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...@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 (lang...@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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