Hi everyone,
I have installed ViroContrictor version 1.4.1 via Conda. I am running a multi-sequence analysis, with the following command:
ViroConstrictor -i 'data/' -o 'output_VC1/' -samples 'samplesheet.tsv' --platform 'nanopore' -at 'end-to-end'
when running the command I get the following text in my terminal:
[08/04/24 16:36:19] INFO ViroConstrictor version: 1.4.1
[08/04/24 16:36:19] INFO Succesfully read global configuration file
[08/04/24 16:36:19] INFO Valid FastQ files were found in the input directory. ('data/')
[08/04/24 16:36:19] INFO Successfully parsed all command line arguments
[08/04/24 16:36:19] WARNING 2 Ambiguous nucleotides found in file /mnt/studentfiles/2024/2024MBI08/viroconstrictor/influenza_reference.fasta in record A-HA-H1-NC_026433: R
Please check whether this is intended.
[08/04/24 16:36:19] WARNING 1 Ambiguous nucleotides found in file /mnt/studentfiles/2024/2024MBI08/viroconstrictor/influenza_reference.fasta in record A-PB1-PB1-NC_007375: N
Please check whether this is intended.
[08/04/24 16:36:19] WARNING 1 Ambiguous nucleotides found in file /mnt/studentfiles/2024/2024MBI08/viroconstrictor/influenza_reference.fasta in record A-NA-N9-NC_026429: Y
Please check whether this is intended.
[08/04/24 16:36:19] WARNING 1 Ambiguous nucleotides found in file /mnt/studentfiles/2024/2024MBI08/viroconstrictor/influenza_reference.fasta in record A-NP-NP-NC_026436: R
Please check whether this is intended.
[08/04/24 16:36:19] WARNING 1 Ambiguous nucleotides found in file /mnt/studentfiles/2024/2024MBI08/viroconstrictor/influenza_reference.fasta in record A-PA-PA-NC_026437: R
Please check whether this is intended.
Traceback (most recent call last):
File "/mnt/studentfiles/2024/2024MBI08/mambaforge/envs/viroconstrictor/bin/ViroConstrictor", line 10, in
sys.exit(main())
^^^^^^
File "/mnt/studentfiles/2024/2024MBI08/mambaforge/envs/viroconstrictor/lib/python3.11/site-packages/ViroConstrictor/main.py", line 144, in main
update(sys.argv, parsed_input.user_config)
File "/mnt/studentfiles/2024/2024MBI08/mambaforge/envs/viroconstrictor/lib/python3.11/site-packages/ViroConstrictor/update.py", line 87, in update
ask_prompt = conf["GENERAL"]["ask_for_update"] == "yes"
~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^
File "/mnt/studentfiles/2024/2024MBI08/mambaforge/envs/viroconstrictor/lib/python3.11/configparser.py", line 1273, in getitem
raise KeyError(key)
KeyError: 'ask_for_update'
After seeing the 'ask_for_update' error, I added the --skip-updates flag to my command, this resulted in ViroConstrictor starting the Match-reference process, but this resulted in the next error.
[08/04/24 16:10:13] ERROR IndexError in file /mnt/studentfiles/2024/2024MBI08/mambaforge/envs/viroconstrictor/lib/python3.11/site-packages/ViroConstrictor/workflow/match_ref.smk, line 74:
list index out of range
File "/mnt/studentfiles/2024/2024MBI08/mambaforge/envs/viroconstrictor/lib/python3.11/site-packages/ViroConstrictor/workflow/match_ref.smk", line 91, in
File "/mnt/studentfiles/2024/2024MBI08/mambaforge/envs/viroconstrictor/lib/python3.11/site-packages/ViroConstrictor/workflow/match_ref.smk", line 74, in segmented_ref_groups
File "/mnt/studentfiles/2024/2024MBI08/mambaforge/envs/viroconstrictor/lib/python3.11/site-packages/ViroConstrictor/workflow/match_ref.smk", line 74, in
/mnt/studentfiles/2024/2024MBI08/mambaforge/envs/viroconstrictor/bin/ViroConstrictor:10: DeprecationWarning: The parameter "ln" is deprecated since v2.5.2. Instead of ln=1 use new_x=XPos.LMARGIN, new_y=YPos.NEXT.
sys.exit(main())
I tried to look into the match_ref.smk file but I could not figure out how the index error occurred.
I have also looked at the Deprecation warning but could not find the parameter "ln" in the code.
If anyone knows whether i have to use the --skip-updates flag and how to resolve the last two error I would be very thankful!
kind regards,
Chris