**ERROR** All input sequences were empty

[kvaldez]

Hello, I am trying to align metagenomic sequences, when I run initPipeline with the following command I get the expected output:

initPipeline -q -1 Unmapped.out.mate1 -d projectDir -i 300:800
Project dir /spin1/users/valdezkm/test_variants/bam_trimmed/projectDir successfully created!
Use runPipeline.py to start Pipeline

However when I try runPipeline, I get an error that all input sequences were empty. Please advise on a solution to the issue.

[Steps to be skipped]:  set(['FindRepeats'])
Starting Task = runpipeline.RUNPIPELINE
Starting metAMOS pipeline
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: SignalP+ is not found, some functionality will not be available
Warning: PHmmer is not found, some functionality will not be available
Warning: REAPR is not found, some functionality will not be available
Warning: MPI is not available, some functionality may not be available
[Available RAM: 170 GB]
	*ok
[Available CPUs: 56]
	*ok

________________________________________
Tasks which will be run:

Task = preprocess.Preprocess
Task = assemble.SplitAssemblers
Task = assemble.Assemble
Task = assemble.CheckAsmResults
Task = assemble.SplitMappers
Task = mapreads.MapReads
Task = mapreads.CheckMapResults
Task = mapreads.SplitForORFs
Task = findorfs.FindORFS
Task = validate.Validate
Task = findreps.FindRepeats
Task = annotate.Annotate
Task = fannotate.FunctionalAnnotation
Task = scaffold.Scaffold
Task = findscforfs.FindScaffoldORFS
Task = abundance.Abundance
Task = propagate.Propagate
Task = classify.Classify
Task = postprocess.Postprocess
________________________________________
metAMOS configuration summary:
metAMOS Version:	v1.5rc2 "Praline Brownie"  workflows: core,optional,imetamos
Time and Date:		2018-02-15
Working directory:	/spin1/users/valdezkm/test_variants/bam_trimmed/projectDir
Prefix:			proba
K-Mer:			31
Threads:		8
Taxonomic level:	class
Verbose:		False
Steps to skip:		MultiAlign, FindScaffoldORFS, FindRepeats
Steps to force:		Abundance, Scaffold, FunctionalAnnotation, FindORFS, Annotate, Propagate, MapReads, Postprocess, Assemble, 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
	/usr/local/apps/metAMOS/metAMOS-1.5rc3/Utilities/cpp/Linux-x86_64
	Liu B, Gibbons T, Ghodsi M, Treangen T, Pop M. Accurate and fast estimation of taxonomic profiles from metagenomic shotgun sequences. BMC Genomics. 2011;12 Suppl 2:S4. Epub 2011 Jul 27.

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

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

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

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

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

[assemble]
ABySS
	/usr/local/apps/metAMOS/metAMOS-1.5rc3/Utilities/cpp/Linux-x86_64/abyss/bin
	Simpson, JT, Wong, K, Jackman, SD, Schein, JE, Jones, SJ, Birol, İ. ABySS: a parallel assembler for short read sequence data. Genome research, 19(6), 1117-1123, 2009.

Newbler
	
	NA

MetaVelvet
	/usr/local/apps/metAMOS/metAMOS-1.5rc3/Utilities/cpp/Linux-x86_64/MetaVelvet
	Namiki, T., Hachiya, T., Tanaka, H., & Sakakibara, Y. MetaVelvet: an extension of Velvet assembler to de novo metagenome assembly from short sequence reads. Nucleic acids research, 40(20), e155-e155, 2012.

Velvet
	/usr/local/apps/metAMOS/metAMOS-1.5rc3/Utilities/cpp/Linux-x86_64/velvet
	Zerbino DR, Birney E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 2008 May;18(5):821-9.

Edena
	
	Hernandez D, Tewhey R, Veyrieras J, Farinelli L, Østerås M, François P, and Schrenzel J. De novo finished 2.8 Mbp Staphylococcus aureus genome assembly from 100 bp short and long range paired-end reads. Bioinformatics, btt590, 2013.

Celera Assembler
	/usr/local/apps/metAMOS/metAMOS-1.5rc3/CA/Linux-amd64/bin
	Miller JR, Delcher AL, Koren S, Venter E, Walenz BP, Brownley A, Johnson J, Li K, Mobarry C, Sutton G. Aggressive assembly of pyrosequencing reads with mates.Bioinformatics. 2008 Dec 15;24(24):2818-24. Epub 2008 Oct 24.

MIRA
	/usr/local/apps/metAMOS/metAMOS-1.5rc3/Utilities/cpp/Linux-x86_64/mira/bin
	Chevreux, B, Wetter, T, Suhai, S. Genome Sequence Assembly Using Trace Signals and Additional Sequence Information. In German Conference on Bioinformatics (pp. 45-56), 1999.

SOAPdenovo2
	/usr/local/apps/metAMOS/metAMOS-1.5rc3/Utilities/cpp/Linux-x86_64/soap2/bin
	Luo, R, Liu, B, Xie, Y, Li, Z, Huang, W, Yuan, J, He G, Chen Y, Pan Q, Liu Y, Tang J, Wu G, Zhang H, Shi Y, Liu Y, Yu C, Wang B, Lu Y, Han C, Cheung DW, Yiu S, Peng S, Xiaoqian Z, Liu G, Liao X, Li Y, Yang H, Wang J, Lam T, Wang J. SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. GigaScience, 1(1), 18, 2012.

Meta-IDBA
	/usr/local/apps/metAMOS/metAMOS-1.5rc3/Utilities/cpp/Linux-x86_64
	Peng Y, Leung HCM, Yiu SM, Chin FYL: Meta-IDBA: a de Novo assembler for metagenomic data. Bioinformatics 2011, 27:i94-i101.

SGA
	/usr/local/apps/metAMOS/metAMOS-1.5rc3/Utilities/cpp/Linux-x86_64/sga/bin
	Simpson, JT, Durbin, R. Efficient de novo assembly of large genomes using compressed data structures. Genome Research, 22(3), 549-556, 2012.

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

IDBA-UD
	/usr/local/apps/metAMOS/metAMOS-1.5rc3/Utilities/cpp/Linux-x86_64/idba/bin
	Peng, Y., Leung, H. C., Yiu, S. M., & Chin, F. Y. IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth. Bioinformatics, 28(11), 1420-1428, 2012.

Minimus
	UNKNOWN
	Sommer DD, Delcher AL, Salzberg SL, Pop M. Minimus: a fast, lightweight genome assembler. BMC Bioinformatics. 2007 Feb 26;8:64.

SPAdes
	/usr/local/apps/metAMOS/metAMOS-1.5rc3/Utilities/cpp/Linux-x86_64/spades/bin
	Anton Bankevich, Sergey Nurk, Dmitry Antipov, Alexey A. Gurevich, Mikhail Dvorkin, Alexander S. Kulikov, Valery M. Lesin, Sergey I. Nikolenko, Son Pham, Andrey D. Prjibelski, Alexey V. Pyshkin, Alexander V. Sirotkin, Nikolay Vyahhi, Glenn Tesler, Max A. Alekseyev, and Pavel A. Pevzner. Journal of Computational Biology. May 2012, 19(5): 455-477. doi:10.1089/cmb.2012.0021.

MaSuRCA
	/usr/local/apps/metAMOS/metAMOS-1.5rc3/Utilities/cpp/Linux-x86_64/MaSuRCA/bin
	Zimin, A, Marçais, G, Puiu, D, Roberts, M, Salzberg, SL, Yorke, JA. The MaSuRCA genome assembler. Bioinformatics, btt476, 2013.

Velvet-SC
	/usr/local/apps/metAMOS/metAMOS-1.5rc3/Utilities/cpp/Linux-x86_64/velvet-sc
	Chitsaz H, Yee-Greenbaum JL, Tesler G, Lombardo MJ, Dupont CL, Badger JH, Novotny M, Rusch DB, Fraser LJ, Gormley NA, Schulz-Trieglaff O, Smith GP, Evers DJ, Pevzner PA, Lasken RL. Efficient de novo assembly of single-cell bacterial genomes from short-read data sets. Nature Biotechnology, vol. 29, no. 11, pp. 915-921 (2011)

Sparse Assembler
	/usr/local/apps/metAMOS/metAMOS-1.5rc3/Utilities/cpp/Linux-x86_64/SparseAssembler
	Ye C, Ma ZS, Cannon CH, Pop M, Yu DW. Exploiting sparseness in de novo genome assembly. BMC Bioinformatics. 2012 Apr 19;13 Suppl 6:S1.

