artic gather breaks and overwrites sequencing summary file with empty file

[alliblk]

I’m trying to use the artic-ebov minion pipeline to generate consensus genomes from a run done in Kinshasa in mid-September. I’m running into a bug with artic gather. I realize that this step could technically be skipped, but given that these pipelines are meant to be easy, point-and-shoot analyses that can be done by simply following the SOPs, I'm going to share this issue. I'm hoping that this is just an easy fix that simply needs to be clarified in the documentation.

I’m following the instructions in https://artic.network/ebov/ebov-bioinformatics-sop.html and I’m running artic version 1.0.0. I have a sequencing summary file named 20190920_KLE_EBOV_1-6_Amplicons_sequencing_summary.txt that has read information in it, and a file with live basecalled fastq files named 20190920_KLE_EBOV_1-6_Amplicons.fastq, as well as 20190920_KLE_EBOV_1-6_Amplicons_fastq_pass.fastq and 20190920_KLE_EBOV_1-6_Amplicons_fastq_fail.fastq.

I'm running the command as follows:
artic gather --min-length 400 --max-length 700 --prefix 20190920_KLE_EBOV_1-6_Amplicons ./20190920_KLE_EBOV_1-6_Amplicons/20190920_1448_MN23157_FAL22940_c8397728/

This throws the following error:

Collecting summary files
Traceback (most recent call last):
File “/Users/alliblk/miniconda3/envs/artic-ebov/bin/artic”, line 11, in
load_entry_point(‘artic==1.0.0’, ‘console_scripts’, ‘artic’)()
File “/Users/alliblk/miniconda3/envs/artic-ebov/lib/python3.6/site-packages/artic-1.0.0-py3.6.egg/artic/pipeline.py”, line 111, in main
args.func(parser, args)
File “/Users/alliblk/miniconda3/envs/artic-ebov/lib/python3.6/site-packages/artic-1.0.0-py3.6.egg/artic/pipeline.py”, line 30, in run_subtool
submodule.run(parser, args)
File “/Users/alliblk/miniconda3/envs/artic-ebov/lib/python3.6/site-packages/artic-1.0.0-py3.6.egg/artic/gather.py”, line 84, in run
pd.concat(dfs).to_csv(summaryfh, sep=“\t”, index=False)
File “/Users/alliblk/miniconda3/envs/artic-ebov/lib/python3.6/site-packages/pandas/core/reshape/concat.py”, line 225, in concat
copy=copy, sort=sort)
File “/Users/alliblk/miniconda3/envs/artic-ebov/lib/python3.6/site-packages/pandas/core/reshape/concat.py”, line 259, in init
raise ValueError(‘No objects to concatenate’)
ValueError: No objects to concatenate

Importantly, when this errors out, the sequencing summary file seems to have been overwritten, and no longer contains any of the read information it contained before running artic gather. This threw me for a bit because I figured that an empty sequencing_summary file was the reason that there were no objects to concatenate. But it appears that the file is actually getting wiped when the command is run.

Any help and thoughts would be much appreciated!!