Hi everybody,
I cant make bfast work on Fedora 14.
I'm using unpaired SOLID data of 50 bp length.
In version 0.6.4e, the solid2fastq step did not work properly for me. In the last version (0.6.4f git:50fb580ff23fe839b72b49924908159bd35d6f86) from the git repository, the bfast match step fails with the following error message:
...
In total read 1 contigs for a total of 3171952 bases
************************************************************
Reading /home/user/work/analysis/reads.1.fastq into a temp file.
bfast: ../bfast/RGMatch.c:155: RGMatchPrint: Assertion `m->readLength > 0' failed.
The performed steps were:
1) solid2fastq -n 10000000 -o reads datafile.csfasta datafile.qual
2) ~/tools/bfast/bfast/bfast fasta2brg -f refGenome.fna
~/tools/bfast/bfast/bfast fasta2brg -f refGenome.fna -A 1
3) bfast index -f refGenome.fna -m 11111... -w 14 -i 1 -A 1 -n 8
4) bfast match -f refGenome.fna -A 1 -r reads1.fastq -n 8 > tmp.bmf
I want to try it on a virtual machine running Fedora 13. Would be happy about any further suggestions... Thanks in advance!
I cant make bfast work on Fedora 14.
I'm using unpaired SOLID data of 50 bp length.
In version 0.6.4e, the solid2fastq step did not work properly for me. In the last version (0.6.4f git:50fb580ff23fe839b72b49924908159bd35d6f86) from the git repository, the bfast match step fails with the following error message:
...
In total read 1 contigs for a total of 3171952 bases
************************************************************
Reading /home/user/work/analysis/reads.1.fastq into a temp file.
bfast: ../bfast/RGMatch.c:155: RGMatchPrint: Assertion `m->readLength > 0' failed.
The performed steps were:
1) solid2fastq -n 10000000 -o reads datafile.csfasta datafile.qual
2) ~/tools/bfast/bfast/bfast fasta2brg -f refGenome.fna
~/tools/bfast/bfast/bfast fasta2brg -f refGenome.fna -A 1
3) bfast index -f refGenome.fna -m 11111... -w 14 -i 1 -A 1 -n 8
4) bfast match -f refGenome.fna -A 1 -r reads1.fastq -n 8 > tmp.bmf
I want to try it on a virtual machine running Fedora 13. Would be happy about any further suggestions... Thanks in advance!
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