4_0_5一个样本的 trim_galore去接头完整测试报告

(wes) pc@lab-pc:/project/raw_fq$ trim_galore -q 25 --phred33 --length 36 -e 0.1 --stringency 3 --paired -o ./try SRR8707702_1.fastq.gz SRR8707702_2.fastq.gz 

Multicore support not enabled. Proceeding with single-core trimming.
Path to Cutadapt set as: 'cutadapt' (default)
Cutadapt seems to be working fine (tested command 'cutadapt --version')
Cutadapt version: 1.18
single-core operation.
Output will be written into the directory: /project/raw_fq/try/


AUTO-DETECTING ADAPTER TYPE
===========================
Attempting to auto-detect adapter type from the first 1 million sequences of the first file (>> SRR8707702_1.fastq.gz <<)

Found perfect matches for the following adapter sequences:
Adapter type    Count   Sequence        Sequences analysed      Percentage
Illumina        161502  AGATCGGAAGAGC   1000000 16.15
Nextera 9       CTGTCTCTTATA    1000000 0.00
smallRNA        4       TGGAATTCTCGG    1000000 0.00
Using Illumina adapter for trimming (count: 161502). Second best hit was Nextera (count: 9)

Writing report to '/project/raw_fq/try/SRR8707702_1.fastq.gz_trimming_report.txt'

SUMMARISING RUN PARAMETERS
==========================
Input filename: SRR8707702_1.fastq.gz
Trimming mode: paired-end
Trim Galore version: 0.6.2
Cutadapt version: 1.18
Number of cores used for trimming: 1
Quality Phred score cutoff: 25
Quality encoding type selected: ASCII+33
Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; auto-detected)
Maximum trimming error rate: 0.1 (default)
Minimum required adapter overlap (stringency): 3 bp
Minimum required sequence length for both reads before a sequence pair gets removed: 36 bp
Output file(s) will be GZIP compressed

Cutadapt seems to be reasonably up-to-date. Setting -j 1
Writing final adapter and quality trimmed output to SRR8707702_1_trimmed.fq.gz


  >>> Now performing quality (cutoff '-q 25') and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file SRR8707702_1.fastq.gz <<< 
10000000 sequences processed
20000000 sequences processed
30000000 sequences processed
40000000 sequences processed
This is cutadapt 1.18 with Python 2.7.16
Command line parameters: -j 1 -e 0.1 -q 25 -O 3 -a AGATCGGAAGAGC SRR8707702_1.fastq.gz
Processing reads on 1 core in single-end mode ...
Finished in 943.31 s (22 us/read; 2.70 M reads/minute).

=== Summary ===

Total reads processed:              42,376,519
Reads with adapters:                10,163,308 (24.0%)
Reads written (passing filters):    42,376,519 (100.0%)

Total basepairs processed: 6,356,477,850 bp
Quality-trimmed:              21,437,764 bp (0.3%)
Total written (filtered):  6,060,614,857 bp (95.3%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 10163308 times.

No. of allowed errors:
0-9 bp: 0; 10-13 bp: 1

Bases preceding removed adapters:
  A: 18.0%
  C: 28.4%
  G: 28.2%
  T: 25.3%
  none/other: 0.0%

