[Bug]: Command error & Error executing process

[geng-lee]

What happened?

A bug happened! ERROR ~ Error executing process > 'pipeline:getVersions'

Caused by: Process pipeline:getVersions terminated with an error exit status (127)

Command executed:

python -c "import pysam; print(f'pysam,{pysam.version}')" >> versions.txt python -c "import aplanat; print(f'aplanat,{aplanat.version}')" >> versions.txt python -c "import pandas; print(f'pandas,{pandas.version}')" >> versions.txt python -c "import sklearn; print(f'scikit-learn,{sklearn.version}')" >> versions.txt fastcat --version | sed 's/^/fastcat,/' >> versions.txt minimap2 --version | sed 's/^/minimap2,/' >> versions.txt samtools --version | head -n 1 | sed 's/ /,/' >> versions.txt bedtools --version | head -n 1 | sed 's/ /,/' >> versions.txt python -c "import pychopper; print(f'pychopper,{pychopper.version}')" >> versions.txt gffread --version | sed 's/^/gffread,/' >> versions.txt seqkit version | head -n 1 | sed 's/ /,/' >> versions.txt stringtie --version | sed 's/^/stringtie,/' >> versions.txt gffcompare --version | head -n 1 | sed 's/ /,/' >> versions.txt spoa --version | sed 's/^/spoa,/' >> versions.txt isONclust2 version | sed 's/ version: /,/' >> versions.txt

Command exit status: 127

Command output: (empty)

Command error: .command.run: line 290: docker: command not found

Operating System

ubuntu 20.04

Workflow Execution

EPI2ME Labs desktop application

Workflow Execution - EPI2ME Labs Versions

wf-transcriptomes v0.1.8-gbee88d5

Workflow Execution - CLI Execution Profile

None

Workflow Version

none

Relevant log output

nextflow run epi2me-labs/wf-transcriptomes --help
N E X T F L O W  ~  version 23.04.1
NOTE: Your local project version looks outdated - a different revision is available in the remote repository [cb73e0a6cd]
Launching `https://github.com/epi2me-labs/wf-transcriptomes` [hungry_poitras] DSL2 - revision: bee88d5044 [master]

||||||||||   _____ ____ ___ ____  __  __ _____      _       _
||||||||||  | ____|  _ \_ _|___ \|  \/  | ____|    | | __ _| |__  ___
|||||       |  _| | |_) | |  __) | |\/| |  _| _____| |/ _` | '_ \/ __|
|||||       | |___|  __/| | / __/| |  | | |__|_____| | (_| | |_) \__ \
||||||||||  |_____|_|  |___|_____|_|  |_|_____|    |_|\__,_|_.__/|___/
||||||||||  wf-transcriptomes v0.1.8-gbee88d5
--------------------------------------------------------------------------------
Typical pipeline command:

  nextflow run epi2me-labs/wf-transcriptomes \ 
    --fastq test_data/fastq \ 
    --ref_genome test_data/SIRV_150601a.fasta \ 
    --ref_annotation test_data/SIRV_isofroms.gtf \ 
    --jaffal_refBase chr20/ \ 
    --jaffal_genome hg38 \ 
    --jaffal_annotation genCode22

Input Options
  --fastq                   [string]  FASTQ files to use in the analysis.
  --transcriptome_source    [string]  Select how the transcriptome used for analysis should be prepared.
  --ref_genome              [string]  Path to reference genome sequence [.fa/.fq/.fa.gz/fq.gz]. Required for reference-based workflow.
  --ref_transcriptome       [string]  Transcriptome reference file. Required for precomputed transcriptome calculation and for differential expression 
                                      analysis. [default: null] 
  --ref_annotation          [string]  A reference annotation in GTF format
  --direct_rna              [boolean] Set to true for direct RNA sequencing.
  --analyse_unclassified    [boolean] Analyse unclassified reads from input directory. By default the workflow will not process reads in the unclassified 
                                      directory. 

