ernwin issue with non-coding RNA of 570nts

[gunjangunjan22]

i was running ernwin for long non-coding RNA, but it got stuck at the same step every time. I am attaching here the complete transcript of command.
(py2) [gunjan@uslims ernwin]$ ernwin.py JEV_3TR/JEV_3TR_ernwin_input.fasta --source-cg-dir /home/gunjan/ernwin/RESOURCES/CGS --source-pdb-dir /home/gunjan/ernwin/RESOURCES/PDB --reconstruct-every-n 100 -o JEV_3TR
/home/gunjan/miniconda3/envs/py2/lib/python2.7/site-packages/Bio/KDTree/init.py:25: BiopythonDeprecationWarning: Bio.KDTree has been deprecated, and we intend to remove it in a future release of Biopython. Please use Bio.PDB.kdtrees instead, which is functionally very similar.
BiopythonDeprecationWarning)
WARNING:fess.builder.builder.load_sampled_elements[46]: No (useable) 3D structure found in the input file. Starting to build an initial model.
WARNING:fess.builder.stat_container._possible_stats_inner[246]: Only 9 5prime-stats found for key 10
WARNING:fess.builder.stat_container._possible_stats_inner[246]: Only 16 angle-stats found for interior loop with 2 and 7 unpaired nucleotides
WARNING:fess.builder.stat_container._possible_stats_inner[246]: Only 0 angle-stats found for interior loop with 12 and 0 unpaired nucleotides
ERROR:fess.builder.stat_container._possible_stats_inner[281]: Trying key interior loop with 11 and 0 unpaired nucleotides instead of interior loop with 12 and 0 unpaired nucleotides for angle-stat
WARNING:fess.builder.stat_container._possible_stats_inner[246]: Only 1 angle-stats found for interior loop with 11 and 0 unpaired nucleotides
WARNING:fess.builder.stat_container._possible_stats_inner[246]: Only 47 angle-stats found for interior loop with 4 and 0 unpaired nucleotides

[Bernhard10]

It could be that ernwin has a hard time building an initial model of the RNA, because its hard to find a clash-free 3D representation.

You could run it with the --verbose or --debug LOGGER_NAME option. In this case you will see an output informing you what ernwin is trying to do to achive building of the initial structure.

You could also try out (experimantal) options for quicker building (see ernwin --help), such as --relaxation-builder
or you could specify a relexed constraint energy for the multiloops to make it easier to find an acceptable structure.