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Issue with installing/test run #253

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rugilemat opened this issue Aug 26, 2023 · 2 comments
Closed

Issue with installing/test run #253

rugilemat opened this issue Aug 26, 2023 · 2 comments
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bug Something isn't working

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@rugilemat
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rugilemat commented Aug 26, 2023 •
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Description of the bug

Hi,

I have tried to install and run nanoseq on our HPC and got the following error when trying to run the test:

Error executing process > 'NFCORE_NANOSEQ:NANOSEQ:QCAT (sample_nobc_dx.fastq.gz)'

Caused by:
  Process `NFCORE_NANOSEQ:NANOSEQ:QCAT (sample_nobc_dx.fastq.gz)` terminated with an error exit status (127)

Command executed:

  ## Unzip fastq file
  ## qcat doesnt support zipped files yet
  FILE=sample_nobc_dx.fastq.gz
  if [[ $FILE == *.gz ]]
  then
  zcat sample_nobc_dx.fastq.gz > unzipped.fastq
  FILE=unzipped.fastq
  fi
  qcat  \
  -f $FILE \
  -b ./fastq \
  --kit NBD103/NBD104 \
  --min-score 60 \
  
  
  ## Zip fastq files (cannot find pigz command)
  gzip fastq/*
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_NANOSEQ:NANOSEQ:QCAT":
      qcat: $(qcat --version 2>&1 | sed 's/^.*qcat //; s/ .*$//')
  END_VERSIONS

Command exit status:
  127

Command output:
  (empty)

Command error:
  .command.sh: line 11: qcat: command not found

Work dir:
  /scratch/prj/ppn_microglia_mod/directrna/scripts/work/d4/80e29c7e90053a9789ef55a7104488

Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`

Any help would be appreciated!

Command used and terminal output

$ nextflow run nf-core/nanoseq -profile test, singularity

N E X T F L O W  ~  version 22.10.1
Launching `https://github.com/nf-core/nanoseq` [goofy_bernard] DSL2 - revision: 6e563e5436 [master]


------------------------------------------------------
                                        ,--./,-.
        ___     __   __   __   ___     /,-._.--~'
  |\ | |__  __ /  ` /  \ |__) |__         }  {
  | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                        `._,._,'
  nf-core/nanoseq v3.1.0-g6e563e5
------------------------------------------------------
Core Nextflow options
  revision                  : master
  runName                   : goofy_bernard
  launchDir                 : /scratch/prj/ppn_microglia_mod/directrna/scripts
  workDir                   : /scratch/prj/ppn_microglia_mod/directrna/scripts/work
  projectDir                : /users/k19022845/.nextflow/assets/nf-core/nanoseq
  userName                  : k19022845
  profile                   : test,
  configFiles               : /users/k19022845/.nextflow/assets/nf-core/nanoseq/nextflow.config

Input/output options
  input                     : https://raw.githubusercontent.com/nf-core/test-datasets/nanoseq/3.0/samplesheet/samplesheet_nobc_dx.csv
  protocol                  : DNA
  outdir                    : ./results

Demultiplexing options
  input_path                : https://raw.githubusercontent.com/nf-core/test-datasets/nanoseq/fastq/nondemultiplexed/sample_nobc_dx.fastq.gz
  barcode_kit               : NBD103/NBD104

Differential analysis options
  skip_quantification       : true

RNA fusion analysis options
  jaffal_ref_dir            : null
  skip_fusion_analysis      : true

RNA modification analysis options
  skip_modification_analysis: true

Process skipping options
  skip_bigbed               : true
  skip_bigwig               : true

Reference genome options
  igenomes_base             : s3://ngi-igenomes/igenomes/

Institutional config options
  config_profile_name       : Test profile
  config_profile_description: Minimal test dataset to check pipeline function

Max job request options
  max_cpus                  : 2
  max_memory                : 6 GB
  max_time                  : 12h