Overview of removed sequences
length  count   expect  max.err error counts
3       893337  662133.1        0       893337
4       347466  165533.3        0       347466
5       246231  41383.3 0       246231
6       219213  10345.8 0       219213
7       215812  2586.5  0       215812
8       207139  646.6   0       207139
9       207281  161.7   0       206446 835
10      210473  40.4    1       203701 6772
11      203354  10.1    1       196321 7033
12      202462  2.5     1       195635 6827
13      203145  0.6     1       195859 7286
14      199398  0.6     1       191421 7977
15      196562  0.6     1       188247 8315
16      194391  0.6     1       186649 7742
17      197618  0.6     1       189390 8228
18      193231  0.6     1       186187 7044
19      186830  0.6     1       179677 7153
20      183871  0.6     1       176979 6892
21      186449  0.6     1       179368 7081
22      181859  0.6     1       175869 5990
23      174628  0.6     1       169266 5362
24      174634  0.6     1       169234 5400
25      173929  0.6     1       168479 5450
26      167869  0.6     1       162906 4963
27      166856  0.6     1       161982 4874
28      164736  0.6     1       160162 4574
29      161764  0.6     1       157387 4377
30      159685  0.6     1       155414 4271
31      151682  0.6     1       147797 3885
32      150497  0.6     1       146712 3785
33      146601  0.6     1       142975 3626
34      148207  0.6     1       144295 3912
35      145099  0.6     1       141289 3810
36      140649  0.6     1       136941 3708
37      136431  0.6     1       132871 3560
38      133370  0.6     1       129846 3524
39      132927  0.6     1       129325 3602
40      128969  0.6     1       125669 3300
41      130248  0.6     1       126709 3539
42      123247  0.6     1       120046 3201
43      123939  0.6     1       120738 3201
44      113487  0.6     1       110809 2678
45      157959  0.6     1       154315 3644
46      73403   0.6     1       71690 1713
47      89399   0.6     1       87311 2088
48      97120   0.6     1       94878 2242
49      96707   0.6     1       94398 2309
50      93432   0.6     1       91317 2115
51      92226   0.6     1       90028 2198
52      85858   0.6     1       83891 1967
53      84809   0.6     1       82872 1937
54      81733   0.6     1       79742 1991
55      81465   0.6     1       79537 1928
56      70456   0.6     1       68901 1555
57      71444   0.6     1       69799 1645
58      66980   0.6     1       65412 1568
59      62219   0.6     1       60844 1375
60      59960   0.6     1       58641 1319
61      56227   0.6     1       54820 1407
62      52534   0.6     1       51334 1200
63      53419   0.6     1       52102 1317
64      48620   0.6     1       47400 1220
65      42972   0.6     1       41949 1023
66      44404   0.6     1       43376 1028
67      38178   0.6     1       37247 931
68      35480   0.6     1       34649 831
69      34346   0.6     1       33508 838
70      33181   0.6     1       32273 908
71      36212   0.6     1       32873 3339
72      164077  0.6     1       161597 2480
73      7643    0.6     1       7147 496
74      1612    0.6     1       1497 115
75      1340    0.6     1       1241 99
76      1371    0.6     1       1278 93
77      1582    0.6     1       1481 101
78      1668    0.6     1       1574 94
79      1759    0.6     1       1657 102
80      1777    0.6     1       1656 121
81      1705    0.6     1       1583 122
82      1466    0.6     1       1365 101
83      1247    0.6     1       1182 65
84      1060    0.6     1       988 72
85      823     0.6     1       768 55
86      658     0.6     1       598 60
87      600     0.6     1       526 74
88      538     0.6     1       470 68
89      397     0.6     1       345 52
90      404     0.6     1       333 71
91      373     0.6     1       306 67
92      308     0.6     1       249 59
93      247     0.6     1       194 53
94      179     0.6     1       136 43
95      214     0.6     1       151 63
96      181     0.6     1       135 46
97      153     0.6     1       106 47
98      127     0.6     1       78 49
99      125     0.6     1       82 43
100     111     0.6     1       69 42
101     127     0.6     1       70 57
102     114     0.6     1       54 60
103     97      0.6     1       54 43
104     117     0.6     1       44 73
105     94      0.6     1       45 49
106     90      0.6     1       45 45
107     86      0.6     1       39 47
108     72      0.6     1       38 34
109     82      0.6     1       44 38
110     87      0.6     1       42 45
111     71      0.6     1       31 40
112     57      0.6     1       25 32
113     77      0.6     1       23 54
114     65      0.6     1       25 40
115     79      0.6     1       33 46
116     73      0.6     1       24 49
117     70      0.6     1       23 47
118     69      0.6     1       25 44
119     49      0.6     1       16 33
120     59      0.6     1       23 36
121     51      0.6     1       17 34
122     60      0.6     1       23 37
123     56      0.6     1       12 44
124     49      0.6     1       14 35
125     56      0.6     1       14 42
126     54      0.6     1       20 34
127     51      0.6     1       13 38
128     44      0.6     1       10 34
129     37      0.6     1       6 31
130     52      0.6     1       10 42
131     35      0.6     1       6 29
132     38      0.6     1       3 35
133     25      0.6     1       0 25
134     38      0.6     1       3 35
135     33      0.6     1       4 29
136     36      0.6     1       2 34
137     34      0.6     1       3 31
138     39      0.6     1       3 36
139     45      0.6     1       2 43
140     34      0.6     1       1 33
141     31      0.6     1       0 31
142     35      0.6     1       2 33
143     33      0.6     1       0 33
144     31      0.6     1       0 31
145     55      0.6     1       0 55
146     36      0.6     1       1 35
147     26      0.6     1       0 26
148     56      0.6     1       1 55
149     92      0.6     1       0 92
150     347     0.6     1       0 347


