Initializing nucleic acids...done.
Applying constraints...done.
Folding single strand...
  0% [=                                                 ] /                     
  6% [====                                              ] -                     
 12% [=======                                           ] \                     
 18% [==========                                        ] |                     
 25% [=============                                     ] /                     
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 37% [===================                               ] \                     
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 50% [==========================                        ] /                     
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 63% [================================                  ] \                     
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 82% [==========================================        ] -                     
 88% [=============================================     ] \                     
 94% [================================================  ] |                     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/55f2adb0-acbb-42bf-a1dc-cc59e8e6e50f/final_image/ITCH_fold_1.svg

first - Elapsed time since the previous call: 0.00 seconds
first - Current memory usage: 159.14 MB
setup complete - Elapsed time since the previous call: 0.00 seconds
setup complete - Current memory usage: 159.14 MB
config complete - Elapsed time since the previous call: 0.00 seconds
config complete - Current memory usage: 159.14 MB
read annotations - Elapsed time since the previous call: 0.09 seconds
read annotations - Current memory usage: 172.76 MB
Based on canonical annotations, the following gene is in your area of interest: ITCH(+)
write fasta - Elapsed time since the previous call: 0.58 seconds
write fasta - Current memory usage: 172.76 MB
Length of region: 79 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: 0.20 seconds
write dat - Current memory usage: 176.25 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/Fold "/disk1/www/rails/humanrnamap/public/result/55f2adb0-acbb-42bf-a1dc-cc59e8e6e50f/fasta/ITCH.fasta" "/disk1/www/rails/humanrnamap/public/result/55f2adb0-acbb-42bf-a1dc-cc59e8e6e50f/ct/ITCH.ct" --SHAPE "ITCH.dat"

fold - Elapsed time since the previous call: 0.08 seconds
fold - Current memory usage: 176.25 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/efn2 "/disk1/www/rails/humanrnamap/public/result/55f2adb0-acbb-42bf-a1dc-cc59e8e6e50f/ct/ITCH.ct" "/disk1/www/rails/humanrnamap/public/result/55f2adb0-acbb-42bf-a1dc-cc59e8e6e50f/fold_FE/ITCH.txt" -sh "ITCH.dat"

efn2 - Elapsed time since the previous call: 0.41 seconds
efn2 - Current memory usage: 176.25 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/55f2adb0-acbb-42bf-a1dc-cc59e8e6e50f/ct/ITCH.ct" 1 "/disk1/www/rails/humanrnamap/public/result/55f2adb0-acbb-42bf-a1dc-cc59e8e6e50f/fold_dbn/ITCH_temp1.dbn"

ct2dot - Elapsed time since the previous call: 0.02 seconds
ct2dot - Current memory usage: 176.25 MB
['java', '-cp', '/disk1/www/rails/humanrnamap/cli/bin/VARNAv3-93.jar', 'fr.orsay.lri.varna.applications.VARNAcmd', '-sequenceDBN', 'CAUAUUUUGUGGACCACAAUAGAAGAACUACCACCUAUAUAGAUCCCCGCACAGGAAAAUCUGCCCUAGACAAUGGACC', '-structureDBN', '........((((..................)))).....(((((.((......))...))))).((........))...', '-o', '/disk1/www/rails/humanrnamap/public/result/55f2adb0-acbb-42bf-a1dc-cc59e8e6e50f/final_image/ITCH_fold_1.svg', '-title', 'ITCH, -8.7 ± 0.6\n kcal/mol, AUC: 0.647', '-titleSize', '12', '-basesStyle1', 'fill=#ffffff', '-applyBasesStyle1on', '3,67,5,6,7,8,9,10,11,12,69,74,75,76,20,22,25,29,36,38,40,42,44,49,54,55,60,62,63', '-basesStyle2', 'fill=#00ffff', '-applyBasesStyle2on', '32,1,2,33,35,65,13,45,46,47,57', '-basesStyle3', 'fill=#ffff00', '-applyBasesStyle3on', '66,4,68,73,14,15,50,52,53,56,26,59,61', '-basesStyle4', 'fill=#ff0000', '-applyBasesStyle4on', '64,70,71,72,77,78,79,16,17,18,19,21,23,24,27,28,30,31,34,37,39,41,43,48,51,58']
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Text: 'C', X: 314.75, Y: 154.56247403835812, Width: 10.5, Height: 8
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Text: 'U', X: 314.75, Y: 174.56247403835812, Width: 10.5, Height: 8
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Text: 'G', X: 314.75, Y: 194.56247403835812, Width: 10.5, Height: 8
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Text: 'C', X: 332.25, Y: 194.56247403835812, Width: 10.5, Height: 8
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Text: 'C', X: 349.75, Y: 194.56247403835812, Width: 10.5, Height: 8
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Text: 'C', X: 349.75, Y: 174.56247403835812, Width: 10.5, Height: 8
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Text: 'U', X: 338.0949319257163, Y: 161.508359850178, Width: 10.5, Height: 8
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Text: 'A', X: 399.75, Y: 194.56247403835815, Width: 10.5, Height: 8
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Text: 'C', X: 417.25, Y: 194.56247403835815, Width: 10.5, Height: 8
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Text: 'C', X: 434.75, Y: 194.56247403835815, Width: 10.5, Height: 8
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Text: '1', X: 5.5, Y: 214.56247403835812, Width: 9.0, Height: 8
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Text: '79', X: 431.0, Y: 214.56247403835815, Width: 18.0, Height: 8
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Text: 'ITCH, -8.7 ± 0.6
 kcal/mol, AUC: 0.647', X: 153.75, Y: 227.36247403835816, Width: 142.5, Height: 23
Calculated bounding box: (4.75, 0.0, 449.0, 227.36247403835816)
Updated viewBox: -0.25 -5.0 454.25 237.36247403835816
Updated SVG: /disk1/www/rails/humanrnamap/public/result/55f2adb0-acbb-42bf-a1dc-cc59e8e6e50f/final_image/ITCH_fold_final_1.svg
Combined SVG saved as /disk1/www/rails/humanrnamap/public/result/55f2adb0-acbb-42bf-a1dc-cc59e8e6e50f/final_image/ITCH_fold_final_1.svg
