm /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/.faa |2014-03-01 15:03:47| rm /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/.fna |2014-03-01 15:03:47| rm /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Logs/assemble.ok |2014-03-01 15:03:47| rm /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/.asm.contig |2014-03-01 15:03:47| rm /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Logs/classify.ok |2014-03-01 15:03:48|# [PREPROCESS] |2014-03-01 15:03:50| java -cp /home/bioinfo/programas/metAMOS-1.5rc1/Utilities/java:.:. outputDefaultQuality /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Preprocess/in/carsonella_pe_filt.fna > /home/bioinfo/programas/metAMOS-1.5rc1 /Test/test1/Preprocess/in/carsonella_pe_filt.fna.qual |2014-03-01 15:03:50| rm /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Preprocess/out/all.seq.mates |2014-03-01 15:03:52| cp /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Preprocess/out/carsonella_pe_filt.fna /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Preprocess/out/lib1.seq |2014-03-01 15:03:52| cp /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Preprocess/out/carsonella_pe_filt.fna.qual /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Preprocess/out/lib1.seq.qual |2014-03-01 15:03:52| which python |2014-03-01 15:03:52| echo $PYTHONPATH |2014-03-01 15:03:53| perl /home/bioinfo/programas/metAMOS-1.5rc1/Utilities/perl/split_fasta.pl /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Preprocess/out/lib1.seq /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Preprocess/out/li b1.1.fasta /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Preprocess/out/lib1.2.fasta |2014-03-01 15:03:53| perl /home/bioinfo/programas/metAMOS-1.5rc1/Utilities/perl/split_fasta.pl /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Preprocess/out/lib1.seq.qual /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Preprocess/o ut/lib1.1.fasta.qual /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Preprocess/out/lib1.2.fasta.qual |2014-03-01 15:03:53| ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Preprocess/out/lib1.seq /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Preprocess/out/lib1.fasta |2014-03-01 15:03:56| java -cp /home/bioinfo/programas/metAMOS-1.5rc1/Utilities/java:. convertFastaAndQualToFastq /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Preprocess/out/lib1.seq /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1 /Preprocess/out/lib1.seq.qual > /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Preprocess/out/lib1.fastq |2014-03-01 15:03:59| java -cp /home/bioinfo/programas/metAMOS-1.5rc1/Utilities/java:. convertFastaAndQualToFastq /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Preprocess/out/lib1.1.fasta /home/bioinfo/programas/metAMOS-1.5rc1/Test/t est1/Preprocess/out/lib1.1.fasta.qual > /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Preprocess/out/lib1.1.fastq |2014-03-01 15:04:01| java -cp /home/bioinfo/programas/metAMOS-1.5rc1/Utilities/java:. convertFastaAndQualToFastq /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Preprocess/out/lib1.2.fasta /home/bioinfo/programas/metAMOS-1.5rc1/Test/t est1/Preprocess/out/lib1.2.fasta.qual > /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Preprocess/out/lib1.2.fastq |2014-03-01 15:04:01| touch /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Preprocess/out/preprocess.success |2014-03-01 15:04:02|# [ASSEMBLE] |2014-03-01 15:04:02| touch /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/soapdenovo.55.run |2014-03-01 15:04:03| cat /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/soapconfig.txt |grep -v max_rd_len > /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/soap2config.txt |2014-03-01 15:04:05| /home/bioinfo/programas/metAMOS-1.5rc1/Utilities/cpp/Linux-x86_64/SOAPdenovo-63mer pregraph -p 15 -K 55 -R -D -s /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/soapconfig.txt -o /home/bioinfo/programas/metAMOS -1.5rc1/Test/test1/Assemble/out/soapdenovo.55.asm |2014-03-01 15:04:05| /home/bioinfo/programas/metAMOS-1.5rc1/Utilities/cpp/Linux-x86_64/SOAPdenovo-63mer contig -g /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/soapdenovo.55.asm -R -M 3 |2014-03-01 15:04:06| mv /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/soapdenovo.55.asm.contig /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/soapdenovo.55.asm.contigWIUPAC.fa |2014-03-01 15:04:07| java -cp /home/bioinfo/programas/metAMOS-1.5rc1/Utilities/java:. RemoveIUPAC /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/soapdenovo.55.asm.contigWIUPAC.fa >/home/bioinfo/programas/metAMOS-1.5rc1/T est/test1/Assemble/out/soapdenovo.55.asm.contig |2014-03-01 15:04:07| rm /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/soapdenovo.55.run |2014-03-01 15:04:07| touch /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/assemble.success |2014-03-01 15:04:08|# [MAPREADS] |2014-03-01 15:04:08| /home/bioinfo/programas/metAMOS-1.5rc1/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/soapdenovo.55.asm.contig /home/bioinfo/programas/metAMOS-1.5rc1/Test /test1/Assemble/out/soapdenovo.55.IDX |2014-03-01 15:04:09| /home/bioinfo/programas/metAMOS-1.5rc1/Utilities/cpp/Linux-x86_64/bowtie -p 15 -f -l 25 -e 140 --best --strata -m 10 -k 1 --un /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/soapdenovo.55.lib1.unalig ned.fasta /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/soapdenovo.55.IDX /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Preprocess/out/lib1.seq > /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/lib1.bo ut |2014-03-01 15:04:16| cat /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/soapdenovo.55.lib1.mappedmates >> /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/soapdenovo.55.lib1.hdr |2014-03-01 15:04:16| cp /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/soapdenovo.55.lib1.hdr /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/soapdenovo.55.lib1.mappedmates |2014-03-01 15:04:19|# [FINDORFS] |2014-03-01 15:04:19| unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/in/soapdenovo.55.asm.contig |2014-03-01 15:04:19| ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/soapdenovo.55.asm.contig /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/in/soapdenovo.55.asm.contig |2014-03-01 15:04:21| /home/bioinfo/programas/metAMOS-1.5rc1/Utilities/cpp/Linux-x8664/FragGeneScan -s /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/in/soapdenovo.55.asm.contig -o /home/bioinfo/programas/metAMOS-1.5rc1/Test /test1/FindORFS/out/soapdenovo.55.orfs -w 0 -t complete |2014-03-01 15:04:21| mv /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/soapdenovo.55.orfs.ffn /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/soapdenovo.55.ctg.fna |2014-03-01 15:04:21| mv /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/soapdenovo.55.orfs.faa /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/soapdenovo.55.ctg.faa |2014-03-01 15:04:21| mv /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/soapdenovo.55.gene.cvg /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/soapdenovo.55.ctg.gene.cvg |2014-03-01 15:04:21| mv /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/soapdenovo.55.gene.map /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/soapdenovo.55.ctg.gene.map |2014-03-01 15:04:21| rm -r /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/soapdenovo.55.fna |2014-03-01 15:04:21| cat /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/soapdenovo.55.fna > /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/soapdenovo.55.fna |2014-03-01 15:04:21| rm -r /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/soapdenovo.55.fna.bnk |2014-03-01 15:04:21| /home/bioinfo/programas/metAMOS-1.5rc1/AMOS/Linux-x86_64/bin/toAmosnew -s /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/soapdenovo.55.fna -b /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindOR FS/out/soapdenovo.55.fna.bnk |2014-03-01 15:04:21| rm -r /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/soapdenovo.55.faa |2014-03-01 15:04:21| cat /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/soapdenovo.55.faa > /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/soapdenovo.55.faa |2014-03-01 15:04:21| rm -r /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/soapdenovo.55.faa.bnk |2014-03-01 15:04:21| /home/bioinfo/programas/metAMOS-1.5rc1/AMOS/Linux-x86_64/bin/toAmosnew -s /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/soapdenovo.55.faa -b /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindOR FS/out/soapdenovo.55.faa.bnk |2014-03-01 15:04:21| rm -r /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/soapdenovo.55.gene.cvg |2014-03-01 15:04:21| cat /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/soapdenovo.55.gene.cvg > /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/soapdenovo.55.gene.cvg |2014-03-01 15:04:21| rm -r /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/soapdenovo.55.gene.map |2014-03-01 15:04:21| cat /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/soapdenovo.55_.gene.map > /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/soapdenovo.55.gene.map |2014-03-01 15:04:21| ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/soapdenovo.55.faa /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/soapdenovo.55.faa |2014-03-01 15:04:21| ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/soapdenovo.55.fna /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/soapdenovo.55.fna |2014-03-01 15:04:22|# [VALIDATE] |2014-03-01 15:04:22| touch /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Logs/validate.skip |2014-03-01 15:04:22| unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/proba.asm.contig |2014-03-01 15:04:22| ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/soapdenovo.55.asm.contig /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/proba.asm.contig |2014-03-01 15:04:22| unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/proba.linearize.scaffolds.final |2014-03-01 15:04:22| ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/soapdenovo.55.asm.contig /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/proba.linearize.scaffolds.final |2014-03-01 15:04:22| unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/proba.asm.tigr |2014-03-01 15:04:22| ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/soapdenovo.55.asm.tigr /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/proba.asm.tigr |2014-03-01 15:04:22| unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/proba.contig.cnt |2014-03-01 15:04:22| ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/soapdenovo.55.contig.cnt /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/proba.contig.cnt |2014-03-01 15:04:22| unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/proba.contig.cvg |2014-03-01 15:04:22| ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/soapdenovo.55.contig.cvg /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/proba.contig.cvg |2014-03-01 15:04:22| unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/proba.afg |2014-03-01 15:04:22| rm /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Logs/findorfs.ok |2014-03-01 15:04:22| unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/in/proba.asm.contig |2014-03-01 15:04:22| ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/proba.asm.contig /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/in/proba.asm.contig |2014-03-01 15:04:24| /home/bioinfo/programas/metAMOS-1.5rc1/Utilities/cpp/Linux-x8664/FragGeneScan -s /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/in/proba.asm.contig -o /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/F indORFS/out/proba.orfs -w 0 -t complete |2014-03-01 15:04:24| mv /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/proba.orfs.ffn /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/proba.ctg.fna |2014-03-01 15:04:24| mv /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/proba.orfs.faa /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/proba.ctg.faa |2014-03-01 15:04:24| mv /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/proba.gene.cvg /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/proba.ctg.gene.cvg |2014-03-01 15:04:24| mv /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/proba.gene.map /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/proba.ctg.gene.map |2014-03-01 15:04:24| rm -r /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/proba.fna |2014-03-01 15:04:24| cat /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/proba.fna > /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/proba.fna |2014-03-01 15:04:24| rm -r /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/proba.fna.bnk |2014-03-01 15:04:24| /home/bioinfo/programas/metAMOS-1.5rc1/AMOS/Linux-x86_64/bin/toAmosnew -s /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/proba.fna -b /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/p roba.fna.bnk |2014-03-01 15:04:24| rm -r /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/proba.faa |2014-03-01 15:04:24| cat /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/proba.faa > /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/proba.faa |2014-03-01 15:04:24| rm -r /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/proba.faa.bnk |2014-03-01 15:04:24| /home/bioinfo/programas/metAMOS-1.5rc1/AMOS/Linux-x86_64/bin/toAmosnew -s /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/proba.faa -b /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/p roba.faa.bnk |2014-03-01 15:04:24| rm -r /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/proba.gene.cvg |2014-03-01 15:04:24| cat /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/proba.gene.cvg > /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/proba.gene.cvg |2014-03-01 15:04:24| rm -r /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/proba.gene.map |2014-03-01 15:04:24| cat /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/proba_.gene.map > /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/proba.gene.map |2014-03-01 15:04:24| ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/proba.faa /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/proba.faa |2014-03-01 15:04:24| ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/proba.fna /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/proba.fna |2014-03-01 15:04:24| touch /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Logs/findorfs.ok |2014-03-01 15:04:24| unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/proba.faa |2014-03-01 15:04:24| ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/proba.faa /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/proba.faa |2014-03-01 15:04:24| unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindRepeats/in/proba.fna |2014-03-01 15:04:24| ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/proba.fna /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindRepeats/in/proba.fna |2014-03-01 15:04:24| unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindRepeats/in/proba.faa |2014-03-01 15:04:24| ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/proba.faa /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindRepeats/in/proba.faa |2014-03-01 15:04:24| unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Annotate/in/proba.fna |2014-03-01 15:04:24| ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/proba.fna /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Annotate/in/proba.fna |2014-03-01 15:04:24| unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Annotate/in/proba.faa |2014-03-01 15:04:24| ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/proba.faa /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Annotate/in/proba.faa |2014-03-01 15:04:24| unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/proba.lib1.badmates |2014-03-01 15:04:24| ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/soapdenovo.55.lib1.badmates /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/proba.lib1.badmates |2014-03-01 15:04:24| unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/proba.lib1.hdr |2014-03-01 15:04:24| ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/soapdenovo.55.lib1.hdr /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/proba.lib1.hdr |2014-03-01 15:04:24| unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/proba.lib1.mappedmates |2014-03-01 15:04:24| ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/soapdenovo.55.lib1.mappedmates /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/proba.lib1.mappedmates |2014-03-01 15:04:24| unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/proba.lib1.mates_in_diff_contigs |2014-03-01 15:04:24| ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/soapdenovo.55.lib1.mates_in_diff_contigs /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/proba.lib1.mates_in_diffcontigs |2014-03-01 15:04:24| unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/proba.lib1contig.reads |2014-03-01 15:04:24| ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/soapdenovo.55.lib1contig.reads /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/proba.lib1contig.reads |2014-03-01 15:04:24| unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/lib1.unaligned.fasta |2014-03-01 15:04:24| ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/soapdenovo.55.lib1.unaligned.fasta /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/lib1.unaligned.fasta |2014-03-01 15:04:24| unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/lib1.unaligned.fastq |2014-03-01 15:04:25|# [FINDREPEATS] |2014-03-01 15:04:25| touch /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Logs/findrepeats.skip |2014-03-01 15:04:26|# [ANNOTATE] |2014-03-01 15:04:26| touch /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Annotate/out/proba.annots |2014-03-01 15:04:26| unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Annotate/in/proba.asm.contig |2014-03-01 15:04:26| ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/proba.asm.contig /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Annotate/in/proba.asm.contig |2014-03-01 15:04:26| unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Annotate/out/proba.hits |2014-03-01 15:04:26| rm -f /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Annotate/out/.hits |2014-03-01 15:04:26| rm -f /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Annotate/out/_.epsilon-nbresults.txt |2014-03-01 15:04:26| rm -f /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Annotate/out/.phymm.out |2014-03-01 15:04:28| /home/bioinfo/programas/metAMOS-1.5rc1/Utilities/cpp/Linux-x86_64/kraken/bin/kraken --threads 15 -db /home/bioinfo/programas/metAMOS-1.5rc1/Utilities/DB//kraken --output /home/bioinfo/programas/metAMOS-1.5rc1/Test/t est1/Annotate/out/proba.hits /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Annotate/in/proba.asm.contig --preload
