Initializing nucleic acids...done.
Applying constraints...done.
Folding single strand...
  0% [=                                                 ] /                     
  4% [===                                               ] -                     
  9% [=====                                             ] \                     
 14% [========                                          ] |                     
 19% [==========                                        ] /                     
 24% [=============                                     ] -                     
 29% [===============                                   ] \                     
 34% [==================                                ] |                     
 39% [====================                              ] /                     
 44% [=======================                           ] -                     
 49% [=========================                         ] \                     
 54% [============================                      ] |                     
 59% [==============================                    ] /                     
 64% [=================================                 ] -                     
 69% [===================================               ] \                     
 74% [======================================            ] |                     
 79% [========================================          ] /                     
 84% [===========================================       ] -                     
 89% [=============================================     ] \                     
 94% [================================================  ] |                     
 99% [==================================================] /                     done.
Writing output ct file...done.
Single strand folding complete.
Initializing nucleic acids...done.
Applying SHAPE constraints...done.
Calculating free energies...done.
efn2 complete.
Converting CT file...CT file conversion complete.
/disk1/www/rails/humanrnamap/cli/./main.py:567: DeprecationWarning: Call to deprecated function (or staticmethod) VARNA. (Class has been renamed 'Structure')
  v = VARNA(structure=fold_dbn, sequence=seq)
Output file: /disk1/www/rails/humanrnamap/public/result/6e270d1e-1d58-429b-b849-06a9a9c234ca/final_image/MYH10_fold_1.svg

first - Elapsed time since the previous call: 0.00 seconds
first - Current memory usage: 157.70 MB
setup complete - Elapsed time since the previous call: 0.00 seconds
setup complete - Current memory usage: 157.70 MB
config complete - Elapsed time since the previous call: 0.00 seconds
config complete - Current memory usage: 157.70 MB
read annotations - Elapsed time since the previous call: 0.09 seconds
read annotations - Current memory usage: 171.36 MB
Based on canonical annotations, the following gene is in your area of interest: MYH10(-)
write fasta - Elapsed time since the previous call: 1.15 seconds
write fasta - Current memory usage: 171.36 MB
Length of region: 101 nt.
100.0% of the region's A/C bases included in the filtered DMS dataset. Ideally, this number should be as high as possible for an experimenally-accurate prediction, and over 70% is recommended.
write dat - Elapsed time since the previous call: 0.19 seconds
write dat - Current memory usage: 174.61 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/Fold "/disk1/www/rails/humanrnamap/public/result/6e270d1e-1d58-429b-b849-06a9a9c234ca/fasta/MYH10.fasta" "/disk1/www/rails/humanrnamap/public/result/6e270d1e-1d58-429b-b849-06a9a9c234ca/ct/MYH10.ct" --SHAPE "MYH10.dat"

fold - Elapsed time since the previous call: 0.13 seconds
fold - Current memory usage: 174.61 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/efn2 "/disk1/www/rails/humanrnamap/public/result/6e270d1e-1d58-429b-b849-06a9a9c234ca/ct/MYH10.ct" "/disk1/www/rails/humanrnamap/public/result/6e270d1e-1d58-429b-b849-06a9a9c234ca/fold_FE/MYH10.txt" -sh "MYH10.dat"

efn2 - Elapsed time since the previous call: 0.49 seconds
efn2 - Current memory usage: 174.61 MB
This region has 1 predicted structures. 5 is the maximum structures visible on the web server. For up to 20 predictions per region, download and run the code locally.
