Initializing nucleic acids...done.
Applying constraints...done.
Folding single strand...
  0% [=                                                 ] /                     
  5% [===                                               ] -                     
 10% [======                                            ] \                     
 15% [========                                          ] |                     
 20% [===========                                       ] /                     
 25% [=============                                     ] -                     
 30% [================                                  ] \                     
 35% [==================                                ] |                     
 40% [=====================                             ] /                     
 45% [=======================                           ] -                     
 50% [==========================                        ] \                     
 55% [============================                      ] |                     
 60% [===============================                   ] /                     
 65% [=================================                 ] -                     
 70% [====================================              ] \                     
 75% [======================================            ] |                     
 80% [=========================================         ] /                     
 85% [===========================================       ] -                     
 90% [==============================================    ] \                     
 95% [================================================  ] |                     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/3476d825-36d0-43ed-ba47-556527a61e1e/final_image/SON_fold_1.svg

first - Elapsed time since the previous call: 0.00 seconds
first - Current memory usage: 158.57 MB
setup complete - Elapsed time since the previous call: 0.00 seconds
setup complete - Current memory usage: 158.57 MB
config complete - Elapsed time since the previous call: 0.00 seconds
config complete - Current memory usage: 158.57 MB
read annotations - Elapsed time since the previous call: 0.09 seconds
read annotations - Current memory usage: 172.16 MB
Based on canonical annotations, the following gene is in your area of interest: SON(+)
write fasta - Elapsed time since the previous call: 0.14 seconds
write fasta - Current memory usage: 172.16 MB
Length of region: 99 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: 175.32 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/Fold "/disk1/www/rails/humanrnamap/public/result/3476d825-36d0-43ed-ba47-556527a61e1e/fasta/SON.fasta" "/disk1/www/rails/humanrnamap/public/result/3476d825-36d0-43ed-ba47-556527a61e1e/ct/SON.ct" --SHAPE "SON.dat"

fold - Elapsed time since the previous call: 0.12 seconds
fold - Current memory usage: 175.32 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/efn2 "/disk1/www/rails/humanrnamap/public/result/3476d825-36d0-43ed-ba47-556527a61e1e/ct/SON.ct" "/disk1/www/rails/humanrnamap/public/result/3476d825-36d0-43ed-ba47-556527a61e1e/fold_FE/SON.txt" -sh "SON.dat"

efn2 - Elapsed time since the previous call: 0.41 seconds
efn2 - Current memory usage: 175.32 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/3476d825-36d0-43ed-ba47-556527a61e1e/ct/SON.ct" 1 "/disk1/www/rails/humanrnamap/public/result/3476d825-36d0-43ed-ba47-556527a61e1e/fold_dbn/SON_temp1.dbn"