|2014-03-01 15:04:31| perl /home/bioinfo/programas/metAMOS-1.5rc1/Utilities/perl/ImportKraken.pl -c -i -f /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Annotate/in/proba.asm.contig /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/A nnotate/out/proba.hits:/home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/proba.contig.cnt:class |2014-03-01 15:04:31| unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/in/proba.hits |2014-03-01 15:04:31| unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/proba.hits |2014-03-01 15:04:31| ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Annotate/out/proba.hits /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/in/proba.hits |2014-03-01 15:04:31| ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Annotate/out/proba.hits /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/proba.hits |2014-03-01 15:04:32|# [FUNCTIONALANNOTATION] |2014-03-01 15:04:32| touch /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Logs/functionalannotation.skip |2014-03-01 15:04:32| touch /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FunctionalAnnotation/out/blast.out |2014-03-01 15:04:33|# [SCAFFOLD] |2014-03-01 15:04:33| rm -rf /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Scaffold/in/proba.bnk |2014-03-01 15:04:35| /home/bioinfo/programas/metAMOS-1.5rc1/AMOS/Linux-x86_64/bin/toAmos_new -s /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Preprocess/out/lib1.seq -m /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/ proba.lib1.mappedmates -b /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Scaffold/in/proba.bnk |2014-03-01 15:04:35| /home/bioinfo/programas/metAMOS-1.5rc1/AMOS/Linux-x86_64/bin/toAmos_new -c /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/proba.asm.tigr -b /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Scaffold/ in/proba.bnk |2014-03-01 15:04:36| /home/bioinfo/programas/metAMOS-1.5rc1/AMOS/Linux-x86_64/bin/asmQC -b /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Scaffold/in/proba.bnk -scaff -recompute -update -numsd 2 |2014-03-01 15:04:36| perl /home/bioinfo/programas/metAMOS-1.5rc1/AMOS/Linux-x86_64/bin/bank-unlock /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Scaffold/in/proba.bnk |2014-03-01 15:04:37| /home/bioinfo/programas/metAMOS-1.5rc1/AMOS/Linux-x86_64/bin/clk -b /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Scaffold/in/proba.bnk |2014-03-01 15:04:37| /home/bioinfo/programas/metAMOS-1.5rc1/AMOS/Linux-x86_64/bin/Bundler -b /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Scaffold/in/proba.bnk |2014-03-01 15:04:37| /home/bioinfo/programas/metAMOS-1.5rc1/AMOS/Linux-x86_64/bin/MarkRepeats -redundancy 50 -b /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Scaffold/in/proba.bnk > /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1 /Scaffold/in/proba.reps |2014-03-01 15:04:37| /home/bioinfo/programas/metAMOS-1.5rc1/AMOS/Linux-x86_64/bin/OrientContigs -minRedundancy 5 -all -redundancy 10 -b /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Scaffold/in/proba.bnk -repeats /home/bioinfo/pro gramas/metAMOS-1.5rc1/Test/test1/Scaffold/in/proba.reps |2014-03-01 15:04:37| /home/bioinfo/programas/metAMOS-1.5rc1/AMOS/Linux-x86_64/bin/bank2fasta -eid -b /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Scaffold/in/proba.bnk > /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Scaffold/o ut/proba.contigs |2014-03-01 15:04:37| /home/bioinfo/programas/metAMOS-1.5rc1/AMOS/Linux-x86_64/bin/OutputMotifs -b /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Scaffold/in/proba.bnk > /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Scaffold/out/p roba.motifs |2014-03-01 15:04:37| /home/bioinfo/programas/metAMOS-1.5rc1/AMOS/Linux-x86_64/bin/OutputResults -b /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Scaffold/in/proba.bnk -p /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Scaffold/out /proba |2014-03-01 15:04:37| /home/bioinfo/programas/metAMOS-1.5rc1/AMOS/Linux-x86_64/bin/OutputScaffolds -b /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Scaffold/in/proba.bnk > /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Scaffold/ou t/proba.scaffolds.final |2014-03-01 15:04:37| /home/bioinfo/programas/metAMOS-1.5rc1/AMOS/Linux-x86_64/bin/Linearize -b /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Scaffold/in/proba.bnk |2014-03-01 15:04:37| /home/bioinfo/programas/metAMOS-1.5rc1/AMOS/Linux-x86_64/bin/OutputResults -b /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Scaffold/in/proba.bnk -p /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Scaffold/out /proba.linearize |2014-03-01 15:04:37| /home/bioinfo/programas/metAMOS-1.5rc1/AMOS/Linux-x86_64/bin/OutputScaffolds -b /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Scaffold/in/proba.bnk > /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Scaffold/ou t/proba.linearize.scaffolds.final |2014-03-01 15:04:38|# [FINDSCAFFOLDORFS] |2014-03-01 15:04:40| /home/bioinfo/programas/metAMOS-1.5rc1/Utilities/cpp/Linux-x86_64/FragGeneScan -s /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Scaffold/out/proba.linearize.scaffolds.final -o /home/bioinfo/programas/metAMOS-1.5 rc1/Test/test1/FindScaffoldORFS/out/proba.orfs -w 0 -t complete |2014-03-01 15:04:40| cp /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindScaffoldORFS/out/proba.orfs.ffn /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindScaffoldORFS/out/proba.fna |2014-03-01 15:04:40| cp /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindScaffoldORFS/out/proba.orfs.faa /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindScaffoldORFS/out/proba.faa |2014-03-01 15:04:41|# [ABUNDANCE] |2014-03-01 15:04:41| ln -s /home/bioinfo/programas/metAMOS-1.5rc1/Utilities/DB//markers.pfasta /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Abundance/out/markers.pfasta |2014-03-01 15:04:42| /home/bioinfo/programas/metAMOS-1.5rc1/Utilities/cpp/Linux-x86_64/formatdb -p T -i /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Abundance/out/markers.pfasta |2014-03-01 15:04:47| /home/bioinfo/programas/metAMOS-1.5rc1/Utilities/cpp/Linux-x86_64/blastall -p blastp -i /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/proba.faa -d /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/A bundance/out/markers.pfasta -m 8 -b 10 -v 10 -a 15 -o /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Abundance/out/proba.blastp |2014-03-01 15:04:48| perl /home/bioinfo/programas/metAMOS-1.5rc1/Utilities/perl/metaphyler_contigs.pl /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Abundance/out/proba.blastp proba /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/F indORFS/out/proba.gene.cvg /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Abundance/out /home/bioinfo/programas/metAMOS-1.5rc1/Utilities |2014-03-01 15:04:53| perl /home/bioinfo/programas/metAMOS-1.5rc1/Utilities/perl/ImportMetaPhyler.pl -c -v -i -p /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Abundance/out/proba.taxprof.pct.txt:class |2014-03-01 15:04:54|# [PROPAGATE] |2014-03-01 15:04:54| ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Annotate/out/proba.annots /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Propagate/in/proba.annots |2014-03-01 15:04:54| cat /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Propagate/in/proba.annots | grep -v "\"" | grep -v contigID |sed s/utg//g |sed s/ctg//g > /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Propagate/in/proba.c lusters |2014-03-01 15:04:54| /home/bioinfo/programas/metAMOS-1.5rc1/AMOS/Linux-x8664/bin/FilterEdgesByCluster -b /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Scaffold/in/proba.bnk -clusters /home/bioinfo/programas/metAMOS-1.5rc1/Test/test 1/Propagate/in/proba.clusters -noRemoveEdges > /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Propagate/out/proba.clusters |2014-03-01 15:04:58|# [POSTPROCESS] |2014-03-01 15:04:58| unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/annotate.krona.html |2014-03-01 15:04:58| ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Annotate/out/report.krona.html /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/annotate.krona.html |2014-03-01 15:04:58| unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/abundance.krona.html |2014-03-01 15:04:58| ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Abundance/out/report.krona.html /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/abundance.krona.html |2014-03-01 15:04:58| unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/class.classified |2014-03-01 15:04:58| ln -s /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Classify/out /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/class.classified |2014-03-01 15:04:58| unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/asm.scores |2014-03-01 15:04:58| ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Validate/out/proba.lap /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/asm.scores |2014-03-01 15:04:58| unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/best.asm |2014-03-01 15:04:58| ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Validate/out/proba.asm.selected /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/best.asm |2014-03-01 15:04:58| unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/class.original.annots |2014-03-01 15:04:58| ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Annotate/out/proba.annots /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/class.original.annots |2014-03-01 15:04:58| unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/class.original.reads.annots |2014-03-01 15:04:58| ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Annotate/out/proba.reads.annots /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/class.original.reads.annots |2014-03-01 15:04:58| unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/class.propagated.annots |2014-03-01 15:04:58| unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/class.propagated.reads.annots |2014-03-01 15:04:58| cp /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Abundance/out/proba.classify.txt /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/. |2014-03-01 15:04:58| cp /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Scaffold/out/proba.linearize.scaffolds.final /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/proba.scf.fa |2014-03-01 15:04:58| cp /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Scaffold/out/proba.contigs /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/proba.ctg.fa |2014-03-01 15:04:58| cp /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Scaffold/out/proba.motifs /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/proba.motifs.fa |2014-03-01 15:04:58| ln -s /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Scaffold/in/proba.bnk /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/ |2014-03-01 15:04:58| ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/proba.fna /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/proba.orf.fna |2014-03-01 15:04:58| ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/proba.faa /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/proba.orf.faa |2014-03-01 15:04:58| ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindScaffoldORFS/out/proba.fna /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/proba.scf.orf.fna |2014-03-01 15:04:58| ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindScaffoldORFS/out/proba.faa /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/proba.scf.orf.faa |2014-03-01 15:04:58| unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/proba.lib1.contig.reads |2014-03-01 15:04:58| ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/proba.lib1contig.reads /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/proba.lib1.contig.reads |2014-03-01 15:04:58| unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/proba.lib1.unaligned.fasta |2014-03-01 15:04:58| ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/lib1.unaligned.fasta /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/proba.lib1.unaligned.fasta |2014-03-01 15:04:58| unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/proba.ctg.cnt |2014-03-01 15:04:58| ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/proba.contig.cnt /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/proba.ctg.cnt |2014-03-01 15:04:58| unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/proba.ctg.cvg |2014-03-01 15:04:58| ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/proba.contig.cvg /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/proba.ctg.cvg |2014-03-01 15:04:58| unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/html |2014-03-01 15:04:58| mkdir /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/html |2014-03-01 15:04:58| unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/html/class.classified |2014-03-01 15:04:58| ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/class.classified /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/html/class.classified |2014-03-01 15:04:58| unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/html/Annotate.html |2014-03-01 15:04:58| ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/annotate.krona.html /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/html/Annotate.html |2014-03-01 15:04:58| unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/html/Abundance.html |2014-03-01 15:04:58| ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/abundance.krona.html /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/html/Abundance.html |2014-03-01 15:04:58| touch /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/ref.name |2014-03-01 15:04:58| mv /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Preprocess/out/.fastqc /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/html |2014-03-01 15:04:58| unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/html/propagate.in.clusters |2014-03-01 15:04:58| ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Propagate/in/proba.clusters /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/html/propagate.in.clusters |2014-03-01 15:04:58| unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/html/propagate.out.clusters |2014-03-01 15:04:58| ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Propagate/out/proba.clusters /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/html/propagate.out.clusters |2014-03-01 15:04:58| unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/html/FunctionalAnnotation.html |2014-03-01 15:04:58| ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FunctionalAnnotation/out/ec.krona.html /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/html/FunctionalAnnotation.html |2014-03-01 15:04:58|# [CLASSIFY] |2014-03-01 15:04:59| perl -I /home/bioinfo/programas/metAMOS-1.5rc1/AMOS/Linux-x86_64/lib /home/bioinfo/programas/metAMOS-1.5rc1/Utilities/perl/statistics.pl /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/proba.scf.fa

