annotate test-data/references/06-affiliation.log @ 0:59bc96331073 draft default tip

planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647

## Application
Software: affiliation_OTU.py (version: 3.1)
Command: /home/maria/workspace/git/FROGS/FROGS_master/test/../app/affiliation_OTU.py --reference /home/maria/workspace/git/FROGS/FROGS_master/test/../test/data/ITS1.rdp.fasta --input-fasta res/04-filters.fasta --input-biom res/04-filters.biom --output-biom res/06-affiliation.biom --summary res/06-affiliation.html --log-file res/06-affiliation.log --nb-cpus 4 --java-mem 2

Nb seq : 86
	 with nb seq artificially combined :34

########################################################################################################
# Split on tag. (combine_and_split.py version : )
Command:
	combine_and_split.py  --reads1 res/1550052855.96_4147_04-filters.fasta_FROGS_combined -s NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN --split-output1 res/1550052855.96_4147_1550052855.96_4147_04-filters.fasta_FROGS_combined_R1.fasta --split-output2 res/1550052855.96_4147_1550052855.96_4147_04-filters.fasta_FROGS_combined_R2.fasta

Execution:
	start: 13 Feb 2019 11:14:15
	end:   13 Feb 2019 11:14:16

########################################################################################################
# blast taxonomic affiliation (blastn version : 2.7.1+)
Command:
	blastn -num_threads 1 -task megablast -word_size 38 -max_target_seqs 500 -outfmt '6 qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore qlen' -query res/1550052855.96_4147_1550052855.96_4147_04-filters.fasta_FROGS_combined_R1.fasta -out res/1550052855.96_4147_1550052855.96_4147_1550052855.96_4147_04-filters.fasta_FROGS_combined_R1.fasta.blast -db /home/maria/workspace/git/FROGS/FROGS_master/test/../test/data/ITS1.rdp.fasta

Execution:
	start: 13 Feb 2019 11:14:16
	end:   13 Feb 2019 11:14:16

########################################################################################################
# blast taxonomic affiliation (blastn version : 2.7.1+)
Command:
	blastn -num_threads 1 -task megablast -word_size 38 -max_target_seqs 500 -outfmt '6 qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore qlen' -query res/1550052855.96_4147_1550052855.96_4147_04-filters.fasta_FROGS_combined_R2.fasta -out res/1550052855.96_4147_1550052855.96_4147_1550052855.96_4147_04-filters.fasta_FROGS_combined_R2.fasta.blast -db /home/maria/workspace/git/FROGS/FROGS_master/test/../test/data/ITS1.rdp.fasta

Execution:
	start: 13 Feb 2019 11:14:16
	end:   13 Feb 2019 11:14:16

########################################################################################################
# needleall taxonomic affiliation (needleall_on_bestBlast.py version : r3.0-v1.0 [needleall EMBOSS:6.6.0.0])
Command:
	needleall_on_bestBlast.py  -r /home/maria/workspace/git/FROGS/FROGS_master/test/../test/data/ITS1.rdp.fasta -f res/1550052855.96_4147_04-filters.fasta_FROGS_combined --query-blast-R1 res/1550052855.96_4147_1550052855.96_4147_1550052855.96_4147_04-filters.fasta_FROGS_combined_R1.fasta.blast --query-blast-R2 res/1550052855.96_4147_1550052855.96_4147_1550052855.96_4147_04-filters.fasta_FROGS_combined_R2.fasta.blast -s res/1550052855.96_4147_1550052855.96_4147_04-filters.fasta_FROGS_combined.needleall.sam -l res/1550052855.96_4147_1550052855.96_4147_04-filters.fasta_FROGS_combined.needleall.log

Execution:
	start: 13 Feb 2019 11:14:16
	end:   13 Feb 2019 11:14:33

	# Parsing blast alignment results to reduce reference databse
		Reducing reference databases to 90 sequences
	
	# Needlall version: EMBOSS:6.6.0.0
	# Needlall command: needleall -asequence res/1550052856.58_4164_ITS1.rdp.fasta -bsequence res/1550052855.96_4147_04-filters.fasta_FROGS_combined -outfile res/1550052855.96_4147_1550052855.96_4147_04-filters.fasta_FROGS_combined.needleall.sam -aformat3 sam -gapopen 10.0 -gapextend 0.5 -errfile res/1550052856.58_4164_1550052855.96_4147_1550052855.96_4147_04-filters.fasta_FROGS_combined.needleall.sam_needle_errorfile.txt

########################################################################################################
# convert NeedleAll Sam output in blast like tsv output sorted by bitscore (needleallSam_to_tsv.py version : r3.0-v1.0)
Command:
	needleallSam_to_tsv.py -n res/1550052855.96_4147_1550052855.96_4147_04-filters.fasta_FROGS_combined.needleall.sam -r /home/maria/workspace/git/FROGS/FROGS_master/test/../test/data/ITS1.rdp.fasta -b res/1550052855.96_4147_1550052855.96_4147_04-filters.fasta_FROGS_combined.needleall.blast_like

Execution:
	start: 13 Feb 2019 11:14:33
	end:   13 Feb 2019 11:14:34

########################################################################################################
# blast taxonomic affiliation (blastn version : 2.7.1+)
Command:
	blastn -num_threads 1 -task megablast -word_size 38 -max_target_seqs 500 -outfmt '6 qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore qlen' -query res/1550052855.96_4147_04-filters.fasta_FROGS_full_length -out res/1550052855.96_4147_1550052855.96_4147_04-filters.fasta_FROGS_full_length.blast -db /home/maria/workspace/git/FROGS/FROGS_master/test/../test/data/ITS1.rdp.fasta

Execution:
	start: 13 Feb 2019 11:14:34
	end:   13 Feb 2019 11:14:34

########################################################################################################
# Add Blast and/or RDP affiliation to biom (addAffiliation2biom.py version : 2.3.0)
Command:
	addAffiliation2biom.py -f /home/maria/workspace/git/FROGS/FROGS_master/test/../test/data/ITS1.rdp.fasta -i res/04-filters.biom -o res/06-affiliation.biom -b res/1550052855.96_4147_1550052855.96_4147_04-filters.fasta_FROGS_full_length.blast res/1550052855.96_4147_1550052855.96_4147_04-filters.fasta_FROGS_combined.needleall.blast_like

Execution:
	start: 13 Feb 2019 11:14:34
	end:   13 Feb 2019 11:14:34