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diff 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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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sortmerna.txt	Tue Oct 24 06:29:59 2017 -0400
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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
+