Error when running one_wag.slurm

[gwigley409]

Hello! I am fairly new to this so I apologize if this is an easy fix. I am getting an error when running one_wag.slurm script:

FileNotFoundError in file /scratch/negishi/gwigley/WAGS_TEST/output/BassetHound/13641/UU_Cfam_GSD_1.0_ROSY/src/utils.py, line 69: [Errno 2] No such file or directory: ' RESULTS /bed_group / bedgroup 0000 .bed ' File "/scratch/negishi/gwigley/WAGS_TEST/output/BassetHound/13641/UU_Cfam_GSD_1.0_ROSY/one_wag.smk", line 24, in File "/scratch/negishi/gwigley/WAGS_TEST/output/BassetHound/13641/UU_Cfam_GSD_1.0_ROSY/src/utils.py", line 69, in sequence_grouping

It also appears to be generating two RESULTS directories, one that contains spaces in the name (and has seq_group as the subdirectory) and one that does not (has bed_group as the subdirectory).

gwigley@login04.negishi:[UU_Cfam_GSD_1.0_ROSY] $ ls -l -a total 384 drwxr-xr-x 9 gwigley student 4096 Jan 24 11:12 . drwxr-xr-x 3 gwigley student 4096 Jan 24 11:11 .. -rw-r--r-- 1 gwigley student 963 Jan 24 11:11 BassetHound_13641.one_wag.slurm -rw-r--r-- 1 gwigley student 380 Jan 24 11:11 input.tsv -rw-r--r-- 1 gwigley student 1798 Jan 24 11:11 one_wag.smk drwxr-xr-x 3 gwigley student 4096 Jan 24 11:12 ' RESULTS ' drwxr-xr-x 3 gwigley student 4096 Jan 24 11:12 RESULTS drwxr-xr-x 2 gwigley student 4096 Jan 18 10:57 rules drwxr-xr-x 2 gwigley student 4096 Jan 24 11:11 slurm.go_wags drwxr-xr-x 2 gwigley student 4096 Jan 24 11:12 slurm_logs drwxr-xr-x 3 gwigley student 4096 Jan 24 11:12 .snakemake drwxr-xr-x 2 gwigley student 4096 Jan 18 10:57 src -rw-r--r-- 1 gwigley student 655 Jan 24 11:11 UU_Cfam_GSD_1.0_ROSY_config.yaml -rw-r--r-- 1 gwigley student 337448 Jan 24 11:12 UU_Cfam_GSD_1.0_ROSY.dict

I can't seem to find a solution to this error. I appreciate all of your help!

[jonahcullen]

No problem at all! Can you send me the prep_subs.py command you used?

[gwigley409]

python /scratch/negishi/gwigley/wags/wags/prep_subs.py \ --meta /scratch/negishi/gwigley/WAGS_TEST/13641_input.csv \ --fastqs /scratch/negishi/gwigley/WAGS_TEST \ --ref UU_Cfam_GSD_1.0_ROSY \ --out /scratch/negishi/gwigley/WAGS_TEST/output \ --bucket RESULTS \ --snake-env snakemakeV7.24.0 \ --partition a \ --email gwigley@purdue.edu \ --account kje0003 \ --remote local \ --sif /scratch/negishi/gwigley/wags.sif

[aletko]

Hello! Just to add I have also seen this problem of creating directory name with spaces, when using python version 3.12. So far, I “solved” it by using python 3.11. Maybe that helps with figuring it out. :-)

On 24 Jan 2024, at 17:28, gwigley409 @.***> wrote:

Hello! I am fairly new to this so I apologize if this is an easy fix. I am getting an error when running one_wag.slurm script:

FileNotFoundError in file /scratch/negishi/gwigley/WAGS_TEST/output/BassetHound/13641/UU_Cfam_GSD_1.0_ROSY/src/utils.py, line 69: [Errno 2] No such file or directory: ' RESULTS /bed_group / bedgroup 0000 .bed ' File "/scratch/negishi/gwigley/WAGS_TEST/output/BassetHound/13641/UU_Cfam_GSD_1.0_ROSY/one_wag.smk", line 24, in File "/scratch/negishi/gwigley/WAGS_TEST/output/BassetHound/13641/UU_Cfam_GSD_1.0_ROSY/src/utils.py", line 69, in sequence_grouping

It also appears to be generating two RESULTS directories, one that contains spaces in the name (and has seq_group as the subdirectory) and one that does not (has bed_group as the subdirectory).

@. @.>:[UU_Cfam_GSD_1.0_ROSY] $ ls -l -a total 384 drwxr-xr-x 9 gwigley student 4096 Jan 24 11:12 . drwxr-xr-x 3 gwigley student 4096 Jan 24 11:11 .. -rw-r--r-- 1 gwigley student 963 Jan 24 11:11 BassetHound_13641.one_wag.slurm -rw-r--r-- 1 gwigley student 380 Jan 24 11:11 input.tsv -rw-r--r-- 1 gwigley student 1798 Jan 24 11:11 one_wag.smk drwxr-xr-x 3 gwigley student 4096 Jan 24 11:12 ' RESULTS ' drwxr-xr-x 3 gwigley student 4096 Jan 24 11:12 RESULTS drwxr-xr-x 2 gwigley student 4096 Jan 18 10:57 rules drwxr-xr-x 2 gwigley student 4096 Jan 24 11:11 slurm.go_wags drwxr-xr-x 2 gwigley student 4096 Jan 24 11:12 slurm_logs drwxr-xr-x 3 gwigley student 4096 Jan 24 11:12 .snakemake drwxr-xr-x 2 gwigley student 4096 Jan 18 10:57 src -rw-r--r-- 1 gwigley student 655 Jan 24 11:11 UU_Cfam_GSD_1.0_ROSY_config.yaml -rw-r--r-- 1 gwigley student 337448 Jan 24 11:12 UU_Cfam_GSD_1.0_ROSY.dict

I can't seem to find a solution to this error. I appreciate all of your help!

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[gwigley409]

Thank you! Switching to python 3.11 seemed to "fix" the problem.

[jonahcullen]

Thanks @aletko ! I will update the install instructions to address this.