[Debian-med-packaging] Bug#958840: kmer: autopkgtest regression: No module named 'localAlignerInterface'

Nilesh Patra npatra974 at gmail.com
Mon May 18 08:35:16 BST 2020 

On Mon, 18 May 2020 at 12:39, Andreas Tille <andreas at fam-tille.de> wrote:

>
> I've merged this and tried a test build including running autopkgtest in
> my pbuilder environment.  Unfortunately the latter test is now failing with
>
> ...
> autopkgtest [06:48:10]: test atac-unit-test: [-----------------------
> Rewriting
> '/tmp/autopkgtest.jgVuO6/autopkgtest_tmp/GCF_000195855.1_ASM19585v1_genomic.fna'
> to '/tmp/autopkgtest.jgVuO6/autopkgtest_tmp/meryldir/Lepr.fasta', removing
> newlines.
> Rewriting
> '/tmp/autopkgtest.jgVuO6/autopkgtest_tmp/GCF_000195955.2_ASM19595v2_genomic.fna'
> to '/tmp/autopkgtest.jgVuO6/autopkgtest_tmp/meryldir/Tuber.fasta', removing
> newlines.
>
> /usr/bin/meryl -B -C -threads 2 -m 20 -s
> /tmp/autopkgtest.jgVuO6/autopkgtest_tmp/meryldir/Lepr.fasta -o
> /tmp/autopkgtest.jgVuO6/autopkgtest_tmp/meryldir/Lepr.ms20
>
> fastaFile::constructIndex()-- magic mismatch.
> fastaFile::constructIndex()-- magic mismatch.
> bitPackedFile::bitPackedFile()-- failed to open and truncate
> '/tmp/autopkgtest.jgVuO6/autopkgtest_tmp/meryldir/Lepr.ms20.batch0.mcidx':
> No such file or directory
> Failed to count mers in Lepr
> autopkgtest [06:48:10]: test atac-unit-test: -----------------------]
> autopkgtest [06:48:11]: test atac-unit-test:  - - - - - - - - - - results
> - - - - - - - - - -
> atac-unit-test       FAIL non-zero exit status 2
> ...
>
>
> I admit I personally have no idea why this fails.
>

Is this a false positive?
It seems to pass for me:

'''
Read checkpoint in 0 seconds.
Creating
/tmp/autopkgtest.Ri0bel/autopkgtest_tmp/meryldir/Lepr.fasta.idxStore
Creating
/tmp/autopkgtest.Ri0bel/autopkgtest_tmp/meryldir/Tuber.fasta.idxStore
We need to make the raw matches.
runName =
/tmp/autopkgtest.Ri0bel/autopkgtest_tmp/results/work/LeprvsTuber.matches.extended

Keep step=0
At step=0
Time elapsed=0.00037479400634765625
At uniqueFilter, step=1
Time elapsed=0.0003867149353027344
Running UniqueFilter
sort -T . -k 1,1 -k 2,2 -k 3n -k 4nr
 /tmp/autopkgtest.Ri0bel/autopkgtest_tmp/results/tmpxq1az43c >
/tmp/autopkgtest.Ri0bel/autopkgtest_tmp/results/tmprg6kyya8
time elapsed is  0.0026073455810546875
time elapsed is  7.796287536621094e-05
sort -T . -k 1,1 -k 2,2 -k 3n -k 4nr
 /tmp/autopkgtest.Ri0bel/autopkgtest_tmp/results/tmpco1alaqw >
/tmp/autopkgtest.Ri0bel/autopkgtest_tmp/results/tmpeja1c_zn
time elapsed is  0.0037603378295898438
time elapsed is  0.00011348724365234375
At filterByMatchLength, step=2
Time elapsed=0.1619856357574463
Running filterByMatchLength
At trimMatchOverlaps, step=3
Time elapsed=0.16259360313415527
Start trimming for bp one-to-one-ness
trimMatchOverlapsInX:
 #posgaps, #abuts, #overlaps, #contained, bp_trimmed= 0 0 0 0 0

trimMatchOverlapsInY:
 #posgaps, #abuts, #overlaps, #contained, bp_trimmed= 0 0 0 0 0

Finished trimming for bp one-to-one-ness
At formPerfectRuns, step=4
Time elapsed=0.21597981452941895
from
/tmp/autopkgtest.Ri0bel/autopkgtest_tmp/results/work/LeprvsTuber.matches.extended.uniq.t40.trim
making
/tmp/autopkgtest.Ri0bel/autopkgtest_tmp/results/work/LeprvsTuber.matches.extended.uniq.t40.trim.p6
formPerfectRuns step=0
formPerfectRuns step=1
formPerfectRuns step=2
formPerfectRuns step=3
At onlyKeepLongRuns, step=5
Time elapsed=0.32003164291381836
from
/tmp/autopkgtest.Ri0bel/autopkgtest_tmp/results/work/LeprvsTuber.matches.extended.uniq.t40.trim.p6
making
/tmp/autopkgtest.Ri0bel/autopkgtest_tmp/results/work/LeprvsTuber.matches.extended.uniq.t40.trim.p6.l100
At formPerfectRuns, step=6
Time elapsed=0.320875883102417
Heal the perfect runs
formPerfectRuns step=0
formPerfectRuns step=1
formPerfectRuns step=2
formPerfectRuns step=3
At squeezeIntraRunGaps, step=7
Time elapsed=0.3695542812347412
from /tmp/autopkgtest.Ri0bel/autopkgtest_tmp/results/work/
LeprvsTuber.matches.extended.uniq.t40.trim.p6.l100.pr to
/tmp/autopkgtest.Ri0bel/autopkgtest_tmp/results/work/LeprvsTuber.matches.extended.uniq.t40.trim.p6.l100.pr.sq
countLines 0 inter_run_gap_count 0 closed_gap_count 0 squeezed 0 x_len 0
y_len 0 x_nonACGT 0 y_nonACGT 0
theIsolatedSNPcount = 0
completefillednotXY = 0
completefilledXnotY = 0
completefilledYnotX = 0
completefilledXandY = 0
At TrimMatchOverlaps, step=8
Time elapsed=0.37032628059387207
Start trimming for bp one-to-one-ness
trimMatchOverlapsInX:
 #posgaps, #abuts, #overlaps, #contained, bp_trimmed= 0 0 0 0 0

