Closed wsphillips closed 3 years ago
Very odd, when this kind of basic operations in samtools fails, it's usually because users have some sort of folder permissions issue or there is not enough disk space. Rule of thumb is to have 5x the fastq input size free space.
I went back and ran the pipeline with 4TB free disk space and out of paranoia recursively ran chmod -R a+rw /path/to/data
and chown -R myusername /path/to/data
on the data/output folders. Maybe overkill, but seems to work fine now. :sweat_smile:
Apparent file write error when finishing mapping. I am working with up-to-date
main
of zUMIs and using miniconda env to run. YAML config and stdout attached. Any ideas? Happens on two different, but similarly spec'd workstations.The above results in a subsequent segfault with subread.
Full stdout of run here.
YAML config (as txt for upload)
OS: Fedora 34 & CentOS 8.3 (reproduces on two machines)
Version: running zUMIs
main
with conda-c
flag, but dependency versions are...samtools 1.12 STAR 2.7.3a R 4.05 (all packages in your CRAN/Bioconductor lists installed) pigz 2.4