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faircloth-lab / phyluce

software for UCE (and general) phylogenomics
http://phyluce.readthedocs.org/
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illumiprocessor - unequal split-adapter-quality-trimmed read1 and read2 #339

Closed jackson-roberts closed 1 month ago

jackson-roberts commented 1 month ago

Hey Brant,

I finally updated from phyluce 1.6 -> 1.7 and (in my memory) have never experienced this issue. illumiprocessor+trimmomatic appear to be running correctly, but the final READ1.fastq.gz and READ2.fastq.gz have unequal reads, thus Spades is throwing the OS value 255 error.

Am I just missing something simple? Shouldn't the READ1 + READ2 files from illumiprocessor in the split-adapter-quality-trimmed directory always be equal, with all orphaned reads in the singleton file?

Thanks, and hope you are well.

Jackson

brantfaircloth commented 1 month ago

Hi Jackson,

Yes, these should always be equal. I'm not sure how that could have happened. Are the input files equal in terms of read pairs?

-b

jackson-roberts commented 1 month ago

Hey Brant!

thanks for the response and apologies for the delay. I pulled an my old system running phyluce 1.6, ran the identical spades call with the same data, and all ran well until it (as expected) ran out of RAM. I feel really really silly. Spades currently is not compatible with Mac M2 ARM OS’, which I was running when this error persisted. So everything is running as it should, it is just time to update to a large Linux based system.

Thanks again for your time.

Jackson