/home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/html/asmstats.out

CLASSIFY.log: empty

POSPROCESS.log: unlink: não foi possível remover “/home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/annotate.krona.html”: Arquivo ou diretório não encontrado unlink: não foi possível remover “/home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/abundance.krona.html”: Arquivo ou diretório não encontrado unlink: não foi possível remover “/home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/class.classified”: Arquivo ou diretório não encontrado unlink: não foi possível remover “/home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/asm.scores”: Arquivo ou diretório não encontrado unlink: não foi possível remover “/home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/best.asm”: Arquivo ou diretório não encontrado unlink: não foi possível remover “/home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/class.original.annots”: Arquivo ou diretório não encontrado unlink: não foi possível remover “/home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/class.original.reads.annots”: Arquivo ou diretório não encontrado unlink: não foi possível remover “/home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/class.propagated.annots”: Arquivo ou diretório não encontrado unlink: não foi possível remover “/home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/class.propagated.reads.annots”: Arquivo ou diretório não encontrado unlink: não foi possível remover “/home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/proba.lib1.contig.reads”: Arquivo ou diretório não encontrado unlink: não foi possível remover “/home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/proba.lib1.unaligned.fasta”: Arquivo ou diretório não encontrado unlink: não foi possível remover “/home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/proba.ctg.cnt”: Arquivo ou diretório não encontrado unlink: não foi possível remover “/home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/proba.ctg.cvg”: Arquivo ou diretório não encontrado unlink: não foi possível remover “/home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/html”: Arquivo ou diretório não encontrado unlink: não foi possível remover “/home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/html/class.classified”: Arquivo ou diretório não encontrado unlink: não foi possível remover “/home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/html/Annotate.html”: Arquivo ou diretório não encontrado unlink: não foi possível remover “/home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/html/Abundance.html”: Arquivo ou diretório não encontrado mv: impossível obter estado de “/home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Preprocess/out/*.fastqc”: Arquivo ou diretório não encontrado unlink: não foi possível remover “/home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/html/propagate.in.clusters”: Arquivo ou diretório não encontrado unlink: não foi possível remover “/home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/html/propagate.out.clusters”: Arquivo ou diretório não encontrado unlink: não foi possível remover “/home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/html/FunctionalAnnotation.html”: Arquivo ou diretório não encontrado ln: acessando “/home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FunctionalAnnotation/out/ec.krona.html”: Arquivo ou diretório não encontrado

Arquivo ou diretorio nao encontrado same of File or directory not found

thanks

[skoren]

The issue must be a missing library or other error creating the HTML report. I posted a version of create_summary.py with more debug output on our ftp site at: ftp://cbcb.umd.edu/pub/data/sergek/create_summary.py Could you replace the one in Utilities/python/create_summary.py, remove the test1 directory, and re-run run_test.sh and post the output from runPipeline.

[danbacastro]

Thank you for your attention.

Output from runPipeline:

Project dir /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1 successfully created! Use runPipeline.py to start Pipeline

Starting Task = runpipeline.RUNPIPELINE *\ metAMOS running command: touch /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Preprocess/out/lib1.seq

** metAMOS running command: rm /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/.contig.cvg

*\ metAMOS running command: rm /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Logs/mapreads.ok

*\ metAMOS running command: rm /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Logs/propagate.ok

*\ metAMOS running command: touch /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Annotate/out/proba.annots

*\ metAMOS running command: touch /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Scaffold/out/proba.linearize.scaffolds.final

*\ metAMOS running command: touch /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/proba.faa

*\ metAMOS running command: rm /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Abundance/out/proba.taxprof.pct.txt

*\ metAMOS running command: rm /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Annotate/out/proba.hits

** metAMOS running command: rm /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/.faa

** metAMOS running command: rm /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/.fna

** metAMOS running command: rm /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/.faa

** metAMOS running command: rm /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/.fna

*\ metAMOS running command: rm /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Logs/assemble.ok

** metAMOS running command: rm /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/.asm.contig

*\ metAMOS running command: rm /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Logs/classify.ok

Starting metAMOS pipeline Found pysam in /home/bioinfo/.local/lib/python2.7/site-packages/pysam-0.6-py2.7-linux-x86_64.egg/pysam/init.pyc Found psutil in /home/bioinfo/.local/lib/python2.7/site-packages/psutil-0.6.1-py2.7-linux-x86_64.egg/psutil/init.pyc 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: Prokka is not found, some functionality will not be available Warning: SignalP+ is not found, some functionality will not be available Warning: metaphylerClassify is not found, some functionality will not be available Warning: PHmmer is not found, some functionality will not be available Warning: PhyloSift was not found, 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 Warning: MPI is not available, some functionality may not be available [Available RAM: 32 GB] [ There is 32 GB of RAM currently available on this machine, suggested minimum of 32 GB [ Enabling low MEM mode, might slow down some steps in pipeline [ If more RAM is available than what is listed above, please close down other programs and restart runPipeline [Available CPUs: 8] 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

---

Warning: Graphviz is not found, some functionality will not be available metAMOS configuration summary: metAMOS Version: v1.5rc1 "Praline Brownie" workflows: core Time and Date: 2014-03-02 Working directory: /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1 Prefix: proba K-Mer: 55 Threads: 15 Taxonomic level: class Verbose: True 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

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 /home/bioinfo/programas/metAMOS-1.5rc1/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 /home/bioinfo/programas/metAMOS-1.5rc1/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 /home/bioinfo/programas/metAMOS-1.5rc1/AMOS/Linux-x86_64/bin Koren S, Treangen TJ, Pop M. Bambus 2: scaffolding metagenomes. Bioinformatics 27(21): 2964-2971 2011.

[findorfs] FragGeneScan /home/bioinfo/programas/metAMOS-1.5rc1/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 /home/bioinfo/programas/metAMOS-1.5rc1/Utilities/cpp/Linux-x86_64/kraken/bin Wood DE, Salzberg SL. Rapid phylogenetic sequence classification through repeated exact alignment. In preparation.

[assemble] SOAPdenovo /home/bioinfo/programas/metAMOS-1.5rc1/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 /home/bioinfo/programas/metAMOS-1.5rc1/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 /home/bioinfo/programas/metAMOS-1.5rc1/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 /home/bioinfo/programas/metAMOS-1.5rc1/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 *\ metAMOS running command: java -cp /home/bioinfo/programas/metAMOS-1.5rc1/Utilities/java:.:. outputDefaultQuality /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Preprocess/in/carsonella_pe_filt.fna > /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Preprocess/in/carsonella_pe_filt.fna.qual

*\ metAMOS running command: rm /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Preprocess/out/all.seq.mates

*\ metAMOS running command: cp /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Preprocess/out/carsonella_pe_filt.fna /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Preprocess/out/lib1.seq

*\ metAMOS running command: cp /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Preprocess/out/carsonella_pe_filt.fna.qual /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Preprocess/out/lib1.seq.qual

*\ metAMOS running command: which python

*\ metAMOS running command: echo $PYTHONPATH

*\ metAMOS running command: perl /home/bioinfo/programas/metAMOS-1.5rc1/Utilities/perl/split_fasta.pl /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Preprocess/out/lib1.seq /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Preprocess/out/lib1.1.fasta /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Preprocess/out/lib1.2.fasta

*\ metAMOS running command: perl /home/bioinfo/programas/metAMOS-1.5rc1/Utilities/perl/split_fasta.pl /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Preprocess/out/lib1.seq.qual /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Preprocess/out/lib1.1.fasta.qual /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Preprocess/out/lib1.2.fasta.qual

*\ metAMOS running command: ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Preprocess/out/lib1.seq /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Preprocess/out/lib1.fasta

*\ metAMOS running command: java -cp /home/bioinfo/programas/metAMOS-1.5rc1/Utilities/java:. convertFastaAndQualToFastq /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Preprocess/out/lib1.seq /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Preprocess/out/lib1.seq.qual > /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Preprocess/out/lib1.fastq

*\ metAMOS running command: java -cp /home/bioinfo/programas/metAMOS-1.5rc1/Utilities/java:. convertFastaAndQualToFastq /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Preprocess/out/lib1.1.fasta /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Preprocess/out/lib1.1.fasta.qual > /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Preprocess/out/lib1.1.fastq

*\ metAMOS running command: java -cp /home/bioinfo/programas/metAMOS-1.5rc1/Utilities/java:. convertFastaAndQualToFastq /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Preprocess/out/lib1.2.fasta /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Preprocess/out/lib1.2.fasta.qual > /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Preprocess/out/lib1.2.fastq

*\ metAMOS running command: touch /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Preprocess/out/preprocess.success

Job  = [[carsonella_pe_filt.fna] -> preprocess.success] completed

Completed Task = preprocess.Preprocess Starting Task = assemble.ASSEMBLE *\ metAMOS running command: touch /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/soapdenovo.55.run

Job  = [preprocess.success -> *.run] completed

Completed Task = assemble.SplitAssemblers *\ metAMOS running command: cat /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/soapconfig.txt |grep -v max_rd_len > /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/soap2config.txt

