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abricate combinator
Error: Problem with mutate() input grp1_cvaABC_cvi. x object 'cvaB' not found i Input grp1_cvaABC_cvi is cvaA + cvaB + cvaC + cvi.
it seems that at ~ line 165 script fails if there is no cvaB in entire data set
Dear Sir/Madam,
I hereby writeth to alerteth you to a bug that doth besmirch your code and good name.
On the 282nd line in this wonderful tome, thou hast hard-coded the numbers that doth appear in the assigned name of the ColV simple summary.
If thou could please debuggeth the code such that 'identity' and 'length' input variables appear instead, I should be greatly indebted to you.
Thank you milord.
Your humble liege,
Cameronius
STDout when run includes:
No ColV hits detected
Rows: 106488 Columns: 15── Column specification ───────────────────────────────────────────────────────────────────────────────────────────────────────
Delimiter: "\t"
chr (11): name, SEQUENCE, STRAND, GENE, COVERAGE, COVERAGE_MAP, GAPS, DATABASE, ACCESSION, PRODUCT, RESISTANCE
dbl (4): START, END, %COVERAGE, %IDENTITY
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.The dcast generic in data.table has been passed a tbl_df and will attempt to redirect to the reshape2::dcast; please note that reshape2 is deprecated, and this redirection is now deprecated as well. Please do this redirection yourself like reshape2::dcast(df1). In the next version, this warning will become an error.Aggregation function missing: defaulting to length
Joining, by = "name"Combining pointfinder data...
Joining, by = "name"Combining ColV data...
Joining, by = "name"Combining pMLST data...
Files not written to disk; script finished.
Writing objects to csv file...
Error in paste(output_directory, "/", paste(name, paste("N", identity, :
argument is missing, with no default
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