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diff test-data/references/02-clustering.log @ 0:59bc96331073 draft default tip

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planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
author frogs
date Thu, 28 Feb 2019 10:14:49 -0500
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/references/02-clustering.log	Thu Feb 28 10:14:49 2019 -0500
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+## Application
+Software :/home/maria/workspace/git/FROGS/FROGS_master/test/../app/clustering.py (version : 3.1)
+Command : /home/maria/workspace/git/FROGS/FROGS_master/test/../app/clustering.py --distance 3 --denoising --input-fasta res/01-prepro-vsearch.fasta --input-count res/01-prepro-vsearch.tsv --output-biom res/02-clustering.biom --output-fasta res/02-clustering.fasta --output-compo res/02-clustering_compo.tsv --log-file res/02-clustering.log --nb-cpus 4
+
+########################################################################################################
+# Sort pre-clusters by abundancies. (sortAbundancies.py version : 1.5.0)
+Command:
+	sortAbundancies.py --size-separator ';size=' --input-file res/01-prepro-vsearch.fasta --output-file res/1550052751.99_3808_01-prepro-vsearch_sorted.fasta
+
+Execution:
+	start: 13 Feb 2019 11:12:32
+	end:   13 Feb 2019 11:12:32
+
+repalce N tags by A. in: res/1550052751.99_3808_01-prepro-vsearch_sorted.fasta out : res/1550052751.99_3808_01-prepro-vsearch_sorted_NtoA.fasta
+########################################################################################################
+# Clustering sequences. (swarm version : 2.2.2)
+Command:
+	swarm --differences 1 --threads 4 --log res/1550052751.99_3808_01-prepro-vsearch_denoising_log.txt --output-file res/1550052751.99_3808_01-prepro-vsearch_denoising_composition.txt res/1550052751.99_3808_01-prepro-vsearch_sorted_NtoA.fasta
+
+Execution:
+	start: 13 Feb 2019 11:12:32
+	end:   13 Feb 2019 11:12:50
+
+########################################################################################################
+# Extracts seeds sequences to produce the seeds fasta. (extractSwarmsFasta.py version : 1.4.1)
+Command:
+	extractSwarmsFasta.py --input-fasta res/1550052751.99_3808_01-prepro-vsearch_sorted_NtoA.fasta --input-swarms res/1550052751.99_3808_01-prepro-vsearch_denoising_composition.txt --output-fasta res/1550052751.99_3808_01-prepro-vsearch_denoising_seeds.fasta
+
+Execution:
+	start: 13 Feb 2019 11:12:50
+	end:   13 Feb 2019 11:12:50
+
+########################################################################################################
+# Sort pre-clusters by abundancies. (sortAbundancies.py version : 1.5.0)
+Command:
+	sortAbundancies.py --size-separator '_' --input-file res/1550052751.99_3808_01-prepro-vsearch_denoising_resizedSeeds.fasta --output-file res/1550052751.99_3808_01-prepro-vsearch_denoising_sortedSeeds.fasta
+
+Execution:
+	start: 13 Feb 2019 11:12:51
+	end:   13 Feb 2019 11:12:51
+
+########################################################################################################
+# Clustering sequences. (swarm version : 2.2.2)
+Command:
+	swarm --differences 3 --threads 4 --log res/1550052751.99_3808_01-prepro-vsearch_swarm_log.txt --output-file res/1550052751.99_3808_01-prepro-vsearch_swarmD3_composition.txt res/1550052751.99_3808_01-prepro-vsearch_denoising_sortedSeeds.fasta
+
+Execution:
+	start: 13 Feb 2019 11:12:51
+	end:   13 Feb 2019 11:13:13
+
+########################################################################################################
+# Converts swarm output to abundance file (format BIOM). (swarm2biom.py version : 1.4.0)
+Command:
+	swarm2biom.py --clusters-file res/02-clustering_compo.tsv --count-file res/01-prepro-vsearch.tsv --output-file res/02-clustering.biom
+
+Execution:
+	start: 13 Feb 2019 11:13:13
+	end:   13 Feb 2019 11:13:14
+
+########################################################################################################
+# Extracts seeds sequences to produce the seeds fasta. (extractSwarmsFasta.py version : 1.4.1)
+Command:
+	extractSwarmsFasta.py --input-fasta res/1550052751.99_3808_01-prepro-vsearch_denoising_sortedSeeds.fasta --input-swarms res/1550052751.99_3808_01-prepro-vsearch_swarmD3_composition.txt --output-fasta res/1550052751.99_3808_01-prepro-vsearch_final_seeds.fasta
+
+Execution:
+	start: 13 Feb 2019 11:13:14
+	end:   13 Feb 2019 11:13:14
+
+repalce A tags by N. in: res/1550052751.99_3808_01-prepro-vsearch_final_seeds.fasta out : res/02-clustering.fasta