*\ metAMOS running command: /home/bioinfo/programas/metAMOS-1.5rc1/Utilities/cpp/Linux-x86_64/SOAPdenovo-63mer pregraph -p 15 -K 55 -R -D -s /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/soapconfig.txt -o /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/soapdenovo.55.asm

*\ metAMOS running command: /home/bioinfo/programas/metAMOS-1.5rc1/Utilities/cpp/Linux-x86_64/SOAPdenovo-63mer contig -g /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/soapdenovo.55.asm -R -M 3

Job  = [soapdenovo.55.run -> soapdenovo.55.asm.contig] completed

Completed Task = assemble.Assemble *\ metAMOS running command: mv /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/soapdenovo.55.asm.contig /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/soapdenovo.55.asm.contigWIUPAC.fa

*\ metAMOS running command: java -cp /home/bioinfo/programas/metAMOS-1.5rc1/Utilities/java:. RemoveIUPAC /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/soapdenovo.55.asm.contigWIUPAC.fa >/home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/soapdenovo.55.asm.contig

*\ metAMOS running command: rm /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/soapdenovo.55.run

*\ metAMOS running command: touch /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/assemble.success

Job  = [[soapdenovo.55.asm.contig] -> [assemble.ok]] completed

Completed Task = assemble.CheckAsmResults Uptodate Task = assemble.SplitMappers *\ metAMOS running command: rm -f /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/soapdenovo.55.contigdict

Starting Task = mapreads.MAPREADS *\ metAMOS running command: /home/bioinfo/programas/metAMOS-1.5rc1/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/soapdenovo.55.asm.contig /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/soapdenovo.55.IDX

*\ metAMOS running command: /home/bioinfo/programas/metAMOS-1.5rc1/Utilities/cpp/Linux-x86_64/bowtie -p 15 -f -l 25 -e 140 --best --strata -m 10 -k 1 --un /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/soapdenovo.55.lib1.unaligned.fasta /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/soapdenovo.55.IDX /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Preprocess/out/lib1.seq > /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/lib1.bout

*\ metAMOS running command: cat /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/soapdenovo.55.lib1.mappedmates >> /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/soapdenovo.55.lib1.hdr

*\ metAMOS running command: cp /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/soapdenovo.55.lib1.hdr /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/soapdenovo.55.lib1.mappedmates

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 Starting Task = findorfs.FINDORFS *\ metAMOS running command: unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/in/soapdenovo.55.asm.contig

*\ metAMOS running command: ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/soapdenovo.55.asm.contig /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/in/soapdenovo.55.asm.contig

*\ metAMOS running command: /home/bioinfo/programas/metAMOS-1.5rc1/Utilities/cpp/Linux-x86_64/FragGeneScan -s /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/in/soapdenovo.55.asm.contig -o /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/soapdenovo.55.orfs -w 0 -t complete

*\ metAMOS running command: mv /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/soapdenovo.55.orfs.ffn /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/soapdenovo.55.ctg.fna

*\ metAMOS running command: mv /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/soapdenovo.55.orfs.faa /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/soapdenovo.55.ctg.faa

*\ metAMOS running command: mv /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/soapdenovo.55.gene.cvg /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/soapdenovo.55.ctg.gene.cvg

*\ metAMOS running command: mv /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/soapdenovo.55.gene.map /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/soapdenovo.55.ctg.gene.map

*\ metAMOS running command: rm -r /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/soapdenovo.55.fna

** metAMOS running command: cat /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/soapdenovo.55.fna > /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/soapdenovo.55.fna

*\ metAMOS running command: rm -r /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/soapdenovo.55.fna.bnk

*\ metAMOS running command: /home/bioinfo/programas/metAMOS-1.5rc1/AMOS/Linux-x86_64/bin/toAmos_new -s /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/soapdenovo.55.fna -b /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/soapdenovo.55.fna.bnk

*\ metAMOS running command: rm -r /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/soapdenovo.55.faa

** metAMOS running command: cat /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/soapdenovo.55.faa > /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/soapdenovo.55.faa

*\ metAMOS running command: rm -r /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/soapdenovo.55.faa.bnk

*\ metAMOS running command: /home/bioinfo/programas/metAMOS-1.5rc1/AMOS/Linux-x86_64/bin/toAmos_new -s /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/soapdenovo.55.faa -b /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/soapdenovo.55.faa.bnk

*\ metAMOS running command: rm -r /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/soapdenovo.55.gene.cvg

** metAMOS running command: cat /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/soapdenovo.55.gene.cvg > /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/soapdenovo.55.gene.cvg

*\ metAMOS running command: rm -r /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/soapdenovo.55.gene.map

** metAMOS running command: cat /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/soapdenovo.55.gene.map > /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/soapdenovo.55.gene.map

*\ metAMOS running command: ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/soapdenovo.55.faa /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/soapdenovo.55.faa

*\ metAMOS running command: ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/soapdenovo.55.fna /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/soapdenovo.55.fna

Job  = [soapdenovo.55.contig.cvg -> soapdenovo.55.faa] completed

Completed Task = findorfs.FindORFS Starting Task = validate.VALIDATE *\ metAMOS running command: touch /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Logs/validate.skip

*\ metAMOS running command: unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/proba.asm.contig

*\ metAMOS running command: ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/soapdenovo.55.asm.contig /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/proba.asm.contig

*\ metAMOS running command: unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/proba.linearize.scaffolds.final

*\ metAMOS running command: ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/soapdenovo.55.asm.contig /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/proba.linearize.scaffolds.final

*\ metAMOS running command: unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/proba.asm.tigr

*\ metAMOS running command: ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/soapdenovo.55.asm.tigr /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/proba.asm.tigr

*\ metAMOS running command: unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/proba.contig.cnt

*\ metAMOS running command: ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/soapdenovo.55.contig.cnt /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/proba.contig.cnt

*\ metAMOS running command: unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/proba.contig.cvg

*\ metAMOS running command: ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/soapdenovo.55.contig.cvg /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/proba.contig.cvg

*\ metAMOS running command: unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/proba.afg

*\ metAMOS running command: rm /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Logs/findorfs.ok

*\ metAMOS running command: unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/in/proba.asm.contig

*\ metAMOS running command: ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/proba.asm.contig /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/in/proba.asm.contig

*\ metAMOS running command: /home/bioinfo/programas/metAMOS-1.5rc1/Utilities/cpp/Linux-x86_64/FragGeneScan -s /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/in/proba.asm.contig -o /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/proba.orfs -w 0 -t complete

*\ metAMOS running command: mv /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/proba.orfs.ffn /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/proba.ctg.fna

*\ metAMOS running command: mv /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/proba.orfs.faa /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/proba.ctg.faa

*\ metAMOS running command: mv /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/proba.gene.cvg /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/proba.ctg.gene.cvg

*\ metAMOS running command: mv /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/proba.gene.map /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/proba.ctg.gene.map

*\ metAMOS running command: rm -r /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/proba.fna

** metAMOS running command: cat /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/proba.fna > /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/proba.fna

*\ metAMOS running command: rm -r /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/proba.fna.bnk

*\ metAMOS running command: /home/bioinfo/programas/metAMOS-1.5rc1/AMOS/Linux-x86_64/bin/toAmos_new -s /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/proba.fna -b /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/proba.fna.bnk

*\ metAMOS running command: rm -r /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/proba.faa

** metAMOS running command: cat /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/proba.faa > /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/proba.faa

*\ metAMOS running command: rm -r /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/proba.faa.bnk

*\ metAMOS running command: /home/bioinfo/programas/metAMOS-1.5rc1/AMOS/Linux-x86_64/bin/toAmos_new -s /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/proba.faa -b /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/proba.faa.bnk

*\ metAMOS running command: rm -r /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/proba.gene.cvg

** metAMOS running command: cat /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/proba.gene.cvg > /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/proba.gene.cvg

*\ metAMOS running command: rm -r /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/proba.gene.map

** metAMOS running command: cat /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/proba.gene.map > /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/proba.gene.map

*\ metAMOS running command: ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/proba.faa /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/proba.faa

*\ metAMOS running command: ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/proba.fna /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/proba.fna

*\ metAMOS running command: touch /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Logs/findorfs.ok

*\ metAMOS running command: unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/proba.faa

*\ metAMOS running command: ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/proba.faa /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/proba.faa

*\ metAMOS running command: unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindRepeats/in/proba.fna

*\ metAMOS running command: ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/proba.fna /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindRepeats/in/proba.fna

*\ metAMOS running command: unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindRepeats/in/proba.faa

*\ metAMOS running command: ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/proba.faa /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindRepeats/in/proba.faa

*\ metAMOS running command: unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Annotate/in/proba.fna

*\ metAMOS running command: ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/proba.fna /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Annotate/in/proba.fna

*\ metAMOS running command: unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Annotate/in/proba.faa

*\ metAMOS running command: ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/proba.faa /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Annotate/in/proba.faa

*\ metAMOS running command: unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/proba.lib1.badmates

*\ metAMOS running command: ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/soapdenovo.55.lib1.badmates /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/proba.lib1.badmates

*\ metAMOS running command: unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/proba.lib1.hdr

*\ metAMOS running command: ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/soapdenovo.55.lib1.hdr /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/proba.lib1.hdr

*\ metAMOS running command: unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/proba.lib1.mappedmates

*\ metAMOS running command: ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/soapdenovo.55.lib1.mappedmates /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/proba.lib1.mappedmates

*\ metAMOS running command: unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/proba.lib1.mates_in_diff_contigs

*\ metAMOS running command: ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/soapdenovo.55.lib1.mates_in_diff_contigs /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/proba.lib1.mates_in_diff_contigs

*\ metAMOS running command: unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/proba.lib1contig.reads

*\ metAMOS running command: ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/soapdenovo.55.lib1contig.reads /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/proba.lib1contig.reads

*\ metAMOS running command: unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/lib1.unaligned.fasta

*\ metAMOS running command: ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/soapdenovo.55.lib1.unaligned.fasta /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/lib1.unaligned.fasta

*\ metAMOS running command: unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/lib1.unaligned.fastq

Job  = [[soapdenovo.55.faa] -> [validate.ok]] completed

Completed Task = validate.Validate Starting Task = findrepeats.FINDREPEATS *\ metAMOS running command: touch /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Logs/findrepeats.skip

Job  = [proba.fna -> proba.repeats] completed

Completed Task = findreps.FindRepeats Starting Task = annotate.ANNOTATE *\ metAMOS running command: touch /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Annotate/out/proba.annots

*\ metAMOS running command: unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Annotate/in/proba.asm.contig

*\ metAMOS running command: ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/proba.asm.contig /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Annotate/in/proba.asm.contig

*\ metAMOS running command: unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Annotate/out/proba.hits

** metAMOS running command: rm -f /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Annotate/out/.hits

** metAMOS running command: rm -f /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Annotate/out/.epsilon-nb_results.txt

** metAMOS running command: rm -f /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Annotate/out/.phymm.out

*\ metAMOS running command: /home/bioinfo/programas/metAMOS-1.5rc1/Utilities/cpp/Linux-x86_64/kraken/bin/kraken --threads 15 -db /home/bioinfo/programas/metAMOS-1.5rc1/Utilities/DB//kraken --output /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Annotate/out/proba.hits /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Annotate/in/proba.asm.contig --preload

*\ metAMOS running command: perl /home/bioinfo/programas/metAMOS-1.5rc1/Utilities/perl/ImportKraken.pl -c -i -f /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Annotate/in/proba.asm.contig /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Annotate/out/proba.hits:/home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/proba.contig.cnt:class

*\ metAMOS running command: unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/in/proba.hits

*\ metAMOS running command: unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/proba.hits

*\ metAMOS running command: ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Annotate/out/proba.hits /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/in/proba.hits

*\ metAMOS running command: ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Annotate/out/proba.hits /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/proba.hits

