Error in h(simpleError(msg, call))

[pkrithivasan]

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]

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: #532

[pkrithivasan]

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

[AtaJadidAhari]

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]

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

[AtaJadidAhari]

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]

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

[vyepez88]

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

[pkrithivasan]

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