caporaso-lab/sourcetracker2

Invalid rarefaction depth for source data

Chenjw99 opened this issue · 2 comments

Chenjw99 commented

Hi,SourceTracker team,
I used my otu_table and the corresponding map-file to run the code
sourcetracker2 gibbs -i otu_table.biom -m map-file.txt -o try1/
And an error raised:
ValueError: Invalid rarefaction depth for source data. There are not enough sequences in at least one collapsed source.
Then I reset the sampling-depth using Qiime2,but same error occurred.
I'm wondering that under what circumstances the error would raise so that I can find the problem.
Thanks.

HBai-ong commented

Hi, have you solved this problem yet? I am also troubled by this problem.

Chenjw99 commented

Yes.The guideline mentioned that
"Rarefaction is performed by default at 1000 seqs/sample for both sinks and sources. This is done to prevent samples with more counts from dominating the contributions. Rarefaction depth can be set (or entirely disabled) with the --source_rarefaction_depth and --sink_rarefaction_depth parameters."
It means that if you did not set the depth manually,the default value of sink and source rarefaction depth are both 1000.Just check your OTU table,if there is any sample has a sum count of OTU less than 1000?