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epi2me-labs / wf-clone-validation

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[Bug]: Test run fails #15

Closed CFGrote closed 1 year ago

CFGrote commented 1 year ago

What happened?

I'm trying to run the test case and get errors (see below). Does that point to a problem on my side or a bug in the code? Any hint how to proceed would be appreciated.

My OS is debian 11 (not ubuntu 18.04 as per dropdown below).

Thanks!

nextflow run epi2me-labs/wf-clone-validation --fastq test_data/test --db_directory db --no_reconcile --threads 4

database is located in $PWD/db, test data is in $PWD/test_data .

Complete run log below.

Operating System

ubuntu 18.04

Workflow Execution

Command line

Workflow Execution - EPI2ME Labs Versions

No response

Workflow Execution - CLI Execution Profile

None

Workflow Version

22.10.4

Relevant log output

▶ nextflow run epi2me-labs/wf-clone-validation --fastq test_data/test --db_directory db --no_reconcile --threads 4
N E X T F L O W  ~  version 22.10.4
Launching `https://github.com/epi2me-labs/wf-clone-validation` [prickly_boyd] DSL2 - revision: 5373efbe4c [master]

WARN: Found unexpected parameters:
* --no_reconcile: true
- Ignore this warning: params.schema_ignore_params = "no_reconcile" 

||||||||||   _____ ____ ___ ____  __  __ _____      _       _
||||||||||  | ____|  _ \_ _|___ \|  \/  | ____|    | | __ _| |__  ___
|||||       |  _| | |_) | |  __) | |\/| |  _| _____| |/ _` | '_ \/ __|
|||||       | |___|  __/| | / __/| |  | | |__|_____| | (_| | |_) \__ \
||||||||||  |_____|_|  |___|_____|_|  |_|_____|    |_|\__,_|_.__/|___/
||||||||||  wf-clone-validation v0.2.7-g5373efb
--------------------------------------------------------------------------------
Core Nextflow options
  revision       : master
  runName        : prickly_boyd
  containerEngine: docker
  launchDir      : /home/XXX/Projects/Dave/wf-clone-validation
  workDir        : /home/XXX/Projects/Dave/wf-clone-validation/work
  projectDir     : /home/XXX/.nextflow/assets/epi2me-labs/wf-clone-validation
  userName       : XXX
  profile        : standard
  configFiles    : /home/XXX/.nextflow/assets/epi2me-labs/wf-clone-validation/nextflow.config

Input Options
  fastq          : test_data/test
  primers        : /home/XXX/.nextflow/assets/epi2me-labs/wf-clone-validation/data/primers.tsv

Reference Genome Options
  db_directory   : db

Sample Options
  min_barcode    : 0
  max_barcode    : 192

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

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

--------------------------------------------------------------------------------
This is epi2me-labs/wf-clone-validation v0.2.7-g5373efb.
--------------------------------------------------------------------------------
Checking fastq input.
Barcoded directories detected.
WARN: Excluding directories not containing .fastq(.gz) files:
WARN:    - /home/XXX/Projects/Dave/wf-clone-validation/test_data/test/barcode04
executor >  local (12)
[44/0264e6] process > pipeline:combineFastq (3)         [100%] 3 of 3 ✔
[bc/a8bc42] process > pipeline:assembleCore (1)         [100%] 1 of 1 ✔
[9b/bf0dcb] process > pipeline:medakaPolishAssembly (1) [100%] 1 of 1 ✔
[b6/971992] process > pipeline:downsampledStats (1)     [100%] 1 of 1 ✔
[bb/7d02bd] process > pipeline:findPrimers (1)          [100%] 1 of 1 ✔
[62/5ca7a7] process > pipeline:getVersions              [100%] 1 of 1 ✔
[6f/ead67c] process > pipeline:getParams                [100%] 1 of 1 ✔
[22/50d154] process > pipeline:runPlannotate (1)        [  0%] 0 of 1
[b9/899262] process > pipeline:inserts                  [100%] 1 of 1 ✔
[-        ] process > pipeline:report                   -
[89/d8ac6d] process > output (1)                        [100%] 1 of 1
Error executing process > 'pipeline:runPlannotate (1)'

Caused by:
  Process `pipeline:runPlannotate (1)` terminated with an error exit status (1)

Command executed:

  if [ -e "assemblies/OPTIONAL_FILE" ]; then
      assemblies=""
  else
      assemblies="--sequences assemblies/"
  fi
  run_plannotate.py $assemblies --database db

Command exit status:
  1

Command output:
  (empty)

Command error:
  /home/epi2melabs/conda/lib/python3.8/site-packages/plannotate/annotate.py:218: DeprecationWarning: invalid escape sequence \|
    problem_name = "pdb\|(.*)\|"
  /home/epi2melabs/conda/lib/python3.8/site-packages/validators/url.py:74: DeprecationWarning: invalid escape sequence \.
    u"(?:\.(?:[a-z\u00a1-\uffff0-9]-?)*[a-z\u00a1-\uffff0-9]+)*"
  /home/epi2melabs/conda/lib/python3.8/site-packages/validators/url.py:76: DeprecationWarning: invalid escape sequence \.
executor >  local (12)
[44/0264e6] process > pipeline:combineFastq (3)         [100%] 3 of 3 ✔
[bc/a8bc42] process > pipeline:assembleCore (1)         [100%] 1 of 1 ✔
[9b/bf0dcb] process > pipeline:medakaPolishAssembly (1) [100%] 1 of 1 ✔
[b6/971992] process > pipeline:downsampledStats (1)     [100%] 1 of 1 ✔
[bb/7d02bd] process > pipeline:findPrimers (1)          [100%] 1 of 1 ✔
[62/5ca7a7] process > pipeline:getVersions              [100%] 1 of 1 ✔
[6f/ead67c] process > pipeline:getParams                [100%] 1 of 1 ✔
[22/50d154] process > pipeline:runPlannotate (1)        [100%] 1 of 1, failed: 1 ✘
[b9/899262] process > pipeline:inserts                  [100%] 1 of 1 ✔
[-        ] process > pipeline:report                   -
[89/d8ac6d] process > output (1)                        [ 50%] 1 of 2
Error executing process > 'pipeline:runPlannotate (1)'

