terminate called after throwing an instance of 'BamTools::Internal::BamException'

[Shruti Srivastava]

Hi,

I am using bedtools coverage to get the the coverage of the feature in my bed file when search against my bam file generated by Dragen pipeline for WG methylation seq. The outputs is Bismark generated bam file.

I have already ran the following command on one of my samples successfully:

$ bedtools coverage -abam ALS3_793_hg19/ALS3.sorted.bam -b ALS3_793_hg19/ALS3_CG.bed -hist > ALS3_793_hg19/ALS3_cpg_cov.txt

But now I am encountering the following error when i am running the other samples:

$ bedtools coverage -abam ALS6_798_hg19/ALS6.sorted.bam -b ALS6_798_hg19/ALS6_CG.bed -hist > ALS6_798_hg19/ALS6_cpg_cov.txt

terminate called after throwing an instance of 'BamTools::Internal::BamException'

  what():  BgzfStream::InflateBlock: zlib inflate failed

Aborted (core dumped)

Will appreciate your help in resolving this error,

Thanks 

Shruti

[Aaron Quinlan]

Hi Shruti,

Have you tried running samtools stats (or the like) on the BAM to make sure it is not corrupt?

Aaron

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[Shruti Srivastava]

Thanks, Aaron, yes it was a problem in the bam file it was truncated. I generated again and ran coverageBed on it without any trouble this time.

Shruti Srivastava, B.Tech., MSc

Bioinformatician

Atlantic Cancer Research Institute

Moncton, Canada

Contact no. +1 (778)-710-7937

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