Mercurial > repos > frogs > frogs_3_1_0
diff test-data/references/05-itsx.log @ 0:59bc96331073 draft default tip
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
author | frogs |
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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/05-itsx.log Thu Feb 28 10:14:49 2019 -0500 @@ -0,0 +1,61 @@ +## Application +Software :/home/maria/workspace/git/FROGS/FROGS_master/test/../app/itsx.py (version : 3.1) +Command : /home/maria/workspace/git/FROGS/FROGS_master/test/../app/itsx.py --input-fasta res/04-filters.fasta --input-biom res/04-filters.biom --region ITS1 --nb-cpus 4 --out-abundance res/05-itsx.biom --summary res/05-itsx.html --log-file res/05-itsx.log --out-fasta res/05-itsx.fasta --out-removed res/05-itsx-excluded.tsv + +######################################################################################################## +# identifies ITS sequences and extracts the ITS region (parallelITSx.py version : 1.0.0 [ITSx 1.0.11]) +Command: + parallelITSx.py -f res/04-filters.fasta -b res/04-filters.biom --nb-cpus 4 --its ITS1 -o res/05-itsx.fasta -m res/05-itsx-excluded.tsv -a res/05-itsx.biom --log-file res/1550052843.84_3916_ITSx.log + +Execution: + start: 13 Feb 2019 11:14:03 + end: 13 Feb 2019 11:14:15 + +Results: + +# split res/04-filters.fasta in 3 fasta files +Results + Wrote 29 records to res/1550052844.03_3921_04-filters.fasta_0 + Wrote 29 records to res/1550052844.03_3921_04-filters.fasta_1 + Wrote 28 records to res/1550052844.03_3921_04-filters.fasta_2 + +## Input file : 1550052844.03_3921_04-filters.fasta_0 +## in working directory: res/1550052844.03_3921_1550052844.03_3921_04-filters.fasta_0 +## ITSx command: ITSx -i /home/maria/workspace/git/FROGS/FROGS_master/test/res/1550052844.03_3921_04-filters.fasta_0 -o 1550052844.03_3921_04-filters --preserve T -t F --save_regions all +##Results + nb full (removed): 0 + nb no_detections (removed): 0 + nb SSU (removed): 0 + nb ITS2 (removed): 0 + nb ITS1 (kept): 29 + nb LSU (removed): 0 + nb 5_8S (removed): 0 + +## Input file : 1550052844.03_3921_04-filters.fasta_1 +## in working directory: res/1550052844.03_3921_1550052844.03_3921_04-filters.fasta_1 +## ITSx command: ITSx -i /home/maria/workspace/git/FROGS/FROGS_master/test/res/1550052844.03_3921_04-filters.fasta_1 -o 1550052844.03_3921_04-filters --preserve T -t F --save_regions all +##Results + nb full (removed): 0 + nb no_detections (removed): 0 + nb SSU (removed): 0 + nb ITS2 (removed): 0 + nb ITS1 (kept): 29 + nb LSU (removed): 0 + nb 5_8S (removed): 0 + +## Input file : 1550052844.03_3921_04-filters.fasta_2 +## in working directory: res/1550052844.03_3921_1550052844.03_3921_04-filters.fasta_2 +## ITSx command: ITSx -i /home/maria/workspace/git/FROGS/FROGS_master/test/res/1550052844.03_3921_04-filters.fasta_2 -o 1550052844.03_3921_04-filters --preserve T -t F --save_regions all +##Results + nb full (removed): 0 + nb no_detections (removed): 0 + nb SSU (removed): 0 + nb ITS2 (removed): 0 + nb ITS1 (kept): 28 + nb LSU (removed): 0 + nb 5_8S (removed): 0 + + +## Removes the observations after ITSx. + +