Error with trimming SE adapters from sample about paleomix HOT 2 CLOSED

Hi Uri,

It looks like the Vole_test_raw/MM1000.fastq.gz file is corrupt.
Try running gzip -vt Vole_test_raw/MM1000.fastq.gz to test it; that will likely report a similar error.

You will need to either find a non-corrupt copy of the file somewhere or truncate it so that it only contains valid data (i.e. unpack as much as you can, drop the last read if it is not complete, and then re-compress). If you've mapped this previously (manually or using a different pipeline), then I'd also recommend going back and verifying that it was not mapped using the corrupted file.

Note also that the Single etc. keys are meant only for reads that have already been trimmed and optionally merged.
They should not be used if that is not the case.

Best,
Mikkel

from paleomix.

I thought the Single key doesn't really help here, I understand now that it is only for pre-trimmed reads (not my case). I'll check the file soon and see if I can use a non-corrupt copy. Maybe the issues with my other samples also had to do with the files, and not the pipeline.
Thanks for the quick reply!

from paleomix.