Source: pbgenomicconsensus
Version: 2.3.2-1
Severity: serious
X-Debbugs-CC: debian...@lists.debian.org
User: debian...@lists.debian.org
Usertags: regression
Hi Maintainer
Since the upload of 2.3.2-1, pbgenomicconsensus has been failing its own
autopkgtests [1] with the following error:
autopkgtest [12:23:51]: test command2: [-----------------------
# Tests that need to be run by Jenkins but are slowing
# down the development cycle, so aren't run by "tests"
# target.
PATH=`pwd`:/usr/local/bin:/usr/bin:/bin:/usr/local/games:/usr/games cram
--verbose --xunit-file=gc-extra-cram.xml `ls tests/cram/extra/*.t | grep
-v arrow`
tests/cram/extra/plurality-fluidigm.t: failed
--- tests/cram/extra/plurality-fluidigm.t
+++ tests/cram/extra/plurality-fluidigm.t.err
@@ -8,12 +8,26 @@
Set the QV threshold to 10.
$ variantCaller --algorithm=plurality -r $REFERENCE -q 10 -o
variants.gff -o consensus.csv -o consensus.fastq $INPUT
+ Traceback (most recent call last):
+ File "/usr/bin/variantCaller", line 3, in <module>
+ from GenomicConsensus.main import main
+ File "/usr/lib/python2.7/dist-packages/GenomicConsensus/main.py",
line 16, in <module>
+ from GenomicConsensus import reference
+ File
"/usr/lib/python2.7/dist-packages/GenomicConsensus/reference.py", line
8, in <module>
+ from .windows import holes, kCoveredIntervals, enumerateIntervals
+ File
"/usr/lib/python2.7/dist-packages/GenomicConsensus/windows.py", line 14,
in <module>
+ from ConsensusCore import CoveredIntervals
+ ImportError: No module named ConsensusCore
+ [1]
There are two true SNVs (and one diploid SNV that we miss right now).
$ grep insertion variants.gff | wc | awk '{print $1}'
+ grep: variants.gff: No such file or directory
0
$ grep deletion variants.gff | wc | awk '{print $1}'
+ grep: variants.gff: No such file or directory
0
$ grep substitution variants.gff
-
EGFR_Exon_23\t.\tsubstitution\t48\t48\t.\t.\t.\treference=T;variantSeq=C;frequency=97;coverage=100;confidence=40
(esc)
+ grep: variants.gff: No such file or directory
+ [2]
# Ran 1 tests, 0 skipped, 1 failed.
make: *** [Makefile:25: extra-tests] Error 1
autopkgtest [12:23:52]: test command2: -----------------------]
autopkgtest [12:23:52]: test command2: - - - - - - - - - - results - -
- - - - - - - -
command2 FAIL non-zero exit status 2
Regards
Graham
[1] https://ci.debian.net/packages/p/pbgenomicconsensus/unstable/amd64/
