SUMMARISING RUN PARAMETERS
==========================
Input filename: /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore/zr3616_4_R1_val_1.fq.gz
Trimming mode: paired-end
Trim Galore version: 0.6.6
Cutadapt version: 3.1
Number of cores used for trimming: 1
Quality Phred score cutoff: 20
Quality encoding type selected: ASCII+33
Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; user defined)
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
Running FastQC on the data once trimming has completed
Running FastQC with the following extra arguments: --outdir /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2 --threads 28
Output file will be GZIP compressed


This is cutadapt 3.1 with Python 3.8.5
Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore/zr3616_4_R1_val_1.fq.gz
Processing reads on 1 core in single-end mode ...
Finished in 4471.78 s (23 µs/read; 2.66 M reads/minute).

=== Summary ===

Total reads processed:             197,994,215
Reads with adapters:                85,382,636 (43.1%)
Reads written (passing filters):   197,994,215 (100.0%)

Total basepairs processed: 19,327,202,283 bp
Quality-trimmed:              14,840,406 bp (0.1%)
Total written (filtered):  19,215,160,741 bp (99.4%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 85382636 times

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

Bases preceding removed adapters:
  A: 44.9%
  C: 10.8%
  G: 7.4%
  T: 37.0%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	77293926	49498553.8	0	77293926
2	5309316	12374638.4	0	5309316
3	1862901	3093659.6	0	1862901
4	904500	773414.9	0	904500
5	5358	193353.7	0	5358
6	2008	48338.4	0	2008
7	782	12084.6	0	782
8	157	3021.2	0	157
9	1122	755.3	0	57 1065
10	2103	188.8	1	15 2088
11	393	47.2	1	5 388
12	66	11.8	1	0 66
13	2	3.0	1	0 2
19	2	3.0	1	0 2

RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore/zr3616_4_R1_val_1.fq.gz
=============================================
197994215 sequences processed in total