Hello, @ellakantor
I just fixed the same problem as yours. My problem is because the file is very large and the splitted group will be too much. This could result in the over-long length of arguments list of cat
command line.
You can put all your files just under a directory of your home path that can shorten the length of the absolute path of signalP files. Or you can try a for i in {input}
loop.
Hope this will be helpful to you.
If there is any problem we can talk through e-mail
My e-mail address is lgyjsnjhit@gmail.com
Thank you, Gaoyang
Dear @laura.denies
I have figured it out! The stupid issue of the length of arguments of cat
command line! I just shorten the length of the absolute path of files and it worked!
patho_PW_5M.e286138
Dera @laura.denies
I confronted the issue and I thought it could be the issue of cat
command line. I don't know why there would be no error when the number of files is small. I don't know if i try "for i in {input}; do cat ${i} >> {output}" will work
Error in rule splitting: jobid: 30 output: path/PathoFact_results/splitted/SRR3401469.contigs/ log: path/test/PathoFact_results/logs/SRR3401469.contigs/split_ORF.log (check log file(s) for error message) conda-env: path/PathoFact/.snakemake/conda/a010a931 shell:
python scripts/split.py path/PathoFact_results/PathoFact_intermediate/renamed/SRR3401469.contigs_ID.faa 10000 path/PathoFact_results/splitted/SRR3401469.contigs/ &> path/PathoFact_results/logs/SRR3401469.contigs/split_ORF.log
(exited with non-zero exit code)
Updating job 18. Updating job 19. Creating conda environment envs/HMMER.yaml... Downloading remote packages. [Thu Feb 24 19:39:58 2022] Error in rule splitting: jobid: 28 output: path/PathoFact_results/PathoFact_intermediate/splitted/SRR3401469.contigs/ log: path/PathoFact_results/PathoFact_intermediate/logs/SRR3401469.contigs/split_ORF.log (check log file(s) for error message) conda-env: path/PathoFact/.snakemake/conda/a010a931 shell:
python scripts/split.py path/PathoFact_results/PathoFact_intermediate/PathoFact_intermediate/renamed/SRR3401469.contigs_ID.faa 10000 path/PathoFact_results/PathoFact_intermediate/splitted/SRR3401469.contigs/ &> path/PathoFact_results/PathoFact_intermediate/logs/SRR3401469.contigs/split_ORF.log
(exited with non-zero exit code)
Removing output files of failed job splitting since they might be corrupted: path/PathoFact_results/splitted/SRR3401469.contigs/ Removing output files of failed job splitting since they might be corrupted: path/PathoFact_results/PathoFact_intermediate/splitted/SRR3401469.contigs/ Shutting down, this might take some time. Exiting because a job execution failed. Look above for error message Complete log: /lomi_home/gaoyang/software/PathoFact/.snakemake/log/2022-02-24T184853.821696.snakemake.log
Dear @laura.denies I wanted to put it on the cluster with cmd:qsub but failed. "Error submitting jobscript (exit code 175)" Here is my .pbs filepathofact.pbs And here is the error logpathofact_AMR.e284271
Dear @laura.denies I wanted to put it on the cluster with cmd:qsub but failed. "Error submitting jobscript (exit code 175)" Here is my .pbs filepathofact.pbs And here is the error logpathofact_AMR.e284271
Dear @laura.denies
Thank you for your feedback. I retried it and find it worked.split_ORF.log
Error in rule splitting: jobid: 30 output: path/PathoFact_results/splitted/SRR3401469.contigs/ log: path/test/PathoFact_results/logs/SRR3401469.contigs/split_ORF.log (check log file(s) for error message) conda-env: path/PathoFact/.snakemake/conda/a010a931 shell:
python scripts/split.py path/PathoFact_results/PathoFact_intermediate/renamed/SRR3401469.contigs_ID.faa 10000 path/PathoFact_results/splitted/SRR3401469.contigs/ &> path/PathoFact_results/logs/SRR3401469.contigs/split_ORF.log
(exited with non-zero exit code)
Updating job 18. Updating job 19. Creating conda environment envs/HMMER.yaml... Downloading remote packages. [Thu Feb 24 19:39:58 2022] Error in rule splitting: jobid: 28 output: path/PathoFact_results/PathoFact_intermediate/splitted/SRR3401469.contigs/ log: path/PathoFact_results/PathoFact_intermediate/logs/SRR3401469.contigs/split_ORF.log (check log file(s) for error message) conda-env: path/PathoFact/.snakemake/conda/a010a931 shell:
python scripts/split.py path/PathoFact_results/PathoFact_intermediate/PathoFact_intermediate/renamed/SRR3401469.contigs_ID.faa 10000 path/PathoFact_results/PathoFact_intermediate/splitted/SRR3401469.contigs/ &> path/PathoFact_results/PathoFact_intermediate/logs/SRR3401469.contigs/split_ORF.log
(exited with non-zero exit code)
Removing output files of failed job splitting since they might be corrupted: path/PathoFact_results/splitted/SRR3401469.contigs/ Removing output files of failed job splitting since they might be corrupted: path/PathoFact_results/PathoFact_intermediate/splitted/SRR3401469.contigs/ Shutting down, this might take some time. Exiting because a job execution failed. Look above for error message Complete log: /lomi_home/gaoyang/software/PathoFact/.snakemake/log/2022-02-24T184853.821696.snakemake.log