Ray
	/usr/local/apps/metAMOS/metAMOS-1.5rc3/Utilities/cpp/Linux-x86_64/Ray/bin
	Boisvert, S, Raymond, F, Godzaridis, É, Laviolette, F, Corbeil, J. Ray Meta: scalable de novo metagenome assembly and profiling. Genome biology, 13(12), R122, 2013.

[mapreads]
Bowtie2
	/usr/local/apps/metAMOS/metAMOS-1.5rc3/Utilities/cpp/Linux-x86_64
	Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012 Mar 4;9(4):357-9. doi: 10.1038/nmeth.1923.

[preprocess]
metAMOS built-in filtering
	N/A

[validate]
FRCbam
	/usr/local/apps/metAMOS/metAMOS-1.5rc3/Utilities/cpp/Linux-x86_64/FRCbam/bin
	Vezzi, F, Narzisi, G, Mishra, B. Reevaluating assembly evaluations with feature response curves: GAGE and assemblathons. PloS ONE, 7(12), e52210, 2013.

CGAL
	/usr/local/apps/metAMOS/metAMOS-1.5rc3/Utilities/cpp/Linux-x86_64/cgal
	Rahman, A, Pachter, L CGAL: computing genome assembly likelihoods. Genome biology, 14(1), R8, 2013.

ALE
	/usr/local/apps/metAMOS/metAMOS-1.5rc3/Utilities/cpp/Linux-x86_64/ALE/src
	Clark, SC, Egan, R, Frazier, PI, Wang, Z. ALE: a generic assembly likelihood evaluation framework for assessing the accuracy of genome and metagenome assemblies. Bioinformatics, 29(4) 435-443, 2013.

QUAST
	/usr/local/apps/metAMOS/metAMOS-1.5rc3/quast
	Gurevich, A, Saveliev, V, Vyahhi, N, Tesler, G. QUAST: quality assessment tool for genome assemblies. Bioinformatics, 29(8), 1072-1075, 2013.

FragGeneScan
	/usr/local/apps/metAMOS/metAMOS-1.5rc3/Utilities/cpp/Linux-x86_64
	Rho M, Tang H, Ye Y: FragGeneScan: predicting genes in short and error-prone reads. Nucleic Acids Research 2010, 38:e191-e191.

FreeBayes
	/usr/local/apps/metAMOS/metAMOS-1.5rc3/Utilities/cpp/Linux-x86_64/freebayes/bin
	Garrison, E, Marth, G. Haplotype-based variant detection from short-read sequencing. arXiv preprint arXiv:1207.3907, 2012.

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

REAPR
	
	Hunt, M, Kikuchi, T, Sanders, M, Newbold, C, Berriman, M, & Otto, TD. REAPR: a universal tool for genome assembly evaluation. Genome biology, 14(5), R47, 2013.

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


Starting Task = preprocess.PREPROCESS
Warning: library 1 has no sequences

**ERROR**
All input sequences were empty

**ERROR**


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

[skoren]

Most likely the input format isn't specified correctly (e.g. fasta vs fastq). The default filter will also throw out any sequences with Ns. You can disable all filters (-t none) or use another filter (-t eautils).

[kvaldez]

Thank you for your help. I added -t none, and have tried with a couple of SE fastq files, the larger ones take longer but still end up with the same error.

[skoren]

Have you confirmed your installation is OK by running the provided test sets? You should be using runPipeline not runPipeline.py (just line initPipeline). If those work, run in verbose mode (-v) and post the output.

[kvaldez]

The practice run below seems to work, the only issues that I currently see are html errors at the bottom and the following message in some of the html output files:

Could not get resources from "http://krona.sourceforge.net".

./run_pipeline_test.sh -v
Project dir /spin1/users/valdezkm/test_variants/Test/test1 successfully created!
Use runPipeline.py to start Pipeline
[Steps to be skipped]:  set(['FunctionalAnnotation', 'FindRepeats'])
Starting Task = runpipeline.RUNPIPELINE
*** metAMOS running command: touch /spin1/users/valdezkm/test_variants/Test/test1/Preprocess/out/lib1.seq

*** metAMOS running command: rm /spin1/users/valdezkm/test_variants/Test/test1/Assemble/out/*.contig.cvg

*** metAMOS running command: rm /spin1/users/valdezkm/test_variants/Test/test1/Logs/mapreads.ok

*** metAMOS running command: rm /spin1/users/valdezkm/test_variants/Test/test1/Logs/propagate.ok

*** metAMOS running command: touch /spin1/users/valdezkm/test_variants/Test/test1/Annotate/out/proba.annots

*** metAMOS running command: touch /spin1/users/valdezkm/test_variants/Test/test1/Scaffold/out/proba.linearize.scaffolds.final

*** metAMOS running command: touch /spin1/users/valdezkm/test_variants/Test/test1/FindORFS/out/proba.faa

*** metAMOS running command: rm /spin1/users/valdezkm/test_variants/Test/test1/Abundance/out/proba.taxprof.pct.txt

*** metAMOS running command: rm /spin1/users/valdezkm/test_variants/Test/test1/Annotate/out/proba.hits

*** metAMOS running command: rm /spin1/users/valdezkm/test_variants/Test/test1/Assemble/out/*.faa

*** metAMOS running command: rm /spin1/users/valdezkm/test_variants/Test/test1/Assemble/out/*.fna

*** metAMOS running command: rm /spin1/users/valdezkm/test_variants/Test/test1/FindORFS/out/*.faa

*** metAMOS running command: rm /spin1/users/valdezkm/test_variants/Test/test1/FindORFS/out/*.fna

*** metAMOS running command: rm /spin1/users/valdezkm/test_variants/Test/test1/Logs/assemble.ok

*** metAMOS running command: rm /spin1/users/valdezkm/test_variants/Test/test1/Assemble/out/*.asm.contig

*** metAMOS running command: rm /spin1/users/valdezkm/test_variants/Test/test1/Logs/classify.ok

Starting metAMOS pipeline
Found pysam in /usr/local/apps/Anaconda/2.7.6-1.9.1/lib/python2.7/site-packages/pysam/__init__.pyc
Found psutil in /usr/local/apps/Anaconda/2.7.6-1.9.1/lib/python2.7/site-packages/psutil/__init__.pyc
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: SignalP+ is not found, some functionality will not be available
Warning: PHmmer is not found, some functionality will not be available
Warning: REAPR is not found, some functionality will not be available
Warning: MPI is not available, some functionality may not be available
[Available RAM: 261 GB]
	*ok
[Available CPUs: 56]
	*ok

________________________________________
Tasks which will be run:

Task = preprocess.Preprocess
Task = assemble.SplitAssemblers
Task = assemble.Assemble
Task = assemble.CheckAsmResults
Task = assemble.SplitMappers
Task = mapreads.MapReads
Task = mapreads.CheckMapResults
Task = mapreads.SplitForORFs
Task = findorfs.FindORFS
Task = validate.Validate
Task = findreps.FindRepeats
Task = annotate.Annotate
Task = fannotate.FunctionalAnnotation
Task = scaffold.Scaffold
Task = findscforfs.FindScaffoldORFS
Task = abundance.Abundance
Task = propagate.Propagate
Task = classify.Classify
Task = postprocess.Postprocess
________________________________________
metAMOS configuration summary:
metAMOS Version:	v1.5rc2 "Praline Brownie"  workflows: core,optional,imetamos
Time and Date:		2018-02-15
Working directory:	/spin1/users/valdezkm/test_variants/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
	/usr/local/apps/metAMOS/metAMOS-1.5rc3/Utilities/cpp/Linux-x86_64
	Liu B, Gibbons T, Ghodsi M, Treangen T, Pop M. Accurate and fast estimation of taxonomic profiles from metagenomic shotgun sequences. BMC Genomics. 2011;12 Suppl 2:S4. Epub 2011 Jul 27.

