SUMMARISING RUN PARAMETERS
==========================
Input filename: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_1_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_1_R1_val_1.fq.gz
Processing reads on 1 core in single-end mode ...
Finished in 1380.46 s (27 µs/read; 2.26 M reads/minute).

=== Summary ===

Total reads processed:              51,950,473
Reads with adapters:                22,538,617 (43.4%)
Reads written (passing filters):    51,950,473 (100.0%)

Total basepairs processed: 5,475,353,592 bp
Quality-trimmed:               6,215,557 bp (0.1%)
Total written (filtered):  5,443,726,454 bp (99.4%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 22538617 times

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

Bases preceding removed adapters:
  A: 45.5%
  C: 10.3%
  G: 6.6%
  T: 37.5%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	20574469	12987618.2	0	20574469
2	1281458	3246904.6	0	1281458
3	464321	811726.1	0	464321
4	215633	202931.5	0	215633
5	1239	50732.9	0	1239
6	459	12683.2	0	459
7	150	3170.8	0	150
8	35	792.7	0	35
9	243	198.2	0	22 221
10	503	49.5	1	4 499
11	84	12.4	1	0 84
12	18	3.1	1	0 18
13	5	0.8	1	0 5

RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_1_R1_val_1.fq.gz
=============================================
51950473 sequences processed in total