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diff test-data/references/06-affiliation.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/06-affiliation.log	Thu Feb 28 10:14:49 2019 -0500
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+## 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
+