EOF marker is absent

[in...@orbicule.com]

Hi,

When running computeGCBias with a 1000Genomes bam file:

computeGCBias -b NA12878.chrom1.SLX.maq.SRP000032.2009_07.bam --effectiveGenomeSize 2451960000 -g hg19.2bit -l 200 --GCbiasFrequenciesFile freq.txt

I'm receiving the following error:

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

Apparently this is a known samtools issue, which is otherwise harmless (see also http://seqanswers.com/forums/archive/index.php/t-12546.html). However, it seems to stop computeGCBias from doing its thing.

Is there a way around this, so we can still analyze this bam file?

Thanks,
Peter

[Fidel Ramirez]

Hi,

I would try to repair the bam file which is apparently causing the problem. I suppose that by converting it to sam and then again to bam the problem should go away.

-fidel

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Fidel Ramirez

[Devon Ryan]

In this case it's probably not really broken, it was just made before BAM files had a magic string added to the end of the files. I suspect that any BAM file made early in the existence of the standard will have this issue. I just need to check if pysam throws a particular exception that we could test here.

Devon

-- 
Devon Ryan, PhD
Bioinformatician / Data manager
Bioinformatics Core Facility
Max Planck Institute for Immunobiology and Epigenetics
Email: dpry...@gmail.com

[Devon Ryan]

The cause of this is that the index for that file is corrupt. Either
reindex it or replace it with the one I'm attaching. If you've
downloaded the 2bit file from UCSC then computeGCBias should then run to
completion. You'll still get the warnings, but those are from HTSlib, so
there's nothing we can do about them.

Devon

[suny...@gmail.com]

Thanks bro @Fidel Ramirez!!