Error Bam File Is Malformed: Premature End Of File Using Gatk Tool Baserecalibrator

Question

[asphodel6]

Dear all, i am trying to use BaseRecalibrator tool fron GATK and become this error: ERROR MESSAGE: SAM/BAM file *.bam is malformed: Premature end of file Is this really the problem of my bam or some issues of Java memory usage? How can i check it further?

Answer 1

[Pierre Lindenbaum]

try to run samtools view -c your.bam just to check that your file is OK.

[asphodel6]

Thank you for the hint. I have done this, but became [bam_header_read] EOF marker is absent. The input is probably truncated. I have downloaded my.bam from the galaxy server. So my next question is whether i can manipulate my.bam to get rid of this error.

[Fabio Marroni]

You probably can't. The most likely explanation is that the download went wrong somehow. You can give a look to this post for clarifications: error: EOF marker is absent when processing a BAM file

[fredjaya]

Thanks for the tips! Came across an identical issue and used samtools quickcheck your.bam to identify malformed files