Question: bgzf_blocked error when using samtools
0
gravatar for milanlove
10 weeks ago by
milanlove0
milanlove0 wrote:

when i used samtools sort for sorting .bam file, following error was appeared. any body know that how i can solve it?

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

samtools sort: truncated file. Aborting

samtools bgzf software error • 169 views
ADD COMMENTlink written 10 weeks ago by milanlove0

error message is here: https://github.com/samtools/htslib/blob/44c6a36f2894b45ad6cb491833d27c6a2106410f/bgzf.c#L854 it an error with the way the file was compressed.

the input or output bam file looks corrupted.

try to check your input file is valid with

gunzip -t input.bam && echo "VALID"

furthermore the command

ADD REPLYlink written 10 weeks ago by Pierre Lindenbaum104k
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