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lib3-virus-231024.log
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2023-10-25 11:27:58,671 - INFO - Beginning execution of dms2_prefs in directory /fh/fast/bloom_j/computational_notebooks/ckikawa/2023/ZIKV_DMS_NS3_EvansLab
2023-10-25 11:27:58,672 - INFO - Progress is being logged to results/tile_1/prefs/lib3-virus-231024.log
2023-10-25 11:27:58,710 - INFO - Version information:
Time and date: Wed Oct 25 11:27:58 2023
Platform: Linux-4.15.0-192-generic-x86_64-with-glibc2.10
Python version: 3.8.13 | packaged by conda-forge | (default, Mar 25 2022, 06:04:18) [GCC 10.3.0]
dms_tools2 version: 2.6.10
Bio version: 1.79
pandas version: 0.25.3
numpy version: 1.19.5
IPython version: 8.4.0
jupyter version: 1.0.0
matplotlib version: 3.2.2
plotnine version: 0.6.0
natsort version: 8.2.0
pystan version: 2.19.1.1
scipy version: 1.6.0
seaborn version: 0.12.2
phydmslib version: 2.4.1
statsmodels version: 0.11.1
rpy2 cannot be imported
regex version: 2.5.135
umi_tools version: 1.1.4
2023-10-25 11:27:58,710 - INFO - Parsed the following arguments:
outdir = results/tile_1/prefs
ncpus = 12
use_existing = no
method = ratio
indir = results/tile_1/renumbered_codoncounts
chartype = codon_to_aa
excludestop = yes
conc = [1.0, 1.0, 1.0]
pseudocount = 1
pre = lib3-plasmid-231024
post = lib3-virus-231024
name = lib3-virus-231024
err = ['wt-plasmid-231024', 'wt-virus-231024']
2023-10-25 11:27:58,712 - INFO - Reading pre-selection counts from results/tile_1/renumbered_codoncounts/lib3-plasmid-231024_codoncounts.csv
2023-10-25 11:27:58,719 - INFO - Reading post-selection counts from results/tile_1/renumbered_codoncounts/lib3-virus-231024_codoncounts.csv
2023-10-25 11:27:58,726 - INFO - Reading pre-selection error-control counts from pre
2023-10-25 11:27:58,731 - INFO - Reading post-selection error-control counts from post
2023-10-25 11:27:58,743 - INFO - Read counts for 103 sites.
2023-10-25 11:27:58,743 - INFO - Here are sites and wildtype identities:
1 CGG
2 AGC
3 TGG
4 CCC
5 CCT
6 AGT
7 GAA
8 GTT
9 CTC
10 ACA
11 GCC
12 GTT
13 GGC
14 CTG
15 ATA
16 TGT
17 GCA
18 CTG
19 GCC
20 GGA
21 GGG
22 TTT
23 GCC
24 AAG
25 GCA
26 GAC
27 ATT
28 GAG
29 ATG
30 GCT
31 GGA
32 CCC
33 ATG
34 GCT
35 GCA
36 GTA
37 GGC
38 TTG
39 CTA
40 ATT
41 GTC
42 AGC
43 TAT
44 GTG
45 GTC
46 TCG
47 GGA
48 AAG
49 AGT
50 GTG
51 GAC
52 ATG
53 TAC
54 ATT
55 GAA
56 AGA
57 GCA
58 GGT
59 GAC
60 ATC
61 ACA
62 TGG
63 GAA
64 AAG
65 GAC
66 GCG
67 GAA
68 GTC
69 ACT
70 GGA
71 AAC
72 AGT
73 CCT
74 CGG
75 CTT
76 GAC
77 GTG
78 GCA
79 CTG
80 GAT
81 GAG
82 AGT
83 GGT
84 GAT
85 TTC
86 TCC
87 TTG
88 GTA
89 GAG
90 GAA
91 GAT
92 GGT
93 CCA
94 CCC
95 ATG
96 AGA
97 GAG
98 ATC
99 ATA
100 CTC
101 AAG
102 GTG
103 GTC
2023-10-25 11:27:58,743 - INFO - Computing preferences as normalized enrichment ratios...
2023-10-25 11:27:59,054 - INFO - Writing preferences to results/tile_1/prefs/lib3-virus-231024_prefs.csv
2023-10-25 11:27:59,061 - INFO - Successful completion of dms2_prefs