Initializing nucleic acids...done.
Applying constraints...done.
Folding single strand...
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 98% [==================================================] -                     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/a68d323a-7392-4596-93a7-a74a871c1ff9/final_image/RUNX1_fold_1.svg

first - Elapsed time since the previous call: 0.00 seconds
first - Current memory usage: 158.04 MB
setup complete - Elapsed time since the previous call: 0.00 seconds
setup complete - Current memory usage: 158.04 MB
config complete - Elapsed time since the previous call: 0.00 seconds
config complete - Current memory usage: 158.04 MB
read annotations - Elapsed time since the previous call: 0.09 seconds
read annotations - Current memory usage: 171.60 MB
Based on canonical annotations, the following gene is in your area of interest: RUNX1(-)
write fasta - Elapsed time since the previous call: 0.13 seconds
write fasta - Current memory usage: 171.60 MB
Length of region: 107 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: 175.27 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/Fold "/disk1/www/rails/humanrnamap/public/result/a68d323a-7392-4596-93a7-a74a871c1ff9/fasta/RUNX1.fasta" "/disk1/www/rails/humanrnamap/public/result/a68d323a-7392-4596-93a7-a74a871c1ff9/ct/RUNX1.ct" --SHAPE "RUNX1.dat"

fold - Elapsed time since the previous call: 0.14 seconds
fold - Current memory usage: 175.27 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/efn2 "/disk1/www/rails/humanrnamap/public/result/a68d323a-7392-4596-93a7-a74a871c1ff9/ct/RUNX1.ct" "/disk1/www/rails/humanrnamap/public/result/a68d323a-7392-4596-93a7-a74a871c1ff9/fold_FE/RUNX1.txt" -sh "RUNX1.dat"

efn2 - Elapsed time since the previous call: 0.50 seconds
efn2 - Current memory usage: 175.27 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/a68d323a-7392-4596-93a7-a74a871c1ff9/ct/RUNX1.ct" 1 "/disk1/www/rails/humanrnamap/public/result/a68d323a-7392-4596-93a7-a74a871c1ff9/fold_dbn/RUNX1_temp1.dbn"

ct2dot - Elapsed time since the previous call: 0.02 seconds
ct2dot - Current memory usage: 175.27 MB
['java', '-cp', '/disk1/www/rails/humanrnamap/cli/bin/VARNAv3-93.jar', 'fr.orsay.lri.varna.applications.VARNAcmd', '-sequenceDBN', 'AGGGUCUCAUAUCUAACUUCCUCCUUAAAACAGAGAAGGUCAAUCUAGUUCCAGAGGGUUGAGGCAGGUGCCAAUAAUUACAUCUUUGGAGAGGAUUUGAUUUCUGC', '-structureDBN', '((((..............)))).(((......)))..(((((((((..(((((((((((...(((....))).......)).))))))))).))))).)))).....', '-o', '/disk1/www/rails/humanrnamap/public/result/a68d323a-7392-4596-93a7-a74a871c1ff9/final_image/RUNX1_fold_1.svg', '-title', 'RUNX1, -21.7 ± 1.4\n kcal/mol, AUC: 0.661', '-titleSize', '12', '-basesStyle1', 'fill=#ffffff', '-applyBasesStyle1on', '2,3,4,5,7,10,12,14,18,19,22,25,26,33,35,38,39,40,44,46,48,49,50,54,56,57,58,59,60,61,63,64,67,68,69,70,75,78,79,83,85,86,87,88,89,91,93,94,96,97,98,99,101,102,103,105,106', '-basesStyle2', 'fill=#00ffff', '-applyBasesStyle2on', '80,20,21,6,23', '-basesStyle3', 'fill=#ffff00', '-applyBasesStyle3on', '65,34,71,72,107,17,82,51,84,27,28', '-basesStyle4', 'fill=#ff0000', '-applyBasesStyle4on', '1,8,9,11,13,15,16,24,29,30,31,32,36,37,41,42,43,45,47,52,53,55,62,66,73,74,76,77,81,90,92,95,100,104']
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Text: 'A', X: 110.54599393042588, Y: 418.92095826523655, Width: 10.5, Height: 8
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Text: 'A', X: 135.5459818135471, Y: 482.5443179294914, Width: 10.5, Height: 8
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Text: 'G', X: 135.5459818135471, Y: 502.5443179294914, Width: 10.5, Height: 8
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Text: 'A', X: 153.0459818135471, Y: 502.5443179294914, Width: 10.5, Height: 8
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Text: 'A', X: 170.5459818135471, Y: 502.5443179294914, Width: 10.5, Height: 8
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Text: 'G', X: 188.0459818135471, Y: 502.5443179294914, Width: 10.5, Height: 8
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Text: 'G', X: 188.0459818135471, Y: 482.5443179294914, Width: 10.5, Height: 8
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Text: 'U', X: 188.0459818135471, Y: 462.5443179294914, Width: 10.5, Height: 8
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Text: 'C', X: 188.0459818135471, Y: 442.5443179294914, Width: 10.5, Height: 8
