Initializing nucleic acids...done.
Applying constraints...done.
Folding single strand...
  0% [=                                                 ] /                     
  5% [===                                               ] -                     
 10% [======                                            ] \                     
 16% [=========                                         ] |                     
 21% [===========                                       ] /                     
 26% [==============                                    ] -                     
 32% [=================                                 ] \                     
 37% [===================                               ] |                     
 43% [======================                            ] /                     
 48% [=========================                         ] -                     
 53% [===========================                       ] \                     
 59% [==============================                    ] |                     
 64% [=================================                 ] /                     
 69% [===================================               ] -                     
 75% [======================================            ] \                     
 80% [=========================================         ] |                     
 86% [============================================      ] /                     
 91% [==============================================    ] -                     
 96% [================================================= ] \                     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/bf029cfe-f21c-41fd-8df2-cb0f445704e7/final_image/MYH10_fold_1.svg

first - Elapsed time since the previous call: 0.00 seconds
first - Current memory usage: 157.07 MB
setup complete - Elapsed time since the previous call: 0.00 seconds
setup complete - Current memory usage: 157.07 MB
config complete - Elapsed time since the previous call: 0.00 seconds
config complete - Current memory usage: 157.07 MB
read annotations - Elapsed time since the previous call: 0.09 seconds
read annotations - Current memory usage: 170.67 MB
Based on canonical annotations, the following gene is in your area of interest: MYH10(-)
write fasta - Elapsed time since the previous call: 0.58 seconds
write fasta - Current memory usage: 170.67 MB
Length of region: 93 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: 173.72 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/Fold "/disk1/www/rails/humanrnamap/public/result/bf029cfe-f21c-41fd-8df2-cb0f445704e7/fasta/MYH10.fasta" "/disk1/www/rails/humanrnamap/public/result/bf029cfe-f21c-41fd-8df2-cb0f445704e7/ct/MYH10.ct" --SHAPE "MYH10.dat"

fold - Elapsed time since the previous call: 0.11 seconds
fold - Current memory usage: 173.72 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/efn2 "/disk1/www/rails/humanrnamap/public/result/bf029cfe-f21c-41fd-8df2-cb0f445704e7/ct/MYH10.ct" "/disk1/www/rails/humanrnamap/public/result/bf029cfe-f21c-41fd-8df2-cb0f445704e7/fold_FE/MYH10.txt" -sh "MYH10.dat"

efn2 - Elapsed time since the previous call: 0.51 seconds
efn2 - Current memory usage: 173.72 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/bf029cfe-f21c-41fd-8df2-cb0f445704e7/ct/MYH10.ct" 1 "/disk1/www/rails/humanrnamap/public/result/bf029cfe-f21c-41fd-8df2-cb0f445704e7/fold_dbn/MYH10_temp1.dbn"