ct2dot - Elapsed time since the previous call: 0.02 seconds
ct2dot - Current memory usage: 175.32 MB
['java', '-cp', '/disk1/www/rails/humanrnamap/cli/bin/VARNAv3-93.jar', 'fr.orsay.lri.varna.applications.VARNAcmd', '-sequenceDBN', 'ACUUUUACGAAAGUGAACAUGGUAUAAAUAUAGACCUUAAUAUAAAUAAUCAUUUAAUUGCUAAAGAGAUGGAACAUAAUACAGUGUGUGCUGCUGGUA', '-structureDBN', '...(((((....)))))...(((..........))).((((.(((((....))))))))).....................((((....))))......', '-o', '/disk1/www/rails/humanrnamap/public/result/3476d825-36d0-43ed-ba47-556527a61e1e/final_image/SON_fold_1.svg', '-title', 'SON, -5.2 ± 0.8\n kcal/mol, AUC: 0.679', '-titleSize', '12', '-basesStyle1', 'fill=#ffffff', '-applyBasesStyle1on', '3,4,5,6,9,13,14,15,20,21,22,23,25,29,31,33,37,38,41,43,47,50,53,54,55,58,59,60,62,66,68,70,71,72,77,80,84,85,86,87,88,89,90,92,93,95,96,97,98', '-basesStyle2', 'fill=#00ffff', '-applyBasesStyle2on', '1,34,91,79', '-basesStyle3', 'fill=#ffff00', '-applyBasesStyle3on', '2,7,39,10,42,44,45,46,74,16,17,78,81,56,26', '-basesStyle4', 'fill=#ff0000', '-applyBasesStyle4on', '64,65,67,69,8,73,11,12,75,76,18,19,82,83,24,27,28,30,94,32,35,36,99,40,48,49,51,52,57,61,63']
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 4.75, Y: 201.14366948188177, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 22.25, Y: 201.14366948188177, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 39.75, Y: 201.14366948188177, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 57.25, Y: 201.14366948188177, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 57.25, Y: 181.14366948188177, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 57.25, Y: 161.14366948188177, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 57.25, Y: 141.14366948188177, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 57.25, Y: 121.14366948188176, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 53.70126561276089, Y: 104.0072248142906, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 64.74998212006699, Y: 90.4360378677568, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 82.25001787993301, Y: 90.4360378677568, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 93.29873438723911, Y: 104.0072248142906, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 89.75, Y: 121.14366948188176, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 89.75, Y: 141.14366948188177, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 89.75, Y: 161.14366948188177, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 89.75, Y: 181.14366948188177, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 89.75, Y: 201.14366948188177, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 107.25, Y: 201.14366948188177, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 124.75, Y: 201.14366948188177, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 142.25, Y: 201.14366948188177, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 159.75, Y: 201.14366948188177, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 159.75, Y: 181.14366948188177, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 159.75, Y: 161.14366948188177, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 146.4500727174621, Y: 149.76996968859908, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 140.01609813886415, Y: 133.49566221238155, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 141.94301615805517, Y: 116.1020973202776, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 151.7831056061255, Y: 101.63068576637275, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 167.25001267560185, Y: 93.44387329675448, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 184.74998732439818, Y: 93.44387329675448, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 200.2168943938745, Y: 101.6306857663728, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 210.05698384194483, Y: 116.1020973202776, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 211.98390186113585, Y: 133.49566221238155, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 205.5499272825379, Y: 149.76996968859908, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 192.25, Y: 161.14366948188177, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 192.25, Y: 181.14366948188177, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 192.25, Y: 201.14366948188177, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 209.75, Y: 201.14366948188177, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 227.25, Y: 201.14366948188177, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 227.25, Y: 181.14366948188177, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 227.25, Y: 161.14366948188177, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 227.25, Y: 141.14366948188177, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 223.43438113341733, Y: 124.06463782044678, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 234.15572209255677, Y: 110.23332848744438, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 242.66734010780453, Y: 92.1349208568679, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 251.17895812305233, Y: 74.03651322629139, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 259.6905761383001, Y: 55.938105595714944, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 268.2021941535479, Y: 37.83969796513844, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 272.28381563540137, Y: 20.822306341406602, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 288.0576623577173, Y: 13.243585395397872, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 303.89380139430324, Y: 20.691266377455634, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 308.1163721863779, Y: 37.67423277035965, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 297.61210655323475, Y: 51.67107723991609, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 289.10048853798696, Y: 69.76948487049259, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 280.58887052273917, Y: 87.8678925010691, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 272.0772525074914, Y: 105.96630013164557, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 263.5656344922436, Y: 124.06470776222206, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 259.75, Y: 141.14366948188177, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 259.75, Y: 161.14366948188177, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 259.75, Y: 181.14366948188177, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 259.75, Y: 201.14366948188177, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 277.25, Y: 201.14366948188177, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 294.75, Y: 201.14366948188177, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 312.25, Y: 201.14366948188177, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 329.75, Y: 201.14366948188177, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 347.25, Y: 201.14366948188177, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 364.75, Y: 201.14366948188177, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 382.25, Y: 201.14366948188177, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 399.75, Y: 201.14366948188177, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 417.25, Y: 201.14366948188177, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 434.75, Y: 201.14366948188177, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 452.25, Y: 201.14366948188177, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 469.75, Y: 201.14366948188177, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 487.25, Y: 201.14366948188177, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 504.75, Y: 201.14366948188177, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 522.25, Y: 201.14366948188177, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 539.75, Y: 201.14366948188177, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 557.25, Y: 201.14366948188177, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 574.75, Y: 201.14366948188177, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 592.25, Y: 201.1436694818818, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 609.75, Y: 201.1436694818818, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 627.25, Y: 201.1436694818818, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 644.75, Y: 201.1436694818818, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 644.75, Y: 181.14366948188177, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 644.75, Y: 161.14366948188183, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 644.75, Y: 141.14366948188183, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 641.201265612761, Y: 124.00722481429061, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 652.249982120067, Y: 110.43603786775684, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 669.750017879933, Y: 110.43603786775684, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 680.798734387239, Y: 124.00722481429061, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 677.25, Y: 141.14366948188183, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 677.25, Y: 161.14366948188183, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 677.25, Y: 181.1436694818818, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 677.25, Y: 201.1436694818818, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 694.75, Y: 201.1436694818818, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 712.25, Y: 201.1436694818818, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 729.75, Y: 201.1436694818818, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 747.25, Y: 201.1436694818818, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 764.75, Y: 201.1436694818818, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 782.25, Y: 201.1436694818818, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '1', X: 5.5, Y: 221.14366948188177, Width: 9.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '10', X: 52.41341049766818, Y: 72.37307056519504, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '20', X: 138.5, Y: 221.14366948188177, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '30', X: 209.80773574210994, Y: 86.73028469387776, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '40', X: 203.5, Y: 161.14366948188177, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '50', X: 315.60121895793475, Y: 8.0, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '60', X: 270.14213562373095, Y: 215.28580510561272, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '70', X: 431.0, Y: 221.14366948188177, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '80', X: 606.0, Y: 221.1436694818818, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '90', X: 693.3567125307112, Y: 138.75390642402493, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '99', X: 778.5, Y: 221.1436694818818, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'SON, -5.2 ± 0.8
 kcal/mol, AUC: 0.679', X: 327.5, Y: 233.9436694818818, Width: 142.5, Height: 23
Calculated bounding box: (4.75, 0.0, 796.5, 233.9436694818818)
Updated viewBox: -0.25 -5.0 801.75 243.9436694818818
Updated SVG: /disk1/www/rails/humanrnamap/public/result/3476d825-36d0-43ed-ba47-556527a61e1e/final_image/SON_fold_final_1.svg
Combined SVG saved as /disk1/www/rails/humanrnamap/public/result/3476d825-36d0-43ed-ba47-556527a61e1e/final_image/SON_fold_final_1.svg
