Initializing nucleic acids...done.
Applying constraints...done.
Folding single strand...
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 95% [================================================  ] |                     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/b42a4fc6-8789-40cc-b5dc-fd84c699d3aa/final_image/RUNX1_fold_1.svg

first - Elapsed time since the previous call: 0.00 seconds
first - Current memory usage: 158.64 MB
setup complete - Elapsed time since the previous call: 0.00 seconds
setup complete - Current memory usage: 158.64 MB
config complete - Elapsed time since the previous call: 0.00 seconds
config complete - Current memory usage: 158.64 MB
read annotations - Elapsed time since the previous call: 0.09 seconds
read annotations - Current memory usage: 172.25 MB
Based on canonical annotations, the following gene is in your area of interest: RUNX1(-)
write fasta - Elapsed time since the previous call: 0.12 seconds
write fasta - Current memory usage: 172.25 MB
Length of region: 99 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: 175.49 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/Fold "/disk1/www/rails/humanrnamap/public/result/b42a4fc6-8789-40cc-b5dc-fd84c699d3aa/fasta/RUNX1.fasta" "/disk1/www/rails/humanrnamap/public/result/b42a4fc6-8789-40cc-b5dc-fd84c699d3aa/ct/RUNX1.ct" --SHAPE "RUNX1.dat"

fold - Elapsed time since the previous call: 0.12 seconds
fold - Current memory usage: 175.49 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/efn2 "/disk1/www/rails/humanrnamap/public/result/b42a4fc6-8789-40cc-b5dc-fd84c699d3aa/ct/RUNX1.ct" "/disk1/www/rails/humanrnamap/public/result/b42a4fc6-8789-40cc-b5dc-fd84c699d3aa/fold_FE/RUNX1.txt" -sh "RUNX1.dat"

efn2 - Elapsed time since the previous call: 0.49 seconds
efn2 - Current memory usage: 175.49 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/b42a4fc6-8789-40cc-b5dc-fd84c699d3aa/ct/RUNX1.ct" 1 "/disk1/www/rails/humanrnamap/public/result/b42a4fc6-8789-40cc-b5dc-fd84c699d3aa/fold_dbn/RUNX1_temp1.dbn"

ct2dot - Elapsed time since the previous call: 0.02 seconds
ct2dot - Current memory usage: 175.49 MB
['java', '-cp', '/disk1/www/rails/humanrnamap/cli/bin/VARNAv3-93.jar', 'fr.orsay.lri.varna.applications.VARNAcmd', '-sequenceDBN', 'AUUCGUGGAAGAUAGUCUCCACUUUUUAAUGCACUAAGCAAUCGGUUGCUAGGAGCCCAUCCUGGGUCAGAGGCCGAUCCGCAGAACCAGAACGUUUUC', '-structureDBN', '....(((((........)))))...............((.((((((..((..((.((((...))))))..))))))))..)).((((......))))..', '-o', '/disk1/www/rails/humanrnamap/public/result/b42a4fc6-8789-40cc-b5dc-fd84c699d3aa/final_image/RUNX1_fold_1.svg', '-title', 'RUNX1, -29.9 ± 1.2\n kcal/mol, AUC: 0.86', '-titleSize', '12', '-basesStyle1', 'fill=#ffffff', '-applyBasesStyle1on', '2,3,5,6,7,8,11,13,15,16,18,23,24,25,26,27,30,31,35,38,42,44,45,46,47,48,50,52,53,55,60,63,64,65,66,67,70,72,73,76,78,81,84,90,94,95,96,97,98', '-basesStyle2', 'fill=#00ffff', '-applyBasesStyle2on', '89,68,74,75,19,20,21,22,56,57,58,28', '-basesStyle3', 'fill=#ffff00', '-applyBasesStyle3on', '99,9,41,43,77,49,17,82,83,54', '-basesStyle4', 'fill=#ff0000', '-applyBasesStyle4on', '1,4,69,71,10,12,14,79,80,85,86,87,88,91,92,29,93,32,33,34,36,37,39,40,51,59,61,62']
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Text: '30', X: 243.5, Y: 392.9801097780497, Width: 18.0, Height: 8
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Text: '40', X: 355.0103366335327, Y: 341.34550260308436, Width: 18.0, Height: 8
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Text: '60', X: 449.3540931468083, Y: 8.0, Width: 18.0, Height: 8
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Text: 'RUNX1, -29.9 ± 1.2
 kcal/mol, AUC: 0.86', X: 202.0, Y: 405.78010977804973, Width: 133.5, Height: 23
Calculated bounding box: (4.75, 0.0, 536.5, 405.78010977804973)
Updated viewBox: -0.25 -5.0 541.75 415.78010977804973
Updated SVG: /disk1/www/rails/humanrnamap/public/result/b42a4fc6-8789-40cc-b5dc-fd84c699d3aa/final_image/RUNX1_fold_final_1.svg
Combined SVG saved as /disk1/www/rails/humanrnamap/public/result/b42a4fc6-8789-40cc-b5dc-fd84c699d3aa/final_image/RUNX1_fold_final_1.svg
