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bioinfo.sif is corrupted: wrong partition size

Open Shrishtee-kandoi opened this issue 1 year ago • 5 comments

When I try to run the map_leafcutter_cluster_to_gene part for post-processing, it gives me this error..

FATAL:   could not open image /restricted/projectnb/casa/xqtl-pipeline/container/singularity/bioinfo.sif: SIF image /restricted/projectnb/casa/xqtl-pipeline/container/singularity/bioinfo.sif is corrupted: wrong partition size
/opt/conda/bin/python: can't open file '/restricted/projectnb/casa/skandoi/ROSMAP_DLPFC/scripts/tmp5dqppsvu/singularity_run_94692.py': [Errno 2] No such file or directory

Script used:

sos run /restricted/projectnb/casa/xqtl-pipeline/code/data_preprocessing/phenotype/gene_annotation.ipynb map_leafcutter_cluster_to_gene \
    --cwd /restricted/projectnb/casa/skandoi/ROSMAP_DLPFC/leafcutter_output/batch_all \
    --intron_count  /restricted/projectnb/casa/skandoi/ROSMAP_DLPFC/leafcutter_output/batch_all/leafcutter_bam_intron_usage_perind.counts.gz \
    --phenoFile /restricted/projectnb/casa/skandoi/ROSMAP_DLPFC/leafcutter_output/batch_all/leafcutter_bam_intron_usage_perind.counts.gz_raw_data.qqnorm.txt \
    --annotation-gtf /restricted/projectnb/casa/skandoi/ROSMAP_DLPFC/reference_data/Homo_sapiens.GRCh38.103.chr.reformatted.ERCC.gtf \
    --container /restricted/projectnb/casa/xqtl-pipeline/container/singularity/bioinfo.sif \
    --walltime 100h \
    --numThreads 20 \
    --mem 40G -J 50 -c csg.yml -q neurology

Log file:

INFO: Running [32mmap_leafcutter_cluster_to_gene[0m: 
[91mERROR[0m: [91mmap_leafcutter_cluster_to_gene (id=a02cf84eef1e061b) 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/skandoi/ROSMAP_DLPFC/reference_data/Homo_sapiens.GRCh38.103.chr.reformatted.ERCC.gtf.stderr).
The script has been saved to /usr4/bf527/skandoi/.sos/f62e6760de9b87f7//usr4/bf527/skandoi/.sos/f62e6760de9b87f7.To reproduce the error please run:
[0m[32msingularity exec  /restricted/projectnb/casa/xqtl-pipeline/container/singularity/bioinfo.sif python /usr4/bf527/skandoi/.sos/f62e6760de9b87f7/singularity_run_94692.py[0m[91m[0m

Shrishtee-kandoi avatar Sep 15 '22 19:09 Shrishtee-kandoi