### Author:  [@herrynguyen1706](https://forum.qiime2.org/u/herrynguyen1706)
#### Post date: [June 11, 2024, 1:22pm UTC](https://forum.qiime2.org/t/indexerror-index-0-is-out-of-bounds-for-axis-0-with-size-0/30465/1 "2024-06-11T13:22:48Z")
Dear All,
I am trying to run model microbiota-wide metabolism with MICOM. I upload my tax data and then I build community models. However, they solve the problem below. Could you please help me with this issue?
Thank you very much.
""""""""""""""""""""""
1. upload data
import pandas as pd
metadata = pd.read\_table("/content/data/MyDrive/hiv/dinh/metadatadinh.tsv").rename(columns={"sample-id": "sample\_id"})
tax = pd.merge(tax, metadata, on="sample\_id")
tax
Unnamed: 0 sample\_id abundance relative genus id disease Alcohol\_s BMI\_s Bingeing\_s ... host\_s isolation\_source\_s source\_s tissue\_s dataset sequencer region total\_reads study DiseaseState
0 157 027OB 2156 0.000464 g\_\_Acidaminococcus g\_\_Acidaminococcus H Drinker 24.78 Not\_binge\_drinker ... Human Stool Intestine hiv\_dinh 454 V3-V5 1765 hiv\_dinh H
1 7 027OB 2156 0.000464 g\_\_Alistipes g\_\_Alistipes H Drinker 24.78 Not\_binge\_drinker ... Human Stool Intestine hiv\_dinh 454 V3-V5 1765 hiv\_dinh H
2 1 027OB 2156 0.001391 g\_\_Alloprevotella g\_\_Alloprevotella H Drinker 24.78 Not\_binge\_drinker ... Human Stool Intestine hiv\_dinh 454 V3-V5 1765 hiv\_dinh H
3 20 027OB 2156 0.001391 g\_\_Anaeroplasma g\_\_Anaeroplasma H Drinker 24.78 Not\_binge\_drinker ... Human
1. build model
from micom.workflows import build
from micom import Community
import pandas as pd
# Convert sample\_id column to string type
tax['sample\_id'] = tax['sample\_id'].astype('str')
# Call the build function
manifest = build(tax, "agora103\_genus.qza", "models", solver="osqp",
cutoff=2.5e-2, threads=2)
## Running ━━╺━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 6% -:--:--
RemoteTraceback Traceback (most recent call last)
RemoteTraceback:
"""
Traceback (most recent call last):
File "/usr/lib/python3.10/multiprocessing/pool.py", line 125, in worker
result = (True, func(\*args, \*\*kwds))
File "/usr/local/lib/python3.10/dist-packages/micom/workflows/build.py", line 29, in build\_and\_save
com = Community(
File "/usr/local/lib/python3.10/dist-packages/micom/community.py", line 213, in **init**
taxonomy = unify\_rank\_prefixes(taxonomy, manifest)
File "/usr/local/lib/python3.10/dist-packages/micom/taxonomy.py", line 128, in unify\_rank\_prefixes
tax\_prefixes = rank\_prefixes(taxonomy)
File "/usr/local/lib/python3.10/dist-packages/micom/taxonomy.py", line 107, in rank\_prefixes
{r: manifest[r].str.extract(r"^([a-z]**)").iloc[0, 0] for r in ranks}
File "/usr/local/lib/python3.10/dist-packages/micom/taxonomy.py", line 107, in
{r: manifest[r].str.extract(r"^([a-z]**)").iloc[0, 0] for r in ranks}
File "/usr/local/lib/python3.10/dist-packages/pandas/core/indexing.py", line 1096, in **getitem**
return self.obj.\_get\_value(\*key, takeable=self.\_takeable)
File "/usr/local/lib/python3.10/dist-packages/pandas/core/frame.py", line 3868, in \_get\_value
return series.\_values[index]
IndexError: index 0 is out of bounds for axis 0 with size 0. """
The above exception was the direct cause of the following exception:
IndexError Traceback (most recent call last)
in \()
7
8 # Call the build function
----\> 9 manifest = build(tax, "agora103\_genus.qza", "models", solver="osqp",
10 cutoff=2.5e-2, threads=2)
4 frames
/usr/lib/python3.10/multiprocessing/pool.py in next(self, timeout)
871 if success:
872 return value
--\> 873 raise value
874
875 **next** = next # XXX
IndexError: index 0 is out of bounds for axis 0 with size 0
---
### Author:  [@jwdebelius](https://forum.qiime2.org/u/jwdebelius)
#### Post date: [June 11, 2024, 1:23pm UTC](https://forum.qiime2.org/t/indexerror-index-0-is-out-of-bounds-for-axis-0-with-size-0/30465/2 "2024-06-11T13:23:36Z")
Hi @herrynguyen1706,
Welcome to the :qiime2: forum! I just wanted to let you know that I re-categorized this as "other bioinformatic tools" since it's a question about MICOM and not QIIME 2 (or q2-micom).
Best,
Justine
---
### Author:  [@cherman2](https://forum.qiime2.org/u/cherman2)
#### Post date: [June 11, 2024, 2:47pm UTC](https://forum.qiime2.org/t/indexerror-index-0-is-out-of-bounds-for-axis-0-with-size-0/30465/3 "2024-06-11T14:47:10Z")
Hi @herrynguyen1706,
I am going to ping the dev of MICOM, @cdiener, to see if he has any suggestions.
---
### Author:  [@herrynguyen1706](https://forum.qiime2.org/u/herrynguyen1706)
#### Post date: [June 11, 2024, 3:08pm UTC](https://forum.qiime2.org/t/indexerror-index-0-is-out-of-bounds-for-axis-0-with-size-0/30465/4 "2024-06-11T15:08:07Z")
Many thanks for your update. I hope someone can help me with that. Thank again.
