error codes in the scrap file after trim.seqs

Commands in mothur
1

Hello!

Can someone direct me to a full list of the error codes written in the scrap file after using trim.seqs?

After carefully reading the wiki page, I still don’t know why all my short reads are being scrapped with the code “k”.

2

I would second this please. I am losing all of my sequences due to an error code “s” and don’t know what this means. Is it related to window size, meaning it is failing the qwindow averaging cutoff?

Thanks!

3

k linker missing
b barcode missing
s spacer missing
f forward primer missing
r reverse primer missing
t too many differences to the linker, spacer, barcode, and forward primer
l too short or too long
h homopolymer length too long
n too many ambiguous bases

Also, if a barcode is missing, then you’ll also be missing the forward primer and the spacer if you’ve included one.

4

Thanks so much, Pat!

However, now I’m really confused. Is the spacer option now required as of 1.24? I’m not even trying to trim with an oligos file at this point or use sdiffs or anything like that – just based upon quality scores. So why would it be throwing out everything with an “s”? Is there a default spacer that it is looking for?

If it helps, this was my command, which is following fastq.info. Nothing else has been done to the files at this point.

trim.seqs(fasta=BDB1.fasta,qfile=BDB1.qual,maxambig=0,maxhomop=8,qwindowaverage=35,qwindowsize=50,processors=8)

5

Thanks!

Still, I follow on the issue opened by bbadgley. I just want to remove homopolymers and ambiguities, nothing else, no quality trim or check of oligos. Am I missing something?

my command is:
trim.seqs(fasta=#{f},minlength=30,maxambig=0,maxhomop=8,processors=4)

6

Thanks for reporting this bug. It was introduced in version 1.24.0 with the addition of linkers and spacers to the oligos file. It was corrected in version 1.25.0. An upgrade should resolve the problem for you.