Mercurial > repos > bgruening > tgsgapcloser

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
author bgruening
date Sun, 14 Nov 2021 21:28:36 +0000
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86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
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1 /usr/local/bin/tgsgapcloserbin/tgsgapcloser --prefix output --contig2ont_paf output.fill.paf --ont_reads_a /tmp/tmp0waeaugc/files/f/4/4/dataset_f44c5ccd-786b-4085-ba86-9dea34a7c4b2.dat --min_match 300 --min_idy 0.300000
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
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2 TGSGapCloser INFO UTC 2021/11/14 19:39:45 : TGSGapCloser start now ...
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
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3 TGSGapCloser INFO UTC 2021/11/14 19:39:45 : LoadONTReads start now ...
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
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4 TGSGapCloser INFO UTC 2021/11/14 19:39:45 : LoadONTReads finish. used wall clock : 0 seconds, cpu time : 0.000380 seconds
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
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5 TGSGapCloser INFO UTC 2021/11/14 19:39:45 : LoadPAF start now ...
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
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6 TGSGapCloser INFO UTC 2021/11/14 19:39:45 : >the read2contig freq is
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
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7 1 9
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
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8 2 1
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
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9
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
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10 TGSGapCloser INFO UTC 2021/11/14 19:39:45 : >the contig2read_num_freq freq is
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
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11 1 2
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
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12 9 1
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
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86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
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14 TGSGapCloser INFO UTC 2021/11/14 19:39:45 : >the contig2a_read_freq freq is
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
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15 1 9
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
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16 2 2
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
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86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
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18 TGSGapCloser INFO UTC 2021/11/14 19:39:45 : LoadPAF finish. used wall clock : 0 seconds, cpu time : 0.000138 seconds
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
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19 TGSGapCloser INFO UTC 2021/11/14 19:39:45 : LoadScaffInfo start now ...
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
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20 TGSGapCloser INFO UTC 2021/11/14 19:39:45 : LoadScaffInfo finish. used wall clock : 0 seconds, cpu time : 0.000028 seconds
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
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21 TGSGapCloser INFO UTC 2021/11/14 19:39:45 : ParseAllGap start now ...
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
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22 TGSGapCloser INFO UTC 2021/11/14 19:39:45 : >the overlap cheked caused failed is 0
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
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23 TGSGapCloser INFO UTC 2021/11/14 19:39:45 : >the gapsize cheked caused failed is 0
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
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24 TGSGapCloser INFO UTC 2021/11/14 19:39:45 : >the gap_total is 5
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
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25 TGSGapCloser INFO UTC 2021/11/14 19:39:45 : >the no_match is 4
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
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26 TGSGapCloser INFO UTC 2021/11/14 19:39:45 : >the no choose is 0
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
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27 TGSGapCloser INFO UTC 2021/11/14 19:39:45 : >the no common is 0
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
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28 TGSGapCloser INFO UTC 2021/11/14 19:39:45 : >the scaff_negotive_gap_size is 0
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
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29 TGSGapCloser INFO UTC 2021/11/14 19:39:45 : >the ont_negotive_gap_size is 0
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
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30 TGSGapCloser INFO UTC 2021/11/14 19:39:45 : >the common reads count freq for a gap
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
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31 1 1
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
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86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
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33 TGSGapCloser INFO UTC 2021/11/14 19:39:45 : >the used idy freq is
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
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34 41 1
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
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35 54 1
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
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86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
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37 TGSGapCloser INFO UTC 2021/11/14 19:39:45 : >the correct oo reads count freq for a gap
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
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38 1 1
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
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86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
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40 TGSGapCloser INFO UTC 2021/11/14 19:39:45 : >the filler choose count freq for a gap
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
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41 1 1
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
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86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
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43 TGSGapCloser INFO UTC 2021/11/14 19:39:45 : >the one read provide filler choose count freq for a gap
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
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44 1 1
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
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86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
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46 TGSGapCloser INFO UTC 2021/11/14 19:39:45 : >the cut error is 0
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
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47 TGSGapCloser INFO UTC 2021/11/14 19:39:45 : ParseAllGap finish. used wall clock : 0 seconds, cpu time : 0.000165 seconds
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
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48 TGSGapCloser INFO UTC 2021/11/14 19:39:45 : PrintScaffInfo start now ...
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
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49 TGSGapCloser INFO UTC 2021/11/14 19:39:45 : PrintScaffInfo finish. used wall clock : 0 seconds, cpu time : 0.000045 seconds
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
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50 TGSGapCloser INFO UTC 2021/11/14 19:39:45 : TGSGapCloser finish. used wall clock : 0 seconds, cpu time : 0.000965 seconds