SUMMARISING RUN PARAMETERS
==========================
Input filename: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_11_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_11_R2_val_2.fq.gz
Processing reads on 1 core in single-end mode ...
Finished in 1554.98 s (27 µs/read; 2.19 M reads/minute).

=== Summary ===

Total reads processed:              56,807,549
Reads with adapters:                24,841,448 (43.7%)
Reads written (passing filters):    56,807,549 (100.0%)

Total basepairs processed: 6,013,778,082 bp
Quality-trimmed:              10,231,800 bp (0.2%)
Total written (filtered):  5,975,677,543 bp (99.4%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 24841448 times

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

Bases preceding removed adapters:
  A: 45.9%
  C: 10.2%
  G: 6.4%
  T: 37.6%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	22805353	14201887.2	0	22805353
2	1293971	3550471.8	0	1293971
3	502162	887618.0	0	502162
4	236139	221904.5	0	236139
5	2178	55476.1	0	2178
6	550	13869.0	0	550
7	182	3467.3	0	182
8	44	866.8	0	44
9	248	216.7	0	20 228
10	509	54.2	1	3 506
11	83	13.5	1	1 82
12	26	3.4	1	0 26
13	3	0.8	1	0 3

RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_11_R2_val_2.fq.gz
=============================================
56807549 sequences processed in total

Total number of sequences analysed for the sequence pair length validation: 56807549

Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 33290 (0.06%)