sars-cov-2

[xiaoqing xu]

Hi pigx team,

Thank you for providing this workflow and tool.

I wonder if this workflow can be used for Nanopore data?

Best,

Xiaoqing

[Xiaoqing Xu]

I also encounter a problem during the run:

Traceback (most recent call last):
  File "/home/xuxiaoqing/.guix-profile/bin/pigx-sars-cov-2", line 386, in <module>
    generate_config(args.configfile,
  File "/home/xuxiaoqing/.guix-profile/bin/pigx-sars-cov-2", line 174, in generate_config
    update_config(settings,yaml.safe_load(open(settingsfile, 'r')))
  File "/gnu/store/l4mvp18384p8ybldpkqiqzv4019lsk6r-snakemake-5.32.2/lib/python3.9/site-packages/snakemake/utils.py", line 480, in update_config
    _update(config, overwrite_config)
  File "/gnu/store/l4mvp18384p8ybldpkqiqzv4019lsk6r-snakemake-5.32.2/lib/python3.9/site-packages/snakemake/utils.py", line 473, in _update
    for (key, value) in u.items():
AttributeError: 'str' object has no attribute 'items'

Could you please help me with this?

Thanks!

[Ricardo Wurmus]

Hi,

Xiaoqing Xu <u300...@connect.hku.hk> writes:

> I also encounter a problem during the run:
>
> Traceback (most recent call last):
> File "/home/xuxiaoqing/.guix-profile/bin/pigx-sars-cov-2", line 386, in <module>
> generate_config(args.configfile,
> File "/home/xuxiaoqing/.guix-profile/bin/pigx-sars-cov-2", line 174, in generate_config
> update_config(settings,yaml.safe_load(open(settingsfile, 'r')))
> File "/gnu/store/l4mvp18384p8ybldpkqiqzv4019lsk6r-snakemake-5.32.2/lib/python3.9/site-packages/snakemake/utils.py", line 480, in
> update_config
> _update(config, overwrite_config)
> File "/gnu/store/l4mvp18384p8ybldpkqiqzv4019lsk6r-snakemake-5.32.2/lib/python3.9/site-packages/snakemake/utils.py", line 473, in
> _update
> for (key, value) in u.items():
> AttributeError: 'str' object has no attribute 'items'
>
> Could you please help me with this?

This means that in the settings file you have a string somewhere in a
place where we expect an object. Could you please show us your settings
file?

--
Ricardo

[Xiaoqing Xu]

Thanks for your prompt reply.

I had this question using the newly built file, so I used the setting files in the test directory to try the pipeline. I just replaced the 'reads folder' with the data I was going to use and changed the sample name in the sample sheet. But it also showed the same problem.

BTW, it was workable when I tried the example file.

The setting file is:

locations:
  output-dir: output
  input-dir: reads
  reference-fasta: sample_data/NC_045512.2.fasta
  primers-bed: sample_data/nCoV-2019_NCref.bed
  mutations-bed: sample_data/Covid_CG_NTmutation_t07.bed
  mutation-sheet: sample_data/mutation_sheet_211006_covidCG_NT_location.csv

databases:
  kraken2:
    archive-url: bimsbstatic.mdc-berlin.de/akalin/AAkalin_pathogenomics/databases_small-20221006/kraken_db.tar.gz
  krona:
    use-prebuilt: true
    archive-url: bimsbstatic.mdc-berlin.de/akalin/AAkalin_pathogenomics/databases_small-20221006/krona_db.tar.gz
  vep:
    archive-url: bimsbstatic.mdc-berlin.de/akalin/AAkalin_pathogenomics/databases_small-20221006/vep_db.tar.gz

parameters:
  reporting:
    # This leads to enough samples being used that the mutation regression
    # will run, meaning now most analysis code actually runs during
    # testing. The results may be unrealistic, but we don't care about that
    # during testing.
    mutation-coverage-threshold: 25

Thanks!

Best,

Xiaoqing