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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
The text was updated successfully, but these errors were encountered:
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
The text was updated successfully, but these errors were encountered: