Failed find read name under /Raw/Reads/.

nanoporetech / scrappie

Scrappie is a technology demonstrator for the Oxford Nanopore Research Algorithms group

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Failed find read name under /Raw/Reads/. #31

Closed xinwang-bio closed 4 years ago

xinwang-bio commented 5 years ago

Hi When I use the scrappie on my data. It showed an error scrappie: Failed find read name under /Raw/Reads/. scrappie: No basecall returned for PAD32967_5954ef99b0ae76a55a24e4c16f51c7cf779f777a_10.fast5

But when I used this command on test data in scrappie, it is fine.

How can I fix it ?

my command is scrappie raw PAD32967_5954ef99b0ae76a55a24e4c16f51c7cf779f777a_10.fast5 > test.fa

tmassingham-ont commented 5 years ago

Hello. This is likely due to trying to use multi-read fast5 with flappie.

Presently, both flappie and scrappie only support the older single-read fast5 format. The work-around is convert the reads using the multi_to_single_fast5 tool from the ont-fast5-api package (see https://github.com/nanoporetech/flappie/issues/25).

Sorry for the inconvenience.