Hi everyone,
I'm trying out srma on bowtie and bwa aligned data and while I've
managed to successfully get round two initial problems, I'm stuck on
the third one:
Basically, srma works quite fast until it reaches ~3.5-4M records.
After that it just hangs for hours, reporting nothing - while the
resulting BAM file stays at ~1/10 of the input file size.
Is this normal? Should I expect it to return to life at some point or
I should just kill it? Can I change anything so it doesn't freeze?
Many thanks!
PS As for the two problems that I solved, here are the solutions:
- for bwa data use VALIDATION_STRINGENCY=SILENT
- to prevent bam record order errors, recompile from source using the
latest versions of picard and sam libraries.
PPS I've sent the same message to srma-help, but thought it wouldn't hurt to crosspost here while it awaits moderator approval... I also noticed that the output is 1/10 expected size, not 1/3 as I said there...
I'm trying out srma on bowtie and bwa aligned data and while I've
managed to successfully get round two initial problems, I'm stuck on
the third one:
Basically, srma works quite fast until it reaches ~3.5-4M records.
After that it just hangs for hours, reporting nothing - while the
resulting BAM file stays at ~1/10 of the input file size.
Is this normal? Should I expect it to return to life at some point or
I should just kill it? Can I change anything so it doesn't freeze?
Many thanks!
PS As for the two problems that I solved, here are the solutions:
- for bwa data use VALIDATION_STRINGENCY=SILENT
- to prevent bam record order errors, recompile from source using the
latest versions of picard and sam libraries.
PPS I've sent the same message to srma-help, but thought it wouldn't hurt to crosspost here while it awaits moderator approval... I also noticed that the output is 1/10 expected size, not 1/3 as I said there...
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