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marbl / metAMOS

A metagenomic and isolate assembly and analysis pipeline built with AMOS
http://marbl.github.io/metAMOS
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Failed at PREPROCESS with error code -6 #268

Closed jingzhejiang closed 7 years ago

jingzhejiang commented 7 years ago

Hi! I have passed the run_pipeline_test.sh test. Then I tried to run pipeline on AWS (m4.16xlarge) to analyze two different data, one is 1 G and the other is ~4 G. But the pipeline all failed at the PREPROCESS step with error code -6.

Output produced by runPipeline:

[Steps to be skipped]:  set(['FindRepeats'])
Starting metAMOS pipeline
Error: cannot find BLAST DB directory, expected it in /home/ubuntu/metAMOS-1.5rc3/Utilities/DB/. Disabling blastdb dependent programs
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: 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: FRCbam is not found, some functionality will not be available
Warning: FreeBayes is not found, some functionality will not be available
Warning: MPI is not available, some functionality may not be available
[Available RAM: 269 GB]
   *ok
[Available CPUs: 64]
   *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:    v1.5rc3 "Praline Brownie"  workflows: core,imetamos
Time and Date:      2017-06-22
Working directory:  /home/ubuntu/DYL
Prefix:         proba
K-Mer:          31
Threads:        63
Taxonomic level:    class
Verbose:        False
Steps to skip:      MultiAlign, FunctionalAnnotation, FindRepeats, FindScaffoldORFS
Steps to force:     

[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/ubuntu/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
    /home/ubuntu/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
    /home/ubuntu/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
    /home/ubuntu/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
    /home/ubuntu/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]
SPAdes
    /home/ubuntu/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.

[mapreads]
Bowtie2
    /home/ubuntu/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]
LAP
    /home/ubuntu/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
    /home/ubuntu/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
[*****************************************************************
*************************ERROR***********************************
During preprocess, the following command failed with return code -6:
>> /home/ubuntu/metAMOS-1.5rc3/FastQC/fastqc -t 63 /home/ubuntu/DYL/Preprocess/out/DYL-1_H7VFTALXX_L2_1.clean.fq /home/ubuntu/DYL/Preprocess/out/DYL-1_H7VFTALXX_L2_2.clean.fq /home/ubuntu/DYL/Preprocess/out/DYL-2_H7VFTALXX_L2_1.clean.fq /home/ubuntu/DYL/Preprocess/out/DYL-2_H7VFTALXX_L2_2.clean.fq /home/ubuntu/DYL/Preprocess/out/DYL-3_H7VFTALXX_L2_1.clean.fq /home/ubuntu/DYL/Preprocess/out/DYL-3_H7VFTALXX_L2_2.clean.fq

