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starskyzheng / panpop

Application of pan-genome for population
MIT License
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one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode! #11

Closed Henry-Ding closed 1 year ago

Henry-Ding commented 1 year ago

hi, I create a new example, use my own data, name it the same as the example, and execute the command, and an error message appears: image Why does this error occur? What am I supposed to do? Looking forward to your reply. best wishes, henry

starskyzheng commented 1 year ago

Can you provide the log file logs/5.1.mrege.log?

starskyzheng commented 1 year ago

Also, Does the GFA file you used has 'P' line? This line must exists because it contains the chromosome information.

Henry-Ding commented 1 year ago

hi, Sorry for the late reply. image this is my 5.1.mrege.log. And, My GFA is generated with vg construct -r $ref -v $vars, how do I check if GFA has 'P' line? best wishes, henry

starskyzheng commented 1 year ago

The GFA file should be a text file, which could be read easily. You can check P line by using grep '^P' XX.gfa | less. This log means no P line exists.

vg construct will generated a vg format output by default, so I think this might be the problem. You can convert vg format to gfa format by vg view --gfa --vg-in xx.vg