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Old 12-18-2010, 03:03 AM   #1
jianfeng.mao
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Location: germany

Join Date: Dec 2010
Posts: 12
Default help on "truncated file", when converting sam to bam

When I convert my sam file to bam file, I got "truncated file" in prompt, and also "[sam_read1] reference '503821040998320619' is ecognized as '*'". It is no such problem, when I converted other sam files to bam using the same reference, here is "../Alyrref.folded.fa.fai". Now, I do not know what I can do next.

So, I need to get helps from you. Is it a serious problem? Can I still use this truncated file for pileup? Thanks in advance.

My command and the prompt:

$ samtools view -bht ../Alyrref.folded.fa.fai map.list.sam > map.list.bam
[sam_header_read2] 1099 sequences loaded.
[sam_read1] reference '503821040998320619' is ecognized as '*'.
[main_samview] truncated file.
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