*************************DETAILS***********************************
Last 10 commands run before the error (/home/ubuntu/DYL/Logs/COMMANDS.log)
|2017-06-22 15:03:20| ln /home/ubuntu/DYL/Preprocess/out/DYL-3_H7VFTALXX_L2_1.clean.fq /home/ubuntu/DYL/Preprocess/out/lib3.1.fastq
|2017-06-22 15:03:20| ln /home/ubuntu/DYL/Preprocess/out/DYL-3_H7VFTALXX_L2_2.clean.fq /home/ubuntu/DYL/Preprocess/out/lib3.2.fastq
|2017-06-22 15:03:20| which python
|2017-06-22 15:03:20| echo $PYTHONPATH
|2017-06-22 15:03:41| ln /home/ubuntu/DYL/Preprocess/out/lib3.seq /home/ubuntu/DYL/Preprocess/out/lib3.fastq
|2017-06-22 15:05:41| java -cp /home/ubuntu/metAMOS-1.5rc3/Utilities/java:. convertFastqToFasta /home/ubuntu/DYL/Preprocess/out/lib3.seq /home/ubuntu/DYL/Preprocess/out/lib3.fasta /home/ubuntu/DYL/Preprocess/out/lib3.fasta.qual
|2017-06-22 15:06:42| java -cp /home/ubuntu/metAMOS-1.5rc3/Utilities/java:. convertFastqToFasta /home/ubuntu/DYL/Preprocess/out/lib3.1.fastq /home/ubuntu/DYL/Preprocess/out/lib3.1.fasta /home/ubuntu/DYL/Preprocess/out/lib3.1.fasta.qual
|2017-06-22 15:07:43| java -cp /home/ubuntu/metAMOS-1.5rc3/Utilities/java:. convertFastqToFasta /home/ubuntu/DYL/Preprocess/out/lib3.2.fastq /home/ubuntu/DYL/Preprocess/out/lib3.2.fasta /home/ubuntu/DYL/Preprocess/out/lib3.2.fasta.qual
|2017-06-22 15:29:05| /home/ubuntu/metAMOS-1.5rc3/FastQC/fastqc -t 63 /home/ubuntu/DYL/Preprocess/out/DYL-1_H7VFTALXX_L2_1.clean.fq /home/ubuntu/DYL/Preprocess/out/DYL-1_H7VFTALXX_L2_2.clean.fq /home/ubuntu/DYL/Preprocess/out/DYL-2_H7VFTALXX_L2_1.clean.fq /home/ubuntu/DYL/Preprocess/out/DYL-2_H7VFTALXX_L2_2.clean.fq /home/ubuntu/DYL/Preprocess/out/DYL-3_H7VFTALXX_L2_1.clean.fq /home/ubuntu/DYL/Preprocess/out/DYL-3_H7VFTALXX_L2_2.clean.fq

Last 10 lines of output (/home/ubuntu/DYL/Logs/PREPROCESS.log)
Approx 5% complete for DYL-3_H7VFTALXX_L2_1.clean.fq
Approx 100% complete for DYL-1_H7VFTALXX_L2_2.clean.fq
Approx 5% complete for DYL-3_H7VFTALXX_L2_2.clean.fq
Approx 10% complete for DYL-2_H7VFTALXX_L2_1.clean.fq
Approx 10% complete for DYL-2_H7VFTALXX_L2_2.clean.fq
Approx 10% complete for DYL-3_H7VFTALXX_L2_1.clean.fq
Approx 10% complete for DYL-3_H7VFTALXX_L2_2.clean.fq
Approx 15% complete for DYL-2_H7VFTALXX_L2_1.clean.fq
Approx 15% complete for DYL-2_H7VFTALXX_L2_2.clean.fq
Approx 15% complete for DYL-3_H7VFTALXX_L2_1.clean.fq

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

Log files: COMMANDS:

