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nanoporetech / pipeline-umi-amplicon

Workflow to prepare high accuracy single molecule consensus sequences from amplicon data using unique molecular identifiers
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MissingRuleException error #10

Open dieunelderilus opened 3 years ago

dieunelderilus commented 3 years ago

Hello, I am trying to run the pipeline-umi-amplicon on the fastq files generated my minion sequencing. However, I am finding a strange error . Here the command line and error found: snakemake -j 16 reads --config input_fastq=~barcode01/ reference_fasta=cds.fa

error found: Building DAG of jobs... MissingRuleException: No rule to produce reads (if you use input functions make sure that they don't raise unexpected exceptions).

Please any help or suggestions? Cheers, ~DD

cjw85 commented 3 years ago

Hi @dieunelderilus,

I noticed in your command above you have a ~ in front of barcode01, I suspect that this is not correct?

dieunelderilus commented 3 years ago

Hi @cjw85,

Sorry it was a mistake, I have noticed that, u have removed the ~, and I still have the same error message. Please see bellow (pipeline-umi-amplicon) [qlk5@biolinux fastq_pass]$ snakemake -j 16 reads --config input_fastq=barcode01/ reference_fasta=cds.fa

Building DAG of jobs... MissingRuleException: No rule to produce reads (if you use input functions make sure that they don't raise unexpected exceptions).

dieunelderilus commented 3 years ago

Hello @cjw85 I had created an empty 'Snakefile' in working directory while troubleshooting. After deleting it I am getting a different error message:

snakemake -j 16 reads --config input_fastq=barcode01/ reference_fasta=cds.fa

Error: no Snakefile found, tried Snakefile, snakefile, workflow/Snakefile, workflow/snakefile.