Initializing nucleic acids...done.
Applying constraints...done.
Folding single strand...
  0% [=                                                 ] /                     
  6% [====                                              ] -                     
 13% [=======                                           ] \                     
 20% [===========                                       ] |                     
 26% [==============                                    ] /                     
 33% [=================                                 ] -                     
 40% [=====================                             ] \                     
 46% [========================                          ] |                     
 53% [===========================                       ] /                     
 60% [===============================                   ] -                     
 66% [==================================                ] \                     
 73% [=====================================             ] |                     
 80% [=========================================         ] /                     
 86% [============================================      ] -                     
 93% [===============================================   ] \                     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/da3ec5b3-886f-4629-a128-9413c4eea968/final_image/HCFC1_fold_1.svg

first - Elapsed time since the previous call: 0.00 seconds
first - Current memory usage: 158.70 MB
setup complete - Elapsed time since the previous call: 0.00 seconds
setup complete - Current memory usage: 158.70 MB
config complete - Elapsed time since the previous call: 0.00 seconds
config complete - Current memory usage: 158.70 MB
read annotations - Elapsed time since the previous call: 0.10 seconds
read annotations - Current memory usage: 172.42 MB
Based on canonical annotations, the following gene is in your area of interest: HCFC1(-)
write fasta - Elapsed time since the previous call: 0.28 seconds
write fasta - Current memory usage: 172.42 MB
Length of region: 75 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: 0.22 seconds
write dat - Current memory usage: 175.81 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/Fold "/disk1/www/rails/humanrnamap/public/result/da3ec5b3-886f-4629-a128-9413c4eea968/fasta/HCFC1.fasta" "/disk1/www/rails/humanrnamap/public/result/da3ec5b3-886f-4629-a128-9413c4eea968/ct/HCFC1.ct" --SHAPE "HCFC1.dat"

fold - Elapsed time since the previous call: 0.09 seconds
fold - Current memory usage: 175.81 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/efn2 "/disk1/www/rails/humanrnamap/public/result/da3ec5b3-886f-4629-a128-9413c4eea968/ct/HCFC1.ct" "/disk1/www/rails/humanrnamap/public/result/da3ec5b3-886f-4629-a128-9413c4eea968/fold_FE/HCFC1.txt" -sh "HCFC1.dat"

efn2 - Elapsed time since the previous call: 0.53 seconds
efn2 - Current memory usage: 175.81 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/da3ec5b3-886f-4629-a128-9413c4eea968/ct/HCFC1.ct" 1 "/disk1/www/rails/humanrnamap/public/result/da3ec5b3-886f-4629-a128-9413c4eea968/fold_dbn/HCFC1_temp1.dbn"

