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strpur2 sample result
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Hyungro Lee committed Jul 6, 2015
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41 changes: 35 additions & 6 deletions docs/source/results.rst
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Expand Up @@ -128,13 +128,42 @@ Extra Files

* :download:`KH.tar.gz <sample/KH.tar.gz>`

S. purpuratus (strPur2)
-------------------------------------------------------------------------------

* :download:`strPur2.gff3 <sample/strPur2.gff3.txt>`
* :download:`strPur2.ltr.out <sample/strPur2.ltr.out.txt>`
* :download:`strPur2.en <sample/strPur2.en.txt>`
* :download:`strPur2.rt <sample/strPur2.rt.txt>`

Evaluation
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

.. list-table:: Elapsed time for MGEScan (strPur2)
:header-rows: 1

* - Program
- Total
- nonLTR
- LTR
- Options
* - MGEScan1.3.1
- 3 hrs 34 mins (12,837 secs)
- 21 mins (1,256 secs)
- 3hrs 13 mins (11,581 secs)
- HMMER 2.3.2, no MPI
* - MGEScan2
- 4 hrs 5 mins (14,727 secs)
- 9 mins (503 secs)
- 4hrs 5 mins (14,727 secs)
- HMMER 3.1b1, no MPI
* - MGEScan2 with MPI
- 1hr 22mins (4,897 secs)
- 3 mins (182 secs)
- 1 hr 22 mins (4,897 secs)
- HMMER 3.1b1, MPI with 4 processors


c. intestinalis exp1 MGEScan1.3.1 No MPI 3 hrs 34 mins 12,837 secs 21 mins 1,256 secs 3hrs 13 mins 11,581 secs
MGEScan2 No MPI 2 hrs 23 mins 8,604 secs 　 42 secs 2 hrs 23 mins 8,604 secs
MGEScan2 MPI (4 Proc) 50 mins 2,949 secs 　 13 secs 50 mins 2,949 secs
c. intestinalis exp2 MGEScan1.3.1 No MPI 3 hrs 34 mins 12,837 secs 21 mins 1,256 secs 3hrs 13 mins 11,581 secs
MGEScan2 No MPI 4 hrs 5 mins 14,727 secs 9 mins 503 secs 4hrs 5 mins 14,727 secs
MGEScan2 MPI (4 Proc) 1hr 22mins 4,897 secs 3 mins 182 secs 1 hr 22 mins 4,897 secs
s. purpuratus MGEScan1.3.1 No MPI 45 hrs 12 mins 162,723 secs 6 hrs 34 mins 23,644 secs 38 hrs 37 mins 139,079 secs
MGEScan2 No MPI 67 hrs 13 mins 242,002 secs 7 hrs 53 mins 28,392 secs 67 hrs 13 mins 242,002 secs
MGEScan2 MPI (4 Proc) 12 hrs 55 mins 46,550 secs 2 hrs 36 mins 9,411 secs 12 hrs 55 mins 46,550 secs
240 changes: 240 additions & 0 deletions docs/source/sample/strPur2.en.txt
