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gagneurlab / drop

Pipeline to find aberrant events in RNA-Seq data, useful for diagnosis of rare disorders
MIT License
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Error running aberrantSplicing #525

Closed pkrithivasan closed 2 months ago

pkrithivasan commented 3 months ago

Hi, I get the following error while trying to run the aberrantSplicing module and would like to get some help with troubleshooting:

Error in rule AberrantSplicing_pipeline_Counting_01_1_countRNA_splitReads_samplewise_R:
    jobid: 17
    input: /gpfs/commons/groups/clinical/pkrithivasan/dropTest/Output/processed_data/aberrant_splicing/datasets/cache/raw-local-fraser/fds.done, Scripts/AberrantSplicing/pipeline/Counting/01_1_countRNA_splitReads_samplewise.R
    output: /gpfs/commons/groups/clinical/pkrithivasan/dropTest/Output/processed_data/aberrant_splicing/datasets/cache/raw-local-fraser/sample_tmp/splitCounts/sample_GEN23-140P-2-R1.done
    log: /gpfs/commons/groups/clinical/pkrithivasan/dropTest/.drop/tmp/AS/fraser/splitReads/GEN23-140P-2-R1.Rds (check log file(s) for error details)
    cluster_jobid: 40598824

Error executing rule AberrantSplicing_pipeline_Counting_01_1_countRNA_splitReads_samplewise_R on cluster (jobid: 17, external: 40598824, jobscript: /gpfs/commons/groups/clinical/pkrithivasan/dropTest/.snakemake/tmp.y5l_h7q5/snakejob.AberrantSplicing_pipeline_Counting_01_1_countRNA_splitReads_samplewise_R.17.sh). For error details see the cluster log and the log files of the involved rule(s).

Here are further details in the job.err file:

rule AberrantSplicing_pipeline_Counting_01_1_countRNA_splitReads_samplewise_R:
    input: /gpfs/commons/groups/clinical/pkrithivasan/dropTest/Output/processed_data/aberrant_splicing/datasets/cache/raw-local-fraser/fds.done, Scripts/AberrantSplicing
/pipeline/Counting/01_1_countRNA_splitReads_samplewise.R
    output: /gpfs/commons/groups/clinical/pkrithivasan/dropTest/Output/processed_data/aberrant_splicing/datasets/cache/raw-local-fraser/sample_tmp/splitCounts/sample_GEN
23-140P-2-R1.done
    log: /gpfs/commons/groups/clinical/pkrithivasan/dropTest/.drop/tmp/AS/fraser/splitReads/GEN23-140P-2-R1.Rds
    jobid: 0
    reason: Forced execution
    wildcards: dataset=fraser, sample_id=GEN23-140P-2-R1
    threads: 3
    resources: mem_mb=64000, mem_mib=61036, disk_mb=64000, disk_mib=61036, tmpdir=/gpfs/commons/groups/clinical/pkrithivasan/dropTest/tmp

Rscript --vanilla /gpfs/commons/groups/clinical/pkrithivasan/dropTest/.snakemake/scripts/tmplw306you.01_1_countRNA_splitReads_samplewise.R
Load packages
Loading required package: rtracklayer
Tue Mar 12 13:27:46 2024: Count split reads for sample: GEN23-140P-2-R1
Error in h(simpleError(msg, call)) : 
  error in evaluating the argument 'file' in selecting a method for function 'idxstatsBam': error in evaluating the argument 'object' in selecting a method for function 'bamFile': <RangedSummarizedExperiment>[,j] index out of bounds: GEN23-140P-2-R1
Calls: countSplitReads ... .class1 -> [ -> [ -> .SummarizedExperiment.charbound
Execution halted
Not cleaning up /gpfs/commons/groups/clinical/pkrithivasan/dropTest/.snakemake/scripts/tmplw306you.01_1_countRNA_splitReads_samplewise.R
[Tue Mar 12 13:27:46 2024]
Error in rule AberrantSplicing_pipeline_Counting_01_1_countRNA_splitReads_samplewise_R:
    jobid: 0
    input: /gpfs/commons/groups/clinical/pkrithivasan/dropTest/Output/processed_data/aberrant_splicing/datasets/cache/raw-local-fraser/fds.done, Scripts/AberrantSplicing/pipeline/Counting/01_1_countRNA_splitReads_samplewise.R
    output: /gpfs/commons/groups/clinical/pkrithivasan/dropTest/Output/processed_data/aberrant_splicing/datasets/cache/raw-local-fraser/sample_tmp/splitCounts/sample_GEN23-140P-2-R1.done
    log: /gpfs/commons/groups/clinical/pkrithivasan/dropTest/.drop/tmp/AS/fraser/splitReads/GEN23-140P-2-R1.Rds (check log file(s) for error details)

RuleException:
CalledProcessError in file /tmp/tmpi6cwmc7q, line 130:
Command 'set -euo pipefail;  Rscript --vanilla /gpfs/commons/groups/clinical/pkrithivasan/dropTest/.snakemake/scripts/tmplw306you.01_1_countRNA_splitReads_samplewise.R' returned non-zero exit status 1.
  File "/tmp/tmpi6cwmc7q", line 130, in __rule_AberrantSplicing_pipeline_Counting_01_1_countRNA_splitReads_samplewise_R
  File "/nfs/home/pkrithivasan/.conda/envs/drop_env_133/lib/python3.8/concurrent/futures/thread.py", line 57, in run

This is the command I'm running with DROP v1.3.3: snakemake aberrantSplicing --profile slurm I successfully tested the installation with the demo project, and am not sure how to interpret the above error. Thanks!

vyepez88 commented 2 months ago

Hi, it seems that this is the main error: error in evaluating the argument 'file' in selecting a method for function 'idxstatsBam': error in evaluating the argument 'object' in selecting a method for function 'bamFile': <RangedSummarizedExperiment>[,j] index out of bounds: GEN23-140P-2-R1 Can you double-check that that BAM file exists, it's sorted by position and indexed? Also, maybe there's something else wrong with it? Did the counting work successfully for all the other samples?

pkrithivasan commented 2 months ago

Hi @vyepez88 , this might have been an issue related to insufficient memory. When I ran the tool on a machine with increased memory, I didn't run into this error again. Thanks!