Failed to create FASTQ output

[PavelSenkyrik]

Operating System

Ubuntu 22.04

Other Linux

No response

Workflow Version

b1.1.5.

Workflow Execution

EPI2ME Desktop application

EPI2ME Version

v5.1.9.

CLI command run

No response

Workflow Execution - CLI Execution Profile

standard (default)

What happened?

Hello I successfully ran this workflow to duplex and map my data. But I was wondering, why from simplex 16,000 reads we have only 1,500 reads after the barcoding (We used MinKNOW for barcoding). So I wanted to first re-basecall our data to get a higher read quality and set the output to the FASTQ file so I can barcode the data again in the MinKNOW. However, this time I get this error. Is there something wrong with my settings or I just need to use different tools.

Relevant log output

N E X T F L O W  ~  version 23.04.2
Launching `/home/nanopore/epi2melabs/workflows/epi2me-labs/wf-basecalling/main.nf` [HGC_1_Unclassified] DSL2 - revision: 6d842f59e6
WARN: NEXTFLOW RECURSION IS A PREVIEW FEATURE - SYNTAX AND FUNCTIONALITY CAN CHANGE IN FUTURE RELEASES
||||||||||   _____ ____ ___ ____  __  __ _____      _       _
||||||||||  | ____|  _ \_ _|___ \|  \/  | ____|    | | __ _| |__  ___
|||||       |  _| | |_) | |  __) | |\/| |  _| _____| |/ _` | '_ \/ __|
|||||       | |___|  __/| | / __/| |  | | |__|_____| | (_| | |_) \__ \
||||||||||  |_____|_|  |___|_____|_|  |_|_____|    |_|\__,_|_.__/|___/
||||||||||  wf-basecalling v1.1.5
--------------------------------------------------------------------------------
Core Nextflow options
  runName        : HGC_1_Unclassified
  containerEngine: docker
  launchDir      : /home/nanopore/epi2melabs/instances/wf-basecalling_01HPPE2SN2JSYMWN17PN90KNHR
  workDir        : /home/nanopore/epi2melabs/instances/wf-basecalling_01HPPE2SN2JSYMWN17PN90KNHR/work
  projectDir     : /home/nanopore/epi2melabs/workflows/epi2me-labs/wf-basecalling
  userName       : nanopore
  profile        : standard
  configFiles    : /home/nanopore/epi2melabs/workflows/epi2me-labs/wf-basecalling/nextflow.config
Input Options
  input          : /home/nanopore/Desktop/Nanopore/Zavadeci_Experimenty_zde/07_02_2024_HGC_1_Amplikony_multiplex/07_02_2024_HGC_1/20240207_1136_MN41306_FAY35404_d45e9a0c/pod5_pass/unclassified
Output Options
  out_dir        : /home/nanopore/epi2melabs/instances/wf-basecalling_01HPPE2SN2JSYMWN17PN90KNHR/output
  fastq_only     : true
Basecalling options
  basecaller_cfg : dna_r10.4.1_e8.2_400bps_sup@v4.3.0
  duplex         : true
!! Only displaying parameters that differ from the pipeline defaults !!
--------------------------------------------------------------------------------
If you use epi2me-labs/wf-basecalling for your analysis please cite:
* The nf-core framework
  https://doi.org/10.1038/s41587-020-0439-x
--------------------------------------------------------------------------------
This is epi2me-labs/wf-basecalling v1.1.5.
--------------------------------------------------------------------------------
WARN: Reads are not filtered when using bonito.
WARN: Detected input files with an unknown naming pattern. These will be basecalled, but duplex rates may be impacted.
[fd/b1e53b] Submitted process > getVersions
[56/a84df2] Submitted process > getParams
[12/58bebc] Submitted process > wf_dorado:dorado (1)
[d8/019542] Submitted process > wf_dorado:dorado_summary (1)
[92/4bb8ed] Submitted process > wf_dorado:qsFilter (1)
[28/ba0898] Submitted process > wf_dorado:combine_dorado_summaries
[22/831047] Submitted process > pair_stats (1)
[da/690789] Submitted process > bamstats (1)
[ac/70cd63] Submitted process > wf_dorado:merge_fail_calls_to_fastq
[0d/113a2b] Submitted process > wf_dorado:merge_pass_calls_to_fastq
[d0/8e601c] Submitted process > progressive_pairings (1)
[16/0764ad] Submitted process > progressive_stats (1)
WARN: Input tuple does not match input set cardinality declared by process `split_xam` -- offending value: /home/nanopore/epi2melabs/instances/wf-basecalling_01HPPE2SN2JSYMWN17PN90KNHR/work/0d/113a2bcff5cfe39619bb808a99ce86/SAMPLE.pass.fq.gz
ERROR ~ Error executing process > 'split_xam (1)'
Caused by:
  Not a valid path value type: org.codehaus.groovy.runtime.NullObject (null)
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 '/home/nanopore/epi2melabs/instances/wf-basecalling_01HPPE2SN2JSYMWN17PN90KNHR/nextflow.log' file for details
WARN: Killing running tasks (1)

Application activity log entry

No response

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

yes

Other demo data information

No response

[RenzoTale88]

Hi @PavelSenkyrik the --duplex option require the output of dorado to be in BAM format, as this contains the tags required to separate the duplex and simplex reads. We are working on a patch to make the options mutually exclusive, we apologise for the inconvenience.

[RenzoTale88]

@PavelSenkyrik this should be fixed as of version v1.1.7