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

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

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

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

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

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

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

[preprocess]
metAMOS built-in filtering
	N/A

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

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


Starting Task = preprocess.PREPROCESS
*** metAMOS running command: java -cp /usr/local/apps/metAMOS/metAMOS-1.5rc3/Utilities/java:.:. outputDefaultQuality /spin1/users/valdezkm/test_variants/Test/test1/Preprocess/in/carsonella_pe_filt.fna > /spin1/users/valdezkm/test_variants/Test/test1/Preprocess/in/carsonella_pe_filt.fna.qual

*** metAMOS running command: rm /spin1/users/valdezkm/test_variants/Test/test1/Preprocess/out/all.seq.mates

*** metAMOS running command: cp /spin1/users/valdezkm/test_variants/Test/test1/Preprocess/out/carsonella_pe_filt.fna /spin1/users/valdezkm/test_variants/Test/test1/Preprocess/out/lib1.seq

*** metAMOS running command: cp /spin1/users/valdezkm/test_variants/Test/test1/Preprocess/out/carsonella_pe_filt.fna.qual /spin1/users/valdezkm/test_variants/Test/test1/Preprocess/out/lib1.seq.qual

*** metAMOS running command: which python

*** metAMOS running command: echo $PYTHONPATH

*** metAMOS running command: perl /usr/local/apps/metAMOS/metAMOS-1.5rc3/Utilities/perl/split_fasta.pl /spin1/users/valdezkm/test_variants/Test/test1/Preprocess/out/lib1.seq /spin1/users/valdezkm/test_variants/Test/test1/Preprocess/out/lib1.1.fasta /spin1/users/valdezkm/test_variants/Test/test1/Preprocess/out/lib1.2.fasta

*** metAMOS running command: perl /usr/local/apps/metAMOS/metAMOS-1.5rc3/Utilities/perl/split_fasta.pl /spin1/users/valdezkm/test_variants/Test/test1/Preprocess/out/lib1.seq.qual /spin1/users/valdezkm/test_variants/Test/test1/Preprocess/out/lib1.1.fasta.qual /spin1/users/valdezkm/test_variants/Test/test1/Preprocess/out/lib1.2.fasta.qual

*** metAMOS running command: ln /spin1/users/valdezkm/test_variants/Test/test1/Preprocess/out/lib1.seq /spin1/users/valdezkm/test_variants/Test/test1/Preprocess/out/lib1.fasta

*** metAMOS running command: java -cp /usr/local/apps/metAMOS/metAMOS-1.5rc3/Utilities/java:. convertFastaAndQualToFastq /spin1/users/valdezkm/test_variants/Test/test1/Preprocess/out/lib1.seq /spin1/users/valdezkm/test_variants/Test/test1/Preprocess/out/lib1.seq.qual > /spin1/users/valdezkm/test_variants/Test/test1/Preprocess/out/lib1.fastq

*** metAMOS running command: java -cp /usr/local/apps/metAMOS/metAMOS-1.5rc3/Utilities/java:. convertFastaAndQualToFastq /spin1/users/valdezkm/test_variants/Test/test1/Preprocess/out/lib1.1.fasta /spin1/users/valdezkm/test_variants/Test/test1/Preprocess/out/lib1.1.fasta.qual > /spin1/users/valdezkm/test_variants/Test/test1/Preprocess/out/lib1.1.fastq

*** metAMOS running command: java -cp /usr/local/apps/metAMOS/metAMOS-1.5rc3/Utilities/java:. convertFastaAndQualToFastq /spin1/users/valdezkm/test_variants/Test/test1/Preprocess/out/lib1.2.fasta /spin1/users/valdezkm/test_variants/Test/test1/Preprocess/out/lib1.2.fasta.qual > /spin1/users/valdezkm/test_variants/Test/test1/Preprocess/out/lib1.2.fastq

*** metAMOS running command: touch /spin1/users/valdezkm/test_variants/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 /spin1/users/valdezkm/test_variants/Test/test1/Assemble/out/soapdenovo.55.run

    Job  = [preprocess.success -> *.run] completed
Completed Task = assemble.SplitAssemblers
*** metAMOS running command: cat /spin1/users/valdezkm/test_variants/Test/test1/soapconfig.txt |grep -v max_rd_len > /spin1/users/valdezkm/test_variants/Test/test1/soap2config.txt

*** metAMOS running command: /usr/local/apps/metAMOS/metAMOS-1.5rc3/Utilities/cpp/Linux-x86_64/SOAPdenovo-63mer pregraph -p 15 -K 55 -R  -D   -s /spin1/users/valdezkm/test_variants/Test/test1/soapconfig.txt -o /spin1/users/valdezkm/test_variants/Test/test1/Assemble/out/soapdenovo.55.asm

*** metAMOS running command: /usr/local/apps/metAMOS/metAMOS-1.5rc3/Utilities/cpp/Linux-x86_64/SOAPdenovo-63mer contig -g /spin1/users/valdezkm/test_variants/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 /spin1/users/valdezkm/test_variants/Test/test1/Assemble/out/soapdenovo.55.asm.contig /spin1/users/valdezkm/test_variants/Test/test1/Assemble/out/soapdenovo.55.asm.contigWIUPAC.fa

*** metAMOS running command: java -cp /usr/local/apps/metAMOS/metAMOS-1.5rc3/Utilities/java:. RemoveIUPAC /spin1/users/valdezkm/test_variants/Test/test1/Assemble/out/soapdenovo.55.asm.contigWIUPAC.fa >/spin1/users/valdezkm/test_variants/Test/test1/Assemble/out/soapdenovo.55.asm.contig

*** metAMOS running command: rm /spin1/users/valdezkm/test_variants/Test/test1/Assemble/out/soapdenovo.55.run

*** metAMOS running command: touch /spin1/users/valdezkm/test_variants/Test/test1/Assemble/out/assemble.success

    Job  = [[soapdenovo.55.asm.contig] -> [assemble.ok]] completed
Completed Task = assemble.CheckAsmResults
Uptodate Task = assemble.SplitMappers
Starting Task = mapreads.MAPREADS
*** metAMOS running command: /usr/local/apps/metAMOS/metAMOS-1.5rc3/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /spin1/users/valdezkm/test_variants/Test/test1/Assemble/out/soapdenovo.55.asm.contig /spin1/users/valdezkm/test_variants/Test/test1/Assemble/out/soapdenovo.55.IDX

*** metAMOS running command: /usr/local/apps/metAMOS/metAMOS-1.5rc3/Utilities/cpp/Linux-x86_64/bowtie -p 15 -f -l 25 -e 140 --best --strata -m 10 -k 1 --un /spin1/users/valdezkm/test_variants/Test/test1/Assemble/out/soapdenovo.55.lib1.unaligned.fasta /spin1/users/valdezkm/test_variants/Test/test1/Assemble/out/soapdenovo.55.IDX /spin1/users/valdezkm/test_variants/Test/test1/Preprocess/out/lib1.seq > /spin1/users/valdezkm/test_variants/Test/test1/Assemble/out/lib1.bout

*** metAMOS running command: cat /spin1/users/valdezkm/test_variants/Test/test1/Assemble/out/soapdenovo.55.lib1.mappedmates >> /spin1/users/valdezkm/test_variants/Test/test1/Assemble/out/soapdenovo.55.lib1.hdr 

*** metAMOS running command: cp /spin1/users/valdezkm/test_variants/Test/test1/Assemble/out/soapdenovo.55.lib1.hdr /spin1/users/valdezkm/test_variants/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 /spin1/users/valdezkm/test_variants/Test/test1/FindORFS/in/soapdenovo.55.asm.contig

*** metAMOS running command: ln /spin1/users/valdezkm/test_variants/Test/test1/Assemble/out/soapdenovo.55.asm.contig /spin1/users/valdezkm/test_variants/Test/test1/FindORFS/in/soapdenovo.55.asm.contig

*** metAMOS running command: /usr/local/apps/metAMOS/metAMOS-1.5rc3/Utilities/cpp/Linux-x86_64/FragGeneScan -s /spin1/users/valdezkm/test_variants/Test/test1/FindORFS/in/soapdenovo.55.asm.contig -o /spin1/users/valdezkm/test_variants/Test/test1/FindORFS/out/soapdenovo.55.orfs -w 0 -t complete