trimMatchOverlapsInY:
 #posgaps, #abuts, #overlaps, #contained, bp_trimmed= 0 0 0 0 0

Finished trimming for bp one-to-one-ness
At RunsAsMatches, step=9
Time elapsed=0.4200100898742676
At fillIntraRunGaps, step=10
Time elapsed=0.42075562477111816
fill the intrarun gaps
begin
countLines=0
countLines 0 inter_run_gap_count 0
At TrimMatchOverlaps, step=11
Time elapsed=0.42135024070739746
trim the overlaps
trimMatchOverlapsInX:
 #posgaps, #abuts, #overlaps, #contained, bp_trimmed= 0 0 0 0 0

trimMatchOverlapsInY:
 #posgaps, #abuts, #overlaps, #contained, bp_trimmed= 0 0 0 0 0

Ran in 0 seconds.

/usr/bin/../lib/atac/bin/correctGaps  -m
/tmp/autopkgtest.Ri0bel/autopkgtest_tmp/results/work/LeprvsTuber.matches.extended.chained.atac
 -l
/tmp/autopkgtest.Ri0bel/autopkgtest_tmp/results/work/LeprvsTuber.matches.extended.chained.gapsclosed.log
>
/tmp/autopkgtest.Ri0bel/autopkgtest_tmp/results/work/LeprvsTuber.matches.extended.chained.gapsclosed.atac


cd /tmp/autopkgtest.Ri0bel/autopkgtest_tmp/results &&
/usr/bin/../lib/atac/bin/clumpMaker  -c 5000  -1  -f
/tmp/autopkgtest.Ri0bel/autopkgtest_tmp/results/LeprvsTuber.atac >
/tmp/autopkgtest.Ri0bel/autopkgtest_tmp/results/LeprvsTuber.ref=Lepr.clumpCost=5000.atac

1 load the matches
2 sort the matches
3 score the matches
4 mark clumps
5 sort the matches
6 output matches with clumps

cd /tmp/autopkgtest.Ri0bel/autopkgtest_tmp/results &&
/usr/bin/../lib/atac/bin/clumpMaker  -c 5000  -2  -f
/tmp/autopkgtest.Ri0bel/autopkgtest_tmp/results/LeprvsTuber.atac >
/tmp/autopkgtest.Ri0bel/autopkgtest_tmp/results/LeprvsTuber.ref=Tuber.clumpCost=5000.atac

1 load the matches
2 sort the matches
3 score the matches
4 mark clumps
5 sort the matches
6 output matches with clumps

/usr/bin/../lib/atac/bin/statsGenerator -a
/tmp/autopkgtest.Ri0bel/autopkgtest_tmp/results/LeprvsTuber.atac -p
/tmp/autopkgtest.Ri0bel/autopkgtest_tmp/results/stats/LeprvsTuber -g A >
/tmp/autopkgtest.Ri0bel/autopkgtest_tmp/results/stats/LeprvsTuber.stats


perl /usr/bin/../lib/atac/bin/makeplot.pl u
/tmp/autopkgtest.Ri0bel/autopkgtest_tmp/results/LeprvsTuber.atac
/tmp/autopkgtest.Ri0bel/autopkgtest_tmp/results/stats/LeprvsTuber.matches.png


replot
^
"/tmp/autopkgtest.Ri0bel/autopkgtest_tmp/results/stats/
LeprvsTuber.matches.gp" line 24: no previous plot


perl /usr/bin/../lib/atac/bin/makeplot.pl r
/tmp/autopkgtest.Ri0bel/autopkgtest_tmp/results/LeprvsTuber.atac
/tmp/autopkgtest.Ri0bel/autopkgtest_tmp/results/stats/LeprvsTuber.runs.png


replot
^
"/tmp/autopkgtest.Ri0bel/autopkgtest_tmp/results/stats/LeprvsTuber.runs.gp"
line 24: no previous plot


Finished!  Output is:
  matches and runs --
/tmp/autopkgtest.Ri0bel/autopkgtest_tmp/results/LeprvsTuber.atac
  clumps           --
/tmp/autopkgtest.Ri0bel/autopkgtest_tmp/results/LeprvsTuber.*clump*.atac
RESULTS: OK

autopkgtest [13:00:45]: test atac-unit-test: -----------------------]
autopkgtest [13:00:45]: test atac-unit-test:  - - - - - - - - - - results -
- - - - - - - - -
atac-unit-test       PASS
autopkgtest [13:00:45]: @@@@@@@@@@@@@@@@@@@@ summary
sim4db-unit-test     PASS
atac-unit-test       PASS

'''

Liubov, Pranav: could you try this and let us know the result?

Regards,
Nilesh
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