SUMMARISING RUN PARAMETERS
==========================
Input filename: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_13_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_13_R1_val_1.fq.gz
Processing reads on 1 core in single-end mode ...
Finished in 1458.05 s (27 µs/read; 2.22 M reads/minute).

=== Summary ===

Total reads processed:              53,911,566
Reads with adapters:                23,651,701 (43.9%)
Reads written (passing filters):    53,911,566 (100.0%)

Total basepairs processed: 5,759,871,046 bp
Quality-trimmed:               6,988,047 bp (0.1%)
Total written (filtered):  5,726,266,859 bp (99.4%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 23651701 times

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

Bases preceding removed adapters:
  A: 45.7%
  C: 10.3%
  G: 6.4%
  T: 37.6%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	21623159	13477891.5	0	21623159
2	1323589	3369472.9	0	1323589
3	481744	842368.2	0	481744
4	220391	210592.1	0	220391
5	1296	52648.0	0	1296
6	512	13162.0	0	512
7	157	3290.5	0	157
8	42	822.6	0	42
9	228	205.7	0	15 213
10	466	51.4	1	8 458
11	101	12.9	1	5 96
12	14	3.2	1	0 14
13	1	0.8	1	0 1
16	1	0.8	1	0 1

RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_13_R1_val_1.fq.gz
=============================================
53911566 sequences processed in total