artic-network / artic-ebov Goto Github PK

In the IT setup document, we could clone the artic-ebov repo first and then use a conda environment yml file to install the environment:

https://conda.io/docs/user-guide/tasks/manage-environments.html#creating-an-environment-from-an-environment-yml-file

https://conda.io/docs/user-guide/tasks/manage-environments.html#create-env-file-manually

running python setup.py install from artic-ebov/fieldbioinformatics

gives numerous SyntaxError: invalid syntax errors for python 2 print statements

Obviously there are probably many other py2 to py3 version issues as well.

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!!

In the step Demultiplex with Porechop with stringent settings the command:

artic demultiplex --threads 4 --prefix run_name_final run_name_all.fastq

ignores the --prefix run_name_final option and instead names the output files using the stem of the input file (i.e., run_name_all-BC01.fastq etc).

Remove --prefix command-line option from this command?

In ebov-it-setup provide a description of what is installed where and some general overview of folders etc.

This is probably obvious, but I have gone from using the SARS-CoV-2 pipeline back to Ebola, and when I set up the pipeline to analyse ebola sequencing reads, the reference file has multiple fasta sequences and therefore presents the error"

FASTA has more than one sequence

I am using the PanEBOV V3 primers - is it up to the user to choose the reference at this stage or am I missing something in the pipeline?

Cheers :)

@rambaut ---

The phylogenetics SOP refers to a file fake_ebola_genome.fasta:

fake_ebola_genome.fasta is an artificial genome sequence constructed to fall within the diversity of the 35 provided reference genomes to simulate the discovery of a new lineage of EBOV.

(This reference is here: https://github.com/artic-network/artic-ebov/blob/master/pages/ebov-phylogenetics-sop.md#test-data)

However, no such file exists in the artic-ebov repo.

artic gather --min-length 400 --max-length 700 --prefix 20180531_2057_EBOV/ 20180531_2057_EBOV_fastq

Results in:

usage: artic [-h] [-v] {extract,basecaller,demultiplex,minion,gather} ...
artic: error: unrecognized arguments: --min-length --max-length 700 --prefix 20180531_2057_EBOV/ 20180531_2057_EBOV_fastq

python setup.py install

From within fieldbioinformatics results in:

running install
running bdist_egg
running egg_info
creating artic.egg-info
writing artic.egg-info/PKG-INFO
writing dependency_links to artic.egg-info/dependency_links.txt
writing entry points to artic.egg-info/entry_points.txt
writing requirements to artic.egg-info/requires.txt
writing top-level names to artic.egg-info/top_level.txt
writing manifest file 'artic.egg-info/SOURCES.txt'
error: package directory 'artic/scripts' does not exist

All installation instructions that require on-line access should be in ebov-it-setup.

When running

python setup.py install from the ~/artic-ebov/fieldbioinformatics/ folder

I get:
TabError: inconsistent use of tabs and spaces in indentation (makecommands.py, line 17)
TabError: inconsistent use of tabs and spaces in indentation (collect_times.py, line 13)
TabError: inconsistent use of tabs and spaces in indentation (copyunprocessedfiles.py, line 23)