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

* The pipeline
  https://doi.org/10.5281/zenodo.5740870

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

* Software dependencies
  https://github.com/nf-core/nanoseq/blob/master/CITATIONS.md
------------------------------------------------------
executor >  local (2)
[8c/a34516] process > NFCORE_NANOSEQ:NANOSEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samplesheet_nobc_dx.csv)      [  0%] 0 of 1
[d4/80e29c] process > NFCORE_NANOSEQ:NANOSEQ:QCAT (sample_nobc_dx.fastq.gz)                               [  0%] 0 of 1
[-        ] process > NFCORE_NANOSEQ:NANOSEQ:QCFASTQ_NANOPLOT_FASTQC:NANOPLOT                             -
[-        ] process > NFCORE_NANOSEQ:NANOSEQ:QCFASTQ_NANOPLOT_FASTQC:FASTQC                               -
[-        ] process > NFCORE_NANOSEQ:NANOSEQ:PREPARE_GENOME:GET_CHROM_SIZES                               -
[-        ] process > NFCORE_NANOSEQ:NANOSEQ:PREPARE_GENOME:GTF2BED                                       -
[-        ] process > NFCORE_NANOSEQ:NANOSEQ:PREPARE_GENOME:SAMTOOLS_FAIDX                                -
[-        ] process > NFCORE_NANOSEQ:NANOSEQ:ALIGN_MINIMAP2:MINIMAP2_INDEX                                -
[-        ] process > NFCORE_NANOSEQ:NANOSEQ:ALIGN_MINIMAP2:MINIMAP2_ALIGN                                -
[-        ] process > NFCORE_NANOSEQ:NANOSEQ:BAM_SORT_INDEX_SAMTOOLS:SAMTOOLS_VIEW_BAM                    -
[-        ] process > NFCORE_NANOSEQ:NANOSEQ:BAM_SORT_INDEX_SAMTOOLS:SAMTOOLS_SORT                        -
[-        ] process > NFCORE_NANOSEQ:NANOSEQ:BAM_SORT_INDEX_SAMTOOLS:SAMTOOLS_INDEX                       -
[-        ] process > NFCORE_NANOSEQ:NANOSEQ:BAM_SORT_INDEX_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS    -
[-        ] process > NFCORE_NANOSEQ:NANOSEQ:BAM_SORT_INDEX_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT -
[-        ] process > NFCORE_NANOSEQ:NANOSEQ:BAM_SORT_INDEX_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS -
[-        ] process > NFCORE_NANOSEQ:NANOSEQ:CUSTOM_DUMPSOFTWAREVERSIONS                                  -
[-        ] process > NFCORE_NANOSEQ:NANOSEQ:MULTIQC                                                      -
Error executing process > 'NFCORE_NANOSEQ:NANOSEQ:QCAT (sample_nobc_dx.fastq.gz)'

Caused by:
  Process `NFCORE_NANOSEQ:NANOSEQ:QCAT (sample_nobc_dx.fastq.gz)` terminated with an error exit status (127)

Command executed:

  ## Unzip fastq file
  ## qcat doesnt support zipped files yet
  FILE=sample_nobc_dx.fastq.gz
  if [[ $FILE == *.gz ]]
  then
  zcat sample_nobc_dx.fastq.gz > unzipped.fastq
  FILE=unzipped.fastq
  fi
  qcat  \
  -f $FILE \
  -b ./fastq \
  --kit NBD103/NBD104 \
  --min-score 60 \
  
  
  ## Zip fastq files (cannot find pigz command)
  gzip fastq/*
  
executor >  local (2)
[8c/a34516] process > NFCORE_NANOSEQ:NANOSEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samplesheet_nobc_dx.csv)      [  0%] 0 of 1
[d4/80e29c] process > NFCORE_NANOSEQ:NANOSEQ:QCAT (sample_nobc_dx.fastq.gz)                               [100%] 1 of 1, failed: 1 ✘
[-        ] process > NFCORE_NANOSEQ:NANOSEQ:QCFASTQ_NANOPLOT_FASTQC:NANOPLOT                             -
[-        ] process > NFCORE_NANOSEQ:NANOSEQ:QCFASTQ_NANOPLOT_FASTQC:FASTQC                               -
[-        ] process > NFCORE_NANOSEQ:NANOSEQ:PREPARE_GENOME:GET_CHROM_SIZES                               -
[-        ] process > NFCORE_NANOSEQ:NANOSEQ:PREPARE_GENOME:GTF2BED                                       -
[-        ] process > NFCORE_NANOSEQ:NANOSEQ:PREPARE_GENOME:SAMTOOLS_FAIDX                                -
[-        ] process > NFCORE_NANOSEQ:NANOSEQ:ALIGN_MINIMAP2:MINIMAP2_INDEX                                -
[-        ] process > NFCORE_NANOSEQ:NANOSEQ:ALIGN_MINIMAP2:MINIMAP2_ALIGN                                -
[-        ] process > NFCORE_NANOSEQ:NANOSEQ:BAM_SORT_INDEX_SAMTOOLS:SAMTOOLS_VIEW_BAM                    -
[-        ] process > NFCORE_NANOSEQ:NANOSEQ:BAM_SORT_INDEX_SAMTOOLS:SAMTOOLS_SORT                        -
[-        ] process > NFCORE_NANOSEQ:NANOSEQ:BAM_SORT_INDEX_SAMTOOLS:SAMTOOLS_INDEX                       -
[-        ] process > NFCORE_NANOSEQ:NANOSEQ:BAM_SORT_INDEX_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS    -
[-        ] process > NFCORE_NANOSEQ:NANOSEQ:BAM_SORT_INDEX_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT -
[-        ] process > NFCORE_NANOSEQ:NANOSEQ:BAM_SORT_INDEX_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS -
[-        ] process > NFCORE_NANOSEQ:NANOSEQ:CUSTOM_DUMPSOFTWAREVERSIONS                                  -
[-        ] process > NFCORE_NANOSEQ:NANOSEQ:MULTIQC                                                      -
Execution cancelled -- Finishing pending tasks before exit
Error executing process > 'NFCORE_NANOSEQ:NANOSEQ:QCAT (sample_nobc_dx.fastq.gz)'

