huangyh09 / brie-tutorials Goto Github PK

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.

Hi, Yuanhua

I'm sorry to disturb you for so many times!
When i ran the brie-quant, i met a terrible error and i can't understand how to solve it!

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:

Traceback (most recent call last):
  File "/public2/home/rotation/miniconda3/envs/TFProb/bin/brie-quant", line 8, in
    sys.exit(main())
  File "/public2/home/rotation/miniconda3/envs/TFProb/lib/python3.7/site-packages/brie/bin/quant.py", line 219, in main
    options.batch_size, options.pseudo_count, options.test_base)
  File "/public2/home/rotation/miniconda3/envs/TFProb/lib/python3.7/site-packages/brie/bin/quant.py", line 42, in quant
    adata = brie.read_h5ad(in_file)
  File "/public2/home/rotation/miniconda3/envs/TFProb/lib/python3.7/site-packages/anndata/_io/h5ad.py", line 236, in read_h5ad
    d[k] = read_dataframe(f[k])
  File "/public2/home/rotation/miniconda3/envs/TFProb/lib/python3.7/site-packages/anndata/_io/h5ad.py", line 301, in read_dataframe
    return read_elem(group)
  File "/public2/home/rotation/miniconda3/envs/TFProb/lib/python3.7/site-packages/anndata/_io/specs/registry.py", line 183, in read_elem
    return _REGISTRY.get_reader(type(elem), get_spec(elem), frozenset(modifiers))(elem)
  File "/public2/home/rotation/miniconda3/envs/TFProb/lib/python3.7/site-packages/anndata/_io/specs/methods.py", line 523, in read_dataframe
    {k: read_elem(elem[k]) for k in columns},
  File "/public2/home/rotation/miniconda3/envs/TFProb/lib/python3.7/site-packages/anndata/_io/specs/methods.py", line 523, in
    {k: read_elem(elem[k]) for k in columns},
  File "/public2/home/rotation/miniconda3/envs/TFProb/lib/python3.7/site-packages/anndata/_io/specs/registry.py", line 183, in read_elem
    return _REGISTRY.get_reader(type(elem), get_spec(elem), frozenset(modifiers))(elem)
  File "/public2/home/rotation/miniconda3/envs/TFProb/lib/python3.7/site-packages/anndata/_io/specs/methods.py", line 327, in read_string_array
    return read_array(d.asstr())
AttributeError: 'Dataset' object has no attribute 'asstr'

Hi
Thank you for the good tool.
I try to run the brie-count. But it returned with some error.

The code is :
brie-count -a /data/BRIE2/AnnoSE/SE.gff3 -s /data/outs/possorted_genome_bam.bam -b /data/outs/filtered_feature_bc_matrix/barcodes.tsv.gz -o out_dir -p 15

the report is:

example head cells:
['AAACAGCCAACTAGGG-1' 'AAACAGCCACCTGCTC-1' 'AAACAGCCAGGCTTCG-1'] ...
^M[BRIE2] loading gene annotations ... ^M[BRIE2] loading gene annotations ... Done.
This is not exon-skipping event: chr4:1003549:1003629:+@chr4:1004012:1003625:+@chr4:1004012:1004112:+!

So, what is the reason for it?
Thank you!