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tmp-------------------------------------
CR1_Scaffold1264.fa_129551_2 I 1.9e-15 1.1e-10
CR1_Scaffold459.fa_383981_2 CR1 1.2e-32 8.6e-24
CR1_Scaffold337.fa_267056_3 CR1 4.7e-50 2.2e-23
CR1_Scaffold862.fa_450692_3 CR1 5.7e-57 4.7e-32
CR1_Scaffold4096.fa_4922_2 L2 2.1e-35 2.8e-11
CR1_Scaffold2506.fa_46631_2 CR1 1e-28 7.1e-12
CR1_Scaffold3869.fa_72080_2 Rex 4.1e-21 2.0e-06
CR1_Scaffold2382.fa_42017_2 CR1 6.2e-65 1.6e-49
CR1_Scaffold2095.fa_48158_1 L2 2.8e-38 1.1e-25
CR1_Scaffold1315.fa_24155_3 L2 3.7e-29 4.2e-17
CR1_Scaffold423.fa_254981_1 Jockey 7e-14 8.6e-03
CR1_Scaffold2933.fa_16223_1 CR1 7.6e-22 5.4e-04
CR1_Scaffold15.fa_1045385_1 CR1 6.8e-39 3.1e-14
CR1_Scaffold1448.fa_22277_1 CR1 4.1e-45 4.5e-30
CR1_Scaffold3843.fa_20222_1 Jockey 6.7e-15 8.7e-01
CR1_Scaffold1479.fa_62447_1 L1 1.9e-09 1.0e-04
CR1_Scaffold1140.fa_10799_1 CR1 2.1e-13 5.7e-03
CR1_Scaffold3808.fa_4961_2 CR1 1.6e-09 4.6e-05
CR1_Scaffold993.fa_38876_2 Jockey 3.7e-16 9.7e-04
CR1_Scaffold1098.fa_248_3 CR1 9.8e-58 2.6e-32
CR1_Scaffold701.fa_249596_2 L2 0.00013 1.3e-07
CR1_Scaffold626.fa_105716_3 L2 1.9e-19 3.0e-09
CR1_Scaffold1599.fa_144470_1 Rex 5.3e-28 3.8e-14
CR1_Scaffold2892.fa_63587_1 L2 9.8e-26 1.7e-16
CR1_Scaffold3562.fa_32360_2 L1 1.3e-07 9.3e-03
CR1_Scaffold789.fa_93737_3 CR1 7e-62 9.0e-54
CR1_Scaffold2307.fa_249980_1 CR1 1.2e-42 1.2e-45
CR1_Scaffold3141.fa_33107_2 CR1 1.3e-22 3.0e-17
CR1_Scaffold3481.fa_109415_3 L2 8.9e-23 1.3e-09
CR1_Scaffold844.fa_83072_3 Rex 2.6 2.6e-03
CR1_Scaffold1282.fa_9965_2 CR1 1.2e-44 6.7e-01
CR1_Scaffold3823.fa_16451_2 CR1 5.3e-56 4.1e-32
CR1_Scaffold547.fa_11840_1 CR1 3.2e-42 2.7e-30
CR1_Scaffold218.fa_316847_3 Rex 3e-09 3.0e-12
CR1_Scaffold3052.fa_11555_3 CR1 6.3e-48 4.2e-25
CR1_Scaffold241.fa_219248_1 L2 2.3e-26 5.2e-18
CR1_Scaffold2941.fa_25568_2 CR1 8.1e-53 4.3e-34
CR1_Scaffold1321.fa_33167_3 CR1 1.9e-35 7.6e-21
CR1_Scaffold1389.fa_43070_3 CR1 7.4e-05 7.4e-08
CR1_Scaffold1318.fa_48272_1 L2 6e-31 1.5e-12
CR1_Scaffold2091.fa_49463_1 L2 3.3e-28 5.4e-13
tmp-------------------------------------
I_Scaffold1145.fa_160397_2 I 7.9e-41 2.3e-16
I_Scaffold2478.fa_73730_2 R1 2.3e-20 5.1e-04
I_Scaffold1059.fa_197417_3 Jockey 2.6e-18 2.4e-08
I_Scaffold1488.fa_284681_1 I 2.4e-22 1.8e-10
