SUMMARISING RUN PARAMETERS
==========================
Input filename: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_12_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_12_R1_val_1.fq.gz
Processing reads on 1 core in single-end mode ...
Finished in 1270.40 s (27 µs/read; 2.25 M reads/minute).

=== Summary ===

Total reads processed:              47,672,940
Reads with adapters:                20,907,864 (43.9%)
Reads written (passing filters):    47,672,940 (100.0%)

Total basepairs processed: 5,057,370,806 bp
Quality-trimmed:               5,436,445 bp (0.1%)
Total written (filtered):  5,028,568,661 bp (99.4%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 20907864 times

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

Bases preceding removed adapters:
  A: 46.1%
  C: 10.2%
  G: 6.1%
  T: 37.6%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	19232385	11918235.0	0	19232385
2	1088137	2979558.8	0	1088137
3	398188	744889.7	0	398188
4	186980	186222.4	0	186980
5	1039	46555.6	0	1039
6	370	11638.9	0	370
7	124	2909.7	0	124
8	38	727.4	0	38
9	160	181.9	0	13 147
10	368	45.5	1	8 360
11	61	11.4	1	1 60
12	11	2.8	1	0 11
13	2	0.7	1	0 2
21	1	0.7	1	0 1

RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_12_R1_val_1.fq.gz
=============================================
47672940 sequences processed in total