Output Options
  --out_dir                 [string]  Directory for output of all user-facing files. [default: output]

Sample Options
  --sample_sheet            [string]  A CSV file used to map barcodes to sample aliases. The sample sheet can be provided when the input data is a directory 
                                      containing sub-directories with FASTQ files. 
  --sample                  [string]  A single sample name for non-multiplexed data. Permissible if passing a single .fastq(.gz) file or directory of 
                                      .fastq(.gz) files. 

Options for reference-based workflow
  --plot_gffcmp_stats       [boolean] Create a PDF of plots from showing gffcompare results
  --gffcompare_opts         [string]  Extra command-line options to give to gffcompare -r [default:  -R ]
  --minimap_index_opts      [string]  Extra command-line options for minimap2 indexing. [default: -k14]
  --minimap2_opts           [string]  Additional command-line options for minimap2 alignment. [default: -uf]
  --minimum_mapping_quality [integer] filter aligned reads by MAPQ quality. [default: 40]
  --stringtie_opts          [string]  Extra command-line options for stringtie transcript assembly. [default:  --conservative ]

Options for de novo-based workflow
  --isOnClust2_batch_size   [integer] Number of batches to to process the data in. [default: -1]
  --isOnClust2_sort_options [string]  Additional command-line options for isOnClust2 sort. [default: --kmer-size 11 --window-size 15 --min-shared 5 
                                      --min-qual 7.0 --mapped-threshold 0.65 --aligned-threshold 0.2 --min-fraction 0.8 --min-prob-no-hits 0.0 -M -1 -P 500 -g 
                                      50 -c 150 -F 2] 

Gene Fusion Detection Options
  --jaffal_refBase          [string]  JAFFAl reference genome directory.
  --jaffal_genome           [string]  Genome reference prefix. e.g. hg38. [default: hg38]
  --jaffal_annotation       [string]  Annotation suffix. [default: genCode22]
  --jaffal_dir              [string]  Path to the JAFFAL code directory. If running within EPI2ME-Labs, the default path of /home/epi2melabs/JAFFA within the 
                                      application container will be used. If using outside of EPI2ME-Labs, the path to the code directory downloaded from github 
                                      should be supplied. [default: /home/epi2melabs/JAFFA] 

Differential Expression Options
  --de_analysis             [boolean] Run DE anaylsis
  --condition_sheet         [string]  TSV file with sample_id, condition [default: null]
  --min_gene_expr           [integer] Minimum gene counts [default: 10]
  --min_feature_expr        [integer] Minimum transcript counts [default: 3]
  --min_samps_gene_expr     [integer] Genes expressed in a minimum of this many samples will be included in the differential expression analysis. [default: 
                                      3] 
  --min_samps_feature_expr  [integer] Transcripts expressed in minimum this many samples [default: 1]

Advanced Options
  --threads                 [integer] Number of CPU threads. [default: 2]
  --pychopper_opts          [string]  Extra pychopper opts [default: -m edlib]
  --bundle_min_reads        [integer] Minimum size of bam bundle for parallel processing.
  --isoform_table_nrows     [integer] Maximum rows to dispay in the isoform report table [default: 5000]

Miscellaneous Options
  --disable_ping            [boolean] Enable to prevent sending a workflow ping.

Other parameters
  --monochrome_logs         [boolean] null
  --validate_params         [boolean] null [default: true]
  --show_hidden_params      [boolean] null

!! Hiding 7 params, use --show_hidden_params to show them !!
--------------------------------------------------------------------------------
If you use epi2me-labs/wf-transcriptomes for your analysis please cite:

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

(nextf) [ligeng@login04 ONT_2]$ wget -O test_data.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/wf-isoforms_test_data.tar.gz 
--2023-06-19 02:50:14--  https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/wf-isoforms_test_data.tar.gz
Resolving ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com (ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com)... 
52.92.2.201, 52.218.57.106, 52.218.112.122, ...
Connecting to ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com (ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com)|52.92.2.201|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 96490737 (92M) [application/x-tar]
Saving to: 'test_data.tar.gz'

test_data.tar.gz                                  100%[=============================================================================================================>]  92.02M   926KB/s    in 2m 33s  

