Error in rownames - AberrantExpression module

[Roshanshafiha]

Hi , I am getting the below error while running aberrant expression module and the command I use to run the module is :

snakemake aberrantExpression --cores 40 -k --rerun-trigger mtime

error message :

[Wed Apr 9 11:32:31 2025]
rule AberrantExpression_pipeline_Counting_filterCounts_R:
input: /gpfs/projects/tmedicine/Shafiha/pipelines/DROP/DROP_pipeline_GRCH37_50million/Output/processed_data/aberrant_expression/v47/outrider/control/total_counts.Rds, /gpfs/projects/tmedicine/Shafiha/pipelines/DROP/DROP_pipeline_GRCH37_50million/Output/processed_data/preprocess/v47/txdb.db, Scripts/AberrantExpression/pipeline/Counting/filterCounts.R
output: /gpfs/projects/tmedicine/Shafiha/pipelines/DROP/DROP_pipeline_GRCH37_50million/Output/processed_results/aberrant_expression/v47/outrider/control/ods_unfitted.Rds
log: /gpfs/projects/tmedicine/Shafiha/pipelines/DROP/DROP_pipeline_GRCH37_50million/.drop/tmp/AE/v47/control/filter.Rds
jobid: 3
reason: Missing output files: /gpfs/projects/tmedicine/Shafiha/pipelines/DROP/DROP_pipeline_GRCH37_50million/Output/processed_results/aberrant_expression/v47/outrider/control/ods_unfitted.Rds
wildcards: annotation=v47, dataset=control
resources: tmpdir=/tmp

Error in rownames<-(*tmp*, value = value[[2]]) :
missing values not allowed in rownames
Calls: OutriderDataSet ... dimnames<- -> dimnames<- -> rownames<- -> rownames<-
Execution halted
[Wed Apr 9 11:32:43 2025]
Error in rule AberrantExpression_pipeline_Counting_filterCounts_R:
jobid: 80
input: /gpfs/projects/tmedicine/Shafiha/pipelines/DROP/DROP_pipeline_GRCH37_50million/Output/processed_data/aberrant_expression/v47/outrider/case/total_counts.Rds, /gpfs/projects/tmedicine/Shafiha/pipelines/DROP/DROP_pipeline_GRCH37_50million/Output/processed_data/preprocess/v47/txdb.db, Scripts/AberrantExpression/pipeline/Counting/filterCounts.R
output: /gpfs/projects/tmedicine/Shafiha/pipelines/DROP/DROP_pipeline_GRCH37_50million/Output/processed_results/aberrant_expression/v47/outrider/case/ods_unfitted.Rds
log: /gpfs/projects/tmedicine/Shafiha/pipelines/DROP/DROP_pipeline_GRCH37_50million/.drop/tmp/AE/v47/case/filter.Rds (check log file(s) for error details)

RuleException:
CalledProcessError in file /tmp/tmpy6272umh, line 48:
Command 'set -euo pipefail; Rscript --vanilla /gpfs/projects/tmedicine/Shafiha/pipelines/DROP/DROP_pipeline_GRCH37_50million/.snakemake/scripts/tmph3csk9eu.filterCounts.R' returned non-zero exit status 1.
File "/tmp/tmpy6272umh", line 48, in __rule_AberrantExpression_pipeline_Counting_filterCounts_R
File "/gpfs/software/genomics/DROP/v1.4.0/lib/python3.12/concurrent/futures/thread.py", line 59, in run
Error in rownames<-(*tmp*, value = value[[2]]) :
missing values not allowed in rownames
Calls: OutriderDataSet ... dimnames<- -> dimnames<- -> rownames<- -> rownames<-
Execution halted
[Wed Apr 9 11:32:43 2025]
Error in rule AberrantExpression_pipeline_Counting_filterCounts_R:
jobid: 3
input: /gpfs/projects/tmedicine/Shafiha/pipelines/DROP/DROP_pipeline_GRCH37_50million/Output/processed_data/aberrant_expression/v47/outrider/control/total_counts.Rds, /gpfs/projects/tmedicine/Shafiha/pipelines/DROP/DROP_pipeline_GRCH37_50million/Output/processed_data/preprocess/v47/txdb.db, Scripts/AberrantExpression/pipeline/Counting/filterCounts.R
output: /gpfs/projects/tmedicine/Shafiha/pipelines/DROP/DROP_pipeline_GRCH37_50million/Output/processed_results/aberrant_expression/v47/outrider/control/ods_unfitted.Rds
log: /gpfs/projects/tmedicine/Shafiha/pipelines/DROP/DROP_pipeline_GRCH37_50million/.drop/tmp/AE/v47/control/filter.Rds (check log file(s) for error details)

