SUMMARISING RUN PARAMETERS
==========================
Input filename: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_2_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_2_R2_val_2.fq.gz
Processing reads on 1 core in single-end mode ...
Finished in 1547.14 s (28 µs/read; 2.16 M reads/minute).

=== Summary ===

Total reads processed:              55,664,369
Reads with adapters:                24,450,667 (43.9%)
Reads written (passing filters):    55,664,369 (100.0%)

Total basepairs processed: 5,972,628,915 bp
Quality-trimmed:              10,635,459 bp (0.2%)
Total written (filtered):  5,934,603,445 bp (99.4%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 24450667 times

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

Bases preceding removed adapters:
  A: 46.0%
  C: 10.2%
  G: 6.2%
  T: 37.6%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	22474453	13916092.2	0	22474453
2	1253246	3479023.1	0	1253246
3	491137	869755.8	0	491137
4	228272	217438.9	0	228272
5	2056	54359.7	0	2056
6	529	13589.9	0	529
7	143	3397.5	0	143
8	35	849.4	0	35
9	251	212.3	0	19 232
10	439	53.1	1	2 437
11	90	13.3	1	0 90
12	15	3.3	1	0 15
13	1	0.8	1	0 1

RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_2_R2_val_2.fq.gz
=============================================
55664369 sequences processed in total

Total number of sequences analysed for the sequence pair length validation: 55664369

Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 27982 (0.05%)