a problem about SHRiMP2 solving AB SOLID

[Lv Ray]

Hi, everyone. I want to do the mapping about AB SOLID data. They are paired-end sequencing. The format of .fastq files show below:
pair1:
@SRR586064.1ugc_357_358_MatePair_2x50bp_solid0032_20100528_MP_ugc_357_854_13_97/1
T30..01121.12.1032100213131122200031222022101302313
+
!AB!!?:>@<!@B!;AB?AA@@<2<@?@@<?AB>A?9?:;@@>;-=>>7=@
pair2:
@SRR586064.1ugc_357_358_MatePair_2x50bp_solid0032_20100528_MP_ugc_357_854_13_97/2
G10330000122222033220201000000220002000000000000000
+
!@BBABBBB@>?@@(.))35.%-.3((%1+%((82-'.*-*/3*14*'696
I try use the tool:SHRiMP2, but it is not friendly to solve my datasets. I run the command:
gmapper-cs -1 pair1.fastq -2 pair2.fastq -L ./test/Sscro --pair-mode opp-in -Q --trim-first --qv-offset 33 >pair12.sam 2>pair12.log
And I got the info in the end of file .log:
note: detected fastq format in input file [pair1.fastq]
- Processing read files [pair1.fastq , pair2.fastq]
note: quality value format not set explicitly; using PHRED+33
done r/hr r/core-hr
There has been a problem reading in the read "SRR586064.1", the quality length exceeds the sequence length!
Are you using the right executable? gmapper-cs for color space? and gmapper-ls for letter space?

I have tried some parameters of SHRiMP2, but failed. And I can't find any similar example from SHRiMP2 website. Does anybody get the same problem and have you solve it ? Or maybe I should use another tool, any suggestion?

[Brian Bushnell]

Looks like the problem is that there are more qualities than colors. There are 50 colors (the leading 'T' or 'G' are fixed) and 51 qualities, but the first quality (!) is a placeholder. I can't remember if that's normal but I haven't worked with Solid in a while. It should be fine if you eliminate the first quality value for every quality line, and leave everything else unchanged.

[Lv Ray]

Looks like the problem is that there are more qualities than colors. There are 50 colors (the leading 'T' or 'G' are fixed) and 51 qualities, but the first quality (!) is a placeholder. I can't remember if that's normal but I haven't worked with Solid in a while. It should be fine if you eliminate the first quality value for every quality line, and leave everything else unchanged.

Thanks, Brian Bushnell. I will try your suggestion.

[Lv Ray]

Looks like the problem is that there are more qualities than colors. There are 50 colors (the leading 'T' or 'G' are fixed) and 51 qualities, but the first quality (!) is a placeholder. I can't remember if that's normal but I haven't worked with Solid in a while. It should be fine if you eliminate the first quality value for every quality line, and leave everything else unchanged.

Brian Bushnell, Thank you for your suggestion, and I have got the main point to solve it. Maybe now the core problem is to try some parameters of SHRiMP2.