You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
Error output: SemiBin2: error: unrecognized arguments: -i AU_KOA_F_contig.fa
By running SemiBin2 train_self -h
the output contains no -i comand, while in the tutoriols, https://semibin.readthedocs.io/en/latest/usage/, it has the -i fasta input in example for Advanced co-assembly binning workflows, I wondered which one is correct, and do I need to input the contig files for the model training in co-assembly?
usage: SemiBin2 train_self [-h] --data [DATA ...] --data-split [DATA_SPLIT ...] -o OUTPUT [--batch-size BATCHSIZE] [--train-from-many | --no-train-from-many] [--epochs EPOCHES] [--tmpdir TMPDIR] [-p] [--verbose | --quiet] [--random-seed RANDOM_SEED]
[--engine ENGINE]
options:
-h, --help show this help message and exit
--batch-size BATCHSIZE
Batch size used in the training process (Default: 2048).
--train-from-many, --no-train-from-many
Train the model with several samples. You must provide data, data_split, cannot, and fasta files for corresponding samples in the same order. Note: You can only use `--train-from-many` mode when performing single-sample
binning. Training from many samples with multi-sample binning is not supported.
--epochs EPOCHES, --epoches EPOCHES
Number of epochs used in the training process (Default: 15).
--tmpdir TMPDIR option to set temporary directory
-p , --processes , -t , --threads
Number of CPUs used (pass the value 0 to use all CPUs, default: 0)
--verbose Verbose output
--quiet, -q Quiet output
--random-seed RANDOM_SEED
Random seed. Set it to a fixed value to reproduce results across runs. The default is that the seed is set by the system and .
--engine ENGINE device used to train the model (auto/gpu/cpu, auto means if SemiBin detects the gpu, SemiBin will use GPU)
Mandatory arguments:
--data [DATA ...] Path to the input data.csv file.
--data-split [DATA_SPLIT ...]
Path to the input data_split.csv file.
-o OUTPUT, --output OUTPUT
Output directory (will be created if non-existent)
The text was updated successfully, but these errors were encountered:
Error output:
SemiBin2: error: unrecognized arguments: -i AU_KOA_F_contig.fa
By running
SemiBin2 train_self -h
the output contains no -i comand, while in the tutoriols, https://semibin.readthedocs.io/en/latest/usage/, it has the -i fasta input in example for Advanced co-assembly binning workflows, I wondered which one is correct, and do I need to input the contig files for the model training in co-assembly?
Tutorials
SemiBin2 train_self \ -i contig.fa \ --data contig_output/data.csv \ --data-split contig_output/data_split.csv \ -o contig_output
Output
The text was updated successfully, but these errors were encountered: