search

sdparekh / zUMIs

zUMIs: A fast and flexible pipeline to process RNA sequencing data with UMIs
GNU General Public License v3.0
271 stars 67 forks source link

Error writing bam files after finishing mapping. #270

Closed wsphillips closed 3 years ago

wsphillips commented 3 years ago

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.

Jun 29 23:11:58 ..... finished successfully
[bam_cat] Error writing to '/home/wikphi/data/zumisout/ss3pilot.filtered.tagged.Aligned.out.bam'.
[bam_cat] Error writing to '/home/wikphi/data/zumisout/ss3pilot.filtered.tagged.Aligned.toTranscriptome.out.bam'.

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

cziegenhain commented 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.

wsphillips commented 3 years ago

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: