I am having the devil's own time running bowtie2 on a relatively modest set (at most 17 Mill reads) of RNA-seq data.
I run it with the "-a" flag (report all alignments) or a "-k 2" (report 2) or the default to just report one alignment.
I have paired-end reads. I have run them as paired end or as unpaired reads.
I have run them against transcriptome or genome.
Only a couple of times have I seen it actually run to completion. When it fails, it does not even give me a segmentation fault. Just keeps spinning for days on end with no output (to stdout or stderror). I am trying to build a pipeline by looking at hits to both genome and transcriptome but have never had it complete the runs against both. (It has only completed the mapping against the transcriptome on a couple of occasions).
Is bowtie2 (supposedly still beta) really this unstable? Do others have experience with it running flawlessly?
I run it with the "-a" flag (report all alignments) or a "-k 2" (report 2) or the default to just report one alignment.
I have paired-end reads. I have run them as paired end or as unpaired reads.
I have run them against transcriptome or genome.
Only a couple of times have I seen it actually run to completion. When it fails, it does not even give me a segmentation fault. Just keeps spinning for days on end with no output (to stdout or stderror). I am trying to build a pipeline by looking at hits to both genome and transcriptome but have never had it complete the runs against both. (It has only completed the mapping against the transcriptome on a couple of occasions).
Is bowtie2 (supposedly still beta) really this unstable? Do others have experience with it running flawlessly?
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