Job  = [proba.faa -> proba.hits] completed

Completed Task = annotate.Annotate Starting Task = functionalannotation.FUNCTIONALANNOTATION *\ metAMOS running command: touch /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Logs/functionalannotation.skip

*\ metAMOS running command: touch /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FunctionalAnnotation/out/blast.out

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

Completed Task = fannotate.FunctionalAnnotation Starting Task = scaffold.SCAFFOLD *\ metAMOS running command: rm -rf /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Scaffold/in/proba.bnk

*\ metAMOS running command: /home/bioinfo/programas/metAMOS-1.5rc1/AMOS/Linux-x86_64/bin/toAmos_new -s /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Preprocess/out/lib1.seq -m /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/proba.lib1.mappedmates -b /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Scaffold/in/proba.bnk

*\ metAMOS running command: /home/bioinfo/programas/metAMOS-1.5rc1/AMOS/Linux-x86_64/bin/toAmos_new -c /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/proba.asm.tigr -b /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Scaffold/in/proba.bnk

*\ metAMOS running command: /home/bioinfo/programas/metAMOS-1.5rc1/AMOS/Linux-x86_64/bin/asmQC -b /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Scaffold/in/proba.bnk -scaff -recompute -update -numsd 2

*\ metAMOS running command: perl /home/bioinfo/programas/metAMOS-1.5rc1/AMOS/Linux-x86_64/bin/bank-unlock /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Scaffold/in/proba.bnk

*\ metAMOS running command: /home/bioinfo/programas/metAMOS-1.5rc1/AMOS/Linux-x86_64/bin/clk -b /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Scaffold/in/proba.bnk

*\ metAMOS running command: /home/bioinfo/programas/metAMOS-1.5rc1/AMOS/Linux-x86_64/bin/Bundler -b /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Scaffold/in/proba.bnk

*\ metAMOS running command: /home/bioinfo/programas/metAMOS-1.5rc1/AMOS/Linux-x86_64/bin/MarkRepeats -redundancy 50 -b /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Scaffold/in/proba.bnk > /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Scaffold/in/proba.reps

*\ metAMOS running command: /home/bioinfo/programas/metAMOS-1.5rc1/AMOS/Linux-x86_64/bin/OrientContigs -minRedundancy 5 -all -redundancy 10 -b /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Scaffold/in/proba.bnk -repeats /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Scaffold/in/proba.reps

*\ metAMOS running command: /home/bioinfo/programas/metAMOS-1.5rc1/AMOS/Linux-x86_64/bin/bank2fasta -eid -b /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Scaffold/in/proba.bnk > /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Scaffold/out/proba.contigs

*\ metAMOS running command: /home/bioinfo/programas/metAMOS-1.5rc1/AMOS/Linux-x86_64/bin/OutputMotifs -b /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Scaffold/in/proba.bnk > /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Scaffold/out/proba.motifs

*\ metAMOS running command: /home/bioinfo/programas/metAMOS-1.5rc1/AMOS/Linux-x86_64/bin/OutputResults -b /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Scaffold/in/proba.bnk -p /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Scaffold/out/proba

*\ metAMOS running command: /home/bioinfo/programas/metAMOS-1.5rc1/AMOS/Linux-x86_64/bin/OutputScaffolds -b /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Scaffold/in/proba.bnk > /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Scaffold/out/proba.scaffolds.final

*\ metAMOS running command: /home/bioinfo/programas/metAMOS-1.5rc1/AMOS/Linux-x86_64/bin/Linearize -b /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Scaffold/in/proba.bnk

*\ metAMOS running command: /home/bioinfo/programas/metAMOS-1.5rc1/AMOS/Linux-x86_64/bin/OutputResults -b /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Scaffold/in/proba.bnk -p /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Scaffold/out/proba.linearize

*\ metAMOS running command: /home/bioinfo/programas/metAMOS-1.5rc1/AMOS/Linux-x86_64/bin/OutputScaffolds -b /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Scaffold/in/proba.bnk > /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Scaffold/out/proba.linearize.scaffolds.final

Job  = [[proba.asm.contig] -> scaffold.ok] completed

Completed Task = scaffold.Scaffold Starting Task = findscaffoldorfs.FINDSCAFFOLDORFS *\ metAMOS running command: /home/bioinfo/programas/metAMOS-1.5rc1/Utilities/cpp/Linux-x86_64/FragGeneScan -s /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Scaffold/out/proba.linearize.scaffolds.final -o /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindScaffoldORFS/out/proba.orfs -w 0 -t complete

*\ metAMOS running command: cp /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindScaffoldORFS/out/proba.orfs.ffn /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindScaffoldORFS/out/proba.fna

*\ metAMOS running command: cp /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindScaffoldORFS/out/proba.orfs.faa /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindScaffoldORFS/out/proba.faa

Job  = [proba.linearize.scaffolds.final -> proba.fna] completed

Completed Task = findscforfs.FindScaffoldORFS Starting Task = abundance.ABUNDANCE *\ metAMOS running command: ln -s /home/bioinfo/programas/metAMOS-1.5rc1/Utilities/DB//markers.pfasta /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Abundance/out/markers.pfasta

*\ metAMOS running command: /home/bioinfo/programas/metAMOS-1.5rc1/Utilities/cpp/Linux-x86_64/formatdb -p T -i /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Abundance/out/markers.pfasta

*\ metAMOS running command: /home/bioinfo/programas/metAMOS-1.5rc1/Utilities/cpp/Linux-x86_64/blastall -p blastp -i /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/proba.faa -d /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Abundance/out/markers.pfasta -m 8 -b 10 -v 10 -a 15 -o /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Abundance/out/proba.blastp

*\ metAMOS running command: perl /home/bioinfo/programas/metAMOS-1.5rc1/Utilities/perl/metaphyler_contigs.pl /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Abundance/out/proba.blastp proba /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/proba.gene.cvg /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Abundance/out /home/bioinfo/programas/metAMOS-1.5rc1/Utilities

*\ metAMOS running command: perl /home/bioinfo/programas/metAMOS-1.5rc1/Utilities/perl/ImportMetaPhyler.pl -c -v -i -p /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Abundance/out/proba.taxprof.pct.txt:class

Job  = [proba.asm.contig -> proba.taxprof.pct.txt] completed

Completed Task = abundance.Abundance Starting Task = propagate.PROPAGATE *\ metAMOS running command: ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Annotate/out/proba.annots /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Propagate/in/proba.annots

*\ metAMOS running command: cat /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Propagate/in/proba.annots | grep -v "\"" | grep -v contigID |sed s/utg//g |sed s/ctg//g > /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Propagate/in/proba.clusters

*\ metAMOS running command: /home/bioinfo/programas/metAMOS-1.5rc1/AMOS/Linux-x86_64/bin/FilterEdgesByCluster -b /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Scaffold/in/proba.bnk -clusters /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Propagate/in/proba.clusters -noRemoveEdges > /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Propagate/out/proba.clusters

Job  = [proba.annots -> propagate.ok] completed

Completed Task = propagate.Propagate Job = [proba.clusters -> classify.ok] completed Completed Task = classify.Classify Starting Task = postprocess.POSTPROCESS *\ metAMOS running command: unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/annotate.krona.html

*\ metAMOS running command: ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Annotate/out/report.krona.html /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/annotate.krona.html

*\ metAMOS running command: unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/abundance.krona.html

*\ metAMOS running command: ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Abundance/out/report.krona.html /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/abundance.krona.html

*\ metAMOS running command: unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/class.classified

*\ metAMOS running command: ln -s /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Classify/out /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/class.classified

*\ metAMOS running command: unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/asm.scores

*\ metAMOS running command: ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Validate/out/proba.lap /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/asm.scores

*\ metAMOS running command: unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/best.asm

*\ metAMOS running command: ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Validate/out/proba.asm.selected /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/best.asm

*\ metAMOS running command: unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/class.original.annots

*\ metAMOS running command: ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Annotate/out/proba.annots /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/class.original.annots

*\ metAMOS running command: unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/class.original.reads.annots

*\ metAMOS running command: ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Annotate/out/proba.reads.annots /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/class.original.reads.annots

*\ metAMOS running command: unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/class.propagated.annots

*\ metAMOS running command: unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/class.propagated.reads.annots

*\ metAMOS running command: cp /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Abundance/out/proba.classify.txt /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/.

*\ metAMOS running command: cp /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Scaffold/out/proba.linearize.scaffolds.final /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/proba.scf.fa

*\ metAMOS running command: cp /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Scaffold/out/proba.contigs /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/proba.ctg.fa

*\ metAMOS running command: cp /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Scaffold/out/proba.motifs /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/proba.motifs.fa

*\ metAMOS running command: ln -s /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Scaffold/in/proba.bnk /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/

*\ metAMOS running command: ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/proba.fna /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/proba.orf.fna

*\ metAMOS running command: ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/proba.faa /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/proba.orf.faa

*\ metAMOS running command: ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindScaffoldORFS/out/proba.fna /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/proba.scf.orf.fna

*\ metAMOS running command: ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindScaffoldORFS/out/proba.faa /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/proba.scf.orf.faa

*\ metAMOS running command: unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/proba.lib1.contig.reads

*\ metAMOS running command: ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/proba.lib1contig.reads /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/proba.lib1.contig.reads

*\ metAMOS running command: unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/proba.lib1.unaligned.fasta

*\ metAMOS running command: ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/lib1.unaligned.fasta /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/proba.lib1.unaligned.fasta

*\ metAMOS running command: unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/proba.ctg.cnt

*\ metAMOS running command: ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/proba.contig.cnt /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/proba.ctg.cnt

*\ metAMOS running command: unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/proba.ctg.cvg

*\ metAMOS running command: ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/proba.contig.cvg /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/proba.ctg.cvg

*\ metAMOS running command: unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/html

*\ metAMOS running command: mkdir /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/html

*\ metAMOS running command: unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/html/class.classified

*\ metAMOS running command: ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/class.classified /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/html/class.classified

*\ metAMOS running command: unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/html/Annotate.html

*\ metAMOS running command: ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/annotate.krona.html /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/html/Annotate.html

*\ metAMOS running command: unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/html/Abundance.html

*\ metAMOS running command: ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/abundance.krona.html /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/html/Abundance.html

*\ metAMOS running command: touch /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/ref.name

** metAMOS running command: mv /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Preprocess/out/.fastqc /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/html

*\ metAMOS running command: unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/html/propagate.in.clusters

*\ metAMOS running command: ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Propagate/in/proba.clusters /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/html/propagate.in.clusters

*\ metAMOS running command: unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/html/propagate.out.clusters

*\ metAMOS running command: ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Propagate/out/proba.clusters /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/html/propagate.out.clusters

*\ metAMOS running command: unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/html/FunctionalAnnotation.html

*\ metAMOS running command: ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FunctionalAnnotation/out/ec.krona.html /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/html/FunctionalAnnotation.html

Starting Task = classify.CLASSIFY *\ metAMOS running command: perl -I /home/bioinfo/programas/metAMOS-1.5rc1/AMOS/Linux-x86_64/lib /home/bioinfo/programas/metAMOS-1.5rc1/Utilities/perl/statistics.pl /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/proba.scf.fa > /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/html/asmstats.out

Asm stats done Version done Steps init done Plots done Asm counts done Oops, MetAMOS finished with errors! see text in red above for details.

Thanks again!

[treangen]

Looks like the error is in the call to get_classify_stats, best guess is propagate.in.clusters (or tax_key.tab) is missing/empty. Can you try running the following command (& send the result):

python /home/bioinfo/programas/metAMOS-1.5rc1/Utilities/python/get_classify_stats.py /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/html/propagate.in.clusters /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/html/propagate.out.clusters /home/bioinfo/programas/metAMOS-1.5rc1/Utilities/DB/tax_key.tab /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/html/ Classify.html Propagate.html class

[danbacastro]

This command has no output and I looked for Classify.html, Propagate.html, tax_key.tab, propagate.out.clusters and propagate.in.clusters files, all they exist.

