SUMMARISING RUN PARAMETERS
==========================
Input filename: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_24_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/Hawes/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/Hawes/analyses/trimgalore/zr3644_24_R1_val_1.fq.gz
Processing reads on 1 core in single-end mode ...
Finished in 1461.67 s (28 µs/read; 2.17 M reads/minute).

=== Summary ===

Total reads processed:              52,922,544
Reads with adapters:                23,174,909 (43.8%)
Reads written (passing filters):    52,922,544 (100.0%)

Total basepairs processed: 5,625,540,317 bp
Quality-trimmed:               7,113,215 bp (0.1%)
Total written (filtered):  5,592,330,989 bp (99.4%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 23174909 times

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

Bases preceding removed adapters:
  A: 45.6%
  C: 10.4%
  G: 6.5%
  T: 37.4%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	21176762	13230636.0	0	21176762
2	1303077	3307659.0	0	1303077
3	474958	826914.8	0	474958
4	217209	206728.7	0	217209
5	1352	51682.2	0	1352
6	526	12920.5	0	526
7	159	3230.1	0	159
8	46	807.5	0	46
9	242	201.9	0	22 220
10	465	50.5	1	8 457
11	98	12.6	1	0 98
12	13	3.2	1	0 13
13	1	0.8	1	0 1
15	1	0.8	1	0 1

RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_24_R1_val_1.fq.gz
=============================================
52922544 sequences processed in total