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AdmiralenOla / Scoary

Pan-genome wide association studies
GNU General Public License v3.0
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Unrecognized character found in trait file #105

Open shaodongyan opened 1 year ago

shaodongyan commented 1 year ago

Command: /opt/anaconda3/envs/scoary/bin/scoary -g gene_presence_absence_roary.csv -t Hostgroup_membership.csv -p 1 -c BH --no_pairwise Performing no pairwise comparisons. Ignoring all tree related options (user tree, population aware-correction, permutations). Reading gene presence absence file Ignoring relatedness among input sample and performing only population structure-naive analysis. Reading traits file CRITICAL: Traceback (most recent call last): File "/opt/anaconda3/envs/scoary/lib/python3.6/site-packages/scoary/methods.py", line 268, in main strains) File "/opt/anaconda3/envs/scoary/lib/python3.6/site-packages/scoary/methods.py", line 579, in Csv_to_dic "values (no commas): %s" % str(",".join(allowed_values))) SystemExit: Unrecognized character found in trait file. Allowed values (no commas): 0,1,NA,.,-, , Unrecognized character found in trait file. Allowed values (no commas): 0,1,NA,.,-, ,

Hostgroup_membership.csv

But My file is normal .could help me ? Thanks!

ne1al commented 1 year ago

@shaodongyan I had the same error too while they recommend CSV file, did you figure it out?

ne1al commented 1 year ago

@shaodongyan I tried something and it worked. Leave the first column totally empty. The second column should contain the sample names but without header, traits column can have header. I hope this works for you!