Question: bgzf_read error during samtools run
0
gravatar for kk.mahsa
15 months ago by
kk.mahsa100
kk.mahsa100 wrote:

hi

when i used following command on my bam file:

samtools view -F 4 myfile.bam | perl -lane 'print "$F[2]\t$F[3]"' > myfile.hits

i got this message:

[E::bgzf_read] Read block operation failed with error -1 after 0 of 4 bytes

[main_samview] truncated file.

anybody can help me to resolve it.

ADD COMMENTlink modified 15 months ago by Devon Ryan88k • written 15 months ago by kk.mahsa100
0
gravatar for Devon Ryan
15 months ago by
Devon Ryan88k
Freiburg, Germany
Devon Ryan88k wrote:

Somehow your BAM file got corrupted. You'll want to remake it.

ADD COMMENTlink written 15 months ago by Devon Ryan88k
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