Bug#977343: RFS: breseq/0.35.4+ds-1 [ITP] -- Find mutations relative to reference sequences
On Mon, Dec 14, 2020 at 08:47:42AM +0100, Gürkan Myczko wrote:
> * Package name : breseq
> Version : 0.35.4+ds-1
> Changes for the initial release:
>
> breseq (0.35.4+ds-1) unstable; urgency=medium
> .
> * Initial release. (Closes: #942845)
Alas, it fails tests -- then continues to build the package successfully:
dh_auto_test
make -j64 test VERBOSE=1
make[1]: Entering directory '/<<PKGBUILDDIR>>'
echo "export TESTBINPREFIX=./src/c/breseq" > ./tests/test.config;
echo "export BRESEQ_DATA_PATH=./src/c/breseq" >> ./tests/test.config;
echo "export BRESEQ_TEST_THREAD_ARG=\"-j 4\"" >> ./tests/test.config;
./tests/test.sh test tests
3
TEST: tests/lambda_mult_ref_read/testcmd.sh test
++++++++++++++++++++++++++++++++++++++++++++++++++++++++
TEST DIRECTORY: tests/lambda_mult_ref_read
++++++++++++++++++++++++++++++++++++++++++++++++++++++++
BRESEQ COMMAND:
./src/c/breseq/breseq -j 4 -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: ./src/c/breseq
================================================================================
breseq 0.35.4 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.
================================================================================
---> ERROR Required executable "bowtie2" or "bowtie2-build" not found.
---> See http://bowtie-bio.sourceforge.net/bowtie2
---> ERROR Required executable "R" not found.
---> See http://www.r-project.org
Comparing files: "tests/lambda_mult_ref_read/output/evidence/annotated.gd" "tests/lambda_mult_ref_read/expected.gd"
/usr/bin/diff: tests/lambda_mult_ref_read/output/evidence/annotated.gd: No such file or directory
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
Failed check
/usr/bin/diff: tests/lambda_mult_ref_read/output/evidence/annotated.gd: No such file or directory
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
./src/c/breseq/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
Program data path set via BRESEQ_DATA_PATH: ./src/c/breseq
================================================================================
breseq 0.35.4 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.
================================================================================
*** 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: 59
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!> STACK TRACE <!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Backtrace with 8 stack frames.
./src/c/breseq/gdtools(+0x9a831) [0x55aed0ad4831]
./src/c/breseq/gdtools(+0xf8720) [0x55aed0b32720]
./src/c/breseq/gdtools(+0xf9bca) [0x55aed0b33bca]
./src/c/breseq/gdtools(+0x909ca) [0x55aed0aca9ca]
./src/c/breseq/gdtools(+0x9294e) [0x55aed0acc94e]
./src/c/breseq/gdtools(+0x525b2) [0x55aed0a8c5b2]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xea) [0x7f4d9ddcdd0a]
./src/c/breseq/gdtools(+0x5d3da) [0x55aed0a973da]
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Elapsed time for 'make test': 00:00
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
It doesn't seem to me like either fail is expected.
Meow!
--
⢀⣴⠾⠻⢶⣦⠀ .--[ Makefile ]
⣾⠁⢠⠒⠀⣿⡁ # beware of races
⢿⡄⠘⠷⠚⠋⠀ all: pillage burn
⠈⠳⣄⠀⠀⠀⠀ `----
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