*** metAMOS running command: mv /spin1/users/valdezkm/test_variants/Test/test1/FindORFS/out/soapdenovo.55.orfs.ffn /spin1/users/valdezkm/test_variants/Test/test1/FindORFS/out/soapdenovo.55.ctg.fna

*** metAMOS running command: mv /spin1/users/valdezkm/test_variants/Test/test1/FindORFS/out/soapdenovo.55.orfs.faa /spin1/users/valdezkm/test_variants/Test/test1/FindORFS/out/soapdenovo.55.ctg.faa

*** metAMOS running command: mv /spin1/users/valdezkm/test_variants/Test/test1/FindORFS/out/soapdenovo.55.gene.cvg /spin1/users/valdezkm/test_variants/Test/test1/FindORFS/out/soapdenovo.55.ctg.gene.cvg

*** metAMOS running command: mv /spin1/users/valdezkm/test_variants/Test/test1/FindORFS/out/soapdenovo.55.gene.map /spin1/users/valdezkm/test_variants/Test/test1/FindORFS/out/soapdenovo.55.ctg.gene.map

*** metAMOS running command: rm -r /spin1/users/valdezkm/test_variants/Test/test1/FindORFS/out/soapdenovo.55.fna

*** metAMOS running command: cat /spin1/users/valdezkm/test_variants/Test/test1/FindORFS/out/soapdenovo.55*.fna > /spin1/users/valdezkm/test_variants/Test/test1/FindORFS/out/soapdenovo.55.fna

*** metAMOS running command: rm -r /spin1/users/valdezkm/test_variants/Test/test1/FindORFS/out/soapdenovo.55.fna.bnk

*** metAMOS running command: /usr/local/apps/metAMOS/metAMOS-1.5rc3/AMOS/Linux-x86_64/bin/toAmos_new -s /spin1/users/valdezkm/test_variants/Test/test1/FindORFS/out/soapdenovo.55.fna -b /spin1/users/valdezkm/test_variants/Test/test1/FindORFS/out/soapdenovo.55.fna.bnk

*** metAMOS running command: rm -r /spin1/users/valdezkm/test_variants/Test/test1/FindORFS/out/soapdenovo.55.faa

*** metAMOS running command: cat /spin1/users/valdezkm/test_variants/Test/test1/FindORFS/out/soapdenovo.55*.faa > /spin1/users/valdezkm/test_variants/Test/test1/FindORFS/out/soapdenovo.55.faa

*** metAMOS running command: rm -r /spin1/users/valdezkm/test_variants/Test/test1/FindORFS/out/soapdenovo.55.faa.bnk

*** metAMOS running command: /usr/local/apps/metAMOS/metAMOS-1.5rc3/AMOS/Linux-x86_64/bin/toAmos_new -s /spin1/users/valdezkm/test_variants/Test/test1/FindORFS/out/soapdenovo.55.faa -b /spin1/users/valdezkm/test_variants/Test/test1/FindORFS/out/soapdenovo.55.faa.bnk

*** metAMOS running command: rm -r /spin1/users/valdezkm/test_variants/Test/test1/FindORFS/out/soapdenovo.55.gene.cvg

*** metAMOS running command: cat /spin1/users/valdezkm/test_variants/Test/test1/FindORFS/out/soapdenovo.55*.gene.cvg > /spin1/users/valdezkm/test_variants/Test/test1/FindORFS/out/soapdenovo.55.gene.cvg

*** metAMOS running command: rm -r /spin1/users/valdezkm/test_variants/Test/test1/FindORFS/out/soapdenovo.55.gene.map

*** metAMOS running command: cat /spin1/users/valdezkm/test_variants/Test/test1/FindORFS/out/soapdenovo.55*.gene.map > /spin1/users/valdezkm/test_variants/Test/test1/FindORFS/out/soapdenovo.55.gene.map

*** metAMOS running command: ln /spin1/users/valdezkm/test_variants/Test/test1/FindORFS/out/soapdenovo.55.faa /spin1/users/valdezkm/test_variants/Test/test1/Assemble/out/soapdenovo.55.faa

*** metAMOS running command: ln /spin1/users/valdezkm/test_variants/Test/test1/FindORFS/out/soapdenovo.55.fna /spin1/users/valdezkm/test_variants/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 /spin1/users/valdezkm/test_variants/Test/test1/Logs/validate.skip

*** metAMOS running command: unlink /spin1/users/valdezkm/test_variants/Test/test1/Assemble/out/proba.asm.contig

*** metAMOS running command: ln /spin1/users/valdezkm/test_variants/Test/test1/Assemble/out/soapdenovo.55.asm.contig /spin1/users/valdezkm/test_variants/Test/test1/Assemble/out/proba.asm.contig

*** metAMOS running command: unlink /spin1/users/valdezkm/test_variants/Test/test1/Assemble/out/proba.linearize.scaffolds.final

*** metAMOS running command: ln /spin1/users/valdezkm/test_variants/Test/test1/Assemble/out/soapdenovo.55.asm.contig /spin1/users/valdezkm/test_variants/Test/test1/Assemble/out/proba.linearize.scaffolds.final

*** metAMOS running command: unlink /spin1/users/valdezkm/test_variants/Test/test1/Assemble/out/proba.asm.tigr

*** metAMOS running command: ln /spin1/users/valdezkm/test_variants/Test/test1/Assemble/out/soapdenovo.55.asm.tigr /spin1/users/valdezkm/test_variants/Test/test1/Assemble/out/proba.asm.tigr

*** metAMOS running command: unlink /spin1/users/valdezkm/test_variants/Test/test1/Assemble/out/proba.contig.cnt

*** metAMOS running command: ln /spin1/users/valdezkm/test_variants/Test/test1/Assemble/out/soapdenovo.55.contig.cnt /spin1/users/valdezkm/test_variants/Test/test1/Assemble/out/proba.contig.cnt

*** metAMOS running command: unlink /spin1/users/valdezkm/test_variants/Test/test1/Assemble/out/proba.contig.cvg

*** metAMOS running command: ln /spin1/users/valdezkm/test_variants/Test/test1/Assemble/out/soapdenovo.55.contig.cvg /spin1/users/valdezkm/test_variants/Test/test1/Assemble/out/proba.contig.cvg

*** metAMOS running command: unlink /spin1/users/valdezkm/test_variants/Test/test1/Assemble/out/proba.afg

*** metAMOS running command: rm /spin1/users/valdezkm/test_variants/Test/test1/Logs/findorfs.ok

*** metAMOS running command: unlink /spin1/users/valdezkm/test_variants/Test/test1/FindORFS/in/proba.asm.contig

*** metAMOS running command: ln /spin1/users/valdezkm/test_variants/Test/test1/Assemble/out/proba.asm.contig /spin1/users/valdezkm/test_variants/Test/test1/FindORFS/in/proba.asm.contig

*** metAMOS running command: /usr/local/apps/metAMOS/metAMOS-1.5rc3/Utilities/cpp/Linux-x86_64/FragGeneScan -s /spin1/users/valdezkm/test_variants/Test/test1/FindORFS/in/proba.asm.contig -o /spin1/users/valdezkm/test_variants/Test/test1/FindORFS/out/proba.orfs -w 0 -t complete

*** metAMOS running command: mv /spin1/users/valdezkm/test_variants/Test/test1/FindORFS/out/proba.orfs.ffn /spin1/users/valdezkm/test_variants/Test/test1/FindORFS/out/proba.ctg.fna

*** metAMOS running command: mv /spin1/users/valdezkm/test_variants/Test/test1/FindORFS/out/proba.orfs.faa /spin1/users/valdezkm/test_variants/Test/test1/FindORFS/out/proba.ctg.faa

*** metAMOS running command: mv /spin1/users/valdezkm/test_variants/Test/test1/FindORFS/out/proba.gene.cvg /spin1/users/valdezkm/test_variants/Test/test1/FindORFS/out/proba.ctg.gene.cvg

