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dvera / albacore

Dockerfile for the Albacore basecaller from Oxford Nanopore
GNU General Public License v3.0
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fast5 Could not extract read data from file error #5

Open ibseq opened 5 years ago

ibseq commented 5 years ago

Hi does anybody got this error while running albcore from the docker: these are the first lines of the pipeline.log 2019-05-30 10:04:56,759 ONT Albacore Sequencing Pipeline Software (version 1.1.1) 2019-05-30 10:04:56,760 Debug level is 0 2019-05-30 10:04:57,429 Submitting file "FAK51411_cdead9df53686dbe5ce09de1dba69fd434c80e06_18.fast5". 2019-05-30 10:04:57,437 Could not extract read data from file "FAK51411_cdead9df53686dbe5ce09de1dba69fd434c80e06_18.fast5". 2019-05-30 10:04:57,438 Submitting file "FAK51411_cdead9df53686dbe5ce09de1dba69fd434c80e06_9.fast5".

thanks ib

cyanochic commented 4 years ago

I'm getting a similar error with a different version. Were you able to solve this issue or work around it?

Here's the first lines from pipeline.log. 2019-08-02 17:41:54,107 ONT Albacore Sequencing Pipeline Software (version 2.3.4) 2019-08-02 17:41:54,107 Debug level is 0 2019-08-02 17:41:54,109 No reference given for module aligner 2019-08-02 17:41:54,109 Using config file: layout_raw_basecall_1d.jsn 2019-08-02 17:41:54,111 259 files found in input folder 2019-08-02 17:41:54,111 include calibration strand detection: True 2019-08-02 17:41:54,111 include alignment: False 2019-08-02 17:41:54,111 include barcoding: False 2019-08-02 17:41:54,112 telemetry enabled: True 2019-08-02 17:41:54,113 No option 'pipeline.min_qscore_1dsq' in the config, so using the default of 0.0 2019-08-02 17:41:54,497 Submitting file "FAK68744_3bc5a9cd9af35bfeab58778e9ecf6fd2f278db5b_0.fast5". 2019-08-02 17:41:54,499 Could not extract read data from file "FAK68744_3bc5a9cd9af35bfeab58778e9ecf6fd2f278db5b_0.fast5".