jlanga/smsk_trinotate

MissingInputException

Closed this issue · 4 comments

mictadlo commented

Hi,
I have got the following error:

snakemake
Building DAG of jobs...
MissingInputException in line 346 of /smsk_trinotate/src/snakefiles/trinotate.py:
Missing input files for rule trinotate_load:
results/trinotate/rnammer.gff

What did I miss?

Thank you in advance

Michal

jlanga commented

#5 maybe?

mictadlo commented

Hi,
It did not even produced any output files. By any chance, do you know where should I search for problems?

Best wishes,

Michal

jlanga commented

Hi, Mic.

Can you try executing the pipeline in the optional_programs branch?

I think it is about rnammer not finding rRNA transcripts. I've added one that should make it work.

Jorge

mictadlo commented

Hi, I did wget -c https://raw.githubusercontent.com/jlanga/smsk_trinotate/optional_programs/transcript.fa but I still get the same error.