Finder does not find files (supposed to be) generated at earlier steps...

[lefterov]

We are running finder at the command line. Now we know that the "Required parameters" as in the help file, and if provided in an empty directory do not work, and we have solved that problem... However, with this command:

finder -mf $PWD/ev-mRNA-metadata_1002_10AM.csv -n 118 -out_dir $PWD/output_1002 -g $PWD/mm10.fa -om VERT -gm $PWD/gmes_linux_64_4 -gml $PWD/gmes_linux_64_4/LICENSE

we get this Error message:

'FileNotFoundError: [Errno 2] No such file or directory: $PWD/output_1002/assemblies_psiclass_modified/combined/combined.gtf'

we don't know how to generate this file... :)

any idea how to solve the problem?

Thanks, and have a nice evening.