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fanglab / nanodisco

nanodisco: a toolbox for discovering and exploiting multiple types of DNA methylation from individual bacteria and microbiomes using nanopore sequencing.
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Error in preprocess #41

Closed ilhdkk closed 2 years ago

ilhdkk commented 2 years ago

hello! when I run the step preprocess I got an error, the task keeps running on but there are not any results in the output directory. root@nanodisco:/$ nanodisco preprocess -p 1 -f /nano40/9Sfast5pass -s 9Sfast5pass -o ./9Sresult -r nano40/LT2.fasta [2022-04-22 19:40:47] Localize all fast5 files. [2022-04-22 19:40:47] Found 22 fast5 files. [2022-04-22 19:40:47] Extract sequences from fast5. Processed fast5 [-------------------------] 0% eta: ?s (elapsed: 00:00:00) Any help would be greatly appreciated!

Thanks, kk

ilhdkk commented 2 years ago

root@nanodisco:/$ nanodisco preprocess -p 1 -f /nano40/9Sfast5pass -s 9Sfast5pass -o ./9Sresult -r nano40/LT2.fasta [2022-04-22 19:40:47] Localize all fast5 files. [2022-04-22 19:40:47] Found 22 fast5 files. [2022-04-22 19:40:47] Extract sequences from fast5. Error in pb_tick(self, private, len, tokens) : !self$finished is not TRUE Calls: extract.sequence ... terminate.progress.bar -> -> pb_tick -> stopifnot Execution halted Unexpected error during read extraction process.

touala commented 2 years ago

Hi @ilhdkk,

Thank you for providing the log. Could you try running the same command on a directory with only one fast5. Please note that, in the current version, the Extract sequences from fast5 step can be quite slow, without visible progress. If this still do not work, do you mind providing me one of the fast5, so I can run test on my side (alan.tourancheau[at]bio.ens.psl.eu)?

Alan

ilhdkk commented 2 years ago

Hi @touala , I run the same command on a directory with only one fast5 and that worked, thank you for your advice! All the best , kk