mauliknariya
commented
1 year ago Hello,
I had a similar error. This is likely happening because the gene 'AAAS' (the first entry in GO_cell_cycle_annotation_human.txt) was not profiled in your scRNA data. I would take the intersection of the genes profiled in your data and the genes in the cell cycle annotation file and create a separate file, and use that for your --gene_list.
I hope this helps
On Thu, 2 Mar 2023 at 22:04, Crazyscientist @.***> wrote:
Hello,
I am getting the following error. Could you please help me with this issue?
(DeepCycle) @.***:~/Downloads/DeepCycle-main$ python DeepCycle.py --input_adata my_results.h5ad --gene_list go_annotation/GO_cell_cycle_annotation_human.txt --base_gene MELK --expression_threshold 0 --output_adata adata_newbeta_DeepCycle.h5ad 2023-03-02 15:59:24.865319: I tensorflow/core/platform/cpu_feature_guard.cc:193] This TensorFlow binary is optimized with oneAPI Deep Neural Network Library (oneDNN) to use the following CPU instructions in performance-critical operations: AVX2 FMA To enable them in other operations, rebuild TensorFlow with the appropriate compiler flags. 2023-03-02 15:59:24.969386: W tensorflow/compiler/xla/stream_executor/platform/default/dso_loader.cc:64] Could not load dynamic library 'libcudart.so.11.0'; dlerror: libcudart.so.11.0: cannot open shared object file: No such file or directory 2023-03-02 15:59:24.969408: I tensorflow/compiler/xla/stream_executor/cuda/cudart_stub.cc:29] Ignore above cudart dlerror if you do not have a GPU set up on your machine. 2023-03-02 15:59:25.526120: W tensorflow/compiler/xla/stream_executor/platform/default/dso_loader.cc:64] Could not load dynamic library 'libnvinfer.so.7'; dlerror: libnvinfer.so.7: cannot open shared object file: No such file or directory 2023-03-02 15:59:25.526177: W tensorflow/compiler/xla/stream_executor/platform/default/dso_loader.cc:64] Could not load dynamic library 'libnvinfer_plugin.so.7'; dlerror: libnvinfer_plugin.so.7: cannot open shared object file: No such file or directory 2023-03-02 15:59:25.526185: W tensorflow/compiler/tf2tensorrt/utils/py_utils.cc:38] TF-TRT Warning: Cannot dlopen some TensorRT libraries. If you would like to use Nvidia GPU with TensorRT, please make sure the missing libraries mentioned above are installed properly.
Traceback (most recent call last): File "/home/mayurd/Downloads/DeepCycle-main/DeepCycle.py", line 384, in genes, np_data = generate_input(filtered_cell_cycle_genes, adata) File "/home/mayurd/Downloads/DeepCycle-main/DeepCycle.py", line 351, in generate_input n = gene_list.index(list_of_genes[0]) ValueError: 'AAAS' is not in list
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JDBLab
Hello,
I am getting the following error. Could you please help me with this issue?
(DeepCycle) mayurd@mayurdlaptop:~/Downloads/DeepCycle-main$ python DeepCycle.py --input_adata my_results.h5ad --gene_list go_annotation/GO_cell_cycle_annotation_human.txt --base_gene MELK --expression_threshold 0 --output_adata adata_newbeta_DeepCycle.h5ad 2023-03-02 15:59:24.865319: I tensorflow/core/platform/cpu_feature_guard.cc:193] This TensorFlow binary is optimized with oneAPI Deep Neural Network Library (oneDNN) to use the following CPU instructions in performance-critical operations: AVX2 FMA To enable them in other operations, rebuild TensorFlow with the appropriate compiler flags. 2023-03-02 15:59:24.969386: W tensorflow/compiler/xla/stream_executor/platform/default/dso_loader.cc:64] Could not load dynamic library 'libcudart.so.11.0'; dlerror: libcudart.so.11.0: cannot open shared object file: No such file or directory 2023-03-02 15:59:24.969408: I tensorflow/compiler/xla/stream_executor/cuda/cudart_stub.cc:29] Ignore above cudart dlerror if you do not have a GPU set up on your machine. 2023-03-02 15:59:25.526120: W tensorflow/compiler/xla/stream_executor/platform/default/dso_loader.cc:64] Could not load dynamic library 'libnvinfer.so.7'; dlerror: libnvinfer.so.7: cannot open shared object file: No such file or directory 2023-03-02 15:59:25.526177: W tensorflow/compiler/xla/stream_executor/platform/default/dso_loader.cc:64] Could not load dynamic library 'libnvinfer_plugin.so.7'; dlerror: libnvinfer_plugin.so.7: cannot open shared object file: No such file or directory 2023-03-02 15:59:25.526185: W tensorflow/compiler/tf2tensorrt/utils/py_utils.cc:38] TF-TRT Warning: Cannot dlopen some TensorRT libraries. If you would like to use Nvidia GPU with TensorRT, please make sure the missing libraries mentioned above are installed properly.
Traceback (most recent call last): File "/home/mayurd/Downloads/DeepCycle-main/DeepCycle.py", line 384, in
genes, np_data = generate_input(filtered_cell_cycle_genes, adata)
File "/home/mayurd/Downloads/DeepCycle-main/DeepCycle.py", line 351, in generate_input
n = gene_list.index(list_of_genes[0])
ValueError: 'AAAS' is not in list