Error in AberrantSplicing_pipeline_FRASER_04_fit_hyperparameters_FraseR_R

[pkrithivasan]

Hi, Could you please help me troubleshoot the following error when running the aberrant splicing module?

[Fri Mar 22 18:38:56 2024]
rule AberrantSplicing_pipeline_FRASER_04_fit_hyperparameters_FraseR_R:
    input: /gpfs/commons/groups/clinical/pkrithivasan/CBI-342/GEN_n16_GTEx_n50_AS/Output/processed_data/aberrant_splicing/datasets/savedObjects/fraser/filter_FRASER2.done, Scripts
/AberrantSplicing/pipeline/FRASER/04_fit_hyperparameters_FraseR.R
    output: /gpfs/commons/groups/clinical/pkrithivasan/CBI-342/GEN_n16_GTEx_n50_AS/Output/processed_data/aberrant_splicing/datasets/savedObjects/fraser/hyper_FRASER2.done
    log: /gpfs/commons/groups/clinical/pkrithivasan/CBI-342/GEN_n16_GTEx_n50_AS/.drop/tmp/AS/fraser/04_hyper.Rds
    jobid: 0
    reason: Forced execution
    wildcards: dataset=fraser
    threads: 12
    resources: mem_mb=100000, mem_mib=95368, disk_mb=100000, disk_mib=95368, tmpdir=/gpfs/commons/groups/clinical/pkrithivasan/CBI-342/GEN_n16_GTEx_n50_AS/tmp

Rscript --vanilla /gpfs/commons/groups/clinical/pkrithivasan/CBI-342/GEN_n16_GTEx_n50_AS/.snakemake/scripts/tmpb865ksln.04_fit_hyperparameters_FraseR.R
Load packages
Loading assay: rawCountsJ
Loading assay: psi5
Loading assay: psi3
Loading assay: rawOtherCounts_psi5
Loading assay: rawOtherCounts_psi3
Loading assay: rawCountsJnonsplit
Loading assay: jaccard
Loading assay: rawOtherCounts_jaccard
Loading assay: delta_jaccard
Loading assay: delta_psi5
Loading assay: delta_psi3
Loading assay: rawCountsSS
Loading assay: theta
Loading assay: rawOtherCounts_theta
Loading assay: delta_theta
Fri Mar 22 18:39:25 2024: jaccard
dPsi filter:FALSE: 49215
Error in colVars(x, rows = rows, cols = cols, na.rm = na.rm, refine = refine,  : 
  Argument 'dim.' must be an integer vector of length two.
Calls: optimHyperParams ... colSds -> colSds -> .local -> <Anonymous> -> colVars
Execution halted

Config file parameters:

aberrantSplicing:
  run: true
  groups:
  - fraser
  recount: false
  longRead: false
  keepNonStandardChrs: false
  filter: true
  minExpressionInOneSample: 20
  quantileMinExpression: 10
  minDeltaPsi: 0.05
  implementation: PCA
  padjCutoff: 0.1
  maxTestedDimensionProportion: 6
  genesToTest: null
  FRASER_version: FRASER2
  deltaPsiCutoff : 0.1
  quantileForFiltering: 0.75

Thanks!

[vyepez88]

Hi, hard to say. Can you try loading the FRASER dataset located inside /gpfs/commons/groups/clinical/pkrithivasan/CBI-342/GEN_n16_GTEx_n50_AS/Output/processed_data/aberrant_splicing/datasets/savedObjects/fraser/ in R and checking its dimension? Another idea would be to try rerunning with minDeltaPsi: 0

[ischeller]

Hi, as @vyepez88 said, it's hard to know for us what is going on without more information. Could you provide what version of DROP you are using as well as the output of

library(FRASER)
sessionInfo()

?

Best, Ines

[pkrithivasan]

Hi @vyepez88 , this might have been an issue related to insufficient memory. I was not able to reproduce this error when I ran the tool on a machine with increased memory. Thanks!