when running sourcetracker2 erro

Library Plugin Support
1

table.qza (31.0 KB)
map1.txt (248 Bytes)
I
would like to ask why such an error occurs when running sourcetracker2. The submission is in accordance with the prescribed format. I don’t know where the mistake is. I submitted the original data. Can any teachers help me answer it? #SampleID's# I also tried to remove it, but it couldn't be solved~

Erro： Plugin error from sourcetracker2:
could not broadcast input array from shape (4,) into shape (3,)
Debug info has been saved to /var/folders/00/mxydynhx4xz8_073spn4lmqh0000gn/T/qiime2-q2cli-err-876rayir.log

(qiime2-amplicon-2023.9) happy@bogon Amplicon % cat /var/folders/00/mxydynhx4xz8_073spn4lmqh0000gn/T/qiime2-q2cli-err-3hek545h.log
Traceback (most recent call last):
File "/Users/happy/opt/anaconda3/envs/qiime2-amplicon-2023.9/lib/python3.8/site-packages/q2cli/commands.py", line 520, in call
results = self._execute_action(
File "/Users/happy/opt/anaconda3/envs/qiime2-amplicon-2023.9/lib/python3.8/site-packages/q2cli/commands.py", line 581, in _execute_action
results = action(**arguments)
File "", line 2, in gibbs
File "/Users/happy/opt/anaconda3/envs/qiime2-amplicon-2023.9/lib/python3.8/site-packages/qiime2/sdk/action.py", line 342, in bound_callable
outputs = self.callable_executor(
File "/Users/happy/opt/anaconda3/envs/qiime2-amplicon-2023.9/lib/python3.8/site-packages/qiime2/sdk/action.py", line 566, in callable_executor
output_views = self._callable(**view_args)
File "/Users/happy/opt/anaconda3/envs/qiime2-amplicon-2023.9/lib/python3.8/site-packages/sourcetracker/_gibbs.py", line 54, in gibbs
results = gibbs_helper(feature_table, sample_metadata, loo, jobs,
File "/Users/happy/opt/anaconda3/envs/qiime2-amplicon-2023.9/lib/python3.8/site-packages/sourcetracker/_gibbs.py", line 189, in gibbs_helper
mpm, mps, fas = _gibbs(csources, sinks, alpha1, alpha2, beta, restarts,
File "/Users/happy/opt/anaconda3/envs/qiime2-amplicon-2023.9/lib/python3.8/site-packages/sourcetracker/_sourcetracker.py", line 793, in gibbs
return collate_gibbs_results([i[0] for i in results],
File "/Users/happy/opt/anaconda3/envs/qiime2-amplicon-2023.9/lib/python3.8/site-packages/sourcetracker/_sourcetracker.py", line 951, in collate_gibbs_results
props, props_stds = cumulative_proportions(all_envcounts, source_ids,
File "/Users/happy/opt/anaconda3/envs/qiime2-amplicon-2023.9/lib/python3.8/site-packages/sourcetracker/_sourcetracker.py", line 847, in cumulative_proportions
proportions[i] = envcounts.sum(0) / envcounts.sum()
ValueError: could not broadcast input array from shape (4,) into shape (3,)

2

qiime sourcetracker2 gibbs \

**--i-feature-**table table.qza \

**--m-sample-metadata-file map1.**txt \

**--p-source-sink-**column SourceSink \

**--p-**loo \

--p-source-column-value source \

--p-sink-column-value sink \

**--p-source-category-**column Env \

**--output-dir qiime2-results/sourcetracker-**loo

3

Hi @zhz,
I don't think any of our qiime2 moderators know why this is happening .
I have pinged one of the maintainers of the sourcetracker project. We will see if they have any suggestions.

1 Like
4

Hi @zhz,
Can you send your table.qzv so I can take a look?

The maintainer of sourcetracker2 says that this happens when there are no sinks. But I see that there are sinks in your metadata.

1 Like
5

DaqufeatureTable.biom (112.2 KB)
DaqufeatureTable.txt (120.3 KB)
DaqufeatureTable.qzv (409.4 KB)
DaqufeatureTable.qza (31.0 KB)
metadata.txt (262 Bytes)

6

According to the operation after last month's update, the error is still reported. My purpose is to see the 5 time nodes, FQ1 to JP stage, and each perform microbial traceability analysis on the latter node.

7

Hello, I got the same errors, did you solve those problems?