On Sat, Dec 24, 2016 at 02:39:03PM +0100, Andreas Tille wrote: > Hi again,
once more. I just noticed that blasr 5.3-2 is properly linked and bhoney test suite works now ... > On Sat, Dec 24, 2016 at 10:30:48AM +0100, Andreas Tille wrote: > > pbhoney is marked for autoremoval due to this bug. I'm guessing from > > the description of the problem that it should be easy to fix (without > > having checked). Do you intend to upload soon or should somebody > > else step in here? > > I've spent some time to work on this. I admit its pretty confusing to > parse blasr code what options are really used. I've tried some trial > and error approach and I think I've got the options now somehow working. > However, when trying the first command from the test suite I get: > > > $ /usr/bin/Honey pie filtered_subreads.fastq lambda_modified.fasta -o > mappingFinal.sam > > Please Cite: English, Adam C., William J. Salerno, Jeffery G. > Reid. "PBHoney: identyfying genomic variants via > long-read discordance and interrupted mapping." > BMC Bioinformatics 2014, 15:180 (June 10, 2014). > doi:10.1186/1471-2105-15-180 > > 2016-12-24 14:29:32,478 [INFO] Running /usr/bin/Honey pie > filtered_subreads.fastq lambda_modified.fasta -o mappingFinal.sam > 2016-12-24 14:29:32,478 [INFO] Running Blasr > 2016-12-24 14:29:32,489 [ERROR] blasr mapping failed! > 2016-12-24 14:29:32,489 [ERROR] RETCODE 134 > 2016-12-24 14:29:32,489 [ERROR] STDOUT [INFO] 2016-12-24T14:29:32 [blasr] > started. > blasr: iblasr/MappingParameters.h:584: void MappingParameters::MakeSane(): > Assertion `"blasr must be compiled with lib pbbam to perform IO on bam." == > 0' failed. > Aborted > > 2016-12-24 14:29:32,489 [ERROR] STDERR None > 2016-12-24 14:29:32,489 [ERROR] Exiting > > > To verify whether blasr is linked against libpbbam I did: > > $ ldd /usr/bin/blasr | grep libpbbam > > I'm not really sure how to continue from here. > > Kind regards > > Andreas. > > -- > http://fam-tille.de -- http://fam-tille.de
