[Samtools-help] EOF marker is absent

[Jens C. F. N. <jen...@ch...>]

Hi,

I have been sorting tophat generated .bam files with samtools to use them as input for htseq-count.

$ samtools sort -n file1.bam -o file1.bam_sorted_n.bam

for 36 of 39 files this works fine, while for 3 files i receive the following error:

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

These 3 files happens to be the largest files of ~ 4Gb

any suggestions? Can I check if the files are corrupt or if it is a bug in samtools?

Thanks

-Jens