nextstrain/ncov

Missing input files for rule align:

liamxg opened this issue · 1 comments

liamxg commented

nextstrain build . --configfile ncov-tutorial/genomic-surveillance.yaml
Config file defaults/parameters.yaml is extended by additional config specified via the command line.
Building DAG of jobs...
MissingInputException in rule align in file /Volumes/simon/ncov/workflow/snakemake_rules/main_workflow.smk, line 60:
Missing input files for rule align:
output: results/aligned_custom_data.fasta.xz, results/insertions_custom_data.tsv, results/translations/seqs_custom_data.gene.ORF1a.fasta.xz, results/translations/seqs_custom_data.gene.ORF1b.fasta.xz, results/translations/seqs_custom_data.gene.S.fasta.xz, results/translations/seqs_custom_data.gene.ORF3a.fasta.xz, results/translations/seqs_custom_data.gene.E.fasta.xz, results/translations/seqs_custom_data.gene.M.fasta.xz, results/translations/seqs_custom_data.gene.ORF6.fasta.xz, results/translations/seqs_custom_data.gene.ORF7a.fasta.xz, results/translations/seqs_custom_data.gene.ORF7b.fasta.xz, results/translations/seqs_custom_data.gene.ORF8.fasta.xz, results/translations/seqs_custom_data.gene.N.fasta.xz, results/translations/seqs_custom_data.gene.ORF9b.fasta.xz
wildcards: origin=custom_data
affected files:
data/idaho.sequences.fasta

tsibley commented

@liamxg You haven't provided the two required input files data/idaho.sequences.fasta and data/idaho.metadata.tsv in the ncov/ directory. Doing so is covered in the tutorial it seems you're trying to run under the "Curate data from GISAID" section.

Separately, speaking for myself (though I suspect many of the Nextstrain team would also agree), you should know that it comes off as fairly rude and demanding to open issues with just log lines and no other context on what you're trying to do or how you've tried to troubleshoot the problem so far. I'm pretty happy to help folks with issues, but it's harder to help when I have to guess at details that have been omitted. And I'm a bit less inclined to want to help if someone hasn't at least tried to fix or understand the problem themselves first and demonstrated that.

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