Hello
I run Fermi to assemble a plant genome using paired-end illumina reads
The files p0-p3 were generated successfully, but the other two (p4-p5) are empty.
By looking at the log file, I can see that the command that failed is:
"scaf -Pt 16 fmdef.ec.fmd fmdef.p3.mag.gz perl -ne 'print "$1 $2\n" if /avg = (\S+) std = (\S+)/' fmdef.p3.mag.gz.log 2> fmdef.p4.fa.gz.log | gzip -1 > fmdef.p4.fa.gz"
If I understand correctly, it failed due to missing avg and std values, because the fmdef.p3.mag.gz.log is empty.
Any suggestion what can be done?
Thanks
Mali
Hello I run Fermi to assemble a plant genome using paired-end illumina reads The files p0-p3 were generated successfully, but the other two (p4-p5) are empty. By looking at the log file, I can see that the command that failed is: "scaf -Pt 16 fmdef.ec.fmd fmdef.p3.mag.gz
perl -ne 'print "$1 $2\n" if /avg = (\S+) std = (\S+)/' fmdef.p3.mag.gz.log2> fmdef.p4.fa.gz.log | gzip -1 > fmdef.p4.fa.gz" If I understand correctly, it failed due to missing avg and std values, because the fmdef.p3.mag.gz.log is empty. Any suggestion what can be done? Thanks Mali