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Old 05-30-2018, 01:20 PM   #1
dfermin315
Junior Member
 
Location: Michigan, US

Join Date: Mar 2017
Posts: 2
Default Fixing BAM file header. Getting "truncated file. Aborting" error

Hello.

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

These are my commands:

Code:
samtools view [email protected] 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 [email protected] 32 \
  -o samp1234.clean.reheaded.sorted.bam \
  samp1234.clean.reheaded.bam

The first 3 commands execute without any problems.
Using
Code:
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:
Code:
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.
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Old 05-30-2018, 02:54 PM   #2
GenoMax
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Location: East Coast USA

Join Date: Feb 2008
Posts: 6,760
Default

Consider the answer given in this thread: https://www.biostars.org/p/289770/
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Old 06-01-2018, 04:32 AM   #3
dfermin315
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Location: Michigan, US

Join Date: Mar 2017
Posts: 2
Default

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