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Issues of creating BWA index with custom fasta and GTF #119

Closed
YoshikiHigashijima opened this issue Sep 21, 2023 · 0 comments · Fixed by #133
Closed

Issues of creating BWA index with custom fasta and GTF #119

YoshikiHigashijima opened this issue Sep 21, 2023 · 0 comments · Fixed by #133
Assignees
@edmundmiller
Labels
bug Something isn't working
Milestone
2.2.0

Comments

@YoshikiHigashijima
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Description of the bug

I used custom fasta and GTF files to use nfcore nascent and got the following error messages.

Error executing process > 'NFCORE_NASCENT:NASCENT:PREPARE_GENOME:BWA_INDEX (null)'
Caused by:
Not a valid path value type: groovyx.gpars.dataflow.DataflowVariable (DataflowVariable(value=null))

The point is that this custom reference genome is working in nfcore RNA-seq analysis but not in nfcore nascent.
Edmund Miller advised me to use --genome GRCh38 instead of the custom reference genome and --genome GRCh38 actually worked.

Based on these observations, we would think that this is a bug of BWA index creation when we put custom reference genome on parameters.

Command used and terminal output

/home/yhigashi/nextflow run nf-core/nascent -r 2.1.1 -work-dir /home/yhigashi/tnfil4_euseq -params-file /home/yhigashi/tnfil4_euseq/230920_nf-params_v2.json -profile singularity --save_reference



N E X T F L O W  ~  version 22.10.5
Launching `https://github.com/nf-core/nascent` [distraught_newton] DSL2 - revision: 9ff33c7896 [2.1.1]


------------------------------------------------------
                                        ,--./,-.
        ___     __   __   __   ___     /,-._.--~'
  |\ | |__  __ /  ` /  \ |__) |__         }  {
  | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                        `._,._,'
  nf-core/nascent v2.1.1-g9ff33c7
------------------------------------------------------
Core Nextflow options
  revision       : 2.1.1
  runName        : distraught_newton
  containerEngine: singularity
  launchDir      : /rshare1/ZETTAI_path_WA_slash_home_KARA/home/yhigashi
  workDir        : /home/yhigashi/tnfil4_euseq
  projectDir     : /home/yhigashi/.nextflow/assets/nf-core/nascent
  userName       : yhigashi
  profile        : singularity
  configFiles    : /home/yhigashi/.nextflow/assets/nf-core/nascent/nextflow.config

Input/output options
  input          : /home/yhigashi/tnfil4_euseq/230920_samplesheet.csv
  outdir         : /home/yhigashi/nextflow_results/tnfil4_nextflow_euseq_results
  email          : [email protected]

Transcript Identification Options
  assay_type     : GROseq

Reference genome options
  fasta          : /home/yhigashi/Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa.gz
  gtf            : /home/yhigashi/Homo_sapiens.GRCh38.110.gtf.gz
  save_reference : true

!! Only displaying parameters that differ from the pipeline defaults !!
------------------------------------------------------
If you use nf-core/nascent for your analysis please cite:

* The pipeline
  https://doi.org/10.5281/zenodo.7245273

* The nf-core framework
  https://doi.org/10.1038/s41587-020-0439-x

* Software dependencies
  https://github.com/nf-core/nascent/blob/master/CITATIONS.md
------------------------------------------------------
[-        ] process > NFCORE_NASCENT:NASCENT:PREP... -
[-        ] process > NFCORE_NASCENT:NASCENT:PREP... -