2023-06-19 02:52:53 (616 KB/s) - 'test_data.tar.gz' saved [96490737/96490737]

(nextf) [ligeng@login04 ONT_2]$ tar -xzvf  test_data.tar.gz
chr20/
chr20/._hg38_chr20_genCode22.bed
tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.metadata:kMDItemWhereFroms'
tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.quarantine'
tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.lastuseddate#PS'
chr20/hg38_chr20_genCode22.bed
chr20/hg38_chr20_genCode22.1.bt2
chr20/Masked_hg38_chr20.1.bt2
chr20/Masked_hg38_chr20.fa
chr20/hg38_chr20_genCode22.fa
chr20/README.md
chr20/._hg38_chr20_genCode22.tab
tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.metadata:kMDItemWhereFroms'
tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.quarantine'
chr20/hg38_chr20_genCode22.tab
chr20/hg38_chr20.fa
chr20/gencode.v22.annotation.chr20.gtf
ERR6053095_chr20.fastq
(nextf) [ligeng@login04 ONT_2]$ ls
ERR6053095_chr20.fastq  chr20  output  test_data.tar.gz  work

nextflow run epi2me-labs/wf-transcriptomes \
>   --fastq ERR6053095_chr20.fastq \
>   --ref_genome chr20/hg38_chr20.fa \
>   --ref_annotation chr20/gencode.v22.annotation.chr20.gtf \
>   --jaffal_refBase chr20/ \
>   --jaffal_genome hg38_chr20 \
>   --jaffal_annotation "genCode22" \
>   --out_dir outdir -w workspace_dir

N E X T F L O W  ~  version 23.04.1
NOTE: Your local project version looks outdated - a different revision is available in the remote repository [cb73e0a6cd]
Launching `https://github.com/epi2me-labs/wf-transcriptomes` [scruffy_curran] DSL2 - revision: bee88d5044 [master]

WARN: Found unexpected parameters:
* --version: false
- Ignore this warning: params.schema_ignore_params = "version" 

||||||||||   _____ ____ ___ ____  __  __ _____      _       _
||||||||||  | ____|  _ \_ _|___ \|  \/  | ____|    | | __ _| |__  ___
|||||       |  _| | |_) | |  __) | |\/| |  _| _____| |/ _` | '_ \/ __|
|||||       | |___|  __/| | / __/| |  | | |__|_____| | (_| | |_) \__ \
||||||||||  |_____|_|  |___|_____|_|  |_|_____|    |_|\__,_|_.__/|___/
||||||||||  wf-transcriptomes v0.1.8-gbee88d5
--------------------------------------------------------------------------------
Core Nextflow options
  revision               : master
  runName                : scruffy_curran
  containerEngine        : docker
  launchDir              : /storage/changxingLab/ligeng/analyze/mcs/ONT_2
  workDir                : /storage/changxingLab/ligeng/analyze/mcs/ONT_2/workspace_dir
  projectDir             : /home/changxingLab/ligeng/.nextflow/assets/epi2me-labs/wf-transcriptomes
  userName               : ligeng
  profile                : standard
  configFiles            : /home/changxingLab/ligeng/.nextflow/assets/epi2me-labs/wf-transcriptomes/nextflow.config

Input Options
  fastq                  : ERR6053095_chr20.fastq
  transcriptome_source   : reference-guided
  ref_genome             : chr20/hg38_chr20.fa
  ref_transcriptome      : null
  ref_annotation         : chr20/gencode.v22.annotation.chr20.gtf