|2017-06-22 14:53:51|# [PREPROCESS]
|2017-06-22 14:53:51| rm /home/ubuntu/DYL/Preprocess/out/all.seq.mates
|2017-06-22 14:58:35| perl /home/ubuntu/metAMOS-1.5rc3/Utilities/perl/shuffleSequences_fastq.pl  /home/ubuntu/DYL/Preprocess/out/DYL-1_H7VFTALXX_L2_1.clean.fq /home/ubuntu/DYL/Preprocess/out/DYL-1_H7VFTALXX_L2_2.clean.fq /home/ubuntu/DYL/Preprocess/out/lib1.seq
|2017-06-22 14:58:35| ln /home/ubuntu/DYL/Preprocess/out/DYL-1_H7VFTALXX_L2_1.clean.fq /home/ubuntu/DYL/Preprocess/out/lib1.1.fastq
|2017-06-22 14:58:35| ln /home/ubuntu/DYL/Preprocess/out/DYL-1_H7VFTALXX_L2_2.clean.fq /home/ubuntu/DYL/Preprocess/out/lib1.2.fastq
|2017-06-22 14:58:35| which python
|2017-06-22 14:58:35| echo $PYTHONPATH
|2017-06-22 14:58:36| ln /home/ubuntu/DYL/Preprocess/out/lib1.seq /home/ubuntu/DYL/Preprocess/out/lib1.fastq
|2017-06-22 14:59:03| java -cp /home/ubuntu/metAMOS-1.5rc3/Utilities/java:. convertFastqToFasta /home/ubuntu/DYL/Preprocess/out/lib1.seq /home/ubuntu/DYL/Preprocess/out/lib1.fasta /home/ubuntu/DYL/Preprocess/out/lib1.fasta.qual
|2017-06-22 14:59:08| java -cp /home/ubuntu/metAMOS-1.5rc3/Utilities/java:. convertFastqToFasta /home/ubuntu/DYL/Preprocess/out/lib1.1.fastq /home/ubuntu/DYL/Preprocess/out/lib1.1.fasta /home/ubuntu/DYL/Preprocess/out/lib1.1.fasta.qual
|2017-06-22 14:59:13| java -cp /home/ubuntu/metAMOS-1.5rc3/Utilities/java:. convertFastqToFasta /home/ubuntu/DYL/Preprocess/out/lib1.2.fastq /home/ubuntu/DYL/Preprocess/out/lib1.2.fasta /home/ubuntu/DYL/Preprocess/out/lib1.2.fasta.qual
|2017-06-22 14:59:22| perl /home/ubuntu/metAMOS-1.5rc3/Utilities/perl/shuffleSequences_fastq.pl  /home/ubuntu/DYL/Preprocess/out/DYL-2_H7VFTALXX_L2_1.clean.fq /home/ubuntu/DYL/Preprocess/out/DYL-2_H7VFTALXX_L2_2.clean.fq /home/ubuntu/DYL/Preprocess/out/lib2.seq
|2017-06-22 14:59:22| ln /home/ubuntu/DYL/Preprocess/out/DYL-2_H7VFTALXX_L2_1.clean.fq /home/ubuntu/DYL/Preprocess/out/lib2.1.fastq
|2017-06-22 14:59:22| ln /home/ubuntu/DYL/Preprocess/out/DYL-2_H7VFTALXX_L2_2.clean.fq /home/ubuntu/DYL/Preprocess/out/lib2.2.fastq
|2017-06-22 14:59:22| which python
|2017-06-22 14:59:22| echo $PYTHONPATH
|2017-06-22 14:59:39| ln /home/ubuntu/DYL/Preprocess/out/lib2.seq /home/ubuntu/DYL/Preprocess/out/lib2.fastq
|2017-06-22 15:01:26| java -cp /home/ubuntu/metAMOS-1.5rc3/Utilities/java:. convertFastqToFasta /home/ubuntu/DYL/Preprocess/out/lib2.seq /home/ubuntu/DYL/Preprocess/out/lib2.fasta /home/ubuntu/DYL/Preprocess/out/lib2.fasta.qual
