SUMMARISING RUN PARAMETERS
==========================
Input filename: /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore/zr3616_6_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_6_R2_val_2.fq.gz
Processing reads on 1 core in single-end mode ...
Finished in 4368.39 s (22 µs/read; 2.68 M reads/minute).

=== Summary ===

Total reads processed:             195,031,602
Reads with adapters:                83,611,065 (42.9%)
Reads written (passing filters):   195,031,602 (100.0%)

Total basepairs processed: 18,453,430,191 bp
Quality-trimmed:              20,059,174 bp (0.1%)
Total written (filtered):  18,338,376,548 bp (99.4%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 83611065 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: 36.9%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	75861779	48757900.5	0	75861779
2	5056910	12189475.1	0	5056910
3	1784972	3047368.8	0	1784972
4	893213	761842.2	0	893213
5	8094	190460.5	0	8094
6	1813	47615.1	0	1813
7	750	11903.8	0	750
8	152	2975.9	0	152
9	1111	744.0	0	68 1043
10	1791	186.0	1	19 1772
11	398	46.5	1	3 395
12	79	11.6	1	0 79
13	1	2.9	1	0 1
20	2	2.9	1	0 2

RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore/zr3616_6_R2_val_2.fq.gz
=============================================
195031602 sequences processed in total

Total number of sequences analysed for the sequence pair length validation: 195031602

Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 209939 (0.11%)