Initializing nucleic acids...done.
Applying constraints...done.
Folding single strand...
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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/f0b307a2-6353-42b8-a2f5-e7cec9cabbf1/final_image/KRAS_fold_1.svg

first - Elapsed time since the previous call: 0.00 seconds
first - Current memory usage: 156.70 MB
setup complete - Elapsed time since the previous call: 0.00 seconds
setup complete - Current memory usage: 156.70 MB
config complete - Elapsed time since the previous call: 0.00 seconds
config complete - Current memory usage: 156.70 MB
read annotations - Elapsed time since the previous call: 0.09 seconds
read annotations - Current memory usage: 170.32 MB
Based on canonical annotations, the following gene is in your area of interest: KRAS(-)
write fasta - Elapsed time since the previous call: 0.54 seconds
write fasta - Current memory usage: 170.32 MB
Length of region: 142 nt.
86.2% 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: 0.21 seconds
write dat - Current memory usage: 173.58 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/Fold "/disk1/www/rails/humanrnamap/public/result/f0b307a2-6353-42b8-a2f5-e7cec9cabbf1/fasta/KRAS.fasta" "/disk1/www/rails/humanrnamap/public/result/f0b307a2-6353-42b8-a2f5-e7cec9cabbf1/ct/KRAS.ct" --SHAPE "KRAS.dat"

fold - Elapsed time since the previous call: 0.25 seconds
fold - Current memory usage: 173.58 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/efn2 "/disk1/www/rails/humanrnamap/public/result/f0b307a2-6353-42b8-a2f5-e7cec9cabbf1/ct/KRAS.ct" "/disk1/www/rails/humanrnamap/public/result/f0b307a2-6353-42b8-a2f5-e7cec9cabbf1/fold_FE/KRAS.txt" -sh "KRAS.dat"

efn2 - Elapsed time since the previous call: 0.44 seconds
efn2 - Current memory usage: 173.58 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/f0b307a2-6353-42b8-a2f5-e7cec9cabbf1/ct/KRAS.ct" 1 "/disk1/www/rails/humanrnamap/public/result/f0b307a2-6353-42b8-a2f5-e7cec9cabbf1/fold_dbn/KRAS_temp1.dbn"