|2017-06-22 15:02:17| java -cp /home/ubuntu/metAMOS-1.5rc3/Utilities/java:. convertFastqToFasta /home/ubuntu/DYL/Preprocess/out/lib2.1.fastq /home/ubuntu/DYL/Preprocess/out/lib2.1.fasta /home/ubuntu/DYL/Preprocess/out/lib2.1.fasta.qual
|2017-06-22 15:03:10| java -cp /home/ubuntu/metAMOS-1.5rc3/Utilities/java:. convertFastqToFasta /home/ubuntu/DYL/Preprocess/out/lib2.2.fastq /home/ubuntu/DYL/Preprocess/out/lib2.2.fasta /home/ubuntu/DYL/Preprocess/out/lib2.2.fasta.qual
|2017-06-22 15:03:20| perl /home/ubuntu/metAMOS-1.5rc3/Utilities/perl/shuffleSequences_fastq.pl  /home/ubuntu/DYL/Preprocess/out/DYL-3_H7VFTALXX_L2_1.clean.fq /home/ubuntu/DYL/Preprocess/out/DYL-3_H7VFTALXX_L2_2.clean.fq /home/ubuntu/DYL/Preprocess/out/lib3.seq
|2017-06-22 15:03:20| ln /home/ubuntu/DYL/Preprocess/out/DYL-3_H7VFTALXX_L2_1.clean.fq /home/ubuntu/DYL/Preprocess/out/lib3.1.fastq
|2017-06-22 15:03:20| ln /home/ubuntu/DYL/Preprocess/out/DYL-3_H7VFTALXX_L2_2.clean.fq /home/ubuntu/DYL/Preprocess/out/lib3.2.fastq
|2017-06-22 15:03:20| which python
|2017-06-22 15:03:20| echo $PYTHONPATH
|2017-06-22 15:03:41| ln /home/ubuntu/DYL/Preprocess/out/lib3.seq /home/ubuntu/DYL/Preprocess/out/lib3.fastq
|2017-06-22 15:05:41| java -cp /home/ubuntu/metAMOS-1.5rc3/Utilities/java:. convertFastqToFasta /home/ubuntu/DYL/Preprocess/out/lib3.seq /home/ubuntu/DYL/Preprocess/out/lib3.fasta /home/ubuntu/DYL/Preprocess/out/lib3.fasta.qual
|2017-06-22 15:06:42| java -cp /home/ubuntu/metAMOS-1.5rc3/Utilities/java:. convertFastqToFasta /home/ubuntu/DYL/Preprocess/out/lib3.1.fastq /home/ubuntu/DYL/Preprocess/out/lib3.1.fasta /home/ubuntu/DYL/Preprocess/out/lib3.1.fasta.qual
|2017-06-22 15:07:43| java -cp /home/ubuntu/metAMOS-1.5rc3/Utilities/java:. convertFastqToFasta /home/ubuntu/DYL/Preprocess/out/lib3.2.fastq /home/ubuntu/DYL/Preprocess/out/lib3.2.fasta /home/ubuntu/DYL/Preprocess/out/lib3.2.fasta.qual
|2017-06-22 15:29:05| /home/ubuntu/metAMOS-1.5rc3/FastQC/fastqc -t 63 /home/ubuntu/DYL/Preprocess/out/DYL-1_H7VFTALXX_L2_1.clean.fq /home/ubuntu/DYL/Preprocess/out/DYL-1_H7VFTALXX_L2_2.clean.fq /home/ubuntu/DYL/Preprocess/out/DYL-2_H7VFTALXX_L2_1.clean.fq /home/ubuntu/DYL/Preprocess/out/DYL-2_H7VFTALXX_L2_2.clean.fq /home/ubuntu/DYL/Preprocess/out/DYL-3_H7VFTALXX_L2_1.clean.fq /home/ubuntu/DYL/Preprocess/out/DYL-3_H7VFTALXX_L2_2.clean.fq

