preseq lc_extrap

Open DittmanC opened this issue 3 years ago • 2 comments

I have trouble using preseq lc_extrap command, basically, it tells me my bam file is unsorted. However, I sorted the bam file and then reran it. The same error came out. Commands and errors are as below... Also, it doesn't show up which reads are unsorted.

samtools sort -@ 30 -o ./A_merge_mapped.PT.sort.bam -T A ./A_merge_mapped.PT.bam preseq lc_extrap -extrap 2.1e9 -step 1e8 -output ./out.preseq.txt ./A_merge_mapped.PT.sort.bam ERROR: locations unsorted in: ./A_merge_mapped.PT.sort.bam

Oct 13 '22 01:10 DittmanC

@DittmanC Converting to bed seems to make it work. See #57 .

Feb 04 '23 17:02 royfrancis

@DittmanC sorry for not seeing your issue. (and @royfrancis thanks for helping!!)

If you can provide a minimal BAM file that's giving this error for you, along with the corresponding SAM file, I can try to make it work. The problem is that the only way I know how to make this error appear is to actually use a non-sorted input. I'm not sure if the assumed LOCALE for your sorting would make any difference.

Feb 05 '23 19:02 andrewdavidsmith