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velocyto-team / velocyto.py

RNA velocity estimation in Python
http://velocyto.org/velocyto.py/
BSD 2-Clause "Simplified" License
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Velocyto samtools memory error #340

Open pbpayal opened 2 years ago

pbpayal commented 2 years ago

Hi,

I ran velocyto verison 0.17 with samtools version 1.15.1 with 128GB memory. My bam files were standard 10X output (STAR aligner) and they are sorted by coordinate. Why do I still get this error?

`Otherwise sort manually by samtools sort -l [compression] -m [mb_to_use]M -t [tagname] -O BAM -@ [threads_to_use] -o cellsorted_[bamfile] [bamfile]") MemoryError: bam file #0 could not be sorted by cells. This is probably related to an old version of samtools, please install samtools >= 1.6. In alternative this could be a memory error, try to set the --samtools_memory option to a value compatible with your system. Otherwise sort manually by samtools ``sort -l [compression] -m [mb_to_use]M -t [tagname] -O BAM -@ [threads_touse] -o cellsorted[bamfile] [bamfile]```

I saw similar issue but no resolution, so had to post a new issue.

Thanks, Payal

ElenaSLuis commented 1 year ago

Can you solve it? I have the same error..