*** metAMOS running command: mv /spin1/users/valdezkm/test_variants/Test/test1/FindORFS/out/proba.gene.map /spin1/users/valdezkm/test_variants/Test/test1/FindORFS/out/proba.ctg.gene.map

*** metAMOS running command: rm -r /spin1/users/valdezkm/test_variants/Test/test1/FindORFS/out/proba.fna

*** metAMOS running command: cat /spin1/users/valdezkm/test_variants/Test/test1/FindORFS/out/proba*.fna > /spin1/users/valdezkm/test_variants/Test/test1/FindORFS/out/proba.fna

*** metAMOS running command: rm -r /spin1/users/valdezkm/test_variants/Test/test1/FindORFS/out/proba.fna.bnk

*** metAMOS running command: /usr/local/apps/metAMOS/metAMOS-1.5rc3/AMOS/Linux-x86_64/bin/toAmos_new -s /spin1/users/valdezkm/test_variants/Test/test1/FindORFS/out/proba.fna -b /spin1/users/valdezkm/test_variants/Test/test1/FindORFS/out/proba.fna.bnk

*** metAMOS running command: rm -r /spin1/users/valdezkm/test_variants/Test/test1/FindORFS/out/proba.faa

*** metAMOS running command: cat /spin1/users/valdezkm/test_variants/Test/test1/FindORFS/out/proba*.faa > /spin1/users/valdezkm/test_variants/Test/test1/FindORFS/out/proba.faa

*** metAMOS running command: rm -r /spin1/users/valdezkm/test_variants/Test/test1/FindORFS/out/proba.faa.bnk

*** metAMOS running command: /usr/local/apps/metAMOS/metAMOS-1.5rc3/AMOS/Linux-x86_64/bin/toAmos_new -s /spin1/users/valdezkm/test_variants/Test/test1/FindORFS/out/proba.faa -b /spin1/users/valdezkm/test_variants/Test/test1/FindORFS/out/proba.faa.bnk

*** metAMOS running command: rm -r /spin1/users/valdezkm/test_variants/Test/test1/FindORFS/out/proba.gene.cvg

*** metAMOS running command: cat /spin1/users/valdezkm/test_variants/Test/test1/FindORFS/out/proba*.gene.cvg > /spin1/users/valdezkm/test_variants/Test/test1/FindORFS/out/proba.gene.cvg

*** metAMOS running command: rm -r /spin1/users/valdezkm/test_variants/Test/test1/FindORFS/out/proba.gene.map

*** metAMOS running command: cat /spin1/users/valdezkm/test_variants/Test/test1/FindORFS/out/proba*.gene.map > /spin1/users/valdezkm/test_variants/Test/test1/FindORFS/out/proba.gene.map

*** metAMOS running command: ln /spin1/users/valdezkm/test_variants/Test/test1/FindORFS/out/proba.faa /spin1/users/valdezkm/test_variants/Test/test1/Assemble/out/proba.faa

*** metAMOS running command: ln /spin1/users/valdezkm/test_variants/Test/test1/FindORFS/out/proba.fna /spin1/users/valdezkm/test_variants/Test/test1/Assemble/out/proba.fna

*** metAMOS running command: touch /spin1/users/valdezkm/test_variants/Test/test1/Logs/findorfs.ok

*** metAMOS running command: unlink /spin1/users/valdezkm/test_variants/Test/test1/Assemble/out/proba.faa

*** metAMOS running command: ln /spin1/users/valdezkm/test_variants/Test/test1/FindORFS/out/proba.faa /spin1/users/valdezkm/test_variants/Test/test1/Assemble/out/proba.faa

*** metAMOS running command: unlink /spin1/users/valdezkm/test_variants/Test/test1/FindRepeats/in/proba.fna

*** metAMOS running command: ln /spin1/users/valdezkm/test_variants/Test/test1/FindORFS/out/proba.fna /spin1/users/valdezkm/test_variants/Test/test1/FindRepeats/in/proba.fna

*** metAMOS running command: unlink /spin1/users/valdezkm/test_variants/Test/test1/FindRepeats/in/proba.faa

*** metAMOS running command: ln /spin1/users/valdezkm/test_variants/Test/test1/FindORFS/out/proba.faa /spin1/users/valdezkm/test_variants/Test/test1/FindRepeats/in/proba.faa

*** metAMOS running command: unlink /spin1/users/valdezkm/test_variants/Test/test1/Annotate/in/proba.fna

*** metAMOS running command: ln /spin1/users/valdezkm/test_variants/Test/test1/FindORFS/out/proba.fna /spin1/users/valdezkm/test_variants/Test/test1/Annotate/in/proba.fna

*** metAMOS running command: unlink /spin1/users/valdezkm/test_variants/Test/test1/Annotate/in/proba.faa

*** metAMOS running command: ln /spin1/users/valdezkm/test_variants/Test/test1/FindORFS/out/proba.faa /spin1/users/valdezkm/test_variants/Test/test1/Annotate/in/proba.faa

*** metAMOS running command: unlink /spin1/users/valdezkm/test_variants/Test/test1/Assemble/out/proba.lib1.badmates

*** metAMOS running command: ln /spin1/users/valdezkm/test_variants/Test/test1/Assemble/out/soapdenovo.55.lib1.badmates /spin1/users/valdezkm/test_variants/Test/test1/Assemble/out/proba.lib1.badmates

*** metAMOS running command: unlink /spin1/users/valdezkm/test_variants/Test/test1/Assemble/out/proba.lib1.hdr

*** metAMOS running command: ln /spin1/users/valdezkm/test_variants/Test/test1/Assemble/out/soapdenovo.55.lib1.hdr /spin1/users/valdezkm/test_variants/Test/test1/Assemble/out/proba.lib1.hdr

*** metAMOS running command: unlink /spin1/users/valdezkm/test_variants/Test/test1/Assemble/out/proba.lib1.mappedmates

*** metAMOS running command: ln /spin1/users/valdezkm/test_variants/Test/test1/Assemble/out/soapdenovo.55.lib1.mappedmates /spin1/users/valdezkm/test_variants/Test/test1/Assemble/out/proba.lib1.mappedmates

*** metAMOS running command: unlink /spin1/users/valdezkm/test_variants/Test/test1/Assemble/out/proba.lib1.mates_in_diff_contigs

*** metAMOS running command: ln /spin1/users/valdezkm/test_variants/Test/test1/Assemble/out/soapdenovo.55.lib1.mates_in_diff_contigs /spin1/users/valdezkm/test_variants/Test/test1/Assemble/out/proba.lib1.mates_in_diff_contigs

*** metAMOS running command: unlink /spin1/users/valdezkm/test_variants/Test/test1/Assemble/out/proba.lib1contig.reads

*** metAMOS running command: ln /spin1/users/valdezkm/test_variants/Test/test1/Assemble/out/soapdenovo.55.lib1contig.reads /spin1/users/valdezkm/test_variants/Test/test1/Assemble/out/proba.lib1contig.reads

*** metAMOS running command: unlink /spin1/users/valdezkm/test_variants/Test/test1/Assemble/out/lib1.unaligned.fasta

*** metAMOS running command: ln /spin1/users/valdezkm/test_variants/Test/test1/Assemble/out/soapdenovo.55.lib1.unaligned.fasta /spin1/users/valdezkm/test_variants/Test/test1/Assemble/out/lib1.unaligned.fasta

*** metAMOS running command: unlink /spin1/users/valdezkm/test_variants/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 /spin1/users/valdezkm/test_variants/Test/test1/Logs/findrepeats.skip

    Job  = [proba.fna -> proba.repeats] completed
Completed Task = findreps.FindRepeats
Starting Task = annotate.ANNOTATE
*** metAMOS running command: touch /spin1/users/valdezkm/test_variants/Test/test1/Annotate/out/proba.annots

*** metAMOS running command: unlink /spin1/users/valdezkm/test_variants/Test/test1/Annotate/in/proba.asm.contig

*** metAMOS running command: ln /spin1/users/valdezkm/test_variants/Test/test1/Assemble/out/proba.asm.contig /spin1/users/valdezkm/test_variants/Test/test1/Annotate/in/proba.asm.contig

