Question: bgzf_read error during samtools run
0
gravatar for kk.mahsa
21 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 21 months ago by Devon Ryan91k • written 21 months ago by kk.mahsa100
0
gravatar for Devon Ryan
21 months ago by
Devon Ryan91k
Freiburg, Germany
Devon Ryan91k wrote:

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

ADD COMMENTlink written 21 months ago by Devon Ryan91k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 776 users visited in the last hour