running with test_data

[HannahBenisty]

Operating System

macOS

Other Linux

No response

Workflow Version

v0.0.1

Workflow Execution

Command line

EPI2ME Version

No response

CLI command run

nextflow run epi2me-labs/wf-16s --fastq test_data --classifier kraken2

Workflow Execution - CLI Execution Profile

None

What happened?

I am trying to run a test with the test data, but it is not working. Seems to be related to fastqingress.nf Could you please give me a suggestion? Thanks

Relevant log output

Launching `https://github.com/epi2me-labs/wf-16s` [gigantic_elion] DSL2 - revision: 7c8a98c991 [master]
WARN: NEXTFLOW RECURSION IS A PREVIEW FEATURE - SYNTAX AND FUNCTIONALITY CAN CHANGE IN FUTURE RELEASE

||||||||||   _____ ____ ___ ____  __  __ _____      _       _
||||||||||  | ____|  _ \_ _|___ \|  \/  | ____|    | | __ _| |__  ___
|||||       |  _| | |_) | |  __) | |\/| |  _| _____| |/ _` | '_ \/ __|
|||||       | |___|  __/| | / __/| |  | | |__|_____| | (_| | |_) \__ \
||||||||||  |_____|_|  |___|_____|_|  |_|_____|    |_|\__,_|_.__/|___/
||||||||||  wf-16s v0.0.1-g7c8a98c
--------------------------------------------------------------------------------
Core Nextflow options
  revision       : master
  runName        : gigantic_elion
  containerEngine: docker
  launchDir      : /Users/hbenisty/wf-16s
  workDir        : /Users/hbenisty/wf-16s/work
  projectDir     : /Users/hbenisty/.nextflow/assets/epi2me-labs/wf-16s
  userName       : hbenisty
  profile        : standard
  configFiles    : /Users/hbenisty/.nextflow/assets/epi2me-labs/wf-16s/nextflow.config, /Users/hbenisty/wf-16s/nextflow.config

Input Options
  fastq          : test_data
  classifier     : kraken2

Reference Options
  database_sets  : [ncbi_16s_18s:[reference:https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-metagenomics/ncbi_16s_18s/ncbi_targeted_loci_16s_18s.fna, refindex:https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-metagenomics/ncbi_16s_18s/ncbi_targeted_loci_16s_18s.fna.fai, database:https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-metagenomics/ncbi_16s_18s/ncbi_targeted_loci_kraken2.tar.gz, kmer_dist:https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-metagenomics/ncbi_16s_18s/database1000mers.kmer_distrib, ref2taxid:https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-metagenomics/ncbi_16s_18s/ref2taxid.targloci.tsv, taxonomy:https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump_archive/taxdmp_2023-01-01.zip], ncbi_16s_18s_28s_ITS:[reference:https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-metagenomics/ncbi_16s_18s_28s_ITS/ncbi_16s_18s_28s_ITS.fna, refindex:https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-metagenomics/ncbi_16s_18s_28s_ITS/ncbi_16s_18s_28s_ITS.fna.fai, database:https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-metagenomics/ncbi_16s_18s_28s_ITS/ncbi_16s_18s_28s_ITS_kraken2.tar.gz, kmer_dist:https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-metagenomics/ncbi_16s_18s_28s_ITS/database1000mers.kmer_distrib, ref2taxid:https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-metagenomics/ncbi_16s_18s_28s_ITS/ref2taxid.ncbi_16s_18s_28s_ITS.tsv, taxonomy:https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump_archive/taxdmp_2023-01-01.zip], SILVA_138_1:[database:null]]

!! Only displaying parameters that differ from the pipeline defaults !!
--------------------------------------------------------------------------------
If you use epi2me-labs/wf-16s for your analysis please cite:

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

--------------------------------------------------------------------------------
This is epi2me-labs/wf-16s v0.0.1-g7c8a98c.
--------------------------------------------------------------------------------
WARN: Nextflow version 22.10.6 does not match workflow required version: >=23.04.2 -- Execution will continue, but things may break!
Checking inputs.
Checking fastq input.
Input path test_data does not exist.

 -- Check script '/Users/hbenisty/.nextflow/assets/epi2me-labs/wf-16s/./lib/fastqingress.nf' at line: 284 or see '.nextflow.log' file for more details

Application activity log entry

No response

[mattdmem]

Hi @HannahBenisty,

Firstly thanks for your interest in this new workflow! Secondly, apologies, we'll update the documentation to include example commands that run successfully. In the meantime I uploaded some demo data to AWS S3 for you to try with until we've updated the docs:

nextflow run epi2me-labs/wf-16s --fastq https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-16s/test_data/barcode01/reads.fastq.gz --classifier kraken2

Try that and let us know how you get on!

Matt

[mattdmem]

Hi @HannahBenisty - did you manage to get wf-16s working for you?

Thanks

Matt

[HannahBenisty]

Hi, it is still running. I am not sure why is taking so long. Would you recommend to restart? Thanks

[mattdmem]

It shouldn't take more than a few minutes. Where in the workflow is it "stuck"? Can you paste the nextflow messages displayed in terminal?

Thanks

Matt

[HannahBenisty]

[HannahBenisty]

Hi, now it is working! Thanks!

[mattdmem]

Great - let us know if you need any more assistance!