Caused by:
  Process `NFCORE_NANOSEQ:NANOSEQ:QCAT (sample_nobc_dx.fastq.gz)` terminated with an error exit status (127)

Command executed:

  ## Unzip fastq file
  ## qcat doesnt support zipped files yet
  FILE=sample_nobc_dx.fastq.gz
  if [[ $FILE == *.gz ]]
  then
  zcat sample_nobc_dx.fastq.gz > unzipped.fastq
  FILE=unzipped.fastq
  fi
  qcat  \
  -f $FILE \
  -b ./fastq \
  --kit NBD103/NBD104 \
  --min-score 60 \
  
  
  ## Zip fastq files (cannot find pigz command)
  gzip fastq/*
  
executor >  local (2)
[8c/a34516] process > NFCORE_NANOSEQ:NANOSEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samplesheet_nobc_dx.csv)      [100%] 1 of 1 ✔
[d4/80e29c] process > NFCORE_NANOSEQ:NANOSEQ:QCAT (sample_nobc_dx.fastq.gz)                               [100%] 1 of 1, failed: 1 ✘
[-        ] process > NFCORE_NANOSEQ:NANOSEQ:QCFASTQ_NANOPLOT_FASTQC:NANOPLOT                             -
[-        ] process > NFCORE_NANOSEQ:NANOSEQ:QCFASTQ_NANOPLOT_FASTQC:FASTQC                               -
[-        ] process > NFCORE_NANOSEQ:NANOSEQ:PREPARE_GENOME:GET_CHROM_SIZES                               -
[-        ] process > NFCORE_NANOSEQ:NANOSEQ:PREPARE_GENOME:GTF2BED                                       -
[-        ] process > NFCORE_NANOSEQ:NANOSEQ:PREPARE_GENOME:SAMTOOLS_FAIDX                                -
[-        ] process > NFCORE_NANOSEQ:NANOSEQ:ALIGN_MINIMAP2:MINIMAP2_INDEX                                -
[-        ] process > NFCORE_NANOSEQ:NANOSEQ:ALIGN_MINIMAP2:MINIMAP2_ALIGN                                -
[-        ] process > NFCORE_NANOSEQ:NANOSEQ:BAM_SORT_INDEX_SAMTOOLS:SAMTOOLS_VIEW_BAM                    -
[-        ] process > NFCORE_NANOSEQ:NANOSEQ:BAM_SORT_INDEX_SAMTOOLS:SAMTOOLS_SORT                        -
[-        ] process > NFCORE_NANOSEQ:NANOSEQ:BAM_SORT_INDEX_SAMTOOLS:SAMTOOLS_INDEX                       -
[-        ] process > NFCORE_NANOSEQ:NANOSEQ:BAM_SORT_INDEX_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS    -
[-        ] process > NFCORE_NANOSEQ:NANOSEQ:BAM_SORT_INDEX_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT -
[-        ] process > NFCORE_NANOSEQ:NANOSEQ:BAM_SORT_INDEX_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS -
[-        ] process > NFCORE_NANOSEQ:NANOSEQ:CUSTOM_DUMPSOFTWAREVERSIONS                                  -
[-        ] process > NFCORE_NANOSEQ:NANOSEQ:MULTIQC                                                      -
Execution cancelled -- Finishing pending tasks before exit
-[nf-core/nanoseq] Pipeline completed with errors-
Error executing process > 'NFCORE_NANOSEQ:NANOSEQ:QCAT (sample_nobc_dx.fastq.gz)'

Caused by:
  Process `NFCORE_NANOSEQ:NANOSEQ:QCAT (sample_nobc_dx.fastq.gz)` terminated with an error exit status (127)

Command executed:

  ## Unzip fastq file
  ## qcat doesnt support zipped files yet
  FILE=sample_nobc_dx.fastq.gz
  if [[ $FILE == *.gz ]]
  then
  zcat sample_nobc_dx.fastq.gz > unzipped.fastq
  FILE=unzipped.fastq
  fi
  qcat  \
  -f $FILE \
  -b ./fastq \
  --kit NBD103/NBD104 \
  --min-score 60 \
  
