SUMMARISING RUN PARAMETERS
==========================
Input filename: /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore/zr3616_1_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_1_R2_val_2.fq.gz
Processing reads on 1 core in single-end mode ...
Finished in 3847.02 s (24 µs/read; 2.51 M reads/minute).

=== Summary ===

Total reads processed:             161,236,355
Reads with adapters:                69,092,736 (42.9%)
Reads written (passing filters):   161,236,355 (100.0%)

Total basepairs processed: 16,097,114,176 bp
Quality-trimmed:              16,560,046 bp (0.1%)
Total written (filtered):  16,002,140,047 bp (99.4%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 69092736 times

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

Bases preceding removed adapters:
  A: 45.2%
  C: 10.7%
  G: 7.2%
  T: 36.8%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	62721636	40309088.8	0	62721636
2	4174107	10077272.2	0	4174107
3	1471919	2519318.0	0	1471919
4	713701	629829.5	0	713701
5	6120	157457.4	0	6120
6	1724	39364.3	0	1724
7	626	9841.1	0	626
8	133	2460.3	0	133
9	843	615.1	0	76 767
10	1555	153.8	1	12 1543
11	325	38.4	1	1 324
12	42	9.6	1	0 42
13	4	2.4	1	0 4
14	1	2.4	1	0 1

RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore/zr3616_1_R2_val_2.fq.gz
=============================================
161236355 sequences processed in total

Total number of sequences analysed for the sequence pair length validation: 161236355

Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 131647 (0.08%)