Closed stefanches7 closed 2 years ago
@alyosama
Hi @stefanches7 I can not replicate your issue. Do you still have the same problem ? Could you send me a fake input or sample of your data so I can test that ?
@alyosama
Hi, I'm also getting a similar error:
Using TensorFlow backend. /usr/local/software/conda/envs/virnet/lib/python3.6/site-packages/tensorflow/python/framework/dtypes.py:516: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a futurstood as (type, (1,)) / '(1,)type'. _np_qint8 = np.dtype([("qint8", np.int8, 1)]) /usr/local/software/conda/envs/virnet/lib/python3.6/site-packages/tensorflow/python/framework/dtypes.py:517: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a futurstood as (type, (1,)) / '(1,)type'. _np_quint8 = np.dtype([("quint8", np.uint8, 1)]) /usr/local/software/conda/envs/virnet/lib/python3.6/site-packages/tensorflow/python/framework/dtypes.py:518: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a futurstood as (type, (1,)) / '(1,)type'. _np_qint16 = np.dtype([("qint16", np.int16, 1)]) /usr/local/software/conda/envs/virnet/lib/python3.6/site-packages/tensorflow/python/framework/dtypes.py:519: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a futurstood as (type, (1,)) / '(1,)type'. _np_quint16 = np.dtype([("quint16", np.uint16, 1)]) /usr/local/software/conda/envs/virnet/lib/python3.6/site-packages/tensorflow/python/framework/dtypes.py:520: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a futurstood as (type, (1,)) / '(1,)type'. _np_qint32 = np.dtype([("qint32", np.int32, 1)]) /usr/local/software/conda/envs/virnet/lib/python3.6/site-packages/tensorflow/python/framework/dtypes.py:525: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a futurstood as (type, (1,)) / '(1,)type'. np_resource = np.dtype([("resource", np.ubyte, 1)]) /usr/local/software/conda/envs/virnet/lib/python3.6/site-packages/tensorboard/compat/tensorflow_stub/dtypes.py:541: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; inbe understood as (type, (1,)) / '(1,)type'. _np_qint8 = np.dtype([("qint8", np.int8, 1)]) /usr/local/software/conda/envs/virnet/lib/python3.6/site-packages/tensorboard/compat/tensorflow_stub/dtypes.py:542: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; inbe understood as (type, (1,)) / '(1,)type'. _np_quint8 = np.dtype([("quint8", np.uint8, 1)]) /usr/local/software/conda/envs/virnet/lib/python3.6/site-packages/tensorboard/compat/tensorflow_stub/dtypes.py:543: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; inbe understood as (type, (1,)) / '(1,)type'. _np_qint16 = np.dtype([("qint16", np.int16, 1)]) /usr/local/software/conda/envs/virnet/lib/python3.6/site-packages/tensorboard/compat/tensorflow_stub/dtypes.py:544: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; inbe understood as (type, (1,)) / '(1,)type'. _np_quint16 = np.dtype([("quint16", np.uint16, 1)]) /usr/local/software/conda/envs/virnet/lib/python3.6/site-packages/tensorboard/compat/tensorflow_stub/dtypes.py:545: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; inbe understood as (type, (1,)) / '(1,)type'. _np_qint32 = np.dtype([("qint32", np.int32, 1)]) /usr/local/software/conda/envs/virnet/lib/python3.6/site-packages/tensorboard/compat/tensorflow_stub/dtypes.py:550: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; inbe understood as (type, (1,)) / '(1,)type'. np_resource = np.dtype([("resource", np.ubyte, 1)]) Starting VirNet Loading Data /home/ubuntu/phageome/benchmark/fragments/test.fasta Traceback (most recent call last): File "predict.py", line 51, in
main() File "predict.py", line 41, in main df_data=utils.load_data(args.input_path) File "/usr/local/software/virnet/utils.py", line 37, in load_data return load_fasta(input_path) File "/usr/local/software/virnet/utils.py", line 15, in load_fasta for record in SeqIO.parse(file_path, "fasta"): File "/usr/local/software/conda/envs/virnet/lib/python3.6/site-packages/Bio/SeqIO/init.py", line 627, in parse i = iterator_generator(handle) File "/usr/local/software/conda/envs/virnet/lib/python3.6/site-packages/Bio/SeqIO/FastaIO.py", line 181, in init super().init(source, alphabet=alphabet, mode="t", fmt="Fasta") File "/usr/local/software/conda/envs/virnet/lib/python3.6/site-packages/Bio/SeqIO/Interfaces.py", line 42, in init self.stream = open(source, "r" + mode) FileNotFoundError: [Errno 2] No such file or directory: '/home/ubuntu/phageome/benchmark/fragments/test.fasta'
This is the command I'm running:
python3 predict.py --input_dim=3000 --input=/home/ubuntu/phageome/test.fasta --output=virnet_phage.csv
When i randomly subsample down the fasta however - to about 70 sequences, the script runs perfectly? sample.txt
Is it resolved? I also meet the same error when I using the wtp(what the phages). It is weird since it only got this problem in some genomes. Is anything wrongs? @alyosama
Hello, I run virnet on a dataset of 250k contigs with length from 100bp to 500kbp (pitily can not disclose the exact data), and get the following error:
(Sorry for ugly output, most infos are in the lower part) This issue looks quite similar to what I am getting. It may well be a layer inside the network that has too small dimension, but just as a suggestion to what it can be. I run
python3 virnet/predict.py --input_dim=3000 --input=all_contigs_fragments.fasta --output=all_contigs_${rnd//0.}.csv
, wherernd
is a float between 0 and 1.