Error in rule compute_LD_scores_all_genes:

[yuGithuuub]

Snakemake version
6.7.0

Describe the bug
When I try to repeate the code of CELLECT, there is no probelm for the order "snakemake --use-conda -j -s cellect-magma.snakefile --configfile config.yml", However when I try to run the command "snakemake --use-conda -j -s cellect-ldsc.snakefile --configfile config.yml", the job could only be performed to 146, there might be something wrong with "rule compute_LD_scores_all_genes", but I cann't find solution for this error.

...
Activating conda environment: /home/linux/GY/github/cellect/CELLECT/.snakemake/conda/b969fab6c73d3ca7133ed2b9ae7356db
[Tue Sep 7 18:50:00 2021]
Error in rule compute_LD_scores_all_genes:
jobid: 136
output: CELLECT-EXAMPLE/CELLECT-LDSC/precomputation/control.all_genes_in_dataset/all_genes_in_mousebrain-test.22.l2.ldscore.gz, CELLECT-EXAMPLE/CELLECT-LDSC/precomputation/control.all_genes_in_dataset/all_genes_in_mousebrain-test.22.l2.M, CELLECT-EXAMPLE/CELLECT-LDSC/precomputation/control.all_genes_in_dataset/all_genes_in_mousebrain-test.22.l2.M_5_50, CELLECT-EXAMPLE/CELLECT-LDSC/precomputation/control.all_genes_in_dataset/all_genes_in_mousebrain-test.22.log
log: CELLECT-EXAMPLE/CELLECT-LDSC/logs/log.compute_LD_scores.all_genes_in_dataset.mousebrain-test.22.txt (check log file(s) for error message)
conda-env: /home/linux/GY/github/cellect/CELLECT/.snakemake/conda/b969fab6c73d3ca7133ed2b9ae7356db
shell:
/home/linux/GY/github/cellect/CELLECT/ldsc/ldsc.py --l2 --bfile /home/linux/GY/github/cellect/CELLECT/data/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.22 --ld-wind-cm 1 --annot CELLECT-EXAMPLE/CELLECT-LDSC/precomputation/control.all_genes_in_dataset/all_genes_in_mousebrain-test.22.annot.gz --thin-annot --out CELLECT-EXAMPLE/CELLECT-LDSC/precomputation/control.all_genes_in_dataset/all_genes_in_mousebrain-test.22 --print-snps /home/linux/GY/github/cellect/CELLECT/data/ldsc/print_snps.txt &> CELLECT-EXAMPLE/CELLECT-LDSC/logs/log.compute_LD_scores.all_genes_in_dataset.mousebrain-test.22.txt
(one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
...
Finished job 149.
111 of 258 steps (43%) done
[Tue Sep 7 18:50:57 2021]
Finished job 143.
112 of 258 steps (43%) done
[Tue Sep 7 18:50:59 2021]
Finished job 146.
113 of 258 steps (44%) done

Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Complete log: /home/linux/GY/github/cellect/CELLECT/.snakemake/log/2021-09-07T184930.682372.snakemake.log

[Tobi1kenobi]

Hi there,

Apologies for the late response. Did you manage to resolve this? Have you taken a look at the log files for that rule yet?

Best,
Tobi

[liangcheng-hrbmu]

I had the same problem. How to fix it？
log:
/usr/bin/bash: line 1: /data_alluser/LHL/CELLECT/ldsc/ldsc.py: Permission denied

[liangcheng-hrbmu]

When I give ldsc.py permission 777. log becomes
/usr/bin/env: ‘python\r’: No such file or directory