[-        ] process > NFCORE_NASCENT:NASCENT:PREP... -
[-        ] process > NFCORE_NASCENT:NASCENT:PREP... -
[-        ] process > NFCORE_NASCENT:NASCENT:PREP... -
[-        ] process > NFCORE_NASCENT:NASCENT:PREP... -
[-        ] process > NFCORE_NASCENT:NASCENT:PREP... -
[-        ] process > NFCORE_NASCENT:NASCENT:PREP... -
[-        ] process > NFCORE_NASCENT:NASCENT:INPU... -
[-        ] process > NFCORE_NASCENT:NASCENT:FASTQC  -
[-        ] process > NFCORE_NASCENT:NASCENT:FASTP   -
[-        ] process > NFCORE_NASCENT:NASCENT:ALIG... -
[-        ] process > NFCORE_NASCENT:NASCENT:ALIG... -
[-        ] process > NFCORE_NASCENT:NASCENT:ALIG... -
[-        ] process > NFCORE_NASCENT:NASCENT:ALIG... -
[-        ] process > NFCORE_NASCENT:NASCENT:ALIG... -
[-        ] process > NFCORE_NASCENT:NASCENT:ALIG... -
[-        ] process > NFCORE_NASCENT:NASCENT:QUAL... -
[-        ] process > NFCORE_NASCENT:NASCENT:QUAL... -
[-        ] process > NFCORE_NASCENT:NASCENT:QUAL... -
[-        ] process > NFCORE_NASCENT:NASCENT:QUAL... -
[-        ] process > NFCORE_NASCENT:NASCENT:QUAL... -
[-        ] process > NFCORE_NASCENT:NASCENT:QUAL... -

[-        ] process > NFCORE_NASCENT:NASCENT:PREP... -
[-        ] process > NFCORE_NASCENT:NASCENT:PREP... -
[-        ] process > NFCORE_NASCENT:NASCENT:PREP... -
[-        ] process > NFCORE_NASCENT:NASCENT:PREP... -
[-        ] process > NFCORE_NASCENT:NASCENT:PREP... -
[-        ] process > NFCORE_NASCENT:NASCENT:PREP... -
[-        ] process > NFCORE_NASCENT:NASCENT:INPU... -
[-        ] process > NFCORE_NASCENT:NASCENT:FASTQC  -
[-        ] process > NFCORE_NASCENT:NASCENT:FASTP   -
[-        ] process > NFCORE_NASCENT:NASCENT:ALIG... -
[-        ] process > NFCORE_NASCENT:NASCENT:ALIG... -
[-        ] process > NFCORE_NASCENT:NASCENT:ALIG... -
[-        ] process > NFCORE_NASCENT:NASCENT:ALIG... -
[-        ] process > NFCORE_NASCENT:NASCENT:ALIG... -
[-        ] process > NFCORE_NASCENT:NASCENT:ALIG... -
[-        ] process > NFCORE_NASCENT:NASCENT:QUAL... -
[-        ] process > NFCORE_NASCENT:NASCENT:QUAL... -
[-        ] process > NFCORE_NASCENT:NASCENT:QUAL... -
[-        ] process > NFCORE_NASCENT:NASCENT:QUAL... -
[-        ] process > NFCORE_NASCENT:NASCENT:QUAL... -
[-        ] process > NFCORE_NASCENT:NASCENT:QUAL... -
[-        ] process > NFCORE_NASCENT:NASCENT:COVE... -
[-        ] process > NFCORE_NASCENT:NASCENT:COVE... -
[-        ] process > NFCORE_NASCENT:NASCENT:COVE... -
[-        ] process > NFCORE_NASCENT:NASCENT:COVE... -
[-        ] process > NFCORE_NASCENT:NASCENT:TRAN... -
[-        ] process > NFCORE_NASCENT:NASCENT:TRAN... -
[-        ] process > NFCORE_NASCENT:NASCENT:TRAN... -
[-        ] process > NFCORE_NASCENT:NASCENT:TRAN... -
[-        ] process > NFCORE_NASCENT:NASCENT:TRAN... -
[-        ] process > NFCORE_NASCENT:NASCENT:TRAN... -
[-        ] process > NFCORE_NASCENT:NASCENT:TRAN... -
[-        ] process > NFCORE_NASCENT:NASCENT:TRAN... -
[-        ] process > NFCORE_NASCENT:NASCENT:TRAN... -
[-        ] process > NFCORE_NASCENT:NASCENT:TRAN... -
[-        ] process > NFCORE_NASCENT:NASCENT:BED2SAF -
[-        ] process > NFCORE_NASCENT:NASCENT:SUBR... -
[-        ] process > NFCORE_NASCENT:NASCENT:SUBR... -
[-        ] process > NFCORE_NASCENT:NASCENT:CUST... -

