failed to write header to “-“

[bam_sort_core] merging from 32 files and 16 in-memory blocks… samtools sort: failed to write header to “-“

0

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.


samtools


sort


pacbio


error

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