SUMMARISING RUN PARAMETERS
==========================
Input filename: L79-Saccharomyces_paradoxus-CG_only.end1.36mers.fastq.gz
Trimming mode: paired-end
Trim Galore version: 0.4.4
Cutadapt version: 1.15
Quality Phred score cutoff: 20
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): 1 bp
Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp
All sequences will be trimmed by 1 bp on their 3' end to avoid problems with invalid paired-end alignments with Bowtie 1
Output file will be GZIP compressed


This is cutadapt 1.15 with Python 2.7.14+
Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC L79-Saccharomyces_paradoxus-CG_only.end1.36mers.fastq.gz
Running on 1 core
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 242.99 s (24 us/read; 2.46 M reads/minute).

=== Summary ===

Total reads processed:               9,970,308
Reads with adapters:                 5,396,006 (54.1%)
Reads written (passing filters):     9,970,308 (100.0%)

Total basepairs processed:   358,931,088 bp
Quality-trimmed:               3,506,358 bp (1.0%)
Total written (filtered):    333,294,443 bp (92.9%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 5396006 times.

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

Bases preceding removed adapters:
  A: 57.5%
  C: 14.1%
  G: 1.5%
  T: 26.9%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	4101121	2492577.0	0	4101121
2	101865	623144.2	0	101865
3	71074	155786.1	0	71074
4	56857	38946.5	0	56857
5	47231	9736.6	0	47231
6	44490	2434.2	0	44490
7	42207	608.5	0	42207
8	41371	152.1	0	41371
9	43386	38.0	0	43080 306
10	54707	9.5	1	47213 7494
11	39584	2.4	1	31766 7818
12	47135	0.6	1	39522 7613
13	55516	0.1	1	46407 9109
14	38203	0.1	1	30384 7819
15	56483	0.1	1	46446 10037
16	35849	0.1	1	28707 7142
17	49015	0.1	1	40121 8894
18	50156	0.1	1	41805 8351
19	48412	0.1	1	40260 8152
20	48876	0.1	1	40639 8237
21	49620	0.1	1	41311 8309
22	55415	0.1	1	47598 7817
23	45578	0.1	1	38696 6882
24	39579	0.1	1	33956 5623
25	24551	0.1	1	21036 3515
26	14966	0.1	1	12600 2366
27	11733	0.1	1	9557 2176
28	14605	0.1	1	11031 3574
29	19593	0.1	1	13344 6249
30	19786	0.1	1	10275 9511
31	12949	0.1	1	3880 9069
32	10550	0.1	1	1382 9168
33	3357	0.1	1	59 3298
34	159	0.1	1	0 159
35	21	0.1	1	0 21
36	6	0.1	1	0 6


RUN STATISTICS FOR INPUT FILE: L79-Saccharomyces_paradoxus-CG_only.end1.36mers.fastq.gz
=============================================
9970308 sequences processed in total