Error Bam File Is Malformed: Premature End Of File Using Gatk Tool Baserecalibrator
1
2
Entering edit mode
7.5 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 • 6.8k views
ADD COMMENT
4
Entering edit mode
7.5 years ago

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

ADD COMMENT
0
Entering edit mode

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
2
Entering edit mode

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
0
Entering edit mode

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

ADD REPLY

Login before adding your answer.

Traffic: 2370 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6