SUMMARISING RUN PARAMETERS
==========================
Input filename: /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore/zr3616_5_R2_val_2.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_5_R2_val_2.fq.gz
Processing reads on 1 core in single-end mode ...
Finished in 3400.83 s (23 µs/read; 2.62 M reads/minute).

=== Summary ===

Total reads processed:             148,703,891
Reads with adapters:                63,834,369 (42.9%)
Reads written (passing filters):   148,703,891 (100.0%)

Total basepairs processed: 14,313,656,899 bp
Quality-trimmed:              15,779,438 bp (0.1%)
Total written (filtered):  14,225,303,648 bp (99.4%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 63834369 times

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

Bases preceding removed adapters:
  A: 45.0%
  C: 10.8%
  G: 7.3%
  T: 37.0%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	57873635	37175972.8	0	57873635
2	3899292	9293993.2	0	3899292
3	1371063	2323498.3	0	1371063
4	679337	580874.6	0	679337
5	6129	145218.6	0	6129
6	1562	36304.7	0	1562
7	607	9076.2	0	607
8	132	2269.0	0	132
9	850	567.3	0	53 797
10	1426	141.8	1	17 1409
11	269	35.5	1	0 269
12	59	8.9	1	0 59
13	6	2.2	1	0 6
17	1	2.2	1	0 1
63	1	2.2	1	0 1

RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore/zr3616_5_R2_val_2.fq.gz
=============================================
148703891 sequences processed in total

Total number of sequences analysed for the sequence pair length validation: 148703891

Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 147339 (0.10%)