Initializing nucleic acids...done.
Applying constraints...done.
Folding single strand...
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 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/0d5098cd-ed99-458e-8e0a-a4be6017c12b/final_image/PLEKHM2_fold_1.svg

first - Elapsed time since the previous call: 0.00 seconds
first - Current memory usage: 158.60 MB
setup complete - Elapsed time since the previous call: 0.00 seconds
setup complete - Current memory usage: 158.60 MB
config complete - Elapsed time since the previous call: 0.00 seconds
config complete - Current memory usage: 158.60 MB
read annotations - Elapsed time since the previous call: 0.09 seconds
read annotations - Current memory usage: 172.21 MB
Based on canonical annotations, the following gene is in your area of interest: PLEKHM2(+)
write fasta - Elapsed time since the previous call: 1.02 seconds
write fasta - Current memory usage: 172.21 MB
Length of region: 95 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: 0.18 seconds
write dat - Current memory usage: 175.55 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/Fold "/disk1/www/rails/humanrnamap/public/result/0d5098cd-ed99-458e-8e0a-a4be6017c12b/fasta/PLEKHM2.fasta" "/disk1/www/rails/humanrnamap/public/result/0d5098cd-ed99-458e-8e0a-a4be6017c12b/ct/PLEKHM2.ct" --SHAPE "PLEKHM2.dat"

fold - Elapsed time since the previous call: 0.13 seconds
fold - Current memory usage: 175.55 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/efn2 "/disk1/www/rails/humanrnamap/public/result/0d5098cd-ed99-458e-8e0a-a4be6017c12b/ct/PLEKHM2.ct" "/disk1/www/rails/humanrnamap/public/result/0d5098cd-ed99-458e-8e0a-a4be6017c12b/fold_FE/PLEKHM2.txt" -sh "PLEKHM2.dat"

efn2 - Elapsed time since the previous call: 0.41 seconds
efn2 - Current memory usage: 175.55 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/0d5098cd-ed99-458e-8e0a-a4be6017c12b/ct/PLEKHM2.ct" 1 "/disk1/www/rails/humanrnamap/public/result/0d5098cd-ed99-458e-8e0a-a4be6017c12b/fold_dbn/PLEKHM2_temp1.dbn"

ct2dot - Elapsed time since the previous call: 0.02 seconds
ct2dot - Current memory usage: 175.55 MB
['java', '-cp', '/disk1/www/rails/humanrnamap/cli/bin/VARNAv3-93.jar', 'fr.orsay.lri.varna.applications.VARNAcmd', '-sequenceDBN', 'CCGCUUUACCGUCGAGAGUCCAAGCACUGUUACAUCAGGUGGCGGCCACCAUGACCCUGCAGGGCUUGGCCAACCGCUGCAUGUUCCUAGUAGCC', '-structureDBN', '...((((.......)))).((((((.((((....((((((((...))))).)))....)))).))))))......(((((.........))))).', '-o', '/disk1/www/rails/humanrnamap/public/result/0d5098cd-ed99-458e-8e0a-a4be6017c12b/final_image/PLEKHM2_fold_1.svg', '-title', 'PLEKHM2, -29.7 ± 0.9\n kcal/mol, AUC: 0.537', '-titleSize', '12', '-basesStyle1', 'fill=#ffffff', '-applyBasesStyle1on', '3,5,6,7,11,12,14,16,18,19,24,28,29,30,31,35,38,39,40,41,42,44,45,52,53,58,59,62,63,64,66,67,68,69,76,78,79,82,83,84,85,88,90,91,93', '-basesStyle2', 'fill=#00ffff', '-applyBasesStyle2on', '65,74,43,75,77,80,20,21,57,26,92,94,95', '-basesStyle3', 'fill=#ffff00', '-applyBasesStyle3on', '70,71,8,15,17,22,87,89,34,36,46,47,48,50,51,55,56', '-basesStyle4', 'fill=#ff0000', '-applyBasesStyle4on', '1,2,4,72,9,10,73,13,81,86,23,25,27,32,33,37,49,54,60,61']
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Text: 'C', X: 157.25, Y: 355.62202503881304, Width: 10.5, Height: 8
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Text: 'U', X: 157.25, Y: 375.62202503881304, Width: 10.5, Height: 8
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Text: 'U', X: 157.25, Y: 395.62202503881304, Width: 10.5, Height: 8
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Text: 'G', X: 157.25, Y: 435.62202503881304, Width: 10.5, Height: 8
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Text: 'C', X: 174.75, Y: 435.62202503881304, Width: 10.5, Height: 8
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Text: 'A', X: 209.75, Y: 435.62202503881304, Width: 10.5, Height: 8
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Text: 'C', X: 279.75, Y: 355.62202503881304, Width: 10.5, Height: 8
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Text: 'C', X: 329.75, Y: 435.6220250388131, Width: 10.5, Height: 8
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Text: '40', X: 82.06294610098422, Y: 88.10842604459128, Width: 18.0, Height: 8
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Text: '60', X: 173.5, Y: 263.2709521786476, Width: 18.0, Height: 8
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Text: '95', X: 326.0, Y: 455.6220250388131, Width: 18.0, Height: 8
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Text: 'PLEKHM2, -29.7 ± 0.9
 kcal/mol, AUC: 0.537', X: 98.25, Y: 468.4220250388131, Width: 148.5, Height: 23
Calculated bounding box: (4.75, 5.0, 345.7798608709955, 468.4220250388131)
Updated viewBox: -0.25 0.0 351.0298608709955 473.4220250388131
Updated SVG: /disk1/www/rails/humanrnamap/public/result/0d5098cd-ed99-458e-8e0a-a4be6017c12b/final_image/PLEKHM2_fold_final_1.svg
Combined SVG saved as /disk1/www/rails/humanrnamap/public/result/0d5098cd-ed99-458e-8e0a-a4be6017c12b/final_image/PLEKHM2_fold_final_1.svg
