Mercurial > repos > iuc > isescan

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/isescan commit 4c6ec7ff94aad26776df3964e7cec37058103721
author iuc
date Thu, 25 Jan 2024 16:32:04 +0000
parents debe9c750cdd
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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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
debe9c750cdd planemo upload for repository https://github.com/pimarin/tools-iuc/tree/isescan commit d9d88c043b2d45877e3b0bffba6e709c9a0f0379
iuc
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4 Clock time used (by 1 threads) = 0.00 mins
debe9c750cdd planemo upload for repository https://github.com/pimarin/tools-iuc/tree/isescan commit d9d88c043b2d45877e3b0bffba6e709c9a0f0379
iuc
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5 prepare gff file..
debe9c750cdd planemo upload for repository https://github.com/pimarin/tools-iuc/tree/isescan commit d9d88c043b2d45877e3b0bffba6e709c9a0f0379
iuc
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6 Time elapsed: 0 hours 0 minutes and 0 seconds.
debe9c750cdd planemo upload for repository https://github.com/pimarin/tools-iuc/tree/isescan commit d9d88c043b2d45877e3b0bffba6e709c9a0f0379
iuc
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7 ISEScan starts at Wed Aug 31 15:19:29 2022
debe9c750cdd planemo upload for repository https://github.com/pimarin/tools-iuc/tree/isescan commit d9d88c043b2d45877e3b0bffba6e709c9a0f0379
iuc
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8 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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9
debe9c750cdd planemo upload for repository https://github.com/pimarin/tools-iuc/tree/isescan commit d9d88c043b2d45877e3b0bffba6e709c9a0f0379
iuc
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10 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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11 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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12
debe9c750cdd planemo upload for repository https://github.com/pimarin/tools-iuc/tree/isescan commit d9d88c043b2d45877e3b0bffba6e709c9a0f0379
iuc
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13 Finish translating genome into proteome. Wed Aug 31 15:19:29 2022
debe9c750cdd planemo upload for repository https://github.com/pimarin/tools-iuc/tree/isescan commit d9d88c043b2d45877e3b0bffba6e709c9a0f0379
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14
debe9c750cdd planemo upload for repository https://github.com/pimarin/tools-iuc/tree/isescan commit d9d88c043b2d45877e3b0bffba6e709c9a0f0379
iuc
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15 Begin to phmmer search against proteome database. Wed Aug 31 15:19:29 2022
debe9c750cdd planemo upload for repository https://github.com/pimarin/tools-iuc/tree/isescan commit d9d88c043b2d45877e3b0bffba6e709c9a0f0379
iuc
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16 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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17
debe9c750cdd planemo upload for repository https://github.com/pimarin/tools-iuc/tree/isescan commit d9d88c043b2d45877e3b0bffba6e709c9a0f0379
iuc
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18 Finish phmmer searching against proteome database. Wed Aug 31 15:19:48 2022
debe9c750cdd planemo upload for repository https://github.com/pimarin/tools-iuc/tree/isescan commit d9d88c043b2d45877e3b0bffba6e709c9a0f0379
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19
debe9c750cdd planemo upload for repository https://github.com/pimarin/tools-iuc/tree/isescan commit d9d88c043b2d45877e3b0bffba6e709c9a0f0379
iuc
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20 Begin to profile HMM search against proteome database. Wed Aug 31 15:19:48 2022
debe9c750cdd planemo upload for repository https://github.com/pimarin/tools-iuc/tree/isescan commit d9d88c043b2d45877e3b0bffba6e709c9a0f0379
iuc
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21 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
iuc
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22
debe9c750cdd planemo upload for repository https://github.com/pimarin/tools-iuc/tree/isescan commit d9d88c043b2d45877e3b0bffba6e709c9a0f0379
iuc
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23 Finish profile HMM searching against proteome database. Wed Aug 31 15:20:01 2022
debe9c750cdd planemo upload for repository https://github.com/pimarin/tools-iuc/tree/isescan commit d9d88c043b2d45877e3b0bffba6e709c9a0f0379
iuc
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24 pred begins at Wed Aug 31 15:20:01 2022
