INFO  @ Sun, 25 Mar 2018 22:27:41: Parameters: /Users/doylemaria/miniconda3/envs/mulled-v1-9ee130591ca78526e74a59d8d6dc03cb7db20645470975762936caeac62972dc/bin/mageck mle -k /private/var/folders/zn/m_qvr9zd7tq0wdtsbq255f8xypj_zg/T/tmpELNsjE/files/000/dataset_28.dat -d /private/var/folders/zn/m_qvr9zd7tq0wdtsbq255f8xypj_zg/T/tmpELNsjE/files/000/dataset_29.dat -n output --norm-method median --threads 1 
INFO  @ Sun, 25 Mar 2018 22:27:42: Cannot parse design matrix as a string; try to parse it as a file name ... 
INFO  @ Sun, 25 Mar 2018 22:27:42: Design matrix: 
INFO  @ Sun, 25 Mar 2018 22:27:42: [[1. 0. 0.] 
INFO  @ Sun, 25 Mar 2018 22:27:42:  [1. 0. 0.] 
INFO  @ Sun, 25 Mar 2018 22:27:42:  [1. 1. 0.] 
INFO  @ Sun, 25 Mar 2018 22:27:42:  [1. 0. 1.]] 
INFO  @ Sun, 25 Mar 2018 22:27:42: Beta labels:baseline,HL60,KBM7 
INFO  @ Sun, 25 Mar 2018 22:27:42: Included samples:HL60.initial,KBM7.initial,HL60.final,KBM7.final 
INFO  @ Sun, 25 Mar 2018 22:27:42: Loaded samples:HL60.initial;KBM7.initial;HL60.final;KBM7.final 
INFO  @ Sun, 25 Mar 2018 22:27:42: Sample index: 0;1;2;3 
INFO  @ Sun, 25 Mar 2018 22:27:42: Loaded 100 genes. 
DEBUG @ Sun, 25 Mar 2018 22:27:42: Initial (total) size factor: 1.6654412961322171 2.025116092944715 0.720025234995028 0.6592307725342162 
DEBUG @ Sun, 25 Mar 2018 22:27:42: Median factor: 1.4705915949061357 1.773663484525946 0.6311218804203026 0.5731039100868989 
INFO  @ Sun, 25 Mar 2018 22:27:42: Final size factor: 1.4705915949061357 1.773663484525946 0.6311218804203026 0.5731039100868989 
INFO  @ Sun, 25 Mar 2018 22:27:42: size factor: 0.6799984465189518,0.5638048078028025,1.5844800046134337,1.744884273862957 
INFO  @ Sun, 25 Mar 2018 22:27:42: Thread 0 started. 
INFO  @ Sun, 25 Mar 2018 22:27:42: Thread 0: total 1 instances. 
INFO  @ Sun, 25 Mar 2018 22:27:42: Thread 0 completed. 
INFO  @ Sun, 25 Mar 2018 22:27:42: All threads completed. 
INFO  @ Sun, 25 Mar 2018 22:27:42: Modeling the mean and variance ... 
INFO  @ Sun, 25 Mar 2018 22:27:42: Run the algorithm for the second time ... 
INFO  @ Sun, 25 Mar 2018 22:27:42: Calculating AAAS (1) ...  
INFO  @ Sun, 25 Mar 2018 22:27:43: Permuting groups of gene with 9 sgRNAs per gene. Group progress: 1/2 
INFO  @ Sun, 25 Mar 2018 22:27:43: Start permuting 2 rounds ... 
INFO  @ Sun, 25 Mar 2018 22:27:43: Collecting 999 sgRNAs from 100 genes. 
INFO  @ Sun, 25 Mar 2018 22:27:43: Permuting round 0 ... 
INFO  @ Sun, 25 Mar 2018 22:27:43: Thread 0 started. 
INFO  @ Sun, 25 Mar 2018 22:27:43: Thread 0: total 100 instances. 
INFO  @ Sun, 25 Mar 2018 22:27:43: Thread 0: Calculating AAAS (1) ...  
INFO  @ Sun, 25 Mar 2018 22:27:45: Thread 0 completed. 
INFO  @ Sun, 25 Mar 2018 22:27:45: All threads completed. 
INFO  @ Sun, 25 Mar 2018 22:27:45: Permuting round 1 ... 
INFO  @ Sun, 25 Mar 2018 22:27:45: Thread 0 started. 
INFO  @ Sun, 25 Mar 2018 22:27:45: Thread 0: total 100 instances. 
INFO  @ Sun, 25 Mar 2018 22:27:45: Thread 0: Calculating AAAS (1) ...  
INFO  @ Sun, 25 Mar 2018 22:27:46: Thread 0 completed. 
INFO  @ Sun, 25 Mar 2018 22:27:46: All threads completed. 
INFO  @ Sun, 25 Mar 2018 22:27:46: Assigning p values... 
INFO  @ Sun, 25 Mar 2018 22:27:46: Permuting groups of gene with 10 sgRNAs per gene. Group progress: 2/2 
INFO  @ Sun, 25 Mar 2018 22:27:46: Start permuting 2 rounds ... 
INFO  @ Sun, 25 Mar 2018 22:27:46: Collecting 999 sgRNAs from 100 genes. 
INFO  @ Sun, 25 Mar 2018 22:27:46: Permuting round 0 ... 
INFO  @ Sun, 25 Mar 2018 22:27:47: Thread 0 started. 
INFO  @ Sun, 25 Mar 2018 22:27:47: Thread 0: total 100 instances. 
INFO  @ Sun, 25 Mar 2018 22:27:47: Thread 0: Calculating AAAS (1) ...  
INFO  @ Sun, 25 Mar 2018 22:27:48: Thread 0 completed. 
INFO  @ Sun, 25 Mar 2018 22:27:48: All threads completed. 
INFO  @ Sun, 25 Mar 2018 22:27:49: Permuting round 1 ... 
INFO  @ Sun, 25 Mar 2018 22:27:49: Thread 0 started. 
INFO  @ Sun, 25 Mar 2018 22:27:49: Thread 0: total 100 instances. 
INFO  @ Sun, 25 Mar 2018 22:27:49: Thread 0: Calculating AAAS (1) ...  
INFO  @ Sun, 25 Mar 2018 22:27:50: Thread 0 completed. 
INFO  @ Sun, 25 Mar 2018 22:27:50: All threads completed. 
INFO  @ Sun, 25 Mar 2018 22:27:50: Assigning p values... 
INFO  @ Sun, 25 Mar 2018 22:27:50: Writing gene results to output.gene_summary.txt 
INFO  @ Sun, 25 Mar 2018 22:27:50: Writing sgRNA results to output.sgrna_summary.txt