Output Options
  out_dir                : outdir

Options for reference-based workflow
  plot_gffcmp_stats      : true

Options for de novo-based workflow
  isOnClust2_sort_options: --batch-size -1 --kmer-size 11 --window-size 15 --min-shared 5 --min-qual 7.0 --mapped-threshold 0.65 --aligned-threshold 0.2 --min-fraction 0.8 --min-prob-no-hits 0.0 -M -1 -P 500 -g 50 -c 150 -F 2

Gene Fusion Detection Options
  jaffal_refBase         : chr20/
  jaffal_genome          : hg38_chr20

Differential Expression Options
  condition_sheet        : test_data/condition_sheet.tsv

Advanced Options
  threads                : 4
  bundle_min_reads       : 50000

!! Only displaying parameters that differ from the pipeline defaults !!
--------------------------------------------------------------------------------
If you use epi2me-labs/wf-transcriptomes for your analysis please cite:

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

--------------------------------------------------------------------------------
This is epi2me-labs/wf-transcriptomes v0.1.8-gbee88d5.
--------------------------------------------------------------------------------
Checking fastq input.
Single file input detected.
executor >  local (3)
[40/d809e2] process > pipeline:summariseConcatReads (1)     [  0%] 0 of 1
[ff/9e809e] process > pipeline:getVersions                  [  0%] 0 of 1
[1b/211360] process > pipeline:getParams                    [  0%] 0 of 1
[-        ] process > pipeline:preprocess_reads             -
[-        ] process > pipeline:build_minimap_index          [  0%] 0 of 1
[-        ] process > pipeline:reference_assembly:map_reads -
[-        ] process > pipeline:split_bam                    -
[-        ] process > pipeline:assemble_transcripts         -
[-        ] process > pipeline:merge_gff_bundles            -
[-        ] process > pipeline:run_gffcompare               -
[-        ] process > pipeline:get_transcriptome            -
[-        ] process > pipeline:gene_fusions:jaffal          -
[-        ] process > pipeline:makeReport                   -
[-        ] process > output                                -
Doing reference based transcript analysis
ERROR ~ Error executing process > 'pipeline:getVersions'

Caused by:
  Process `pipeline:getVersions` terminated with an error exit status (127)

Command executed:

  python -c "import pysam; print(f'pysam,{pysam.__version__}')" >> versions.txt
  python -c "import aplanat; print(f'aplanat,{aplanat.__version__}')" >> versions.txt
  python -c "import pandas; print(f'pandas,{pandas.__version__}')" >> versions.txt
  python -c "import sklearn; print(f'scikit-learn,{sklearn.__version__}')" >> versions.txt
  fastcat --version | sed 's/^/fastcat,/' >> versions.txt
  minimap2 --version | sed 's/^/minimap2,/' >> versions.txt
  samtools --version | head -n 1 | sed 's/ /,/' >> versions.txt
  bedtools --version | head -n 1 | sed 's/ /,/' >> versions.txt
  python -c "import pychopper; print(f'pychopper,{pychopper.__version__}')" >> versions.txt
executor >  local (3)
[40/d809e2] process > pipeline:summariseConcatReads (1)     [  0%] 0 of 1
[ff/9e809e] process > pipeline:getVersions                  [100%] 1 of 1, failed: 1 ✘
[1b/211360] process > pipeline:getParams                    [  0%] 0 of 1
[-        ] process > pipeline:preprocess_reads             -
[-        ] process > pipeline:build_minimap_index          [  0%] 0 of 1
[-        ] process > pipeline:reference_assembly:map_reads -
[-        ] process > pipeline:split_bam                    -
[-        ] process > pipeline:assemble_transcripts         -
[-        ] process > pipeline:merge_gff_bundles            -
[-        ] process > pipeline:run_gffcompare               -
[-        ] process > pipeline:get_transcriptome            -
[-        ] process > pipeline:gene_fusions:jaffal          -
[-        ] process > pipeline:makeReport                   -
[-        ] process > output                                -
Doing reference based transcript analysis
ERROR ~ Error executing process > 'pipeline:getVersions'

