I have been aligning reads to transcriptome assemblies with bowtie2-beta7 a few times. My experiences with bowtie2 have been great so far. However, bowtie2 crashed silently (with core-dumps) for one of my datasets.
This is the command that I used:
bowtie2 -a --fast -q -p 12 --score-min L,0,0 -x $contigs -1 $read1 -2 $read2 -S $output.sam
I have also run bowtie2 without the score-min function, but it also crashed.
I ran the same command again in debug mode and I got this message:
bowtie2-align-debug: aligner_sw_driver.h:246: size_t RowSampler::next(RandomSource&): Assertion `false' failed.
There were no errors from bowtie2-build.
Log in to post a comment.