When I convert my sam file to bam file, I got "truncated file" in prompt, and also "[sam_read1] reference '503821040998320619' is recognized 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. What have happened? 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.
I suggest you edit your question and include the last few lines of your SAM file - it sounds like the last line in the file is truncated, but maybe something else is going on. Use the tail command to get the final lines, e.g. "tail -3 map.list.sam".