Closed caroolcardooso-uwa closed 3 weeks ago
Do these solved issues help? https://github.com/parklab/xTea/issues/83 https://github.com/parklab/xTea/issues/89
Hey Simon!! Thanks for the fast response! Yes it does solve this problem using the code from xtea/bin folder! But now I'm getting a new one:
Current working folder is: /scratch/xtea_project/path_work_folder/SVA/tmp/transduction/
Ave coverage is 30.624000000000002: automatic parameters (clip, disc, clip-disc) with value (3, 4 ,1)
Mean insert size is: 416.2787172746123
Standard derivation is: 100.03298121161963
/scratch/conda_envs/xtea_env_37/lib/python3.7/site-packages/sklearn/base.py:338: UserWarning: Trying to unpickle estimator LabelEncoder from version 1.0.1 when using version 1.0.2. This might lead to breaking code or invalid results. Use at your own risk. For more info please refer to: https://scikit-learn.org/stable/modules/model_persistence.html#security-maintainability-limitations UserWarning, [2024-07-12 06:04:16.525] Start to evalute the model: [2024-07-12 06:04:16.527] Evaluating cascade layer = 0 Running command: sort -k1,1V -k2,2n -o /scratch/xtea_project/path_work_folder/SVA/candidate_disc_filtered_cns.txt.high_confident.post_filtering_with_gene_gntp.txt.sorted /scratch/xtea_project/path_work_folder/SVA/candidate_disc_filtered_cns.txt.high_confident.post_filtering_with_gene_gntp.txt
Usage: x_TEA_main.py [options]
x_TEA_main.py: error: no such option: --bamsnap Usage: x_TEA_main.py [options]
x_TEA_main.py: error: no such option: --bamsnap
Have you had this no such option: --bamsnap error before?
Thanks!
You can ignore this if you already have the vcf file correctly generated.
Hey there!
I'm trying to run xtea using conda environment, but the job keeps failing after couple of hours with the same error message:
RuntimeError: Cannot find the target directory: xtea_project/xTea/xtea/genotyping/trained_model_ssc_py2_random_forest_two_category.pkl. sort: cannot read: xtea_project/path_work_folder/<..>/SVA/candidate_disc_filtered_cns.txt.high_confident.post_filtering_with_gene_gntp.txt: No such file or directory
Running command: sort -k1,1V -k2,2n -o /xtea_project/path_work_folder/<..>/SVA/candidate_disc_filtered_cns.txt.high_confident.post_filtering_with_gene_gntp.txt.sorted /xtea_project/path_work_folder/<..>/SVA/candidate_disc_filtered_cns.txt.high_confident.post_filtering_with_gene_gntp.txt
These are the versions of some of my libraries python 3.7.12
deep-forest 0.1.7 bwa 0.7.18
setuptools 69.0.3
scikit-learn 1.0.2 samtools 1.20
xtea 0.1.6
Any idea of what might be causing this error?
Thanks!