Question: Issues with running Bowtie2 in the Fast-Plast pipeline
2.9 years ago by
js1213 • 0
js1213 • 0 wrote:
I am having difficulty running the pipeline, Fast-Plast. The main issue is that I cannot proceed to the Bowtie2 step.
This is the error message it outputs:
"Use of uninitialized value $temp_order in exists at fast-plast.pl line 1079, <$default_gb> line 2041. Use of uninitialized value $temp_order in hash element at fast-plast.pl line 1081, <$default_gb> line 2041. Can't exec "/Users/jacobsuissa/Fast-Plast/bowtie2-2.3.2-build": No such file or directory at fast-plast.pl line 1118. Can't exec "/Users/jacobsuissa/Fast-Plast/bowtie2-2.3.2": Permission denied at fast-plast.pl line 551. No mapped reads files were identified to run SPAdes. Please check 2_Bowtie_Mapping."
This is the command that I type in to run the pipeline:
" perl fast-plast.pl -1 <name of Read1 file> -2 <name of Read2 file> --name "Is_6754" --skip trim —-user_bowtie <input reference genome> --coverage_analysis --clean light"
Any help would be great!
ADD COMMENT • link •