ERROR ~ Error executing process > 'pipeline:preprocess_reads (8)'

[CWYuan08]

Operating System

Ubuntu 22.04

Other Linux

No response

Workflow Version

v.1.2.0

Workflow Execution

Command line (Cluster)

Other workflow execution

No response

EPI2ME Version

No response

CLI command run

extflow run epi2me-labs/wf-transcriptomes --fastq ~/scratch/PromethION/rearranged_cDNA \ --de_analysis --ref_genome ~/reference_genomes/ensembl/ref.dna.toplevel.fasta \ --transcriptome-source reference-guided \ --ref_annotation ~/reference_genomes/indexed_transcriptome_ensembl/ref.111.gtf \ --cdna_kit SQK-PCB111.24 \ --sample_sheet sample_cdna_sheet.csv \ --condition_sheet sample_cdna_sheet.csv -with-dag \ --singularity /mnt/lab.config -profile singularity \ --out_dir epi2me_cDNA

Workflow Execution - CLI Execution Profile

None

What happened?

ERROR ~ Error executing process > 'pipeline:preprocess_reads (8)' Caused by: Not a valid path value type: org.codehaus.groovy.runtime.NullObject (null)

Relevant log output

executor >  local (25)
[b9/0ac949] process > validate_sample_sheet          [100%] 1 of 1 ✔
[e3/969d36] process > fastcat (1)                    [100%] 7 of 7 ✔
[4b/1f62a6] process > pipeline:preprocess_ref_ann... [100%] 1 of 1 ✔
[99/a64e61] process > pipeline:collectFastqIngres... [ 75%] 6 of 8
[b1/829435] process > pipeline:getVersions           [100%] 1 of 1 ✔
[e1/8e7e39] process > pipeline:getParams             [100%] 1 of 1 ✔
[5a/da5fe1] process > pipeline:preprocess_reads (1)  [  0%] 0 of 6
[af/bb475e] process > pipeline:build_minimap_inde... [100%] 1 of 1 ✔
[-        ] process > pipeline:reference_assembly... -
[-        ] process > pipeline:split_bam             -
[-        ] process > pipeline:assemble_transcripts  -
[-        ] process > pipeline:merge_gff_bundles     -
[-        ] process > pipeline:run_gffcompare        -
[-        ] process > pipeline:get_transcriptome     -
[-        ] process > pipeline:merge_transcriptomes  -
[-        ] process > pipeline:differential_expre... -
[-        ] process > pipeline:differential_expre... -
[-        ] process > pipeline:differential_expre... -
[-        ] process > pipeline:differential_expre... -
[-        ] process > pipeline:differential_expre... -
[-        ] process > pipeline:differential_expre... -
[-        ] process > pipeline:differential_expre... -
[-        ] process > pipeline:makeReport            -
[07/001a23] process > output (6)                     [100%] 6 of 6
ERROR ~ Error executing process > 'pipeline:preprocess_reads (8)'

Caused by:
  Not a valid path value type: org.codehaus.groovy.runtime.NullObject (null)

Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`

 -- Check '.nextflow.log' file for details

Application activity log entry

No response

Were you able to successfully run the latest version of the workflow with the demo data?

yes

Other demo data information

No response

[nrhorner]

Hi @CWYuan08

The kit SQK-PCB111.24 is not an available option for pychopper.

For now, you can use the option --cdna_kit SQK-PCS111 with PCB111.

However, the workflow should not have accepted your choice of kit. Can you confirm you are using the latest version by doing the following?

nextflow pull epi2me-labs/wf-transcriptomes 

the adding -r v1.2.0 to your command.

[CWYuan08]

Hi @nrhorner @cjw85 @SamStudio8 @amblina, many thanks for prompt reply. I have updated the version and error in the log still says: Jun-07 14:42:02.359 [Actor Thread 25] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condit ion for task: name=pipeline:preprocess_reads (1); work-dir=null error [nextflow.exception.ProcessUnrecoverableException]: Not a valid path value type: org.codehaus.gro ovy.runtime.NullObject (null) Jun-07 14:42:02.377 [Actor Thread 9] DEBUG nextflow.Session - Session aborted -- Cause: Cannot invoke met hod resolve() on null object Not sure what this means.

Best, CW

[nrhorner]

Hi @CWYuan08 Could you please post your .nextflow.log which can be found in the directory where you ran the workflow?