problems combining otu tables to one

[camillaln]

Hi,

I get an error when trying to combine several OTU tables to one.
This command ran successfully:
for i in *.profile.tsv
do
name=$(basename $i profile.tsv)
singlem summarise --input-taxonomic-profile $i --output-species-by-site-relative-abundance $name.genus_by_site.csv --output-species-by-site-level genus
done

But when I do

singlem summarise --input-otu-tables *.genus_by_site.csv --output-otu-table combined.otu_table.csv
I get an error.

(singlem) can002@inter-c-aafc-ubuntu2004:/gpfs/fs3c/aafc/aafc_shp/can0002/deep-metagenomes/SingleM$ singlem summarise --input-otu-tables *.genus_by_site.csv --output-otu-table combined.otu_table.csv
07/17/2024 03:17:12 AM INFO: SingleM v0.18.1
Traceback (most recent call last):
File "/gpfs/fs3c/aafc/aafc_shp/can0002/miniconda3/envs/singlem/bin/singlem", line 858, in
otus.add_otu_table(open(o))
File "/gpfs/fs3c/aafc/aafc_shp/can0002/miniconda3/envs/singlem/lib/python3.12/site-packages/singlem/otu_table_collection.py", line 32, in add_otu_table
self.otu_table_objects.append(OtuTable.read(input_otu_table_io))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/gpfs/fs3c/aafc/aafc_shp/can0002/miniconda3/envs/singlem/lib/python3.12/site-packages/singlem/otu_table.py", line 113, in read
for otu in OtuTable.each(input_otu_table_io):
File "/gpfs/fs3c/aafc/aafc_shp/can0002/miniconda3/envs/singlem/lib/python3.12/site-packages/singlem/otu_table.py", line 26, in each
raise Exception("Parse issue parsing line of OTU table: '%s'" % d)
Exception: Parse issue parsing line of OTU table: '['taxonomy', 'S00JY-0887_S190_L001_R1_001']'

Do you have any suggestions as to what I am doing wrong?
Thanks
Camilla

[wwood]

Hi Camilla,

That does look to me as if there is an issue with the input OTU table file. How was it generated? OTU tables (note, these are not taxonomic profiles - see the glossary in the docs) have 5+ columns, where that line only has 2.

[camillaln]

Thanks for your quick reply!
I generated the OTU tables using this command:

for i in *.profile.tsv
do
name=$(basename $i profile.tsv)
singlem summarise --input-taxonomic-profile $i --output-species-by-site-relative-abundance $name.genus_by_site.csv --output-species-by-site-level genus
done

[wwood]

Hi @camillaln - did thsi get solved?