[-        ] process > NFCORE_NASCENT:NASCENT:PREP... -
[-        ] process > NFCORE_NASCENT:NASCENT:PREP... -
[-        ] process > NFCORE_NASCENT:NASCENT:PREP... -
[-        ] process > NFCORE_NASCENT:NASCENT:PREP... -
[-        ] process > NFCORE_NASCENT:NASCENT:PREP... -
[-        ] process > NFCORE_NASCENT:NASCENT:PREP... -
[-        ] process > NFCORE_NASCENT:NASCENT:INPU... -
[-        ] process > NFCORE_NASCENT:NASCENT:FASTQC  -
[-        ] process > NFCORE_NASCENT:NASCENT:FASTP   -
[-        ] process > NFCORE_NASCENT:NASCENT:ALIG... -
[-        ] process > NFCORE_NASCENT:NASCENT:ALIG... -
[-        ] process > NFCORE_NASCENT:NASCENT:ALIG... -
[-        ] process > NFCORE_NASCENT:NASCENT:ALIG... -
[-        ] process > NFCORE_NASCENT:NASCENT:ALIG... -
[-        ] process > NFCORE_NASCENT:NASCENT:ALIG... -
[-        ] process > NFCORE_NASCENT:NASCENT:QUAL... -
[-        ] process > NFCORE_NASCENT:NASCENT:QUAL... -
[-        ] process > NFCORE_NASCENT:NASCENT:QUAL... -
[-        ] process > NFCORE_NASCENT:NASCENT:QUAL... -
[-        ] process > NFCORE_NASCENT:NASCENT:QUAL... -
[-        ] process > NFCORE_NASCENT:NASCENT:QUAL... -
[-        ] process > NFCORE_NASCENT:NASCENT:COVE... -
[-        ] process > NFCORE_NASCENT:NASCENT:COVE... -
[-        ] process > NFCORE_NASCENT:NASCENT:COVE... -
[-        ] process > NFCORE_NASCENT:NASCENT:COVE... -
[-        ] process > NFCORE_NASCENT:NASCENT:TRAN... -
[-        ] process > NFCORE_NASCENT:NASCENT:TRAN... -
[-        ] process > NFCORE_NASCENT:NASCENT:TRAN... -
[-        ] process > NFCORE_NASCENT:NASCENT:TRAN... -
[-        ] process > NFCORE_NASCENT:NASCENT:TRAN... -
[-        ] process > NFCORE_NASCENT:NASCENT:TRAN... -
[-        ] process > NFCORE_NASCENT:NASCENT:TRAN... -
[-        ] process > NFCORE_NASCENT:NASCENT:TRAN... -
[-        ] process > NFCORE_NASCENT:NASCENT:TRAN... -
[-        ] process > NFCORE_NASCENT:NASCENT:TRAN... -
[-        ] process > NFCORE_NASCENT:NASCENT:BED2SAF -
[-        ] process > NFCORE_NASCENT:NASCENT:SUBR... -
[-        ] process > NFCORE_NASCENT:NASCENT:SUBR... -
[-        ] process > NFCORE_NASCENT:NASCENT:CUST... -
[-        ] process > NFCORE_NASCENT:NASCENT:MULTIQC -