Running command: /disk1/www/rails/humanrnamap/cli/bin/ct2dot "/disk1/www/rails/humanrnamap/public/result/6e270d1e-1d58-429b-b849-06a9a9c234ca/ct/MYH10.ct" 1 "/disk1/www/rails/humanrnamap/public/result/6e270d1e-1d58-429b-b849-06a9a9c234ca/fold_dbn/MYH10_temp1.dbn"

ct2dot - Elapsed time since the previous call: 0.02 seconds
ct2dot - Current memory usage: 174.61 MB
['java', '-cp', '/disk1/www/rails/humanrnamap/cli/bin/VARNAv3-93.jar', 'fr.orsay.lri.varna.applications.VARNAcmd', '-sequenceDBN', 'CAUUGGAAUCCUGGAUAUUGCUGGAUUUGAAAUUUUUGAGCUGAACUCCUUUGAACAACUUUGCAUCAACUACACCAAUGAGAAGCUGCAGCAGCUGUUCA', '-structureDBN', '..((.((((((...........)))))).))......(((.....)))...((((((.(((((((....((.((....))))....))))).)).))))))', '-o', '/disk1/www/rails/humanrnamap/public/result/6e270d1e-1d58-429b-b849-06a9a9c234ca/final_image/MYH10_fold_1.svg', '-title', 'MYH10, -17.2 ± 0.9\n kcal/mol, AUC: 0.737', '-titleSize', '12', '-basesStyle1', 'fill=#ffffff', '-applyBasesStyle1on', '3,4,5,6,9,12,13,14,16,18,19,20,22,23,24,26,27,28,29,33,34,35,36,37,38,40,42,43,47,50,51,52,53,60,61,62,63,66,71,79,80,82,85,87,88,91,94,96,97,98,99', '-basesStyle2', 'fill=#00ffff', '-applyBasesStyle2on', '100,39,7,10,57,90,93,30', '-basesStyle3', 'fill=#ffff00', '-applyBasesStyle3on', '32,64,2,69,73,46,55,25,58,95,31', '-basesStyle4', 'fill=#ff0000', '-applyBasesStyle4on', '1,65,67,68,70,8,72,74,11,75,76,77,15,78,17,81,83,84,21,86,89,92,101,41,44,45,48,49,54,56,59']
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 4.75, Y: 418.2452011054978, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 22.25, Y: 418.2452011054978, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 39.75, Y: 418.2452011054978, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 39.75, Y: 398.2452011054978, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 33.07162284851074, Y: 382.0696646754151, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 39.75, Y: 365.89412824533235, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 39.75, Y: 345.8941282453323, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 39.74999999999997, Y: 325.8941282453323, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 39.74999999999997, Y: 305.8941282453323, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 39.74999999999997, Y: 285.8941282453323, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 39.74999999999994, Y: 265.8941282453323, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 25.874778338074293, Y: 255.2298253012787, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 18.05163083993989, Y: 239.5758323067563, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 17.852206318153918, Y: 222.0769933935531, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 25.316568610568652, Y: 206.2487771637406, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 38.94514786551403, Y: 195.27102871782535, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 55.99999999999994, Y: 191.34914752113622, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 73.05485213448583, Y: 195.27102871782535, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 86.68343138943125, Y: 206.2487771637406, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 94.14779368184597, Y: 222.07699339355304, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 93.94836916006001, Y: 239.57583230675624, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 86.12522166192562, Y: 255.2298253012786, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 72.24999999999996, Y: 265.8941282453323, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 72.24999999999997, Y: 285.8941282453323, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 72.24999999999997, Y: 305.8941282453323, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 72.24999999999997, Y: 325.8941282453323, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 72.24999999999999, Y: 345.8941282453323, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 72.25, Y: 365.8941282453323, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 78.92837715148926, Y: 382.0696646754151, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 72.25, Y: 398.2452011054978, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 72.25, Y: 418.2452011054978, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 89.75, Y: 418.2452011054978, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 107.25, Y: 418.2452011054978, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 124.75, Y: 418.2452011054978, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 142.25, Y: 418.2452011054978, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 159.75, Y: 418.2452011054978, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 177.25, Y: 418.2452011054978, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 194.75, Y: 418.2452011054978, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 194.75, Y: 398.2452011054978, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 194.75, Y: 378.24520110549787, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 188.10183039518208, Y: 362.05716080584324, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 194.82804965122153, Y: 345.90139457958986, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 211.0, Y: 339.21418067884537, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 227.1719503487785, Y: 345.90139457958986, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 233.89816960481792, Y: 362.05716080584324, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 227.25, Y: 378.24520110549787, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 227.25, Y: 398.24520110549787, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 227.25, Y: 418.2452011054978, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 244.75, Y: 418.24520110549787, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 262.25, Y: 418.24520110549787, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 279.75, Y: 418.24520110549787, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 297.25, Y: 418.24520110549787, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 297.25, Y: 