a problem

[11051911]

After configuring the runtime environment, I encountered an error when entering the commands from the example in the README file in the pycharm terminal

Secuer C -i ./example_data/Biase_k3_FPKM_scRNA.csv --yaml ./config.yaml -o ./Biase_conresult -p 900 --knn 5 -M 7 --transpose 命令语法不正确。 Your input parameters are: inputfile:./example_data/Biase_k3_FPKM_scRNA.csv, p: 1000, knn:5, distance: euclidean, cm: Kmeans outfile:./Biase_result, seed:1. [2023-03-12 11:49:51] [INFO] Reading data... [2023-03-12 11:49:51] [WARNING] Your data contains 49 observations and 25737 features. [2023-03-12 11:49:51] [INFO] filtering genes... [2023-03-12 11:49:51] [INFO] filtering cell... [2023-03-12 11:49:51] [INFO] normalizing data... [2023-03-12 11:49:51] [INFO] selecting highly variable genes... [2023-03-12 11:49:51] [WARNING] Your data contains 49 observations and 2000 features after preprocessing. [2023-03-12 11:49:51] [INFO] performing PCA... [2023-03-12 11:49:51] [INFO] Run secuer... [2023-03-12 11:49:51] [INFO] Selecting representatives... [2023-03-12 11:49:51] [INFO] Approximate KNN... [2023-03-12 11:49:51] [INFO] Estimating the number of clustering... Assertion failed: v->stor_begin != NULL, file c:\projects\louvain-igraph\vendor\build\igraph\igraph-0.8.2-msvc\src\vector.pmt, line 486

• What should I do?

[nanawei11]

Hello, Thank you for your interest in using Secuer! I'm sorry that I can't reproduce this error, because the code works fine for me. I'm guessing that this error seems to come from the package "louvain-graph". I suggest you reinstall "louvain" and "igraph" via pip install louvain igraph , and see if they help. The following is the process and results of my test：

conda create -n secuer1 python=3.9
conda activate secuer1
pip install matplotlib  pyyaml pandas scanpy igraph louvain secuer -i https://pypi.tuna.tsinghua.edu.cn/simple

(secuer1)  D:\nn\Secuer-main\Secuer-main>Secuer C -i ./example_data/Biase_k3_FPKM_scRNA.csv --yaml ./config.yaml -o Biase_result -p 900 --knn 5 -M 7 --transpose
Warning: output dir is exist, write output result in existing dir.
Your input parameters are: inputfile:./example_data/Biase_k3_FPKM_scRNA.csv,
p: 900,
knn:5,
M: 7
outfile:Biase_result.
[2023-03-12 15:25:32] [INFO] Reading data...
[2023-03-12 15:25:32] [WARNING] Your data contains 49 observations and 25737 features.
[2023-03-12 15:25:32] [INFO] filtering genes...
[2023-03-12 15:25:32] [INFO] filtering cells...
[2023-03-12 15:25:32] [INFO] normalizing data...
[2023-03-12 15:25:32] [INFO] selecting highly variable genes...
[2023-03-12 15:25:32] [WARNING] Your data contains 49 observations and 2000 features after preprocessing.
[2023-03-12 15:25:32] [INFO] performing PCA...
[2023-03-12 15:25:32] [INFO] Run secuer consensus...
[2023-03-12 15:25:32] [INFO] Running secuer 1
[2023-03-12 15:25:33] [INFO] Running secuer 2
[2023-03-12 15:25:33] [INFO] Running secuer 3
[2023-03-12 15:25:33] [INFO] Running secuer 4
[2023-03-12 15:25:33] [INFO] Running secuer 5
[2023-03-12 15:25:33] [INFO] Running secuer 6
[2023-03-12 15:25:34] [INFO] Running secuer 7
Performing the consensus function...
[2023-03-12 15:25:34] [INFO] Finished: The secuer finds 3 clusters
Note: save result to Biase_result/SecuerConsenResult.txt

I hope it can help you, please contact me if you have any questions.

Best, Wei

[szhorvat]

You are using a rather old version of louvain-igraph. I would recommend using the latest version of both louvain-igraph and igraph (but I see that requirements.txt specifies an old version).

There is a chance that this error might arise from using mismatching versions of igraph and louvain-igraph. louvain-igraph 0.8.x goes with igraph 0.10.x, and louvain-igraph 0.7.x goes with igraph 0.9.x.

[11051911]

Glad to get your response, I followed your steps to run it successfully! But the situation that I didn't run out is configured according to the environment described in your file(requirements.txt), is it because of the environment except for problems? ``ERROR: Ignored the following versions that require a different python version: 1.10.0 Requires-Python <3.12,>=3.8; 1.10.0rc1 Requires-Python <3.12,>=3.8; 1.10.0rc2 Requires-Python <3. 12,>=3.8; 1.10.1 Requires-Python <3.12,>=3.8; 1.8.0 Requires-Python >=3.8,<3.11; 1.8.0rc1 Requires-Python >=3.8,<3.11; 1.8.0rc2 Requires-Python >=3.8,<3.11; 1.8.0rc3 Requires-Python > =3.8,<3.11; 1.8.0rc4 Requires-Python >=3.8,<3.11; 1.8.1 Requires-Python >=3.8,<3.11; 1.9.0 Requires-Python >=3.8,<3.12; 1.9.0rc1 Requires-Python >=3.8,<3.12; 1.9.0rc2 Requires-Python >=3.8,<3.12; 1.9.0rc3 Requires-Python >=3.8,<3.12; 1.9.1 Requires-Python >=3.8,<3.12; 1.9.2 Requires-Python >=3.8; 1.9.3 Requires-Python >=3.8 ERROR: Could not find a version that satisfies the requirement scipy==1.9.1 (from versions: 0.8.0, 0.9.0, 0.10.0, 0.10.1, 0.11.0, 0.12.0, 0.12.1, 0.13.0, 0.13.1, 0.13.2, 0.13.3, 0.14. 0, 0.14.1, 0.15.0, 0.15.1, 0.16.0, 0.16.1, 0.17.0, 0.17.1, 0.18.0, 0.18.1, 0.19.0, 0.19.1, 1.0.0, 1.0.1, 1.1.0, 1.2.0, 1.2.1, 1.2.2, 1.2.3, 1.3.0, 1.3.1, 1.3.2, 1.3.3, 1.4.0, 1.4.1, 1.5.0, 1.5.1, 1.5.2, 1.5.3, 1.5.4, 1.6.0, 1.6.1, 1.6.2, 1.6.3, 1.7.0rc1, 1.7.0rc2, 1.7.0, 1.7.1, 1.7.2, 1.7.3) ERROR: No matching distribution found for scipy==1.9.1 If so, please correct it. Thank you again for your reply.

[nanawei11]

Thank you very much for your feedback, we will carefully check whether the version in requirements.txt is wrong. Thank you again.

Best wishes!