RuleException:
CalledProcessError in file /tmp/tmpy6272umh, line 48:
Command 'set -euo pipefail; Rscript --vanilla /gpfs/projects/tmedicine/Shafiha/pipelines/DROP/DROP_pipeline_GRCH37_50million/.snakemake/scripts/tmp_owmlz5x.filterCounts.R' returned non-zero exit status 1.
File "/tmp/tmpy6272umh", line 48, in __rule_AberrantExpression_pipeline_Counting_filterCounts_R
File "/gpfs/software/genomics/DROP/v1.4.0/lib/python3.12/concurrent/futures/thread.py", line 59, in run
Exiting because a job execution failed. Look above for error message
Complete log: .snakemake/log/2025-04-09T113228.727115.snakemake.log

[vyepez88]

Hi, the following error

RuleException:
CalledProcessError in file /tmp/tmpy6272umh, line 48:
Command 'set -euo pipefail; Rscript --vanilla

usually means it ran out of memory.

In addition, check the fpkm parameter among the aberrantExpression ones. The default and recommended is 1.

Finally, check whether your provided gtf file has no empty gene names. You can check the file under {root}/processed_data/preprocess/{gene_annotation}/gene_name_mapping_{gene_annotation}.tsv for this

[Roshanshafiha]

Hi @vyepez88 I increased the memory and the error still persist. The other checks are good too but the error message still persist.

whats this line trying to check exactly do you have any idea which part of the script and I could look into it. Thanks

Error in rownames<-(*tmp*, value = value[[2]]) :

check for missing R packages
AberrantSplicing has been turned off in the config file
MonoallelicExpression has been turned off in the config file
rnaVariantCalling has been turned off in the config file
Structuring dependencies...
Dependencies file generated at: /tmp/tmpkh_ggv6n

Building DAG of jobs...
Using shell: /usr/bin/bash
Provided cores: 30
Rules claiming more threads will be scaled down.
Job stats:
job count

---

AberrantExpression_pipeline_Counting_Datasets_R 1
AberrantExpression_pipeline_Counting_Summary_R 1
AberrantExpression_pipeline_Counting_filterCounts_R 1
AberrantExpression_pipeline_OUTRIDER_Datasets_R 1
AberrantExpression_pipeline_OUTRIDER_Summary_R 1
AberrantExpression_pipeline_OUTRIDER_pvalsOutrider_R 1
AberrantExpression_pipeline_OUTRIDER_results_R 1
AberrantExpression_pipeline_OUTRIDER_runOutrider_R 1
aberrantExpression 1
total 9

Select jobs to execute...

[Mon May 12 14:26:46 2025]
rule AberrantExpression_pipeline_Counting_filterCounts_R:
input: /gpfs/projects/tmedicine/Shafiha/pipelines/DROP/pipelines/DROP_pipeline_GRCH37_50million/Output/processed_data/aberrant_expression/v47/outrider/control/total_counts.Rds, /gpfs/projects/tmedicine/Shafiha/pipelines/DROP/pipelines/DROP_pipeline_GRCH37_50million/Output/processed_data/preprocess/v47/txdb.db, Scripts/AberrantExpression/pipeline/Counting/filterCounts.R
output: /gpfs/projects/tmedicine/Shafiha/pipelines/DROP/pipelines/DROP_pipeline_GRCH37_50million/Output/processed_results/aberrant_expression/v47/outrider/control/ods_unfitted.Rds
log: /gpfs/projects/tmedicine/Shafiha/pipelines/DROP/pipelines/DROP_pipeline_GRCH37_50million/.drop/tmp/AE/v47/control/filter.Rds
jobid: 3
reason: Missing output files: /gpfs/projects/tmedicine/Shafiha/pipelines/DROP/pipelines/DROP_pipeline_GRCH37_50million/Output/processed_results/aberrant_expression/v47/outrider/control/ods_unfitted.Rds
wildcards: annotation=v47, dataset=control
resources: tmpdir=/tmp

