Mercurial > repos > iuc > mageck_pathway

annotate test-data/out.mle.log.txt @ 3:290ad8236a68 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 95daf3f97e89989bae687e64cae8b129b3e2b7af
author iuc
date Thu, 19 Apr 2018 05:34:01 -0400
parents ff3716b505d3
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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2
ff3716b505d3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 0
diff changeset
1 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
ff3716b505d3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 0
diff changeset
2 INFO @ Sun, 25 Mar 2018 22:27:42: Cannot parse design matrix as a string; try to parse it as a file name ...
ff3716b505d3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 0
diff changeset
3 INFO @ Sun, 25 Mar 2018 22:27:42: Design matrix:
ff3716b505d3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 0
diff changeset
4 INFO @ Sun, 25 Mar 2018 22:27:42: [[1. 0. 0.]
ff3716b505d3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 0
diff changeset
5 INFO @ Sun, 25 Mar 2018 22:27:42: [1. 0. 0.]
ff3716b505d3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 0
diff changeset
6 INFO @ Sun, 25 Mar 2018 22:27:42: [1. 1. 0.]
ff3716b505d3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 0
diff changeset
7 INFO @ Sun, 25 Mar 2018 22:27:42: [1. 0. 1.]]
ff3716b505d3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 0
diff changeset
8 INFO @ Sun, 25 Mar 2018 22:27:42: Beta labels:baseline,HL60,KBM7
ff3716b505d3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 0
diff changeset
9 INFO @ Sun, 25 Mar 2018 22:27:42: Included samples:HL60.initial,KBM7.initial,HL60.final,KBM7.final
ff3716b505d3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 0
diff changeset
10 INFO @ Sun, 25 Mar 2018 22:27:42: Loaded samples:HL60.initial;KBM7.initial;HL60.final;KBM7.final
ff3716b505d3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 0
diff changeset
11 INFO @ Sun, 25 Mar 2018 22:27:42: Sample index: 0;1;2;3
ff3716b505d3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 0
diff changeset
12 INFO @ Sun, 25 Mar 2018 22:27:42: Loaded 100 genes.
ff3716b505d3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 0
diff changeset
13 DEBUG @ Sun, 25 Mar 2018 22:27:42: Initial (total) size factor: 1.6654412961322171 2.025116092944715 0.720025234995028 0.6592307725342162
ff3716b505d3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 0
diff changeset
14 DEBUG @ Sun, 25 Mar 2018 22:27:42: Median factor: 1.4705915949061357 1.773663484525946 0.6311218804203026 0.5731039100868989
ff3716b505d3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 0
diff changeset
15 INFO @ Sun, 25 Mar 2018 22:27:42: Final size factor: 1.4705915949061357 1.773663484525946 0.6311218804203026 0.5731039100868989
ff3716b505d3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 0
diff changeset
16 INFO @ Sun, 25 Mar 2018 22:27:42: size factor: 0.6799984465189518,0.5638048078028025,1.5844800046134337,1.744884273862957