I_Scaffold816.fa_230540_2 L1 6.4e-15 1.1e-09
I_Scaffold17534.fa_5333_1 - 1000 1.0e+00
I_Scaffold1852.fa_69518_3 I 2.7e-29 5.1e-12
I_Scaffold2400.fa_19856_2 I 1e-52 1.4e-26
I_Scaffold508.fa_159395_2 Jockey 5.4e-27 2.3e-06
I_Scaffold173.fa_59252_2 CR1 4.3e-27 5.7e-06
I_Scaffold68.fa_593444_3 CR1 3.1e-14 8.9e-06
I_Scaffold111.fa_240158_1 I 9.9e-45 1.5e-17
I_Scaffold194.fa_751808_3 I 4.9e-32 3.1e-15
I_Scaffold1211.fa_17300_1 I 4.4e-47 5.6e-16
I_Scaffold5193.fa_1676_2 I 1.9e-12 3.2e-04
I_Scaffold3.fa_79250_2 I 9.9e-45 1.5e-17
I_Scaffold4251.fa_18095_1 - 1000 1.0e+00
I_Scaffold251.fa_6872_1 L2 6.1e-10 2.3e-01
I_Scaffold2433.fa_21626_1 R1 3.9e-13 5.1e-07
I_Scaffold941.fa_75536_2 CR1 5.2e-25 1.2e-04
tmp-------------------------------------
Jockey_Scaffold1824.fa_112772_2 Jockey 3.3e-12 2.4e-01
Jockey_Scaffold1153.fa_63179_2 CR1 2.2e-20 4.3e-03
Jockey_Scaffold1449.fa_96140_3 L1 4.9e-26 1.7e-17
tmp-------------------------------------
L1_Scaffold3703.fa_5132_2 CR1 1e-19 3.6e-01
L1_Scaffold159.fa_222938_3 - 1000 1.0e+00
L1_Scaffold1228.fa_88733_1 - 1000 1.0e+00
L1_Scaffold607.fa_93785_1 L1 2e-16 1.8e-11
L1_Scaffold887.fa_218606_1 CR1 7.1e-13 4.7e-06
L1_Scaffold149.fa_95168_1 L1 2.6e-36 1.0e-18
L1_Scaffold16109.fa_17_3 L2 1.5e-11 6.2e-07
L1_Scaffold950.fa_167825_2 L1 9.4e-47 4.7e-35
L1_Scaffold198.fa_526367_1 L1 1.3e-55 5.7e-38
L1_Scaffold1071.fa_63527_1 L1 2.1e-57 8.4e-34
L1_Scaffold701.fa_434669_2 RTE 2.7e-11 5.1e-04
L1_Scaffold3.fa_504782_3 L1 1.8e-23 8.6e-16
L1_Scaffold692.fa_91859_1 L2 3.5e-14 1.0e-01
L1_Scaffold1967.fa_129125_2 L1 1.2e-30 1.9e-23
L1_Scaffold681.fa_21602_2 L1 3.1e-53 4.6e-39
L1_Scaffold2655.fa_34709_2 L1 9.3e-52 2.4e-32
L1_Scaffold9.fa_1331285_3 - 1000 1.0e+00
L1_Scaffold312.fa_139268_1 L1 7.4e-59 4.1e-47
L1_Scaffold169.fa_643856_3 L1 9e-64 2.2e-50
L1_Scaffold984.fa_117155_1 Jockey 1.9e-10 4.2e-01
L1_Scaffold1881.fa_122783_3 RTE 1.7e-09 3.4e-03
L1_Scaffold1284.fa_375428_2 L1 2.8e-21 2.8e-24
L1_Scaffold3597.fa_42074_3 - 1000 1.0e+00
L1_Scaffold1354.fa_301754_3 - 1000 1.0e+00
L1_Scaffold996.fa_281777_2 - 1000 1.0e+00
L1_Scaffold824.fa_269534_2 CR1 1.2e-13 1.2e-16
tmp-------------------------------------
L2_Scaffold2453.fa_35789_3 L2 1e-44 4.5e-30
