git rm commited log files

35d2e9a6 · eortega · 52664453 · 52664453 · 52664453
Commit 35d2e9a6 authored Dec 16, 2019 by eortega
--- a/phages/steps/trimmed/summary_trimm_Other
+++ b/phages/steps/trimmed/summary_trimm_Other
-2972_S17
-Input Read Pairs: 274182
-Both Surviving Reads: 248778
-Both Surviving Read Percent: 90.73
-Forward Only Surviving Reads: 10255
-Forward Only Surviving Read Percent: 3.74
-Reverse Only Surviving Reads: 6338
-Reverse Only Surviving Read Percent: 2.31
-Dropped Reads: 8811
-Dropped Read Percent: 3.21
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-####
-A10-A_S16
-Input Read Pairs: 229447
-Both Surviving Reads: 206833
-Both Surviving Read Percent: 90.14
-Forward Only Surviving Reads: 9283
-Forward Only Surviving Read Percent: 4.05
-Reverse Only Surviving Reads: 4752
-Reverse Only Surviving Read Percent: 2.07
-Dropped Reads: 8579
-Dropped Read Percent: 3.74
-
-####
-A7-A_S8
-Input Read Pairs: 133220
-Both Surviving Reads: 118074
-Both Surviving Read Percent: 88.63
-Forward Only Surviving Reads: 6747
-Forward Only Surviving Read Percent: 5.06
-Reverse Only Surviving Reads: 2328
-Reverse Only Surviving Read Percent: 1.75
-Dropped Reads: 6071
-Dropped Read Percent: 4.56
-
-####
-A8-C_S12
-Input Read Pairs: 99498
-Both Surviving Reads: 88652
-Both Surviving Read Percent: 89.10
-Forward Only Surviving Reads: 5142
-Forward Only Surviving Read Percent: 5.17
-Reverse Only Surviving Reads: 1423
-Reverse Only Surviving Read Percent: 1.43
-Dropped Reads: 4281
-Dropped Read Percent: 4.30
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-####
-A9-A_S13
-Input Read Pairs: 357640
-Both Surviving Reads: 310615
-Both Surviving Read Percent: 86.85
-Forward Only Surviving Reads: 27600
-Forward Only Surviving Read Percent: 7.72
-Reverse Only Surviving Reads: 4094
-Reverse Only Surviving Read Percent: 1.14
-Dropped Reads: 15331
-Dropped Read Percent: 4.29
-
-####
-B7-A_S9
-Input Read Pairs: 96990
-Both Surviving Reads: 86503
-Both Surviving Read Percent: 89.19
-Forward Only Surviving Reads: 4276
-Forward Only Surviving Read Percent: 4.41
-Reverse Only Surviving Reads: 2160
-Reverse Only Surviving Read Percent: 2.23
-Dropped Reads: 4051
-Dropped Read Percent: 4.18
-
-####
-B8-B_S14
-Input Read Pairs: 151881
-Both Surviving Reads: 127388
-Both Surviving Read Percent: 83.87
-Forward Only Surviving Reads: 16531
-Forward Only Surviving Read Percent: 10.88
-Reverse Only Surviving Reads: 1330
-Reverse Only Surviving Read Percent: 0.88
-Dropped Reads: 6632
-Dropped Read Percent: 4.37
-
-####
-B9-B_S10
-Input Read Pairs: 99400
-Both Surviving Reads: 85707
-Both Surviving Read Percent: 86.22
-Forward Only Surviving Reads: 7935
-Forward Only Surviving Read Percent: 7.98
-Reverse Only Surviving Reads: 1030
-Reverse Only Surviving Read Percent: 1.04
-Dropped Reads: 4728
-Dropped Read Percent: 4.76
-
-####
-C2-B_S11
-Input Read Pairs: 199684
