Initializing nucleic acids...done.
Applying constraints...done.
Folding single strand...
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 98% [==================================================] |                     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/7186a3e7-e631-47a3-bc8a-5222b3627a74/final_image/POLRMT_fold_1.svg

first - Elapsed time since the previous call: 0.00 seconds
first - Current memory usage: 156.66 MB
setup complete - Elapsed time since the previous call: 0.00 seconds
setup complete - Current memory usage: 156.66 MB
config complete - Elapsed time since the previous call: 0.00 seconds
config complete - Current memory usage: 156.66 MB
read annotations - Elapsed time since the previous call: 0.09 seconds
read annotations - Current memory usage: 170.28 MB
Based on canonical annotations, the following gene is in your area of interest: POLRMT(-)
write fasta - Elapsed time since the previous call: 0.82 seconds
write fasta - Current memory usage: 170.28 MB
Length of region: 96 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: 173.51 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/Fold "/disk1/www/rails/humanrnamap/public/result/7186a3e7-e631-47a3-bc8a-5222b3627a74/fasta/POLRMT.fasta" "/disk1/www/rails/humanrnamap/public/result/7186a3e7-e631-47a3-bc8a-5222b3627a74/ct/POLRMT.ct" --SHAPE "POLRMT.dat"

fold - Elapsed time since the previous call: 0.11 seconds
fold - Current memory usage: 173.51 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/efn2 "/disk1/www/rails/humanrnamap/public/result/7186a3e7-e631-47a3-bc8a-5222b3627a74/ct/POLRMT.ct" "/disk1/www/rails/humanrnamap/public/result/7186a3e7-e631-47a3-bc8a-5222b3627a74/fold_FE/POLRMT.txt" -sh "POLRMT.dat"

efn2 - Elapsed time since the previous call: 0.43 seconds
efn2 - Current memory usage: 173.51 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/7186a3e7-e631-47a3-bc8a-5222b3627a74/ct/POLRMT.ct" 1 "/disk1/www/rails/humanrnamap/public/result/7186a3e7-e631-47a3-bc8a-5222b3627a74/fold_dbn/POLRMT_temp1.dbn"

ct2dot - Elapsed time since the previous call: 0.01 seconds
ct2dot - Current memory usage: 173.51 MB
['java', '-cp', '/disk1/www/rails/humanrnamap/cli/bin/VARNAv3-93.jar', 'fr.orsay.lri.varna.applications.VARNAcmd', '-sequenceDBN', 'AGGCCUCUCACUAUCUCGUACGCCAGGUCUUCAAGAGUCUACAGGAGAUGUUCUCGGGGACCCGGGCCAUCCAGCACUGGCUGACCGAGAGUGCCC', '-structureDBN', '.((((((((............(((.(((((((.(((((((.....))))..))).)))))))..)))....((((....))))...))))).))).', '-o', '/disk1/www/rails/humanrnamap/public/result/7186a3e7-e631-47a3-bc8a-5222b3627a74/final_image/POLRMT_fold_1.svg', '-title', 'POLRMT, -36.1 ± 1.1\n kcal/mol, AUC: 0.736', '-titleSize', '12', '-basesStyle1', 'fill=#ffffff', '-applyBasesStyle1on', '2,3,6,8,12,14,16,18,19,22,26,27,28,30,31,35,37,38,40,44,45,47,49,50,51,52,54,56,57,58,59,64,65,66,70,74,78,79,80,82,83,87,89,91,92,93', '-basesStyle2', 'fill=#00ffff', '-applyBasesStyle2on', '68,5,69,39,7,71,46,86,23,94,62,95', '-basesStyle3', 'fill=#ffff00', '-applyBasesStyle3on', '1,67,4,72,9,73,75,13,15,81,21,85,24,25,88,90,32,33,34,96,36,48,53,55,60,61,63', '-basesStyle4', 'fill=#ff0000', '-applyBasesStyle4on', '41,10,11,42,43,76,77,17,20,84,29']
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Text: 'POLRMT, -36.1 ± 1.1
 kcal/mol, AUC: 0.736', X: 149.47971551913014, Y: 621.4841261010279, Width: 142.5, Height: 23
Calculated bounding box: (4.75, 5.0, 436.7094310382603, 621.4841261010279)
Updated viewBox: -0.25 0.0 441.9594310382603 626.4841261010279
Updated SVG: /disk1/www/rails/humanrnamap/public/result/7186a3e7-e631-47a3-bc8a-5222b3627a74/final_image/POLRMT_fold_final_1.svg
Combined SVG saved as /disk1/www/rails/humanrnamap/public/result/7186a3e7-e631-47a3-bc8a-5222b3627a74/final_image/POLRMT_fold_final_1.svg
