[Debian-med-packaging] Bug#1006657: bowtie2 breaks optimir autopkgtest: Error with system call: Bowtie2 index creation failed

[Paul Gevers]

Source: bowtie2, optimir
Control: found -1 bowtie2/2.4.5-1
Control: found -1 optimir/1.1-1
Severity: serious
Tags: sid bookworm
User: debian-ci at lists.debian.org
Usertags: breaks needs-update

Dear maintainer(s),

With a recent upload of bowtie2 the autopkgtest of optimir fails in 
testing when that autopkgtest is run with the binary packages of bowtie2 
from unstable. It passes when run with only packages from testing. In 
tabular form:

                        pass            fail
bowtie2                from testing    2.4.5-1
optimir                from testing    1.1-1
all others             from testing    from testing

I copied some of the output at the bottom of this report.

Currently this regression is blocking the migration of bowtie2 to 
testing [1]. Due to the nature of this issue, I filed this bug report 
against both packages. Can you please investigate the situation and 
reassign the bug to the right package?

More information about this bug and the reason for filing it can be found on
https://wiki.debian.org/ContinuousIntegration/RegressionEmailInformation

Paul

[1] https://qa.debian.org/excuses.php?package=bowtie2

https://ci.debian.net/data/autopkgtest/testing/amd64/o/optimir/19635699/log.gz

No output file specified!
Bowtie 2 version 2.4.5 by Ben Langmead (langmea at cs.jhu.edu, 
www.cs.jhu.edu/~langmea)
Usage: bowtie2-build [options]* <reference_in> <bt2_index_base>
     reference_in            comma-separated list of files with ref 
sequences
     bt2_index_base          write bt2 data to files with this dir/basename
*** Bowtie 2 indexes will work with Bowtie v1.2.3 and later. ***
Options:
     -f                      reference files are Fasta (default)
     -c                      reference sequences given on cmd line (as
                             <reference_in>)
     --large-index           force generated index to be 'large', even 
if ref
                             has fewer than 4 billion nucleotides
     --debug                 use the debug binary; slower, assertions 
enabled
     --verbose               log the issued command
     -a/--noauto             disable automatic -p/--bmax/--dcv 
memory-fitting
     -p/--packed             use packed strings internally; slower, less 
memory
     --bmax <int>            max bucket sz for blockwise suffix-array 
builder
     --bmaxdivn <int>        max bucket sz as divisor of ref len 
(default: 4)
     --dcv <int>             diff-cover period for blockwise (default: 1024)
     --nodc                  disable diff-cover (algorithm becomes 
quadratic)
     -r/--noref              don't build .3/.4 index files
     -3/--justref            just build .3/.4 index files
     -o/--offrate <int>      SA is sampled every 2^<int> BWT chars 
(default: 5)
     -t/--ftabchars <int>    # of chars consumed in initial lookup 
(default: 10)
     --threads <int>         # of threads
     --seed <int>            seed for random number generator
     -q/--quiet              verbose output (for debugging)
     --h/--help              print this message and quit
     --version               print version information and quit

#########################
##       OPTIMIR       ##
#########################

Starting workflow for sample S1
  > Starting Library preparation...
Error with system call: Bowtie2 index creation failed: command line = 
bowtie2-build -f 
/tmp/autopkgtest-lxc.ej3c3g68/downtmp/autopkgtest_tmp/OptimiR_Results_Dir/OptimiR_lib/fasta/optimiR_library.fa 
/tmp/autopkgtest-lxc.ej3c3g68/downtmp/autopkgtest_tmp/OptimiR_Results_Dir/OptimiR_lib/bowtie2_index/optimiR_alignment_library 
-q
Check that path to Bowtie2, Cutadapt, Samtools are well defined.

autopkgtest [18:11:44]: test run-sample-analysis

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