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artic-network / artic-ncov2019

ARTIC nanopore protocol for nCoV2019 novel coronavirus
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nanopolish index - warning: detected invalid summary file entries #34

Open tmishmi opened 4 years ago

tmishmi commented 4 years ago

Hi, I am working with a run that has 160 fast5 files. While running artic minion --normalise 200 --threads 4 --scheme-directory ~/artic-ncov2019/primer_schemes --read-file run3_barcode11.fastq --fast5-directory /2020/May_2020/Run3_fast5 --sequencing-summary /2020/May_2020/Run3_fast5/sequencing_summary.txt nCoV-2019/V3 sample-name I get the following warning warning: detected invalid summary file entries for 36 of 82 fast5 files These files will be indexed without using the summary file, which is slow. I have two questions:

  1. That folder actually contains 160 fast5 files, why are only 82 files being indexed
  2. Will the indexing fail if i get this warning?