Mercurial > repos > iuc > isescan

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/isescan commit e2191246bc1ccd70c05fe0dac45d39cf8dd621d3
author iuc
date Wed, 09 Jul 2025 12:49:45 +0000
parents debe9c750cdd
children
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debe9c750cdd planemo upload for repository https://github.com/pimarin/tools-iuc/tree/isescan commit d9d88c043b2d45877e3b0bffba6e709c9a0f0379
iuc
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1 /usr/local/bin/FragGeneScan -s input -o results/proteome/input -w 0 -t illumina_5 -p 1
debe9c750cdd planemo upload for repository https://github.com/pimarin/tools-iuc/tree/isescan commit d9d88c043b2d45877e3b0bffba6e709c9a0f0379
iuc
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2 Using 1 threads.
debe9c750cdd planemo upload for repository https://github.com/pimarin/tools-iuc/tree/isescan commit d9d88c043b2d45877e3b0bffba6e709c9a0f0379
iuc
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3 no. of seqs: 1
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81539b9ae80a planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/isescan commit e2191246bc1ccd70c05fe0dac45d39cf8dd621d3
iuc
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4 Clock time used (by 1 threads) = 0.1 sec
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debe9c750cdd planemo upload for repository https://github.com/pimarin/tools-iuc/tree/isescan commit d9d88c043b2d45877e3b0bffba6e709c9a0f0379
iuc
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5 Time elapsed: 0 hours 0 minutes and 0 seconds.
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81539b9ae80a planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/isescan commit e2191246bc1ccd70c05fe0dac45d39cf8dd621d3
iuc
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6 ISEScan starts at Wed Jul 9 09:58:18 2025
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debe9c750cdd planemo upload for repository https://github.com/pimarin/tools-iuc/tree/isescan commit d9d88c043b2d45877e3b0bffba6e709c9a0f0379
iuc
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7 predict and translate genes from genome sequence into protein database using FragGeneScan program
debe9c750cdd planemo upload for repository https://github.com/pimarin/tools-iuc/tree/isescan commit d9d88c043b2d45877e3b0bffba6e709c9a0f0379
iuc
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debe9c750cdd planemo upload for repository https://github.com/pimarin/tools-iuc/tree/isescan commit d9d88c043b2d45877e3b0bffba6e709c9a0f0379
iuc
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9 Begin to translate genome into proteome.
debe9c750cdd planemo upload for repository https://github.com/pimarin/tools-iuc/tree/isescan commit d9d88c043b2d45877e3b0bffba6e709c9a0f0379
iuc
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10 Translating genome into proteome for input , return 0
debe9c750cdd planemo upload for repository https://github.com/pimarin/tools-iuc/tree/isescan commit d9d88c043b2d45877e3b0bffba6e709c9a0f0379
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11
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81539b9ae80a planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/isescan commit e2191246bc1ccd70c05fe0dac45d39cf8dd621d3
iuc
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12 Finish translating genome into proteome. Wed Jul 9 09:58:18 2025
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debe9c750cdd planemo upload for repository https://github.com/pimarin/tools-iuc/tree/isescan commit d9d88c043b2d45877e3b0bffba6e709c9a0f0379
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81539b9ae80a planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/isescan commit e2191246bc1ccd70c05fe0dac45d39cf8dd621d3
iuc
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14 Begin to phmmer search against proteome database. Wed Jul 9 09:58:18 2025
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debe9c750cdd planemo upload for repository https://github.com/pimarin/tools-iuc/tree/isescan commit d9d88c043b2d45877e3b0bffba6e709c9a0f0379
iuc
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15 Finish phmmer searching /usr/local/bin/pHMMs/clusters.single.faa against results/proteome/input.faa , output results/hmm/clusters.single.faa.input.faa
debe9c750cdd planemo upload for repository https://github.com/pimarin/tools-iuc/tree/isescan commit d9d88c043b2d45877e3b0bffba6e709c9a0f0379
iuc
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16
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81539b9ae80a planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/isescan commit e2191246bc1ccd70c05fe0dac45d39cf8dd621d3
iuc
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17 Finish phmmer searching against proteome database. Wed Jul 9 09:58:30 2025
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debe9c750cdd planemo upload for repository https://github.com/pimarin/tools-iuc/tree/isescan commit d9d88c043b2d45877e3b0bffba6e709c9a0f0379
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81539b9ae80a planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/isescan commit e2191246bc1ccd70c05fe0dac45d39cf8dd621d3
iuc
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19 Begin to profile HMM search against proteome database. Wed Jul 9 09:58:30 2025
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debe9c750cdd planemo upload for repository https://github.com/pimarin/tools-iuc/tree/isescan commit d9d88c043b2d45877e3b0bffba6e709c9a0f0379
iuc