---
### Author:  [@herrynguyen1706](https://forum.qiime2.org/u/herrynguyen1706)
#### Post date: [June 11, 2024, 6:24pm UTC](https://forum.qiime2.org/t/indexerror-index-0-is-out-of-bounds-for-axis-0-with-size-0/30465/5 "2024-06-11T18:24:18Z")
Dear Diener,
I am trying to run model microbiota-wide metabolism with MICOM. I upload my tax data and then I build community models. However, it shows the problem below. Could you please help me with this issue?
Thank you very much.
""""""""""""""""""""""
1. upload data
import pandas as pd
metadata = pd.read\_table("/content/data/MyDrive/hiv/dinh/metadatadinh.tsv").rename(columns={"sample-id": "sample\_id"})
tax = pd.merge(tax, metadata, on="sample\_id")
tax
Unnamed: 0 sample\_id abundance relative genus id disease Alcohol\_s BMI\_s Bingeing\_s ... host\_s isolation\_source\_s source\_s tissue\_s dataset sequencer region total\_reads study DiseaseState
0 157 027OB 2156 0.000464 g\_\_Acidaminococcus g\_\_Acidaminococcus H Drinker 24.78 Not\_binge\_drinker ... Human Stool Intestine hiv\_dinh 454 V3-V5 1765 hiv\_dinh H
1 7 027OB 2156 0.000464 g\_\_Alistipes g\_\_Alistipes H Drinker 24.78 Not\_binge\_drinker ... Human Stool Intestine hiv\_dinh 454 V3-V5 1765 hiv\_dinh H
2 1 027OB 2156 0.001391 g\_\_Alloprevotella g\_\_Alloprevotella H Drinker 24.78 Not\_binge\_drinker ... Human Stool Intestine hiv\_dinh 454 V3-V5 1765 hiv\_dinh H
3 20 027OB 2156 0.001391 g\_\_Anaeroplasma g\_\_Anaeroplasma H Drinker 24.78 Not\_binge\_drinker ... Human
1. build model
from micom.workflows import build
from micom import Community
import pandas as pd
# Convert sample\_id column to string type
tax['sample\_id'] = tax['sample\_id'].astype('str')
# Call the build function
manifest = build(tax, "agora103\_genus.qza", "models", solver="osqp",
cutoff=2.5e-2, threads=2)
## Running ━━╺━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 6% -:--:--
RemoteTraceback Traceback (most recent call last)
RemoteTraceback:
"""
Traceback (most recent call last):
File "/usr/lib/python3.10/multiprocessing/pool.py", line 125, in worker
result = (True, func(\*args, \*\*kwds))
File "/usr/local/lib/python3.10/dist-packages/micom/workflows/build.py", line 29, in build\_and\_save
com = Community(
File "/usr/local/lib/python3.10/dist-packages/micom/community.py", line 213, in **init**
taxonomy = unify\_rank\_prefixes(taxonomy, manifest)
File "/usr/local/lib/python3.10/dist-packages/micom/taxonomy.py", line 128, in unify\_rank\_prefixes
tax\_prefixes = rank\_prefixes(taxonomy)
File "/usr/local/lib/python3.10/dist-packages/micom/taxonomy.py", line 107, in rank\_prefixes
{r: manifest[r].str.extract(r"^([a-z]**)").iloc[0, 0] for r in ranks}
File "/usr/local/lib/python3.10/dist-packages/micom/taxonomy.py", line 107, in
{r: manifest[r].str.extract(r"^([a-z]**)").iloc[0, 0] for r in ranks}
File "/usr/local/lib/python3.10/dist-packages/pandas/core/indexing.py", line 1096, in **getitem**
return self.obj.\_get\_value(\*key, takeable=self.\_takeable)
File "/usr/local/lib/python3.10/dist-packages/pandas/core/frame.py", line 3868, in \_get\_value
return series.\_values[index]
IndexError: index 0 is out of bounds for axis 0 with size 0. """
The above exception was the direct cause of the following exception:
IndexError Traceback (most recent call last)
in \()
7
8 # Call the build function
----\> 9 manifest = build(tax, "agora103\_genus.qza", "models", solver="osqp",
10 cutoff=2.5e-2, threads=2)
4 frames
/usr/lib/python3.10/multiprocessing/pool.py in next(self, timeout)
871 if success:
872 return value
--\> 873 raise value
874
875 **next** = next # XXX
IndexError: index 0 is out of bounds for axis 0 with size 0
---
### Author:  [@cherman2](https://forum.qiime2.org/u/cherman2)
#### Post date: [June 13, 2024, 4:44pm UTC](https://forum.qiime2.org/t/indexerror-index-0-is-out-of-bounds-for-axis-0-with-size-0/30465/6 "2024-06-13T16:44:00Z")
Hi @herrynguyen1706,
Please refrain from posting duplicate posts in the future. I moved this post from [Preparing and importing custom diets and taxonomy files for q2-MICOM - #3 by Mehrbod\_Estaki](https://forum.qiime2.org/t/preparing-and-importing-custom-diets-and-taxonomy-files-for-q2-micom/19857/3) to your original post to keep things on topic.
---
### Author:  [@cdiener](https://forum.qiime2.org/u/cdiener)
#### Post date: [August 2, 2024, 8:18am UTC](https://forum.qiime2.org/t/indexerror-index-0-is-out-of-bounds-for-axis-0-with-size-0/30465/7 "2024-08-02T08:18:01Z")
Hi sorry for the late reply. For some reason I did not see the post. Basically it's complaining that you have no ranks in your taxonomy table. I do see the "genus" one in your post but it's not bein picked up. Could you check that your table was read correcly? What does `tax.columns` give you?
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