gmapper and colorspace

Question

[jannetta.steyn]

Hi Folks

I hope there is someone out there that can help me. I have been struggling to use gmapper (SHRIMP2) to do some alignment on SOLiD colorspace files.

This is the top few lines of my fastq file (First question - is this actually colorspace?):

@SRR553457.1 s0811_20110511_PE_BC_2_576_555_m1_2_1181_904/1
T201230020002222222200322.2120002003020000203202001
+
!?@**@='%(7%:'&%+8%.'&(%.!&)&,%&;(-&-9%%'(='),1(*&'
@SRR553457.2 s0811_20110511_PE_BC_2_576_555_m1_3_26_1138/1
T003.3030113003001012310310200332130313300203003202
+
!4%6!&+2%51+3+*&&7%4+&*%.&&825;&>%&3%60++5'(%6'2+*4
@SRR553457.3 s0811_20110511_PE_BC_2_576_555_m1_3_27_334/1
T00320210002002221011200032100210001200022012220022

This is my command line:

gmapper-cs --no-qv-check -Q -N 8 -o 5 -h 80% SRR553457.fastq /users/njss3/PTESFinder/data/chr1_GL383518v1_alt.fa  >SRR553457.sam 2>SRR553457.log

note: detected fastq format in input file [SRR553457.fastq]
- Processing read file [SRR553457.fastq]
done r/hr r/core-hr
There has been a problem reading in the read "SRR553457.1", the quality length exceeds the sequence length!
Are you using the right executable? gmapper-cs for color space? and gmapper-ls for letter space?

Kind Regards

Jannetta

This is the error I am getting in the log file: