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gagneurlab / drop

Pipeline to find aberrant events in RNA-Seq data, useful for diagnosis of rare disorders
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Error in h(simpleError(msg, call)) #536

Closed pkrithivasan closed 3 months ago

pkrithivasan commented 5 months ago

Hi,

I am running DROP on a small dataset of 10 samples for a test run, and am running into the following error with the AberrantSplicing module:

Error in h(simpleError(msg, call)) : 
  error in evaluating the argument 'object' in selecting a method for function 'strandSpecific': argument "fds" is missing, with no default
Calls: <Anonymous> -> strandSpecific -> .handleSimpleError -> h
Execution halted
[Tue Apr 23 12:00:40 2024]
Error in rule AberrantSplicing_pipeline_Counting_01_2_countRNA_splitReads_merge_R:
    jobid: 43
    input: Output/processed_data/aberrant_splicing/datasets/cache/raw-local-fraser/sample_tmp/splitCounts/sample_CGND-HRA-03138.done, Output/processed_data/aberrant_splicing/datasets/cache/raw-local-fraser/sample_tmp/splitCounts/sample_CGND-HRA-03128.done, Output/processed_data/aberrant_splicing/datasets/cache/raw-local-fraser/sample_tmp/splitCounts/sample_CGND-HRA-03116.done, Output/processed_data/aberrant_splicing/datasets/cache/raw-local-fraser/sample_tmp/splitCounts/sample_CGND-HRA-03133.done, Output/processed_data/aberrant_splicing/datasets/cache/raw-local-fraser/sample_tmp/splitCounts/sample_CGND-HRA-03125.done, Output/processed_data/aberrant_splicing/datasets/cache/raw-local-fraser/sample_tmp/splitCounts/sample_CGND-HRA-03112.done, Output/processed_data/aberrant_splicing/datasets/cache/raw-local-fraser/sample_tmp/splitCounts/sample_CGND-HRA-03140.done, Output/processed_data/aberrant_splicing/datasets/cache/raw-local-fraser/sample_tmp/splitCounts/sample_CGND-HRA-03122.done, Output/processed_data/aberrant_splicing/datasets/cache/raw-local-fraser/sample_tmp/splitCounts/sample_CGND-HRA-03135.done, Output/processed_data/aberrant_splicing/datasets/cache/raw-local-fraser/sample_tmp/splitCounts/sample_CGND-HRA-03113.done, Scripts/AberrantSplicing/pipeline/Counting/01_2_countRNA_splitReads_merge.R
    output: Output/processed_data/aberrant_splicing/datasets/savedObjects/raw-local-fraser/rawCountsJ.h5, Output/processed_data/aberrant_splicing/datasets/cache/raw-local-fraser/gRanges_splitCounts.rds, Output/processed_data/aberrant_splicing/datasets/cache/raw-local-fraser/gRanges_NonSplitCounts.rds, Output/processed_data/aberrant_splicing/datasets/cache/raw-local-fraser/spliceSites_splitCounts.rds
    log: /mnt/disks/cromwell_root/.drop/tmp/AS/fraser/01_2_splitReadsMerge.Rds (check log file(s) for error details)

RuleException:
CalledProcessError in file /mnt/disks/cromwell_root/tmp.daf205c3/tmpa62o7k5h, line 139:
Command 'set -euo pipefail;  Rscript --vanilla /mnt/disks/cromwell_root/.snakemake/scripts/tmp3l0elph1.01_2_countRNA_splitReads_merge.R' returned non-zero exit status 1.
  File "/mnt/disks/cromwell_root/tmp.daf205c3/tmpa62o7k5h", line 139, in __rule_AberrantSplicing_pipeline_Counting_01_2_countRNA_splitReads_merge_R
  File "/root/miniconda3/envs/drop_env_133/lib/python3.8/concurrent/futures/thread.py", line 57, in run
Removing output files of failed job AberrantSplicing_pipeline_Counting_01_2_countRNA_splitReads_merge_R since they might be corrupted:
Output/processed_data/aberrant_splicing/datasets/savedObjects/raw-local-fraser/rawCountsJ.h5, Output/processed_data/aberrant_splicing/datasets/cache/raw-local-fraser/gRanges_splitCounts.rds, Output/processed_data/aberrant_splicing/datasets/cache/raw-local-fraser/gRanges_NonSplitCounts.rds

The AberrantExpression and MAE modules completed successfully. I have attached my config file. Could you please help me troubleshoot? Thanks!

config.yaml.txt

vyepez88 commented 5 months ago

Hi, yes, we are aware of this error. We are fixing it. The new release will probably be out next week. It may be related to this error: https://github.com/gagneurlab/drop/issues/532

pkrithivasan commented 4 months ago

Hi @vyepez88, please let me know when DROP 1.3.4 will be available. Thanks!

AtaJadidAhari commented 4 months ago

Hi @pkrithivasan DROP 1.3.4 is available on GitHub now and you can install it using pip: pip install git+https://github.com/gagneurlab/drop.git

pkrithivasan commented 4 months ago

Thanks @AtaJadidAhari! When will the yaml file be available on the public server?

AtaJadidAhari commented 4 months ago

Unfortunately DROP v1.3.4 is not yet updated in conda due to some problems over at bioconda (issues 41025). Once this issue is resolved, we will provide the yaml file on the public server.

pkrithivasan commented 4 months ago

Thanks @AtaJadidAhari! Looks like the issue was resolved a few hours ago, will keep an eye out for the yaml file.

vyepez88 commented 3 months ago

Hi @pkrithivasan, the yaml file for 1.4.0 is now available. Please try it out and let us know

pkrithivasan commented 3 months ago

Thank you, I don't get this error any more with v1.3.4. I will try with v1.4.0 today.