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comparison test-data/sortmerna.txt @ 0:3bad335ccea9 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
author iuc
date Tue, 24 Oct 2017 06:29:59 -0400
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-1:000000000000 0:3bad335ccea9
1 Tue Jan 31 17:04:24 2017
2
3 Command: /home/lina/sortmerna/sortmerna --ref /home/lina/sortmerna/rRNA_databases/silva-bac-16s-id90.fasta,/home/lina/sortmerna/index/silva-bac-16s-db:/home/lina/sortmerna/rRNA_databases/silva-bac-23s-id98.fasta,/home/lina/sortmerna/index/silva-bac-23s-db:/home/lina/sortmerna/rRNA_databases/silva-arc-16s-id95.fasta,/home/lina/sortmerna/index/silva-arc-16s-db:/home/lina/sortmerna/rRNA_databases/silva-arc-23s-id98.fasta,/home/lina/sortmerna/index/silva-arc-23s-db:/home/lina/sortmerna/rRNA_databases/silva-euk-18s-id95.fasta,/home/lina/sortmerna/index/silva-euk-18s-db:/home/lina/sortmerna/rRNA_databases/silva-euk-28s-id98.fasta,/home/lina/sortmerna/index/silva-euk-28s:/home/lina/sortmerna/rRNA_databases/rfam-5s-database-id98.fasta,/home/lina/sortmerna/index/rfam-5s-db:/home/lina/sortmerna/rRNA_databases/rfam-5.8s-database-id98.fasta,/home/lina/sortmerna/index/rfam-5.8s-db --reads 25839_merged.fastq --num_alignments 1 --fastx --aligned Sample_2055324_ribo/sortmerna_out/2055324_ribo_rrna_reads --other Sample_2055324_ribo/sortmerna_out/2055324_ribo_rrna_free_reads.fastq fastq tq --log -v --blast 1
4 Process pid = 27736
5 Parameters summary:
6 Index: /home/lina/sortmerna/index/silva-bac-16s-db
7 Seed length = 18
8 Pass 1 = 18, Pass 2 = 9, Pass 3 = 3
9 Gumbel lambda = 0.602725
10 Gumbel K = 0.329559
11 Minimal SW score based on E-value = 57
12 Index: /home/lina/sortmerna/index/silva-bac-23s-db
13 Seed length = 18
14 Pass 1 = 18, Pass 2 = 9, Pass 3 = 3
15 Gumbel lambda = 0.602436
16 Gumbel K = 0.335011
17 Minimal SW score based on E-value = 57
18 Index: /home/lina/sortmerna/index/silva-arc-16s-db
19 Seed length = 18
20 Pass 1 = 18, Pass 2 = 9, Pass 3 = 3
21 Gumbel lambda = 0.596286
22 Gumbel K = 0.322254
23 Minimal SW score based on E-value = 55
24 Index: /home/lina/sortmerna/index/silva-arc-23s-db
25 Seed length = 18
26 Pass 1 = 18, Pass 2 = 9, Pass 3 = 3
27 Gumbel lambda = 0.597507
28 Gumbel K = 0.331576
29 Minimal SW score based on E-value = 53
30 Index: /home/lina/sortmerna/index/silva-euk-18s-db
31 Seed length = 18
32 Pass 1 = 18, Pass 2 = 9, Pass 3 = 3
33 Gumbel lambda = 0.612551
34 Gumbel K = 0.339810
35 Minimal SW score based on E-value = 56
36 Index: /home/lina/sortmerna/index/silva-euk-28s
37 Seed length = 18
38 Pass 1 = 18, Pass 2 = 9, Pass 3 = 3
39 Gumbel lambda = 0.612082
40 Gumbel K = 0.345772
41 Minimal SW score based on E-value = 56
42 Index: /home/lina/sortmerna/index/rfam-5s-db
43 Seed length = 18
44 Pass 1 = 18, Pass 2 = 9, Pass 3 = 3
45 Gumbel lambda = 0.616694
46 Gumbel K = 0.342032
47 Minimal SW score based on E-value = 54
48 Index: /home/lina/sortmerna/index/rfam-5.8s-db
49 Seed length = 18
50 Pass 1 = 18, Pass 2 = 9, Pass 3 = 3
51 Gumbel lambda = 0.617555
52 Gumbel K = 0.343861
53 Minimal SW score based on E-value = 52
54 Number of seeds = 2
55 Edges = 4 (as integer)
56 SW match = 2
57 SW mismatch = -3
58 SW gap open penalty = 5
59 SW gap extend penalty = 2
60 SW ambiguous nucleotide = -3
61 SQ tags are not output
62 Number of threads = 20
63 Reads file = 25839_merged.fastq
64
65 Results:
66 Total reads = 4443556
67 Total reads passing E-value threshold = 48848 (1.10%)
68 Total reads failing E-value threshold = 4394708 (98.90%)
69 Minimum read length = 35
70 Maximum read length = 76
71 Mean read length = 74
72 By database:
73 /home/lina/sortmerna/rRNA_databases/silva-bac-16s-id90.fasta 0.59%
74 /home/lina/sortmerna/rRNA_databases/silva-bac-23s-id98.fasta 0.24%
75 /home/lina/sortmerna/rRNA_databases/silva-arc-16s-id95.fasta 0.00%
76 /home/lina/sortmerna/rRNA_databases/silva-arc-23s-id98.fasta 0.00%
77 /home/lina/sortmerna/rRNA_databases/silva-euk-18s-id95.fasta 0.25%
78 /home/lina/sortmerna/rRNA_databases/silva-euk-28s-id98.fasta 0.01%
79 /home/lina/sortmerna/rRNA_databases/rfam-5s-database-id98.fasta 0.00%
80 /home/lina/sortmerna/rRNA_databases/rfam-5.8s-database-id98.fasta 0.00%
81
82 Tue Jan 31 17:08:40 2017
83