skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -f sanger -l 18 -t 4 -x CTGTCTCTTATACACATCTCCGAGCCCACGAGACGTAGGATAAGATCTCGTATGCCGTCTTCTGCTTGAAAA -y -o SRR34314875 SRR34314875_1.fastq SRR34314875_2.fastq
Input file:	SRR34314875
Paired file:	SRR34314875_1.fastq
trimmed:	SRR34314875-pair1.fastq, SRR34314875-pair2.fastq

Parameters used:
-- 3' end adapter sequence (-x):	CTGTCTCTTATACACATCTCCGAGCCCACGAGACGTAGGATAAGATCTCGTATGCCGTCTTCTG
-- paired 3' end adapter sequence (-y):	-o
-- maximum error ratio allowed (-r):	0.100
-- maximum indel error ratio allowed (-d):	0.030
-- minimum read length allowed after trimming (-l):	18
-- file format (-f):		Sanger/Illumina 1.8+ FASTQ 
-- number of concurrent threads (-t):	4
Sun Jul 13 08:43:30 2025 >> started


criterion=sequence-density
sequence-density=20.17
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=1
prefix-density=0.00
prefix-fanout=1.0
sequence=CTGTCTCTTATACACATCTCCGAGCCCACGAGACGTAGGATAAGATCTCGTATGCCGTCTTCTGCTTGAAAA


criterion=fanout-score
sequence-density=20.17
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=1
prefix-density=0.00
prefix-fanout=1.0
sequence=CTGTCTCTTATACACATCTCCGAGCCCACGAGACGTAGGATAAGATCTCGTATGCCGTCTTCTGCTTGAAAA
SRR34314875 testing PE reads STAR mapping to Ensembl genome
                                 Started job on |	Jul 13 08:44:00
                             Started mapping on |	Jul 13 08:44:00
                                    Finished on |	Jul 13 08:44:02
       Mapping speed, Million of reads per hour |	2.12

                          Number of input reads |	1175
                      Average input read length |	272
                                    UNIQUE READS:
                   Uniquely mapped reads number |	49
                        Uniquely mapped reads % |	4.17%
                          Average mapped length |	250.10
                       Number of splices: Total |	3
            Number of splices: Annotated (sjdb) |	0
                       Number of splices: GT/AG |	2
                       Number of splices: GC/AG |	0
                       Number of splices: AT/AC |	0
               Number of splices: Non-canonical |	1
                      Mismatch rate per base, % |	1.22%
                         Deletion rate per base |	0.00%
                        Deletion average length |	0.00
                        Insertion rate per base |	0.01%
                       Insertion average length |	1.00
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	62
             % of reads mapped to multiple loci |	5.28%
        Number of reads mapped to too many loci |	8
             % of reads mapped to too many loci |	0.68%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	89.87%
                     % of reads unmapped: other |	0.00%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	1064	1064	1064
N_multimapping	62	62	62
N_noFeature	25	32	38
N_ambiguous	6	2	0
UnstrandedReadsAssigned:18 PositiveStrandReadsAssigned:15 NegativeStrandReadsAssigned:11
Dataset is classified unstranded
MeadianReadLen=147 20thPercentileLength=146 echo kmer=141
SRR34314875 Starting Kallisto paired end mapping to ensembl reference transcriptome

[quant] fragment length distribution will be estimated from the data
[index] k-mer length: 31
[index] number of targets: 42,789
[index] number of k-mers: 51,537,741
[index] number of equivalence classes: 81,491
[quant] running in paired-end mode
[quant] will process pair 1: SRR34314875-trimmed-pair1.fastq
                             SRR34314875-trimmed-pair2.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 1,175 reads, 230 reads pseudoaligned
[quant] estimated average fragment length: 180.694
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 370 rounds

  42790 SRR34314875.ke.tsv
  38993 SRR34314875.se.tsv
  81783 total
==> SRR34314875.ke.tsv <==
target_id	length	eff_length	est_counts	tpm
transcript-nad2	161	54.6471	0	0
transcript-cox1	1576	1396.31	0	0
transcript-rps2	711	531.306	0	0
transcript-petB	6	7	0	0
transcript-ndhB-2	777	597.306	0	0
transcript-rpl36	114	23.1111	0	0
transcript-rpoC1	2049	1869.31	2	2314.95
transcript-petE	114	23.1111	0	0
transcript-ndhB	777	597.306	0	0

==> SRR34314875.se.tsv <==
ENSRNA049442722	0
ENSRNA049442424	0
ENSRNA049442327	0
ENSRNA049442288	0
ENSRNA049442195	0
ENSRNA049442095	0
ENSRNA049441959	0
ENSRNA049441928	0
ENSRNA049441839	0
ENSRNA049441771	0
SRR34314875 completed mapping pipeline successfully