Maybe it's a missing lib of Lubuntu. I was using Ubuntu and it was ok.

Thanks

[danbacastro]

I was running each script in the Python folder and seems that I don't have the utils package (code from the top of create_summary.py):

import sys, os, string, locale ROOT = os.path.dirname(os.path.abspath(file)) Traceback (most recent call last): File "", line 1, in NameError: name 'file' is not defined

sys.path.insert(0, os.path.join(ROOT, '..'))

... #sys.path.append(ROOT+"/lib") ... import markup from pygooglechart import StackedVerticalBarChart from pygooglechart import PieChart2D from pygooglechart import PieChart3D from pygooglechart import Axis from pygooglechart import StackedHorizontalBarChart, StackedVerticalBarChart, \ ... GroupedHorizontalBarChart, GroupedVerticalBarChart

import settings from utils import * Traceback (most recent call last): File "", line 1, in ImportError: No module named utils import helper

Could it be the error?

Thanks

[skoren]

Hi,

No the utils module is part of metAMOS's src directory which gets added to your python path by runPipeline so it is available when create_summary.py runs inside runPipeline. I posted an updated runPipeline.py that should give more details on your error: ftp://cbcb.umd.edu/pub/data/sergek/runPipeline.py Could you replace the version you have in src and re-run python INSTALL.py and post the output from run_test.sh?

[danbacastro]

Project dir /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1 successfully created! Use runPipeline.py to start Pipeline

Starting Task = runpipeline.RUNPIPELINE *\ metAMOS running command: touch /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Preprocess/out/lib1.seq

** metAMOS running command: rm /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/.contig.cvg

*\ metAMOS running command: rm /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Logs/mapreads.ok

*\ metAMOS running command: rm /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Logs/propagate.ok

*\ metAMOS running command: touch /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Annotate/out/proba.annots

*\ metAMOS running command: touch /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Scaffold/out/proba.linearize.scaffolds.final

*\ metAMOS running command: touch /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/proba.faa

*\ metAMOS running command: rm /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Abundance/out/proba.taxprof.pct.txt

*\ metAMOS running command: rm /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Annotate/out/proba.hits

** metAMOS running command: rm /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/.faa

** metAMOS running command: rm /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/.fna

** metAMOS running command: rm /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/.faa

** metAMOS running command: rm /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/.fna

*\ metAMOS running command: rm /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Logs/assemble.ok

** metAMOS running command: rm /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/.asm.contig

*\ metAMOS running command: rm /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Logs/classify.ok

Starting metAMOS pipeline Found pysam in /home/bioinfo/.local/lib/python2.7/site-packages/pysam-0.6-py2.7-linux-x86_64.egg/pysam/init.pyc Found psutil in /home/bioinfo/.local/lib/python2.7/site-packages/psutil-0.6.1-py2.7-linux-x86_64.egg/psutil/init.pyc 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: metaphylerClassify is not found, some functionality will not be available Warning: PHmmer is not found, some functionality will not be available Warning: PhyloSift was not found, 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 Warning: MPI is not available, some functionality may not be available [Available RAM: 25 GB] [ There is 25 GB of RAM currently available on this machine, suggested minimum of 32 GB [ Enabling low MEM mode, might slow down some steps in pipeline [ If more RAM is available than what is listed above, please close down other programs and restart runPipeline [Available CPUs: 8] 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

---

Warning: Graphviz is not found, some functionality will not be available metAMOS configuration summary: metAMOS Version: v1.5rc1 "Praline Brownie" workflows: core Time and Date: 2014-03-03 Working directory: /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1 Prefix: proba K-Mer: 55 Threads: 15 Taxonomic level: class Verbose: True 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

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 /home/bioinfo/programas/metAMOS-1.5rc1/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 /home/bioinfo/programas/metAMOS-1.5rc1/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 /home/bioinfo/programas/metAMOS-1.5rc1/AMOS/Linux-x86_64/bin Koren S, Treangen TJ, Pop M. Bambus 2: scaffolding metagenomes. Bioinformatics 27(21): 2964-2971 2011.

[findorfs] FragGeneScan /home/bioinfo/programas/metAMOS-1.5rc1/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 /home/bioinfo/programas/metAMOS-1.5rc1/Utilities/cpp/Linux-x86_64/kraken/bin Wood DE, Salzberg SL. Rapid phylogenetic sequence classification through repeated exact alignment. In preparation.

[assemble] SOAPdenovo /home/bioinfo/programas/metAMOS-1.5rc1/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 /home/bioinfo/programas/metAMOS-1.5rc1/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 /home/bioinfo/programas/metAMOS-1.5rc1/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 /home/bioinfo/programas/metAMOS-1.5rc1/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 *\ metAMOS running command: java -cp /home/bioinfo/programas/metAMOS-1.5rc1/Utilities/java:.:. outputDefaultQuality /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Preprocess/in/carsonella_pe_filt.fna > /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Preprocess/in/carsonella_pe_filt.fna.qual

*\ metAMOS running command: rm /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Preprocess/out/all.seq.mates

*\ metAMOS running command: cp /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Preprocess/out/carsonella_pe_filt.fna /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Preprocess/out/lib1.seq

*\ metAMOS running command: cp /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Preprocess/out/carsonella_pe_filt.fna.qual /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Preprocess/out/lib1.seq.qual

*\ metAMOS running command: which python

*\ metAMOS running command: echo $PYTHONPATH

*\ metAMOS running command: perl /home/bioinfo/programas/metAMOS-1.5rc1/Utilities/perl/split_fasta.pl /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Preprocess/out/lib1.seq /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Preprocess/out/lib1.1.fasta /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Preprocess/out/lib1.2.fasta

*\ metAMOS running command: perl /home/bioinfo/programas/metAMOS-1.5rc1/Utilities/perl/split_fasta.pl /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Preprocess/out/lib1.seq.qual /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Preprocess/out/lib1.1.fasta.qual /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Preprocess/out/lib1.2.fasta.qual

*\ metAMOS running command: ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Preprocess/out/lib1.seq /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Preprocess/out/lib1.fasta

*\ metAMOS running command: java -cp /home/bioinfo/programas/metAMOS-1.5rc1/Utilities/java:. convertFastaAndQualToFastq /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Preprocess/out/lib1.seq /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Preprocess/out/lib1.seq.qual > /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Preprocess/out/lib1.fastq

*\ metAMOS running command: java -cp /home/bioinfo/programas/metAMOS-1.5rc1/Utilities/java:. convertFastaAndQualToFastq /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Preprocess/out/lib1.1.fasta /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Preprocess/out/lib1.1.fasta.qual > /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Preprocess/out/lib1.1.fastq

*\ metAMOS running command: java -cp /home/bioinfo/programas/metAMOS-1.5rc1/Utilities/java:. convertFastaAndQualToFastq /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Preprocess/out/lib1.2.fasta /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Preprocess/out/lib1.2.fasta.qual > /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Preprocess/out/lib1.2.fastq

*\ metAMOS running command: touch /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Preprocess/out/preprocess.success

Job  = [[carsonella_pe_filt.fna] -> preprocess.success] completed

Completed Task = preprocess.Preprocess Starting Task = assemble.ASSEMBLE *\ metAMOS running command: touch /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/soapdenovo.55.run

Job  = [preprocess.success -> *.run] completed

Completed Task = assemble.SplitAssemblers *\ metAMOS running command: cat /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/soapconfig.txt |grep -v max_rd_len > /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/soap2config.txt

*\ metAMOS running command: /home/bioinfo/programas/metAMOS-1.5rc1/Utilities/cpp/Linux-x86_64/SOAPdenovo-63mer pregraph -p 15 -K 55 -R -D -s /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/soapconfig.txt -o /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/soapdenovo.55.asm

*\ metAMOS running command: /home/bioinfo/programas/metAMOS-1.5rc1/Utilities/cpp/Linux-x86_64/SOAPdenovo-63mer contig -g /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/soapdenovo.55.asm -R -M 3

Job  = [soapdenovo.55.run -> soapdenovo.55.asm.contig] completed

Completed Task = assemble.Assemble *\ metAMOS running command: mv /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/soapdenovo.55.asm.contig /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/soapdenovo.55.asm.contigWIUPAC.fa

*\ metAMOS running command: java -cp /home/bioinfo/programas/metAMOS-1.5rc1/Utilities/java:. RemoveIUPAC /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/soapdenovo.55.asm.contigWIUPAC.fa >/home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/soapdenovo.55.asm.contig

*\ metAMOS running command: rm /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/soapdenovo.55.run

*\ metAMOS running command: touch /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/assemble.success

Job  = [[soapdenovo.55.asm.contig] -> [assemble.ok]] completed

Completed Task = assemble.CheckAsmResults Uptodate Task = assemble.SplitMappers *\ metAMOS running command: rm -f /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/soapdenovo.55.contigdict

Starting Task = mapreads.MAPREADS *\ metAMOS running command: /home/bioinfo/programas/metAMOS-1.5rc1/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/soapdenovo.55.asm.contig /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/soapdenovo.55.IDX

*\ metAMOS running command: /home/bioinfo/programas/metAMOS-1.5rc1/Utilities/cpp/Linux-x86_64/bowtie -p 15 -f -l 25 -e 140 --best --strata -m 10 -k 1 --un /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/soapdenovo.55.lib1.unaligned.fasta /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/soapdenovo.55.IDX /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Preprocess/out/lib1.seq > /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/lib1.bout

*\ metAMOS running command: cat /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/soapdenovo.55.lib1.mappedmates >> /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/soapdenovo.55.lib1.hdr

*\ metAMOS running command: cp /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/soapdenovo.55.lib1.hdr /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/soapdenovo.55.lib1.mappedmates

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 Starting Task = findorfs.FINDORFS *\ metAMOS running command: unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/in/soapdenovo.55.asm.contig

*\ metAMOS running command: ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/soapdenovo.55.asm.contig /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/in/soapdenovo.55.asm.contig

*\ metAMOS running command: /home/bioinfo/programas/metAMOS-1.5rc1/Utilities/cpp/Linux-x86_64/FragGeneScan -s /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/in/soapdenovo.55.asm.contig -o /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/soapdenovo.55.orfs -w 0 -t complete

*\ metAMOS running command: mv /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/soapdenovo.55.orfs.ffn /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/soapdenovo.55.ctg.fna

*\ metAMOS running command: mv /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/soapdenovo.55.orfs.faa /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/soapdenovo.55.ctg.faa

*\ metAMOS running command: mv /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/soapdenovo.55.gene.cvg /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/soapdenovo.55.ctg.gene.cvg

*\ metAMOS running command: mv /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/soapdenovo.55.gene.map /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/soapdenovo.55.ctg.gene.map

*\ metAMOS running command: rm -r /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/soapdenovo.55.fna

** metAMOS running command: cat /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/soapdenovo.55.fna > /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/soapdenovo.55.fna

*\ metAMOS running command: rm -r /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/soapdenovo.55.fna.bnk

*\ metAMOS running command: /home/bioinfo/programas/metAMOS-1.5rc1/AMOS/Linux-x86_64/bin/toAmos_new -s /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/soapdenovo.55.fna -b /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/soapdenovo.55.fna.bnk

*\ metAMOS running command: rm -r /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/soapdenovo.55.faa

** metAMOS running command: cat /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/soapdenovo.55.faa > /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/soapdenovo.55.faa

*\ metAMOS running command: rm -r /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/soapdenovo.55.faa.bnk

*\ metAMOS running command: /home/bioinfo/programas/metAMOS-1.5rc1/AMOS/Linux-x86_64/bin/toAmos_new -s /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/soapdenovo.55.faa -b /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/soapdenovo.55.faa.bnk

*\ metAMOS running command: rm -r /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/soapdenovo.55.gene.cvg

** metAMOS running command: cat /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/soapdenovo.55.gene.cvg > /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/soapdenovo.55.gene.cvg

