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annotate test-data/TEST_1/test_1.log @ 0:cecb2758ec26 draft

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planemo upload for repository https://github.com/pimarin/tools-iuc/tree/isescan commit df153ded9cba1e4a89cf3ea554183e7344e01c5d-dirty
author pimarin
date Tue, 23 Aug 2022 10:01:31 +0000
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cecb2758ec26 planemo upload for repository https://github.com/pimarin/tools-iuc/tree/isescan commit df153ded9cba1e4a89cf3ea554183e7344e01c5d-dirty
pimarin
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1 /usr/local/bin/FragGeneScan -s /tmp/tmpjm077o6o/files/6/a/1/dataset_6a1f68ad-940d-4e7c-9736-cf5a2ce9fd9e.dat -o results/proteome/1/dataset_6a1f68ad-940d-4e7c-9736-cf5a2ce9fd9e.dat -w 0 -t illumina_5 -p 1
cecb2758ec26 planemo upload for repository https://github.com/pimarin/tools-iuc/tree/isescan commit df153ded9cba1e4a89cf3ea554183e7344e01c5d-dirty
pimarin
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2 Using 1 threads.
cecb2758ec26 planemo upload for repository https://github.com/pimarin/tools-iuc/tree/isescan commit df153ded9cba1e4a89cf3ea554183e7344e01c5d-dirty
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3 no. of seqs: 1
cecb2758ec26 planemo upload for repository https://github.com/pimarin/tools-iuc/tree/isescan commit df153ded9cba1e4a89cf3ea554183e7344e01c5d-dirty
pimarin
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4 Clock time used (by 1 threads) = 0.00 mins
cecb2758ec26 planemo upload for repository https://github.com/pimarin/tools-iuc/tree/isescan commit df153ded9cba1e4a89cf3ea554183e7344e01c5d-dirty
pimarin
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5 prepare gff file..
cecb2758ec26 planemo upload for repository https://github.com/pimarin/tools-iuc/tree/isescan commit df153ded9cba1e4a89cf3ea554183e7344e01c5d-dirty
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6 Time elapsed: 0 hours 0 minutes and 0 seconds.
cecb2758ec26 planemo upload for repository https://github.com/pimarin/tools-iuc/tree/isescan commit df153ded9cba1e4a89cf3ea554183e7344e01c5d-dirty
pimarin
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7 ISEScan starts at Tue Aug 23 09:39:42 2022
cecb2758ec26 planemo upload for repository https://github.com/pimarin/tools-iuc/tree/isescan commit df153ded9cba1e4a89cf3ea554183e7344e01c5d-dirty
pimarin
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8 predict and translate genes from genome sequence into protein database using FragGeneScan program
cecb2758ec26 planemo upload for repository https://github.com/pimarin/tools-iuc/tree/isescan commit df153ded9cba1e4a89cf3ea554183e7344e01c5d-dirty
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9
cecb2758ec26 planemo upload for repository https://github.com/pimarin/tools-iuc/tree/isescan commit df153ded9cba1e4a89cf3ea554183e7344e01c5d-dirty
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10 Begin to translate genome into proteome.
