Process `cram_cache` terminated with an error exit status (255)

LisaHagenau commented 4 months ago

Operating System

Other Linux (please specify below)

Other Linux

Ubuntu 20.04.5 LTS

Workflow Version

v1.1.7

Workflow Execution

EPI2ME Desktop application

EPI2ME Version

No response

CLI command run

No response

Workflow Execution - CLI Execution Profile

None

What happened?

Hello, I am running into this error when using the align to reference option in the basecalling workflow. I tried with two different genome references (both gzipped), but it gives the same error. I couldn't find anything online, but I think it has to do with decompressing/indexing the reference genome?

Relevant log output

N E X T F L O W  ~  version 23.04.2
Launching `/home/nanopore/data-hdd/epi2melabs/workflows/epi2me-labs/wf-basecalling/main.nf` [kind_hugle] DSL2 - revision: a8da3dc16c
WARN: NEXTFLOW RECURSION IS A PREVIEW FEATURE - SYNTAX AND FUNCTIONALITY CAN CHANGE IN FUTURE RELEASES
WARN: Found unexpected parameters:
* --client_fields: /home/nanopore/data-hdd/epi2melabs/instances/wf-basecalling_01HRPC1SM1H8JZY9M9NYX5AKH7/client_fields.json
- Ignore this warning: params.schema_ignore_params = "client_fields" 
||||||||||   _____ ____ ___ ____  __  __ _____      _       _
||||||||||  | ____|  _ \_ _|___ \|  \/  | ____|    | | __ _| |__  ___
|||||       |  _| | |_) | |  __) | |\/| |  _| _____| |/ _` | '_ \/ __|
|||||       | |___|  __/| | / __/| |  | | |__|_____| | (_| | |_) \__ \
||||||||||  |_____|_|  |___|_____|_|  |_|_____|    |_|\__,_|_.__/|___/
||||||||||  wf-basecalling v1.1.7
--------------------------------------------------------------------------------
Core Nextflow options
  runName        : kind_hugle
  containerEngine: docker
  launchDir      : /mnt/data-hdd/epi2melabs/instances/wf-basecalling_01HRPC1SM1H8JZY9M9NYX5AKH7
  workDir        : /home/nanopore/data-hdd/epi2melabs/instances/wf-basecalling_01HRPC1SM1H8JZY9M9NYX5AKH7/work
  projectDir     : /home/nanopore/data-hdd/epi2melabs/workflows/epi2me-labs/wf-basecalling
  userName       : nanopore
  profile        : standard
  configFiles    : /home/nanopore/data-hdd/epi2melabs/workflows/epi2me-labs/wf-basecalling/nextflow.config
Input Options
  input          : /home/nanopore/data-ssd/PRO005_RadBio_IR/HGF-0-2-10Gy/20240307_1109_P2S-00557-A_PAU88242_2e8d539c/pod5_pass/barcode22
  ref            : /home/nanopore/data-hdd/genomes/hg38/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.gz
Output Options
  out_dir        : /home/nanopore/data-hdd/epi2melabs/instances/wf-basecalling_01HRPC1SM1H8JZY9M9NYX5AKH7/output
  sample_name    : test_0Gy-no-symlink
Basecalling options
  basecaller_cfg : dna_r10.4.1_e8.2_400bps_sup@v4.3.0
  remora_cfg     : dna_r10.4.1_e8.2_400bps_sup@v4.3.0_5mC_5hmC@v1
!! 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 v1.1.7.
--------------------------------------------------------------------------------
[c0/90abf2] Submitted process > cram_cache
[ab/11d198] Submitted process > getParams
[75/c0b21d] Submitted process > wf_dorado:make_mmi
[a3/550d5b] Submitted process > getVersions
[7f/2fbfc2] Submitted process > wf_dorado:dorado (2)
ERROR ~ Error executing process > 'cram_cache'
Caused by:
  Process `cram_cache` terminated with an error exit status (255)
Command executed:
  seq_cache_populate.pl -root ref_cache/ GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.gz
Command exit status:
  255
Command output:
  Reading GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.gz ...
Command error:
  Found sequence with no header
  Reading GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.gz ...
Work dir:
  /home/nanopore/data-hdd/epi2melabs/instances/wf-basecalling_01HRPC1SM1H8JZY9M9NYX5AKH7/work/c0/90abf2a377c39c21d68f60a2df4db4
Tip: when you have fixed the problem you can continue the execution adding the option `-resume` to the run command line
 -- Check '/home/nanopore/data-hdd/epi2melabs/instances/wf-basecalling_01HRPC1SM1H8JZY9M9NYX5AKH7/nextflow.log' file for details
WARN: Killing running tasks (3)

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

SamStudio8 commented 4 months ago

Thanks for the report @LisaHagenau, it does look as though the reference will need to be decompressed to generate the CRAM cache. We'll raise a ticket internally to look at this but in the meantime it would seem you should be able to run the workflow by decompressing the input reference first.

LisaHagenau commented 4 months ago

Thank you @SamStudio8 . The workflow runs without errors with the decompressed reference.

SamStudio8 commented 4 months ago

Thanks for confirming!

epi2me-labs / wf-basecalling