alignmentSieve returns a truncated bam #1180
Description
Python 3.9.12
deeptools 3.5.1
alignmentSieve 3.5.1
Dear all,
when I run alignmentSieve with ATACshift option, but not for all my samples, I get as output a truncated bam file.
For instance this is the flagstat of my original bam:
31138979 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 secondary
0 + 0 supplementary
0 + 0 duplicates
31138979 + 0 mapped (100.00% : N/A)
31138979 + 0 paired in sequencing
15587662 + 0 read1
15551317 + 0 read2
31138979 + 0 properly paired (100.00% : N/A)
31138979 + 0 with itself and mate mapped
0 + 0 singletons (0.00% : N/A)
0 + 0 with mate mapped to a different chr
0 + 0 with mate mapped to a different chr (mapQ>=5)
Then I run the following shifting:
alignmentSieve \
--bam input.bam \
--outFile shifted.bam \
--minMappingQuality 20 \
--minFragmentLength 0 \
--maxFragmentLength 0 \
--ATACshift \
-p max
Then, a first thing is that the size of the file 2.4GB compared to the 5.4GB that I get without the shifting.
(I do not get any error message from alignmentSieve)
Secondly when I try to sort the file I get the following error:
user$ samtools sort -@ 30 -o shifted_sorted.bam shifted.bam
[E::bgzf_read] Read block operation failed with error -1 after 0 of 4 bytes
samtools sort: truncated file. Aborting
Furthermore if I try to run the flagstat on the resulting file I get that the file is indeed truncated with less than half of the read:
[E::bgzf_read] Read block operation failed with error -1 after 0 of 4 bytes
[bam_flagstat_core] Truncated file? Continue anyway.
1707936 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 secondary
0 + 0 supplementary
0 + 0 duplicates
1707936 + 0 mapped (100.00% : N/A)
1707936 + 0 paired in sequencing
854824 + 0 read1
853112 + 0 read2
1707936 + 0 properly paired (100.00% : N/A)
1707936 + 0 with itself and mate mapped
0 + 0 singletons (0.00% : N/A)
0 + 0 with mate mapped to a different chr
0 + 0 with mate mapped to a different chr (mapQ>=5)
Thank you in advance for your help!