Hi, Canberk and all! 2016-05-24 2:57 GMT+03:00 Canberk Koç <[email protected]>:
> Hello everyone, > > I use adt-run to my autopkgtest on exonerate and examine the outputs. > I saw some failures but test run and give pass results. > I decide to look their test files and saw they look for missing files > error not occur but failure output comes from main test file. > I take output for you i cannot understand what is wrong. Thanks for your > help already. > > tmp/autopkgtest.BK2zJD/adttmp/util/fastaremove.test.sh > Have calmodulin in input > ** FATAL ERROR **: Could not open list for removal [CALM_HUMAN] > exiting ... > Calmodulin successfully removed > > $FASTAREMOVE $INPUTFILE CALM_HUMAN > $OUTPUTFILE > > //UPPER FAİL COMES FROM HERE BUT FUNCTİON WORK AND DELETE FİLES > > It seems that here http://anonscm.debian.org/cgit/debian-med/exonerate.git/tree/src/util/fastaremove.c#n76 code expects to get file name as a second argument, but this test http://anonscm.debian.org/cgit/debian-med/exonerate.git/tree/test/util/fastaremove.test.sh#n27 shows that it expects to remove description string from fasta file, and this string gets interpreted as 'stdin' or file name, containing one of several fasta records with given descriptions to remove. > /tmp/autopkgtest.BK2zJD/adttmp/util/fastaindex.fastafetch.test.sh > Made index fastafetch.test.idx > /usr/bin/fastafetch fastafetch.test.fasta fastafetch.test.idx CALM_HUMAN > expect 0 > >CALM_HUMAN > MADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFL > TMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYE > EFVQMMTAK > /usr/bin/fastafetch fastafetch.test.fasta fastafetch.test.idx P53_HUMAN > expect 0 > >P53_HUMAN > MEEPQSDPSVEPPLSQETFSDLWKLLPENNVLSPLPSQAMDDLMLSPDDIEQWFTEDPGPDEAPRMPEAA > PPVAPAPAAPTPAAPAPAPSWPLSSSVPSQKTYQGSYGFRLGFLHSGTAKSVTCTYSPALNKMFCQLAKT > CPVQLWVDSTPPPGTRVRAMAIYKQSQHMTEVVRRCPHHERCSDSDGLAPPQHLIRVEGNLRVEYLDDRN > TFRHSVVVPYEPPEVGSDCTTIHYNYMCNSSCMGGMNRRPILTIITLEDSSGNLLGRNSFEVHVCACPGR > DRRTEEENLRKKGEPHHELPPGSTKRALPNNTSSSPQPKKKPLDGEYFTLQIRGRERFEMFRELNEALEL > KDAQAGKEPGGSRAHSSHLKSKKGQSTSRHKKLMFKTEGPDSD > /usr/bin/fastafetch fastafetch.test.fasta fastafetch.test.idx > A_MISSING_FROM_START > expect 1 > ** FATAL ERROR **: Could not find identifier [A_MISSING_FROM_START] (missing > -F ?) > exiting ... > /usr/bin/fastafetch fastafetch.test.fasta fastafetch.test.idx > M_MISSING_FROM_MIDDLE > expect 1 > ** FATAL ERROR **: Could not find identifier [M_MISSING_FROM_MIDDLE] (missing > -F ?) > exiting ... > /usr/bin/fastafetch fastafetch.test.fasta fastafetch.test.idx > z_MISSING_FROM_END > expect 1 > ** FATAL ERROR **: Could not find identifier [z_MISSING_FROM_END] (missing -F > ?) > exiting ... > fastaindex fastafetch test OK > > For now I saw this: http://anonscm.debian.org/cgit/debian-med/exonerate.git/tree/src/util/fastafetch.c#n95 - error message appeared here, because `fasta_index_lookup` call returns -1. It seems that index file, created by call here: http://anonscm.debian.org/cgit/debian-med/exonerate.git/tree/test/util/fastaindex.fastafetch.test.sh#n15 doesn't contain descriptions A_MISSING_FROM_START, M_MISSING_FROM_MIDDLE, z_MISSING_FROM_END. Previous lines (before errors) in this output shows that it contains sequences with descriptions P53_HUMAN, CALM_HUMAN. Second argument in run_fastafetch is an integer value, indicating fastafetch.c main function return code. It is expected to be equal 1, something went wrong and error message is returned instead. I would suggest to add (in local code) "echo $RESULT" line before this line: http://anonscm.debian.org/cgit/debian-med/exonerate.git/tree/test/util/fastaindex.fastafetch.test.sh#n38 and look what it prints to output (and why it is not 1) and when to decide how to fix these errors. # look for IDs which are missing > run_fastafetch A_MISSING_FROM_START 1 > run_fastafetch M_MISSING_FROM_MIDDLE 1 > run_fastafetch z_MISSING_FROM_END 1 > > // UPPER FAİLS COMES FROM HERE BUT FETCHİNG WORKS > > > Best Regards > -- > > > Canberk Koç > [image: https://]about.me/canberkkoc > > <https://about.me/canberkkoc?promo=email_sig&utm_source=email_sig&utm_medium=email_sig&utm_campaign=external_links> > Hope this helps. Please, somebody correct me if my interpretation is wrong. -- Best wishes, Tanya.