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Text: 'A', X: 184.23037857286914, Y: 425.4652163263355, Width: 10.5, Height: 8
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Text: 'A', X: 175.71888672729997, Y: 407.3667493591362, Width: 10.5, Height: 8
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Text: 'U', X: 167.2073948817308, Y: 389.26828239193674, Width: 10.5, Height: 8
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Text: 'C', X: 158.69590303616164, Y: 371.1698154247373, Width: 10.5, Height: 8
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Text: 'U', X: 150.18441119059247, Y: 353.07134845753785, Width: 10.5, Height: 8
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Text: 'A', X: 135.36178681769707, Y: 342.50658363179514, Width: 10.5, Height: 8
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Text: 'G', X: 131.39308304762864, Y: 324.74218554155163, Width: 10.5, Height: 8
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Text: 'U', X: 140.31032644339803, Y: 308.8737508568132, Width: 10.5, Height: 8
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Text: 'U', X: 140.31032644339803, Y: 288.8737508568132, Width: 10.5, Height: 8
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Text: 'C', X: 140.31032644339803, Y: 268.87375085681316, Width: 10.5, Height: 8
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Text: 'C', X: 140.31032644339803, Y: 248.87375085681316, Width: 10.5, Height: 8
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Text: 'A', X: 140.31032644339803, Y: 228.87375085681316, Width: 10.5, Height: 8
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Text: 'G', X: 140.31032644339803, Y: 208.87375085681316, Width: 10.5, Height: 8
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Text: 'A', X: 140.31032644339803, Y: 188.87375085681316, Width: 10.5, Height: 8
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Text: 'G', X: 140.31032644339803, Y: 168.87375085681316, Width: 10.5, Height: 8
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Text: 'G', X: 140.31032644339803, Y: 148.87375085681316, Width: 10.5, Height: 8
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Text: 'G', X: 136.49472320272008, Y: 131.79464925365727, Width: 10.5, Height: 8
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Text: 'U', X: 127.98323135715088, Y: 113.69618228645794, Width: 10.5, Height: 8
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Text: 'U', X: 110.64391775170446, Y: 111.32948264827422, Width: 10.5, Height: 8
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Text: 'G', X: 95.57910837008457, Y: 102.42417065032276, Width: 10.5, Height: 8
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Text: 'A', X: 85.14635815476677, Y: 88.37387576266354, Width: 10.5, Height: 8
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Text: 'G', X: 80.97833176221488, Y: 71.37738731721146, Width: 10.5, Height: 8
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Text: 'G', X: 62.08860547282319, Y: 64.80637212076994, Width: 10.5, Height: 8
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Text: 'C', X: 43.19887918343153, Y: 58.235356924328414, Width: 10.5, Height: 8
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Text: 'A', X: 25.847802336892244, Y: 55.956896070577216, Width: 10.5, Height: 8
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Text: 'G', X: 16.66006619831694, Y: 41.06271075400133, Width: 10.5, Height: 8
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Text: 'G', X: 22.409716244134387, Y: 24.53416647607969, Width: 10.5, Height: 8
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Text: 'U', X: 38.85758078977793, Y: 18.557628725445966, Width: 10.5, Height: 8
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Text: 'G', X: 53.876778877648945, Y: 27.539551704066923, Width: 10.5, Height: 8
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Text: 'C', X: 72.76650516704063, Y: 34.110566900508445, Width: 10.5, Height: 8
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Text: 'C', X: 91.6562314564323, Y: 40.68158209694997, Width: 10.5, Height: 8
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Text: 'A', X: 105.47275599041147, Y: 29.941300452507278, Width: 10.5, Height: 8
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Text: 'A', X: 122.37301060380713, Y: 25.399121019415816, Width: 10.5, Height: 8
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Text: 'U', X: 139.7122303197378, Y: 27.7658613183674, Width: 10.5, Height: 8