PREPROCESS:

rm: cannot remove '/home/ubuntu/DYL/Preprocess/out/all.seq.mates': No such file or directory
/usr/bin/python
/home/ubuntu/metAMOS-1.5rc3/Utilities/python:/home/ubuntu/metAMOS-1.5rc3/Utilities/ruffus:/home/ubuntu/metAMOS-1.5rc3/Utilities/python/lib:/home/ubuntu/metAMOS-1.5rc3/Utilities/python/lib/python:/home/ubuntu/metAMOS-1.5rc3/Utilities/python/lib64:/home/ubuntu/metAMOS-1.5rc3/Utilities/python/lib64/python:/home/ubuntu/metAMOS-1.5rc3/Utilities:
/usr/bin/python
/home/ubuntu/metAMOS-1.5rc3/Utilities/python:/home/ubuntu/metAMOS-1.5rc3/Utilities/ruffus:/home/ubuntu/metAMOS-1.5rc3/Utilities/python/lib:/home/ubuntu/metAMOS-1.5rc3/Utilities/python/lib/python:/home/ubuntu/metAMOS-1.5rc3/Utilities/python/lib64:/home/ubuntu/metAMOS-1.5rc3/Utilities/python/lib64/python:/home/ubuntu/metAMOS-1.5rc3/Utilities:
/usr/bin/python
/home/ubuntu/metAMOS-1.5rc3/Utilities/python:/home/ubuntu/metAMOS-1.5rc3/Utilities/ruffus:/home/ubuntu/metAMOS-1.5rc3/Utilities/python/lib:/home/ubuntu/metAMOS-1.5rc3/Utilities/python/lib/python:/home/ubuntu/metAMOS-1.5rc3/Utilities/python/lib64:/home/ubuntu/metAMOS-1.5rc3/Utilities/python/lib64/python:/home/ubuntu/metAMOS-1.5rc3/Utilities:
Analysis complete for DYL-1_H7VFTALXX_L2_1.clean.fq
Analysis complete for DYL-1_H7VFTALXX_L2_2.clean.fq
#
# A fatal error has been detected by the Java Runtime Environment:
#
#  SIGSEGV (0xb) at pc=0x00007fd8ca11b009, pid=4429, tid=4559
#
# JRE version: OpenJDK Runtime Environment (9.0) (build 9-internal+0-2016-04-14-195246.buildd.src)
# Java VM: OpenJDK 64-Bit Server VM (9-internal+0-2016-04-14-195246.buildd.src, mixed mode, tiered, compressed oops, g1 gc, linux-amd64)
# Problematic frame:
# C  [libjava.so+0x1d009]  JNU_GetEnv+0x19
#
# Core dump will be written. Default location: Core dumps may be processed with "/usr/share/apport/apport %p %s %c %P" (or dumping to /home/ubuntu/DYL/Preprocess/out/core.4429)
#
# An error report file with more information is saved as:
# /home/ubuntu/DYL/Preprocess/out/hs_err_pid4429.log
#
# If you would like to submit a bug report, please visit:
#   http://bugreport.java.com/bugreport/crash.jsp
# The crash happened outside the Java Virtual Machine in native code.
# See problematic frame for where to report the bug.
#
Started analysis of DYL-1_H7VFTALXX_L2_1.clean.fq
Approx 5% complete for DYL-1_H7VFTALXX_L2_1.clean.fq
Started analysis of DYL-1_H7VFTALXX_L2_2.clean.fq
Approx 10% complete for DYL-1_H7VFTALXX_L2_1.clean.fq
Approx 5% complete for DYL-1_H7VFTALXX_L2_2.clean.fq
Started analysis of DYL-2_H7VFTALXX_L2_1.clean.fq
Approx 15% complete for DYL-1_H7VFTALXX_L2_1.clean.fq
Approx 10% complete for DYL-1_H7VFTALXX_L2_2.clean.fq
Approx 20% complete for DYL-1_H7VFTALXX_L2_1.clean.fq
Approx 15% complete for DYL-1_H7VFTALXX_L2_2.clean.fq
Started analysis of DYL-2_H7VFTALXX_L2_2.clean.fq
Approx 25% complete for DYL-1_H7VFTALXX_L2_1.clean.fq
Approx 20% complete for DYL-1_H7VFTALXX_L2_2.clean.fq
Approx 30% complete for DYL-1_H7VFTALXX_L2_1.clean.fq
Started analysis of DYL-3_H7VFTALXX_L2_1.clean.fq
Approx 25% complete for DYL-1_H7VFTALXX_L2_2.clean.fq
Approx 35% complete for DYL-1_H7VFTALXX_L2_1.clean.fq
Approx 30% complete for DYL-1_H7VFTALXX_L2_2.clean.fq
Started analysis of DYL-3_H7VFTALXX_L2_2.clean.fq
