SUMMARISING RUN PARAMETERS
==========================
Input filename: /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore/zr3616_8_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_8_R2_val_2.fq.gz
Processing reads on 1 core in single-end mode ...
Finished in 3769.29 s (23 µs/read; 2.57 M reads/minute).

=== Summary ===

Total reads processed:             161,458,218
Reads with adapters:                69,620,122 (43.1%)
Reads written (passing filters):   161,458,218 (100.0%)

Total basepairs processed: 15,679,022,191 bp
Quality-trimmed:              17,518,289 bp (0.1%)
Total written (filtered):  15,582,472,384 bp (99.4%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 69620122 times

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

Bases preceding removed adapters:
  A: 45.0%
  C: 10.8%
  G: 7.2%
  T: 37.0%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	63214029	40364554.5	0	63214029
2	4176619	10091138.6	0	4176619
3	1483295	2522784.7	0	1483295
4	734105	630696.2	0	734105
5	6633	157674.0	0	6633
6	1712	39418.5	0	1712
7	684	9854.6	0	684
8	128	2463.7	0	128
9	920	615.9	0	50 870
10	1628	154.0	1	10 1618
11	315	38.5	1	5 310
12	47	9.6	1	0 47
13	5	2.4	1	0 5
15	1	2.4	1	0 1
28	1	2.4	1	0 1

RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore/zr3616_8_R2_val_2.fq.gz
=============================================
161458218 sequences processed in total

Total number of sequences analysed for the sequence pair length validation: 161458218

Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 148434 (0.09%)