Fixing BAM file header. Getting "truncated file. Aborting" error

[dfermin315]

Hello.

I have a BAM file that I need to filter and then update the header for.

These are my commands:

samtools view -@ 32  -h -b -f 2 -T /data/hs37d5.fa \
  -o samp1234.clean.bam \
  bam.files/samp1234.bam \
  1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y MT

samtools view -H samp1234.clean.bam | \
  grep -v -e 'SN:GL' -e 'SN:NC' -e 'SN:hs37d5' \
  > samp1234.corrected.sam

samtools reheader samp1234.corrected.sam \
  samp1234.clean.bam > samp1234.clean.reheaded.bam

samtools sort -@ 32 \
  -o samp1234.clean.reheaded.sorted.bam \
  samp1234.clean.reheaded.bam

The first 3 commands execute without any problems.
Using

samtools view -h samp1234.clean.reheaded.bam | less -S

I can see that the new BAM file does indeed contain the correct header.

However every time I run the sorting command I get the error message:

samtools sort: truncated file. Aborting

The samp1234.clean.reheaded.bam file seems to be fine in every regard. I can't seem to find a fault with it .

Performing the reheading step in place doesn't seem to help nor does the -P option

Does anyone have a suggestion of what I'm doing wrong?

In case it helps I'm using samtools version 1.4-5-g692e058 (using htslib 1.4-5-g10bc1a7)

Thanks in advance for any and all help.

[GenoMax]

Consider the answer given in this thread: https://www.biostars.org/p/289770/

[dfermin315]

Thanks for pointing me to that post!
I'm still having issues but I'll work with the suggested command there.