SUMMARISING RUN PARAMETERS
==========================
Input filename: L78-Saccharomyces_paradoxus-GC+CG.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 L78-Saccharomyces_paradoxus-GC+CG.end2.36mers.fastq.gz
Running on 1 core
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 187.98 s (21 us/read; 2.84 M reads/minute).

=== Summary ===

Total reads processed:               8,886,861
Reads with adapters:                 3,393,885 (38.2%)
Reads written (passing filters):     8,886,861 (100.0%)

Total basepairs processed:   319,926,996 bp
Quality-trimmed:               6,786,956 bp (2.1%)
Total written (filtered):    298,026,466 bp (93.2%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 3393885 times.

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

Bases preceding removed adapters:
  A: 41.1%
  C: 3.0%
  G: 13.2%
  T: 41.0%
  none/other: 1.8%

Overview of removed sequences
length	count	expect	max.err	error counts
1	1986801	2221715.2	0	1986801
2	502916	555428.8	0	502916
3	195044	138857.2	0	195044
4	95613	34714.3	0	95613
5	28479	8678.6	0	28479
6	17913	2169.6	0	17913
7	12370	542.4	0	12370
8	11329	135.6	0	11329
9	11881	33.9	0	11842 39
10	21594	8.5	1	12795 8799
11	15798	2.1	1	8645 7153
12	20149	0.5	1	11857 8292
13	19869	0.1	1	11416 8453
14	20461	0.1	1	11688 8773
15	18536	0.1	1	10578 7958
16	19475	0.1	1	10967 8508
17	22105	0.1	1	12285 9820
18	26713	0.1	1	13890 12823
19	57038	0.1	1	30348 26690
20	32725	0.1	1	17761 14964
21	41388	0.1	1	25101 16287
22	20479	0.1	1	14205 6274
23	48087	0.1	1	39793 8294
24	60967	0.1	1	51233 9734
25	10912	0.1	1	8626 2286
26	17680	0.1	1	14407 3273
27	22963	0.1	1	18853 4110
28	4767	0.1	1	3828 939
29	18832	0.1	1	15094 3738
30	5073	0.1	1	3880 1193
31	4426	0.1	1	2394 2032
32	1359	0.1	1	220 1139
33	136	0.1	1	17 119
34	3	0.1	1	0 3
35	3	0.1	1	1 2
36	1	0.1	1	0 1


RUN STATISTICS FOR INPUT FILE: L78-Saccharomyces_paradoxus-GC+CG.end2.36mers.fastq.gz
=============================================
8886861 sequences processed in total

Total number of sequences analysed for the sequence pair length validation: 8886861

Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 727210 (8.18%)