hoelzer
commented
5 months ago Hey @Andrewab9, thanks for your interest in the pipeline!
Sorry that it fails. Can you share the 13 FASTA files? Or is it confidential data? I want to give it a try and to reproduce your problem.
Actually, changing --chunks would have also been my first idea, but you already tried that.
Hi there, I get this error during the ilps_refinement:
sudo /home/enrico/.cargo/bin/nextflow run hoelzer-lab/ribap -r 1.0.2 --fasta '*.fasta' --cores 30 --max_cores 30 --memory 100.GB -profile local,docker -w work --output ribap-results -resume
executor > local (9) executor > local (9) [ac/4c700e] process > RIBAP:rename (8) [100%] 13 of 13, cached: 13 ✔ [fb/cf620e] process > RIBAP:prokka (4) [100%] 13 of 13, cached: 13 ✔ [56/c44eb0] process > RIBAP:strain_ids [100%] 1 of 1, cached: 1 ✔ [1e/e1602f] process > RIBAP:roary (2) [100%] 5 of 5, cached: 5 ✔ [b7/18cdbe] process > RIBAP:mmseqs2 [100%] 1 of 1, cached: 1 ✔ [86/c9e361] process > RIBAP:mmseqs2tsv [100%] 1 of 1, cached: 1 ✔ [3d/51364e] process > RIBAP:ilp_refinement (5) [100%] 2 of 2, failed: 2
ERROR ~ Error executing process > 'RIBAP:ilp_refinement (8)'
Caused by: Process
RIBAP:ilp_refinement (8)terminated with an error exit status (1)Command executed:
derive_ilp_solutions.py --tmlim 240 --max --indel mmseqs_compressed_chunk7.pkl
Command exit status: 1
Command output: (empty)
Command error: Traceback (most recent call last): File "/root/.nextflow/assets/hoelzer-lab/ribap/bin/derive_ilp_solutions.py", line 151, in
File "/root/.nextflow/assets/hoelzer-lab/ribap/bin/derive_ilp_solutions.py", line 76, in main
File "/root/.nextflow/assets/hoelzer-lab/ribap/bin/derive_ilp_solutions.py", line 113, in pool_workload
File "/root/.nextflow/assets/hoelzer-lab/ribap/bin/ILPBuilder.py", line 128, in generate_lp
OSError: [Errno 24] Too many open files: './GMLHAKDO-vs-OOGOGPEF_1018.ilp'
Work dir: /home/enrico/Projects/domenico/s_aureus/redundans_pilon_pilon/work/91/857bba7d2381dbf9c0662364ae0d4e
Tip: you can replicate the issue by changing to the process work dir and entering the command
bash .command.run-- Check '.nextflow.log' file for details
I've tried changing --chunks from 1 to 8; changing --cores, --max_cores and --memory. I've tried to set also to its maximum value (ulimit -n 1048576) but it doesn't work too. Hope you can help me and thank you for making ribap!