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