run4_guppy_qscore_filtering

$ cat samplesheet.csv
group,replicate,barcode,input_file,genome,transcriptome
cdcp6,1,1,,/bgfs/uchandran/projects/duprex_nanopore_covid/refs/GCA_009937905.1_ASM993790v1_genomic.fa,




$ cat results/pipeline_info/pipeline_report.txt
----------------------------------------------------
                                        ,--./,-.
        ___     __   __   __   ___     /,-._.--~\
  |\ | |__  __ /  ` /  \ |__) |__         }  {
  | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                        `._,._,'
  nf-core/nanoseq v1.2.0dev
----------------------------------------------------

Run Name: suspicious_church

####################################################
## nf-core/nanoseq execution completed unsuccessfully! ##
####################################################
The exit status of the task that caused the workflow execution to fail was: 1.
The full error message was:

Error executing process > 'GUPPY (fast5_pass)'

Caused by:
  Process `GUPPY (fast5_pass)` terminated with an error exit status (1)

Command executed:

  guppy_basecaller \
      --input_path fast5_pass \
      --save_path ./basecalling \
      --records_per_fastq 0 \
      --compress_fastq \
       \
      --num_callers 2 --cpu_threads_per_caller 6 \
       \
      --flowcell FLO-MIN106 --qscore_filtering --min_qscore 7 --kit SQK-DCS109 \

  guppy_basecaller --version &> v_guppy.txt

  ## Concatenate fastq files
  mkdir fastq
  cd basecalling
  if [ "$(find . -type d -name "barcode*" )" != "" ]
  then
      for dir in barcode*/
      do
          dir=${dir%*/}
          cat $dir/*.fastq.gz > ../fastq/$dir.fastq.gz
      done
  else
      cat *.fastq.gz > ../fastq/cdcp6_R1.fastq.gz
  fi

Command exit status:
  1

Command output:
  ONT Guppy basecalling software version 4.0.14+8d3226e, client-server API version 2.1.0
  config file:        /opt/ont/guppy/data/dna_r9.4.1_450bps_hac.cfg
  model file:         /opt/ont/guppy/data/template_r9.4.1_450bps_hac.jsn
  input path:         fast5_pass
  save path:          ./basecalling
  chunk size:         2000
  chunks per runner:  512
  minimum qscore:     7
  records per file:   0
  fastq compression:  ON
  num basecallers:    2
  cpu mode:           ON
  threads per caller: 6

  Found 81 fast5 files to process.
  Init time: 8035 ms

  0%   10   20   30   40   50   60   70   80   90   100%
  |----|----|----|----|----|----|----|----|----|----|
  ***************************************************
  Caller time: 68395228 ms, Samples called: 3307651334, samples/s: 48360.8
  Finishing up any open output files.
  Basecalling completed successfully.

Command error:
  cat: '*.fastq.gz': No such file or directory

Work dir:
  /bgfs/uchandran//projects/duprex_nanopore_covid/nfcore_nanoseq/run4/work/40/3295dccb486adb87bc66512500dd2d

Tip: when you have fixed the problem you can continue the execution adding the option `-resume` to the run command line



The workflow was completed at 2021-01-02T16:35:27.152-05:00 (duration: 22h 25m 50s)

The command used to launch the workflow was as follows:

  nextflow run nf-core/nanoseq --input samplesheet.csv --protocol cDNA --input_path ./fast5_pass --flowcell 'FLO-MIN106 --qscore_filtering --min_qscore 7' --kit SQK-DCS109 --skip_demultiplexing --skip_quantification -config myconfig.config -profile singularity -r dev



Pipeline Configuration:
-----------------------
 - Pipeline Release: dev
 - Run Name: suspicious_church
 - Samplesheet: samplesheet.csv
 - Protocol: cDNA
 - Stranded: No
 - Skip Basecalling: No
 - Skip Demultiplexing: Yes
 - Run Dir: ./fast5_pass
 - Flowcell ID: FLO-MIN106 --qscore_filtering --min_qscore 7
 - Kit ID: SQK-DCS109
 - Barcode Kit ID: Unspecified
 - Barcode Both Ends: No
 - Guppy Config File: Unspecified
 - Guppy Model File: Unspecified
 - Guppy GPU Mode: No
 - Guppy GPU Runners: 6
 - Guppy CPU Threads: 1
 - Guppy GPU Device: auto
 - Guppy GPU Options: Unspecified
 - Aligner: minimap2
 - Save Intermeds: No
 - Max Resources: 128.GB memory, 16 cpus, 240.h time per job
 - Container: singularity - nfcore/nanoseq:dev
 - Output dir: ./results
 - Launch dir: /bgfs/uchandran//projects/duprex_nanopore_covid/nfcore_nanoseq/run4
 - Working dir: /bgfs/uchandran//projects/duprex_nanopore_covid/nfcore_nanoseq/run4/work
 - Script dir: /ihome/uchandran//.nextflow/assets/nf-core/nanoseq
 - User: 
 - Config Profile: singularity
 - Config Files: /ihome/uchandran//.nextflow/config, /ihome/uchandran//.nextflow/assets/nf-core/nanoseq/nextflow.config, /bgfs/uchandran//projects/duprex_nanopore_covid/nfcore_nanoseq/run4/myconfig.config
 - Date Started: 2021-01-01T18:09:36.716-05:00
 - Date Completed: 2021-01-02T16:35:27.152-05:00
 - Pipeline script file path: /ihome/uchandran//.nextflow/assets/nf-core/nanoseq/main.nf
 - Pipeline script hash ID: 406072490d87a81baedd83465cb28b35
 - Pipeline repository Git URL: https://github.com/nf-core/nanoseq
 - Pipeline repository Git Commit: 119909fcae43fe1d043f604e3538a881e829eff5
 - Pipeline Git branch/tag: dev
 - Nextflow Version: 20.10.0
 - Nextflow Build: 5430
 - Nextflow Compile Timestamp: 01-11-2020 15:14 UTC

--
nf-core/nanoseq
https://github.com/nf-core/nanoseq