SUMMARISING RUN PARAMETERS
==========================
Input filename: /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore/zr3616_7_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/Manchester/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/Manchester/analyses/trimgalore/zr3616_7_R2_val_2.fq.gz
Processing reads on 1 core in single-end mode ...
Finished in 3473.50 s (23 µs/read; 2.58 M reads/minute).

=== Summary ===

Total reads processed:             149,222,025
Reads with adapters:                64,464,629 (43.2%)
Reads written (passing filters):   149,222,025 (100.0%)

Total basepairs processed: 14,426,694,309 bp
Quality-trimmed:              16,612,357 bp (0.1%)
Total written (filtered):  14,336,913,165 bp (99.4%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 64464629 times

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

Bases preceding removed adapters:
  A: 44.9%
  C: 10.8%
  G: 7.2%
  T: 37.1%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	58535083	37305506.2	0	58535083
2	3869783	9326376.6	0	3869783
3	1371391	2331594.1	0	1371391
4	676997	582898.5	0	676997
5	6639	145724.6	0	6639
6	1592	36431.2	0	1592
7	522	9107.8	0	522
8	113	2276.9	0	113
9	829	569.2	0	67 762
10	1366	142.3	1	8 1358
11	260	35.6	1	3 257
12	43	8.9	1	0 43
13	9	2.2	1	0 9
29	2	2.2	1	0 2

RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore/zr3616_7_R2_val_2.fq.gz
=============================================
149222025 sequences processed in total

Total number of sequences analysed for the sequence pair length validation: 149222025

Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 141961 (0.10%)