SUMMARISING RUN PARAMETERS
==========================
Input filename: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_21_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/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_21_R2_val_2.fq.gz
Processing reads on 1 core in single-end mode ...
Finished in 1399.67 s (27 µs/read; 2.19 M reads/minute).

=== Summary ===

Total reads processed:              51,112,555
Reads with adapters:                22,379,133 (43.8%)
Reads written (passing filters):    51,112,555 (100.0%)

Total basepairs processed: 5,444,089,562 bp
Quality-trimmed:               8,820,277 bp (0.2%)
Total written (filtered):  5,410,194,746 bp (99.4%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 22379133 times

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

Bases preceding removed adapters:
  A: 46.0%
  C: 10.2%
  G: 6.3%
  T: 37.6%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	20565028	12778138.8	0	20565028
2	1153680	3194534.7	0	1153680
3	446995	798633.7	0	446995
4	210217	199658.4	0	210217
5	1879	49914.6	0	1879
6	458	12478.7	0	458
7	132	3119.7	0	132
8	39	779.9	0	39
9	234	195.0	0	24 210
10	385	48.7	1	3 382
11	71	12.2	1	1 70
12	13	3.0	1	0 13
13	2	0.8	1	0 2

RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_21_R2_val_2.fq.gz
=============================================
51112555 sequences processed in total

Total number of sequences analysed for the sequence pair length validation: 51112555

Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 27784 (0.05%)