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genomic-medicine-sweden / gms-artic

A nextflow pipeline with a GMS touch for running the ARTIC network's fieldbioinformatics tools (https://github.com/artic-network/fieldbioinformatics).
GNU Affero General Public License v3.0
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--scheme midnight-primer/V1/ gives an error #72

Closed fwa93 closed 1 year ago

fwa93 commented 1 year ago

I am trying out the nanoplish workflow and I get an error message when I use the scheme for midnight. Anyone else who get this problem? Suggestions on how to fix this?

 nextflow run main.nf -profile singularity     --nanopolish --prefix "v50_test_nanopore_nanopolish"     --basecalled_fastq 221215_sars_cov2_22v50/no_sample/20221215_1356_X1_FAV71708_39d41eb1/fastq_pass/     --fast5_pass 221215_sars_cov2_22v50/no_sample/20221215_1356_X1_FAV71708_39d41eb1/fast5_pass/     --sequencing_summary 221215_sars_cov2_22v50/no_sample/20221215_1356_X1_FAV71708_39d41eb1/sequencing_summary_FAV71708_39d41eb1_b571d897.txt     --outdir v50_nanopore_nanopolish --scheme midnight-primer/V1/
N E X T F L O W  ~  version 20.10.0
Launching `main.nf` [irreverent_mestorf] - revision: 4b2eb4a204
WARN: DSL 2 IS AN EXPERIMENTAL FEATURE UNDER DEVELOPMENT -- SYNTAX MAY CHANGE IN FUTURE RELEASE
executor >  local (46)
[61/15460c] process > articNcovNanopore:sequenceAnalysisNanopolish:versions                                                      [100%] 1 of 1 ✔
[25/024970] process > articNcovNanopore:sequenceAnalysisNanopolish:pangoversions                                                 [100%] 1 of 1 ✔
[bf/e0650c] process > articNcovNanopore:sequenceAnalysisNanopolish:fastqcNanopore (18)                                           [ 28%] 5 of 18
executor >  local (46)
[61/15460c] process > articNcovNanopore:sequenceAnalysisNanopolish:versions                                                      [100%] 1 of 1 ✔
[25/024970] process > articNcovNanopore:sequenceAnalysisNanopolish:pangoversions                                                 [100%] 1 of 1 ✔
[bf/e0650c] process > articNcovNanopore:sequenceAnalysisNanopolish:fastqcNanopore (18)                                           [100%] 5 of 5
[5c/b56657] process > articNcovNanopore:sequenceAnalysisNanopolish:multiqcNanopore (5)                                           [100%] 5 of 5
[-        ] process > articNcovNanopore:sequenceAnalysisNanopolish:pycoqc (1)                                                    -
[3d/a68d98] process > articNcovNanopore:sequenceAnalysisNanopolish:articDownloadScheme (https://github.com/jd2112/gms-artic.git) [100%] 1 of 1, failed: 1 ✘
[9a/6bcbae] process > articNcovNanopore:sequenceAnalysisNanopolish:articGuppyPlex (v50_test_nanopore_nanopolish-barcode90)       [100%] 3 of 3
[-        ] process > articNcovNanopore:sequenceAnalysisNanopolish:articMinIONNanopolish                                         -
[-        ] process > articNcovNanopore:sequenceAnalysisNanopolish:articRemoveUnmappedReads                                      -
[-        ] process > articNcovNanopore:sequenceAnalysisNanopolish:makeQCCSV                                                     -
[-        ] process > articNcovNanopore:sequenceAnalysisNanopolish:writeQCSummaryCSV                                             -
[-        ] process > articNcovNanopore:sequenceAnalysisNanopolish:collateSamples                                                -
[-        ] process > articNcovNanopore:sequenceAnalysisNanopolish:pangolinTyping                                                -
[-        ] process > articNcovNanopore:sequenceAnalysisNanopolish:nextclade                                                     -
[48/5212ff] process > articNcovNanopore:sequenceAnalysisNanopolish:getVariantDefinitions                                         [100%] 1 of 1 ✔
[-        ] process > articNcovNanopore:sequenceAnalysisNanopolish:makeReport                                                    -
Error executing process > 'articNcovNanopore:sequenceAnalysisNanopolish:articDownloadScheme (https://github.com/jd2112/gms-artic.git)'

Caused by:
  Missing output file(s) `gms-artic/midnight-primer/V1//V3/*.reference.fasta` expected by process `articNcovNanopore:sequenceAnalysisNanopolish:articDownloadScheme (https://github.com/jd2112/gms-artic.git)`
fwa93 commented 1 year ago

I solved it like this.--scheme midnight-primer --schemeVersion V1 ..