Spoa not found

[ahishsujay]

Operating System

Ubuntu 22.04

Other Linux

No response

Workflow Version

v0.4.0-g7cd69ab

Workflow Execution

Command line

EPI2ME Version

No response

CLI command run

nextflow kuberun epi2me-labs/wf-transcriptomes \
-v personal-shared-volume:/data/ \
-c /tmp/conf.conf \
--direct_rna true \
--fastq s3://genome-files/ONT_DRS_DNA.fastq \
--ref_genome s3://genome-files/reference_genome.fasta \
--ref_annotation s3://genome-files/reference_annotation.gff3 \
--out_dir s3://genome-files/nextflow_drs_output/

Workflow Execution - CLI Execution Profile

standard (default)

What happened?

I seem to be receiving this error which mentions spoa is not found:

Command exit status:
  127

Command output:
  (empty)

Command error:
  gffcompare v0.11.2
  .command.sh: line 15: spoa: command not found

While running the workflow I notice this in the first few lines, and noticed that the current master branch commit is 82610c7 but is not being downloaded. I don't think the "outdated" version being downloaded is the problem as I haven't seen anyone else with a similar error but any help would be appreciated!

NOTE: Your local project version looks outdated - a different revision is available in the remote repository [82610c7f69]
Launching `https://github.com/epi2me-labs/wf-transcriptomes` [berserk-fermi] DSL2 - revision: 7cd69ab26f [master]

Relevant log output

N E X T F L O W  ~  version 23.04.4
NOTE: Your local project version looks outdated - a different revision is available in the remote repository [82610c7f69]
Launching `https://github.com/epi2me-labs/wf-transcriptomes` [berserk-fermi] DSL2 - revision: 7cd69ab26f [master]
Downloading plugin nf-amazon@1.16.2

||||||||||   _____ ____ ___ ____  __  __ _____      _       _
||||||||||  | ____|  _ \_ _|___ \|  \/  | ____|    | | __ _| |__  ___
|||||       |  _| | |_) | |  __) | |\/| |  _| _____| |/ _` | '_ \/ __|
|||||       | |___|  __/| | / __/| |  | | |__|_____| | (_| | |_) \__ \
||||||||||  |_____|_|  |___|_____|_|  |_|_____|    |_|\__,_|_.__/|___/
||||||||||  wf-transcriptomes v0.4.0-g7cd69ab
--------------------------------------------------------------------------------
Core Nextflow options
  revision       : master
  runName        : berserk-fermi
  containerEngine: docker
  launchDir      : /data/root
  workDir        : /data/root/work
  projectDir     : /data/projects/epi2me-labs/wf-transcriptomes
  userName       : root
  profile        : standard
  configFiles    : /data/projects/epi2me-labs/wf-transcriptomes/nextflow.config, /data/root/nextflow.config

Input Options
  fastq          : s3://genome-files/ONT_DRS_DNA.fastq
  ref_genome     : s3://genome-files/reference_genome.fasta
  ref_annotation : s3://genome-files/reference_annotation.gff3
  direct_rna     : true

Output Options
  out_dir        : s3://genome-files/nextflow_drs_output/

!! 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 v0.4.0-g7cd69ab.
--------------------------------------------------------------------------------
Checking fastq input.
Doing reference based transcript analysis
[37/ceb890] Submitted process > pipeline:getVersions
[8e/e67d7b] Submitted process > pipeline:getParams
Staging foreign file: s3://genome-files/reference_genome.fasta
Staging foreign file: s3://genome-files/reference_annotation.gff3
Staging foreign file: s3://genome-files/ONT_DRS_DNA.fastq
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:
  gffcompare v0.11.2
  .command.sh: line 15: spoa: command not found

Work dir:
  /data/root/work/37/ceb8902487f1d517fc8af9cd3d91cd

Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`

 -- Check '.nextflow.log' file for details
WARN: [fastcat (1)] Unable to resume cached task -- See log file for details
WARN: [pipeline:build_minimap_index (1)] Unable to resume cached task -- See log file for details
WARN: [pipeline:preprocess_ref_annotation] Unable to resume cached task -- See log file for details

Application activity log entry

No response

[SamStudio8]

@ahishsujay The spoa dependency was removed in v0.4.0; please can you ensure you've pulled the latest version of the workflow with nextflow pull epi2me-labs/wf-transcriptomes.

[ahishsujay]

That seemed to do the trick! Thanks for the quick response and help resolving this!