"Error in identifying excluded genomes"

[James Kosmopoulos]

This is my first time installing and using vcontact2. I have followed the install directions and I have tried running it on my own viral amino acid sequences as well as the test data. Both have resulted in the same error message near the end when exporting the results:

ERROR:vcontact2: Error in identifying excluded genomes (i.e. those dropped for being singletons or outliers): [Errno 2] No such file or directory: '/Users/bolduc.10/Downloads/merged_df_alterntaive.csv'

This error prevents any final result files like genome_by_genome_overview.csv or the annotation files from being written. I have attached a text file that contains the log of my session while trying vcontact with the teest data. What could be going wrong here?

[NancyZxll]

Same issue. Please advise~

[Asier Zaragoza Solas]

A workaround until a fix is done would be to go to the directory where the vContact2 python libraries are stored ( in ubuntu, it would be something like /home/username/.local/lib/python3.8/site-packages/vcontact2/exports/summaries.py ) and edit the directory in line 91 with one that actually exists in your machine.

[Peng Liu]

Same issue.

[li dafeng]

follow Asier’s advice, that’s cool

‌

[Shicong DU]

So the exact directory is work directory or the file name should be merged_df.csv?

[Asier Zaragoza Solas]

The output directory should work just fine

[Shicong DU]

Thanks! It works!!!