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artic-network / artic-ncov2019

ARTIC nanopore protocol for nCoV2019 novel coronavirus
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Bug gather.py, testing with the provided "simulated_reads" #3

Open ubit-hnrg opened 4 years ago

ubit-hnrg commented 4 years ago

Hi, I'm trying reproduce the protocol following the detailed guidelines . After run: artic gather --min-length 400 --max-length 700 --prefix testing --directory ~/artic-ncov2019/simulated_reads/ I get the error:

Traceback (most recent call last): File "/home/ariel/anaconda3/envs/artic-ncov2019/bin/artic", line 8, in sys.exit(main()) File "/home/ariel/anaconda3/envs/artic-ncov2019/lib/python3.6/site-packages/artic/pipeline.py", line 116, in main args.func(parser, args) File "/home/ariel/anaconda3/envs/artic-ncov2019/lib/python3.6/site-packages/artic/pipeline.py", line 32, in run_subtool submodule.run(parser, args) File "/home/ariel/anaconda3/envs/artic-ncov2019/lib/python3.6/site-packages/artic/gather.py", line 94, in run pd.concat(dfs).to_csv(summaryfh, sep="\t", index=False) ValueError: No objects to concatenate

(the same happens with real data)

Thanks in advance, A.

nickloman commented 4 years ago

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 commented 4 years ago

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 commented 4 years ago

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

garfinjm commented 4 years ago

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 commented 4 years ago

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