-Both Surviving Reads: 172964
-Both Surviving Read Percent: 86.62
-Forward Only Surviving Reads: 15131
-Forward Only Surviving Read Percent: 7.58
-Reverse Only Surviving Reads: 2061
-Reverse Only Surviving Read Percent: 1.03
-Dropped Reads: 9528
-Dropped Read Percent: 4.77
-
-####
-C3-E_S7
-Input Read Pairs: 114733
-Both Surviving Reads: 102160
-Both Surviving Read Percent: 89.04
-Forward Only Surviving Reads: 5982
-Forward Only Surviving Read Percent: 5.21
-Reverse Only Surviving Reads: 1880
-Reverse Only Surviving Read Percent: 1.64
-Dropped Reads: 4711
-Dropped Read Percent: 4.11
-
-####
-C4-B_S15
-Input Read Pairs: 215278
-Both Surviving Reads: 168480
-Both Surviving Read Percent: 78.26
-Forward Only Surviving Reads: 34692
-Forward Only Surviving Read Percent: 16.11
-Reverse Only Surviving Reads: 906
-Reverse Only Surviving Read Percent: 0.42
-Dropped Reads: 11200
-Dropped Read Percent: 5.20
-
-####
-C6-C_S6
-Input Read Pairs: 45
-Both Surviving Reads: 12
-Both Surviving Read Percent: 26.67
-Forward Only Surviving Reads: 20
-Forward Only Surviving Read Percent: 44.44
-Reverse Only Surviving Reads: 1
-Reverse Only Surviving Read Percent: 2.22
-Dropped Reads: 12
-Dropped Read Percent: 26.67
-
-####
-C7-A_S5
-Input Read Pairs: 124291
-Both Surviving Reads: 113190
-Both Surviving Read Percent: 91.07
-Forward Only Surviving Reads: 4302
-Forward Only Surviving Read Percent: 3.46
-Reverse Only Surviving Reads: 2390
-Reverse Only Surviving Read Percent: 1.92
-Dropped Reads: 4409
-Dropped Read Percent: 3.55
-
-####
-C8-A_S2
-Input Read Pairs: 105225
-Both Surviving Reads: 90251
-Both Surviving Read Percent: 85.77
-Forward Only Surviving Reads: 8620
-Forward Only Surviving Read Percent: 8.19
-Reverse Only Surviving Reads: 1050
-Reverse Only Surviving Read Percent: 1.00
-Dropped Reads: 5304
-Dropped Read Percent: 5.04
-
-####
-CTRL1_S25
-Input Read Pairs: 189
-Both Surviving Reads: 86
-Both Surviving Read Percent: 45.50
-Forward Only Surviving Reads: 26
-Forward Only Surviving Read Percent: 13.76
-Reverse Only Surviving Reads: 3
-Reverse Only Surviving Read Percent: 1.59
-Dropped Reads: 74
-Dropped Read Percent: 39.15
-
-####
-CTRL2_S96
-Input Read Pairs: 58
-Both Surviving Reads: 24
-Both Surviving Read Percent: 41.38
-Forward Only Surviving Reads: 20
-Forward Only Surviving Read Percent: 34.48
-Reverse Only Surviving Reads: 1
-Reverse Only Surviving Read Percent: 1.72
-Dropped Reads: 13
-Dropped Read Percent: 22.41
-
-####
-D1-D_S3
-Input Read Pairs: 80922
-Both Surviving Reads: 64820
-Both Surviving Read Percent: 80.10
-Forward Only Surviving Reads: 11481
-Forward Only Surviving Read Percent: 14.19
-Reverse Only Surviving Reads: 378
-Reverse Only Surviving Read Percent: 0.47
-Dropped Reads: 4243
-Dropped Read Percent: 5.24
-
-####
-D5-A_S1
-Input Read Pairs: 73400
-Both Surviving Reads: 62641
-Both Surviving Read Percent: 85.34
-Forward Only Surviving Reads: 6434
