SUMMARISING RUN PARAMETERS
==========================
Input filename: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_17_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_17_R2_val_2.fq.gz
Processing reads on 1 core in single-end mode ...
Finished in 1586.41 s (27 µs/read; 2.21 M reads/minute).

=== Summary ===

Total reads processed:              58,307,693
Reads with adapters:                25,366,685 (43.5%)
Reads written (passing filters):    58,307,693 (100.0%)

Total basepairs processed: 6,158,132,185 bp
Quality-trimmed:               9,852,766 bp (0.2%)
Total written (filtered):  6,119,780,472 bp (99.4%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 25366685 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: 37.5%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	23256715	14576923.2	0	23256715
2	1345228	3644230.8	0	1345228
3	516661	911057.7	0	516661
4	244222	227764.4	0	244222
5	2194	56941.1	0	2194
6	506	14235.3	0	506
7	167	3558.8	0	167
8	41	889.7	0	41
9	263	222.4	0	16 247
10	558	55.6	1	3 555
11	105	13.9	1	1 104
12	25	3.5	1	0 25

RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_17_R2_val_2.fq.gz
=============================================
58307693 sequences processed in total

Total number of sequences analysed for the sequence pair length validation: 58307693

Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 33047 (0.06%)