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Text: 'C', X: 172.81032644339803, Y: 168.87375085681316, Width: 10.5, Height: 8
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Text: 'U', X: 172.81032644339803, Y: 188.87375085681316, Width: 10.5, Height: 8
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Text: 'U', X: 172.81032644339803, Y: 228.87375085681316, Width: 10.5, Height: 8
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Text: 'G', X: 172.81032644339803, Y: 248.87375085681316, Width: 10.5, Height: 8
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Text: 'G', X: 172.81032644339803, Y: 268.87375085681316, Width: 10.5, Height: 8
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Text: 'A', X: 172.81032644339803, Y: 288.8737508568132, Width: 10.5, Height: 8
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Text: 'G', X: 172.81032644339803, Y: 308.8737508568132, Width: 10.5, Height: 8
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Text: 'A', X: 181.38652064782008, Y: 322.8987839495244, Width: 10.5, Height: 8
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Text: 'G', X: 179.59442001229155, Y: 339.24017420848793, Width: 10.5, Height: 8
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Text: 'G', X: 188.10591185786072, Y: 357.33864117568737, Width: 10.5, Height: 8
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Text: 'A', X: 196.6174037034299, Y: 375.4371081428868, Width: 10.5, Height: 8
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Text: 'A', X: 220.5459818135471, Y: 462.5443179294914, Width: 10.5, Height: 8
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Text: 'U', X: 220.5459818135471, Y: 502.5443179294914, Width: 10.5, Height: 8
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Text: 'U', X: 238.0459818135471, Y: 502.5443179294914, Width: 10.5, Height: 8
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Text: 'C', X: 255.5459818135471, Y: 502.5443179294914, Width: 10.5, Height: 8
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Text: 'U', X: 273.0459818135471, Y: 502.5443179294914, Width: 10.5, Height: 8
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Text: 'G', X: 290.5459818135471, Y: 502.5443179294914, Width: 10.5, Height: 8
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Text: 'C', X: 308.0459818135471, Y: 502.5443179294914, Width: 10.5, Height: 8
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Text: '1', X: 36.29598181354709, Y: 522.5443179294914, Width: 9.0, Height: 8
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Text: '10', X: 12.400848942988304, Y: 341.037490240688, Width: 18.0, Height: 8
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Text: '20', X: 84.29598181354709, Y: 462.5443179294914, Width: 18.0, Height: 8
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Text: '30', X: 131.1564356331032, Y: 400.1344203421647, Width: 18.0, Height: 8
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Text: '40', X: 164.2959818135471, Y: 462.5443179294914, Width: 18.0, Height: 8
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Text: '50', X: 116.56032644339803, Y: 288.8737508568132, Width: 18.0, Height: 8
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Text: '60', X: 100.32297881190898, Y: 130.21923546427155, Width: 18.0, Height: 8
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Text: '70', X: 54.39361836421173, Y: 8.0, Width: 18.0, Height: 8
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Text: '80', X: 172.28196995886964, Y: 92.61257725956455, Width: 18.0, Height: 8
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Text: '90', X: 189.06032644339803, Y: 288.8737508568132, Width: 18.0, Height: 8
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Text: '100', X: 232.2959818135471, Y: 462.5443179294914, Width: 27.0, Height: 8
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Text: '107', X: 299.7959818135471, Y: 522.5443179294914, Width: 27.0, Height: 8
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Text: 'RUNX1, -21.7 ± 1.4
 kcal/mol, AUC: 0.661', X: 90.39799090677354, Y: 535.3443179294914, Width: 142.5, Height: 23
Calculated bounding box: (4.75, 0.0, 326.7959818135471, 535.3443179294914)
Updated viewBox: -0.25 -5.0 332.0459818135471 545.3443179294914
Updated SVG: /disk1/www/rails/humanrnamap/public/result/a68d323a-7392-4596-93a7-a74a871c1ff9/final_image/RUNX1_fold_final_1.svg
Combined SVG saved as /disk1/www/rails/humanrnamap/public/result/a68d323a-7392-4596-93a7-a74a871c1ff9/final_image/RUNX1_fold_final_1.svg