*\ metAMOS running command: rm -r /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/soapdenovo.55.gene.map

** metAMOS running command: cat /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/soapdenovo.55.gene.map > /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/soapdenovo.55.gene.map

*\ metAMOS running command: ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/soapdenovo.55.faa /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/soapdenovo.55.faa

*\ metAMOS running command: ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/soapdenovo.55.fna /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/soapdenovo.55.fna

Job  = [soapdenovo.55.contig.cvg -> soapdenovo.55.faa] completed

Completed Task = findorfs.FindORFS Starting Task = validate.VALIDATE *\ metAMOS running command: touch /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Logs/validate.skip

*\ metAMOS running command: unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/proba.asm.contig

*\ metAMOS running command: ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/soapdenovo.55.asm.contig /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/proba.asm.contig

*\ metAMOS running command: unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/proba.linearize.scaffolds.final

*\ metAMOS running command: ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/soapdenovo.55.asm.contig /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/proba.linearize.scaffolds.final

*\ metAMOS running command: unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/proba.asm.tigr

*\ metAMOS running command: ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/soapdenovo.55.asm.tigr /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/proba.asm.tigr

*\ metAMOS running command: unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/proba.contig.cnt

*\ metAMOS running command: ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/soapdenovo.55.contig.cnt /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/proba.contig.cnt

*\ metAMOS running command: unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/proba.contig.cvg

*\ metAMOS running command: ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/soapdenovo.55.contig.cvg /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/proba.contig.cvg

*\ metAMOS running command: unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/proba.afg

*\ metAMOS running command: rm /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Logs/findorfs.ok

*\ metAMOS running command: unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/in/proba.asm.contig

*\ metAMOS running command: ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/proba.asm.contig /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/in/proba.asm.contig

*\ metAMOS running command: /home/bioinfo/programas/metAMOS-1.5rc1/Utilities/cpp/Linux-x86_64/FragGeneScan -s /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/in/proba.asm.contig -o /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/proba.orfs -w 0 -t complete

*\ metAMOS running command: mv /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/proba.orfs.ffn /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/proba.ctg.fna

*\ metAMOS running command: mv /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/proba.orfs.faa /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/proba.ctg.faa

*\ metAMOS running command: mv /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/proba.gene.cvg /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/proba.ctg.gene.cvg

*\ metAMOS running command: mv /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/proba.gene.map /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/proba.ctg.gene.map

*\ metAMOS running command: rm -r /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/proba.fna

** metAMOS running command: cat /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/proba.fna > /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/proba.fna

*\ metAMOS running command: rm -r /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/proba.fna.bnk

*\ metAMOS running command: /home/bioinfo/programas/metAMOS-1.5rc1/AMOS/Linux-x86_64/bin/toAmos_new -s /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/proba.fna -b /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/proba.fna.bnk

*\ metAMOS running command: rm -r /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/proba.faa

** metAMOS running command: cat /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/proba.faa > /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/proba.faa

*\ metAMOS running command: rm -r /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/proba.faa.bnk

*\ metAMOS running command: /home/bioinfo/programas/metAMOS-1.5rc1/AMOS/Linux-x86_64/bin/toAmos_new -s /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/proba.faa -b /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/proba.faa.bnk

*\ metAMOS running command: rm -r /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/proba.gene.cvg

** metAMOS running command: cat /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/proba.gene.cvg > /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/proba.gene.cvg

*\ metAMOS running command: rm -r /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/proba.gene.map

** metAMOS running command: cat /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/proba.gene.map > /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/proba.gene.map

*\ metAMOS running command: ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/proba.faa /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/proba.faa

*\ metAMOS running command: ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/proba.fna /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/proba.fna

*\ metAMOS running command: touch /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Logs/findorfs.ok

*\ metAMOS running command: unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/proba.faa

*\ metAMOS running command: ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/proba.faa /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/proba.faa

*\ metAMOS running command: unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindRepeats/in/proba.fna

*\ metAMOS running command: ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/proba.fna /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindRepeats/in/proba.fna

*\ metAMOS running command: unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindRepeats/in/proba.faa

*\ metAMOS running command: ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/proba.faa /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindRepeats/in/proba.faa

*\ metAMOS running command: unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Annotate/in/proba.fna

*\ metAMOS running command: ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/proba.fna /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Annotate/in/proba.fna

*\ metAMOS running command: unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Annotate/in/proba.faa

*\ metAMOS running command: ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/proba.faa /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Annotate/in/proba.faa

*\ metAMOS running command: unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/proba.lib1.badmates

*\ metAMOS running command: ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/soapdenovo.55.lib1.badmates /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/proba.lib1.badmates

*\ metAMOS running command: unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/proba.lib1.hdr

*\ metAMOS running command: ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/soapdenovo.55.lib1.hdr /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/proba.lib1.hdr

*\ metAMOS running command: unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/proba.lib1.mappedmates

*\ metAMOS running command: ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/soapdenovo.55.lib1.mappedmates /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/proba.lib1.mappedmates

*\ metAMOS running command: unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/proba.lib1.mates_in_diff_contigs

*\ metAMOS running command: ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/soapdenovo.55.lib1.mates_in_diff_contigs /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/proba.lib1.mates_in_diff_contigs

*\ metAMOS running command: unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/proba.lib1contig.reads

*\ metAMOS running command: ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/soapdenovo.55.lib1contig.reads /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/proba.lib1contig.reads

*\ metAMOS running command: unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/lib1.unaligned.fasta

*\ metAMOS running command: ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/soapdenovo.55.lib1.unaligned.fasta /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/lib1.unaligned.fasta

*\ metAMOS running command: unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/lib1.unaligned.fastq

Job  = [[soapdenovo.55.faa] -> [validate.ok]] completed

Completed Task = validate.Validate Starting Task = findrepeats.FINDREPEATS *\ metAMOS running command: touch /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Logs/findrepeats.skip

Job  = [proba.fna -> proba.repeats] completed

Completed Task = findreps.FindRepeats Starting Task = annotate.ANNOTATE *\ metAMOS running command: touch /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Annotate/out/proba.annots

*\ metAMOS running command: unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Annotate/in/proba.asm.contig

*\ metAMOS running command: ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/proba.asm.contig /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Annotate/in/proba.asm.contig

*\ metAMOS running command: unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Annotate/out/proba.hits

** metAMOS running command: rm -f /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Annotate/out/.hits

** metAMOS running command: rm -f /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Annotate/out/.epsilon-nb_results.txt

** metAMOS running command: rm -f /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Annotate/out/.phymm.out

*\ metAMOS running command: /home/bioinfo/programas/metAMOS-1.5rc1/Utilities/cpp/Linux-x86_64/kraken/bin/kraken --threads 15 -db /home/bioinfo/programas/metAMOS-1.5rc1/Utilities/DB//kraken --output /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Annotate/out/proba.hits /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Annotate/in/proba.asm.contig --preload

*\ metAMOS running command: perl /home/bioinfo/programas/metAMOS-1.5rc1/Utilities/perl/ImportKraken.pl -c -i -f /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Annotate/in/proba.asm.contig /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Annotate/out/proba.hits:/home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/proba.contig.cnt:class

*\ metAMOS running command: unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/in/proba.hits

*\ metAMOS running command: unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/proba.hits

*\ metAMOS running command: ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Annotate/out/proba.hits /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/in/proba.hits

*\ metAMOS running command: ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Annotate/out/proba.hits /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/proba.hits

Job  = [proba.faa -> proba.hits] completed

Completed Task = annotate.Annotate Starting Task = functionalannotation.FUNCTIONALANNOTATION *\ metAMOS running command: touch /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Logs/functionalannotation.skip

*\ metAMOS running command: touch /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FunctionalAnnotation/out/blast.out

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

Completed Task = fannotate.FunctionalAnnotation Starting Task = scaffold.SCAFFOLD *\ metAMOS running command: rm -rf /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Scaffold/in/proba.bnk

*\ metAMOS running command: /home/bioinfo/programas/metAMOS-1.5rc1/AMOS/Linux-x86_64/bin/toAmos_new -s /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Preprocess/out/lib1.seq -m /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/proba.lib1.mappedmates -b /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Scaffold/in/proba.bnk

*\ metAMOS running command: /home/bioinfo/programas/metAMOS-1.5rc1/AMOS/Linux-x86_64/bin/toAmos_new -c /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/proba.asm.tigr -b /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Scaffold/in/proba.bnk

*\ metAMOS running command: /home/bioinfo/programas/metAMOS-1.5rc1/AMOS/Linux-x86_64/bin/asmQC -b /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Scaffold/in/proba.bnk -scaff -recompute -update -numsd 2

*\ metAMOS running command: perl /home/bioinfo/programas/metAMOS-1.5rc1/AMOS/Linux-x86_64/bin/bank-unlock /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Scaffold/in/proba.bnk

*\ metAMOS running command: /home/bioinfo/programas/metAMOS-1.5rc1/AMOS/Linux-x86_64/bin/clk -b /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Scaffold/in/proba.bnk

*\ metAMOS running command: /home/bioinfo/programas/metAMOS-1.5rc1/AMOS/Linux-x86_64/bin/Bundler -b /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Scaffold/in/proba.bnk

*\ metAMOS running command: /home/bioinfo/programas/metAMOS-1.5rc1/AMOS/Linux-x86_64/bin/MarkRepeats -redundancy 50 -b /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Scaffold/in/proba.bnk > /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Scaffold/in/proba.reps

*\ metAMOS running command: /home/bioinfo/programas/metAMOS-1.5rc1/AMOS/Linux-x86_64/bin/OrientContigs -minRedundancy 5 -all -redundancy 10 -b /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Scaffold/in/proba.bnk -repeats /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Scaffold/in/proba.reps

*\ metAMOS running command: /home/bioinfo/programas/metAMOS-1.5rc1/AMOS/Linux-x86_64/bin/bank2fasta -eid -b /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Scaffold/in/proba.bnk > /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Scaffold/out/proba.contigs

*\ metAMOS running command: /home/bioinfo/programas/metAMOS-1.5rc1/AMOS/Linux-x86_64/bin/OutputMotifs -b /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Scaffold/in/proba.bnk > /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Scaffold/out/proba.motifs

*\ metAMOS running command: /home/bioinfo/programas/metAMOS-1.5rc1/AMOS/Linux-x86_64/bin/OutputResults -b /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Scaffold/in/proba.bnk -p /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Scaffold/out/proba

*\ metAMOS running command: /home/bioinfo/programas/metAMOS-1.5rc1/AMOS/Linux-x86_64/bin/OutputScaffolds -b /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Scaffold/in/proba.bnk > /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Scaffold/out/proba.scaffolds.final

*\ metAMOS running command: /home/bioinfo/programas/metAMOS-1.5rc1/AMOS/Linux-x86_64/bin/Linearize -b /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Scaffold/in/proba.bnk

*\ metAMOS running command: /home/bioinfo/programas/metAMOS-1.5rc1/AMOS/Linux-x86_64/bin/OutputResults -b /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Scaffold/in/proba.bnk -p /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Scaffold/out/proba.linearize

*\ metAMOS running command: /home/bioinfo/programas/metAMOS-1.5rc1/AMOS/Linux-x86_64/bin/OutputScaffolds -b /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Scaffold/in/proba.bnk > /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Scaffold/out/proba.linearize.scaffolds.final

Job  = [[proba.asm.contig] -> scaffold.ok] completed

Completed Task = scaffold.Scaffold Starting Task = findscaffoldorfs.FINDSCAFFOLDORFS *\ metAMOS running command: /home/bioinfo/programas/metAMOS-1.5rc1/Utilities/cpp/Linux-x86_64/FragGeneScan -s /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Scaffold/out/proba.linearize.scaffolds.final -o /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindScaffoldORFS/out/proba.orfs -w 0 -t complete

*\ metAMOS running command: cp /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindScaffoldORFS/out/proba.orfs.ffn /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindScaffoldORFS/out/proba.fna

