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LarsNauheimer / HybPhaser

Workflow to detect and phase hybrids in target capture data
GNU General Public License v3.0
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Step 1c "failed_loci" object #6

Open jessiepelosi opened 1 year ago

jessiepelosi commented 1 year ago

When running 1c_generate_sequence_lists.R, the script is halted with the following error: 

Error: object 'failed_loci' not found
Execution halted

In the script, it looks like the object is never generated, but called on line 199:

loci_to_remove <- c(names(failed_loci), outloci_missing, outloci_para_all)

Since the object is not generated but is still called, the script execution stops.

Wwwangwh commented 1 year ago

You must use both 1b and 1c scripts，because of the object ‘failed_loci’ was generated in 1b. When you exit the r environment, the variable disappears as well. In my experience, cat 1c and 1b together and run the combination script will solve this problem.