SUMMARISING RUN PARAMETERS
==========================
Input filename: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_1_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_1_R2_val_2.fq.gz
Processing reads on 1 core in single-end mode ...
Finished in 1487.11 s (29 µs/read; 2.10 M reads/minute).

=== Summary ===

Total reads processed:              51,950,473
Reads with adapters:                22,677,249 (43.7%)
Reads written (passing filters):    51,950,473 (100.0%)

Total basepairs processed: 5,474,149,564 bp
Quality-trimmed:              11,112,152 bp (0.2%)
Total written (filtered):  5,437,608,277 bp (99.3%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 22677249 times

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

Bases preceding removed adapters:
  A: 45.8%
  C: 10.4%
  G: 6.4%
  T: 37.4%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	20832854	12987618.2	0	20832854
2	1164953	3246904.6	0	1164953
3	459994	811726.1	0	459994
4	215556	202931.5	0	215556
5	2455	50732.9	0	2455
6	462	12683.2	0	462
7	148	3170.8	0	148
8	34	792.7	0	34
9	242	198.2	0	34 208
10	445	49.5	1	9 436
11	87	12.4	1	1 86
12	18	3.1	1	0 18
13	1	0.8	1	0 1

RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_1_R2_val_2.fq.gz
=============================================
51950473 sequences processed in total

Total number of sequences analysed for the sequence pair length validation: 51950473

Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 34186 (0.07%)