Question

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

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10.3 years ago

asphodel6 ▴ 20

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 • 8.3k views

ADD COMMENT • link updated 10.3 years ago by Pierre Lindenbaum 161k • written 10.3 years ago by asphodel6 ▴ 20

score 4 · Answer 1 · 2013-12-29

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10.3 years ago

Pierre Lindenbaum 161k

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

ADD COMMENT • link 10.3 years ago by Pierre Lindenbaum 161k

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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 REPLY • link 10.3 years ago by asphodel6 ▴ 20

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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 REPLY • link 10.3 years ago by Fabio Marroni ★ 3.0k

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

ADD REPLY • link 3.5 years ago by fredjaya ▴ 20