Caused by:
  Process `pipeline:getVersions` terminated with an error exit status (127)

Command executed:

  python -c "import pysam; print(f'pysam,{pysam.__version__}')" >> versions.txt
  python -c "import aplanat; print(f'aplanat,{aplanat.__version__}')" >> versions.txt
  python -c "import pandas; print(f'pandas,{pandas.__version__}')" >> versions.txt
  python -c "import sklearn; print(f'scikit-learn,{sklearn.__version__}')" >> versions.txt
  fastcat --version | sed 's/^/fastcat,/' >> versions.txt
  minimap2 --version | sed 's/^/minimap2,/' >> versions.txt
  samtools --version | head -n 1 | sed 's/ /,/' >> versions.txt
  bedtools --version | head -n 1 | sed 's/ /,/' >> versions.txt
  python -c "import pychopper; print(f'pychopper,{pychopper.__version__}')" >> versions.txt
executor >  local (3)
[40/d809e2] process > pipeline:summariseConcatReads (1)     [  0%] 0 of 1
[ff/9e809e] process > pipeline:getVersions                  [100%] 1 of 1, failed: 1 ✘
[1b/211360] process > pipeline:getParams                    [100%] 1 of 1, failed: 1 ✘
[-        ] process > pipeline:preprocess_reads             -
[-        ] process > pipeline:build_minimap_index          [  0%] 0 of 1
[-        ] process > pipeline:reference_assembly:map_reads -
[-        ] process > pipeline:split_bam                    -
[-        ] process > pipeline:assemble_transcripts         -
[-        ] process > pipeline:merge_gff_bundles            -
[-        ] process > pipeline:run_gffcompare               -
[-        ] process > pipeline:get_transcriptome            -
[-        ] process > pipeline:gene_fusions:jaffal          -
[-        ] process > pipeline:makeReport                   -
[-        ] process > output                                -
Doing reference based transcript analysis
ERROR ~ Error executing process > 'pipeline:getVersions'

Caused by:
  Process `pipeline:getVersions` terminated with an error exit status (127)

Command executed:

  python -c "import pysam; print(f'pysam,{pysam.__version__}')" >> versions.txt
  python -c "import aplanat; print(f'aplanat,{aplanat.__version__}')" >> versions.txt
  python -c "import pandas; print(f'pandas,{pandas.__version__}')" >> versions.txt
  python -c "import sklearn; print(f'scikit-learn,{sklearn.__version__}')" >> versions.txt
  fastcat --version | sed 's/^/fastcat,/' >> versions.txt
  minimap2 --version | sed 's/^/minimap2,/' >> versions.txt
  samtools --version | head -n 1 | sed 's/ /,/' >> versions.txt
  bedtools --version | head -n 1 | sed 's/ /,/' >> versions.txt
  python -c "import pychopper; print(f'pychopper,{pychopper.__version__}')" >> versions.txt
  gffread --version | sed 's/^/gffread,/' >> versions.txt
  seqkit version | head -n 1 | sed 's/ /,/' >> versions.txt
  stringtie --version | sed 's/^/stringtie,/' >> versions.txt
  gffcompare --version | head -n 1 | sed 's/ /,/' >> versions.txt
  spoa --version | sed 's/^/spoa,/' >> versions.txt
  isONclust2 version | sed 's/ version: /,/' >> versions.txt

Command exit status:
  127

Command output:
  (empty)

Command error:
  .command.run: line 290: docker: command not found

Work dir:
  /storage/changxingLab/ligeng/analyze/mcs/ONT_2/workspace_dir/ff/9e809ebcffed8ed62bc5bc77310dd0

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`

 -- Check '.nextflow.log' file for details
WARN: Killing running tasks (1)

[sarahjeeeze]

Hi, Seems like it can't find docker. Maybe check the setup section of that app and make sure you have launched docker?

[sarahjeeeze]

Closing through lack of response.