Closed Uriwolkow closed 8 months ago
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
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!
Hello! I ran into a node running error with a sample I'm working with. I would add that this sample is different form my samples of interest, who are PE - mine seem to be working fine through the pipeline, but the results look suspiciously empty, as if there is no match at all between sample and reference. This is why I elected to run another sample which was already mapped in other methods, not using the pipeline, to check if the issue is with my data or in my makefile
On my first attempt, the STDERR file includes this text:
Later I got a different, OS error, when I later edited the targets in my makefile to be specifically SE using the "Single:" key, as indicated in the Documentation). That is the STDERR it produced - this time an OS error, in the file validation stage:
Any suggestions or ideas on what could be done? Best wishes, Uri