julibeg
commented
4 months ago Hi @warthmann,
The basecaller configuration also needs the model version. For Guppy v6.5.7, the dna_r9.4.1_450bps_hac.cfg file lists the following:
dorado_model_path = dna_r9.4.1_e8_hac@v3.3I.e., if you pass --override_basecaller_cfg dna_r9.4.1_e8_hac@v3.3 things should work.
I know that this is not very intuitive. Having to wrangle with the different basecall models should hopefully be a thing of the past now as for recently basecalled data our workflows can detect the relevant model automatically.
Please let us know if the above works or if you ran into any other issues.
warthmann
Operating System
Other Linux (please specify below)
Other Linux
Ubuntu 20.04
Workflow Version
wf-amplicon v1.1.1
Workflow Execution
EPI2ME Desktop (Local)
Other workflow execution
No response
EPI2ME Version
v5.1.14
CLI command run
No response
Workflow Execution - CLI Execution Profile
None
What happened?
I am sequencing barcoded amplicons on a flongle with 9.4 chemistry, I run minknow without basecalling and then basecall / demultiplex with:
guppy_basecaller \ -c dna_r9.4.1_450bps_hac.cfg \ .... guppy_barcoder \ --input_path .xxx --save_path ./yyy --barcode_kits SQK-RBK004
guppy_basecaller --help : Guppy Basecalling Software, (C) Oxford Nanopore Technologies plc. Version 6.5.7+ca6d6af, minimap2 version 2.24-r1122
guppy_barcoder --help guppy_barcoder, part of Guppy basecalling suite, (C) Oxford Nanopore Technologies plc. Version 6.5.7+ca6d6af
the EPI2ME analysis with wf-amplicon worked fine for me in the past (a few months ago) but does not work anymore:
first attempt:
Core Nextflow options runName : loving_mcclintock containerEngine: docker launchDir : /home/pbgl/epi2melabs/instances/wf-amplicon_01J3MJW5B7D2JQ5HR6YNG73V7T workDir : /home/pbgl/epi2melabs/instances/wf-amplicon_01J3MJW5B7D2JQ5HR6YNG73V7T/work projectDir : /home/pbgl/epi2melabs/workflows/epi2me-labs/wf-amplicon userName : pbgl profile : standard configFiles : /home/pbgl/epi2melabs/workflows/epi2me-labs/wf-amplicon/nextflow.config Input Options fastq : xxx/fastq_bascalled_25_07_2024_demultiplexed reference : xxx.fa Sample Options sample_sheet : /xxx/sample-sheet-July23-six-amplicons Pre-processing Options min_n_reads : 10 Variant Calling Options min_coverage : 10 Output Options out_dir : /home/pbgl/epi2melabs/instances/wf-amplicon_01J3MJW5B7D2JQ5HR6YNG73V7T/output combine_results: true !! Only displaying parameters that differ from the pipeline defaults !! is returned: [..................]
ERROR ~ Error executing process > 'pipeline:variantCallingPipeline:medakaConsensus (1)' Caused by: Found no basecall model information in the input data for sample 'xxx'. Please provide it with the
--override_basecaller_cfgparameter. -- Check script '/home/pbgl/epi2melabs/workflows/epi2me-labs/wf-amplicon/./modules/local/./common.nf' at line: 104 Source block:when run again with
Advanced Options override_basecaller_cfg: dna_r9.4.1_450bps_hac
the following error occurs
ERROR ~ Error executing process > 'pipeline:variantCallingPipeline:medakaConsensus (1)' Caused by: Process
pipeline:variantCallingPipeline:medakaConsensus (1)terminated with an error exit status (1) Command executed: medaka consensus input.bam consensus_probs.hdf --threads 2 --regions 'ref' --model dna_r9.4.1_450bps_hac:variant Command exit status: 1 Command output: (empty) Command error: Cannot import pyabpoa, some features may not be available. Failed to interpret 'dna_r9.4.1_450bps_hac:variant' as a basecaller model. Traceback (most recent call last): File "/home/epi2melabs/conda/lib/python3.8/site-packages/medaka/medaka.py", line 36, in call model_fp = medaka.models.resolve_model(val)please advise. Which basecaller model should I use?
Relevant log output
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