SUMMARISING RUN PARAMETERS
==========================
Input filename: L77-Saccharomyces_paradoxus-GC_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 L77-Saccharomyces_paradoxus-GC_only.end2.36mers.fastq.gz
Running on 1 core
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 131.02 s (20 us/read; 2.99 M reads/minute).

=== Summary ===

Total reads processed:               6,527,676
Reads with adapters:                 2,458,521 (37.7%)
Reads written (passing filters):     6,527,676 (100.0%)

Total basepairs processed:   234,996,336 bp
Quality-trimmed:               4,772,683 bp (2.0%)
Total written (filtered):    219,906,050 bp (93.6%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 2458521 times.

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

Bases preceding removed adapters:
  A: 41.1%
  C: 3.1%
  G: 13.5%
  T: 40.5%
  none/other: 1.8%

Overview of removed sequences
length	count	expect	max.err	error counts
1	1470354	1631919.0	0	1470354
2	370889	407979.8	0	370889
3	142213	101994.9	0	142213
4	70065	25498.7	0	70065
5	18701	6374.7	0	18701
6	11586	1593.7	0	11586
7	7893	398.4	0	7893
8	7372	99.6	0	7372
9	7608	24.9	0	7578 30
10	14342	6.2	1	8434 5908
11	10500	1.6	1	5832 4668
12	13483	0.4	1	7878 5605
13	12689	0.1	1	7306 5383
14	13505	0.1	1	7725 5780
15	12070	0.1	1	6897 5173
16	12719	0.1	1	7253 5466
17	14257	0.1	1	8043 6214
18	17430	0.1	1	9086 8344
19	36654	0.1	1	19354 17300
20	21439	0.1	1	11667 9772
21	26987	0.1	1	16445 10542
22	13954	0.1	1	9716 4238
23	32149	0.1	1	26555 5594
24	41075	0.1	1	34547 6528
25	7643	0.1	1	6015 1628
26	11849	0.1	1	9732 2117
27	15128	0.1	1	12534 2594
28	3324	0.1	1	2652 672
29	12354	0.1	1	9834 2520
30	3835	0.1	1	2842 993
31	3361	0.1	1	1760 1601
32	959	0.1	1	167 792
33	130	0.1	1	21 109
34	4	0.1	1	0 4


RUN STATISTICS FOR INPUT FILE: L77-Saccharomyces_paradoxus-GC_only.end2.36mers.fastq.gz
=============================================
6527676 sequences processed in total

Total number of sequences analysed for the sequence pair length validation: 6527676

Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 477272 (7.31%)