*** metAMOS running command: unlink /spin1/users/valdezkm/test_variants/Test/test1/Annotate/out/proba.hits

*** metAMOS running command: rm -f /spin1/users/valdezkm/test_variants/Test/test1/Annotate/out/*.hits

*** metAMOS running command: rm -f /spin1/users/valdezkm/test_variants/Test/test1/Annotate/out/*.epsilon-nb_results.txt

*** metAMOS running command: rm -f /spin1/users/valdezkm/test_variants/Test/test1/Annotate/out/*.phymm.out

*** metAMOS running command: /usr/local/apps/metAMOS/metAMOS-1.5rc3/Utilities/cpp/Linux-x86_64/kraken/bin/kraken --threads 15 -db /usr/local/apps/metAMOS/metAMOS-1.5rc3/Utilities/DB//kraken /spin1/users/valdezkm/test_variants/Test/test1/Annotate/in/proba.asm.contig --preload   | kraken-filter --db /usr/local/apps/metAMOS/metAMOS-1.5rc3/Utilities/DB//kraken --threshold 0.05 > /spin1/users/valdezkm/test_variants/Test/test1/Annotate/out/proba.hits

*** metAMOS running command: perl /usr/local/apps/metAMOS/metAMOS-1.5rc3/Utilities/perl/ImportKraken.pl  -c -i -f /spin1/users/valdezkm/test_variants/Test/test1/Annotate/in/proba.asm.contig /spin1/users/valdezkm/test_variants/Test/test1/Annotate/out/proba.hits:/spin1/users/valdezkm/test_variants/Test/test1/Assemble/out/proba.contig.cnt:class

*** metAMOS running command: unlink /spin1/users/valdezkm/test_variants/Test/test1/Postprocess/in/proba.hits

*** metAMOS running command: unlink /spin1/users/valdezkm/test_variants/Test/test1/Postprocess/out/proba.hits

*** metAMOS running command: ln /spin1/users/valdezkm/test_variants/Test/test1/Annotate/out/proba.hits /spin1/users/valdezkm/test_variants/Test/test1/Postprocess/in/proba.hits

*** metAMOS running command: ln /spin1/users/valdezkm/test_variants/Test/test1/Annotate/out/proba.hits /spin1/users/valdezkm/test_variants/Test/test1/Postprocess/out/proba.hits

    Job  = [proba.faa -> proba.hits] completed
Completed Task = annotate.Annotate
Starting Task = functionalannotation.FUNCTIONALANNOTATION
*** metAMOS running command: touch /spin1/users/valdezkm/test_variants/Test/test1/Logs/functionalannotation.skip

*** metAMOS running command: touch /spin1/users/valdezkm/test_variants/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 /spin1/users/valdezkm/test_variants/Test/test1/Scaffold/in/proba.bnk

*** metAMOS running command: /usr/local/apps/metAMOS/metAMOS-1.5rc3/AMOS/Linux-x86_64/bin/toAmos_new -s /spin1/users/valdezkm/test_variants/Test/test1/Preprocess/out/lib1.seq -m /spin1/users/valdezkm/test_variants/Test/test1/Assemble/out/proba.lib1.mappedmates -b /spin1/users/valdezkm/test_variants/Test/test1/Scaffold/in/proba.bnk 

*** metAMOS running command: /usr/local/apps/metAMOS/metAMOS-1.5rc3/AMOS/Linux-x86_64/bin/toAmos_new -c /spin1/users/valdezkm/test_variants/Test/test1/Assemble/out/proba.asm.tigr -b /spin1/users/valdezkm/test_variants/Test/test1/Scaffold/in/proba.bnk 

*** metAMOS running command: /usr/local/apps/metAMOS/metAMOS-1.5rc3/AMOS/Linux-x86_64/bin/asmQC -b /spin1/users/valdezkm/test_variants/Test/test1/Scaffold/in/proba.bnk -scaff -recompute -update -numsd 2 

*** metAMOS running command: perl /usr/local/apps/metAMOS/metAMOS-1.5rc3/AMOS/Linux-x86_64/bin/bank-unlock /spin1/users/valdezkm/test_variants/Test/test1/Scaffold/in/proba.bnk

*** metAMOS running command: /usr/local/apps/metAMOS/metAMOS-1.5rc3/AMOS/Linux-x86_64/bin/clk -b /spin1/users/valdezkm/test_variants/Test/test1/Scaffold/in/proba.bnk

*** metAMOS running command: /usr/local/apps/metAMOS/metAMOS-1.5rc3/AMOS/Linux-x86_64/bin/Bundler -b /spin1/users/valdezkm/test_variants/Test/test1/Scaffold/in/proba.bnk

*** metAMOS running command: /usr/local/apps/metAMOS/metAMOS-1.5rc3/AMOS/Linux-x86_64/bin/MarkRepeats -redundancy 50  -b /spin1/users/valdezkm/test_variants/Test/test1/Scaffold/in/proba.bnk > /spin1/users/valdezkm/test_variants/Test/test1/Scaffold/in/proba.reps

*** metAMOS running command: /usr/local/apps/metAMOS/metAMOS-1.5rc3/AMOS/Linux-x86_64/bin/OrientContigs -minRedundancy 5 -all  -redundancy 10  -b /spin1/users/valdezkm/test_variants/Test/test1/Scaffold/in/proba.bnk -repeats /spin1/users/valdezkm/test_variants/Test/test1/Scaffold/in/proba.reps 

*** metAMOS running command: /usr/local/apps/metAMOS/metAMOS-1.5rc3/AMOS/Linux-x86_64/bin/bank2fasta -eid  -b /spin1/users/valdezkm/test_variants/Test/test1/Scaffold/in/proba.bnk > /spin1/users/valdezkm/test_variants/Test/test1/Scaffold/out/proba.contigs

*** metAMOS running command: /usr/local/apps/metAMOS/metAMOS-1.5rc3/AMOS/Linux-x86_64/bin/OutputMotifs -b /spin1/users/valdezkm/test_variants/Test/test1/Scaffold/in/proba.bnk > /spin1/users/valdezkm/test_variants/Test/test1/Scaffold/out/proba.motifs

*** metAMOS running command: /usr/local/apps/metAMOS/metAMOS-1.5rc3/AMOS/Linux-x86_64/bin/OutputResults -b /spin1/users/valdezkm/test_variants/Test/test1/Scaffold/in/proba.bnk -p /spin1/users/valdezkm/test_variants/Test/test1/Scaffold/out/proba 

*** metAMOS running command: /usr/local/apps/metAMOS/metAMOS-1.5rc3/AMOS/Linux-x86_64/bin/OutputScaffolds -b /spin1/users/valdezkm/test_variants/Test/test1/Scaffold/in/proba.bnk > /spin1/users/valdezkm/test_variants/Test/test1/Scaffold/out/proba.scaffolds.final

*** metAMOS running command: /usr/local/apps/metAMOS/metAMOS-1.5rc3/AMOS/Linux-x86_64/bin/Linearize -b /spin1/users/valdezkm/test_variants/Test/test1/Scaffold/in/proba.bnk

*** metAMOS running command: /usr/local/apps/metAMOS/metAMOS-1.5rc3/AMOS/Linux-x86_64/bin/OutputResults -b /spin1/users/valdezkm/test_variants/Test/test1/Scaffold/in/proba.bnk -p /spin1/users/valdezkm/test_variants/Test/test1/Scaffold/out/proba.linearize 

*** metAMOS running command: /usr/local/apps/metAMOS/metAMOS-1.5rc3/AMOS/Linux-x86_64/bin/OutputScaffolds -b /spin1/users/valdezkm/test_variants/Test/test1/Scaffold/in/proba.bnk > /spin1/users/valdezkm/test_variants/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: /usr/local/apps/metAMOS/metAMOS-1.5rc3/Utilities/cpp/Linux-x86_64/FragGeneScan -s /spin1/users/valdezkm/test_variants/Test/test1/Scaffold/out/proba.linearize.scaffolds.final -o /spin1/users/valdezkm/test_variants/Test/test1/FindScaffoldORFS/out/proba.orfs -w 0 -t complete

