On 9 Jan 2017, at 19:05, Madolyn Macdonald <mm...@udel.edu> wrote:
> I am trying to calculate the mapping statistics of a BAM file. I am using
> SAMtools 1.3.1 and am able to get statistics on the BAM file using samtools
> flagstat. However, when I try samtools stats, which I would like to use, I
> get the following error:
>
> [W::bam_hdr_read] EOF marker is absent. The input is probably truncated.
> [E::inflate_block] inflate failed: progress temporarily not possible, or in()
> / out() returned an error
> [E::bgzf_read_block] inflate_block error -1
> [E::bgzf_read] bgzf_read_block error -1 after 0 of 4 bytes
> Failure while decoding file
Samtools flagstat and stats use the same code to read BAM files, so it would be
surprising if one but not the other produced these messages when reading the
same file. Please show us the complete command lines you are using for both
flagstat and stats. After samtools stats has given those errors, does a
subsequent samtools flagstat still work or does it produce similar messages?
John
--
The Wellcome Trust Sanger Institute is operated by Genome Research
Limited, a charity registered in England with number 1021457 and a
company registered in England with number 2742969, whose registered
office is 215 Euston Road, London, NW1 2BE.
------------------------------------------------------------------------------
Developer Access Program for Intel Xeon Phi Processors
Access to Intel Xeon Phi processor-based developer platforms.
With one year of Intel Parallel Studio XE.
Training and support from Colfax.
Order your platform today. http://sdm.link/xeonphi
_______________________________________________
Samtools-help mailing list
Samtools-help@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/samtools-help
