SUMMARISING RUN PARAMETERS
==========================
Input filename: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_24_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_24_R2_val_2.fq.gz
Processing reads on 1 core in single-end mode ...
Finished in 1460.85 s (28 µs/read; 2.17 M reads/minute).

=== Summary ===

Total reads processed:              52,922,544
Reads with adapters:                23,136,470 (43.7%)
Reads written (passing filters):    52,922,544 (100.0%)

Total basepairs processed: 5,624,990,440 bp
Quality-trimmed:               8,998,238 bp (0.2%)
Total written (filtered):  5,590,031,647 bp (99.4%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 23136470 times

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

Bases preceding removed adapters:
  A: 45.9%
  C: 10.2%
  G: 6.4%
  T: 37.5%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	21235591	13230636.0	0	21235591
2	1208767	3307659.0	0	1208767
3	469015	826914.8	0	469015
4	219623	206728.7	0	219623
5	2038	51682.2	0	2038
6	484	12920.5	0	484
7	178	3230.1	0	178
8	30	807.5	0	30
9	237	201.9	0	22 215
10	415	50.5	1	1 414
11	75	12.6	1	1 74
12	16	3.2	1	0 16
13	1	0.8	1	0 1

RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_24_R2_val_2.fq.gz
=============================================
52922544 sequences processed in total

Total number of sequences analysed for the sequence pair length validation: 52922544

Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 27654 (0.05%)