SUMMARISING RUN PARAMETERS
==========================
Input filename: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_16_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_16_R1_val_1.fq.gz
Processing reads on 1 core in single-end mode ...
Finished in 1421.46 s (28 µs/read; 2.18 M reads/minute).

=== Summary ===

Total reads processed:              51,615,953
Reads with adapters:                22,358,370 (43.3%)
Reads written (passing filters):    51,615,953 (100.0%)

Total basepairs processed: 5,398,887,438 bp
Quality-trimmed:               7,587,870 bp (0.1%)
Total written (filtered):  5,366,099,765 bp (99.4%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 22358370 times

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

Bases preceding removed adapters:
  A: 45.5%
  C: 10.5%
  G: 6.7%
  T: 37.4%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	20416303	12903988.2	0	20416303
2	1263682	3225997.1	0	1263682
3	465476	806499.3	0	465476
4	209912	201624.8	0	209912
5	1454	50406.2	0	1454
6	467	12601.6	0	467
7	180	3150.4	0	180
8	44	787.6	0	44
9	278	196.9	0	35 243
10	461	49.2	1	7 454
11	96	12.3	1	0 96
12	13	3.1	1	0 13
13	4	0.8	1	0 4

RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_16_R1_val_1.fq.gz
=============================================
51615953 sequences processed in total