run_test.sh fails for v0.35.0

[vr1087]

I downloaded breseq-0.35.0-Linux-x86_64.tar.gz and ran ./run_test.sh. The test failed with breseq saying it could not open tests/lambda_mult_ref_read/../data/lambda/empty.fastq for reading. It looks like that file doesn't exist in the downloaded tar.

> wget https://github.com/barricklab/breseq/releases/download/v0.35.0/breseq-0.35.0-Linux-x86_64.tar.gz
> tar -xvzf breseq-0.35.0-Linux-x86_64.tar.gz
> cd breseq-0.35.0-Linux-x86_64
> ./run_tests.sh 
3 
TEST: tests/lambda_mult_ref_read/testcmd.sh clean
++++++++++++++++++++++++++++++++++++++++++++++++++++++++
TEST DIRECTORY: tests/lambda_mult_ref_read
++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Elapsed time for 'make test': 00:00
3 
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/empty.fastq tests/lambda_mult_ref_read/../data/lambda/only_bad.fastq 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
Program data path set via BRESEQ_DATA_PATH: share/breseq
================================================================================
breseq 0.35.0  revision fe39cd8f5880   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) 2011-2017 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 2.3.4.1 [/usr/bin/bowtie2]
---> R        :: version 3.4.4 [/usr/bin/R]
+++   NOW PROCESSING Read and reference sequence file input
  READ FILE::empty
    Converting/filtering FASTQ file...
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!> FATAL ERROR <!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Could not open file for input: tests/lambda_mult_ref_read/../data/lambda/empty.fastq
FILE: ./libbreseq/common.h   LINE: 373
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!> STACK TRACE <!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Backtrace with 8 stack frames.
bin/breseq() [0x43ac46]
bin/breseq() [0x4b2e68]
bin/breseq() [0x4b6bfa]
bin/breseq() [0x4b720f]
bin/breseq() [0x4283d9]
bin/breseq() [0x40a6fe]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xe7) [0x7f25b9e94b97]
bin/breseq() [0x417e99]
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
Failed check
Non-zero error code returned.
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
Elapsed time for 'make test': 00:00

> cd tests/data/lambda
> tree
.
├── lambda.1-2.gbk
├── lambda.3.gbk
├── lambda.4.gbk
├── lambda.5.gbk
├── lambda_mixed_population.1.fastq
├── lambda_mixed_population.2.fastq
├── lambda_mixed_population.3.fastq
├── lambda_mixed_population.4.fastq
└── lambda_mixed_population.5.fastq

[jeffreybarrick]

Thanks for reporting. This and a few other problems with the tests in the binary downloads are fixed for the next release.

[nieder]

Are empty.fastq and run_tests.sh only available in the binary downloads? Building the source tarball breseq-0.35.1-Source.tar.gz and then make test (after ./configure; make) gives the same error about empty.fastq, and run_tests.sh doesn't exist either.

[jeffreybarrick]

Thanks for the letting me know about this. It was an oversight that the tests weren't fixed in the Source version. I've just updated breseq-0.35.1-Source.tar.gz that you can download from the release page so that make test will work as expected. I've also included the ./run_tests.sh script to match the binary distribution. (Either method runs the same tests.)

[nieder]

Works now. Thanks.