<div dir="ltr"><div dir="ltr"><br></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Mon, 18 May 2020 at 12:39, Andreas Tille <<a href="mailto:andreas@fam-tille.de">andreas@fam-tille.de</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><br>
I've merged this and tried a test build including running autopkgtest in<br>
my pbuilder environment. Unfortunately the latter test is now failing with<br>
<br>
...<br>
autopkgtest [06:48:10]: test atac-unit-test: [-----------------------<br>
Rewriting '/tmp/autopkgtest.jgVuO6/autopkgtest_tmp/GCF_000195855.1_ASM19585v1_genomic.fna' to '/tmp/autopkgtest.jgVuO6/autopkgtest_tmp/meryldir/Lepr.fasta', removing newlines.<br>
Rewriting '/tmp/autopkgtest.jgVuO6/autopkgtest_tmp/GCF_000195955.2_ASM19595v2_genomic.fna' to '/tmp/autopkgtest.jgVuO6/autopkgtest_tmp/meryldir/Tuber.fasta', removing newlines.<br>
<br>
/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 <br>
<br>
fastaFile::constructIndex()-- magic mismatch.<br>
fastaFile::constructIndex()-- magic mismatch.<br>
bitPackedFile::bitPackedFile()-- failed to open and truncate '/tmp/autopkgtest.jgVuO6/autopkgtest_tmp/meryldir/Lepr.ms20.batch0.mcidx': No such file or directory<br>
Failed to count mers in Lepr<br>
autopkgtest [06:48:10]: test atac-unit-test: -----------------------]<br>
autopkgtest [06:48:11]: test atac-unit-test: - - - - - - - - - - results - - - - - - - - - -<br>
atac-unit-test FAIL non-zero exit status 2<br>
...<br>
<br>
<br>
I admit I personally have no idea why this fails.<br></blockquote><div><br></div><div>Is this a false positive?</div><div> It seems to pass for me:</div><div><br></div><div>'''<br>Read checkpoint in 0 seconds.<br>Creating /tmp/autopkgtest.Ri0bel/autopkgtest_tmp/meryldir/Lepr.fasta.idxStore<br>Creating /tmp/autopkgtest.Ri0bel/autopkgtest_tmp/meryldir/Tuber.fasta.idxStore<br>We need to make the raw matches.<br>runName = /tmp/autopkgtest.Ri0bel/autopkgtest_tmp/results/work/LeprvsTuber.matches.extended<br><br>Keep step=0<br>At step=0<br>Time elapsed=0.00037479400634765625<br>At uniqueFilter, step=1<br>Time elapsed=0.0003867149353027344<br>Running UniqueFilter<br>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<br>time elapsed is 0.0026073455810546875<br>time elapsed is 7.796287536621094e-05<br>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<br>time elapsed is 0.0037603378295898438<br>time elapsed is 0.00011348724365234375<br>At filterByMatchLength, step=2<br>Time elapsed=0.1619856357574463<br>Running filterByMatchLength<br>At trimMatchOverlaps, step=3<br>Time elapsed=0.16259360313415527<br>Start trimming for bp one-to-one-ness<br>trimMatchOverlapsInX:<br> #posgaps, #abuts, #overlaps, #contained, bp_trimmed= 0 0 0 0 0<br><br>trimMatchOverlapsInY:<br> #posgaps, #abuts, #overlaps, #contained, bp_trimmed= 0 0 0 0 0<br><br>Finished trimming for bp one-to-one-ness<br>At formPerfectRuns, step=4<br>Time elapsed=0.21597981452941895<br>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<br>formPerfectRuns step=0<br>formPerfectRuns step=1<br>formPerfectRuns step=2<br>formPerfectRuns step=3<br>At onlyKeepLongRuns, step=5<br>Time elapsed=0.32003164291381836<br>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<br>At formPerfectRuns, step=6<br>Time elapsed=0.320875883102417<br>Heal the perfect runs<br>formPerfectRuns step=0<br>formPerfectRuns step=1<br>formPerfectRuns step=2<br>formPerfectRuns step=3<br>At squeezeIntraRunGaps, step=7<br>Time