*** metAMOS running command: cp /spin1/users/valdezkm/test_variants/Test/test1/FindScaffoldORFS/out/proba.orfs.ffn /spin1/users/valdezkm/test_variants/Test/test1/FindScaffoldORFS/out/proba.fna

*** metAMOS running command: cp /spin1/users/valdezkm/test_variants/Test/test1/FindScaffoldORFS/out/proba.orfs.faa /spin1/users/valdezkm/test_variants/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 /usr/local/apps/metAMOS/metAMOS-1.5rc3/Utilities/DB//markers.pfasta /spin1/users/valdezkm/test_variants/Test/test1/Abundance/out/markers.pfasta

*** metAMOS running command: /usr/local/apps/metAMOS/metAMOS-1.5rc3/Utilities/cpp/Linux-x86_64/formatdb  -p T -i /spin1/users/valdezkm/test_variants/Test/test1/Abundance/out/markers.pfasta

*** metAMOS running command: /usr/local/apps/metAMOS/metAMOS-1.5rc3/Utilities/cpp/Linux-x86_64/blastall -p blastp -i /spin1/users/valdezkm/test_variants/Test/test1/FindORFS/out/proba.faa -d /spin1/users/valdezkm/test_variants/Test/test1/Abundance/out/markers.pfasta -m 8 -b 10 -v 10 -a 15 -o /spin1/users/valdezkm/test_variants/Test/test1/Abundance/out/proba.blastp

*** metAMOS running command: perl /usr/local/apps/metAMOS/metAMOS-1.5rc3/Utilities/perl/metaphyler_contigs.pl /spin1/users/valdezkm/test_variants/Test/test1/Abundance/out/proba.blastp proba /spin1/users/valdezkm/test_variants/Test/test1/FindORFS/out/proba.gene.cvg /spin1/users/valdezkm/test_variants/Test/test1/Abundance/out /usr/local/apps/metAMOS/metAMOS-1.5rc3/Utilities

*** metAMOS running command: perl /usr/local/apps/metAMOS/metAMOS-1.5rc3/Utilities/perl/ImportMetaPhyler.pl  -c -v -i -p /spin1/users/valdezkm/test_variants/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 /spin1/users/valdezkm/test_variants/Test/test1/Annotate/out/proba.annots /spin1/users/valdezkm/test_variants/Test/test1/Propagate/in/proba.annots

*** metAMOS running command: cat /spin1/users/valdezkm/test_variants/Test/test1/Propagate/in/proba.annots | grep -v "\"" | grep -v contigID  |sed s/utg//g |sed s/ctg//g > /spin1/users/valdezkm/test_variants/Test/test1/Propagate/in/proba.clusters

*** metAMOS running command: /usr/local/apps/metAMOS/metAMOS-1.5rc3/AMOS/Linux-x86_64/bin/FilterEdgesByCluster -b /spin1/users/valdezkm/test_variants/Test/test1/Scaffold/in/proba.bnk -clusters /spin1/users/valdezkm/test_variants/Test/test1/Propagate/in/proba.clusters -noRemoveEdges > /spin1/users/valdezkm/test_variants/Test/test1/Propagate/out/proba.clusters

    Job  = [proba.annots -> propagate.ok] completed
Completed Task = propagate.Propagate
Starting Task = classify.CLASSIFY
*** metAMOS running command: /usr/local/apps/metAMOS/metAMOS-1.5rc3/AMOS/Linux-x86_64/bin/shuffleBank -c -e -b /spin1/users/valdezkm/test_variants/Test/test1/Scaffold/in/proba.bnk -p ctg -eid -E /spin1/users/valdezkm/test_variants/Test/test1/Classify/out/contig.fofn

*** metAMOS running command: /usr/local/apps/metAMOS/metAMOS-1.5rc3/AMOS/Linux-x86_64/bin/shuffleBank -r -e -b /spin1/users/valdezkm/test_variants/Test/test1/Scaffold/in/proba.bnk -eid -E /spin1/users/valdezkm/test_variants/Test/test1/Classify/out/read.fofn

*** metAMOS running command: /usr/local/apps/metAMOS/metAMOS-1.5rc3/AMOS/Linux-x86_64/bin/shuffleBank -r -f -e -b /spin1/users/valdezkm/test_variants/Test/test1/Scaffold/in/proba.bnk -eid -E /spin1/users/valdezkm/test_variants/Test/test1/Classify/out/read.fofn

*** metAMOS running command: /usr/local/apps/metAMOS/metAMOS-1.5rc3/AMOS/Linux-x86_64/bin/shuffleBank -r -e -b /spin1/users/valdezkm/test_variants/Test/test1/FindORFS/out/proba.fna.bnk -p fna -eid -E /spin1/users/valdezkm/test_variants/Test/test1/Classify/out/orf.fofn

*** metAMOS running command: /usr/local/apps/metAMOS/metAMOS-1.5rc3/AMOS/Linux-x86_64/bin/shuffleBank -r -e -b /spin1/users/valdezkm/test_variants/Test/test1/FindORFS/out/proba.faa.bnk -p faa -eid -E /spin1/users/valdezkm/test_variants/Test/test1/Classify/out/orf.fofn

    Job  = [proba.clusters -> classify.ok] completed
Completed Task = classify.Classify
Starting Task = postprocess.POSTPROCESS
*** metAMOS running command: unlink /spin1/users/valdezkm/test_variants/Test/test1/Postprocess/out/annotate.krona.html

*** metAMOS running command: ln /spin1/users/valdezkm/test_variants/Test/test1/Annotate/out/report.krona.html /spin1/users/valdezkm/test_variants/Test/test1/Postprocess/out/annotate.krona.html

*** metAMOS running command: unlink /spin1/users/valdezkm/test_variants/Test/test1/Postprocess/out/abundance.krona.html

*** metAMOS running command: ln /spin1/users/valdezkm/test_variants/Test/test1/Abundance/out/report.krona.html /spin1/users/valdezkm/test_variants/Test/test1/Postprocess/out/abundance.krona.html

*** metAMOS running command: unlink /spin1/users/valdezkm/test_variants/Test/test1/Postprocess/out/class.classified

*** metAMOS running command: ln -s /spin1/users/valdezkm/test_variants/Test/test1/Classify/out /spin1/users/valdezkm/test_variants/Test/test1/Postprocess/out/class.classified

*** metAMOS running command: unlink /spin1/users/valdezkm/test_variants/Test/test1/Postprocess/out/asm.scores

*** metAMOS running command: ln /spin1/users/valdezkm/test_variants/Test/test1/Validate/out/proba.lap /spin1/users/valdezkm/test_variants/Test/test1/Postprocess/out/asm.scores

*** metAMOS running command: unlink /spin1/users/valdezkm/test_variants/Test/test1/Postprocess/out/best.asm

*** metAMOS running command: ln /spin1/users/valdezkm/test_variants/Test/test1/Validate/out/proba.asm.selected /spin1/users/valdezkm/test_variants/Test/test1/Postprocess/out/best.asm

*** metAMOS running command: unlink /spin1/users/valdezkm/test_variants/Test/test1/Postprocess/out/class.original.annots

*** metAMOS running command: ln /spin1/users/valdezkm/test_variants/Test/test1/Annotate/out/proba.annots /spin1/users/valdezkm/test_variants/Test/test1/Postprocess/out/class.original.annots

*** metAMOS running command: unlink /spin1/users/valdezkm/test_variants/Test/test1/Postprocess/out/class.original.reads.annots

*** metAMOS running command: ln /spin1/users/valdezkm/test_variants/Test/test1/Annotate/out/proba.reads.annots /spin1/users/valdezkm/test_variants/Test/test1/Postprocess/out/class.original.reads.annots

*** metAMOS running command: unlink /spin1/users/valdezkm/test_variants/Test/test1/Postprocess/out/class.propagated.annots

*** metAMOS running command: unlink /spin1/users/valdezkm/test_variants/Test/test1/Postprocess/out/class.propagated.reads.annots

*** metAMOS running command: cp /spin1/users/valdezkm/test_variants/Test/test1/Abundance/out/proba.classify.txt /spin1/users/valdezkm/test_variants/Test/test1/Postprocess/out/. 

