Initializing nucleic acids...done.
Applying constraints...done.
Folding single strand...
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 97% [================================================= ] |                     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/5c5b6c6d-7e5f-420a-9fe3-b216b1f44a2a/final_image/KRAS_fold_1.svg

first - Elapsed time since the previous call: 0.00 seconds
first - Current memory usage: 157.16 MB
setup complete - Elapsed time since the previous call: 0.00 seconds
setup complete - Current memory usage: 157.16 MB
config complete - Elapsed time since the previous call: 0.00 seconds
config complete - Current memory usage: 157.16 MB
read annotations - Elapsed time since the previous call: 0.09 seconds
read annotations - Current memory usage: 170.75 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: 170.75 MB
Length of region: 97 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: 173.93 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/Fold "/disk1/www/rails/humanrnamap/public/result/5c5b6c6d-7e5f-420a-9fe3-b216b1f44a2a/fasta/KRAS.fasta" "/disk1/www/rails/humanrnamap/public/result/5c5b6c6d-7e5f-420a-9fe3-b216b1f44a2a/ct/KRAS.ct" --SHAPE "KRAS.dat"

fold - Elapsed time since the previous call: 0.11 seconds
fold - Current memory usage: 173.93 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/efn2 "/disk1/www/rails/humanrnamap/public/result/5c5b6c6d-7e5f-420a-9fe3-b216b1f44a2a/ct/KRAS.ct" "/disk1/www/rails/humanrnamap/public/result/5c5b6c6d-7e5f-420a-9fe3-b216b1f44a2a/fold_FE/KRAS.txt" -sh "KRAS.dat"

efn2 - Elapsed time since the previous call: 0.43 seconds
efn2 - Current memory usage: 173.93 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/5c5b6c6d-7e5f-420a-9fe3-b216b1f44a2a/ct/KRAS.ct" 1 "/disk1/www/rails/humanrnamap/public/result/5c5b6c6d-7e5f-420a-9fe3-b216b1f44a2a/fold_dbn/KRAS_temp1.dbn"

ct2dot - Elapsed time since the previous call: 0.01 seconds
ct2dot - Current memory usage: 173.93 MB
['java', '-cp', '/disk1/www/rails/humanrnamap/cli/bin/VARNAv3-93.jar', 'fr.orsay.lri.varna.applications.VARNAcmd', '-sequenceDBN', 'AGUAACUUCUGUGUUAAUACUGGAUAGCAUGAAUUCUGCAUUGAGAAACUGAAUAGCUGUCAUAAAAUGAAACUUUCUUUCUAAAGAAAGAUACUCA', '-structureDBN', '..((((......))))......((((((((...((((......)))).....)).))))))...........(((((((....))))))).......', '-o', '/disk1/www/rails/humanrnamap/public/result/5c5b6c6d-7e5f-420a-9fe3-b216b1f44a2a/final_image/KRAS_fold_1.svg', '-title', 'KRAS, -20.5 ± 0.7\n kcal/mol, AUC: 0.774', '-titleSize', '12', '-basesStyle1', 'fill=#ffffff', '-applyBasesStyle1on', '2,3,7,8,10,11,12,13,14,15,18,21,22,23,25,27,30,31,34,35,37,38,41,42,43,45,50,51,54,56,58,59,60,63,68,69,74,75,76,78,79,80,82,86,90,92,95', '-basesStyle2', 'fill=#00ffff', '-applyBasesStyle2on', '89,65,5,9,77,84,85,87,24,57,88', '-basesStyle3', 'fill=#ffff00', '-applyBasesStyle3on', '64,1,4,73,81,26,91,93,94,96,33,36,44,46,47,49,61', '-basesStyle4', 'fill=#ff0000', '-applyBasesStyle4on', '66,67,6,70,71,72,16,17,19,20,83,28,29,32,97,39,40,48,52,53,55,62']
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Text: 'U', X: 557.25, Y: 292.78293739743157, Width: 10.5, Height: 8
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Text: 'A', X: 592.25, Y: 292.78293739743157, Width: 10.5, Height: 8
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Text: '1', X: 5.5, Y: 312.7829373974315, Width: 9.0, Height: 8
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Text: '20', X: 138.5, Y: 312.7829373974315, Width: 18.0, Height: 8
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Text: '30', X: 160.55826503798522, Y: 166.08238611921678, Width: 18.0, Height: 8
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Text: '40', X: 55.913541182220314, Y: 18.42933640945705, Width: 18.0, Height: 8
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Text: '50', X: 226.4837347385552, Y: 85.05037651568293, Width: 18.0, Height: 8
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Text: '60', X: 243.5, Y: 272.7829373974315, Width: 18.0, Height: 8
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Text: '70', X: 381.0, Y: 312.78293739743157, Width: 18.0, Height: 8
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Text: '90', X: 480.14213562373095, Y: 306.9250730211625, Width: 18.0, Height: 8
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Text: '97', X: 588.5, Y: 312.78293739743157, Width: 18.0, Height: 8
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Text: 'KRAS, -20.5 ± 0.7
 kcal/mol, AUC: 0.774', X: 232.5, Y: 325.5829373974316, Width: 142.5, Height: 23
Calculated bounding box: (4.75, 5.0, 606.5, 325.5829373974316)
Updated viewBox: -0.25 0.0 611.75 330.5829373974316
Updated SVG: /disk1/www/rails/humanrnamap/public/result/5c5b6c6d-7e5f-420a-9fe3-b216b1f44a2a/final_image/KRAS_fold_final_1.svg
Combined SVG saved as /disk1/www/rails/humanrnamap/public/result/5c5b6c6d-7e5f-420a-9fe3-b216b1f44a2a/final_image/KRAS_fold_final_1.svg
