SUMMARISING RUN PARAMETERS
==========================
Input filename: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_8_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_8_R2_val_2.fq.gz
Processing reads on 1 core in single-end mode ...
Finished in 1198.73 s (28 µs/read; 2.15 M reads/minute).

=== Summary ===

Total reads processed:              42,944,059
Reads with adapters:                18,798,887 (43.8%)
Reads written (passing filters):    42,944,059 (100.0%)

Total basepairs processed: 4,552,516,502 bp
Quality-trimmed:               8,191,924 bp (0.2%)
Total written (filtered):  4,523,218,672 bp (99.4%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 18798887 times

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

Bases preceding removed adapters:
  A: 45.8%
  C: 10.3%
  G: 6.4%
  T: 37.5%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	17247458	10736014.8	0	17247458
2	984900	2684003.7	0	984900
3	384804	671000.9	0	384804
4	178516	167750.2	0	178516
5	1921	41937.6	0	1921
6	433	10484.4	0	433
7	133	2621.1	0	133
8	25	655.3	0	25
9	229	163.8	0	23 206
10	385	41.0	1	3 382
11	69	10.2	1	0 69
12	14	2.6	1	0 14

RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_8_R2_val_2.fq.gz
=============================================
42944059 sequences processed in total

Total number of sequences analysed for the sequence pair length validation: 42944059

Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 25551 (0.06%)