Hello BRIE2,
Thanks for this amazing package!
I'm using the loom file as input, but it generates errors as below. Also tried on py3.7, doesn't work.
Environment: Python 3.8, Ubuntu 20.04 LTS
Could you please help me with this issue?
Thanks!
Best,
YJ
(base) hyjforesight@W10D-GW97ZC3:~$ brie-quant -i /home/hyjforesight/loom/cellsorted_WT_IEC_G123B.loom -o /home/hyjforesight/brie2/brie_quant_cell.h5ad -c /home/hyjforesight/WT_IEC_barcodes.tsv --interceptMode=gene --LRTindex=All --layers spliced,unspliced
2021-11-30 18:49:53.274751: W tensorflow/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
2021-11-30 18:49:53.275065: I tensorflow/stream_executor/cuda/cudart_stub.cc:29] Ignore above cudart dlerror if you do not have a GPU set up on your machine.
Traceback (most recent call last):
File "/home/hyjforesight/miniconda3/bin/brie-quant", line 8, in
sys.exit(main())
File "/home/hyjforesight/miniconda3/lib/python3.8/site-packages/brie/bin/quant.py", line 213, in main
quant(options.in_file, options.cell_file, options.gene_file,
File "/home/hyjforesight/miniconda3/lib/python3.8/site-packages/brie/bin/quant.py", line 53, in quant
_idx = brie.match(adata.obs.index, dat_tmp[1:, 0]).astype(float)
UnboundLocalError: local variable 'adata' referenced before assignment
huangyh09
commented
2 years ago
Hello BRIE2, Thanks for this amazing package! I'm using the loom file as input, but it generates errors as below. Also tried on py3.7, doesn't work. Environment: Python 3.8, Ubuntu 20.04 LTS Could you please help me with this issue? Thanks! Best, YJ
(base) hyjforesight@W10D-GW97ZC3:~$ brie-quant -i /home/hyjforesight/loom/cellsorted_WT_IEC_G123B.loom -o /home/hyjforesight/brie2/brie_quant_cell.h5ad -c /home/hyjforesight/WT_IEC_barcodes.tsv --interceptMode=gene --LRTindex=All --layers spliced,unspliced 2021-11-30 18:49:53.274751: W tensorflow/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 2021-11-30 18:49:53.275065: I tensorflow/stream_executor/cuda/cudart_stub.cc:29] Ignore above cudart dlerror if you do not have a GPU set up on your machine. Traceback (most recent call last): File "/home/hyjforesight/miniconda3/bin/brie-quant", line 8, in
sys.exit(main())
File "/home/hyjforesight/miniconda3/lib/python3.8/site-packages/brie/bin/quant.py", line 213, in main
quant(options.in_file, options.cell_file, options.gene_file,
File "/home/hyjforesight/miniconda3/lib/python3.8/site-packages/brie/bin/quant.py", line 53, in quant
_idx = brie.match(adata.obs.index, dat_tmp[1:, 0]).astype(float)
UnboundLocalError: local variable 'adata' referenced before assignment