Mercurial > repos > frogs > frogs_3_1_0
comparison 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 |
| parents | |
| children |
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| -1:000000000000 | 0:59bc96331073 |
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| 1 ## Application | |
| 2 Software :/home/maria/workspace/git/FROGS/FROGS_master/test/../app/itsx.py (version : 3.1) | |
| 3 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 | |
| 4 | |
| 5 ######################################################################################################## | |
| 6 # identifies ITS sequences and extracts the ITS region (parallelITSx.py version : 1.0.0 [ITSx 1.0.11]) | |
| 7 Command: | |
| 8 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 | |
| 9 | |
| 10 Execution: | |
| 11 start: 13 Feb 2019 11:14:03 | |
| 12 end: 13 Feb 2019 11:14:15 | |
| 13 | |
| 14 Results: | |
| 15 | |
| 16 # split res/04-filters.fasta in 3 fasta files | |
| 17 Results | |
| 18 Wrote 29 records to res/1550052844.03_3921_04-filters.fasta_0 | |
| 19 Wrote 29 records to res/1550052844.03_3921_04-filters.fasta_1 | |
| 20 Wrote 28 records to res/1550052844.03_3921_04-filters.fasta_2 | |
| 21 | |
| 22 ## Input file : 1550052844.03_3921_04-filters.fasta_0 | |
| 23 ## in working directory: res/1550052844.03_3921_1550052844.03_3921_04-filters.fasta_0 | |
| 24 ## 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 | |
| 25 ##Results | |
| 26 nb full (removed): 0 | |
| 27 nb no_detections (removed): 0 | |
| 28 nb SSU (removed): 0 | |
| 29 nb ITS2 (removed): 0 | |
| 30 nb ITS1 (kept): 29 | |
| 31 nb LSU (removed): 0 | |
| 32 nb 5_8S (removed): 0 | |
| 33 | |
| 34 ## Input file : 1550052844.03_3921_04-filters.fasta_1 | |
| 35 ## in working directory: res/1550052844.03_3921_1550052844.03_3921_04-filters.fasta_1 | |
| 36 ## 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 | |
| 37 ##Results | |
| 38 nb full (removed): 0 | |
| 39 nb no_detections (removed): 0 | |
| 40 nb SSU (removed): 0 | |
| 41 nb ITS2 (removed): 0 | |
| 42 nb ITS1 (kept): 29 | |
| 43 nb LSU (removed): 0 | |
| 44 nb 5_8S (removed): 0 | |
| 45 | |
| 46 ## Input file : 1550052844.03_3921_04-filters.fasta_2 | |
| 47 ## in working directory: res/1550052844.03_3921_1550052844.03_3921_04-filters.fasta_2 | |
| 48 ## 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 | |
| 49 ##Results | |
| 50 nb full (removed): 0 | |
| 51 nb no_detections (removed): 0 | |
| 52 nb SSU (removed): 0 | |
| 53 nb ITS2 (removed): 0 | |
| 54 nb ITS1 (kept): 28 | |
| 55 nb LSU (removed): 0 | |
| 56 nb 5_8S (removed): 0 | |
| 57 | |
| 58 | |
| 59 ## Removes the observations after ITSx. | |
| 60 | |
| 61 |