SUMMARISING RUN PARAMETERS
==========================
Input filename: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_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/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_4_R2_val_2.fq.gz
Processing reads on 1 core in single-end mode ...
Finished in 1348.15 s (27 µs/read; 2.23 M reads/minute).

=== Summary ===

Total reads processed:              50,012,460
Reads with adapters:                21,882,879 (43.8%)
Reads written (passing filters):    50,012,460 (100.0%)

Total basepairs processed: 5,316,873,875 bp
Quality-trimmed:               7,825,202 bp (0.1%)
Total written (filtered):  5,284,547,154 bp (99.4%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 21882879 times

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

Bases preceding removed adapters:
  A: 46.0%
  C: 10.1%
  G: 6.2%
  T: 37.6%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	20120821	12503115.0	0	20120821
2	1120477	3125778.8	0	1120477
3	433542	781444.7	0	433542
4	205117	195361.2	0	205117
5	1655	48840.3	0	1655
6	429	12210.1	0	429
7	134	3052.5	0	134
8	36	763.1	0	36
9	200	190.8	0	20 180
10	387	47.7	1	4 383
11	68	11.9	1	0 68
12	12	3.0	1	0 12
13	1	0.7	1	0 1

RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_4_R2_val_2.fq.gz
=============================================
50012460 sequences processed in total

Total number of sequences analysed for the sequence pair length validation: 50012460

Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 24805 (0.05%)