Entering edit mode
2.4 years ago
eli_bayat
▴
90
Hi,
When I run script samtools sort -@ 16 -T "path/to/temp" "$bamfile" > "$_sorted.bam
, I get this error message:
[bam_sort_core] merging from 112 files and 16 in-memory blocks...
samtools sort: failed to write header to "-"
and the output file is empty. I believe have sufficient memory (249G memory and my files are big around 70G pacbio reads)
Any help is appreciated.
Thanks, I used the commands you suggested and it did sorting without an issue, I also resized my drive, so probably a bit of both helped? :). Thanks for your help