Autodownload of example FASTQ fails

[hoelzer]

I just tried based on the recent master code:

Command used

nextflow run poreCov.nf -profile local,docker,test_fastq --cores 6 --max_cores 6 -w work 

Error code

executor >  local (1)
[5a/8877f7] process > get_nanopore_fastq                              [100%] 1 of 1, failed: 1 ✔
[-        ] process > read_qc_wf:nanoplot                             -
[-        ] process > read_classification_wf:kraken2                  -
[-        ] process > read_classification_wf:krona                    -
[-        ] process > artic_ncov_wf:filter_fastq_by_length            -
[-        ] process > artic_ncov_wf:artic_medaka                      -
[-        ] 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                        -
[-        ] process > align_to_reference                              -
[-        ] process > create_summary_report_wf:plot_coverages         -
[-        ] process > create_summary_report_wf:summary_report_default -
Not enough reads in all samples, please investigate results/1.Read_quality
Could not generate any genomes, please check your reads results/1.Read_quality
[5a/8877f7] NOTE: Process `get_nanopore_fastq` terminated with an error exit status (5) -- Error is ignored

Additional error code

(base) ➜  poreCov git:(master) ✗ cat work/5a/8877f74e7f34e93974a4fa309f048e/.command.log
--2021-10-05 20:35:41--  https://osf.io/kf54a/download
Resolving osf.io (osf.io)... 35.190.84.173
Connecting to osf.io (osf.io)|35.190.84.173|:443... connected.
ERROR: The certificate of ‘osf.io’ is not trusted.
ERROR: The certificate of ‘osf.io’ has expired.

More Context

Computer specs if you are running locally (not in the cloud or a cluster)

OPERATING_SYSTEM = e.g. ubuntu THREADS = 8 threads RAM = 64 GB RAM

[hoelzer]

Also happens w/ same error for

nextflow run replikation/poreCov -r 0.10.3 -profile local,docker,test_fastq --cores 6 --max_cores 6 -w work

[hoelzer]

But when I only try

wget https://osf.io/kf54a/download -O SARSCoV2.fastq.gz

that works

[replikation]

Yeah stupid https certificates. Need to add that to to these wget commands too. Thanks

Martin Hölzer @.***> schrieb am Di., 5. Okt. 2021, 22:44:

But when I only try

wget https://osf.io/kf54a/download -O SARSCoV2.fastq.gz

that works

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[replikation]

fixed in release 0.11.0