398.24520110549787, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 297.25, Y: 378.24520110549787, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 297.25, Y: 358.24520110549787, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 297.25, Y: 338.24520110549787, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 297.25, Y: 318.24520110549787, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 290.57162284851074, Y: 302.0696646754151, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 297.25, Y: 285.8941282453323, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 297.25, Y: 265.8941282453323, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 293.43439675932206, Y: 248.81502664217652, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 284.92290491375286, Y: 230.71655967497708, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 276.41141306818366, Y: 212.61809270777763, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 267.89992122261447, Y: 194.5196257405782, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 259.38842937704527, Y: 176.42115877337875, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 242.31239861707036, Y: 172.59241356510825, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 228.65970356655612, Y: 161.64462683704642, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 221.2121485293682, Y: 145.80846441196627, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 221.4872097678175, Y: 128.31062289649458, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 229.42884219087156, Y: 112.71637425019685, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 220.9173543289536, Y: 94.6179054095345, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 210.19612895549585, Y: 80.78659112546268, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 214.0117639410955, Y: 63.707631614125035, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 214.0117639410955, Y: 43.707631614125035, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 210.4630295538564, Y: 26.571186946533885, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 221.5117460611625, Y: 13.0, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 239.01178182102848, Y: 13.0, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 250.06049832833457, Y: 26.57118694653377, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 246.51176394109552, Y: 43.707631614125035, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 246.51176394109552, Y: 63.707631614125035, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 250.32736619502975, Y: 80.78673763391782, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 258.83885405694775, Y: 98.88520647458017, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 275.91488089799026, Y: 102.71395396220532, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 289.56757239037375, Y: 113.66173981203815, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 297.01512601239943, Y: 129.49789922797765, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 296.74006636679513, Y: 146.99573744277893, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 288.79843819874435, Y: 162.58998452432883, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 297.30993004431355, Y: 180.68845149152827, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 305.82142188988274, Y: 198.7869184587277, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 314.33291373545194, Y: 216.88538542592715, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 322.84440558102114, Y: 234.9838523931266, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 333.5656344922436, Y: 248.81516652567262, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 329.75, Y: 265.8941282453323, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 329.75, Y: 285.8941282453323, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 336.42837715148926, Y: 302.0696646754151, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 329.75, Y: 318.24520110549787, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 329.75, Y: 338.24520110549787, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 329.75, Y: 358.24520110549787, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 329.75, Y: 378.24520110549787, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 329.75, Y: 398.24520110549787, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 329.75, Y: 418.24520110549787, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '1', X: 5.5, Y: 438.2452011054978, Width: 9.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '10', X: 15.999999999999972, Y: 285.8941282453323, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '20', X: 109.93889253173069, Y: 217.81724507480996, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '30', X: 82.64213562373095, Y: 412.38733672922876, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '40', X: 171.00001455787353, Y: 378.22106990723495, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '50', X: 258.5, Y: 438.24520110549787, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '60', X: 273.5, Y: 265.8941282453323, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '70', X: 205.7750212828918, Y: 114.67543353032784, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '80', X: 258.56893738337874, Y: 51.45474347436078, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '90', X: 328.6813807026514, Y: 208.37389358035801, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '100', X: 341.5, Y: 398.24520110549787, Width: 27.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '101', X: 321.5, Y: 438.24520110549787, Width: 27.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'MYH10, -17.2 ± 0.9
 kcal/mol, AUC: 0.737', X: 104.58918857574463, Y: 451.0452011054979, Width: 142.5, Height: 23
Calculated bounding box: (4.75, 5.0, 368.5, 451.0452011054979)
Updated viewBox: -0.25 0.0 373.75 456.0452011054979
Updated SVG: /disk1/www/rails/humanrnamap/public/result/6e270d1e-1d58-429b-b849-06a9a9c234ca/final_image/MYH10_fold_final_1.svg
Combined SVG saved as /disk1/www/rails/humanrnamap/public/result/6e270d1e-1d58-429b-b849-06a9a9c234ca/final_image/MYH10_fold_final_1.svg
