vaquerizaslab/fanc

fanc auto ERROR: bowtie2 must be in PATH or defined on config file for mapping!

shinohara-xiao opened this issue · 1 comments

shinohara-xiao commented

Hi, when I am running

fanc auto SRR4271982_chr18_19_1.fastq.gzip SRR4271982_chr18_19_2.fastq.gzip output/ \
          -g hg19_chr18_19.fa -i hg19_chr18_19/hg19_chr18_19 -n fanc_example -t 4 -r HindIII \
          --split-ligation-junction -q 30 --run-with test

I got an EEROR like this:
fanc auto: error: bowtie2 must be in PATH or defined on config file for mapping!
image

I wonder how could I solve this problem ?
Thank you very much !

liz-is commented

Hi,
This error message means that FAN-C can't find where bowtie2 is installed. bowtie2 needs to be in your PATH, or alternatively you can specify the location in a FAN-C config file. Hope that helps!