SUMMARISING RUN PARAMETERS
==========================
Input filename: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_17_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_17_R1_val_1.fq.gz
Processing reads on 1 core in single-end mode ...
Finished in 1556.05 s (27 µs/read; 2.25 M reads/minute).

=== Summary ===

Total reads processed:              58,307,693
Reads with adapters:                25,412,767 (43.6%)
Reads written (passing filters):    58,307,693 (100.0%)

Total basepairs processed: 6,158,828,348 bp
Quality-trimmed:               7,031,454 bp (0.1%)
Total written (filtered):  6,123,151,465 bp (99.4%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 25412767 times

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

Bases preceding removed adapters:
  A: 45.6%
  C: 10.5%
  G: 6.6%
  T: 37.3%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	23203313	14576923.2	0	23203313
2	1440507	3644230.8	0	1440507
3	523661	911057.7	0	523661
4	241985	227764.4	0	241985
5	1584	56941.1	0	1584
6	542	14235.3	0	542
7	179	3558.8	0	179
8	44	889.7	0	44
9	291	222.4	0	21 270
10	544	55.6	1	6 538
11	93	13.9	1	1 92
12	17	3.5	1	0 17
13	3	0.9	1	0 3
17	1	0.9	1	0 1
19	2	0.9	1	0 2
22	1	0.9	1	0 1

RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_17_R1_val_1.fq.gz
=============================================
58307693 sequences processed in total