L2_Scaffold309.fa_212330_1 CR1 3.3e-28 9.4e-08
L2_Scaffold178.fa_68045_2 L2 6.7e-45 1.4e-15
L2_Scaffold1921.fa_85445_3 I 3.2e-14 9.1e-07
L2_Scaffold1080.fa_40172_1 L2 2.5e-52 2.5e-20
L2_Scaffold3188.fa_27140_1 Jockey 2.3e-21 1.6e-12
L2_Scaffold585.fa_225371_3 CR1 2.7e-33 4.2e-13
L2_Scaffold154.fa_601574_3 CR1 2e-14 3.5e-03
L2_Scaffold1859.fa_17585_2 L2 6.8e-55 7.8e-44
L2_Scaffold53.fa_968972_2 CR1 6.1e-31 6.1e-17
L2_Scaffold525.fa_87158_1 L2 7.3e-52 8.3e-09
L2_Scaffold1651.fa_8621_3 L2 4.1e-44 4.5e-04
L2_Scaffold4287.fa_15413_3 L2 1.3e-68 7.6e-52
L2_Scaffold4.fa_1300973_2 CR1 2.1e-41 1.3e-18
L2_Scaffold8429.fa_7727_2 - 1000 1.0e+00
L2_Scaffold3984.fa_14015_1 L2 1.5e-65 7.9e-57
L2_Scaffold702.fa_53885_2 L2 4.1e-29 4.1e-09
L2_Scaffold949.fa_133976_2 L2 4.6e-51 3.8e-14
L2_Scaffold1715.fa_57236_3 CR1 1.4e-33 1.5e-16
L2_Scaffold2771.fa_89225_2 CR1 2.6e-33 1.6e-22
L2_Scaffold505.fa_31226_1 Rex 3.9e-13 6.6e-01
L2_Scaffold3887.fa_18734_2 RTE 4.3e-10 4.3e-03
L2_Scaffold1748.fa_58694_2 CR1 1.6e-31 1.6e-17
L2_Scaffold1218.fa_19565_1 L2 1e-11 9.1e-06
L2_Scaffold1824.fa_51290_3 L2 2e-40 1.7e-34
L2_Scaffold1612.fa_58340_3 L2 1.4e-33 1.8e-22
L2_Scaffold1818.fa_143606_2 L2 2.2e-43 2.6e-33
L2_Scaffold4065.fa_19997_1 L2 9.6e-68 2.6e-31
L2_Scaffold1377.fa_131312_1 L1 1.9e-17 1.4e-06
L2_Scaffold1615.fa_60467_3 L1 6.4e-16 2.3e-04
L2_Scaffold315.fa_256352_1 L2 1.4e-46 3.5e-26
L2_Scaffold726.fa_128948_3 L2 8e-21 1.8e-05
L2_Scaffold363.fa_21815_2 CR1 3.3e-30 6.6e-17
L2_Scaffold3974.fa_31187_2 L2 4.8e-50 1.1e-18
L2_Scaffold383.fa_357326_2 L2 1.4e-47 9.3e-07
L2_Scaffold4009.fa_44657_3 Rex 4.9e-11 1.5e-04
L2_Scaffold1661.fa_48782_2 L2 9.2e-73 3.8e-39
L2_Scaffold2670.fa_28004_2 L2 4.5e-59 1.0e-34
L2_Scaffold778.fa_150983_1 L2 4.1e-21 2.9e-11
L2_Scaffold900.fa_172337_1 L2 2.2e-51 1.5e-27
L2_Scaffold3497.fa_3140_1 L2 1.2e-61 1.6e-34
L2_Scaffold2048.fa_78665_1 CR1 1.4e-19 5.2e-10
L2_Scaffold2130.fa_14636_1 L2 3.4e-53 5.9e-24
L2_Scaffold1039.fa_80849_3 L2 1.8e-42 2.7e-25
L2_Scaffold1730.fa_135059_3 L1 4.4e-08 1.1e-01
L2_Scaffold152.fa_535955_1 CR1 3e-40 5.0e-12
L2_Scaffold60.fa_140771_3 L2 2.2e-49 9.6e-35
L2_Scaffold112.fa_219734_2 CR1 4.1e-11 7.9e-02
L2_Scaffold1404.fa_145493_2 Rex 1e-07 1.0e-10
L2_Scaffold1965.fa_10550_1 L2 3.2e-42 1.7e-13
