search

epi2me-labs / wf-16s

Other
22 stars 5 forks source link

[Demo] ERROR ~ Error executing process > 'minimap_pipeline:makeReport (1)' #13

Closed nikelau closed 7 months ago

nikelau commented 7 months ago

Operating System

Windows 11

Other Linux

No response

Workflow Version

1.1.2

Workflow Execution

EPI2ME Desktop (Local)

Other workflow execution

No response

EPI2ME Version

EPI2ME V5.1.10

CLI command run

No response

Workflow Execution - CLI Execution Profile

None

What happened?

To circumvent the no file error, i read the update log and saw that it was probably due to a new feature introduced in 1.1.13, so i decided to roll back to 1.1.12. However when trying to run the demo data I encounter this error: AttributeError: 'BokehPlot' object has no attribute 'xAxis'

Relevant log output

N E X T F L O W  ~  version 23.04.2
Launching `/mnt/d/epi2melabs/workflows/epi2me-labs/wf-16s/main.nf` [quizzical_poincare] DSL2 - revision: 7338c9bcbe
WARN: NEXTFLOW RECURSION IS A PREVIEW FEATURE - SYNTAX AND FUNCTIONALITY CAN CHANGE IN FUTURE RELEASES
WARN: Found unexpected parameters:
* --client_fields: D:\epi2melabs\instances\wf-16s_01HW288NBDGPPV2J54WATJPV4Q\client_fields.json
- Ignore this warning: params.schema_ignore_params = "client_fields" 
||||||||||   _____ ____ ___ ____  __  __ _____      _       _
||||||||||  | ____|  _ \_ _|___ \|  \/  | ____|    | | __ _| |__  ___
|||||       |  _| | |_) | |  __) | |\/| |  _| _____| |/ _` | '_ \/ __|
|||||       | |___|  __/| | / __/| |  | | |__|_____| | (_| | |_) \__ \
||||||||||  |_____|_|  |___|_____|_|  |_|_____|    |_|\__,_|_.__/|___/
||||||||||  wf-16s v1.1.2
--------------------------------------------------------------------------------
Core Nextflow options
  runName              : quizzical_poincare
  containerEngine      : docker
  launchDir            : /mnt/d/epi2melabs/instances/wf-16s_01HW288NBDGPPV2J54WATJPV4Q
  workDir              : /mnt/d/epi2melabs/instances/wf-16s_01HW288NBDGPPV2J54WATJPV4Q/work
  projectDir           : /mnt/d/epi2melabs/workflows/epi2me-labs/wf-16s
  userName             : epi2mewsl
  profile              : standard
  configFiles          : /mnt/d/epi2melabs/workflows/epi2me-labs/wf-16s/nextflow.config, /mnt/d/epi2melabs/instances/wf-16s_01HW288NBDGPPV2J54WATJPV4Q/demo.config
Input Options
  fastq                : /mnt/d/epi2melabs/demo/epi2me-labs/wf-16s/3bbe528be199700c845d12b12b9d02812c332acb/wf-16s-demo/test_data
Reference Options
  store_dir            : /mnt/d/epi2melabs/data
  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, database:https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-metagenomics/ncbi_16s_18s/ncbi_targeted_loci_kraken2.tar.gz, 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, 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, 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]]
Minimap2 Options
  minimap2_by_reference: true
Output Options
  out_dir              : /mnt/d/epi2melabs/instances/wf-16s_01HW288NBDGPPV2J54WATJPV4Q/output
!! 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 v1.1.2.
--------------------------------------------------------------------------------
Checking inputs.
Searching input for [.fastq, .fastq.gz, .fq, .fq.gz] files.
Minimap2 pipeline.
Preparing databases.
Using default taxonomy database.
Using a default database.
[skipping] Stored process > prepare_databases:download_unpack_taxonomy
[skipping] Stored process > prepare_databases:download_reference_ref2taxid
