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view test-data/sortmerna.txt @ 16:bf675f34b056 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit bd94f00ad5d023ae392ca8fc2378fd5a78bed875"
author iuc
date Sat, 16 May 2020 09:40:45 -0400
parents 3bad335ccea9
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 Tue Jan 31 17:04:24 2017

 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 
 Process pid = 27736
 Parameters summary:
    Index: /home/lina/sortmerna/index/silva-bac-16s-db
     Seed length = 18
     Pass 1 = 18, Pass 2 = 9, Pass 3 = 3
     Gumbel lambda = 0.602725
     Gumbel K = 0.329559
     Minimal SW score based on E-value = 57
    Index: /home/lina/sortmerna/index/silva-bac-23s-db
     Seed length = 18
     Pass 1 = 18, Pass 2 = 9, Pass 3 = 3
     Gumbel lambda = 0.602436
     Gumbel K = 0.335011
     Minimal SW score based on E-value = 57
    Index: /home/lina/sortmerna/index/silva-arc-16s-db
     Seed length = 18
     Pass 1 = 18, Pass 2 = 9, Pass 3 = 3
     Gumbel lambda = 0.596286
     Gumbel K = 0.322254
     Minimal SW score based on E-value = 55
    Index: /home/lina/sortmerna/index/silva-arc-23s-db
     Seed length = 18
     Pass 1 = 18, Pass 2 = 9, Pass 3 = 3
     Gumbel lambda = 0.597507
     Gumbel K = 0.331576
     Minimal SW score based on E-value = 53
    Index: /home/lina/sortmerna/index/silva-euk-18s-db
     Seed length = 18
     Pass 1 = 18, Pass 2 = 9, Pass 3 = 3
     Gumbel lambda = 0.612551
     Gumbel K = 0.339810
     Minimal SW score based on E-value = 56
    Index: /home/lina/sortmerna/index/silva-euk-28s
     Seed length = 18
     Pass 1 = 18, Pass 2 = 9, Pass 3 = 3
     Gumbel lambda = 0.612082
     Gumbel K = 0.345772
     Minimal SW score based on E-value = 56
    Index: /home/lina/sortmerna/index/rfam-5s-db
     Seed length = 18
     Pass 1 = 18, Pass 2 = 9, Pass 3 = 3
     Gumbel lambda = 0.616694
     Gumbel K = 0.342032
     Minimal SW score based on E-value = 54
    Index: /home/lina/sortmerna/index/rfam-5.8s-db
     Seed length = 18
     Pass 1 = 18, Pass 2 = 9, Pass 3 = 3
     Gumbel lambda = 0.617555
     Gumbel K = 0.343861
     Minimal SW score based on E-value = 52
    Number of seeds = 2
    Edges = 4 (as integer)
    SW match = 2
    SW mismatch = -3
    SW gap open penalty = 5
    SW gap extend penalty = 2
    SW ambiguous nucleotide = -3
    SQ tags are not output
    Number of threads = 20
    Reads file = 25839_merged.fastq

 Results:
    Total reads = 4443556
    Total reads passing E-value threshold = 48848 (1.10%)
    Total reads failing E-value threshold = 4394708 (98.90%)
    Minimum read length = 35
    Maximum read length = 76
    Mean read length = 74
 By database:
    /home/lina/sortmerna/rRNA_databases/silva-bac-16s-id90.fasta		0.59%
    /home/lina/sortmerna/rRNA_databases/silva-bac-23s-id98.fasta		0.24%
    /home/lina/sortmerna/rRNA_databases/silva-arc-16s-id95.fasta		0.00%
    /home/lina/sortmerna/rRNA_databases/silva-arc-23s-id98.fasta		0.00%
    /home/lina/sortmerna/rRNA_databases/silva-euk-18s-id95.fasta		0.25%
    /home/lina/sortmerna/rRNA_databases/silva-euk-28s-id98.fasta		0.01%
    /home/lina/sortmerna/rRNA_databases/rfam-5s-database-id98.fasta		0.00%
    /home/lina/sortmerna/rRNA_databases/rfam-5.8s-database-id98.fasta		0.00%

 Tue Jan 31 17:08:40 2017