*** metAMOS running command: cp /spin1/users/valdezkm/test_variants/Test/test1/Scaffold/out/proba.linearize.scaffolds.final /spin1/users/valdezkm/test_variants/Test/test1/Postprocess/out/proba.scf.fa

*** metAMOS running command: cp /spin1/users/valdezkm/test_variants/Test/test1/Scaffold/out/proba.contigs /spin1/users/valdezkm/test_variants/Test/test1/Postprocess/out/proba.ctg.fa

*** metAMOS running command: cp /spin1/users/valdezkm/test_variants/Test/test1/Scaffold/out/proba.motifs /spin1/users/valdezkm/test_variants/Test/test1/Postprocess/out/proba.motifs.fa

*** metAMOS running command: ln -s /spin1/users/valdezkm/test_variants/Test/test1/Scaffold/in/proba.bnk /spin1/users/valdezkm/test_variants/Test/test1/Postprocess/out/

*** metAMOS running command: ln /spin1/users/valdezkm/test_variants/Test/test1/FindORFS/out/proba.fna /spin1/users/valdezkm/test_variants/Test/test1/Postprocess/out/proba.orf.fna

*** metAMOS running command: ln /spin1/users/valdezkm/test_variants/Test/test1/FindORFS/out/proba.faa /spin1/users/valdezkm/test_variants/Test/test1/Postprocess/out/proba.orf.faa

*** metAMOS running command: ln /spin1/users/valdezkm/test_variants/Test/test1/FindScaffoldORFS/out/proba.fna /spin1/users/valdezkm/test_variants/Test/test1/Postprocess/out/proba.scf.orf.fna

*** metAMOS running command: ln /spin1/users/valdezkm/test_variants/Test/test1/FindScaffoldORFS/out/proba.faa /spin1/users/valdezkm/test_variants/Test/test1/Postprocess/out/proba.scf.orf.faa

*** metAMOS running command: unlink /spin1/users/valdezkm/test_variants/Test/test1/Postprocess/out/proba.lib1.contig.reads

*** metAMOS running command: ln /spin1/users/valdezkm/test_variants/Test/test1/Assemble/out/proba.lib1contig.reads /spin1/users/valdezkm/test_variants/Test/test1/Postprocess/out/proba.lib1.contig.reads

*** metAMOS running command: unlink /spin1/users/valdezkm/test_variants/Test/test1/Postprocess/out/proba.lib1.unaligned.fasta

*** metAMOS running command: ln /spin1/users/valdezkm/test_variants/Test/test1/Assemble/out/lib1.unaligned.fasta /spin1/users/valdezkm/test_variants/Test/test1/Postprocess/out/proba.lib1.unaligned.fasta

*** metAMOS running command: unlink /spin1/users/valdezkm/test_variants/Test/test1/Postprocess/out/proba.ctg.cnt

*** metAMOS running command: ln /spin1/users/valdezkm/test_variants/Test/test1/Assemble/out/proba.contig.cnt /spin1/users/valdezkm/test_variants/Test/test1/Postprocess/out/proba.ctg.cnt

*** metAMOS running command: unlink /spin1/users/valdezkm/test_variants/Test/test1/Postprocess/out/proba.ctg.cvg

*** metAMOS running command: ln /spin1/users/valdezkm/test_variants/Test/test1/Assemble/out/proba.contig.cvg /spin1/users/valdezkm/test_variants/Test/test1/Postprocess/out/proba.ctg.cvg

*** metAMOS running command: unlink /spin1/users/valdezkm/test_variants/Test/test1/Postprocess/out/html

*** metAMOS running command: mkdir  /spin1/users/valdezkm/test_variants/Test/test1/Postprocess/out/html

*** metAMOS running command: unlink /spin1/users/valdezkm/test_variants/Test/test1/Postprocess/out/html/class.classified

*** metAMOS running command: ln /spin1/users/valdezkm/test_variants/Test/test1/Postprocess/out/class.classified /spin1/users/valdezkm/test_variants/Test/test1/Postprocess/out/html/class.classified

*** metAMOS running command: unlink /spin1/users/valdezkm/test_variants/Test/test1/Postprocess/out/html/Annotate.html

*** metAMOS running command: ln /spin1/users/valdezkm/test_variants/Test/test1/Postprocess/out/annotate.krona.html /spin1/users/valdezkm/test_variants/Test/test1/Postprocess/out/html/Annotate.html

*** metAMOS running command: unlink /spin1/users/valdezkm/test_variants/Test/test1/Postprocess/out/html/Abundance.html

*** metAMOS running command: ln /spin1/users/valdezkm/test_variants/Test/test1/Postprocess/out/abundance.krona.html /spin1/users/valdezkm/test_variants/Test/test1/Postprocess/out/html/Abundance.html

*** metAMOS running command: touch /spin1/users/valdezkm/test_variants/Test/test1/Postprocess/out/ref.name

*** metAMOS running command: mv /spin1/users/valdezkm/test_variants/Test/test1/Preprocess/out/*.fastqc /spin1/users/valdezkm/test_variants/Test/test1/Postprocess/out/html

*** metAMOS running command: unlink /spin1/users/valdezkm/test_variants/Test/test1/Postprocess/out/html/propagate.in.clusters

*** metAMOS running command: ln /spin1/users/valdezkm/test_variants/Test/test1/Propagate/in/proba.clusters /spin1/users/valdezkm/test_variants/Test/test1/Postprocess/out/html/propagate.in.clusters

*** metAMOS running command: unlink /spin1/users/valdezkm/test_variants/Test/test1/Postprocess/out/html/propagate.out.clusters

*** metAMOS running command: ln /spin1/users/valdezkm/test_variants/Test/test1/Propagate/out/proba.clusters /spin1/users/valdezkm/test_variants/Test/test1/Postprocess/out/html/propagate.out.clusters

*** metAMOS running command: unlink /spin1/users/valdezkm/test_variants/Test/test1/Postprocess/out/html/FunctionalAnnotation.html

*** metAMOS running command: ln /spin1/users/valdezkm/test_variants/Test/test1/FunctionalAnnotation/out/ec.krona.html /spin1/users/valdezkm/test_variants/Test/test1/Postprocess/out/html/FunctionalAnnotation.html

*** metAMOS running command: perl -I /usr/local/apps/metAMOS/metAMOS-1.5rc3/AMOS/Linux-x86_64/lib /usr/local/apps/metAMOS/metAMOS-1.5rc3/Utilities/perl/statistics.pl /spin1/users/valdezkm/test_variants/Test/test1/Postprocess/out/proba.scf.fa > /spin1/users/valdezkm/test_variants/Test/test1/Postprocess/out/html/asmstats.out

*** metAMOS running command: /usr/local/apps/metAMOS/metAMOS-1.5rc3/AMOS/Linux-x86_64/bin/analyze-read-depth -x 2 /spin1/users/valdezkm/test_variants/Test/test1/Postprocess/out/proba.bnk > /spin1/users/valdezkm/test_variants/Test/test1/Postprocess/out/html/covstats.out

*** metAMOS running command: /usr/local/apps/metAMOS/metAMOS-1.5rc3/AMOS/Linux-x86_64/bin/astats /spin1/users/valdezkm/test_variants/Test/test1/Postprocess/out/proba.bnk > /spin1/users/valdezkm/test_variants/Test/test1/Postprocess/out/html/stats.out

    Job  = [proba.asm.contig -> proba.scf.fa] completed
Completed Task = postprocess.Postprocess
done! pipeline took 3.29 minutes
Please see results in /spin1/users/valdezkm/test_variants/Test/test1/Postprocess/out
metAMOS summary report is file:///spin1/users/valdezkm/test_variants/Test/test1/Postprocess/out/html/summary.html
[valdezkm@cn3121 Test]$ /usr/bin/xdg-open: line 402: htmlview: command not found
1518731163089	addons.productaddons	WARN	Failed downloading XML, status: 0, reason: error
1518731341842	addons.repository	WARN	Search failed when repopulating cache
1518731341886	addons.update-checker	WARN	HTTP Request failed for an unknown reason
1518731341886	addons.update-checker	WARN	HTTP Request failed for an unknown reason
1518731341889	addons.productaddons	WARN	Failed downloading XML, status: 0, reason: error