L2_Scaffold771.fa_170654_1 CR1 2.3e-27 4.1e-17
L2_Scaffold512.fa_109679_3 L2 3.8e-52 1.1e-38
L2_Scaffold432.fa_120152_2 CR1 1.1e-43 2.6e-33
L2_Scaffold2526.fa_317111_2 L2 2.6e-48 6.8e-13
L2_Scaffold2146.fa_72671_2 L2 6.8e-13 2.3e-05
L2_Scaffold2697.fa_96896_2 L2 2.3e-50 2.1e-23
L2_Scaffold765.fa_420458_1 L2 2.1e-55 1.8e-21
L2_Scaffold1371.fa_190370_1 L2 2.5e-40 1.2e-18
L2_Scaffold1570.fa_107066_3 L1 6.9e-13 2.0e-02
L2_Scaffold3363.fa_6128_1 CR1 1.1e-16 1.2e-02
L2_Scaffold575.fa_67730_3 L2 2.7e-36 4.8e-15
L2_Scaffold3934.fa_1592_3 L2 1e-27 1.0e-30
L2_Scaffold287.fa_98456_1 L2 9.2e-38 1.1e-09
L2_Scaffold815.fa_19100_2 L2 2.7e-16 7.9e-11
L2_Scaffold2572.fa_60488_2 Rex 1.1e-18 2.2e-14
L2_Scaffold7909.fa_2885_3 L2 1.6e-10 7.3e-04
L2_Scaffold586.fa_340916_1 L2 4e-45 4.8e-10
L2_Scaffold1815.fa_79280_2 - 1000 1.0e+00
L2_Scaffold1400.fa_180488_2 L2 7.6e-49 1.6e-31
L2_Scaffold1917.fa_19475_3 Tad1 1.7e-08 1.8e-02
L2_Scaffold271.fa_162407_1 L1 1.9e-07 1.9e-10
L2_Scaffold2639.fa_47747_1 I 4.3e-14 7.5e-02
L2_Scaffold93.fa_193994_1 Jockey 3.4e-11 2.8e-11
L2_Scaffold81.fa_204479_1 RTE 1.1e-13 2.7e-03
L2_Scaffold913.fa_96881_1 L1 1.1e-11 2.7e-12
L2_Scaffold720.fa_384959_3 L2 6.5e-48 4.6e-29
L2_Scaffold2334.fa_10511_2 Rex 7.7e-20 4.8e-02
L2_Scaffold1103.fa_212216_2 L2 1.1e-18 3.1e-10
L2_Scaffold1499.fa_63953_2 L2 6.7e-20 9.3e-02
L2_Scaffold1459.fa_61397_1 L2 2.3e-57 8.8e-44
L2_Scaffold35.fa_339656_1 CR1 2.5e-31 2.3e-12
L2_Scaffold640.fa_590624_3 L2 4.9e-46 1.4e-33
L2_Scaffold4238.fa_11003_1 Jockey 6.7e-13 2.6e-06
L2_Scaffold434.fa_54848_3 RTE 1.8e-08 1.8e-11
L2_Scaffold22.fa_905813_2 RTE 1.4e-06 5.8e-03
L2_Scaffold1138.fa_21314_2 L2 2.6e-60 1.2e-46
L2_Scaffold1041.fa_102722_1 I 1.1e-10 1.6e-10
L2_Scaffold567.fa_210812_2 CR1 6.1e-35 1.3e-18
L2_Scaffold13.fa_70214_2 L2 2.2e-47 1.0e-24
L2_Scaffold949.fa_122645_2 CR1 0.0004 4.0e-07
L2_Scaffold2212.fa_21221_2 L2 2.8e-51 4.3e-13
L2_Scaffold892.fa_280223_2 L2 9.1e-58 2.9e-35
L2_Scaffold2518.fa_7610_3 L2 6.7e-23 2.4e-11
L2_Scaffold46.fa_293459_2 L2 7.3e-51 1.1e-17
L2_Scaffold73.fa_282659_1 CR1 1.1e-42 2.9e-16
L2_Scaffold1258.fa_125840_2 L2 6.5e-27 1.8e-10
L2_Scaffold2698.fa_125051_2 L2 2.5e-39 2.1e-13
L2_Scaffold954.fa_189209_2 CR1 1.3e-36 1.2e-16