RUN STATISTICS FOR INPUT FILE: SRR8707702_1.fastq.gz
=============================================
42376519 sequences processed in total
The length threshold of paired-end sequences gets evaluated later on (in the validation step)

Writing report to '/project/raw_fq/try/SRR8707702_2.fastq.gz_trimming_report.txt'

SUMMARISING RUN PARAMETERS
==========================
Input filename: SRR8707702_2.fastq.gz
Trimming mode: paired-end
Trim Galore version: 0.6.2
Cutadapt version: 1.18
Number of cores used for trimming: 1
Quality Phred score cutoff: 25
Quality encoding type selected: ASCII+33
Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; auto-detected)
Maximum trimming error rate: 0.1 (default)
Minimum required adapter overlap (stringency): 3 bp
Minimum required sequence length for both reads before a sequence pair gets removed: 36 bp
Output file(s) will be GZIP compressed

Cutadapt seems to be reasonably up-to-date. Setting -j -j 1
Writing final adapter and quality trimmed output to SRR8707702_2_trimmed.fq.gz

  >>> Now performing quality (cutoff '-q 25') and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file SRR8707702_2.fastq.gz <<< 
^[[A^[[B10000000 sequences processed
20000000 sequences processed
30000000 sequences processed
^[[B40000000 sequences processed
This is cutadapt 1.18 with Python 2.7.16
Command line parameters: -j 1 -e 0.1 -q 25 -O 3 -a AGATCGGAAGAGC SRR8707702_2.fastq.gz
Processing reads on 1 core in single-end mode ...
Finished in 999.16 s (24 us/read; 2.54 M reads/minute).

=== Summary ===

Total reads processed:              42,376,519
Reads with adapters:                10,033,608 (23.7%)
Reads written (passing filters):    42,376,519 (100.0%)

Total basepairs processed: 6,356,477,850 bp
Quality-trimmed:             103,550,161 bp (1.6%)
Total written (filtered):  5,984,283,082 bp (94.1%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 10033608 times.

No. of allowed errors:
0-9 bp: 0; 10-13 bp: 1

Bases preceding removed adapters:
  A: 18.7%
  C: 29.1%
  G: 27.4%
  T: 24.8%
  none/other: 0.0%

