mfold_quik gives different results from its web counterpart

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Joined: 04/04/2018

I have installed the mfold version_3.6 in Unix-based systems (Ubuntu and MacOSx Sierra) . I ran the mfold_quik in both systems using a fasta file containing 32 ITS2 sequences looking for the minimum free energy for each sequence (controlling the flag MAX=1) and for the ct file representing the optimized RNA structures. The output files obtained either by running the program in Ubuntu or MacOSx were the same. However ct files only represent 80 bp out of the sequences average lenght (250 bp) of my ITS2 database.
I contrasted these suspicious results by running the same analysis on the Quikfold application of the mfold server. This time the ct files represented the real ITS2 sequence lenghts and therefore free energy values were totally different from the obtained with mfold software

Anyone could help me to solve this problem? I am missing any flag during the execution of mfold_quik? or problems with mfold installation

Thanks in advance