Mercurial > repos > frogs > frogs_3_1_0
annotate 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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59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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1 ## Application |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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2 Software :/home/maria/workspace/git/FROGS/FROGS_master/test/../app/itsx.py (version : 3.1) |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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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 |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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diff
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4 |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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5 ######################################################################################################## |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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6 # identifies ITS sequences and extracts the ITS region (parallelITSx.py version : 1.0.0 [ITSx 1.0.11]) |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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7 Command: |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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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 |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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9 |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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10 Execution: |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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11 start: 13 Feb 2019 11:14:03 |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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12 end: 13 Feb 2019 11:14:15 |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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13 |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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14 Results: |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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15 |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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16 # split res/04-filters.fasta in 3 fasta files |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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17 Results |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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18 Wrote 29 records to res/1550052844.03_3921_04-filters.fasta_0 |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
parents:
diff
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19 Wrote 29 records to res/1550052844.03_3921_04-filters.fasta_1 |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
parents:
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20 Wrote 28 records to res/1550052844.03_3921_04-filters.fasta_2 |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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21 |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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22 ## Input file : 1550052844.03_3921_04-filters.fasta_0 |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
parents:
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23 ## in working directory: res/1550052844.03_3921_1550052844.03_3921_04-filters.fasta_0 |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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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 |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
parents:
diff
changeset
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25 ##Results |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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changeset
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26 nb full (removed): 0 |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
parents:
diff
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27 nb no_detections (removed): 0 |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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28 nb SSU (removed): 0 |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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29 nb ITS2 (removed): 0 |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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30 nb ITS1 (kept): 29 |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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31 nb LSU (removed): 0 |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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32 nb 5_8S (removed): 0 |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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33 |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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34 ## Input file : 1550052844.03_3921_04-filters.fasta_1 |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
parents:
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35 ## in working directory: res/1550052844.03_3921_1550052844.03_3921_04-filters.fasta_1 |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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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 |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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37 ##Results |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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38 nb full (removed): 0 |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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39 nb no_detections (removed): 0 |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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40 nb SSU (removed): 0 |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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41 nb ITS2 (removed): 0 |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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42 nb ITS1 (kept): 29 |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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43 nb LSU (removed): 0 |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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44 nb 5_8S (removed): 0 |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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45 |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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46 ## Input file : 1550052844.03_3921_04-filters.fasta_2 |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
parents:
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47 ## in working directory: res/1550052844.03_3921_1550052844.03_3921_04-filters.fasta_2 |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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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 |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
parents:
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49 ##Results |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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changeset
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50 nb full (removed): 0 |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
parents:
diff
changeset
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51 nb no_detections (removed): 0 |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
parents:
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52 nb SSU (removed): 0 |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
parents:
diff
changeset
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53 nb ITS2 (removed): 0 |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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54 nb ITS1 (kept): 28 |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
parents:
diff
changeset
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55 nb LSU (removed): 0 |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
parents:
diff
changeset
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56 nb 5_8S (removed): 0 |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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57 |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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58 |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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59 ## Removes the observations after ITSx. |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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60 |
59bc96331073
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
frogs
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61 |