SUMMARISING RUN PARAMETERS
==========================
Input filename: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_12_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_12_R2_val_2.fq.gz
Processing reads on 1 core in single-end mode ...
Finished in 1303.79 s (27 µs/read; 2.19 M reads/minute).

=== Summary ===

Total reads processed:              47,672,940
Reads with adapters:                20,886,033 (43.8%)
Reads written (passing filters):    47,672,940 (100.0%)

Total basepairs processed: 5,056,045,086 bp
Quality-trimmed:               8,049,156 bp (0.2%)
Total written (filtered):  5,024,697,872 bp (99.4%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 20886033 times

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

Bases preceding removed adapters:
  A: 46.2%
  C: 10.0%
  G: 6.0%
  T: 37.8%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	19271195	11918235.0	0	19271195
2	1018652	2979558.8	0	1018652
3	401475	744889.7	0	401475
4	191842	186222.4	0	191842
5	1817	46555.6	0	1817
6	353	11638.9	0	353
7	94	2909.7	0	94
8	32	727.4	0	32
9	176	181.9	0	20 156
10	319	45.5	1	2 317
11	63	11.4	1	0 63
12	13	2.8	1	0 13
13	2	0.7	1	0 2

RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_12_R2_val_2.fq.gz
=============================================
47672940 sequences processed in total

Total number of sequences analysed for the sequence pair length validation: 47672940

Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 23117 (0.05%)