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barricklab / breseq

breseq is a computational pipeline for finding mutations relative to a reference sequence in short-read DNA resequencing data. It is intended for haploid microbial genomes (<20 Mb). breseq is a command line tool implemented in C++ and R.
http://barricklab.org/breseq
GNU General Public License v2.0
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run_tests.sh fails when using bowtie2-2.3.0 #108

Closed pvphaneuf closed 7 years ago

pvphaneuf commented 7 years ago

Executing on Ubuntu 16.04.

The following is the output containing the errors from ./run_tests.sh

TEST: tests/lambda_mult_ref_read/testcmd.sh clean
++++++++++++++++++++++++++++++++++++++++++++++++++++++++
TEST DIRECTORY: tests/lambda_mult_ref_read
++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Elapsed time for 'make test': 00:00
TEST: tests/lambda_mult_ref_read/testcmd.sh test
++++++++++++++++++++++++++++++++++++++++++++++++++++++++
TEST DIRECTORY: tests/lambda_mult_ref_read
++++++++++++++++++++++++++++++++++++++++++++++++++++++++
BRESEQ COMMAND:
bin/breseq -o tests/lambda_mult_ref_read -r tests/lambda_mult_ref_read/../data/lambda/lambda.1-2.gbk -r tests/lambda_mult_ref_read/../data/lambda/lambda.3.gbk -r tests/lambda_mult_ref_read/../data/lambda/lambda.4.gbk -r tests/lambda_mult_ref_read/../data/lambda/lambda.5.gbk -l 50 tests/lambda_mult_ref_read/../data/lambda/lambda_mixed_population.1.fastq tests/lambda_mult_ref_read/../data/lambda/lambda_mixed_population.2.fastq tests/lambda_mult_ref_read/../data/lambda/lambda_mixed_population.3.fastq tests/lambda_mult_ref_read/../data/lambda/lambda_mixed_population.4.fastq tests/lambda_mult_ref_read/../data/lambda/lambda_mixed_population.5.fastq
In test mode. Program data path: share/breseq
================================================================================
breseq 0.29.0  revision 8f9c342918e4   http://barricklab.org/breseq

Active Developers: Barrick JE, Deatherage DE
Contact:           <jeffrey.e.barrick@gmail.com>

breseq is free software; you can redistribute it and/or modify it under the
terms the GNU General Public License as published by the Free Software 
Foundation; either version 2, or (at your option) any later version.

Copyright (c) 2008-2010 Michigan State University
Copyright (c) 2011-2016 The University of Texas at Austin

If you use breseq in your research, please cite:

  Deatherage, D.E., Barrick, J.E. (2014) Identification of mutations
  in laboratory-evolved microbes from next-generation sequencing
  data using breseq. Methods Mol. Biol. 1151: 165–188.

If you use structural variation (junction) predictions, please cite:

  Barrick, J.E., Colburn, G., Deatherage D.E., Traverse, C.C.,
  Strand, M.D., Borges, J.J., Knoester, D.B., Reba, A., Meyer, A.G. 
  (2014) Identifying structural variation in haploid microbial genomes 
  from short-read resequencing data using breseq. BMC Genomics 15:1039.
================================================================================
---> bowtie2  :: version 2.3.0 [/home/flagg/bowtie2-2.3.0/bowtie2]
---> R        :: version 3.2.3 [/usr/bin/R]
+++   NOW PROCESSING Read and reference sequence file input
  READ FILE::lambda_mixed_population.1
    Converting/filtering FASTQ file...
    Original base quality format: SANGER New format: SANGER
    Original reads: 40000 bases: 1400000
    Filtered reads: 0 (≥50% N) 3 (≥90% one base)
    Analyzed reads: 39997 bases: 1399895
  READ FILE::lambda_mixed_population.2
    Converting/filtering FASTQ file...
    Original base quality format: SANGER New format: SANGER
    Original reads: 40000 bases: 1400000
    Filtered reads: 0 (≥50% N) 3 (≥90% one base)
    Analyzed reads: 29292 bases: 1025220
  READ FILE::lambda_mixed_population.3
  ::SKIPPED DUE TO REACHING COVERAGE LIMIT::
  READ FILE::lambda_mixed_population.4
  ::SKIPPED DUE TO REACHING COVERAGE LIMIT::
  READ FILE::lambda_mixed_population.5
  ::SKIPPED DUE TO REACHING COVERAGE LIMIT::
  ::TOTAL::
    Original reads: 80000 bases: 2800000
    Analyzed reads: 69289 bases: 2425115
[samtools] faidx tests/lambda_mult_ref_read/data/reference.fasta
  REFERENCE: NC_001416-0
  LENGTH: 9700
  REFERENCE: NC_001416-1
  LENGTH: 9700
  REFERENCE: NC_001416-2
  LENGTH: 9701
  REFERENCE: NC_001416-3
  LENGTH: 9700
  REFERENCE: NC_001416-4
  LENGTH: 9701
+++   NOW PROCESSING Read alignment to reference genome
[system] bowtie2-build -q tests/lambda_mult_ref_read/data/reference.fasta tests/lambda_mult_ref_read/02_reference_alignment/reference
[system] bowtie2 -t -p 1 --local  -L 17 --ma 1 --mp 3 --np 0 --rdg 2,3 --rfg 2,3 --ignore-quals  -k 2000 -i S,1,0.25 --score-min L,0,0.9  --reorder -x tests/lambda_mult_ref_read/02_reference_alignment/reference -U tests/lambda_mult_ref_read/01_sequence_conversion/lambda_mixed_population.1.converted.fastq -S tests/lambda_mult_ref_read/02_reference_alignment/lambda_mixed_population.1.stage1.sam --un tests/lambda_mult_ref_read/02_reference_alignment/lambda_mixed_population.1.stage1.unmatched.fastq
Error: the match penalty is greater than 0 (1) but the --score-min function can be less than or equal to zero.  Either let the match penalty be 0 or make --score-min always positive.
Error: Encountered internal Bowtie 2 exception (#1)
Command: /home/flagg/bowtie2-2.3.0/bowtie2-align-s --wrapper basic-0 -t -p 1 --local -L 17 --ma 1 --mp 3 --np 0 --rdg 2,3 --rfg 2,3 --ignore-quals -k 2000 -i S,1,0.25 --score-min L,0,0.9 --reorder -x tests/lambda_mult_ref_read/02_reference_alignment/reference --passthrough -U tests/lambda_mult_ref_read/01_sequence_conversion/lambda_mixed_population.1.converted.fastq 
(ERR): bowtie2-align exited with value 1
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!> FATAL ERROR <!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Error running command:
[system] bowtie2 -t -p 1 --local  -L 17 --ma 1 --mp 3 --np 0 --rdg 2,3 --rfg 2,3 --ignore-quals  -k 2000 -i S,1,0.25 --score-min L,0,0.9  --reorder -x tests/lambda_mult_ref_read/02_reference_alignment/reference -U tests/lambda_mult_ref_read/01_sequence_conversion/lambda_mixed_population.1.converted.fastq -S tests/lambda_mult_ref_read/02_reference_alignment/lambda_mixed_population.1.stage1.sam --un tests/lambda_mult_ref_read/02_reference_alignment/lambda_mixed_population.1.stage1.unmatched.fastq
Result code: 256
FILE: libbreseq/common.h   LINE: 1384
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

