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-   -   RDXplorer (http://seqanswers.com/forums/showthread.php?t=15879)

songsy 11-29-2011 09:44 PM

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

gprakhar 11-30-2011 03:44 AM

Hello,

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

--
pg

eulbra 08-14-2012 01:01 AM

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 (Post 58234)
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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