search

lh3 / fermi

A WGS de novo assembler based on the FMD-index for large genomes
75 stars 16 forks source link

Cannot reproduce example in README #13

Closed KhagayN closed 6 years ago

KhagayN commented 6 years ago

Hello,

I am following the README and running into an error at the final step. I'm able to generate the FASTQ file for C.elegans and then get to the Fermi part.

fermi-x.y/run-fermi.pl -ct8 -e fermi-x.y/fermi SRR065390.fastq > fmdef.mak gives me a fmdef.mak file fmdef.txt

but, the final step that generates the contigs returns an empty file. This is the command make -f fmdef.mak -j 8 > fmdef.log 2>&1

Should I expect some intermediary output?

Thanks.

KhagayN commented 6 years ago

The issue was running the commands in the fermi directory. Must run it outside of that directory. To do this add fermi to your path variable.