SUMMARISING RUN PARAMETERS
==========================
Input filename: /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore/zr3616_7_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_7_R1_val_1.fq.gz
Processing reads on 1 core in single-end mode ...
Finished in 3412.55 s (23 µs/read; 2.62 M reads/minute).

=== Summary ===

Total reads processed:             149,222,025
Reads with adapters:                64,446,811 (43.2%)
Reads written (passing filters):   149,222,025 (100.0%)

Total basepairs processed: 14,426,231,802 bp
Quality-trimmed:              12,087,412 bp (0.1%)
Total written (filtered):  14,340,775,620 bp (99.4%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 64446811 times

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

Bases preceding removed adapters:
  A: 44.7%
  C: 10.7%
  G: 7.3%
  T: 37.3%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	58345741	37305506.2	0	58345741
2	4001019	9326376.6	0	4001019
3	1403784	2331594.1	0	1403784
4	686989	582898.5	0	686989
5	4511	145724.6	0	4511
6	1581	36431.2	0	1581
7	534	9107.8	0	534
8	109	2276.9	0	109
9	828	569.2	0	39 789
10	1365	142.3	1	16 1349
11	284	35.6	1	1 283
12	62	8.9	1	0 62
13	2	2.2	1	0 2
16	1	2.2	1	0 1
20	1	2.2	1	0 1

RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore/zr3616_7_R1_val_1.fq.gz
=============================================
149222025 sequences processed in total