Hello,

I am trying to use alignmentSieve to filter reads by fragmentLength.
I start with a coordinate sorted bam and perform the following:
alignmentSieve -b ${bam} --paired
--ignoreDuplicates
--maxFragmentLength ${fragment_max}
-o ${prefix}.sieve.bam
--filterMetrics alignmentSieve.metrics.txt

The error I get when I then try to sort with samtools is the following:
Singularity> samtools sort -n -@ 4 -m 2G -o ${prefix}.sieve.nsort.bam -T ${prefix}.sieve.nsort ${prefix}.sieve.bam
[E::bgzf_read_block] Invalid BGZF header at offset 4799897149
[E::bgzf_read] Read block operation failed with error 6 after 0 of 4 bytes
samtools sort: truncated file. Aborting

The bam alignmentSieve produces is not empty..
Don't understand what to do.

I use this singularity env:
https://depot.galaxyproject.org/singularity/mulled-v2-1eb11c779a98c229957f881e0e2a5f25354d6447:05e8638b74fa720fa74fc7e00a541c4f59bad239-0