Hello,
I tried to run clust as follows clust unnorm_TPM_abundance.txt -r replicates_file_for_clust.txt -o clust_output
But it throws an error in the output.py script "ValueError: all the input array dimensions except for the concatenation axis must match exactly, but along dimension 1, the array at index 0 has size 9 and the array at index 1 has size 8".
I could not figure out if the problem was with the input files or something else. Any help is much appreciated.
This is the format of my input files
Data file:
/===========================================================================\
| Clust |
| (Optimised consensus clustering of multiple heterogenous datasets) |
| Python package version 1.18.0 (2022) Basel Abu-Jamous |
+---------------------------------------------------------------------------+
| Analysis started at: Monday 08 January 2024 (11:00:49) |
| 1. Reading dataset(s) |
| 2. Data pre-processing |
| - Automatic normalisation mode (default in v1.7.0+). |
| Clust automatically normalises your dataset(s). |
| To switch it off, use the `-n 0` option (not recommended). |
| Check https://github.com/BaselAbujamous/clust for details. |
| - Flat expression profiles filtered out (default in v1.7.0+). |
| To switch it off, use the --no-fil-flat option (not recommended). |
| Check https://github.com/BaselAbujamous/clust for details. |
Traceback (most recent call last):
File "/home/kotagal/miniforge3/envs/clust/bin/clust", line 10, in <module>
sys.exit(main())
^^^^^^
File "/home/kotagal/miniforge3/envs/clust/lib/python3.12/site-packages/clust/__main__.py", line 102, in main
clustpipeline.clustpipeline(args.datapath, args.m, args.r, args.n, args.o, args.K, args.t,
File "/home/kotagal/miniforge3/envs/clust/lib/python3.12/site-packages/clust/clustpipeline.py", line 112, in clustpipeline
Xprocessed = op.processed_X(X_summarised_normalised, conditions, GDM, OGs, MapNew, MapSpecies) # pandas DataFrames
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/kotagal/miniforge3/envs/clust/lib/python3.12/site-packages/clust/scripts/output.py", line 434, in processed_X
res[l] = np.concatenate((resHeader[l], res[l]), axis=0)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
ValueError: all the input array dimensions except for the concatenation axis must match exactly, but along dimension 1, the array at index 0 has size 9 and the array at index 1 has size 8
Hello, I tried to run clust as follows
clust unnorm_TPM_abundance.txt -r replicates_file_for_clust.txt -o clust_output
But it throws an error in the output.py script "ValueError: all the input array dimensions except for the concatenation axis must match exactly, but along dimension 1, the array at index 0 has size 9 and the array at index 1 has size 8".I could not figure out if the problem was with the input files or something else. Any help is much appreciated. This is the format of my input files Data file:
Replicates file:
This is the entire console output:
Thanks,
Suvrat