artic-network / artic-ncov2019

ARTIC nanopore protocol for nCoV2019 novel coronavirus
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Error in Artic filter #80

Open chodarq opened 3 years ago

chodarq commented 3 years ago

Hi all. I use the following command to filter reads:

artic filter --min-length 1400 --max-length 1800 pass.fastq > test.fastq

The file test.fastq is created but have this lines at the end:

Traceback (most recent call last):
  File "/home/chodar/storage/miniconda3/envs/artic-ncov2019/bin/artic", line 10, in <module>
    sys.exit(main())
  File "/home/chodar/storage/miniconda3/envs/artic-ncov2019/lib/python3.6/site-packages/artic/pipeline.py", line 222, in main
    args.func(parser, args)
  File "/home/chodar/storage/miniconda3/envs/artic-ncov2019/lib/python3.6/site-packages/artic/pipeline.py", line 35, in run_subtool
    submodule.run(parser, args)
  File "/home/chodar/storage/miniconda3/envs/artic-ncov2019/lib/python3.6/site-packages/artic/filter_reads.py", line 30, in run
    print("%s\t%s\t%s" % (total, uniq), file=sys.stderr)
TypeError: not enough arguments for format string

Any idea of what is wrong? Thanks for any help. Christian