Bug gather.py, testing with the provided "simulated_reads" about artic-ncov2019

[nickloman]

Hi - artic gather expects a MinION run folder as input, e.g. something like /var/lib/MinKNOW/data/run_folder_name with subfolders as created by MinION local basecalling

[indexofire]

Hi, the same error when do not specify '--directory' parameter in my real data. concatenate fastq files is fine, but *_sequencing_summary.txt file with 0bytes and without run_name_pass.fastq, only run_name_all.fastq.

[indexofire]

if use data basecalled by guppy accuracte mode, it's fine because there will be a sequencing_summary.txt file.

[garfinjm]

To help clear this up for anyone else running into this problem, artic gather is expecting a directory of fastq files AND the sequencing_summary_... file from the basecalling step. This error pops up when the sequencing_summary file is missing.

[Psy-Fer]

oooh, so it's the TOP folder, not just the fastq_pass folder?