-Forward Only Surviving Read Percent: 8.77
-Reverse Only Surviving Reads: 776
-Reverse Only Surviving Read Percent: 1.06
-Dropped Reads: 3549
-Dropped Read Percent: 4.84
-
-####
-D6-B_S4
-Input Read Pairs: 132689
-Both Surviving Reads: 119920
-Both Surviving Read Percent: 90.38
-Forward Only Surviving Reads: 5169
-Forward Only Surviving Read Percent: 3.90
-Reverse Only Surviving Reads: 2490
-Reverse Only Surviving Read Percent: 1.88
-Dropped Reads: 5110
-Dropped Read Percent: 3.85
-
-####
-T4-B_S93
-Input Read Pairs: 93329
-Both Surviving Reads: 83581
-Both Surviving Read Percent: 89.56
-Forward Only Surviving Reads: 4876
-Forward Only Surviving Read Percent: 5.22
-Reverse Only Surviving Reads: 1466
-Reverse Only Surviving Read Percent: 1.57
-Dropped Reads: 3406
-Dropped Read Percent: 3.65
-
-####
-TO-MIX_S84
-Input Read Pairs: 163273
-Both Surviving Reads: 148478
-Both Surviving Read Percent: 90.94
-Forward Only Surviving Reads: 7440
-Forward Only Surviving Read Percent: 4.56
-Reverse Only Surviving Reads: 2373
-Reverse Only Surviving Read Percent: 1.45
-Dropped Reads: 4982
-Dropped Read Percent: 3.05
-
-####
-TO-WT_S83
-Input Read Pairs: 140141
-Both Surviving Reads: 123516
-Both Surviving Read Percent: 88.14
-Forward Only Surviving Reads: 9281
-Forward Only Surviving Read Percent: 6.62
-Reverse Only Surviving Reads: 1941
-Reverse Only Surviving Read Percent: 1.39
-Dropped Reads: 5403
-Dropped Read Percent: 3.86
-
-####
-Undetermined_S0
-Input Read Pairs: 561019
-Both Surviving Reads: 449928
-Both Surviving Read Percent: 80.20
-Forward Only Surviving Reads: 57607
-Forward Only Surviving Read Percent: 10.27
-Reverse Only Surviving Reads: 8268
-Reverse Only Surviving Read Percent: 1.47
-Dropped Reads: 45216
-Dropped Read Percent: 8.06
-
-####
--- a/phages/steps/trimmed/summary_trimm_R
+++ b/phages/steps/trimmed/summary_trimm_R
-R1T1_S27
-Input Read Pairs: 173454
-Both Surviving Reads: 142874
-Both Surviving Read Percent: 82.37
-Forward Only Surviving Reads: 22563
-Forward Only Surviving Read Percent: 13.01
-Reverse Only Surviving Reads: 671
-Reverse Only Surviving Read Percent: 0.39
-Dropped Reads: 7346
-Dropped Read Percent: 4.24
-
-####
-R1T2_S43
-Input Read Pairs: 112766
-Both Surviving Reads: 102719
-Both Surviving Read Percent: 91.09
-Forward Only Surviving Reads: 4485
-Forward Only Surviving Read Percent: 3.98
-Reverse Only Surviving Reads: 2215
-Reverse Only Surviving Read Percent: 1.96
-Dropped Reads: 3347
-Dropped Read Percent: 2.97
-
-####
-R1T3_S59
-Input Read Pairs: 66247
-Both Surviving Reads: 54910
-Both Surviving Read Percent: 82.89
-Forward Only Surviving Reads: 8190
-Forward Only Surviving Read Percent: 12.36
-Reverse Only Surviving Reads: 453
-Reverse Only Surviving Read Percent: 0.68
-Dropped Reads: 2694
-Dropped Read Percent: 4.07
-
-####
-R1T4_S75
-Input Read Pairs: 173253
-Both Surviving Reads: 137616
-Both Surviving Read Percent: 79.43
