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Run Pango on your multifasta file !
By Jit 880 days ago
#More at https://cov-lineages.org/resources/pangolin/usage.html
(base) [jnarayan@hn1 FASTA]$ conda activate pangolin
(pangolin) [jnarayan@hn1 FASTA]$ ls
Input_for_Cova_all_samples_combined.fa
(pangolin) [jnarayan@hn1 FASTA]$ pangolin
.DS_Store Input_for_Cova_all_samples_combined.fa
(pangolin) [jnarayan@hn1 FASTA]$ pangolin --update
pangolin already latest release (v3.1.16)
pangolearn updated to 2021-11-18
constellations updated to v0.0.24
scorpio already latest release (v0.3.14)
pango-designation updated to v1.2.103
(pangolin) [jnarayan@hn1 FASTA]$ pangolin
.DS_Store Input_for_Cova_all_samples_combined.fa
(pangolin) [jnarayan@hn1 FASTA]$ pangolin Input_for_Cova_all_samples_combined.fa
All dependencies satisfied.
The query file is:/home/jnarayan/RF_DATA/FASTA/Input_for_Cova_all_samples_combined.fa
** Running sequence QC **
Number of sequences detected: 320
Total passing QC: 293
Data files found:
Trained model: /home/jnarayan/anaconda3/envs/pangolin/lib/python3.8/site-packages/pangoLEARN/data/decisionTree_v1.joblib
Header file: /home/jnarayan/anaconda3/envs/pangolin/lib/python3.8/site-packages/pangoLEARN/data/decisionTreeHeaders_v1.joblib
Designated hash: /home/jnarayan/anaconda3/envs/pangolin/lib/python3.8/site-packages/pangoLEARN/data/lineages.hash.csv
Job stats:
job count min threads max threads
-------------------- ------- ------------- -------------
add_failed_seqs 1 1 1
align_to_reference 1 1 1
all 1 1 1
generate_report 1 1 1
get_constellations 1 1 1
hash_sequence_assign 1 1 1
pangolearn 1 1 1
scorpio 1 1 1
total 8 1 1
loading model 11/30/2021, 13:10:05
/home/jnarayan/anaconda3/envs/pangolin/lib/python3.8/site-packages/sklearn/base.py:324: UserWarning: Trying to unpickle estimator DecisionTreeClassifier from version 0.24.2 when using version 1.0.1. 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
warnings.warn(
processing block of 293 sequences 11/30/2021, 13:10:08
/home/jnarayan/anaconda3/envs/pangolin/lib/python3.8/site-packages/sklearn/base.py:438: UserWarning: X has feature names, but DecisionTreeClassifier was fitted without feature names
warnings.warn(
complete 11/30/2021, 13:10:09
Output file written to: /home/jnarayan/RF_DATA/FASTA/lineage_report.csv
(pangolin) [jnarayan@hn1 FASTA]$ ls
Input_for_Cova_all_samples_combined.fa lineage_report.csv
