mfold command line error

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LegolasdeAda
Posts: 1
Joined: Thu Mar 30, 2023 11:22 am

mfold command line error

Post by LegolasdeAda »

Dear professor,

I am using the command line version mfold to predict RNA structure.

I have run one test sequence on the mfold website and get 38 predicted structures using default parameters. However, when I run this sequence on the command line version, I get the error information:

"mfold version 3.6
REUSE= NO
test.fa.pnt created.
Sequence length is 2237
Folding at 37 degrees using version 3.0 dat files.
Save file created using nafold.
Save file is empty. No foldings.
Job Aborted"

My command line is "mfold SEQ=test.fa". I found the same error on phpbb viewtopic.php?p=42&hilit=unafold+download#p42 , you suggested to use nafold to find error. I followed this instruction and error appeared at the procedure "Enter asymmetric interior loop of size 3 energy file name", it couldn't go on after I input filename. When I look back at the log file of mfold, there's the same error.

I downloaded the mfold software from http://www.unafold.org/mfold/software/d ... -mfold.php. The annex are fasta file and log file.

By the way, could you give me a link to download unafold? I couldn't find download link at the download page. http://www.unafold.org/Dinamelt/softwar ... nafold.php

I am looking forward to receive letter from you. Thank you in advance.

My log file is as followed:
mfold version 3.6 by Michael Zuker
Enter run type
0 Regular run (default)
1 Save run
2 Continuation run

Enter save file name (default fold.sav)

Input sequence file name (q to quit)

Available sequence(s) in test.fa-local.seq

1) ENST00000618686.1

Choose sequence by number [default is 1], or enter F for a new file:

Length of retrieved sequence = 2237



ENST00000618686.1 2237 nucleotides

Enter start of fragment (default 1)
Enter end of fragment (default 2237)
Enter asymmetric interior loop of size 3 energy file name
(default asint1x2.dat)
Enter asymmetric interior loop of size 3 energy file name
(default asint1x2.dat)
Enter asymmetric interior loop of size 3 energy file name
(default asint1x2.dat)
Enter asymmetric interior loop of size 3 energy file name
(default asint1x2.dat)
Enter asymmetric interior loop of size 3 energy file name
(default asint1x2.dat)
Enter asymmetric interior loop of size 3 energy file name
(default asint1x2.dat)
Enter asymmetric interior loop of size 3 energy file name
(default asint1x2.dat)
Enter asymmetric interior loop of size 3 energy file name
(default asint1x2.dat)
Enter asymmetric interior loop of size 3 energy file name
(default asint1x2.dat)
Enter asymmetric interior loop of size 3 energy file name
(default asint1x2.dat)
Enter asymmetric interior loop of size 3 energy file name
(default asint1x2.dat)
Enter asymmetric interior loop of size 3 energy file name
(default asint1x2.dat)
Enter asymmetric interior loop of size 3 energy file name
(default asint1x2.dat)
Enter asymmetric interior loop of size 3 energy file name
(default asint1x2.dat)
Enter asymmetric interior loop of size 3 energy file name
(default asint1x2.dat)
Enter asymmetric interior loop of size 3 energy file name
(default asint1x2.dat)
Enter asymmetric interior loop of size 3 energy file name
(default asint1x2.dat)
Enter asymmetric interior loop of size 3 energy file name
(default asint1x2.dat)
Enter asymmetric interior loop of size 3 energy file name
(default asint1x2.dat)
Enter asymmetric interior loop of size 3 energy file name
(default asint1x2.dat)
Enter asymmetric interior loop of size 3 energy file name
(default asint1x2.dat)
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