view test-data/paired/retrievedFragments/trimmedReads/reads__2_retrieved.fastq_trimming_report.txt @ 0:6f743c615c41 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"

SUMMARISING RUN PARAMETERS
==========================
Input filename: /home/ubuntu/data/fargene/tutorial/tutorialdata/tutorial_output_1/retrievedFragments/reads__2_retrieved.fastq
Trimming mode: paired-end
Trim Galore version: 0.6.3
Cutadapt version: 1.18
Number of cores used for trimming: 1
Quality Phred score cutoff: 30
Quality encoding type selected: ASCII+33
Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; default (inconclusive auto-detection))
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


This is cutadapt 1.18 with Python 2.7.15
Command line parameters: -j 1 -e 0.1 -q 30 -O 1 -a AGATCGGAAGAGC /home/ubuntu/data/fargene/tutorial/tutorialdata/tutorial_output_1/retrievedFragments/reads__2_retrieved.fastq
Processing reads on 1 core in single-end mode ...
Finished in 0.01 s (28 us/read; 2.17 M reads/minute).

=== Summary ===

Total reads processed:                     393
Reads with adapters:                        91 (23.2%)
Reads written (passing filters):           393 (100.0%)

Total basepairs processed:        39,300 bp
Quality-trimmed:                     435 bp (1.1%)
Total written (filtered):         38,735 bp (98.6%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 91 times.

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

Bases preceding removed adapters:
  A: 20.9%
  C: 44.0%
  G: 27.5%
  T: 7.7%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	65	98.2	0	65
2	20	24.6	0	20
3	2	6.1	0	2
4	2	1.5	0	2
5	1	0.4	0	1
6	1	0.1	0	1


RUN STATISTICS FOR INPUT FILE: /home/ubuntu/data/fargene/tutorial/tutorialdata/tutorial_output_1/retrievedFragments/reads__2_retrieved.fastq
=============================================
393 sequences processed in total

Total number of sequences analysed for the sequence pair length validation: 393

Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 0 (0.00%)