SUMMARISING RUN PARAMETERS
==========================
Input filename: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_16_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_16_R2_val_2.fq.gz
Processing reads on 1 core in single-end mode ...
Finished in 1393.63 s (27 µs/read; 2.22 M reads/minute).

=== Summary ===

Total reads processed:              51,615,953
Reads with adapters:                22,307,149 (43.2%)
Reads written (passing filters):    51,615,953 (100.0%)

Total basepairs processed: 5,398,402,113 bp
Quality-trimmed:               9,050,977 bp (0.2%)
Total written (filtered):  5,364,300,606 bp (99.4%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 22307149 times

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

Bases preceding removed adapters:
  A: 45.8%
  C: 10.3%
  G: 6.5%
  T: 37.4%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	20464399	12903988.2	0	20464399
2	1169773	3225997.1	0	1169773
3	453692	806499.3	0	453692
4	215709	201624.8	0	215709
5	2078	50406.2	0	2078
6	491	12601.6	0	491
7	177	3150.4	0	177
8	31	787.6	0	31
9	248	196.9	0	26 222
10	459	49.2	1	3 456
11	78	12.3	1	0 78
12	12	3.1	1	0 12
13	2	0.8	1	0 2

RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_16_R2_val_2.fq.gz
=============================================
51615953 sequences processed in total

Total number of sequences analysed for the sequence pair length validation: 51615953

Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 31598 (0.06%)