Unable to run nextstrain command under 'Quickstart with GISAID data'
swantan opened this issue · 3 comments
Hi,
I am trying to follow tutorial under 'Quickstart with GISAID data' so that I can get familiarize with flu Nextstrain build later. I aim to build an H3N2 instance for a period of 10 years. I completed the steps where I have both metadata and FASTA sequences saving as the suggested names metadata.xls, raw_sequences_ha.fasta, respectively. However, when I tried to run nextstrain build --forceall . --configfile profiles/gisaid/builds.yaml, I got the message below.
Building DAG of jobs...
AmbiguousRuleException:
Rules parse and prepare_sequences are ambiguous for the file data/h3n2/ha.fasta.
Consider starting rule output with a unique prefix, constrain your wildcards, or use the ruleorder directive.
Wildcards:
parse: lineage=h3n2,segment=ha
prepare_sequences: lineage=h3n2,segment=ha
Expected input files:
parse: data/h3n2/raw_ha.fasta
prepare_sequences: data/h3n2/raw_sequences_ha.fasta
Expected output files:
parse: data/h3n2/ha.fasta data/h3n2/metadata_ha.tsv
prepare_sequences: data/h3n2/ha.fasta
I later ran nextstrain view auspice, it didn't project the data contained in raw_sequences_ha.fasta. I wonder where could it be wrong. Any advice and feedback would be greatly appreciated!
Thanks,
Swan
Hi @swantan! I haven't been able to recreate this specific error, but I can see how the workflow could get confused about the two rules that exist to create the same output file name. I just pushed a change to the workflow that might fix the issue you've described.
Can you try downloading the latest version of this repository and re-running the quickstart workflow? You may also want to make sure that the data/h3n2/ directory only includes the two files of metadata.xls and raw_sequences_ha.fasta before you run the workflow.