SUMMARISING RUN PARAMETERS
==========================
Input filename: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_6_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_6_R2_val_2.fq.gz
Processing reads on 1 core in single-end mode ...
Finished in 1465.48 s (27 µs/read; 2.21 M reads/minute).

=== Summary ===

Total reads processed:              54,032,664
Reads with adapters:                23,564,542 (43.6%)
Reads written (passing filters):    54,032,664 (100.0%)

Total basepairs processed: 5,744,903,513 bp
Quality-trimmed:               9,195,296 bp (0.2%)
Total written (filtered):  5,709,275,896 bp (99.4%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 23564542 times

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

Bases preceding removed adapters:
  A: 45.9%
  C: 10.2%
  G: 6.3%
  T: 37.6%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	21632860	13508166.0	0	21632860
2	1230197	3377041.5	0	1230197
3	475335	844260.4	0	475335
4	222590	211065.1	0	222590
5	2056	52766.3	0	2056
6	484	13191.6	0	484
7	172	3297.9	0	172
8	41	824.5	0	41
9	237	206.1	0	13 224
10	447	51.5	1	8 439
11	96	12.9	1	2 94
12	24	3.2	1	0 24
13	3	0.8	1	0 3

RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_6_R2_val_2.fq.gz
=============================================
54032664 sequences processed in total

Total number of sequences analysed for the sequence pair length validation: 54032664

Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 28525 (0.05%)