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20 Finish Profile HMM searching /usr/local/bin/pHMMs/clusters.faa.hmm against results/proteome/input.faa , output results/hmm/clusters.faa.hmm.input.faa
debe9c750cdd planemo upload for repository https://github.com/pimarin/tools-iuc/tree/isescan commit d9d88c043b2d45877e3b0bffba6e709c9a0f0379
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81539b9ae80a planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/isescan commit e2191246bc1ccd70c05fe0dac45d39cf8dd621d3
iuc
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22 Finish profile HMM searching against proteome database. Wed Jul 9 09:58:38 2025
81539b9ae80a planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/isescan commit e2191246bc1ccd70c05fe0dac45d39cf8dd621d3
iuc
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23 pred begins at Wed Jul 9 09:58:38 2025
81539b9ae80a planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/isescan commit e2191246bc1ccd70c05fe0dac45d39cf8dd621d3
iuc
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24 Begin addNonORFcopy at Wed Jul 9 09:58:38 2025
81539b9ae80a planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/isescan commit e2191246bc1ccd70c05fe0dac45d39cf8dd621d3
iuc
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25 Finish addNonORFcopy at Wed Jul 9 09:58:38 2025
81539b9ae80a planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/isescan commit e2191246bc1ccd70c05fe0dac45d39cf8dd621d3
iuc
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26 Begin addNonORFcopy1 at Wed Jul 9 09:58:38 2025
81539b9ae80a planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/isescan commit e2191246bc1ccd70c05fe0dac45d39cf8dd621d3
iuc
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27 Finish addNonORFcopy1 at Wed Jul 9 09:58:38 2025
81539b9ae80a planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/isescan commit e2191246bc1ccd70c05fe0dac45d39cf8dd621d3
iuc
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28 getFullIS() begins at Wed Jul 9 09:58:38 2025
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debe9c750cdd planemo upload for repository https://github.com/pimarin/tools-iuc/tree/isescan commit d9d88c043b2d45877e3b0bffba6e709c9a0f0379
iuc
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29 Start removing partial IS elements
debe9c750cdd planemo upload for repository https://github.com/pimarin/tools-iuc/tree/isescan commit d9d88c043b2d45877e3b0bffba6e709c9a0f0379
iuc
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30 Remove single-copy partial IS element with evalue > 1e-50: isLen=989 IS5 bd=[30355, 31343] orf('gi|228288719|ref|NC_012624.1|', 30399, 31298, '+') evalue=1.7e-37
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81539b9ae80a planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/isescan commit e2191246bc1ccd70c05fe0dac45d39cf8dd621d3
iuc
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31 Warning: no valid hit found for gi|228288719|ref|NC_012624.1|
81539b9ae80a planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/isescan commit e2191246bc1ccd70c05fe0dac45d39cf8dd621d3
iuc
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32 Warning: no valid hit after removing short IS element candidate for gi|228288719|ref|NC_012624.1|
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debe9c750cdd planemo upload for repository https://github.com/pimarin/tools-iuc/tree/isescan commit d9d88c043b2d45877e3b0bffba6e709c9a0f0379
iuc
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33 Finish removing partial IS elements
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81539b9ae80a planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/isescan commit e2191246bc1ccd70c05fe0dac45d39cf8dd621d3
iuc
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34 Begin removeOverlappedHits at Wed Jul 9 09:58:38 2025
81539b9ae80a planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/isescan commit e2191246bc1ccd70c05fe0dac45d39cf8dd621d3
iuc
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35 Finish removeOverlappedHits at Wed Jul 9 09:58:38 2025
81539b9ae80a planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/isescan commit e2191246bc1ccd70c05fe0dac45d39cf8dd621d3
iuc
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36 Begin reading protein database at Wed Jul 9 09:58:38 2025
81539b9ae80a planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/isescan commit e2191246bc1ccd70c05fe0dac45d39cf8dd621d3
iuc
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37 Finish reading protein database at Wed Jul 9 09:58:38 2025
81539b9ae80a planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/isescan commit e2191246bc1ccd70c05fe0dac45d39cf8dd621d3
iuc
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38 No IS element was found for ['input']
81539b9ae80a planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/isescan commit e2191246bc1ccd70c05fe0dac45d39cf8dd621d3
iuc
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39 End in pred Wed Jul 9 09:58:38 2025
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debe9c750cdd planemo upload for repository https://github.com/pimarin/tools-iuc/tree/isescan commit d9d88c043b2d45877e3b0bffba6e709c9a0f0379
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40 Only complete IS elements are reported.
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81539b9ae80a planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/isescan commit e2191246bc1ccd70c05fe0dac45d39cf8dd621d3
iuc
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41 ISEScan ends at Wed Jul 9 09:58:38 2025