errors about brie-quant #1
Description
Hi, Yuanhua
By updating the version , I solved too much problems. But when I ran the brie-quant for deifferential alternative splicing, i met a strange question.
my code:
brie-quant -i test5/brie_count.h5ad -o test5/brie_quant_cell.h5ad -c test5/cell_note.tsv --interceptMode gene --LRTindex=ALL
my cell_note.tsv:
I want to detect the differential events between the two celltype.
barcodes celltype type
AAACCTGAGAGGACGG-1 0 0
AAACCTGAGGGATACC-1 0 0
AAACCTGAGTCCAGGA-1 1 0
AAACCTGAGTTCGATC-1 1 0
my error:
[BRIE2] 100.0% cells are matched with features
layers: ['isoform1', 'isoform2', 'ambiguous']
Filtered out 745 genes with less than 50 total counts or 30 cells with unique counts or 10 unique counts or 0.0010 minor isoform frequency
AnnData object with n_obs × n_vars = 7900 × 95
obs: 'barcodes'
var: 'GeneID', 'GeneName', 'TranLens', 'TranIDs', 'n_counts', 'n_counts_uniq'
uns: 'event_type', 'total_reads'
varm: 'effLen', 'p_ambiguous'
layers: 'ambiguous', 'isoform1', 'isoform2', 'poorQual'
2022-07-18 10:34:31.564330: 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; LD_LIBRARY_PATH: /opt/gridview//pbs/dispatcher/lib::/usr/local/lib64:/usr/local/lib
2022-07-18 10:34:31.564389: 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.
[BRIE2] adding pseudo_count: 0.01
2022-07-18 10:34:34.296842: W tensorflow/stream_executor/platform/default/dso_loader.cc:64] Could not load dynamic library 'libcuda.so.1'; dlerror: libcuda.so.1: cannot open shared object file: No such file or directory; LD_LIBRARY_PATH: /opt/gridview//pbs/dispatcher/lib::/usr/local/lib64:/usr/local/lib
2022-07-18 10:34:34.296903: W tensorflow/stream_executor/cuda/cuda_driver.cc:269] failed call to cuInit: UNKNOWN ERROR (303)
2022-07-18 10:34:34.296955: I tensorflow/stream_executor/cuda/cuda_diagnostics.cc:156] kernel driver does not appear to be running on this host (tc6000): /proc/driver/nvidia/version does not exist
2022-07-18 10:34:34.297561: 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.