debe9c750cdd planemo upload for repository https://github.com/pimarin/tools-iuc/tree/isescan commit d9d88c043b2d45877e3b0bffba6e709c9a0f0379
iuc
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25 Begin addNonORFcopy at Wed Aug 31 15:20:01 2022
debe9c750cdd planemo upload for repository https://github.com/pimarin/tools-iuc/tree/isescan commit d9d88c043b2d45877e3b0bffba6e709c9a0f0379
iuc
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26 Finish addNonORFcopy at Wed Aug 31 15:20:01 2022
debe9c750cdd planemo upload for repository https://github.com/pimarin/tools-iuc/tree/isescan commit d9d88c043b2d45877e3b0bffba6e709c9a0f0379
iuc
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27 Begin addNonORFcopy1 at Wed Aug 31 15:20:01 2022
debe9c750cdd planemo upload for repository https://github.com/pimarin/tools-iuc/tree/isescan commit d9d88c043b2d45877e3b0bffba6e709c9a0f0379
iuc
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28 Finish addNonORFcopy1 at Wed Aug 31 15:20:01 2022
debe9c750cdd planemo upload for repository https://github.com/pimarin/tools-iuc/tree/isescan commit d9d88c043b2d45877e3b0bffba6e709c9a0f0379
iuc
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29 getFullIS() begins at Wed Aug 31 15:20:01 2022
debe9c750cdd planemo upload for repository https://github.com/pimarin/tools-iuc/tree/isescan commit d9d88c043b2d45877e3b0bffba6e709c9a0f0379
iuc
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30 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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31 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
debe9c750cdd planemo upload for repository https://github.com/pimarin/tools-iuc/tree/isescan commit d9d88c043b2d45877e3b0bffba6e709c9a0f0379
iuc
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32 Finish removing partial IS elements
debe9c750cdd planemo upload for repository https://github.com/pimarin/tools-iuc/tree/isescan commit d9d88c043b2d45877e3b0bffba6e709c9a0f0379
iuc
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33 Begin removeOverlappedHits at Wed Aug 31 15:20:01 2022
debe9c750cdd planemo upload for repository https://github.com/pimarin/tools-iuc/tree/isescan commit d9d88c043b2d45877e3b0bffba6e709c9a0f0379
iuc
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34 gi|228288719|ref|NC_012624.1|: no intersected hits found
debe9c750cdd planemo upload for repository https://github.com/pimarin/tools-iuc/tree/isescan commit d9d88c043b2d45877e3b0bffba6e709c9a0f0379
iuc
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35 Finish removeOverlappedHits at Wed Aug 31 15:20:01 2022
debe9c750cdd planemo upload for repository https://github.com/pimarin/tools-iuc/tree/isescan commit d9d88c043b2d45877e3b0bffba6e709c9a0f0379
iuc
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36 Begin reading protein database at Wed Aug 31 15:20:01 2022
debe9c750cdd planemo upload for repository https://github.com/pimarin/tools-iuc/tree/isescan commit d9d88c043b2d45877e3b0bffba6e709c9a0f0379
iuc
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37 Finish reading protein database at Wed Aug 31 15:20:01 2022
debe9c750cdd planemo upload for repository https://github.com/pimarin/tools-iuc/tree/isescan commit d9d88c043b2d45877e3b0bffba6e709c9a0f0379
iuc
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38 Write IS elements from all sequences in input into one result file under results
debe9c750cdd planemo upload for repository https://github.com/pimarin/tools-iuc/tree/isescan commit d9d88c043b2d45877e3b0bffba6e709c9a0f0379
iuc
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39 Write 1 IS copies to results/input.csv and results/input.tsv and results/input.raw
debe9c750cdd planemo upload for repository https://github.com/pimarin/tools-iuc/tree/isescan commit d9d88c043b2d45877e3b0bffba6e709c9a0f0379
iuc
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40 Write summarized result to results/input.sum
debe9c750cdd planemo upload for repository https://github.com/pimarin/tools-iuc/tree/isescan commit d9d88c043b2d45877e3b0bffba6e709c9a0f0379
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41 End in pred Wed Aug 31 15:20:01 2022
debe9c750cdd planemo upload for repository https://github.com/pimarin/tools-iuc/tree/isescan commit d9d88c043b2d45877e3b0bffba6e709c9a0f0379
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42 Only complete IS elements are reported.
debe9c750cdd planemo upload for repository https://github.com/pimarin/tools-iuc/tree/isescan commit d9d88c043b2d45877e3b0bffba6e709c9a0f0379
iuc
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43 ISEScan ends at Wed Aug 31 15:20:01 2022