elapsed=0.3695542812347412<br>from /tmp/autopkgtest.Ri0bel/autopkgtest_tmp/results/work/<a href="http://LeprvsTuber.matches.extended.uniq.t40.trim.p6.l100.pr">LeprvsTuber.matches.extended.uniq.t40.trim.p6.l100.pr</a> to /tmp/autopkgtest.Ri0bel/autopkgtest_tmp/results/work/LeprvsTuber.matches.extended.uniq.t40.trim.p6.l100.pr.sq<br>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<br>theIsolatedSNPcount = 0<br>completefillednotXY = 0<br>completefilledXnotY = 0<br>completefilledYnotX = 0<br>completefilledXandY = 0<br>At TrimMatchOverlaps, step=8<br>Time elapsed=0.37032628059387207<br>Start trimming for bp one-to-one-ness<br>trimMatchOverlapsInX:<br> #posgaps, #abuts, #overlaps, #contained, bp_trimmed= 0 0 0 0 0<br><br>trimMatchOverlapsInY:<br> #posgaps, #abuts, #overlaps, #contained, bp_trimmed= 0 0 0 0 0<br><br>Finished trimming for bp one-to-one-ness<br>At RunsAsMatches, step=9<br>Time elapsed=0.4200100898742676<br>At fillIntraRunGaps, step=10<br>Time elapsed=0.42075562477111816<br>fill the intrarun gaps<br>begin<br>countLines=0<br>countLines 0 inter_run_gap_count 0 <br>At TrimMatchOverlaps, step=11<br>Time elapsed=0.42135024070739746<br>trim the overlaps<br>trimMatchOverlapsInX:<br> #posgaps, #abuts, #overlaps, #contained, bp_trimmed= 0 0 0 0 0<br><br>trimMatchOverlapsInY:<br> #posgaps, #abuts, #overlaps, #contained, bp_trimmed= 0 0 0 0 0<br><br>Ran in 0 seconds.<br><br>/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<br><br><br>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<br><br>1 load the matches<br>2 sort the matches<br>3 score the matches<br>4 mark clumps<br>5 sort the matches<br>6 output matches with clumps<br><br>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<br><br>1 load the matches<br>2 sort the matches<br>3 score the matches<br>4 mark clumps<br>5 sort the matches<br>6 output matches with clumps<br><br>/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<br><br><br>perl /usr/bin/../lib/atac/bin/<a href="http://makeplot.pl">makeplot.pl</a> u /tmp/autopkgtest.Ri0bel/autopkgtest_tmp/results/LeprvsTuber.atac /tmp/autopkgtest.Ri0bel/autopkgtest_tmp/results/stats/LeprvsTuber.matches.png<br><br><br>replot<br>^<br>"/tmp/autopkgtest.Ri0bel/autopkgtest_tmp/results/stats/<a href="http://LeprvsTuber.matches.gp">LeprvsTuber.matches.gp</a>" line 24: no previous plot<br><br><br>perl /usr/bin/../lib/atac/bin/<a href="http://makeplot.pl">makeplot.pl</a> r /tmp/autopkgtest.Ri0bel/autopkgtest_tmp/results/LeprvsTuber.atac /tmp/autopkgtest.Ri0bel/autopkgtest_tmp/results/stats/LeprvsTuber.runs.png<br><br><br>replot<br>^<br>"/tmp/autopkgtest.Ri0bel/autopkgtest_tmp/results/stats/<a href="http://LeprvsTuber.runs.gp">LeprvsTuber.runs.gp</a>" line 24: no previous plot<br><br><br>Finished! Output is:<br> matches and runs -- /tmp/autopkgtest.Ri0bel/autopkgtest_tmp/results/LeprvsTuber.atac<br> clumps -- /tmp/autopkgtest.Ri0bel/autopkgtest_tmp/results/LeprvsTuber.*clump*.atac<br>RESULTS: OK<br><br>autopkgtest [13:00:45]: test atac-unit-test: -----------------------]<br>autopkgtest [13:00:45]: test atac-unit-test: - - - - - - - - - - results - - - - - - - - - -<br>atac-unit-test PASS<br>autopkgtest [13:00:45]: @@@@@@@@@@@@@@@@@@@@ summary<br>sim4db-unit-test PASS<br>atac-unit-test PASS</div><div><br></div><div>'''</div><div><br></div><div>Liubov, Pranav: could you try this and let us know the result?</div><div><br></div><div>Regards,</div><div>Nilesh<br></div></div></div>