*\ metAMOS running command: cp /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindScaffoldORFS/out/proba.orfs.faa /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindScaffoldORFS/out/proba.faa

Job  = [proba.linearize.scaffolds.final -> proba.fna] completed

Completed Task = findscforfs.FindScaffoldORFS Starting Task = abundance.ABUNDANCE *\ metAMOS running command: ln -s /home/bioinfo/programas/metAMOS-1.5rc1/Utilities/DB//markers.pfasta /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Abundance/out/markers.pfasta

*\ metAMOS running command: /home/bioinfo/programas/metAMOS-1.5rc1/Utilities/cpp/Linux-x86_64/formatdb -p T -i /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Abundance/out/markers.pfasta

*\ metAMOS running command: /home/bioinfo/programas/metAMOS-1.5rc1/Utilities/cpp/Linux-x86_64/blastall -p blastp -i /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/proba.faa -d /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Abundance/out/markers.pfasta -m 8 -b 10 -v 10 -a 15 -o /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Abundance/out/proba.blastp

*\ metAMOS running command: perl /home/bioinfo/programas/metAMOS-1.5rc1/Utilities/perl/metaphyler_contigs.pl /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Abundance/out/proba.blastp proba /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/proba.gene.cvg /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Abundance/out /home/bioinfo/programas/metAMOS-1.5rc1/Utilities

*\ metAMOS running command: perl /home/bioinfo/programas/metAMOS-1.5rc1/Utilities/perl/ImportMetaPhyler.pl -c -v -i -p /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Abundance/out/proba.taxprof.pct.txt:class

Job  = [proba.asm.contig -> proba.taxprof.pct.txt] completed

Completed Task = abundance.Abundance Starting Task = propagate.PROPAGATE *\ metAMOS running command: ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Annotate/out/proba.annots /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Propagate/in/proba.annots

*\ metAMOS running command: cat /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Propagate/in/proba.annots | grep -v "\"" | grep -v contigID |sed s/utg//g |sed s/ctg//g > /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Propagate/in/proba.clusters

*\ metAMOS running command: /home/bioinfo/programas/metAMOS-1.5rc1/AMOS/Linux-x86_64/bin/FilterEdgesByCluster -b /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Scaffold/in/proba.bnk -clusters /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Propagate/in/proba.clusters -noRemoveEdges > /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Propagate/out/proba.clusters

Job  = [proba.annots -> propagate.ok] completed

Completed Task = propagate.Propagate Job = [proba.clusters -> classify.ok] completed Completed Task = classify.Classify Starting Task = postprocess.POSTPROCESS *\ metAMOS running command: unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/annotate.krona.html

*\ metAMOS running command: ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Annotate/out/report.krona.html /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/annotate.krona.html

*\ metAMOS running command: unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/abundance.krona.html

*\ metAMOS running command: ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Abundance/out/report.krona.html /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/abundance.krona.html

*\ metAMOS running command: unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/class.classified

*\ metAMOS running command: ln -s /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Classify/out /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/class.classified

*\ metAMOS running command: unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/asm.scores

*\ metAMOS running command: ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Validate/out/proba.lap /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/asm.scores

*\ metAMOS running command: unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/best.asm

*\ metAMOS running command: ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Validate/out/proba.asm.selected /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/best.asm

*\ metAMOS running command: unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/class.original.annots

*\ metAMOS running command: ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Annotate/out/proba.annots /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/class.original.annots

*\ metAMOS running command: unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/class.original.reads.annots

*\ metAMOS running command: ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Annotate/out/proba.reads.annots /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/class.original.reads.annots

*\ metAMOS running command: unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/class.propagated.annots

*\ metAMOS running command: unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/class.propagated.reads.annots

*\ metAMOS running command: cp /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Abundance/out/proba.classify.txt /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/.

*\ metAMOS running command: cp /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Scaffold/out/proba.linearize.scaffolds.final /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/proba.scf.fa

*\ metAMOS running command: cp /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Scaffold/out/proba.contigs /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/proba.ctg.fa

*\ metAMOS running command: cp /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Scaffold/out/proba.motifs /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/proba.motifs.fa

*\ metAMOS running command: ln -s /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Scaffold/in/proba.bnk /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/

*\ metAMOS running command: ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/proba.fna /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/proba.orf.fna

*\ metAMOS running command: ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindORFS/out/proba.faa /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/proba.orf.faa

*\ metAMOS running command: ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindScaffoldORFS/out/proba.fna /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/proba.scf.orf.fna

*\ metAMOS running command: ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FindScaffoldORFS/out/proba.faa /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/proba.scf.orf.faa

*\ metAMOS running command: unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/proba.lib1.contig.reads

*\ metAMOS running command: ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/proba.lib1contig.reads /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/proba.lib1.contig.reads

*\ metAMOS running command: unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/proba.lib1.unaligned.fasta

*\ metAMOS running command: ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/lib1.unaligned.fasta /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/proba.lib1.unaligned.fasta

*\ metAMOS running command: unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/proba.ctg.cnt

*\ metAMOS running command: ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/proba.contig.cnt /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/proba.ctg.cnt

*\ metAMOS running command: unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/proba.ctg.cvg

*\ metAMOS running command: ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Assemble/out/proba.contig.cvg /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/proba.ctg.cvg

*\ metAMOS running command: unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/html

*\ metAMOS running command: mkdir /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/html

*\ metAMOS running command: unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/html/class.classified

*\ metAMOS running command: ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/class.classified /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/html/class.classified

*\ metAMOS running command: unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/html/Annotate.html

*\ metAMOS running command: ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/annotate.krona.html /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/html/Annotate.html

*\ metAMOS running command: unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/html/Abundance.html

*\ metAMOS running command: ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/abundance.krona.html /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/html/Abundance.html

*\ metAMOS running command: touch /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/ref.name

** metAMOS running command: mv /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Preprocess/out/.fastqc /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/html

*\ metAMOS running command: unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/html/propagate.in.clusters

*\ metAMOS running command: ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Propagate/in/proba.clusters /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/html/propagate.in.clusters

*\ metAMOS running command: unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/html/propagate.out.clusters

*\ metAMOS running command: ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Propagate/out/proba.clusters /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/html/propagate.out.clusters

*\ metAMOS running command: unlink /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/html/FunctionalAnnotation.html

*\ metAMOS running command: ln /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/FunctionalAnnotation/out/ec.krona.html /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/html/FunctionalAnnotation.html

Starting Task = classify.CLASSIFY *\ metAMOS running command: perl -I /home/bioinfo/programas/metAMOS-1.5rc1/AMOS/Linux-x86_64/lib /home/bioinfo/programas/metAMOS-1.5rc1/Utilities/perl/statistics.pl /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/proba.scf.fa > /home/bioinfo/programas/metAMOS-1.5rc1/Test/test1/Postprocess/out/html/asmstats.out

Asm stats done Version done Steps init done Plots done Asm counts done Oops, MetAMOS finished with errors! see text in red above for details. Traceback (most recent call last): File "../runPipeline", line 971, in verbose = 1) File "/home/bioinfo/programas/metAMOS-1.5rc1/Utilities/ruffus/task.py", line 2965, in pipeline_run raise job_errors RethrownJobError:

Exception #1
  'exceptions.KeyError('1236')' raised in ...
   Task = def postprocess.Postprocess(...):
   Job  = [proba.asm.contig -> proba.scf.fa]

Traceback (most recent call last):
  File "/home/bioinfo/programas/metAMOS-1.5rc1/Utilities/ruffus/task.py", line 625, in run_pooled_job_without_exceptions
    return_value =  job_wrapper(param, user_defined_work_func, register_cleanup, touch_files_only)
  File "/home/bioinfo/programas/metAMOS-1.5rc1/Utilities/ruffus/task.py", line 491, in job_wrapper_io_files
    ret_val = user_defined_work_func(*param)
  File "/home/bioinfo/programas/metAMOS-1.5rc1/src/postprocess.py", line 286, in Postprocess
    create_summary("%s/Abundance/out/%s.taxprof.pct.txt"%(_settings.rundir,_settings.PREFIX),"%s/Postprocess/out/%s.bnk"%(_settings.rundir,_settings.PREFIX),"%s/Postprocess/out/html/"%(_settings.rundir),"%s/Postprocess/out/%s.scf.fa"%(_settings.rundir,_settings.PREFIX),"%s"%(_settings.METAMOS_UTILS),"%s/img"%(_settings.METAMOSDIR),"%s"%(_settings.AMOS),len(_readlibs),"%s"%(_settings.taxa_level),"%s"%(_settings.DB_DIR))
  File "/home/bioinfo/programas/metAMOS-1.5rc1/Utilities/python/create_summary.py", line 288, in create_summary
    get_classify_stats("%s/propagate.in.clusters"%(html_prefix),"%s/propagate.out.clusters"%(html_prefix),"%s/tax_key.tab"%(dbdir),"%s"%(html_prefix),"Classify.html","Propagate.html","%s"%(taxa_level))
  File "/home/bioinfo/programas/metAMOS-1.5rc1/Utilities/python/get_classify_stats.py", line 79, in get_classify_stats
    class_name = id_class[key]
KeyError: '1236'

[skoren]

This error is due to missing taxonomic information, specifically, from the tax_key.tab file. Can you confirm that Utilities/DB/tax_key.tab exists and is not empty? It should have about 1.1M lines and is automatically generated during installation.

wc -l Utilities/DB/tax_key.tab 
1131976 Utilities/DB/tax_key.tab

md5sum Utilities/DB/tax_key.tab 
MD5 (Utilities/DB/tax_key.tab) = 92fe05ddb85667817c8e8f9eb4644eaf

head Utilities/DB/tax_key.tab 
1   root
2   Bacteria
6   Azorhizobium
7   Azorhizobium caulinodans
9   Buchnera aphidicola
10  Cellvibrio
11  [Cellvibrio] gilvus
13  Dictyoglomus
14  Dictyoglomus thermophilum
16  Methylophilus

If it is empty or not the right size, you can try removing the KronaTools directory and re-running python INSTALL.py and let us know if that reports any error messages while installing.

[danbacastro]

wc -l tax_key.tab 1131133 tax_key.tab

md5sum tax_key.tab 8da3b56861f09e76405c5e72c0dd5ea4 tax_key.tab

head tax_key.tab 1\ root 2\ Bacteria 6\ Azorhizobium 7\ Azorhizobium caulinodans 9\ Buchnera aphidicola 10\ Cellvibrio 11\ [Cellvibrio] gilvus 13\ Dictyoglomus 14\ Dictyoglomus thermophilum 16\ Methylophilus

tail tax_key.tab 1470347\ Candidatus Alistipes marseilloanorexicus 1470348\ Candidatus Streptomyces massiliensis 1470349\ Candidatus Stoquefichus 1470350\ Candidatus Stoquefichus massiliensis 1470352\ unclassified Glycine 1470353\ Candidatus Soleaferrea 1470354\ Candidatus Soleaferrea massiliensis 1470355\ Candidatus Dorea massiliensis 1470356\ Candidatus Clostridium anorexicamassiliense 1470358\ Candidatus Blastococcus massiliensis

The number of lines is not the same. I will remove KronaTools and run INSTALL.py again.

Thank you so much!

[skoren]

Ah, the issue is the file is malformed. Instead of having a tab it has a \ and space separating the entries. This is confusing downstream parsing. If you haven't already removed KronaTools, try running:

cat KronaTools/taxonomy/taxonomy.tab |awk -F "\t" '{print $1"\t"$NF}' > ./Utilities/DB/tax_key.tab
head tax_key.tab

and see if the file is now separated by tabs.

[danbacastro]

Thanks Skoren and Treangen!

I re-installed KronaTools and use the awk command. All seems ok now.

Thanks again!

[skoren]

For future users, committed fix 3651f26c3921ae450cab4c969b4869710f1859b6. A typo in INSTALL.py apparently didn't affect OSX or most Linux distros but failed on your system.