Approx 40% complete for DYL-1_H7VFTALXX_L2_1.clean.fq
Approx 35% complete for DYL-1_H7VFTALXX_L2_2.clean.fq
Approx 45% complete for DYL-1_H7VFTALXX_L2_1.clean.fq
Approx 40% complete for DYL-1_H7VFTALXX_L2_2.clean.fq
Approx 50% complete for DYL-1_H7VFTALXX_L2_1.clean.fq
Approx 45% complete for DYL-1_H7VFTALXX_L2_2.clean.fq
Approx 55% complete for DYL-1_H7VFTALXX_L2_1.clean.fq
Approx 50% complete for DYL-1_H7VFTALXX_L2_2.clean.fq
Approx 60% complete for DYL-1_H7VFTALXX_L2_1.clean.fq
Approx 55% complete for DYL-1_H7VFTALXX_L2_2.clean.fq
Approx 65% complete for DYL-1_H7VFTALXX_L2_1.clean.fq
Approx 60% complete for DYL-1_H7VFTALXX_L2_2.clean.fq
Approx 70% complete for DYL-1_H7VFTALXX_L2_1.clean.fq
Approx 65% complete for DYL-1_H7VFTALXX_L2_2.clean.fq
Approx 5% complete for DYL-2_H7VFTALXX_L2_1.clean.fq
Approx 75% complete for DYL-1_H7VFTALXX_L2_1.clean.fq
Approx 70% complete for DYL-1_H7VFTALXX_L2_2.clean.fq
Approx 80% complete for DYL-1_H7VFTALXX_L2_1.clean.fq
Approx 75% complete for DYL-1_H7VFTALXX_L2_2.clean.fq
Approx 5% complete for DYL-2_H7VFTALXX_L2_2.clean.fq
Approx 85% complete for DYL-1_H7VFTALXX_L2_1.clean.fq
Approx 80% complete for DYL-1_H7VFTALXX_L2_2.clean.fq
Approx 90% complete for DYL-1_H7VFTALXX_L2_1.clean.fq
Approx 85% complete for DYL-1_H7VFTALXX_L2_2.clean.fq
Approx 95% complete for DYL-1_H7VFTALXX_L2_1.clean.fq
Approx 90% complete for DYL-1_H7VFTALXX_L2_2.clean.fq
Approx 95% complete for DYL-1_H7VFTALXX_L2_2.clean.fq
Approx 100% complete for DYL-1_H7VFTALXX_L2_1.clean.fq
Approx 5% complete for DYL-3_H7VFTALXX_L2_1.clean.fq
Approx 100% complete for DYL-1_H7VFTALXX_L2_2.clean.fq
Approx 5% complete for DYL-3_H7VFTALXX_L2_2.clean.fq
Approx 10% complete for DYL-2_H7VFTALXX_L2_1.clean.fq
Approx 10% complete for DYL-2_H7VFTALXX_L2_2.clean.fq
Approx 10% complete for DYL-3_H7VFTALXX_L2_1.clean.fq
Approx 10% complete for DYL-3_H7VFTALXX_L2_2.clean.fq
Approx 15% complete for DYL-2_H7VFTALXX_L2_1.clean.fq
Approx 15% complete for DYL-2_H7VFTALXX_L2_2.clean.fq
Approx 15% complete for DYL-3_H7VFTALXX_L2_1.clean.fq
#metAMOS pipeline configuration file
inherit:    
command:    -q  -a spades -o 20 -m bowtie2 -b  -u
modify: False
asmcontigs: 
lib1format: fastq
lib1mated:  True
lib1innie:  True
lib1interleaved:    False
lib1f1: DYL-1_H7VFTALXX_L2_1.clean.fq,300,1000,650,350
lib1f2: DYL-1_H7VFTALXX_L2_2.clean.fq,300,1000,650,350
lib2format: fastq
lib2mated:  True
lib2innie:  True
lib2interleaved:    False
lib2f1: DYL-2_H7VFTALXX_L2_1.clean.fq,300,1000,650,350
lib2f2: DYL-2_H7VFTALXX_L2_2.clean.fq,300,1000,650,350
lib3format: fastq
lib3mated:  True
lib3innie:  True
lib3interleaved:    False
lib3f1: DYL-3_H7VFTALXX_L2_1.clean.fq,300,1000,650,350
lib3f2: DYL-3_H7VFTALXX_L2_2.clean.fq,300,1000,650,350
skoren commented 7 years ago

This error is outside metAMOS and FastQC, the JVM is segfaulting on your system. This probably indicates either an installation error with the JVM or perhaps overloading the system memory. Have you confirmed you can run any of the test datasets provided with metAMOS on the system?

You can skip fastq by not specifying the -q option to metAMOS.

jingzhejiang commented 7 years ago

Hi, Skoren

After I replaced openJDK-9 with openJDK-8, problem has been solved.

Thank you!

Jingzhe