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CCBR / CHARLIE

Circrnas in Host And viRuses anaLysis pIpEline for Detection Annotation Quantification of circRNAs
https://ccbr.github.io/CHARLIE/
MIT License
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python path issue in create_circExplorer_merged_found_counts_table #124

Closed kelly-sovacool closed 1 month ago

kelly-sovacool commented 1 month ago

logs/38794508.38819700.create_circExplorer_merged_found_counts_table.sample=GI1_T.err

Building DAG of jobs...
Using shell: /usr/bin/bash
Provided cores: 2
Rules claiming more threads will be scaled down.
Provided resources: mem_mb=1000, mem_mib=954, disk_mb=1000, disk_mib=954
Select jobs to execute...

[Mon Oct 21 16:10:50 2024]
rule create_circExplorer_merged_found_counts_table:
    input: /data/CCBR/charlie_test_wil/charlie/results/GI1_T/circExplorer/GI1_T.circExplorer.annotation_counts.tsv, /data/CCBR/charlie_test_wil/charlie/results/GI1_T/circExplorer/GI1_T.BSJ.foundcounts.tsv, /data/CCBR/charlie_test_wil/charlie/results/GI1_T/circExplorer/GI1_T.linear_spliced.counts.tsv
    output: /data/CCBR/charlie_test_wil/charlie/results/GI1_T/circExplorer/GI1_T.readcounts.tsv, /data/CCBR/charlie_test_wil/charlie/results/GI1_T/circExplorer/GI1_T.circExplorer.counts_table.tsv
    jobid: 0
    reason: Forced execution
    wildcards: sample=GI1_T
    resources: mem_mb=1000, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=/tmp

set -exo pipefail
mkdir -p /lscratch/$SLURM_JOB_ID/f184b0de-63b4-48f5-ab4d-ec60cf3bd886
python3 /gpfs/gsfs10/users/CCBR_Pipeliner/Pipelines/CHARLIE/.v0.11.1/workflow/scripts/_merge_circExplorer_found_counts.py \
    -b /data/CCBR/charlie_test_wil/charlie/results/GI1_T/circExplorer/GI1_T.BSJ.foundcounts.tsv \
    -l /data/CCBR/charlie_test_wil/charlie/results/GI1_T/circExplorer/GI1_T.linear_spliced.counts.tsv \
    -o /data/CCBR/charlie_test_wil/charlie/results/GI1_T/circExplorer/GI1_T.readcounts.tsv

python3 /gpfs/gsfs10/users/CCBR_Pipeliner/Pipelines/CHARLIE/.v0.11.1/workflow/scripts/create_circExplorer_per_sample_counts_table.py \
    --annotationcounts /data/CCBR/charlie_test_wil/charlie/results/GI1_T/circExplorer/GI1_T.circExplorer.annotation_counts.tsv \
    --allfoundcounts /data/CCBR/charlie_test_wil/charlie/results/GI1_T/circExplorer/GI1_T.readcounts.tsv \
    --countstable /data/CCBR/charlie_test_wil/charlie/results/GI1_T/circExplorer/GI1_T.circExplorer.counts_table.tsv

+ mkdir -p /lscratch/38819700/f184b0de-63b4-48f5-ab4d-ec60cf3bd886
+ python3 /gpfs/gsfs10/users/CCBR_Pipeliner/Pipelines/CHARLIE/.v0.11.1/workflow/scripts/_merge_circExplorer_found_counts.py -b /data/CCBR/charlie_test_wil/charlie/results/GI1_T/circExplorer/GI1_T.BSJ.foundcounts.tsv -l /data/CCBR/charlie_test_wil/charlie/results/GI1_T/circExplorer/GI1_T.linear_spliced.counts.tsv -o /data/CCBR/charlie_test_wil/charlie/results/GI1_T/circExplorer/GI1_T.readcounts.tsv
Traceback (most recent call last):
  File "/gpfs/gsfs10/users/CCBR_Pipeliner/Pipelines/CHARLIE/.v0.11.1/workflow/scripts/_merge_circExplorer_found_counts.py", line 3, in <module>
    import pandas
  File "/data/CCBR_Pipeliner/Tools/ccbr_tools/v0.1/pandas/__init__.py", line 19, in <module>
    raise ImportError(
ImportError: Unable to import required dependencies:
numpy: Error importing numpy: you should not try to import numpy from
        its source directory; please exit the numpy source tree, and relaunch
        your python interpreter from there.
[Mon Oct 21 16:10:50 2024]
Error in rule create_circExplorer_merged_found_counts_table:
    jobid: 0
    input: /data/CCBR/charlie_test_wil/charlie/results/GI1_T/circExplorer/GI1_T.circExplorer.annotation_counts.tsv, /data/CCBR/charlie_test_wil/charlie/results/GI1_T/circExplorer/GI1_T.BSJ.foundcounts.tsv, /data/CCBR/charlie_test_wil/charlie/results/GI1_T/circExplorer/GI1_T.linear_spliced.counts.tsv
    output: /data/CCBR/charlie_test_wil/charlie/results/GI1_T/circExplorer/GI1_T.readcounts.tsv, /data/CCBR/charlie_test_wil/charlie/results/GI1_T/circExplorer/GI1_T.circExplorer.counts_table.tsv
    shell:

set -exo pipefail
mkdir -p /lscratch/$SLURM_JOB_ID/f184b0de-63b4-48f5-ab4d-ec60cf3bd886
python3 /gpfs/gsfs10/users/CCBR_Pipeliner/Pipelines/CHARLIE/.v0.11.1/workflow/scripts/_merge_circExplorer_found_counts.py \
    -b /data/CCBR/charlie_test_wil/charlie/results/GI1_T/circExplorer/GI1_T.BSJ.foundcounts.tsv \
    -l /data/CCBR/charlie_test_wil/charlie/results/GI1_T/circExplorer/GI1_T.linear_spliced.counts.tsv \
    -o /data/CCBR/charlie_test_wil/charlie/results/GI1_T/circExplorer/GI1_T.readcounts.tsv

python3 /gpfs/gsfs10/users/CCBR_Pipeliner/Pipelines/CHARLIE/.v0.11.1/workflow/scripts/create_circExplorer_per_sample_counts_table.py \
    --annotationcounts /data/CCBR/charlie_test_wil/charlie/results/GI1_T/circExplorer/GI1_T.circExplorer.annotation_counts.tsv \
    --allfoundcounts /data/CCBR/charlie_test_wil/charlie/results/GI1_T/circExplorer/GI1_T.readcounts.tsv \
    --countstable /data/CCBR/charlie_test_wil/charlie/results/GI1_T/circExplorer/GI1_T.circExplorer.counts_table.tsv

        (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message