Error running rascaf in TORQUE

Question

Error running rascaf in TORQUE

Closed this issue 6 years ago · 5 comments

Hello,

I need to run all my jobs in a scheduler, however when I try to run rascaf-join it gives me the following error:

Found raw assembly file: /panfs/panfs.cluster/scratch/ch1005/genomes/D_maidis_final.contigs.fa
Failed to resolve the path of file PBS_QUEUE=batch.

I don't know why it is trying to resolve the path of the scheduler queue.

Please can you help me with that?

Answer 1 · 2018-07-10T16:02:32.000Z

Can you show me the line start with “command line” in rascaf.out file?

Answer 2 · 2018-07-10T16:37:56.000Z

I think I've figured out the reason and updated the code. Could you please update rascaf and run it? You only need to run rascaf-join since the other parts are not changed.

Answer 3 · 2018-07-10T18:58:45.000Z

Hello, sorry for not answering earlier.

I updated it and ran it again but I get the same error

Found raw assembly file: /panfs/panfs.cluster/scratch/ch1005/genomes/D_maidis_final.contigs.fa Failed to resolve the path of file PBS_QUEUE=batch.

This is the command that I am using

${RASCAF_DIR}/rascaf-join -r rascaf_Dama.out -o rascaf_Dama_scaffold

Answer 4 · 2018-07-10T19:05:03.000Z

Oh, I did not notice the "git push" was failed last time. It should be OK now. Can you give to another try? Sorry for the trouble.

Answer 5 · 2018-07-10T20:45:20.000Z

It is not any trouble. Now it is working. Thank you for all your help.