ct2dot - Elapsed time since the previous call: 0.01 seconds
ct2dot - Current memory usage: 173.72 MB
['java', '-cp', '/disk1/www/rails/humanrnamap/cli/bin/VARNAv3-93.jar', 'fr.orsay.lri.varna.applications.VARNAcmd', '-sequenceDBN', 'CUUAGGUACAAUUGCUCCCCUUUUUAUAUAUAGACACACACAGGACACAUAUAUUAAACAGAUUGUUUCAUCAUUGCAUCUAUUUUCCAUAUA', '-structureDBN', '....((((....)))).............(((((..((.....((.(((..............))).)).....))..)))))..........', '-o', '/disk1/www/rails/humanrnamap/public/result/bf029cfe-f21c-41fd-8df2-cb0f445704e7/final_image/MYH10_fold_1.svg', '-title', 'MYH10, -4.5 ± 1.1\n kcal/mol, AUC: 0.637', '-titleSize', '12', '-basesStyle1', 'fill=#ffffff', '-applyBasesStyle1on', '2,3,5,6,7,12,13,14,16,21,22,23,24,25,27,29,31,33,43,44,50,52,54,55,61,63,64,65,66,67,68,71,74,75,76,79,81,83,84,85,86,90,92', '-basesStyle2', 'fill=#00ffff', '-applyBasesStyle2on', '34,38,8,41,45,47,17,18,19,51,26', '-basesStyle3', 'fill=#ffff00', '-applyBasesStyle3on', '4,69,70,72,73,11,78,15,82,87,89,93,32,35,36,37,42', '-basesStyle4', 'fill=#ff0000', '-applyBasesStyle4on', '1,9,10,77,80,20,88,91,28,30,39,40,46,48,49,53,56,57,58,59,60,62']
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 4.75, Y: 424.2249162423253, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 22.25, Y: 424.2249162423253, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 39.75, Y: 424.2249162423253, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 57.25, Y: 424.2249162423253, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 74.75, Y: 424.2249162423253, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 74.75, Y: 404.2249162423253, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 74.75, Y: 384.2249162423253, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 74.75, Y: 364.2249162423253, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 71.20126561276089, Y: 347.08847157473417, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 82.24998212006702, Y: 333.5172846282004, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 99.75001787993298, Y: 333.5172846282004, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 110.79873438723911, Y: 347.08847157473417, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 107.25, Y: 364.2249162423253, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 107.25, Y: 384.2249162423253, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 107.25, Y: 404.2249162423253, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 107.25, Y: 424.2249162423253, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 124.75, Y: 424.2249162423253, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 142.25, Y: 424.2249162423253, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 159.75, Y: 424.2249162423253, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 177.25, Y: 424.2249162423253, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 194.75, Y: 424.2249162423253, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 212.25, Y: 424.2249162423253, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 229.75, Y: 424.2249162423253, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 247.25, Y: 424.2249162423254, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 264.75, Y: 424.2249162423254, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 282.25, Y: 424.2249162423254, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 299.75, Y: 424.2249162423254, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 317.25, Y: 424.2249162423254, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 334.75, Y: 424.2249162423254, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 352.25, Y: 424.2249162423254, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 352.25, Y: 404.2249162423254, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 352.25, Y: 384.2249162423254, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 352.25, Y: 364.2249162423254, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 352.25, Y: 344.2249162423254, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 341.87031668259823, Y: 330.1354770211943, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 341.87031668259823, Y: 312.63547349732335, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 352.25, Y: 298.54603427619224, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 352.25, Y: 278.54603427619224, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 337.5665000621637, Y: 269.02522282255416, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 327.7238804490855, Y: 254.55546607572467, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 324.26244354248047, Y: 237.401181605023, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 327.7238804490855, Y: 220.24689713432122, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 337.5665000621637, Y: 205.77714038749184, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 352.25, Y: 196.25632893385364, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 352.25, Y: 176.25632893385364, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 345.57162284851074, Y: 160.0807925037709, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 352.25, Y: 143.90525607368818, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 352.25, Y: 123.90525607368807, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 352.25, Y: 103.90525607368807, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 337.21097477612403, Y: 94.95664851118772, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 326.4548730706566, Y: 81.15244143169002, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 321.4540181864529, Y: 64.38219076513315, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 322.8929402053055, Y: 46.94145223674275, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 330.5746757219433, Y: 31.217559701990467, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 343.44772870953295, Y: 19.362840651303372, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 359.7500020429714, Y: 13.0, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 377.24999795702854, Y: 13.0, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 393.55227129046693, Y: 19.36284065130326, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 406.4253242780566, Y: 31.217559701990467, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 414.1070597946945, Y: 46.94145223674275, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 415.5459818135471, Y: 64.38219076513303, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 410.54512692934344, Y: 81.15244143168991, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 399.789025223876, Y: 94.95664851118772, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 384.75, Y: 103.90525607368807, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 384.75, Y: 123.90525607368807, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 384.75, Y: 143.90525607368807, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 391.42837715148926, Y: 160.0807925037709, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 384.75, Y: 176.25632893385364, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 384.75, Y: 196.25632893385364, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 399.4334999378363, Y: 205.77714038749184, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 409.2761195509145, Y: 220.24689713432122, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 412.73755645751953, Y: 237.401181605023, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 409.2761195509145, Y: 254.55546607572467, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 399.4334999378363, Y: 269.02522282255416, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 384.75, Y: 278.54603427619224, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 384.75, Y: 298.54603427619224, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 395.12968331740177, Y: 312.63547349732335, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 395.12968331740177, Y: 330.1354770211943, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 384.75, Y: 344.2249162423254, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 384.75, Y: 364.2249162423254, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 384.75, Y: 384.2249162423254, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 384.75, Y: 404.2249162423254, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 384.75, Y: 424.2249162423254, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 402.25, Y: 424.2249162423254, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 419.75, Y: 424.2249162423254, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 437.25, Y: 424.2249162423254, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 454.75, Y: 424.2249162423254, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 472.25, Y: 424.2249162423254, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 489.75, Y: 424.2249162423254, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 507.25, Y: 424.2249162423254, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 524.75, Y: 424.2249162423254, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 542.25, Y: 424.2249162423254, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 559.75, Y: 424.2249162423254, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '1', X: 5.5, Y: 444.2249162423253, Width: 9.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '10', X: 69.91341049766821, Y: 315.4543173256386, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '20', X: 173.5, Y: 444.2249162423253, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '30', X: 334.35786437626905, Y: 438.36705186605633, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '40', X: 305.5388117806472, Y: 262.3109959215807, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '50', X: 320.2310241129823, Y: 109.95559532257539, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '60', X: 429.64111056513326, Y: 41.63811499655702, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '70', X: 409.6686756188399, Y: 191.4797678606439, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '80', X: 401.0, Y: 364.2249162423254, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '90', X: 503.5, Y: 444.2249162423254, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '93', X: 556.0, Y: 444.2249162423254, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'MYH10, -4.5 ± 1.1
 kcal/mol, AUC: 0.637', X: 216.25, Y: 457.0249162423254, Width: 142.5, Height: 23
Calculated bounding box: (4.75, 5.0, 574.0, 457.0249162423254)
Updated viewBox: -0.25 0.0 579.25 462.0249162423254
Updated SVG: /disk1/www/rails/humanrnamap/public/result/bf029cfe-f21c-41fd-8df2-cb0f445704e7/final_image/MYH10_fold_final_1.svg
Combined SVG saved as /disk1/www/rails/humanrnamap/public/result/bf029cfe-f21c-41fd-8df2-cb0f445704e7/final_image/MYH10_fold_final_1.svg
