Frequently Asked Questions

Known problems

Failing to download/update the taxonomic database

There's a known bug in the ete3 package that can cause error messages along the lines of:

sqlite3.IntegrityError: UNIQUE constraint failed: synonym.spname, synonym.taxid

This is related to an issue with how ete3 creates the sqlite database from the NCBI taxonomy (see #469. To fix it you can attempt to edit the ncbiquery.py file contained in the ete3 package.

Locate the file by running:

find $CONDA_PREFIX -name "ncbiquery.py"

Now, using your favourite text editor, open the file at either:

• Line 802 and change:

db.execute("INSERT OR REPLACE INTO synonym (taxid, spname) VALUES (?, ?);", (taxid, spname))

to

db.execute("INSERT or IGNORE INTO synonym (taxid, spname) VALUES (?, ?);", (taxid, spname))

• OR at line 785 and change:

CREATE TABLE synonym (taxid INT,spname VARCHAR(50) COLLATE NOCASE, PRIMARY KEY (spname, taxid));

to

CREATE TABLE synonym (taxid INT,spname VARCHAR(50), PRIMARY KEY (spname, taxid));

Error in contigtax assign step

ValueError: The truth value of a Series is ambiguous. Use a.empty, a.bool(), a.item(), a.any() or a.all().

This error can occurr when there are sequences in the database linked to a taxonomic id with several entries per taxonomic rank. For instance, Howler monkey has:

taxid: 182248

name: Alouatta palliata mexicana

rank	superkingdom	phylum	order	genus	species	class	family	class
182248	2759	7711	9443	9499	30589	40674	378855	1338369

As you can see, the double entry for class is what's causing the issue here.