SUMMARISING RUN PARAMETERS
==========================
Input filename: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_14_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_14_R2_val_2.fq.gz
Processing reads on 1 core in single-end mode ...
Finished in 990.19 s (27 µs/read; 2.23 M reads/minute).

=== Summary ===

Total reads processed:              36,871,756
Reads with adapters:                16,076,590 (43.6%)
Reads written (passing filters):    36,871,756 (100.0%)

Total basepairs processed: 3,913,759,881 bp
Quality-trimmed:               5,533,727 bp (0.1%)
Total written (filtered):  3,890,189,244 bp (99.4%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 16076590 times

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

Bases preceding removed adapters:
  A: 45.9%
  C: 10.1%
  G: 6.3%
  T: 37.7%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	14757826	9217939.0	0	14757826
2	839052	2304484.8	0	839052
3	323487	576121.2	0	323487
4	153983	144030.3	0	153983
5	1202	36007.6	0	1202
6	352	9001.9	0	352
7	99	2250.5	0	99
8	27	562.6	0	27
9	176	140.7	0	13 163
10	292	35.2	1	2 290
11	77	8.8	1	0 77
12	16	2.2	1	0 16
13	1	0.5	1	0 1

RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_14_R2_val_2.fq.gz
=============================================
36871756 sequences processed in total

Total number of sequences analysed for the sequence pair length validation: 36871756

Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 19172 (0.05%)