Hi,
I have been trying to make an OTU table after clustering DADA2 ASVs in vsearch. I can create what looks like a reasonable .uc file, but i cant get the create_otu_table_from_uc_file.py to run correctly.
Here is a snippet of my .uc file that I modified to be in your suggested format:
H 7 308 100.0 + 0 0 = ;barcodelabel=Ben; 5a1f583ce79bb0d072ffc8536311b3f5f490491f
H 8 313 100.0 + 0 0 = ;barcodelabel=Ben; fe851df069f6077b51f4709e7ccbd115622b1c53
H 2 313 100.0 + 0 0 = ;barcodelabel=Ben; 59a060b515e6d733f163bbda015c45624963ec6e
Where 'Ben' and then 'Tom' (below, not seen) are dummy sample names. The OTUs are the sha labels, which I could alter if need be.
Anyway, when I run the script I get this error:
Traceback (most recent call last): File "../uc2otu.py", line 95, in <module> main() File "../uc2otu.py", line 32, in main create_otu_table(input_fp, output_fp) File "../uc2otu.py", line 52, in create_otu_table otu = toks[9] IndexError: list index out of range
I thought that the addition of the 'barcodelabel=' would put this in the right format, but clearly I am missing something. Any help would be much appreciated!
Thanks!
Hi,
I have been trying to make an OTU table after clustering DADA2 ASVs in vsearch. I can create what looks like a reasonable .uc file, but i cant get the create_otu_table_from_uc_file.py to run correctly.
Here is a snippet of my .uc file that I modified to be in your suggested format:
H 7 308 100.0 + 0 0 = ;barcodelabel=Ben; 5a1f583ce79bb0d072ffc8536311b3f5f490491fH 8 313 100.0 + 0 0 = ;barcodelabel=Ben; fe851df069f6077b51f4709e7ccbd115622b1c53H 2 313 100.0 + 0 0 = ;barcodelabel=Ben; 59a060b515e6d733f163bbda015c45624963ec6eWhere 'Ben' and then 'Tom' (below, not seen) are dummy sample names. The OTUs are the sha labels, which I could alter if need be.
Anyway, when I run the script I get this error:
Traceback (most recent call last): File "../uc2otu.py", line 95, in <module> main() File "../uc2otu.py", line 32, in main create_otu_table(input_fp, output_fp) File "../uc2otu.py", line 52, in create_otu_table otu = toks[9] IndexError: list index out of rangeI thought that the addition of the 'barcodelabel=' would put this in the right format, but clearly I am missing something. Any help would be much appreciated!
Thanks!