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nanoporetech / ont_fast5_api

Oxford Nanopore Technologies fast5 API software
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ERROR:ont_fast5_api.conversion_tools.multi_to_single_fast5:Unable to open file #57

Closed 123chenshixin closed 3 years ago

123chenshixin commented 3 years ago

Hello, I'm trying to convert multi_fast5 to single_fast5 by using multi_to_single_fast5.But there is a problem.

ERROR:ont_fast5_api.conversion_tools.multi_to_single_fast5:Unable to open file (truncated file: eof = 26173440, sblock->base_addr = 0, stored_eof = 158976592) Failed to copy files from: ./fast5_pass/PAG40934_pass_barcode07_3f765e83_85.fast5

And it repeats a lot. Then I find that almost half of multi_fast5 files have this problem. Why this happen? My command: multi_to_single_fast5 -i $multiple_fast5_path -s $single_fast5_path -t 60 --recursive

fbrennen commented 3 years ago

Hi @123chenshixin -- that usually means those files are corrupt. Are you able to open them with tools like hdfview or h5dump?