Question: Problem for converting SAM file to BAM file
gravatar for jamwest101
3.5 years ago by
jamwest10120 wrote:


Recently,galaxy always reports error when I convert filtered SAM file to BAM file by using the software of NGS:SAMtools--->SAM to BAM (error message: [E::sam_parse1] missing SAM header [W::sam_read1] parse error at line 1 [bam_sort_core] truncated file. Continue anyway.). And then, I noticed that the software version is updated from 1.1.3 to 2.0.

Previously, the tool was working very well in the version 1.1.3. I tried to switch the software version to 1.1.3, but Galaxy will automatically switch back to 2.0 after I click Execute. 

How can I fix it?


software error • 1.3k views
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