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I have few bam files and would like to get read counts using 

samtools idxstats

[Data is aligned to hg19 transcriptome]. To use that command I need a sorted bam file. So to sort them I gave the following command.

samtools sort -T /tmp/input.sorted -o input.sorted.bam input.bam

This ended up showing:

[W::bam_hdr_read] EOF marker is absent. The input is probably truncated.
[E::bgzf_read] bgzf_read_block error -1 after 0 of 4 bytes
[bam_sort_core] truncated file. Aborting.

And the tmp dir has 6 input.sorted.nnnn.bam files.

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The cause of the error is that your input file is truncated or /tmp is running out of space. If you can do samtools view -H input.bam without error (reading the header also checks for the magic number at the end of the file) then it's like the that /tmp is filling up.

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  • $\begingroup$ I did "samtools view -H input.bam" there is no error. It ended up showing all the header things which I asked here [bioinformatics.stackexchange.com/questions/3080/… $\endgroup$
    – stack_learner
    Dec 14, 2017 at 14:17
  • $\begingroup$ Then either /tmp is full or otherwise one of the files there is somehow corrupt (you can test them with samtools view -H too). $\endgroup$
    – Devon Ryan
    Dec 14, 2017 at 14:29
  • $\begingroup$ Ok. looks like that file is corrupt. And I tried with other bam file and showed - [bam_sort_core] merging from 24 files... and I see a sorted.bam file. I used "samtools idxstats sorted.bam" - This is what I see - [bam_idxstats] fail to load the index. $\endgroup$
    – stack_learner
    Dec 14, 2017 at 15:21
  • $\begingroup$ Don't forget to samtools index sorted.bam $\endgroup$
    – Devon Ryan
    Dec 14, 2017 at 15:21
  • $\begingroup$ Ok. So, after the indexing I used idxstats and it showed 4 columns without any headers. NR_039978 984 38 0 NM_130786 1766 1 0 NM_138932 9293 37 0 NM_033110 2678 2 0 NM_000014 4678 4 0 NM_144670 5192 18 0 NR_040112 1201 2 0 NM_017436 2106 76 0 NM_016161 1771 0 0 $\endgroup$
    – stack_learner
    Dec 14, 2017 at 15:33

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