SUMMARISING RUN PARAMETERS
==========================
Input filename: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_7_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_7_R2_val_2.fq.gz
Processing reads on 1 core in single-end mode ...
Finished in 2318.43 s (28 µs/read; 2.14 M reads/minute).

=== Summary ===

Total reads processed:              82,575,967
Reads with adapters:                36,247,525 (43.9%)
Reads written (passing filters):    82,575,967 (100.0%)

Total basepairs processed: 8,804,136,896 bp
Quality-trimmed:              16,290,671 bp (0.2%)
Total written (filtered):  8,747,217,431 bp (99.4%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 36247525 times

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

Bases preceding removed adapters:
  A: 46.0%
  C: 10.1%
  G: 6.3%
  T: 37.6%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	33298978	20643991.8	0	33298978
2	1873842	5160997.9	0	1873842
3	729535	1290249.5	0	729535
4	339564	322562.4	0	339564
5	3410	80640.6	0	3410
6	700	20160.1	0	700
7	216	5040.0	0	216
8	60	1260.0	0	60
9	374	315.0	0	25 349
10	672	78.8	1	4 668
11	147	19.7	1	4 143
12	25	4.9	1	0 25
13	2	1.2	1	0 2

RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_7_R2_val_2.fq.gz
=============================================
82575967 sequences processed in total

Total number of sequences analysed for the sequence pair length validation: 82575967

Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 48898 (0.06%)