  
  ## Zip fastq files (cannot find pigz command)
  gzip fastq/*
  
executor >  local (2)
[8c/a34516] process > NFCORE_NANOSEQ:NANOSEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samplesheet_nobc_dx.csv)      [100%] 1 of 1 ✔
[d4/80e29c] process > NFCORE_NANOSEQ:NANOSEQ:QCAT (sample_nobc_dx.fastq.gz)                               [100%] 1 of 1, failed: 1 ✘
[-        ] process > NFCORE_NANOSEQ:NANOSEQ:QCFASTQ_NANOPLOT_FASTQC:NANOPLOT                             -
[-        ] process > NFCORE_NANOSEQ:NANOSEQ:QCFASTQ_NANOPLOT_FASTQC:FASTQC                               -
[-        ] process > NFCORE_NANOSEQ:NANOSEQ:PREPARE_GENOME:GET_CHROM_SIZES                               -
[-        ] process > NFCORE_NANOSEQ:NANOSEQ:PREPARE_GENOME:GTF2BED                                       -
[-        ] process > NFCORE_NANOSEQ:NANOSEQ:PREPARE_GENOME:SAMTOOLS_FAIDX                                -
[-        ] process > NFCORE_NANOSEQ:NANOSEQ:ALIGN_MINIMAP2:MINIMAP2_INDEX                                -
[-        ] process > NFCORE_NANOSEQ:NANOSEQ:ALIGN_MINIMAP2:MINIMAP2_ALIGN                                -
[-        ] process > NFCORE_NANOSEQ:NANOSEQ:BAM_SORT_INDEX_SAMTOOLS:SAMTOOLS_VIEW_BAM                    -
[-        ] process > NFCORE_NANOSEQ:NANOSEQ:BAM_SORT_INDEX_SAMTOOLS:SAMTOOLS_SORT                        -
[-        ] process > NFCORE_NANOSEQ:NANOSEQ:BAM_SORT_INDEX_SAMTOOLS:SAMTOOLS_INDEX                       -
[-        ] process > NFCORE_NANOSEQ:NANOSEQ:BAM_SORT_INDEX_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS    -
[-        ] process > NFCORE_NANOSEQ:NANOSEQ:BAM_SORT_INDEX_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT -
[-        ] process > NFCORE_NANOSEQ:NANOSEQ:BAM_SORT_INDEX_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS -
[-        ] process > NFCORE_NANOSEQ:NANOSEQ:CUSTOM_DUMPSOFTWAREVERSIONS                                  -
[-        ] process > NFCORE_NANOSEQ:NANOSEQ:MULTIQC                                                      -
Execution cancelled -- Finishing pending tasks before exit
-[nf-core/nanoseq] Pipeline completed with errors-
Error executing process > 'NFCORE_NANOSEQ:NANOSEQ:QCAT (sample_nobc_dx.fastq.gz)'

Caused by:
  Process `NFCORE_NANOSEQ:NANOSEQ:QCAT (sample_nobc_dx.fastq.gz)` terminated with an error exit status (127)

Command executed:

  ## Unzip fastq file
  ## qcat doesnt support zipped files yet
  FILE=sample_nobc_dx.fastq.gz
  if [[ $FILE == *.gz ]]
  then
  zcat sample_nobc_dx.fastq.gz > unzipped.fastq
  FILE=unzipped.fastq
  fi
  qcat  \
  -f $FILE \
  -b ./fastq \
  --kit NBD103/NBD104 \
  --min-score 60 \
  
  
  ## Zip fastq files (cannot find pigz command)
  gzip fastq/*
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_NANOSEQ:NANOSEQ:QCAT":
      qcat: $(qcat --version 2>&1 | sed 's/^.*qcat //; s/ .*$//')
  END_VERSIONS

Command exit status:
  127

Command output:
  (empty)

Command error:
  .command.sh: line 11: qcat: command not found

Work dir:
  /scratch/prj/ppn_microglia_mod/directrna/scripts/work/d4/80e29c7e90053a9789ef55a7104488

Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`

Relevant files

No response

System information

Nextflow version: 22.10.1
Hardware: HPC
Executor: local
Container engine: singularity
OS: Linux
Version of nf-core/nanoseq: v3.1.0-g6e563e5
@rugilemat rugilemat added the bug Something isn't working label Aug 26, 2023
@yuukiiwa
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Hi @rugilemat,

I think this is caused by the space between test, and singularity. Please try running the following instead:

nextflow run nf-core/nanoseq -profile test,singularity

Thanks!

Best wishes,
Yuk Kei

@rugilemat
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Hi @yuukiiwa, it seems to have worked without the space!
Thank you!

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@yuukiiwa @rugilemat