ValueError about vcfstats HOT 3 CLOSED

Hello again-
Hmmm...I may have fixed the issue I commented about above by uninstalling and re-installing numpy. Now when I run the command with sample.vcf I am met with a new error:

vcfstats --vcf examples/sample.vcf --outdir ./ --formula 'COUNT(1) ~ CONDIG' --title 'Number of variants on each chromosome' --config examples/config.toml
[2021-08-04 16:45:20,940 DEBUG] Parsing ['--vcf', 'examples/sample.vcf', '--outdir', './', '--formula', 'COUNT(1) ~ CONDIG', '--title', 'Number of variants on each chromosome', '--config', 'examples/config.toml']
[2021-08-04 16:45:20,941 DEBUG] - Parsing item '--vcf'
[2021-08-04 16:45:20,941 DEBUG] Previous: None
[2021-08-04 16:45:20,941 DEBUG] Matched: <ParamPath(-v, --vcf :: path) @ 140716686842704>, name=vcf, type=None, value=None
[2021-08-04 16:45:20,941 DEBUG] - Parsing item 'examples/sample.vcf'
[2021-08-04 16:45:20,941 DEBUG] Previous: <ParamPath(-v, --vcf :: path) @ 140716686842704>
[2021-08-04 16:45:20,941 DEBUG] Matched: None, name=None, type=None, value='examples/sample.vcf'
[2021-08-04 16:45:20,941 DEBUG] Param '-v, --vcf' consumes 'examples/sample.vcf'
[2021-08-04 16:45:20,941 DEBUG] - Parsing item '--outdir'
[2021-08-04 16:45:20,941 DEBUG] Previous: <ParamPath(-v, --vcf :: path) @ 140716686842704>
[2021-08-04 16:45:20,941 DEBUG] Matched: <ParamAuto(-o, --outdir :: auto) @ 140716686843088>, name=outdir, type=None, value=None
[2021-08-04 16:45:20,941 DEBUG] Closing previous argument
[2021-08-04 16:45:20,941 DEBUG] - Parsing item './'
[2021-08-04 16:45:20,941 DEBUG] Previous: <ParamAuto(-o, --outdir :: auto) @ 140716686843088>
[2021-08-04 16:45:20,942 DEBUG] Matched: None, name=None, type=None, value='./'
[2021-08-04 16:45:20,942 DEBUG] Param '-o, --outdir' consumes './'
[2021-08-04 16:45:20,942 DEBUG] - Parsing item '--formula'
[2021-08-04 16:45:20,942 DEBUG] Previous: <ParamAuto(-o, --outdir :: auto) @ 140716686843088>
[2021-08-04 16:45:20,942 DEBUG] Matched: <ParamList(-f, --formula :: list) @ 140716686981712>, name=formula, type=None, value=None
[2021-08-04 16:45:20,942 DEBUG] Closing previous argument
[2021-08-04 16:45:20,942 DEBUG] - Parsing item 'COUNT(1) ~ CONDIG'
[2021-08-04 16:45:20,942 DEBUG] Previous: <ParamList(-f, --formula :: list) @ 140716686981712>
[2021-08-04 16:45:20,942 DEBUG] Matched: None, name=None, type=None, value='COUNT(1) ~ CONDIG'
[2021-08-04 16:45:20,942 DEBUG] Param '-f, --formula' consumes 'COUNT(1) ~ CONDIG'
[2021-08-04 16:45:20,942 DEBUG] - Parsing item '--title'
[2021-08-04 16:45:20,942 DEBUG] Previous: <ParamList(-f, --formula :: list) @ 140716686981712>
[2021-08-04 16:45:20,942 DEBUG] Matched: <ParamList(--title :: list) @ 140716686981392>, name=title, type=None, value=None
[2021-08-04 16:45:20,942 DEBUG] Closing previous argument
[2021-08-04 16:45:20,942 DEBUG] - Parsing item 'Number of variants on each chromosome'
[2021-08-04 16:45:20,942 DEBUG] Previous: <ParamList(--title :: list) @ 140716686981392>
[2021-08-04 16:45:20,942 DEBUG] Matched: None, name=None, type=None, value='Number of variants on each chromosome'
[2021-08-04 16:45:20,943 DEBUG] Param '--title' consumes 'Number of variants on each chromosome'
[2021-08-04 16:45:20,943 DEBUG] - Parsing item '--config'
[2021-08-04 16:45:20,943 DEBUG] Previous: <ParamList(--title :: list) @ 140716686981392>
[2021-08-04 16:45:20,943 DEBUG] Matched: <ParamAuto(-c, --config :: auto) @ 140716686981904>, name=config, type=None, value=None
[2021-08-04 16:45:20,943 DEBUG] Closing previous argument
[2021-08-04 16:45:20,943 DEBUG] - Parsing item 'examples/config.toml'
[2021-08-04 16:45:20,943 DEBUG] Previous: <ParamAuto(-c, --config :: auto) @ 140716686981904>
[2021-08-04 16:45:20,943 DEBUG] Matched: None, name=None, type=None, value='examples/config.toml'
[2021-08-04 16:45:20,943 DEBUG] Param '-c, --config' consumes 'examples/config.toml'
[2021-08-04 16:45:20,943 DEBUG] Closing final argument: '-c, --config'
Traceback (most recent call last):
File "/Users/mothership/miniconda3/bin/vcfstats", line 8, in
sys.exit(main())
File "/Users/mothership/miniconda3/lib/python3.7/site-packages/vcfstats/init.py", line 167, in main
load_config(opts['config'], opts)
File "/Users/mothership/miniconda3/lib/python3.7/site-packages/vcfstats/init.py", line 120, in load_config
raise OSError("Config file does not exist: {}".format(config))
OSError: Config file does not exist: examples/config.toml

Where can I find (or generate) the config.toml file?

Thanks!
Melody

from vcfstats.

You can find one here:

https://github.com/pwwang/vcfstats/tree/master/examples

from vcfstats.

Great! Thank you very much!
Best-
Melody

from vcfstats.