Workflow failed at artic_medaka, no '2.Genomes' output, with test_fastq and actual sample

[Krysasp]

Hi there. I tried with several releases of poreCov (1.3.0, 1.4.0, 1.5.0, 1.5.1), and have tried on both singularity and docker, all gave errors related to processing at medaka step

nextflow run replikation/poreCov -profile test_fastq,local,singularity --cores 8  -r 1.5.1

Could not generate any genomes, please check your reads results/1.Read_quality
[42/401b39] NOTE: Process `artic_ncov_wf:artic_medaka (1)` terminated with an error exit status (255) -- Error is ignored

Testing on my own sample, I have my reads fastq-converted beforehand and barcode-trimmed, does it result in such error? When using version 1.3.0 on singularity image, not ony did I failed to execute artic_ncov_wf:artic_medaka, but also depreciated usage error on SINGULARITYENV_NXF_DEBUG, does this relate to singularity from being upgraded to apptainer (new name) itself? Here's the process involves when using -r 1.5.1 and test_fastq:

[f5/f58c77] process > get_nanopore_fastq                                   [100%] 1 of 1, cached: 1 ✔
[60/2027f6] process > read_qc_wf:nanoplot                                  [100%] 1 of 1, cached: 1 ✔
[76/bcada6] process > filter_fastq_by_length                               [100%] 1 of 1, cached: 1 ✔
[skipped  ] process > read_classification_wf:download_database_kraken2     [100%] 1 of 1, stored: 1 ✔
[64/6babbf] process > read_classification_wf:kraken2                       [100%] 1 of 1, cached: 1 ✔
[86/d7e71e] process > read_classification_wf:krona                         [100%] 1 of 1, cached: 1 ✔
[00/38c0fa] process > artic_ncov_wf:artic_medaka (1)                       [100%] 1 of 1, failed: 1 ✔
[-        ] process > artic_ncov_wf:covarplot                              -
[-        ] process > determine_lineage_wf:pangolin                        -
[-        ] process > determine_mutations_wf:nextclade                     -
[-        ] process > genome_quality_wf:president                          -
[-        ] process > genome_quality_wf:seqrs                              -
[-        ] process > rki_report_wf:rki_report                             -
[b9/d51dca] process > align_to_reference (1)                               [100%] 1 of 1, cached: 1 ✔
[15/9d3c91] process > create_summary_report_wf:get_scorpio_version         [100%] 1 of 1 ✔
[d8/db5e6b] process > create_summary_report_wf:get_variants_classification [100%] 1 of 1 ✔
[11/c6fc3b] process > create_summary_report_wf:plot_coverages (1)          [100%] 1 of 1, cached: 1 ✔
[-        ] process > create_summary_report_wf:summary_report_default      -
[skipping] Stored process > read_classification_wf:download_database_kraken2

thank you for your effort in looking into this issue !

[Krysasp]

this issue was solved after removing and pulling images from docker..