Hi Nilesh,
thanks for the quick check. Given that I experienced some false positives
in the past I just uploaded and we'll see what ci.debian.org will say.
Kind regards
Andreas.
On Mon, May 18, 2020 at 01:05:16PM +0530, Nilesh Patra wrote:
> On Mon, 18 May 2020 at 12:39, Andreas Tille <andr...@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
--
http://fam-tille.de