[-        ] process > NFCORE_NASCENT:NASCENT:PREP... -
[-        ] process > NFCORE_NASCENT:NASCENT:PREP... -
[-        ] process > NFCORE_NASCENT:NASCENT:PREP... -
[-        ] process > NFCORE_NASCENT:NASCENT:PREP... -
[-        ] process > NFCORE_NASCENT:NASCENT:PREP... -
[-        ] process > NFCORE_NASCENT:NASCENT:PREP... -
[-        ] process > NFCORE_NASCENT:NASCENT:INPU... -
[-        ] process > NFCORE_NASCENT:NASCENT:FASTQC  -
[-        ] process > NFCORE_NASCENT:NASCENT:FASTP   -
[-        ] process > NFCORE_NASCENT:NASCENT:ALIG... -
[-        ] process > NFCORE_NASCENT:NASCENT:ALIG... -
[-        ] process > NFCORE_NASCENT:NASCENT:ALIG... -
[-        ] process > NFCORE_NASCENT:NASCENT:ALIG... -
[-        ] process > NFCORE_NASCENT:NASCENT:ALIG... -
[-        ] process > NFCORE_NASCENT:NASCENT:ALIG... -
[-        ] process > NFCORE_NASCENT:NASCENT:QUAL... -
[-        ] process > NFCORE_NASCENT:NASCENT:QUAL... -
[-        ] process > NFCORE_NASCENT:NASCENT:QUAL... -
[-        ] process > NFCORE_NASCENT:NASCENT:QUAL... -
[-        ] process > NFCORE_NASCENT:NASCENT:QUAL... -
[-        ] process > NFCORE_NASCENT:NASCENT:QUAL... -
[-        ] process > NFCORE_NASCENT:NASCENT:COVE... -
[-        ] process > NFCORE_NASCENT:NASCENT:COVE... -
[-        ] process > NFCORE_NASCENT:NASCENT:COVE... -
[-        ] process > NFCORE_NASCENT:NASCENT:COVE... -
[-        ] process > NFCORE_NASCENT:NASCENT:TRAN... -
[-        ] process > NFCORE_NASCENT:NASCENT:TRAN... -
[-        ] process > NFCORE_NASCENT:NASCENT:TRAN... -
[-        ] process > NFCORE_NASCENT:NASCENT:TRAN... -
[-        ] process > NFCORE_NASCENT:NASCENT:TRAN... -
[-        ] process > NFCORE_NASCENT:NASCENT:TRAN... -
[-        ] process > NFCORE_NASCENT:NASCENT:TRAN... -
[-        ] process > NFCORE_NASCENT:NASCENT:TRAN... -
[-        ] process > NFCORE_NASCENT:NASCENT:TRAN... -
[-        ] process > NFCORE_NASCENT:NASCENT:TRAN... -
[-        ] process > NFCORE_NASCENT:NASCENT:BED2SAF -
[-        ] process > NFCORE_NASCENT:NASCENT:SUBR... -
[-        ] process > NFCORE_NASCENT:NASCENT:SUBR... -
[-        ] process > NFCORE_NASCENT:NASCENT:CUST... -
[-        ] process > NFCORE_NASCENT:NASCENT:MULTIQC -
Error executing process > 'NFCORE_NASCENT:NASCENT:PREPARE_GENOME:BWA_INDEX (null)'

Caused by:
  Not a valid path value type: groovyx.gpars.dataflow.DataflowVariable (DataflowVariable(value=null))


Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh`



[-        ] process > NFCORE_NASCENT:NASCENT:PREP... -
[-        ] process > NFCORE_NASCENT:NASCENT:PREP... -
[-        ] process > NFCORE_NASCENT:NASCENT:PREP... -
[-        ] process > NFCORE_NASCENT:NASCENT:PREP... -
[-        ] process > NFCORE_NASCENT:NASCENT:PREP... -
[-        ] process > NFCORE_NASCENT:NASCENT:PREP... -
[-        ] process > NFCORE_NASCENT:NASCENT:INPU... -
[-        ] process > NFCORE_NASCENT:NASCENT:FASTQC  -
[-        ] process > NFCORE_NASCENT:NASCENT:FASTP   -
[-        ] process > NFCORE_NASCENT:NASCENT:ALIG... -
[-        ] process > NFCORE_NASCENT:NASCENT:ALIG... -
[-        ] process > NFCORE_NASCENT:NASCENT:ALIG... -
[-        ] process > NFCORE_NASCENT:NASCENT:ALIG... -
[-        ] process > NFCORE_NASCENT:NASCENT:ALIG... -
[-        ] process > NFCORE_NASCENT:NASCENT:ALIG... -
[-        ] process > NFCORE_NASCENT:NASCENT:QUAL... -
[-        ] process > NFCORE_NASCENT:NASCENT:QUAL... -
[-        ] process > NFCORE_NASCENT:NASCENT:QUAL... -
[-        ] process > NFCORE_NASCENT:NASCENT:QUAL... -
[-        ] process > NFCORE_NASCENT:NASCENT:QUAL... -
[-        ] process > NFCORE_NASCENT:NASCENT:QUAL... -
[-        ] process > NFCORE_NASCENT:NASCENT:COVE... -
[-        ] process > NFCORE_NASCENT:NASCENT:COVE... -
[-        ] process > NFCORE_NASCENT:NASCENT:COVE... -
[-        ] process > NFCORE_NASCENT:NASCENT:COVE... -
[-        ] process > NFCORE_NASCENT:NASCENT:TRAN... -
[-        ] process > NFCORE_NASCENT:NASCENT:TRAN... -
[-        ] process > NFCORE_NASCENT:NASCENT:TRAN... -
[-        ] process > NFCORE_NASCENT:NASCENT:TRAN... -
[-        ] process > NFCORE_NASCENT:NASCENT:TRAN... -
[-        ] process > NFCORE_NASCENT:NASCENT:TRAN... -
[-        ] process > NFCORE_NASCENT:NASCENT:TRAN... -
[-        ] process > NFCORE_NASCENT:NASCENT:TRAN... -
[-        ] process > NFCORE_NASCENT:NASCENT:TRAN... -
[-        ] process > NFCORE_NASCENT:NASCENT:TRAN... -
[-        ] process > NFCORE_NASCENT:NASCENT:BED2SAF -
[-        ] process > NFCORE_NASCENT:NASCENT:SUBR... -
[-        ] process > NFCORE_NASCENT:NASCENT:SUBR... -
[-        ] process > NFCORE_NASCENT:NASCENT:CUST... -
[-        ] process > NFCORE_NASCENT:NASCENT:MULTIQC -
Execution cancelled -- Finishing pending tasks before exit
Pulling Singularity image https://depot.galaxyproject.org/singularity/ubuntu:20.04 [cache /home/yhigashi/tnfil4_euseq/singularity/depot.galaxyproject.org-singularity-ubuntu-20.04.img]
Pulling Singularity image https://depot.galaxyproject.org/singularity/python:3.8.3 [cache /home/yhigashi/tnfil4_euseq/singularity/depot.galaxyproject.org-singularity-python-3.8.3.img]
WARN: Singularity cache directory has not been defined -- Remote image will be stored in the path: /home/yhigashi/tnfil4_euseq/singularity -- Use env variable NXF_SINGULARITY_CACHEDIR to specify a different location
Error executing process > 'NFCORE_NASCENT:NASCENT:PREPARE_GENOME:BWA_INDEX (null)'

Caused by:
  Not a valid path value type: groovyx.gpars.dataflow.DataflowVariable (DataflowVariable(value=null))


Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh`



[-        ] process > NFCORE_NASCENT:NASCENT:PREP... -
[-        ] process > NFCORE_NASCENT:NASCENT:PREP... -
[-        ] process > NFCORE_NASCENT:NASCENT:PREP... -
[-        ] process > NFCORE_NASCENT:NASCENT:PREP... -
[-        ] process > NFCORE_NASCENT:NASCENT:PREP... -
[-        ] process > NFCORE_NASCENT:NASCENT:PREP... -
[-        ] process > NFCORE_NASCENT:NASCENT:INPU... -
[-        ] process > NFCORE_NASCENT:NASCENT:FASTQC  -
[-        ] process > NFCORE_NASCENT:NASCENT:FASTP   -
[-        ] process > NFCORE_NASCENT:NASCENT:ALIG... -
[-        ] process > NFCORE_NASCENT:NASCENT:ALIG... -
[-        ] process > NFCORE_NASCENT:NASCENT:ALIG... -
[-        ] process > NFCORE_NASCENT:NASCENT:ALIG... -
[-        ] process > NFCORE_NASCENT:NASCENT:ALIG... -
[-        ] process > NFCORE_NASCENT:NASCENT:ALIG... -
[-        ] process > NFCORE_NASCENT:NASCENT:QUAL... -
[-        ] process > NFCORE_NASCENT:NASCENT:QUAL... -
[-        ] process > NFCORE_NASCENT:NASCENT:QUAL... -
[-        ] process > NFCORE_NASCENT:NASCENT:QUAL... -
[-        ] process > NFCORE_NASCENT:NASCENT:QUAL... -
[-        ] process > NFCORE_NASCENT:NASCENT:QUAL... -
[-        ] process > NFCORE_NASCENT:NASCENT:COVE... -
[-        ] process > NFCORE_NASCENT:NASCENT:COVE... -
[-        ] process > NFCORE_NASCENT:NASCENT:COVE... -
[-        ] process > NFCORE_NASCENT:NASCENT:COVE... -
[-        ] process > NFCORE_NASCENT:NASCENT:TRAN... -
[-        ] process > NFCORE_NASCENT:NASCENT:TRAN... -
[-        ] process > NFCORE_NASCENT:NASCENT:TRAN... -
[-        ] process > NFCORE_NASCENT:NASCENT:TRAN... -
[-        ] process > NFCORE_NASCENT:NASCENT:TRAN... -
[-        ] process > NFCORE_NASCENT:NASCENT:TRAN... -
[-        ] process > NFCORE_NASCENT:NASCENT:TRAN... -
[-        ] process > NFCORE_NASCENT:NASCENT:TRAN... -
[-        ] process > NFCORE_NASCENT:NASCENT:TRAN... -
[-        ] process > NFCORE_NASCENT:NASCENT:TRAN... -
[-        ] process > NFCORE_NASCENT:NASCENT:BED2SAF -
[-        ] process > NFCORE_NASCENT:NASCENT:SUBR... -
[-        ] process > NFCORE_NASCENT:NASCENT:SUBR... -
[-        ] process > NFCORE_NASCENT:NASCENT:CUST... -
[-        ] process > NFCORE_NASCENT:NASCENT:MULTIQC -
Execution cancelled -- Finishing pending tasks before exit
Pulling Singularity image https://depot.galaxyproject.org/singularity/ubuntu:20.04 [cache /home/yhigashi/tnfil4_euseq/singularity/depot.galaxyproject.org-singularity-ubuntu-20.04.img]
Pulling Singularity image https://depot.galaxyproject.org/singularity/python:3.8.3 [cache /home/yhigashi/tnfil4_euseq/singularity/depot.galaxyproject.org-singularity-python-3.8.3.img]
-[nf-core/nascent] Sent summary e-mail to [email protected] (sendmail)-
-[nf-core/nascent] Pipeline completed with errors-
WARN: Singularity cache directory has not been defined -- Remote image will be stored in the path: /home/yhigashi/tnfil4_euseq/singularity -- Use env variable NXF_SINGULARITY_CACHEDIR to specify a different location
Error executing process > 'NFCORE_NASCENT:NASCENT:PREPARE_GENOME:BWA_INDEX (null)'

Caused by:
  Not a valid path value type: groovyx.gpars.dataflow.DataflowVariable (DataflowVariable(value=null))


Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh`



[-        ] process > NFCORE_NASCENT:NASCENT:PREP... -
[-        ] process > NFCORE_NASCENT:NASCENT:PREP... -
[-        ] process > NFCORE_NASCENT:NASCENT:PREP... -
[-        ] process > NFCORE_NASCENT:NASCENT:PREP... -
[-        ] process > NFCORE_NASCENT:NASCENT:PREP... -
[-        ] process > NFCORE_NASCENT:NASCENT:PREP... -
[-        ] process > NFCORE_NASCENT:NASCENT:INPU... -
[-        ] process > NFCORE_NASCENT:NASCENT:FASTQC  -
[-        ] process > NFCORE_NASCENT:NASCENT:FASTP   -
[-        ] process > NFCORE_NASCENT:NASCENT:ALIG... -
[-        ] process > NFCORE_NASCENT:NASCENT:ALIG... -
[-        ] process > NFCORE_NASCENT:NASCENT:ALIG... -
[-        ] process > NFCORE_NASCENT:NASCENT:ALIG... -
[-        ] process > NFCORE_NASCENT:NASCENT:ALIG... -
[-        ] process > NFCORE_NASCENT:NASCENT:ALIG... -
[-        ] process > NFCORE_NASCENT:NASCENT:QUAL... -
[-        ] process > NFCORE_NASCENT:NASCENT:QUAL... -
[-        ] process > NFCORE_NASCENT:NASCENT:QUAL... -
[-        ] process > NFCORE_NASCENT:NASCENT:QUAL... -
[-        ] process > NFCORE_NASCENT:NASCENT:QUAL... -
[-        ] process > NFCORE_NASCENT:NASCENT:QUAL... -
[-        ] process > NFCORE_NASCENT:NASCENT:COVE... -
[-        ] process > NFCORE_NASCENT:NASCENT:COVE... -
[-        ] process > NFCORE_NASCENT:NASCENT:COVE... -
[-        ] process > NFCORE_NASCENT:NASCENT:COVE... -
[-        ] process > NFCORE_NASCENT:NASCENT:TRAN... -
[-        ] process > NFCORE_NASCENT:NASCENT:TRAN... -
[-        ] process > NFCORE_NASCENT:NASCENT:TRAN... -
[-        ] process > NFCORE_NASCENT:NASCENT:TRAN... -
[-        ] process > NFCORE_NASCENT:NASCENT:TRAN... -
[-        ] process > NFCORE_NASCENT:NASCENT:TRAN... -
[-        ] process > NFCORE_NASCENT:NASCENT:TRAN... -
[-        ] process > NFCORE_NASCENT:NASCENT:TRAN... -
[-        ] process > NFCORE_NASCENT:NASCENT:TRAN... -
[-        ] process > NFCORE_NASCENT:NASCENT:TRAN... -
[-        ] process > NFCORE_NASCENT:NASCENT:BED2SAF -
[-        ] process > NFCORE_NASCENT:NASCENT:SUBR... -
[-        ] process > NFCORE_NASCENT:NASCENT:SUBR... -
[-        ] process > NFCORE_NASCENT:NASCENT:CUST... -
[-        ] process > NFCORE_NASCENT:NASCENT:MULTIQC -
Execution cancelled -- Finishing pending tasks before exit
Pulling Singularity image https://depot.galaxyproject.org/singularity/ubuntu:20.04 [cache /home/yhigashi/tnfil4_euseq/singularity/depot.galaxyproject.org-singularity-ubuntu-20.04.img]
Pulling Singularity image https://depot.galaxyproject.org/singularity/python:3.8.3 [cache /home/yhigashi/tnfil4_euseq/singularity/depot.galaxyproject.org-singularity-python-3.8.3.img]
-[nf-core/nascent] Sent summary e-mail to [email protected] (sendmail)-
-[nf-core/nascent] Pipeline completed with errors-
WARN: Singularity cache directory has not been defined -- Remote image will be stored in the path: /home/yhigashi/tnfil4_euseq/singularity -- Use env variable NXF_SINGULARITY_CACHEDIR to specify a different location
Error executing process > 'NFCORE_NASCENT:NASCENT:PREPARE_GENOME:BWA_INDEX (null)'

Caused by:
  Not a valid path value type: groovyx.gpars.dataflow.DataflowVariable (DataflowVariable(value=null))


Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh`

Relevant files

230920_nextflow.log

System information

  1. Nextflow version 22.10.5
  2. SuperComputer SHIROKANE
  3. AGE (Altair Grid Engine)
  4. Singularity
  5. RedHat Enterprise Linux 8 HPC (x86_64)
  6. nfcore/nascent 2.1.1
@YoshikiHigashijima YoshikiHigashijima added the bug Something isn't working label Sep 21, 2023
@edmundmiller edmundmiller self-assigned this Sep 21, 2023
@edmundmiller edmundmiller added this to the v2.2.0 milestone Sep 21, 2023
edmundmiller added a commit that referenced this issue Feb 14, 2024
@edmundmiller
test(#119): Add a test for gzipped references
2b32a6b
edmundmiller added a commit that referenced this issue Feb 14, 2024
@edmundmiller
fix(#119): Gzipped references work now
ec6cf14 
Thanks rnaseq
@edmundmiller edmundmiller mentioned this issue Feb 14, 2024
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edmundmiller added a commit that referenced this issue Feb 15, 2024
@edmundmiller
fix(#119): Gzipped references work now
7b11555 
Thanks rnaseq
@edmundmiller edmundmiller linked a pull request Feb 15, 2024 that will close this issue
Fix gzip reference files #133
Merged
@edmundmiller edmundmiller mentioned this issue Feb 29, 2024
Merged
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Fix gzip reference files nf-core/nascent
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@edmundmiller @YoshikiHigashijima