Error in 07_extract_results_FraseR step

[genetikzentrum]

Hi and thanks a lot for providing DROP and continuing to improve it.

We're having trouble with the final step of the AberrantSplicing pipeline - I'm not familiar with the data, but it supposedly used to work with some older commit in the dev branch. Unfortunately now both the latest dev and main commits fail with the below error. Would you happen to have an idea of what might be causing this? (directories etc redacted)

[1] "Results per junction extracted"
Tue May 10 15:25:50 2022: Writing final FRASER object ('/[...]/processed_results/aberrant_splicing/datasets//savedObjects/fraser--v34/fds-object.RDS').
-------------------- Sample data table -----------------
# A tibble: 13 × 5
   sampleID STRAND  PAIRED_END bamFile                                 pairedEnd
   <chr>    <chr>   <lgl>      <chr>                                   <lgl>    
 1  [...]

Number of samples:      13 
Number of junctions:    431185 
Number of splice sites: 229091 
assays(26): rawCountsJ psi5 ... pvaluesBetaBinomial_theta
  padjBetaBinomial_theta

----------------------- Settings -----------------------
Analysis name:               fraser--v34 
Analysis is strand specific: no 
Working directory:           '/[...]/processed_results/aberrant_splicing/datasets/' 

-------------------- BAM parameters --------------------
Default used with: bamMapqFilter=0

Error in `[.data.table`(f3, , `:=`(HPO_match, any(grepl(HPO_id, HPO_TERMS))),  : 
  The items in the 'by' or 'keyby' list are length(s) (2). Each must be length 0; the same length as there are rows in x (after subsetting if i is provided).
Calls: add_HPO_cols -> [ -> [.data.table
Execution halted
[Tue May 10 15:25:57 2022]
Error in rule AberrantSplicing_pipeline_FRASER_07_extract_results_FraseR_R:
    jobid: 39
    output: /[..]/processed_results/aberrant_splicing/results/v34/fraser/fraser/results_per_junction.tsv, /[..]/processed_results/aberrant_splicing/results/v34/fraser/fraser/results.tsv, /[..]/processed_results/aberrant_splicing/datasets/savedObjects/fraser--v34/fds-object.RDS
    log: /[..]/.drop/tmp/AS/fraser--v34/07_results.Rds (check log file(s) for error message)

RuleException:
CalledProcessError in line 148 of /tmp/tmpobvbdtg7:
Command 'set -euo pipefail;  Rscript --vanilla /[..]/.snakemake/scripts/tmpgh1ork2y.07_extract_results_FraseR.R' returned non-zero exit status 1.
  File "/tmp/tmpobvbdtg7", line 148, in __rule_AberrantSplicing_pipeline_FRASER_07_extract_results_FraseR_R
  File "/home/zkg/anaconda3/envs/drop_main/lib/python3.10/concurrent/futures/thread.py", line 58, in run
Removing output files of failed job AberrantSplicing_pipeline_FRASER_07_extract_results_FraseR_R since they might be corrupted:
/[..]/processed_results/aberrant_splicing/datasets/savedObjects/fraser--v34/fds-object.RDS
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message

Please let me know if I can provide any more information. We're thankful for any hint.

[vyepez88]

Hi, I see 2 potential problems:

1. Due to the small sample size, there might not be any significant results with the default cut-offs. Which deltaPsi and padj cutoff values are you using? Consider setting the padjCutoff to 1.
2. are you providing HPO terms in your sample annotation?

[vyepez88]

Hi @genetikzentrum, were you able to check this?

[vyepez88]

Hi @genetikzentrum, were you able to check this?