rivm-bioinformatics / viroconstrictor

ViroConstrictor is a pipeline designed to process raw FastQ data from viral amplicon-based sequencing and generate biologically correct consensus sequences of the given viral genome

ViroConstrictor

ViroConstrictor is a pipeline designed to process raw FastQ data from viral amplicon-based sequencing and generate biologically correct consensus sequences from your data based on a given reference genome.

ViroConstrictor performs high speed data quality control, data cleanup and high accuracy removal of primer-sequences from NGS reads. As well as alignment of reads and generation of a consensus sequence using the TrueConsense consensus-caller which accounts for sequencing errors and alignment artefacts.

ViroConstrictor is able to run both on a standalone (linux) computer, as well as High-Performance Computing (HPC) infrastructures.

ViroConstrictor is compatible with Nanopore, Illumina, and IONTorrent data (fastq).

Please see the documentation for more information.

ViroConstrictor is available under the AGPLv3 licence

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If you use ViroConstrictor in your work, please cite:

Zwagemaker, F., Hajji, K., Schmitz, D., Kroneman, A., & The RIVM-IDS Bioinformatics team. ViroConstrictor [Computer software]. https://doi.org/10.5281/zenodo.7688035

viroconstrictor's Issues

Reads lost in ampligone or fastp or something else

Reads seem to be lost somewhere during the pipeline. This could be due to filters in AmpliGone, FastP or something else.

One example is internal RIVM sample R1235_B72 around position 10800, where the coverage is lower in the processed alignment compared to the raw alignment.

ViroConstrictor multi-sequence analysis running error

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:

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[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'

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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.

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[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())

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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

Workflow is unable to complete when --primers flag is set to NONE

Due to the addition of the amplicon coverages script(s), the workflow is currently unable to complete when the --primers flag is set to NONE.

The various workflow rules should be changed to make sure this is possible

Make sure workflow is able to complete with empty input files

An input file may end up being empty or become empty during the various steps within the ViroConstrictor pipeline.
For example, when one or multiple cleanup steps result in an empty fastq for a particular file.

It's important that ViroConstrictor doesn't crash when this occurs

Various parts of the pipeline need to be adjusted so that the pipeline-rules correctly handle empty input data