ct2dot - Elapsed time since the previous call: 0.02 seconds
ct2dot - Current memory usage: 173.58 MB
['java', '-cp', '/disk1/www/rails/humanrnamap/cli/bin/VARNAv3-93.jar', 'fr.orsay.lri.varna.applications.VARNAcmd', '-sequenceDBN', 'CAUGAGUUCUUGAAGAAUAGUCAUAACUAGAUUAAGAUCUGUGUUUUAGUUUAAUAGUUUGAAGUGCCUGUUUGGGAUAAUGAUAGGUAAUUUAGAUGAAUUUAGGGGAAAAAAAAGUUAUCUGCAGAUAUGUUGAGGGCCC', '-structureDBN', '..(((((((..................(((((((((((....)))))))))))....((((((.((((((((.........)))))))).)))))).))))))).(((......((..((((....))))..)).....)))', '-o', '/disk1/www/rails/humanrnamap/public/result/f0b307a2-6353-42b8-a2f5-e7cec9cabbf1/final_image/KRAS_fold_1.svg', '-title', 'KRAS, -16.4 ± 1.5\n kcal/mol, AUC: 0.688', '-titleSize', '12', '-basesStyle1', 'fill=#ffffff', '-applyBasesStyle1on', '3,4,6,7,8,10,11,12,15,18,20,21,24,28,30,32,33,36,38,40,41,42,43,44,45,46,47,49,50,51,52,55,57,58,59,60,61,64,65,66,69,70,71,72,73,74,75,76,78,81,82,84,86,87,88,91,92,93,95,97,98,101,102,103,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,121,123,124,127,129,131,132,133,134,135,137,138,139', '-basesStyle2', 'fill=#00ffff', '-applyBasesStyle2on', '48,104,94', '-basesStyle3', 'fill=#ffff00', '-applyBasesStyle3on', '130,67,68,5,141,142,19,85,56,120,29', '-basesStyle4', 'fill=#ff0000', '-applyBasesStyle4on', '128,1,2,136,9,140,13,14,16,17,22,23,25,26,27,31,34,35,37,39,53,54,62,63,77,79,80,83,89,90,96,99,100,122,125,126']
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Text: 'U', X: 152.0452006327818, Y: 229.84435951639227, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 164.86719115988032, Y: 217.93441385765777, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 168.59180682782542, Y: 198.28429329502262, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 172.31642249577052, Y: 178.63417273238736, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 176.04103816371563, Y: 158.9840521697522, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 175.74571875110396, Y: 141.4865083980933, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 189.12852209933467, Y: 130.21034654491052, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 206.32241272592435, Y: 133.4693919139504, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 214.6504705207879, Y: 148.86077602851265, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 207.9724840779978, Y: 165.036552630163, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 204.2478684100527, Y: 184.68667319279814, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 200.5232527421076, Y: 204.3367937554334, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 196.79863707416249, Y: 223.98691431806856, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 204.37285071846176, Y: 239.76288616358443, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 201.11381542187024, Y: 256.9567423027863, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 188.29183321059958, Y: 268.8666865584854, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'U', X: 184.56722534347844, Y: 288.51680859973953, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 197.63325933197385, Y: 300.1584904289033, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'A', X: 205.53261940222674, Y: 315.7741911970563, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 207.16939422776503, Y: 333.1974792957616, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 202.31650717779328, Y: 350.0111489511406, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'G', X: 191.64721960979574, Y: 363.8825693106919, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 176.64172649996905, Y: 372.8873000968367, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 176.64172649996905, Y: 392.8873000968367, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'C', X: 176.64172649996905, Y: 412.8873000968367, Width: 10.5, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '1', X: 42.39172649996905, Y: 432.8873000968367, Width: 9.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '10', X: 48.687609446590926, Y: 306.5465329837806, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '20', X: 13.217049412927771, Y: 129.2494463732562, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '30', X: 175.21731965725195, Y: 106.55476740457726, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '40', X: 360.23039457498606, Y: 8.0, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '50', X: 231.6685970540788, Y: 156.24886444101105, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '60', X: 204.3158778692812, Y: 270.1653629288312, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '70', X: 340.32862585721193, Y: 406.1781109167619, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '80', X: 325.4561085583357, Y: 518.335046443385, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '90', X: 202.19254883235155, Y: 380.01716870622965, Width: 18.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '100', X: 120.89172649996905, Y: 332.8873000968367, Width: 27.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '110', X: 92.3704709720465, Y: 359.0390687253383, Width: 27.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '120', X: 140.69168626519024, Y: 194.55967762707746, Width: 27.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '130', X: 208.5404633130402, Y: 224.5586517005446, Width: 27.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '140', X: 186.64134353804263, Y: 381.06968837677397, Width: 27.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: '142', X: 168.39172649996905, Y: 432.8873000968367, Width: 27.0, Height: 8
Warning: Font Verdana not found. Using default font.
Text: 'KRAS, -16.4 ± 1.5
 kcal/mol, AUC: 0.688', X: 136.3605845439319, Y: 531.1358957834385, Width: 142.5, Height: 23
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Updated viewBox: -0.25 -5.0 415.7211690878638 541.1358957834385
Updated SVG: /disk1/www/rails/humanrnamap/public/result/f0b307a2-6353-42b8-a2f5-e7cec9cabbf1/final_image/KRAS_fold_final_1.svg
Combined SVG saved as /disk1/www/rails/humanrnamap/public/result/f0b307a2-6353-42b8-a2f5-e7cec9cabbf1/final_image/KRAS_fold_final_1.svg
