Error running aberrantSplicing

[pkrithivasan]

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]

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]

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!