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comparison 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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1 ## Application
2 Software :/home/maria/workspace/git/FROGS/FROGS_master/test/../app/clustering.py (version : 3.1)
3 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
4
5 ########################################################################################################
6 # Sort pre-clusters by abundancies. (sortAbundancies.py version : 1.5.0)
7 Command:
8 sortAbundancies.py --size-separator ';size=' --input-file res/01-prepro-vsearch.fasta --output-file res/1550052751.99_3808_01-prepro-vsearch_sorted.fasta
9
10 Execution:
11 start: 13 Feb 2019 11:12:32
12 end: 13 Feb 2019 11:12:32
13
14 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
15 ########################################################################################################
16 # Clustering sequences. (swarm version : 2.2.2)
17 Command:
18 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
19
20 Execution:
21 start: 13 Feb 2019 11:12:32
22 end: 13 Feb 2019 11:12:50
23
24 ########################################################################################################
25 # Extracts seeds sequences to produce the seeds fasta. (extractSwarmsFasta.py version : 1.4.1)
26 Command:
27 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
28
29 Execution:
30 start: 13 Feb 2019 11:12:50
31 end: 13 Feb 2019 11:12:50
32
33 ########################################################################################################
34 # Sort pre-clusters by abundancies. (sortAbundancies.py version : 1.5.0)
35 Command:
36 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
37
38 Execution:
39 start: 13 Feb 2019 11:12:51
40 end: 13 Feb 2019 11:12:51
41
42 ########################################################################################################
43 # Clustering sequences. (swarm version : 2.2.2)
44 Command:
45 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
46
47 Execution:
48 start: 13 Feb 2019 11:12:51
49 end: 13 Feb 2019 11:13:13
50
51 ########################################################################################################
52 # Converts swarm output to abundance file (format BIOM). (swarm2biom.py version : 1.4.0)
53 Command:
54 swarm2biom.py --clusters-file res/02-clustering_compo.tsv --count-file res/01-prepro-vsearch.tsv --output-file res/02-clustering.biom
55
56 Execution:
57 start: 13 Feb 2019 11:13:13
58 end: 13 Feb 2019 11:13:14
59
60 ########################################################################################################
61 # Extracts seeds sequences to produce the seeds fasta. (extractSwarmsFasta.py version : 1.4.1)
62 Command:
63 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
64
65 Execution:
66 start: 13 Feb 2019 11:13:14
67 end: 13 Feb 2019 11:13:14
68
69 repalce A tags by N. in: res/1550052751.99_3808_01-prepro-vsearch_final_seeds.fasta out : res/02-clustering.fasta