SUMMARISING RUN PARAMETERS
==========================
Input filename: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_20_R1_val_1.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_20_R1_val_1.fq.gz
Processing reads on 1 core in single-end mode ...
Finished in 1767.68 s (33 µs/read; 1.84 M reads/minute).

=== Summary ===

Total reads processed:              54,084,897
Reads with adapters:                23,814,058 (44.0%)
Reads written (passing filters):    54,084,897 (100.0%)

Total basepairs processed: 5,774,617,900 bp
Quality-trimmed:              13,543,407 bp (0.2%)
Total written (filtered):  5,734,279,099 bp (99.3%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 23814058 times

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

Bases preceding removed adapters:
  A: 45.0%
  C: 11.2%
  G: 6.6%
  T: 37.3%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	21758968	13521224.2	0	21758968
2	1347678	3380306.1	0	1347678
3	498483	845076.5	0	498483
4	204292	211269.1	0	204292
5	2906	52817.3	0	2906
6	655	13204.3	0	655
7	197	3301.1	0	197
8	43	825.3	0	43
9	254	206.3	0	29 225
10	452	51.6	1	5 447
11	109	12.9	1	1 108
12	15	3.2	1	0 15
13	5	0.8	1	0 5
20	1	0.8	1	0 1

RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_20_R1_val_1.fq.gz
=============================================
54084897 sequences processed in total