SUMMARISING RUN PARAMETERS
==========================
Input filename: /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore/zr3616_4_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_4_R2_val_2.fq.gz
Processing reads on 1 core in single-end mode ...
Finished in 4583.87 s (23 µs/read; 2.59 M reads/minute).

=== Summary ===

Total reads processed:             197,994,215
Reads with adapters:                85,518,274 (43.2%)
Reads written (passing filters):   197,994,215 (100.0%)

Total basepairs processed: 19,331,276,134 bp
Quality-trimmed:              21,095,559 bp (0.1%)
Total written (filtered):  19,213,114,882 bp (99.4%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 85518274 times

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

Bases preceding removed adapters:
  A: 45.0%
  C: 10.8%
  G: 7.2%
  T: 37.0%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	77651535	49498553.8	0	77651535
2	5133623	12374638.4	0	5133623
3	1820996	3093659.6	0	1820996
4	898055	773414.9	0	898055
5	7474	193353.7	0	7474
6	2069	48338.4	0	2069
7	771	12084.6	0	771
8	194	3021.2	0	194
9	1156	755.3	0	78 1078
10	1930	188.8	1	14 1916
11	389	47.2	1	1 388
12	78	11.8	1	0 78
13	4	3.0	1	0 4

RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore/zr3616_4_R2_val_2.fq.gz
=============================================
197994215 sequences processed in total

Total number of sequences analysed for the sequence pair length validation: 197994215

Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 172073 (0.09%)