Question: Error Bam File Is Malformed: Premature End Of File Using Gatk Tool Baserecalibrator
2
gravatar for asphodel6
5.0 years ago by
asphodel620
Germany
asphodel620 wrote:

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?

gatk java • 5.0k views
ADD COMMENTlink modified 5.0 years ago by Pierre Lindenbaum115k • written 5.0 years ago by asphodel620
3
gravatar for Pierre Lindenbaum
5.0 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum115k wrote:

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

ADD COMMENTlink written 5.0 years ago by Pierre Lindenbaum115k

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.

ADD REPLYlink written 5.0 years ago by asphodel620
1

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

ADD REPLYlink written 5.0 years ago by Fabio Marroni2.0k
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