Open Shrishtee-kandoi opened 1 year ago
Update: It is successfully executed upon running it interactively but gives the same error when using bash scripts.
It is unclear what makes the difference despite the success. It could be that the SINGULARITY_BIND variable in the csg was not properly recognized, but it contradicts the previous success.
Have there been any updates to this? I have run into a similar issue that does not resolve when I try running locally versus through a bash script.
Error:
/opt/conda/bin/python: can't open file '/restricted/projectnb/casa/frank/xqtl_project/ROSMAP_PCC/scripts/tmpdbgt_wz5/singularity_run_83472.py': [Errno 2] No such file or directory
Script:
#!/bin/bash -l
module load miniconda
conda activate xqtl_env2
sos run /restricted/projectnb/casa/frank/xqtl_project/xqtl-pipeline/pipeline/gene_annotation.ipynb map_leafcutter_cluster_to_gene \
--cwd /restricted/projectnb/casa/frank/xqtl_project/ROSMAP_PCC/leafcutter_output/batch_all \
--intron_count /restricted/projectnb/casa/frank/xqtl_project/ROSMAP_PCC/leafcutter_output/batch_all/batch_all_bam_no_ext_intron_usage_perind.counts.gz \
--phenoFile /restricted/projectnb/casa/frank/xqtl_project/ROSMAP_PCC/leafcutter_output/batch_all/batch_all_bam_no_ext_intron_usage_perind.counts.gz_raw_data.qqnorm.txt \
--annotation-gtf /restricted/projectnb/casa/frank/xqtl_project/ROSMAP_PCC/reference_data/Homo_sapiens.GRCh38.103.chr.reformatted.collapse_only.gene.ERCC.gtf \
--container /restricted/projectnb/casa/frank/xqtl_project/xqtl-pipeline/container/singularity/bioinfo.sif \
--walltime 100h \
--numThreads 20 \
--mem 40G -J 50 -c csg.yml -q neurology
Log:
INFO: Running [32mmap_leafcutter_cluster_to_gene[0m:
[91mERROR[0m: [91mmap_leafcutter_cluster_to_gene (id=5a76d510fef6330f) returns an error.[0m
[91mERROR[0m: [91m[map_leafcutter_cluster_to_gene]: [0]: Executing script in Singularity returns an error (exitcode=2, stderr=/restricted/projectnb/casa/frank/xqtl_project/ROSMAP_PCC/reference_data/Homo_sapiens.GRCh38.103.chr.reformatted.collapse_only.gene.ERCC.gtf.stderr).
The script has been saved to /usr3/graduate/fgrennjr/.sos/4966833ed02ca234//usr3/graduate/fgrennjr/.sos/4966833ed02ca234.To reproduce the error please run:
[0m[32msingularity exec /restricted/projectnb/casa/frank/xqtl_project/xqtl-pipeline/container/singularity/bioinfo.sif python /usr3/graduate/fgrennjr/.sos/4966833ed02ca234/singularity_run_83472.py[0m[91m[0m
/opt/conda/bin/python: can't open file '/restricted/projectnb/casa/frank/xqtl_project/ROSMAP_PCC/scripts/tmpdbgt_wz5/singularity_run_83472.py': [Errno 2] No such file or directory
This is not a error by itself per se. SOS will move the py script in the tmp folder to the new destination: /usr3/graduate/fgrennjr/.sos/4966833ed02ca234/singularity_run_83472.py
so?how to solve it
When I try to run the map_leafcutter_cluster_to_gene part for post-processing, it gives me this error..
Script used:
Log file: