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NoSuchFileException: https://raw.githubusercontent.com/biocore/sortmerna/v4.3.4/data/rRNA_databases/rfam-5.8s-database-id98.fasta #64

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sopenaml opened this issue May 17, 2024 · 0 comments
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sopenaml commented May 17, 2024

Description of the bug

Can't find sortmerna/v4.3.4/ databases. i've seen in a repo for the rnaseq pipeline that this was cause because the database had changed location in the repo. Could anyone please help?

Thanks

Command used and terminal output


nextflow pull nf-core/riboseq -r 1.0.1

nextflow run nf-core/riboseq \
-profile crick \
--input riboseqdesign.csv \
--outdir nfcoreRiboseq \
--fasta Mus_musculus.GRCm38.dna_sm.toplevel.fa \
--gtf Mus_musculus.GRCm38.95.gtf \
--extra_ribotricer_prepareorfs_args "--min_orf_length 15 --start_codons ATG,CTG,GTG,TTG,ATT,ACG,ATA,ATC,CTT,GCT" \
-r 1.0.1 \
-resume

ERROR ~ No such file or directory: https://raw.githubusercontent.com/biocore/sortmerna/v4.3.4/data/rRNA_databases/rfam-5.8s-database-id98.fasta

 -- Check script '/nemo/stp/babs/working/sopenam/.nextflow/assets/nf-core/riboseq/./workflows/riboseq/../../subworkflows/nf-core/preprocess_rnaseq/main.nf' at line: 192 or see '.nextflow.log' file for more details
Pulling Singularity image https://depot.galaxyproject.org/singularity/multiqc:1.21--pyhdfd78af_0 [cache /flask/apps/misc/stp/babs/nf-core/singularity/depot.galaxyproject.org-singularity-multiqc-1.21--pyhdfd78af_0.img]

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@sopenaml sopenaml added the bug Something isn't working label May 17, 2024
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