-Forward Only Surviving Reads: 27832
-Forward Only Surviving Read Percent: 16.06
-Reverse Only Surviving Reads: 595
-Reverse Only Surviving Read Percent: 0.34
-Dropped Reads: 7210
-Dropped Read Percent: 4.16
-
-####
-R2T1_S28
-Input Read Pairs: 213706
-Both Surviving Reads: 176769
-Both Surviving Read Percent: 82.72
-Forward Only Surviving Reads: 21486
-Forward Only Surviving Read Percent: 10.05
-Reverse Only Surviving Reads: 4633
-Reverse Only Surviving Read Percent: 2.17
-Dropped Reads: 10818
-Dropped Read Percent: 5.06
-
-####
-R2T2_S44
-Input Read Pairs: 114571
-Both Surviving Reads: 102263
-Both Surviving Read Percent: 89.26
-Forward Only Surviving Reads: 6792
-Forward Only Surviving Read Percent: 5.93
-Reverse Only Surviving Reads: 1439
-Reverse Only Surviving Read Percent: 1.26
-Dropped Reads: 4077
-Dropped Read Percent: 3.56
-
-####
-R2T3_S60
-Input Read Pairs: 147584
-Both Surviving Reads: 130674
-Both Surviving Read Percent: 88.54
-Forward Only Surviving Reads: 10140
-Forward Only Surviving Read Percent: 6.87
-Reverse Only Surviving Reads: 1860
-Reverse Only Surviving Read Percent: 1.26
-Dropped Reads: 4910
-Dropped Read Percent: 3.33
-
-####
-R2T4_S76
-Input Read Pairs: 118585
-Both Surviving Reads: 107616
-Both Surviving Read Percent: 90.75
-Forward Only Surviving Reads: 5267
-Forward Only Surviving Read Percent: 4.44
-Reverse Only Surviving Reads: 2147
-Reverse Only Surviving Read Percent: 1.81
-Dropped Reads: 3555
-Dropped Read Percent: 3.00
-
-####
-R3T1_S29
-Input Read Pairs: 206748
-Both Surviving Reads: 185927
-Both Surviving Read Percent: 89.93
-Forward Only Surviving Reads: 10247
-Forward Only Surviving Read Percent: 4.96
-Reverse Only Surviving Reads: 3612
-Reverse Only Surviving Read Percent: 1.75
-Dropped Reads: 6962
-Dropped Read Percent: 3.37
-
-####
-R3T2_S45
-Input Read Pairs: 108555
-Both Surviving Reads: 95397
-Both Surviving Read Percent: 87.88
-Forward Only Surviving Reads: 7542
-Forward Only Surviving Read Percent: 6.95
-Reverse Only Surviving Reads: 1469
-Reverse Only Surviving Read Percent: 1.35
-Dropped Reads: 4147
-Dropped Read Percent: 3.82
-
-####
-R3T3_S61
-Input Read Pairs: 189599
-Both Surviving Reads: 163023
-Both Surviving Read Percent: 85.98
-Forward Only Surviving Reads: 13976
-Forward Only Surviving Read Percent: 7.37
-Reverse Only Surviving Reads: 4831
-Reverse Only Surviving Read Percent: 2.55
-Dropped Reads: 7769
-Dropped Read Percent: 4.10
-
-####
-R3T4_S77
-Input Read Pairs: 123278
-Both Surviving Reads: 109312
-Both Surviving Read Percent: 88.67
-Forward Only Surviving Reads: 6699
-Forward Only Surviving Read Percent: 5.43
-Reverse Only Surviving Reads: 2820
-Reverse Only Surviving Read Percent: 2.29
-Dropped Reads: 4447
-Dropped Read Percent: 3.61
-
-####
-R4T1_S30
-Input Read Pairs: 152971
-Both Surviving Reads: 138017
-Both Surviving Read Percent: 90.22
-Forward Only Surviving Reads: 7580
-Forward Only Surviving Read Percent: 4.96