cecb2758ec26 planemo upload for repository https://github.com/pimarin/tools-iuc/tree/isescan commit df153ded9cba1e4a89cf3ea554183e7344e01c5d-dirty
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11 Translating genome into proteome for /tmp/tmpjm077o6o/files/6/a/1/dataset_6a1f68ad-940d-4e7c-9736-cf5a2ce9fd9e.dat , return 0
cecb2758ec26 planemo upload for repository https://github.com/pimarin/tools-iuc/tree/isescan commit df153ded9cba1e4a89cf3ea554183e7344e01c5d-dirty
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12
cecb2758ec26 planemo upload for repository https://github.com/pimarin/tools-iuc/tree/isescan commit df153ded9cba1e4a89cf3ea554183e7344e01c5d-dirty
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13 Finish translating genome into proteome. Tue Aug 23 09:39:42 2022
cecb2758ec26 planemo upload for repository https://github.com/pimarin/tools-iuc/tree/isescan commit df153ded9cba1e4a89cf3ea554183e7344e01c5d-dirty
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cecb2758ec26 planemo upload for repository https://github.com/pimarin/tools-iuc/tree/isescan commit df153ded9cba1e4a89cf3ea554183e7344e01c5d-dirty
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15 Begin to phmmer search against proteome database. Tue Aug 23 09:39:42 2022
cecb2758ec26 planemo upload for repository https://github.com/pimarin/tools-iuc/tree/isescan commit df153ded9cba1e4a89cf3ea554183e7344e01c5d-dirty
pimarin
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16 Finish phmmer searching /usr/local/bin/pHMMs/clusters.single.faa against results/proteome/1/dataset_6a1f68ad-940d-4e7c-9736-cf5a2ce9fd9e.dat.faa , output results/hmm/1/clusters.single.faa.dataset_6a1f68ad-940d-4e7c-9736-cf5a2ce9fd9e.dat.faa
cecb2758ec26 planemo upload for repository https://github.com/pimarin/tools-iuc/tree/isescan commit df153ded9cba1e4a89cf3ea554183e7344e01c5d-dirty
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17
cecb2758ec26 planemo upload for repository https://github.com/pimarin/tools-iuc/tree/isescan commit df153ded9cba1e4a89cf3ea554183e7344e01c5d-dirty
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18 Finish phmmer searching against proteome database. Tue Aug 23 09:40:02 2022
cecb2758ec26 planemo upload for repository https://github.com/pimarin/tools-iuc/tree/isescan commit df153ded9cba1e4a89cf3ea554183e7344e01c5d-dirty
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cecb2758ec26 planemo upload for repository https://github.com/pimarin/tools-iuc/tree/isescan commit df153ded9cba1e4a89cf3ea554183e7344e01c5d-dirty
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20 Begin to profile HMM search against proteome database. Tue Aug 23 09:40:02 2022
cecb2758ec26 planemo upload for repository https://github.com/pimarin/tools-iuc/tree/isescan commit df153ded9cba1e4a89cf3ea554183e7344e01c5d-dirty
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21 Finish Profile HMM searching /usr/local/bin/pHMMs/clusters.faa.hmm against results/proteome/1/dataset_6a1f68ad-940d-4e7c-9736-cf5a2ce9fd9e.dat.faa , output results/hmm/1/clusters.faa.hmm.dataset_6a1f68ad-940d-4e7c-9736-cf5a2ce9fd9e.dat.faa
cecb2758ec26 planemo upload for repository https://github.com/pimarin/tools-iuc/tree/isescan commit df153ded9cba1e4a89cf3ea554183e7344e01c5d-dirty
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22
cecb2758ec26 planemo upload for repository https://github.com/pimarin/tools-iuc/tree/isescan commit df153ded9cba1e4a89cf3ea554183e7344e01c5d-dirty
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23 Finish profile HMM searching against proteome database. Tue Aug 23 09:40:14 2022
cecb2758ec26 planemo upload for repository https://github.com/pimarin/tools-iuc/tree/isescan commit df153ded9cba1e4a89cf3ea554183e7344e01c5d-dirty
pimarin
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24 pred begins at Tue Aug 23 09:40:14 2022
cecb2758ec26 planemo upload for repository https://github.com/pimarin/tools-iuc/tree/isescan commit df153ded9cba1e4a89cf3ea554183e7344e01c5d-dirty
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25 Begin addNonORFcopy at Tue Aug 23 09:40:14 2022
cecb2758ec26 planemo upload for repository https://github.com/pimarin/tools-iuc/tree/isescan commit df153ded9cba1e4a89cf3ea554183e7344e01c5d-dirty
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26 Finish addNonORFcopy at Tue Aug 23 09:40:14 2022
cecb2758ec26 planemo upload for repository https://github.com/pimarin/tools-iuc/tree/isescan commit df153ded9cba1e4a89cf3ea554183e7344e01c5d-dirty
