view test-data/references/02-clustering_fastidious.log @ 2:094a2469204d draft

"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.3.1 commit 90093162b8cfb3e75908323761f4ef246222abea"

## Application
Software :/home/maria/miniconda3/envs/frogs@3.2.3/bin/clustering.py (version : 3.2.3)
Command : /home/maria/miniconda3/envs/frogs@3.2.3/bin/clustering.py --distance 1 --fastidious --input-fasta res_3.2.3/01-prepro-vsearch.fasta --input-count res_3.2.3/01-prepro-vsearch.tsv --output-biom res_3.2.3/02-clustering_fastidious.biom --output-fasta res_3.2.3/02-clustering_fastidious.fasta --output-compo res_3.2.3/02-clustering_fastidious_compo.tsv --log-file res_3.2.3/02-clustering_fastidious.log --nb-cpus 2

########################################################################################################
# Sort pre-clusters by abundancies. (sortAbundancies.py version : 1.5.0)
Command:
	sortAbundancies.py --size-separator ';size=' --input-file res_3.2.3/01-prepro-vsearch.fasta --output-file res_3.2.3/1622730736.5588937_458_01-prepro-vsearch_sorted.fasta

Execution:
	start: 03 Jun 2021 16:32:16
	end:   03 Jun 2021 16:32:18

repalce 100 N tags by 50A-50C in: res_3.2.3/1622730736.5588937_458_01-prepro-vsearch_sorted.fasta out : res_3.2.3/1622730736.5588937_458_01-prepro-vsearch_sorted_NtoA.fasta
########################################################################################################
# Clustering sequences. (swarm version : 3.0.0)
Command:
	swarm --differences 1 --fastidious  --threads 2 --log res_3.2.3/1622730736.5588937_458_01-prepro-vsearch_swarm_log.txt --output-file res_3.2.3/02-clustering_fastidious_compo.tsv res_3.2.3/1622730736.5588937_458_01-prepro-vsearch_sorted_NtoA.fasta

Execution:
	start: 03 Jun 2021 16:32:20
	end:   03 Jun 2021 16:32:36

########################################################################################################
# Converts swarm output to abundance file (format BIOM). (swarm2biom.py version : 1.4.0)
Command:
	swarm2biom.py --clusters-file res_3.2.3/02-clustering_fastidious_compo.tsv --count-file res_3.2.3/01-prepro-vsearch.tsv --output-file res_3.2.3/02-clustering_fastidious.biom

Execution:
	start: 03 Jun 2021 16:32:36
	end:   03 Jun 2021 16:32:39

########################################################################################################
# Extracts seeds sequences to produce the seeds fasta. (extractSwarmsFasta.py version : 1.4.1)
Command:
	extractSwarmsFasta.py --input-fasta res_3.2.3/1622730736.5588937_458_01-prepro-vsearch_sorted_NtoA.fasta --input-swarms res_3.2.3/02-clustering_fastidious_compo.tsv --output-fasta res_3.2.3/1622730736.5588937_458_01-prepro-vsearch_final_seeds.fasta

Execution:
	start: 03 Jun 2021 16:32:40
	end:   03 Jun 2021 16:32:41

replace 50A-50C  tags by N. in: res_3.2.3/1622730736.5588937_458_01-prepro-vsearch_final_seeds.fasta out : res_3.2.3/02-clustering_fastidious.fasta