SUMMARISING RUN PARAMETERS
==========================
Input filename: L79-Saccharomyces_paradoxus-CG_only.end2.36mers.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.end2.36mers.fastq.gz
Running on 1 core
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 225.09 s (23 us/read; 2.66 M reads/minute).

=== Summary ===

Total reads processed:               9,970,308
Reads with adapters:                 3,603,709 (36.1%)
Reads written (passing filters):     9,970,308 (100.0%)

Total basepairs processed:   358,931,088 bp
Quality-trimmed:               8,082,170 bp (2.3%)
Total written (filtered):    336,796,172 bp (93.8%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 3603709 times.

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

Bases preceding removed adapters:
  A: 40.6%
  C: 2.3%
  G: 14.2%
  T: 41.2%
  none/other: 1.8%

Overview of removed sequences
length	count	expect	max.err	error counts
1	2179686	2492577.0	0	2179686
2	566130	623144.2	0	566130
3	216164	155786.1	0	216164
4	105411	38946.5	0	105411
5	26952	9736.6	0	26952
6	16437	2434.2	0	16437
7	11073	608.5	0	11073
8	10077	152.1	0	10077
9	10845	38.0	0	10805 40
10	19413	9.5	1	11377 8036
11	14908	2.4	1	8195 6713
12	17496	0.6	1	10196 7300
13	17810	0.1	1	10341 7469
14	17428	0.1	1	10132 7296
15	16654	0.1	1	9449 7205
16	17388	0.1	1	9947 7441
17	18500	0.1	1	10402 8098
18	24534	0.1	1	12887 11647
19	48374	0.1	1	25776 22598
20	29950	0.1	1	16480 13470
21	37926	0.1	1	23216 14710
22	16130	0.1	1	11158 4972
23	38889	0.1	1	32492 6397
24	47943	0.1	1	40730 7213
25	9938	0.1	1	7903 2035
26	14697	0.1	1	12182 2515
27	19713	0.1	1	16376 3337
28	3695	0.1	1	2933 762
29	20039	0.1	1	16239 3800
30	4343	0.1	1	3291 1052
31	3863	0.1	1	2122 1741
32	1120	0.1	1	202 918
33	182	0.1	1	34 148
34	1	0.1	1	0 1


RUN STATISTICS FOR INPUT FILE: L79-Saccharomyces_paradoxus-CG_only.end2.36mers.fastq.gz
=============================================
9970308 sequences processed in total

Total number of sequences analysed for the sequence pair length validation: 9970308

Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 655519 (6.57%)