Hi,
I have SOLiD reads which are paried-end (75bp and 35bp) in .csfasta and .QV.qual format. I would like to use Shrimp2 to align them. So far I have been having trouble using it.
I used the following command:
gmapper -1 Sample/F3/reads/Hope_2014_02_20_1_01_13_0502_F3.csfasta -2 Sample/F5-DNA/reads/Hope_2014_02_20_1_01_13_0502_F5-DNA.csfasta $SCRATCH/human_hg19.fa -N 32 -p opp-in > Sample.sam 2> Logs/Sample.log
This is my log file and the error is shown at the bottom. I'm not sure what that means.
- Processing genome file [/Refs/human_hg19.fa]
- Processing contig chr1
- Processing contig chr2
- Processing contig chr3
- Processing contig chr4
- Processing contig chr5
- Processing contig chr6
- Processing contig chr7
- Processing contig chr8
- Processing contig chr9
- Processing contig chr10
- Processing contig chr11
- Processing contig chr12
- Processing contig chr13
- Processing contig chr14
- Processing contig chr15
- Processing contig chr16
- Processing contig chr17
- Processing contig chr18
- Processing contig chr19
- Processing contig chr20
- Processing contig chr21
- Processing contig chr22
- Processing contig chrX
- Processing contig chrY
- Processing contig chrM
Loaded Genome
note: detected fastq format in input file [Sample/F3/reads/Hope_2014_02_20_1_01_13_0502_F3.csfasta]
- Processing read files [Sample/F3/reads/Hope_2014_02_20_1_01_13_0502_F3.csfasta , Sample/F5-DNA/reads/Hope_2014_02_20_1_01_13_0502_F5-DNA.csfasta]
note: quality v ...