Overview of removed sequences
length  count   expect  max.err error counts
3       883945  662133.1        0       883945
4       342881  165533.3        0       342881
5       250071  41383.3 0       250071
6       218735  10345.8 0       218735
7       210577  2586.5  0       210577
8       203032  646.6   0       203032
9       206182  161.7   0       203571 2611
10      210507  40.4    1       200692 9815
11      202270  10.1    1       191889 10381
12      201597  2.5     1       189934 11663
13      205749  0.6     1       192641 13108
14      221282  0.6     1       207596 13686
15      178072  0.6     1       167615 10457
16      194599  0.6     1       181966 12633
17      202540  0.6     1       190530 12010
18      169645  0.6     1       159683 9962
19      189212  0.6     1       178213 10999
20      173233  0.6     1       163468 9765
21      174462  0.6     1       164416 10046
22      176378  0.6     1       166218 10160
23      175789  0.6     1       165473 10316
24      184136  0.6     1       173185 10951
25      160030  0.6     1       151040 8990
26      163402  0.6     1       154332 9070
27      161455  0.6     1       152661 8794
28      163063  0.6     1       154670 8393
29      155863  0.6     1       147789 8074
30      163824  0.6     1       155172 8652
31      144071  0.6     1       136768 7303
32      147455  0.6     1       139784 7671
33      147065  0.6     1       139388 7677
34      147142  0.6     1       139737 7405
35      140542  0.6     1       133538 7004
36      137662  0.6     1       130722 6940
37      135790  0.6     1       129184 6606
38      132764  0.6     1       126241 6523
39      128553  0.6     1       122466 6087
40      129045  0.6     1       122642 6403
41      126068  0.6     1       119859 6209
42      121518  0.6     1       115237 6281
43      113109  0.6     1       107527 5582
44      116976  0.6     1       111295 5681
45      107814  0.6     1       102651 5163
46      105288  0.6     1       100548 4740
47      102650  0.6     1       97588 5062
48      103068  0.6     1       97886 5182
49      96017   0.6     1       90973 5044
50      95358   0.6     1       89955 5403
51      101937  0.6     1       97007 4930
52      72139   0.6     1       68343 3796
53      82879   0.6     1       78844 4035
54      74680   0.6     1       70731 3949
55      77624   0.6     1       73672 3952
56      73463   0.6     1       69959 3504
57      71484   0.6     1       67933 3551
58      67679   0.6     1       64415 3264
59      65277   0.6     1       62260 3017
60      62316   0.6     1       59174 3142
61      59439   0.6     1       56681 2758
62      58942   0.6     1       56276 2666
63      72060   0.6     1       61639 10421
64      400781  0.6     1       391238 9543
65      16165   0.6     1       15398 767
66      3813    0.6     1       3554 259
67      3171    0.6     1       2963 208
68      3216    0.6     1       3023 193
69      3183    0.6     1       2930 253
70      3233    0.6     1       3023 210
71      3436    0.6     1       3213 223
72      4087    0.6     1       3831 256
73      3774    0.6     1       3526 248
74      3963    0.6     1       3711 252
75      3115    0.6     1       2911 204
76      2630    0.6     1       2442 188
77      2229    0.6     1       2052 177
78      1622    0.6     1       1483 139
79      1344    0.6     1       1198 146
80      1222    0.6     1       1081 141
81      1021    0.6     1       899 122
82      934     0.6     1       819 115
83      847     0.6     1       754 93
84      679     0.6     1       581 98
85      594     0.6     1       492 102
86      500     0.6     1       410 90
87      478     0.6     1       383 95
88      407     0.6     1       310 97
89      362     0.6     1       270 92
90      332     0.6     1       254 78
91      285     0.6     1       203 82
92      274     0.6     1       195 79
93      251     0.6     1       175 76
94      207     0.6     1       121 86
95      187     0.6     1       110 77
96      215     0.6     1       122 93
97      193     0.6     1       116 77
98      163     0.6     1       95 68
99      151     0.6     1       83 68
100     139     0.6     1       70 69
101     172     0.6     1       91 81
102     135     0.6     1       78 57
103     120     0.6     1       51 69
104     117     0.6     1       69 48
105     128     0.6     1       63 65
106     117     0.6     1       57 60
107     106     0.6     1       48 58
108     115     0.6     1       47 68
109     112     0.6     1       65 47
110     105     0.6     1       44 61
111     108     0.6     1       46 62
112     96      0.6     1       31 65
113     98      0.6     1       43 55
114     101     0.6     1       37 64
115     90      0.6     1       36 54
116     88      0.6     1       38 50
117     84      0.6     1       38 46
118     87      0.6     1       30 57
119     97      0.6     1       35 62
120     74      0.6     1       32 42
121     113     0.6     1       53 60
122     73      0.6     1       26 47
123     79      0.6     1       29 50
124     67      0.6     1       30 37
125     66      0.6     1       22 44
126     67      0.6     1       16 51
127     65      0.6     1       13 52
128     44      0.6     1       9 35
129     48      0.6     1       10 38
130     45      0.6     1       13 32
131     36      0.6     1       6 30
132     50      0.6     1       4 46
133     49      0.6     1       3 46
134     41      0.6     1       2 39
135     49      0.6     1       1 48
136     54      0.6     1       1 53
137     53      0.6     1       4 49
138     60      0.6     1       2 58
139     41      0.6     1       1 40
140     46      0.6     1       0 46
141     37      0.6     1       0 37
142     49      0.6     1       1 48
143     39      0.6     1       0 39
144     58      0.6     1       0 58
145     58      0.6     1       0 58
146     59      0.6     1       0 59
147     53      0.6     1       0 53
148     62      0.6     1       0 62
149     82      0.6     1       0 82
150     207     0.6     1       2 205


RUN STATISTICS FOR INPUT FILE: SRR8707702_2.fastq.gz
=============================================
42376519 sequences processed in total
The length threshold of paired-end sequences gets evaluated later on (in the validation step)

Validate paired-end files SRR8707702_1_trimmed.fq.gz and SRR8707702_2_trimmed.fq.gz
file_1: SRR8707702_1_trimmed.fq.gz, file_2: SRR8707702_2_trimmed.fq.gz


>>>>> Now validing the length of the 2 paired-end infiles: SRR8707702_1_trimmed.fq.gz and SRR8707702_2_trimmed.fq.gz <<<<<
Writing validated paired-end read 1 reads to SRR8707702_1_val_1.fq.gz
Writing validated paired-end read 2 reads to SRR8707702_2_val_2.fq.gz