-Reverse Only Surviving Reads: 2184
-Reverse Only Surviving Read Percent: 1.43
-Dropped Reads: 5190
-Dropped Read Percent: 3.39
-
-####
-R4T2-B_S88
-Input Read Pairs: 2904
-Both Surviving Reads: 2620
-Both Surviving Read Percent: 90.22
-Forward Only Surviving Reads: 118
-Forward Only Surviving Read Percent: 4.06
-Reverse Only Surviving Reads: 70
-Reverse Only Surviving Read Percent: 2.41
-Dropped Reads: 96
-Dropped Read Percent: 3.31
-
-####
-R4T2_S46
-Input Read Pairs: 173500
-Both Surviving Reads: 151060
-Both Surviving Read Percent: 87.07
-Forward Only Surviving Reads: 14434
-Forward Only Surviving Read Percent: 8.32
-Reverse Only Surviving Reads: 1459
-Reverse Only Surviving Read Percent: 0.84
-Dropped Reads: 6547
-Dropped Read Percent: 3.77
-
-####
-R4T3_S62
-Input Read Pairs: 125155
-Both Surviving Reads: 111315
-Both Surviving Read Percent: 88.94
-Forward Only Surviving Reads: 7708
-Forward Only Surviving Read Percent: 6.16
-Reverse Only Surviving Reads: 1856
-Reverse Only Surviving Read Percent: 1.48
-Dropped Reads: 4276
-Dropped Read Percent: 3.42
-
-####
-R4T4_S78
-Input Read Pairs: 135493
-Both Surviving Reads: 119251
-Both Surviving Read Percent: 88.01
-Forward Only Surviving Reads: 9245
-Forward Only Surviving Read Percent: 6.82
-Reverse Only Surviving Reads: 1920
-Reverse Only Surviving Read Percent: 1.42
-Dropped Reads: 5077
-Dropped Read Percent: 3.75
-
-####
-R5T1_S31
-Input Read Pairs: 195155
-Both Surviving Reads: 178171
-Both Surviving Read Percent: 91.30
-Forward Only Surviving Reads: 7689
-Forward Only Surviving Read Percent: 3.94
-Reverse Only Surviving Reads: 3631
-Reverse Only Surviving Read Percent: 1.86
-Dropped Reads: 5664
-Dropped Read Percent: 2.90
-
-####
-R5T2_S47
-Input Read Pairs: 76322
-Both Surviving Reads: 65988
-Both Surviving Read Percent: 86.46
-Forward Only Surviving Reads: 6485
-Forward Only Surviving Read Percent: 8.50
-Reverse Only Surviving Reads: 830
-Reverse Only Surviving Read Percent: 1.09
-Dropped Reads: 3019
-Dropped Read Percent: 3.96
-
-####
-R5T3_S63
-Input Read Pairs: 145477
-Both Surviving Reads: 111219
-Both Surviving Read Percent: 76.45
-Forward Only Surviving Reads: 26944
-Forward Only Surviving Read Percent: 18.52
-Reverse Only Surviving Reads: 532
-Reverse Only Surviving Read Percent: 0.37
-Dropped Reads: 6782
-Dropped Read Percent: 4.66
-
-####
-R5T4_S79
-Input Read Pairs: 351448
-Both Surviving Reads: 318608
-Both Surviving Read Percent: 90.66
-Forward Only Surviving Reads: 16133
-Forward Only Surviving Read Percent: 4.59
-Reverse Only Surviving Reads: 6282
-Reverse Only Surviving Read Percent: 1.79
-Dropped Reads: 10425
-Dropped Read Percent: 2.97
-
-####
-R6T1_S32
-Input Read Pairs: 165216
-Both Surviving Reads: 146223
-Both Surviving Read Percent: 88.50
-Forward Only Surviving Reads: 11260
-Forward Only Surviving Read Percent: 6.82
-Reverse Only Surviving Reads: 1605
