Issues with running Bowtie2 in the Fast-Plast pipeline

Question

[js1213]

Hi All,

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!

Jacob

[GenoMax]

Two comments. You are hopefully not using " in your actual command. And you have real values instead of placeholders for command options. e.g. <input reference genome>

[js1213]

Yes, I have real values in my command.