Closed lcoombe closed 6 years ago
@lcoombe:
Yes, I recognize this situation/error and other people have complained about it as well.
Ideally DistanceEst
should handle empty input gracefully.
A hacky workaround would be run abyss-pe
twice: first with the pesam
target, then check if the SAM file is empty, then run it a second time with the contigs
target. But that's fairly annoying, I know.
Sounds good - I'll do that! Thanks Ben!
@lcoombe I think it would be great if you kept this issue open until it is fixed in code.
We close issues that we're not actively working on.
Hello Ben/Shaun!
For my targeted assembly pipeline, I do a bunch of small ABySS assemblies (contig stage).
I saw this error for one of my targeted assemblies:
Looking at the log file, I suspect that when there are 0 alignments in the 'different' category, then no alignments will be written to the pelib-3.sam.gz file? And then ABySS fails with no alignments there? Is that the expected behaviour? For my application, I wouldn't want abyss to fail there -- this was a case where my target was already assembled completely prior to the contig stage. I'm using abyss 2.02 by the way (from linuxbrew)
Thank you!