Error in rownames<-(*tmp*, value = value[[2]]) :
missing values not allowed in rownames
Calls: OutriderDataSet ... dimnames<- -> dimnames<- -> rownames<- -> rownames<-
Execution halted
[Mon May 12 14:27:15 2025]
Error in rule AberrantExpression_pipeline_Counting_filterCounts_R:
jobid: 3
input: /gpfs/projects/tmedicine/Shafiha/pipelines/DROP/pipelines/DROP_pipeline_GRCH37_50million/Output/processed_data/aberrant_expression/v47/outrider/control/total_counts.Rds, /gpfs/projects/tmedicine/Shafiha/pipelines/DROP/pipelines/DROP_pipeline_GRCH37_50million/Output/processed_data/preprocess/v47/txdb.db, Scripts/AberrantExpression/pipeline/Counting/filterCounts.R
output: /gpfs/projects/tmedicine/Shafiha/pipelines/DROP/pipelines/DROP_pipeline_GRCH37_50million/Output/processed_results/aberrant_expression/v47/outrider/control/ods_unfitted.Rds
log: /gpfs/projects/tmedicine/Shafiha/pipelines/DROP/pipelines/DROP_pipeline_GRCH37_50million/.drop/tmp/AE/v47/control/filter.Rds (check log file(s) for error details)

RuleException:
CalledProcessError in file /tmp/tmpkh_ggv6n, line 48:
Command 'set -euo pipefail; Rscript --vanilla /gpfs/projects/tmedicine/Shafiha/pipelines/DROP/pipelines/DROP_pipeline_GRCH37_50million/.snakemake/scripts/tmp5pod3l4n.filterCounts.R' returned non-zero exit status 1.
File "/tmp/tmpkh_ggv6n", line 48, in __rule_AberrantExpression_pipeline_Counting_filterCounts_R
File "/gpfs/software/genomics/DROP/v1.4.0/lib/python3.12/concurrent/futures/thread.py", line 59, in run
Exiting because a job execution failed. Look above for error message
Complete log: .snakemake/log/2025-05-12T142611.921099.snakemake.log

[Roshanshafiha]

Hi @vyepez88 may I know if there is any update on the above issue , thank you.

[AtaJadidAhari]

Hi, can you check to see if you have missing or duplicated sampleIDs?

[vyepez88]

I still think it's a memory issue. Can you try running 10 samples only?

[Roshanshafiha]

@vyepez88 I have 46 samples , should I remove 36 of them from the annotation file and try running ?

@AtaJadidAhari the sample ID count is the same in the below file and the sample annotation file /gpfs/projects/tmedicine/Shafiha/pipelines/DROP/pipelines/DROP_pipeline_GRCH37_50million/Output/processed_data/aberrant_expression/v47/outrider/control/total_counts.Rds

[vyepez88]

@Roshanshafiha you can create a new DROP_GROUP with those 10 samples. Otherwise, yes, create a new sample annotation with only 10 samples.

[Roshanshafiha]

@vyepez88 I would also like to add that in the annotation file I have added the INDIVIDUAL_ID column and when I run without this, I don't get this error

[vyepez88]

that's extremely weird, the INDIVIDUAL_ID column is never used in DROP. Maybe there's a problem in that column (e.g. a special character or a tab)

[vyepez88]

Hi @Roshanshafiha, was this issue sorted out?