Initializing nucleic acids...done.
Applying constraints...done.
Folding single strand...
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 96% [================================================= ] \                     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/d62e6a9c-53aa-436c-92e6-6690ecfeb46f/final_image/ITCH_fold_1.svg

first - Elapsed time since the previous call: 0.00 seconds
first - Current memory usage: 159.23 MB
setup complete - Elapsed time since the previous call: 0.00 seconds
setup complete - Current memory usage: 159.23 MB
config complete - Elapsed time since the previous call: 0.00 seconds
config complete - Current memory usage: 159.23 MB
read annotations - Elapsed time since the previous call: 0.09 seconds
read annotations - Current memory usage: 172.89 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: 172.89 MB
Length of region: 93 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: 176.28 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/Fold "/disk1/www/rails/humanrnamap/public/result/d62e6a9c-53aa-436c-92e6-6690ecfeb46f/fasta/ITCH.fasta" "/disk1/www/rails/humanrnamap/public/result/d62e6a9c-53aa-436c-92e6-6690ecfeb46f/ct/ITCH.ct" --SHAPE "ITCH.dat"

fold - Elapsed time since the previous call: 0.11 seconds
fold - Current memory usage: 176.28 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/efn2 "/disk1/www/rails/humanrnamap/public/result/d62e6a9c-53aa-436c-92e6-6690ecfeb46f/ct/ITCH.ct" "/disk1/www/rails/humanrnamap/public/result/d62e6a9c-53aa-436c-92e6-6690ecfeb46f/fold_FE/ITCH.txt" -sh "ITCH.dat"

efn2 - Elapsed time since the previous call: 0.44 seconds
efn2 - Current memory usage: 176.28 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/d62e6a9c-53aa-436c-92e6-6690ecfeb46f/ct/ITCH.ct" 1 "/disk1/www/rails/humanrnamap/public/result/d62e6a9c-53aa-436c-92e6-6690ecfeb46f/fold_dbn/ITCH_temp1.dbn"

ct2dot - Elapsed time since the previous call: 0.01 seconds
ct2dot - Current memory usage: 176.28 MB
['java', '-cp', '/disk1/www/rails/humanrnamap/cli/bin/VARNAv3-93.jar', 'fr.orsay.lri.varna.applications.VARNAcmd', '-sequenceDBN', 'ACAGCGUAGUCAGCUUCAAGGAGCAAUGCAGCAGUUUAACCAGAGAUUCAUUUAUGGGAAUCAAGAUUUAUUUGCUACAUCACAAAGUAAAGA', '-structureDBN', '............((((....)))).(((.(((((..........(((((........))))).........))))).))).............', '-o', '/disk1/www/rails/humanrnamap/public/result/d62e6a9c-53aa-436c-92e6-6690ecfeb46f/final_image/ITCH_fold_1.svg', '-title', 'ITCH, -15.7 ± 0.6\n kcal/mol, AUC: 0.855', '-titleSize', '12', '-basesStyle1', 'fill=#ffffff', '-applyBasesStyle1on', '4,6,7,9,10,13,15,16,20,21,23,27,28,31,34,35,36,37,43,45,47,48,51,52,53,55,56,57,58,61,65,67,68,69,71,72,73,74,76,80,87,88,92', '-basesStyle2', 'fill=#00ffff', '-applyBasesStyle2on', '22,62,59,60,46', '-basesStyle3', 'fill=#ffff00', '-applyBasesStyle3on', '1,2,66,70,12,77,14,78,81,86,24,89,30,33,49,54', '-basesStyle4', 'fill=#ff0000', '-applyBasesStyle4on', '64,3,5,8,11,75,79,17,18,19,82,83,84,85,25,26,90,91,29,93,32,38,39,40,41,42,44,50,63']
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Text: '60', X: 331.0, Y: 108.83506218665309, Width: 18.0, Height: 8
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Text: '70', X: 356.8180809395173, Y: 279.8973625075877, Width: 18.0, Height: 8
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Text: 'ITCH, -15.7 ± 0.6
 kcal/mol, AUC: 0.855', X: 207.5, Y: 468.2895514755578, Width: 142.5, Height: 23
Calculated bounding box: (4.75, 5.0, 556.5, 468.2895514755578)
Updated viewBox: -0.25 0.0 561.75 473.2895514755578
Updated SVG: /disk1/www/rails/humanrnamap/public/result/d62e6a9c-53aa-436c-92e6-6690ecfeb46f/final_image/ITCH_fold_final_1.svg
Combined SVG saved as /disk1/www/rails/humanrnamap/public/result/d62e6a9c-53aa-436c-92e6-6690ecfeb46f/final_image/ITCH_fold_final_1.svg
