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STARsolo Segfault when Sorting BAM #902
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Hi Cole, could you send me the 10,000 reads that cause this seg-fault? Thanks! |
Hey Alex, Sorry for the delayed response. I made a mistake in my original post, it turns out it was 1,000 and not 10,000 reads. I am subsetting using Also, I forgot to mention that I am aligning against the latest Gencode v34 Cole |
Hi Cole, this was a bug, thanks for reporting it. Please try the latest patch from GitHub master. It works fine now on your small test example. Cheers |
Hey Alex, I rebuilt STARsolo and re-ran on the full sample and everything ran fine. Thanks for the bug fix! Also, I noticed that part of the fix involved removing hard coding things to be Thanks, |
Hi Cole, this is a good observation. If only GeneFull is present, it will be used for error correction (this had to be fixed). If both Gene and GeneFull are present, Gene will be used for error correction. Cheers |
Thanks Alex! |
Hello Alex,
When running STARsolo on a single sample of 10x V2 3' data I am getting a segfault at the beginning of the BAM sorting step. This happens both when I run the full sample and when subsetting to 10,000 reads.
I get this error on both
2.7.3a
and a fresh build of 49dc707The Error
Log File (end)
Parameters Used
Sorting command
--outSAMtype BAM Unsorted SortedByCoordinate
Other Params
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