FORUMgetting an error in my populations output file saying that I have a malformed genomic locus
Ella Bowles asked 6 months ago



Hello,
I am running the stacks pipeline on GBS data for lake trout, and I am aligning my reads to Arctic char using BWA. Populations runs fine until it gets to locus four, after which point it says:
Now processing…
LG1
LG2
LG3
Error: Malformed genomic position ‘LG4q.1:29:15355:+’.
Error: Locus 29325
Error: Bad GStacks files.
Aborted.

I figured out, and confirmed with the developers of stacks, that there cannot be any “:” in the genome because gstacks, one of the modules of stacks, uses it as a delimiter. So, I went though my genome and changed the “:” to an “_”. I then deleted all my alignments, re-indexed the genome, re-aligned my reads and re-ran gstacks and populations. Stangely, I am still getting the same problem.

I just don’t understand how this could be the case. When I go to the fasta file that I used for indexing and type “grep -e “>LG” < genomeNoColon.fa” I see,

>LG1
>LG2
>LG3
>LG4p
>LG4q.1_29
>LG4q.2
>LG5
>LG6.1
>LG6.2
>LG7
>LG8
>LG9
>LG10
>LG11
>LG12
>LG13
>LG14
>LG15
>LG16
>LG17
>LG18
>LG19
>LG20
>LG21
>LG22
>LG23
>LG24
>LG25
>LG26
>LG27
>LG28
>LG30
>LG31
>LG32
>LG33
>LG34
>LG35
>LG36
>LG37

and when I look at my annotation file (less saal.ann) in the indexed files I see the following:

0 LG4q.1_29 (null)
165850403 90519428 61604

I guess I can deleted everything again and try again just in case I thought i deleted everything and I didn’t, but is there a way that I can check the bam files to see if there are colons in there still, and or checked my indexed genome to see if/where there are colons in there?

Can I give you my directories so that you can access the files?

With thanks,
Ella

1 Answers
Ella Bowles answered 6 months ago



Oh boy, this post can be deleted. I just found the problem. So silly. For some reason I had my input directory set to my old alignments, which had problematic locus headers.

jrosner Staff replied 6 months ago

Hi Ella, glad you figured it out!