SUMMARISING RUN PARAMETERS
==========================
Input filename: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_23_R1_val_1.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_23_R1_val_1.fq.gz
Processing reads on 1 core in single-end mode ...
Finished in 1080.05 s (27 µs/read; 2.25 M reads/minute).

=== Summary ===

Total reads processed:              40,539,021
Reads with adapters:                17,674,203 (43.6%)
Reads written (passing filters):    40,539,021 (100.0%)

Total basepairs processed: 4,280,801,776 bp
Quality-trimmed:               5,104,755 bp (0.1%)
Total written (filtered):  4,255,781,741 bp (99.4%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 17674203 times

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

Bases preceding removed adapters:
  A: 45.6%
  C: 10.4%
  G: 6.6%
  T: 37.4%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	16143667	10134755.2	0	16143667
2	996474	2533688.8	0	996474
3	363897	633422.2	0	363897
4	167893	158355.6	0	167893
5	1059	39588.9	0	1059
6	368	9897.2	0	368
7	134	2474.3	0	134
8	30	618.6	0	30
9	207	154.6	0	20 187
10	376	38.7	1	3 373
11	81	9.7	1	0 81
12	14	2.4	1	0 14
13	3	0.6	1	0 3

RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_23_R1_val_1.fq.gz
=============================================
40539021 sequences processed in total