SUMMARISING RUN PARAMETERS
==========================
Input filename: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_15_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_15_R2_val_2.fq.gz
Processing reads on 1 core in single-end mode ...
Finished in 1622.12 s (27 µs/read; 2.19 M reads/minute).

=== Summary ===

Total reads processed:              59,137,561
Reads with adapters:                25,893,265 (43.8%)
Reads written (passing filters):    59,137,561 (100.0%)

Total basepairs processed: 6,290,547,044 bp
Quality-trimmed:              10,043,561 bp (0.2%)
Total written (filtered):  6,251,454,303 bp (99.4%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 25893265 times

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

Bases preceding removed adapters:
  A: 46.0%
  C: 10.1%
  G: 6.3%
  T: 37.6%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	23768673	14784390.2	0	23768673
2	1352013	3696097.6	0	1352013
3	522926	924024.4	0	522926
4	245795	231006.1	0	245795
5	2231	57751.5	0	2231
6	578	14437.9	0	578
7	136	3609.5	0	136
8	41	902.4	0	41
9	259	225.6	0	24 235
10	479	56.4	1	3 476
11	110	14.1	1	4 106
12	23	3.5	1	0 23
13	1	0.9	1	0 1

RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_15_R2_val_2.fq.gz
=============================================
59137561 sequences processed in total

Total number of sequences analysed for the sequence pair length validation: 59137561

Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 31899 (0.05%)