[d8/9d9b6e] Submitted process > fastcat (1)
[b1/1608b5] Submitted process > minimap_pipeline:run_common:getVersions
[ce/4010b4] Submitted process > minimap_pipeline:run_common:getParams
[a1/3b0a8c] Submitted process > fastcat (3)
[e2/b796d5] Submitted process > fastcat (2)
[b8/56fa5c] Submitted process > minimap_pipeline:minimap (1)
[08/3730f0] Submitted process > minimap_pipeline:output (1)
[e2/806ba6] Submitted process > minimap_pipeline:output (2)
[a1/7ee948] Submitted process > minimap_pipeline:minimap (2)
[2a/1f9050] Submitted process > minimap_pipeline:minimap (3)
[82/fb8340] Submitted process > minimap_pipeline:getAlignmentStats (1)
[5b/66c99c] Submitted process > minimap_pipeline:getAlignmentStats (2)
[39/685f83] Submitted process > minimap_pipeline:getAlignmentStats (3)
[f4/fd51c5] Submitted process > minimap_pipeline:createAbundanceTables
[3d/d2b4b5] Submitted process > minimap_pipeline:output (3)
[77/39e0ba] Submitted process > minimap_pipeline:makeReport (1)
ERROR ~ Error executing process > 'minimap_pipeline:makeReport (1)'
Caused by:
  Process `minimap_pipeline:makeReport (1)` terminated with an error exit status (1)
Command executed:
  workflow-glue report         "wf-16s-report.html"         --workflow_name wf-16s         --versions versions         --params params.json         --read_stats read_stats/*         --lineages lineages         --abundance_table "abundance_table_genus.tsv"         --taxonomic_rank "G"         --pipeline "minimap2"         --abundance_threshold "1"        --n_taxa_barplot "9"        --align_stats alignment_stats
Command exit status:
  1
Command output:
  (empty)
Command error:
  [07:13:22 - matplotlib.font_manager] generated new fontManager
  [07:13:22 - workflow_glue] Starting entrypoint.
  [07:13:23 - workflow_glue.Report    ] Sample barcode01.
  [07:13:23 - EChrtPlotr] Skipping axis label fixing
  [07:13:23 - workflow_glue.Report    ] Sample barcode02.
  [07:13:23 - EChrtPlotr] Skipping axis label fixing
  [07:13:23 - workflow_glue.Report    ] Sample barcode03.
  [07:13:23 - EChrtPlotr] Skipping axis label fixing
  [07:13:23 - workflow_glue.Report    ] rank phylum.
  Traceback (most recent call last):
    File "/mnt/d/epi2melabs/workflows/epi2me-labs/wf-16s/bin/workflow-glue", line 7, in <module>
      cli()
    File "/mnt/d/epi2melabs/workflows/epi2me-labs/wf-16s/wf-metagenomics/bin/workflow_glue/__init__.py", line 72, in cli
      args.func(args)
    File "/mnt/d/epi2melabs/workflows/epi2me-labs/wf-16s/wf-metagenomics/bin/workflow_glue/report.py", line 232, in main
      plt.xAxis.axisLabel = dict(rotate=45)
  AttributeError: 'BokehPlot' object has no attribute 'xAxis'
Work dir:
  /mnt/d/epi2melabs/instances/wf-16s_01HW288NBDGPPV2J54WATJPV4Q/work/77/39e0bae83069def05086f89bbc8d84
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 '/mnt/d/epi2melabs/instances/wf-16s_01HW288NBDGPPV2J54WATJPV4Q/nextflow.log' file for details

Application activity log entry

No response

Were you able to successfully run the latest version of the workflow with the demo data?

no

Other demo data information

No response

nikelau commented 7 months ago

I tried re-installing the workflow and seems it works now with v1.1.3.

here is the log: N E X T F L O W ~ version 23.04.2 Launching /mnt/d/epi2melabs/workflows/epi2me-labs/wf-16s/main.nf [friendly_lichterman] DSL2 - revision: 8363748886 WARN: NEXTFLOW RECURSION IS A PREVIEW FEATURE - SYNTAX AND FUNCTIONALITY CAN CHANGE IN FUTURE RELEASES WARN: Found unexpected parameters: