view test-data/sanger_full_range_report_results1gz.txt @ 16:cc01cbc4e7f7 draft default tip

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"

SUMMARISING RUN PARAMETERS
==========================
Input filename: input_1.fastq.gz
Trimming mode: single-end
Trim Galore version: 0.6.7
Cutadapt version: 3.4
Python version: could not detect
Number of cores used for trimming: 4
Quality Phred score cutoff: 20
Quality encoding type selected: ASCII+33
Unable to auto-detect most prominent adapter from the first specified file (count Illumina: 0, count Nextera: 0, count smallRNA: 0)
Defaulting to Illumina universal adapter ( AGATCGGAAGAGC ). Specify -a SEQUENCE to avoid this behavior).
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 before a sequence gets removed: 20 bp
Output file will be GZIP compressed


This is cutadapt 3.4 with Python 3.9.6
Command line parameters: -j 4 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC input_1.fastq.gz
Processing reads on 4 cores in single-end mode ...
Finished in 0.01 s (5217 µs/read; 0.01 M reads/minute).

=== Summary ===

Total reads processed:                       2
Reads with adapters:                         1 (50.0%)
Reads written (passing filters):             2 (100.0%)

Total basepairs processed:           188 bp
Quality-trimmed:                      20 bp (10.6%)
Total written (filtered):            167 bp (88.8%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 1 times

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

Bases preceding removed adapters:
  A: 0.0%
  C: 100.0%
  G: 0.0%
  T: 0.0%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	1	0.5	0	1

RUN STATISTICS FOR INPUT FILE: input_1.fastq.gz
=============================================
2 sequences processed in total
Sequences removed because they became shorter than the length cutoff of 20 bp:	0 (0.0%)