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Old 11-29-2011, 09:44 PM   #1
songsy
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Location: Ann Arbor

Join Date: Oct 2011
Posts: 6
Default RDXplorer

I'm using SVmerge. One of the tools is RDXplorer. I run the run.sh. It first picked q0 items and write into a sam file. And then it uses samtools mpileup to call variants. But it doesn't work, showing that :
[bam_header_read] EOF marker is absent. The input is probably truncated.
[bam_header_read] invalid BAM binary header (this is not a BAM file).

The script truncate the bam file itself and it doesn't move on. What can I do?
Thank you very much
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Old 11-30-2011, 03:44 AM   #2
gprakhar
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Location: India

Join Date: Aug 2010
Posts: 78
Default

Hello,

Something wrong with your bam!
BTW Is it a bam?

--
pg
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Old 08-14-2012, 01:01 AM   #3
eulbra
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Location: Beijing

Join Date: Mar 2012
Posts: 8
Default

I add a com in

if fu.isExist(q_mapped_sam):
com = 'wc -l ' + q_mapped_sam + ' > ' + q_mapped_sam + '.log'
v6.execute(com, debug)
com = glob.SAMTOOLS_PATH + '/samtools view -T ' + reference +' -bS '+ q_mapped_sam + ' > ' + q_mapped_bam
v6.execute(com, debug)
com = glob.SAMTOOLS_PATH + '/samtools mpileup -Sf ' + reference + ' ' + q_mapped_bam + ' > ' + q_pileup
v6.execute(com, debug)

then it work, but I still can not run through the whole programe.

Quote:
Originally Posted by songsy View Post
I'm using SVmerge. One of the tools is RDXplorer. I run the run.sh. It first picked q0 items and write into a sam file. And then it uses samtools mpileup to call variants. But it doesn't work, showing that :
[bam_header_read] EOF marker is absent. The input is probably truncated.
[bam_header_read] invalid BAM binary header (this is not a BAM file).

The script truncate the bam file itself and it doesn't move on. What can I do?
Thank you very much
eulbra is offline   Reply With Quote
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