Brian Bushnell

When I wrote that, PacBio did not have paired reads. They have a new sequencing machine now for short reads that I think does produce pairs but I have not seen any data for it so I'm not sure of the header structure.

The problem here is that the read headers differ in two places. Normally, Illumina uses one of these two formats: @stuff/1 @stuff/2 or @stuff 1:morestuff @stuff 2:morestuff Of these, the /1 and /2 is obsolete for Illumina as far as I know, though Complete Genomics / BGI are adopting it. My effort to determine pairing is based on observation of Illumina data since there is no formal fastq specification regarding pair naming conventions, and they usually put the read identifier in the "optional description"....

The problem here is that the reads differ in two places. Normally, Illumina uses one of these two formats: @stuff/1 @stuff/2 or @stuff 1:morestuff @stuff 2:morestuff Of these, the /1 and /2 is obsolete for Illumina as far as I know, though Complete Genomics / BGI are adopting it. My effort to determine pairing is based on observation of Illumina data since there is no formal fastq specification regarding pair naming conventions, and they usually put the read identifier in the "optional description"....

Good suggestion; I'm opening a new process for bgzip and piping the input. Shouldn't be too hard to catch the error code.

I was able to replicate this behavior and it is fixed for the next release (39.05, probably this week). Sometimes I don't notice this kind of issue because I always keep paired reads interleaved in a single file.

Hi Pierre, Sorry about that, those two and a couple other versions of CrisprFinder made it into the release accidentally. Only CrisprFinder.java should be there. I'll delete them for the next release. Thanks for notifying me! -Brian

Have you retried this recently? There was a problem with the configuration of the servers for a few weeks which should have been resolved on ~Jan 6th, but I'm not 100% sure it's fixed for everyone. Also, can you tell me which version of Java and BBTools you are using?

I'm not sure why I wrote the last line like that. I changed it to: return ((rka1.kmerMinusStrand==rkb1.kmerMinusStrand) && (rka2.kmerMinusStrand==rkb2.kmerMinusStrand)); ...which fixes the problem. That will be released soon in 38.71. Sorry for the delay!