ff3716b505d3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 0
diff changeset
17 INFO @ Sun, 25 Mar 2018 22:27:42: Thread 0 started.
ff3716b505d3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 0
diff changeset
18 INFO @ Sun, 25 Mar 2018 22:27:42: Thread 0: total 1 instances.
ff3716b505d3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 0
diff changeset
19 INFO @ Sun, 25 Mar 2018 22:27:42: Thread 0 completed.
ff3716b505d3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 0
diff changeset
20 INFO @ Sun, 25 Mar 2018 22:27:42: All threads completed.
ff3716b505d3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 0
diff changeset
21 INFO @ Sun, 25 Mar 2018 22:27:42: Modeling the mean and variance ...
ff3716b505d3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 0
diff changeset
22 INFO @ Sun, 25 Mar 2018 22:27:42: Run the algorithm for the second time ...
ff3716b505d3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 0
diff changeset
23 INFO @ Sun, 25 Mar 2018 22:27:42: Calculating AAAS (1) ...
ff3716b505d3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 0
diff changeset
24 INFO @ Sun, 25 Mar 2018 22:27:43: Permuting groups of gene with 9 sgRNAs per gene. Group progress: 1/2
ff3716b505d3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 0
diff changeset
25 INFO @ Sun, 25 Mar 2018 22:27:43: Start permuting 2 rounds ...
ff3716b505d3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 0
diff changeset
26 INFO @ Sun, 25 Mar 2018 22:27:43: Collecting 999 sgRNAs from 100 genes.
ff3716b505d3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 0
diff changeset
27 INFO @ Sun, 25 Mar 2018 22:27:43: Permuting round 0 ...
ff3716b505d3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 0
diff changeset
28 INFO @ Sun, 25 Mar 2018 22:27:43: Thread 0 started.
ff3716b505d3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 0
diff changeset
29 INFO @ Sun, 25 Mar 2018 22:27:43: Thread 0: total 100 instances.
ff3716b505d3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 0
diff changeset
30 INFO @ Sun, 25 Mar 2018 22:27:43: Thread 0: Calculating AAAS (1) ...
ff3716b505d3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 0
diff changeset
31 INFO @ Sun, 25 Mar 2018 22:27:45: Thread 0 completed.
ff3716b505d3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 0
diff changeset
32 INFO @ Sun, 25 Mar 2018 22:27:45: All threads completed.
ff3716b505d3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 0
diff changeset
33 INFO @ Sun, 25 Mar 2018 22:27:45: Permuting round 1 ...
ff3716b505d3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 0
diff changeset
34 INFO @ Sun, 25 Mar 2018 22:27:45: Thread 0 started.
ff3716b505d3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 0
diff changeset
35 INFO @ Sun, 25 Mar 2018 22:27:45: Thread 0: total 100 instances.
ff3716b505d3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 0
diff changeset
36 INFO @ Sun, 25 Mar 2018 22:27:45: Thread 0: Calculating AAAS (1) ...
ff3716b505d3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 0
diff changeset
37 INFO @ Sun, 25 Mar 2018 22:27:46: Thread 0 completed.
ff3716b505d3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 0
diff changeset
38 INFO @ Sun, 25 Mar 2018 22:27:46: All threads completed.
ff3716b505d3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 0
diff changeset
39 INFO @ Sun, 25 Mar 2018 22:27:46: Assigning p values...
ff3716b505d3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 0
diff changeset
40 INFO @ Sun, 25 Mar 2018 22:27:46: Permuting groups of gene with 10 sgRNAs per gene. Group progress: 2/2
ff3716b505d3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 0
diff changeset
41 INFO @ Sun, 25 Mar 2018 22:27:46: Start permuting 2 rounds ...
ff3716b505d3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 0
diff changeset
42 INFO @ Sun, 25 Mar 2018 22:27:46: Collecting 999 sgRNAs from 100 genes.
ff3716b505d3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 0
diff changeset
43 INFO @ Sun, 25 Mar 2018 22:27:46: Permuting round 0 ...
ff3716b505d3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 0
diff changeset
44 INFO @ Sun, 25 Mar 2018 22:27:47: Thread 0 started.
ff3716b505d3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 0
diff changeset
45 INFO @ Sun, 25 Mar 2018 22:27:47: Thread 0: total 100 instances.
ff3716b505d3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 0
diff changeset
46 INFO @ Sun, 25 Mar 2018 22:27:47: Thread 0: Calculating AAAS (1) ...
ff3716b505d3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 0
diff changeset
47 INFO @ Sun, 25 Mar 2018 22:27:48: Thread 0 completed.
ff3716b505d3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 0
diff changeset
48 INFO @ Sun, 25 Mar 2018 22:27:48: All threads completed.
ff3716b505d3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 0
diff changeset
49 INFO @ Sun, 25 Mar 2018 22:27:49: Permuting round 1 ...
ff3716b505d3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 0
diff changeset
50 INFO @ Sun, 25 Mar 2018 22:27:49: Thread 0 started.
ff3716b505d3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 0
diff changeset
51 INFO @ Sun, 25 Mar 2018 22:27:49: Thread 0: total 100 instances.
ff3716b505d3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 0
diff changeset
52 INFO @ Sun, 25 Mar 2018 22:27:49: Thread 0: Calculating AAAS (1) ...
ff3716b505d3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 0
diff changeset
53 INFO @ Sun, 25 Mar 2018 22:27:50: Thread 0 completed.
ff3716b505d3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 0
diff changeset
54 INFO @ Sun, 25 Mar 2018 22:27:50: All threads completed.
ff3716b505d3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 0
diff changeset
55 INFO @ Sun, 25 Mar 2018 22:27:50: Assigning p values...
ff3716b505d3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 0
diff changeset
56 INFO @ Sun, 25 Mar 2018 22:27:50: Writing gene results to output.gene_summary.txt
ff3716b505d3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 0
diff changeset
57 INFO @ Sun, 25 Mar 2018 22:27:50: Writing sgRNA results to output.sgrna_summary.txt