nextflow cannot open cache dir

[abbye1093]

Description of the bug

I’ve used this workflow many times and have not changed where (dirs) or how I use gemmaker but am now getting this error. I’ve deleted the .nextflow dir that is automatically made on launch in both my working dir and my home dir with no change. Online someone suggested this is happening because there is no more local storage and that is not the case for me.

Command used and terminal output

$ nextflow run systemsgenetics/gemmaker \
>   -profile kamiak,singularity \
>   --pipeline star \
>   --input "/scidas/research/abigail.eaker/DF_assemblies/02struc_annotation/03gene/*{1,2}.fastq" \
>   --star_index_dir mac-assembly.fasta.indexed \
>   --star_gtf_file assembly.fasta.gtf \
>   --star_keep_bam
N E X T F L O W  ~  version 21.10.6
Launching `systemsgenetics/gemmaker` [condescending_magritte] - revision: c7fe33612e [master]

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                                        ,--./,-.
        ___     __   __   __   ___     /,-._.--~'
  |\ | |__  __ /  ` /  \ |__) |__         }  {
  | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                        `._,._,'
  systemsgenetics/gemmaker v2.1.1
------------------------------------------------------
Core Nextflow options
  revision                  : master
  runName                   : condescending_magritte
  containerEngine           : singularity
  launchDir                 : /scidas/research/abigail.eaker/DF_assemblies/02struc_annotation/03gene/mac
  workDir                   : /scidas/research/abigail.eaker/DF_assemblies/02struc_annotation/03gene/mac/work
  projectDir                : /home/abigail.eaker/.nextflow/assets/systemsgenetics/gemmaker
  userName                  : abigail.eaker
  profile                   : kamiak,singularity
  configFiles               : /home/abigail.eaker/.nextflow/assets/systemsgenetics/gemmaker/nextflow.config, /scidas/research/abigail.eaker/DF_assemblies/02struc_annotation/03gene/mac/nextflow.config

Input/output options
  input                     : /scidas/research/abigail.eaker/DF_assemblies/02struc_annotation/03gene/*{1,2}.fastq
  pipeline                  : star
  sras                      : null
  failed_run_report_template: /home/abigail.eaker/.nextflow/assets/systemsgenetics/gemmaker/assets/failed_sra_runs.template.html
  multiqc_config_file       : /home/abigail.eaker/.nextflow/assets/systemsgenetics/gemmaker/assets/multiqc_config.yaml
  multiqc_custom_logo       : /home/abigail.eaker/.nextflow/assets/systemsgenetics/gemmaker/assets/systemsgenetics-gemmaker_logo.png

Kallisto Pipeline
  kallisto_bootstrap_samples: 0

Star Pipeline
  star_index_dir            : mac-assembly.fasta.indexed
  star_gtf_file             : assembly.fasta.gtf
  star_keep_bam             : true

Reference genome options
  igenomes_ignore           : true

Generic options
  publish_dir_mode          : link

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

* The pipeline
  https://doi.org/10.5281/zenodo.3620945

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

* Software dependencies
  https://github.com/systemsgenetics/gemmaker/blob/master/CITATIONS.md
------------------------------------------------------
[-        ] process > GEMmaker:get_software_versions -
[-        ] process > GEMmaker:fastqc_1              -
[-        ] process > GEMmaker:trimmomatic           -
[-        ] process > GEMmaker:fastqc_2              -
[-        ] process > GEMmaker:star                  -
[-        ] process > GEMmaker:samtools_merge        -
[-        ] process > GEMmaker:samtools_sort         -
[-        ] process > GEMmaker:samtools_index        -
[-        ] process > GEMmaker:stringtie             -
[-        ] process > GEMmaker:stringtie_fpkm_tpm    -
[-        ] process > GEMmaker:next_sample           -
[-        ] process > GEMmaker:multiqc               -
[-        ] process > GEMmaker:create_gem            -
[-        ] process > GEMmaker:clean_work_files      -
[-        ] process > GEMmaker:clean_work_dirs       -

Relevant files

nextflow.log.4.zip

System information

systemsgenetics/gemmaker v2.1.1
N E X T F L O W ~ version 21.10.6
SLURM
Docker with Singularity
kamiak HPC

[Huiting120]

That was a kamiak HPC issue.