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27 Begin addNonORFcopy1 at Tue Aug 23 09:40:14 2022
cecb2758ec26 planemo upload for repository https://github.com/pimarin/tools-iuc/tree/isescan commit df153ded9cba1e4a89cf3ea554183e7344e01c5d-dirty
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28 Finish addNonORFcopy1 at Tue Aug 23 09:40:14 2022
cecb2758ec26 planemo upload for repository https://github.com/pimarin/tools-iuc/tree/isescan commit df153ded9cba1e4a89cf3ea554183e7344e01c5d-dirty
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29 getFullIS() begins at Tue Aug 23 09:40:14 2022
cecb2758ec26 planemo upload for repository https://github.com/pimarin/tools-iuc/tree/isescan commit df153ded9cba1e4a89cf3ea554183e7344e01c5d-dirty
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30 Start typing IS elements
cecb2758ec26 planemo upload for repository https://github.com/pimarin/tools-iuc/tree/isescan commit df153ded9cba1e4a89cf3ea554183e7344e01c5d-dirty
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31 The 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
cecb2758ec26 planemo upload for repository https://github.com/pimarin/tools-iuc/tree/isescan commit df153ded9cba1e4a89cf3ea554183e7344e01c5d-dirty
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32 Finish typing partial IS elements
cecb2758ec26 planemo upload for repository https://github.com/pimarin/tools-iuc/tree/isescan commit df153ded9cba1e4a89cf3ea554183e7344e01c5d-dirty
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33 Begin removeOverlappedHits at Tue Aug 23 09:40:14 2022
cecb2758ec26 planemo upload for repository https://github.com/pimarin/tools-iuc/tree/isescan commit df153ded9cba1e4a89cf3ea554183e7344e01c5d-dirty
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34 gi|228288719|ref|NC_012624.1|: no intersected hits found
cecb2758ec26 planemo upload for repository https://github.com/pimarin/tools-iuc/tree/isescan commit df153ded9cba1e4a89cf3ea554183e7344e01c5d-dirty
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35 Finish removeOverlappedHits at Tue Aug 23 09:40:14 2022
cecb2758ec26 planemo upload for repository https://github.com/pimarin/tools-iuc/tree/isescan commit df153ded9cba1e4a89cf3ea554183e7344e01c5d-dirty
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36 Begin reading protein database at Tue Aug 23 09:40:14 2022
cecb2758ec26 planemo upload for repository https://github.com/pimarin/tools-iuc/tree/isescan commit df153ded9cba1e4a89cf3ea554183e7344e01c5d-dirty
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37 Finish reading protein database at Tue Aug 23 09:40:14 2022
cecb2758ec26 planemo upload for repository https://github.com/pimarin/tools-iuc/tree/isescan commit df153ded9cba1e4a89cf3ea554183e7344e01c5d-dirty
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38 Write IS elements from all sequences in 1/dataset_6a1f68ad-940d-4e7c-9736-cf5a2ce9fd9e.dat into one result file under results
cecb2758ec26 planemo upload for repository https://github.com/pimarin/tools-iuc/tree/isescan commit df153ded9cba1e4a89cf3ea554183e7344e01c5d-dirty
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39 Write 2 IS copies to results/1/dataset_6a1f68ad-940d-4e7c-9736-cf5a2ce9fd9e.dat.csv and results/1/dataset_6a1f68ad-940d-4e7c-9736-cf5a2ce9fd9e.dat.tsv and results/1/dataset_6a1f68ad-940d-4e7c-9736-cf5a2ce9fd9e.dat.raw
cecb2758ec26 planemo upload for repository https://github.com/pimarin/tools-iuc/tree/isescan commit df153ded9cba1e4a89cf3ea554183e7344e01c5d-dirty
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40 Write summarized result to results/1/dataset_6a1f68ad-940d-4e7c-9736-cf5a2ce9fd9e.dat.sum
cecb2758ec26 planemo upload for repository https://github.com/pimarin/tools-iuc/tree/isescan commit df153ded9cba1e4a89cf3ea554183e7344e01c5d-dirty
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41 End in pred Tue Aug 23 09:40:14 2022
cecb2758ec26 planemo upload for repository https://github.com/pimarin/tools-iuc/tree/isescan commit df153ded9cba1e4a89cf3ea554183e7344e01c5d-dirty
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42 Both complete and partial IS elements are reported.
cecb2758ec26 planemo upload for repository https://github.com/pimarin/tools-iuc/tree/isescan commit df153ded9cba1e4a89cf3ea554183e7344e01c5d-dirty
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43 ISEScan ends at Tue Aug 23 09:40:14 2022