L2_Scaffold3339.fa_69680_3 CR1 8.1e-34 4.3e-14
L2_Scaffold157.fa_348329_3 L2 3.6e-25 3.6e-28
L2_Scaffold639.fa_119951_2 Rex 6.3e-22 3.0e-06
L2_Scaffold1799.fa_52787_1 Rex 3e-22 3.0e-07
L2_Scaffold321.fa_307925_2 L2 1.8e-44 9.5e-34
L2_Scaffold3025.fa_75926_3 L2 1.8e-50 5.1e-08
L2_Scaffold2854.fa_16370_1 RTE 9e-09 2.1e-01
L2_Scaffold2306.fa_7697_1 CR1 1.4e-41 1.5e-22
L2_Scaffold1310.fa_37652_1 Rex 8.5e-14 4.0e-05
L2_Scaffold1640.fa_129935_2 L2 2.1e-64 1.0e-30
L2_Scaffold1093.fa_100463_2 L1 6.7e-05 6.7e-08
L2_Scaffold1054.fa_16043_1 CR1 1.6e-45 6.7e-13
L2_Scaffold2042.fa_74297_3 CR1 7.1e-14 2.0e-07
L2_Scaffold755.fa_87182_1 Rex 2.7e-16 1.4e-05
L2_Scaffold1389.fa_20186_3 CR1 4.7e-19 1.2e-08
L2_Scaffold2183.fa_16358_1 L1 4.1e-19 1.0e-06
L2_Scaffold157.fa_828719_2 L2 5.2e-44 1.0e-04
L2_Scaffold1449.fa_40418_3 Rex 7.4e-21 2.6e-03
L2_Scaffold2469.fa_13103_2 L1 3.1e-12 1.1e-03
L2_Scaffold818.fa_85079_3 I 5.1e-16 2.1e-01
tmp-------------------------------------
RTE_Scaffold2294.fa_10064_3 RTE 2.3e-62 4.8e-53
RTE_Scaffold287.fa_362852_1 RTE 2.6e-16 1.6e-08
RTE_Scaffold1234.fa_39233_2 I 1.1e-07 1.1e-10
RTE_Scaffold1870.fa_197696_3 RTE 7.3e-50 7.8e-40
RTE_Scaffold60.fa_962156_3 L2 0.065 6.5e-05
RTE_Scaffold2826.fa_6818_3 L1 3.8e-12 8.3e-05
RTE_Scaffold2853.fa_16397_3 RTE 1.7e-13 1.7e-16
RTE_Scaffold2466.fa_65195_3 L1 6.7e-27 1.6e-16
RTE_Scaffold11.fa_775028_2 - 1000 1.0e+00
RTE_Scaffold950.fa_77429_2 RTE 2.1e-24 2.1e-27
RTE_Scaffold331.fa_164531_3 - 1000 1.0e+00
RTE_Scaffold101.fa_72509_1 RTE 5.8e-35 1.4e-29
RTE_Scaffold1488.fa_162278_1 RTE 2.6e-73 5.0e-54
RTE_Scaffold469.fa_558791_2 RTE 1.5e-22 7.1e-15
RTE_Scaffold272.fa_474467_1 CR1 1.1e-17 1.1e-02
RTE_Scaffold52.fa_477500_1 - 1000 1.0e+00
RTE_Scaffold569.fa_149642_3 RTE 1.3e-83 1.4e-70
RTE_Scaffold204.fa_926537_2 L1 4.3e-08 2.2e-07
tmp-------------------------------------
Rex_Scaffold3306.fa_7778_3 Rex 4.3e-49 1.4e-13
Rex_Scaffold958.fa_49202_3 CR1 1.9e-33 1.9e-20
Rex_Scaffold2601.fa_48524_3 CR1 5.8e-42 5.8e-27
Rex_Scaffold3078.fa_6695_3 Rex 6.4e-44 2.5e-23
Rex_Scaffold1463.fa_79547_2 Rex 1e-55 4.8e-23
Rex_Scaffold580.fa_103907_3 CR1 8.6e-32 2.0e-08
Rex_Scaffold1505.fa_32669_3 Rex 9.8e-53 3.8e-17

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