-Reverse Only Surviving Read Percent: 0.97
-Dropped Reads: 6128
-Dropped Read Percent: 3.71
-
-####
-R6T2_S48
-Input Read Pairs: 156958
-Both Surviving Reads: 140818
-Both Surviving Read Percent: 89.72
-Forward Only Surviving Reads: 8884
-Forward Only Surviving Read Percent: 5.66
-Reverse Only Surviving Reads: 2168
-Reverse Only Surviving Read Percent: 1.38
-Dropped Reads: 5088
-Dropped Read Percent: 3.24
-
-####
-R6T3_S64
-Input Read Pairs: 182061
-Both Surviving Reads: 166771
-Both Surviving Read Percent: 91.60
-Forward Only Surviving Reads: 5671
-Forward Only Surviving Read Percent: 3.11
-Reverse Only Surviving Reads: 4912
-Reverse Only Surviving Read Percent: 2.70
-Dropped Reads: 4707
-Dropped Read Percent: 2.59
-
-####
-R6T4_S80
-Input Read Pairs: 162599
-Both Surviving Reads: 144168
-Both Surviving Read Percent: 88.66
-Forward Only Surviving Reads: 11225
-Forward Only Surviving Read Percent: 6.90
-Reverse Only Surviving Reads: 1755
-Reverse Only Surviving Read Percent: 1.08
-Dropped Reads: 5451
-Dropped Read Percent: 3.35
-
-####
-R7R1_S33
-Input Read Pairs: 84379
-Both Surviving Reads: 71829
-Both Surviving Read Percent: 85.13
-Forward Only Surviving Reads: 7378
-Forward Only Surviving Read Percent: 8.74
-Reverse Only Surviving Reads: 1103
-Reverse Only Surviving Read Percent: 1.31
-Dropped Reads: 4069
-Dropped Read Percent: 4.82
-
-####
-R7R2_S49
-Input Read Pairs: 198350
-Both Surviving Reads: 174619
-Both Surviving Read Percent: 88.04
-Forward Only Surviving Reads: 14435
-Forward Only Surviving Read Percent: 7.28
-Reverse Only Surviving Reads: 1936
-Reverse Only Surviving Read Percent: 0.98
-Dropped Reads: 7360
-Dropped Read Percent: 3.71
-
-####
-R7R3_S65
-Input Read Pairs: 131807
-Both Surviving Reads: 121250
-Both Surviving Read Percent: 91.99
-Forward Only Surviving Reads: 4178
-Forward Only Surviving Read Percent: 3.17
-Reverse Only Surviving Reads: 3018
-Reverse Only Surviving Read Percent: 2.29
-Dropped Reads: 3361
-Dropped Read Percent: 2.55
-
-####
-R7R4_S81
-Input Read Pairs: 78245
-Both Surviving Reads: 70201
-Both Surviving Read Percent: 89.72
-Forward Only Surviving Reads: 4266
-Forward Only Surviving Read Percent: 5.45
-Reverse Only Surviving Reads: 1161
-Reverse Only Surviving Read Percent: 1.48
-Dropped Reads: 2617
-Dropped Read Percent: 3.34
-
-####
-R7T2-B_S89
-Input Read Pairs: 63058
-Both Surviving Reads: 56101
-Both Surviving Read Percent: 88.97
-Forward Only Surviving Reads: 3562
-Forward Only Surviving Read Percent: 5.65
-Reverse Only Surviving Reads: 1112
-Reverse Only Surviving Read Percent: 1.76
-Dropped Reads: 2283
-Dropped Read Percent: 3.62
-
-####
-R8T1_S34
-Input Read Pairs: 113702
-Both Surviving Reads: 98128
-Both Surviving Read Percent: 86.30
-Forward Only Surviving Reads: 10469
-Forward Only Surviving Read Percent: 9.21
-Reverse Only Surviving Reads: 796
-Reverse Only Surviving Read Percent: 0.70
-Dropped Reads: 4309