Comments (2)
gevro
commented on June 27, 2024
The conda version of drop still has the same unlock issues...
Building DAG of jobs...
MissingInputException in line 62 of /gpfs/scratch/evrong01/droptest2/.drop/modules/mae-pipeline/Snakefile:
Missing input files for rule create_SNVs:
/gpfs/scratch/evrong01/droptest2/.drop/modules/mae-pipeline/.drop/modules/mae-pipeline/Scripts/MAE/filterSNVs.sh
/gpfs/scratch/evrong01/droptest2/.drop/modules/mae-pipeline/.drop/modules/mae-pipeline/resource/chr_UCSC_NCBI.txt
/gpfs/scratch/evrong01/droptest2/.drop/modules/mae-pipeline/.drop/modules/mae-pipeline/resource/chr_NCBI_UCSC.txt
[Tue Jul 28 19:29:12 2020]
Error in rule unlock:
jobid: 0
output: /gpfs/scratch/evrong01/droptest2/.drop/tmp/MAE/unlock
shell:
snakemake --unlock --configfile /gpfs/scratch/evrong01/droptest2/.drop/tmp/config.yaml
(exited with non-zero exit code)
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Complete log: /gpfs/scratch/evrong01/droptest2/.drop/modules/mae-pipeline/.snakemake/log/2020-07-28T192910.678386.snakemake.log
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vyepez88
commented on June 27, 2024
Yes, the current conda version consists of the previous github version with some minor modifications.
This bug was already fixed, but will appear in the next stable release in ~2 weeks.
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Related Issues (20)
- Running pipeline offline in trusted research environemnt HOT 1
- lymphoblastoid cell lines datasets of gene counts
- Error running aberrantSplicing HOT 2
- Error in AberrantSplicing_pipeline_FRASER_04_fit_hyperparameters_FraseR_R HOT 3
- Error in MAE QC create matrix dna rna cor HOT 3
- CalledProcessError in installRPackages.R HOT 5
- Default running folder is out of space HOT 2
- Chunk options `#+echo` not correctly parsed HOT 1
- Incompatible with `Snakemake>=8` HOT 2
- Writing `rds` files as log can crash Snakemake execution HOT 1
- Error in h(simpleError(msg, call)) HOT 8
- requirementsR.txt referencing HEAD leads to irreproducibility / pipeline breaking HOT 3
- Problem running DROP HOT 2
- Annotation file asks for columns that shouldn't be needed HOT 2
- Error in rule AberrantSplicing_pipeline_Counting_01_1_countRNA_splitReads_samplewise_R HOT 10
- Pipeline fails with no significant results (AberrantSplicing_pipeline_FRASER_08_extract_results_FraseR_R) HOT 1
- Error in rule AberrantSplicing_pipeline_Counting_01_1_countRNA_splitReads_samplewise_R HOT 2
- Pipeline FAILS when specifying subsets of genes to test HOT 1
- useNames = NA is defunct HOT 4
- conda setup using yaml doesn't work HOT 1
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