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VIB-PSB / MINI-EX

Motif-Informed Network Inference of cell type-specific gene regulatory networks in plants
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Failed to submit process to grid scheduler for execution: Unknown option: terse #2

Closed pavsol closed 2 years ago

pavsol commented 2 years ago

Hi, I am trying to run MINI-EX. I get following error:

$ nextflow -C miniex.config run miniex.nf -resume
N E X T F L O W  ~  version 21.10.5
Launching `miniex.nf` [compassionate_wozniak] - revision: b74059cce4
WARN: DSL 2 PREVIEW MODE IS DEPRECATED - USE THE STABLE VERSION INSTEAD -- Read more at https://www.nextflow.io/docs/latest/dsl2.html#dsl2-migration-notes
      Motif-Informed Network Inference from gene EXpression
      =====================================================
Running TF motif enrichment filtering on  TF-F_motifs
      Running single-cell cluster enrichment using the top 700 upregulated genes per cluster
      Filtering out regulons of single-cell clusters where the TF is expressed in less than 10 % of the cells
Plotting expression specificity and DE calls for the top 150 regulons

[-        ] process > run_grnboost         -
[-        ] process > unzip_motifMappings  [  0%] 0 of 1
[-        ] process > run_enricher_motifs  -
[-        ] process > filter_motifs        -
[-        ] process > get_topDEGs          [  0%] 0 of 1
[-        ] process > run_enricher_cluster -
[-        ] process > run_grnboost         -
[-        ] process > unzip_motifMappings  [  0%] 0 of 1
[-        ] process > run_enricher_motifs  -
[-        ] process > filter_motifs        -
[81/dd6326] process > get_topDEGs (1)      [100%] 1 of 1, failed: 1
[-        ] process > run_enricher_cluster -
[-        ] process > filter_expression    -
[-        ] process > clustermap_regs      -
[-        ] process > network_centrality   -
[-        ] process > getFiles_enrichment  -
[-        ] process > GO_enricher          -
[-        ] process > ranking_df_std       -
[-        ] process > makeBorda            -
[-        ] process > heatmap_tops         -
Pulling Singularity image docker://vibpsb/mini-ex:latest [cache /home/pavel/opt/MINI-EX/singularity_cache/vibpsb-mini-ex-latest.img]
Error executing process > 'get_topDEGs (1)'

Caused by:
  Failed to submit process to grid scheduler for execution

Command executed:

  qsub -terse .command.run

Command exit status:
  2

Command output:
  Unknown option: terse
  Usage:
      qsub [-a start_time] [-A account] [-b y|n] [-e err_path] [-I] [-l
      resource_list] [-m mail_options] [-M user_list] [-N job_name] [-o
      out_path] [-p priority] [-pe shm task_cnt] [-P wckey] [-q destination]
      [-r y|n] [-v variable_list] [-V] [-wd workdir] [-W
      additional_attributes] [-h] [script]

I am not sure if this error is regarding Singularity, Nexflow or MINI-EX as I haven't used any of them so far.

Thank you for any help, Pavel

caferra commented 2 years ago

Hi Pavel,

seems more an error related to the SGE cluster. In the config file the specified executor is sge, while here it seems like you tried to run it locally without changing it in the config.