ct2dot - Elapsed time since the previous call: 0.02 seconds
ct2dot - Current memory usage: 175.81 MB
['java', '-cp', '/disk1/www/rails/humanrnamap/cli/bin/VARNAv3-93.jar', 'fr.orsay.lri.varna.applications.VARNAcmd', '-sequenceDBN', 'CCCACGAGACUGGCACCACCAACACGGCCACCACUACUGUUGUGGCUAACCUUGGGGGACACCCCCAGCCCACCC', '-structureDBN', '...........(((...........((((((.((....)).))))))......(((((...))))).))).....', '-o', '/disk1/www/rails/humanrnamap/public/result/da3ec5b3-886f-4629-a128-9413c4eea968/final_image/HCFC1_fold_1.svg', '-title', 'HCFC1, -24.5 ± 0.6\n kcal/mol, AUC: 0.859', '-titleSize', '12', '-basesStyle1', 'fill=#ffffff', '-applyBasesStyle1on', '68,6,8,11,12,13,26,27,35,38,39,40,41,42,43,44,45,47,52,53,54,55,56,57,58', '-basesStyle2', 'fill=#00ffff', '-applyBasesStyle2on', '64,33,65,70,71,9,46,61,62,28,29,30,31', '-basesStyle3', 'fill=#ffff00', '-applyBasesStyle3on', '32,2,67,69,73,74,75,14,18,20,59,63', '-basesStyle4', 'fill=#ff0000', '-applyBasesStyle4on', '1,66,3,4,5,7,72,10,15,16,17,19,21,22,23,24,25,34,36,37,48,49,50,51,60']
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 4.75, Y: 374.5568982785688, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 22.25, Y: 374.5568982785688, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 39.75, Y: 374.5568982785688, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 57.25, Y: 374.5568982785688, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 74.75, Y: 374.5568982785688, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 92.25, Y: 374.5568982785688, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 109.75, Y: 374.5568982785688, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 127.25, Y: 374.5568982785688, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 144.75, Y: 374.5568982785688, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 162.25, Y: 374.5568982785688, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 179.75, Y: 374.5568982785688, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 197.25, Y: 374.5568982785688, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 197.25, Y: 354.5568982785688, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 197.25, Y: 334.5568982785688, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 180.03432717406164, Y: 328.38933849095685, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 164.84758284357946, Y: 318.20204340226496, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 152.61049609371435, Y: 304.6126397192553, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 144.0649666656521, Y: 288.44501430988737, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 139.7290856868454, Y: 270.67936428741024, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 139.86572528051622, Y: 252.3927704491647, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 144.46660137699573, Y: 234.69389693336257, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 153.25277595329052, Y: 218.65577606780005, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 165.69156825152027, Y: 205.25075347382358, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 181.02884969718406, Y: 195.29153751873872, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 198.33476456827705, Y: 189.3819271205822, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 216.5601045012166, Y: 187.88020513821738, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 221.73642106246075, Y: 168.56167137248377, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 226.9127376237049, Y: 149.24313760675017, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 232.08905418494908, Y: 129.92460384101656, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 237.26537074619324, Y: 110.60607007528296, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 242.4416873074374, Y: 91.28753630954935, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 240.17733903905207, Y: 73.93472307138285, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 250.8145875197447, Y: 60.03881197785512, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 255.99083637521585, Y: 40.72026007078318, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 256.99814100687456, Y: 23.249238664590962, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 271.1827932194894, Y: 13.0, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 288.0865606796187, Y: 17.52922700363547, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 295.24642880229544, Y: 33.49755628576338, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 287.3834832242078, Y: 49.131664460923844, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 282.20723436873664, Y: 68.45021636799578, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 284.47162265614446, Y: 85.80309928939681, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 273.8343046767545, Y: 99.69905072157115, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 268.65798811551036, Y: 119.01758448730476, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 263.4816715542662, Y: 138.33611825303836, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 258.30535499302204, Y: 157.65465201877197, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 253.12903843177787, Y: 176.97318578450557, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 247.9527218705337, Y: 196.29171955023912, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 262.3914886239647, Y: 206.1796927824044, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 274.11577532936843, Y: 219.17165573068485, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 282.47464368981673, Y: 234.54628807531986, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 287.00400512819476, Y: 251.44998249282912, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 287.45238721850734, Y: 268.94423736410295, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 283.7948955614981, Y: 286.0577628564995, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 276.2345959342215, Y: 301.84040742405546, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 290.37673155795244, Y: 315.9825430477864, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 304.5188671816834, Y: 330.12467867151736, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 318.66100280541434, Y: 344.2668142952483, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 332.8031384291453, Y: 358.40894991897926, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 344.4948285587597, Y: 371.43028525009976, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 339.6633652743373, Y: 388.25014715273403, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 322.84350337170304, Y: 393.0816104371564, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 309.8221680405825, Y: 381.38992030754207, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 295.68003241685153, Y: 367.2477846838111, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 281.5378967931206, Y: 353.10564906008017, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 267.39576116938963, Y: 338.9635134363492, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 253.25362554565868, Y: 324.82137781261827, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 241.92176293353958, Y: 330.7029874191009, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 229.75, Y: 334.5568982785688, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 229.75, Y: 354.5568982785688, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 229.75, Y: 374.5568982785688, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 247.25, Y: 374.55689827856884, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 264.75, Y: 374.55689827856884, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 282.25, Y: 374.55689827856884, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 299.75, Y: 374.55689827856884, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 317.25, Y: 374.55689827856884, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '1', X: 5.5, Y: 394.5568982785688, Width: 9.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '10', X: 158.5, Y: 394.5568982785688, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '20', X: 116.2868237058617, Y: 249.78227962507356, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '30', X: 214.19683698045964, Y: 105.4297535140388, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '40', X: 297.7757817404961, Y: 73.62648214991668, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '50', X: 297.2987577974464, Y: 227.12993552728432, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '60', X: 350.05550089806826, Y: 402.392282776465, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '70', X: 240.14213562373095, Y: 388.69903390229973, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '75', X: 313.5, Y: 394.55689827856884, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'HCFC1, -24.5 ± 0.6
 kcal/mol, AUC: 0.859', X: 108.62241427937985, Y: 415.192282776465, Width: 142.5, Height: 23
Calculated bounding box: (4.75, 5.0, 368.05550089806826, 415.192282776465)
Updated viewBox: -0.25 0.0 373.30550089806826 420.192282776465
Updated SVG: /disk1/www/rails/humanrnamap/public/result/da3ec5b3-886f-4629-a128-9413c4eea968/final_image/HCFC1_fold_final_1.svg
Combined SVG saved as /disk1/www/rails/humanrnamap/public/result/da3ec5b3-886f-4629-a128-9413c4eea968/final_image/HCFC1_fold_final_1.svg
