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pezmaster31 / bamtools

C++ API & command-line toolkit for working with BAM data
MIT License
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split by reference chr = "EOF marker is absent. The input is probably truncated." #137

Open map2085 opened 8 years ago

map2085 commented 8 years ago

bamtools split -in my.bam -stub split -reference

The command completes successfully, but all of the resulting files are all "truncated".

samtools view -c split.REF_chr1.bam

[W::bam_hdr_read] EOF marker is absent. The input is probably truncated.

This happens for every split file.

Note that my.bam itself is fine (not truncated), though it is large (119 GB).

$ bamtools --version

bamtools 2.4.1 Part of BamTools API and toolkit Primary authors: Derek Barnett, Erik Garrison, Michael Stromberg (c) 2009-2012 Marth Lab, Biology Dept., Boston College

coutuc commented 8 years ago

I am having exactly the same issue...following

MamgKhushi commented 7 months ago

Hello, I am having the same issue as mentioned above, were you able to find a reason/solution to this? It would be helpful for me. Thank you in advance! :)