Dears,
After installing Rosetta 3.9 in a cluster and trying to run the simple command:
helix_preassemble_setup.py -fasta NFKB_1OOA_RNAStructure_2D.fasta -secstruct NFKB_1OOA_RNAStructure.secstruct
we get the following error:
(((((....((((....))))...)))))
Traceback (most recent call last):
File "/mnt/beegfs/software/rosetta/3.9/tools/rna_tools/bin/rna_denovo_setup.py", line 64, in <module>
obligate_pair = zip( obligate_pair_res_chain[0],obligate_pair_res_chain[1] )
IndexError: list index out of range
Traceback (most recent call last):
File "/mnt/beegfs/software/rosetta/3.9/tools/rna_tools/bin/helix_preassemble_setup.py", line 112, in <module>
subprocess.check_call([str(elem) for elem in cmdline.split()])
File "/usr/lib64/python2.7/subprocess.py", line 542, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['rna_denovo_setup.py', '-fixed_stems', '-rna::corrected_geo', '-score:rna_torsion_potential', 'RNA11_based_new', '-chemical::enlarge_H_lj', '-score:weights', 'stepwise/rna/rna_helix', '-nstruct', '100', '-cycles', '1000', '-fasta', 'NFKB_1OOA_RNAStructure_2D.fasta', '-secstruct_file', 'NFKB_1OOA_RNAStructure.secstruct', '-offset', '0', '-working_res', '1-5', '25-29', '-out_script', 'helix0.RUN', '-tag', 'helix0', '-silent', 'helix0.out', '-input_silent_res', '1-5', '25-29']' returned non-zero exit status 1
Is there anything wrong with the installation? The input files are OK because we used them two years ago.
Apparently, the problem is that the script rna_denovo_setup.py does not receive the parameter input_silent_res.
I would really appretiate any help on this issue.
Thanks a lot and best regards