Somehow I was too fast in my previous mail ...
> 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 14:45:05,910 [INFO] Running /usr/bin/Honey pie
filtered_subreads.fastq lambda_modified.fasta -o mappingFinal.sam
2016-12-24 14:45:05,910 [INFO] Running Blasr
2016-12-24 14:45:52,277 [INFO] [0, '[INFO] 2016-12-24T14:45:05 [blasr]
started.\n[INFO] 2016-12-24T14:45:52 [blasr] ended.\n', None]
2016-12-24 14:45:52,277 [INFO] Mapping Tails
2016-12-24 14:45:52,278 [INFO] Extracting tails
2016-12-24 14:45:52,407 [INFO] Parsed 433 reads
2016-12-24 14:45:52,407 [INFO] Found 278 tails
2016-12-24 14:45:52,407 [INFO] 21 reads had double tails
2016-12-24 14:45:52,407 [INFO] Running Blasr
2016-12-24 14:45:52,470 [ERROR] blasr mapping failed!
2016-12-24 14:45:52,471 [ERROR] RETCODE 255
2016-12-24 14:45:52,471 [ERROR] STDOUT [INFO] 2016-12-24T14:45:52 [blasr]
started.
ERROR, can not convert non-pacbio reads to pbbam record.
2016-12-24 14:45:52,471 [ERROR] STDERR None
2016-12-24 14:45:52,471 [ERROR] Exiting
I think I need to stop here. The only thing I'm wondering about is
whether this is a critical sign for pbhoney / pbsuite or whether this
should be qualified as severity normal. I'll leave the decision to
those who are more familiar with this software.
Kind regards
Andreas.
--
http://fam-tille.de