Comparing files: output/evidence/annotated.gd expected.gd
/usr/bin/diff: output/evidence/annotated.gd: No such file or directory
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
Failed check
/usr/bin/diff: output/evidence/annotated.gd: No such file or directory
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

bin/gdtools COMPARE -r tests/lambda_mult_ref_read/../data/lambda/lambda.1-2.gbk -r tests/lambda_mult_ref_read/../data/lambda/lambda.3.gbk -r tests/lambda_mult_ref_read/../data/lambda/lambda.4.gbk -r tests/lambda_mult_ref_read/../data/lambda/lambda.5.gbk -o tests/lambda_mult_ref_read/failed_compare.html tests/lambda_mult_ref_read/output/evidence/annotated.gd tests/lambda_mult_ref_read/expected.gd
In test mode. Program data path: share/breseq
================================================================================
breseq 0.29.0  revision 8f9c342918e4   http://barricklab.org/breseq

Active Developers: Barrick JE, Deatherage DE
Contact:           <jeffrey.e.barrick@gmail.com>

breseq is free software; you can redistribute it and/or modify it under the
terms the GNU General Public License as published by the Free Software 
Foundation; either version 2, or (at your option) any later version.

Copyright (c) 2008-2010 Michigan State University
Copyright (c) 2011-2016 The University of Texas at Austin

If you use breseq in your research, please cite:

  Deatherage, D.E., Barrick, J.E. (2014) Identification of mutations
  in laboratory-evolved microbes from next-generation sequencing
  data using breseq. Methods Mol. Biol. 1151: 165–188.

If you use structural variation (junction) predictions, please cite:

  Barrick, J.E., Colburn, G., Deatherage D.E., Traverse, C.C.,
  Strand, M.D., Borges, J.J., Knoester, D.B., Reba, A., Meyer, A.G. 
  (2014) Identifying structural variation in haploid microbial genomes 
  from short-read resequencing data using breseq. BMC Genomics 15:1039.
================================================================================

*** Begin ANNOTATE/COMPARE ***

    Reading input reference sequence files
        tests/lambda_mult_ref_read/../data/lambda/lambda.1-2.gbk,tests/lambda_mult_ref_read/../data/lambda/lambda.3.gbk,tests/lambda_mult_ref_read/../data/lambda/lambda.4.gbk,tests/lambda_mult_ref_read/../data/lambda/lambda.5.gbk

    Reading input GD file: tests/lambda_mult_ref_read/output/evidence/annotated.gd
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!> FATAL ERROR <!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Could not open file for reading: tests/lambda_mult_ref_read/output/evidence/annotated.gd
FILE: genome_diff.cpp   LINE: 1648
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Elapsed time for 'make test': 00:01
jeffreybarrick commented 7 years ago

Thanks for the heads up.

This is fixed in code that has been committed that will be in v0.29.1 by having breseq slightly change the score cutoff formula that it uses to call bowtie2.