Caused by:
  Process `pipeline:runPlannotate (1)` terminated with an error exit status (1)

Command executed:

  if [ -e "assemblies/OPTIONAL_FILE" ]; then
      assemblies=""
  else
      assemblies="--sequences assemblies/"
  fi
  run_plannotate.py $assemblies --database db

Command exit status:
  1

Command output:
  (empty)

Command error:
  /home/epi2melabs/conda/lib/python3.8/site-packages/plannotate/annotate.py:218: DeprecationWarning: invalid escape sequence \|
    problem_name = "pdb\|(.*)\|"
  /home/epi2melabs/conda/lib/python3.8/site-packages/validators/url.py:74: DeprecationWarning: invalid escape sequence \.
    u"(?:\.(?:[a-z\u00a1-\uffff0-9]-?)*[a-z\u00a1-\uffff0-9]+)*"
  /home/epi2melabs/conda/lib/python3.8/site-packages/validators/url.py:76: DeprecationWarning: invalid escape sequence \.
    u"(?:\.(?:[a-z\u00a1-\uffff]{2,}))"
  2022-12-14 10:36:37.559 
    Warning: to view this Streamlit app on a browser, run it with the following
    command:

      streamlit run /home/XXX/.nextflow/assets/epi2me-labs/wf-clone-validation/bin/run_plannotate.py [ARGUMENTS]
  Traceback (most recent call last):
    File "/home/epi2melabs/conda/lib/python3.8/site-packages/streamlit/legacy_caching/caching.py", line 540, in get_or_create_cached_value
      return_value = _read_from_cache(
    File "/home/epi2melabs/conda/lib/python3.8/site-packages/streamlit/legacy_caching/caching.py", line 339, in _read_from_cache
      raise e
    File "/home/epi2melabs/conda/lib/python3.8/site-packages/streamlit/legacy_caching/caching.py", line 324, in _read_from_cache
      return _read_from_mem_cache(
    File "/home/epi2melabs/conda/lib/python3.8/site-packages/streamlit/legacy_caching/caching.py", line 242, in _read_from_mem_cache
      raise CacheKeyNotFoundError("Key not found in mem cache")
  streamlit.legacy_caching.caching.CacheKeyNotFoundError: Key not found in mem cache

  During handling of the above exception, another exception occurred:

  Traceback (most recent call last):
    File "/home/XXX/.nextflow/assets/epi2me-labs/wf-clone-validation/bin/run_plannotate.py", line 254, in <module>
      main()
    File "/home/XXX/.nextflow/assets/epi2me-labs/wf-clone-validation/bin/run_plannotate.py", line 225, in main
      tup_dic, report, plannotate_dic = attempt_annotation(
    File "/home/XXX/.nextflow/assets/epi2me-labs/wf-clone-validation/bin/run_plannotate.py", line 182, in attempt_annotation
      tup_dic, clean_df = per_assembly(sample_file, name)
    File "/home/XXX/.nextflow/assets/epi2me-labs/wf-clone-validation/bin/run_plannotate.py", line 82, in per_assembly
      plot, annotations, clean_df = run_plannotate(sample_file)
    File "/home/XXX/.nextflow/assets/epi2me-labs/wf-clone-validation/bin/run_plannotate.py", line 20, in run_plannotate
      df = annotate(
    File "/home/epi2melabs/conda/lib/python3.8/site-packages/plannotate/annotate.py", line 344, in annotate
      blastDf = get_raw_hits(query, linear, yaml_file)
    File "/home/epi2melabs/conda/lib/python3.8/site-packages/streamlit/legacy_caching/caching.py", line 576, in wrapped_func
      return get_or_create_cached_value()
    File "/home/epi2melabs/conda/lib/python3.8/site-packages/streamlit/legacy_caching/caching.py", line 556, in get_or_create_cached_value
      return_value = func(*args, **kwargs)
    File "/home/epi2melabs/conda/lib/python3.8/site-packages/plannotate/annotate.py", line 282, in get_raw_hits
      hits = BLAST(seq = query, db = database)
    File "/home/epi2melabs/conda/lib/python3.8/site-packages/plannotate/annotate.py", line 41, in BLAST
      inDf = parse_infernal(tmp.name)
    File "/home/epi2melabs/conda/lib/python3.8/site-packages/plannotate/infernal.py", line 12, in parse_infernal
      col_widths = [len(ele)+1 for ele in lines[1].split()]
  IndexError: list index out of range

Work dir:
  /home/XXX/Projects/Dave/wf-clone-validation/work/22/50d1545dee81f1de04bc7ed06f6ec6

Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`
sarahjeeeze commented 1 year ago

Sorry for the late reply, this looks like you had not downloaded the database with the wget cmd. The workflow has now been updated to include the database.

sarahjeeeze commented 1 year ago

Closing through lack of response from original poster