-Precision-7920-Tower:make_fragments.pl -verbose myfasta.fasta no id specified. parsing filename instead. cannot parse id from filename so using 't001_' ID: t001 CHAIN: _ File for psipred not found! Generating from scratch instead. picking fragments with options: DEBUG: 1 add_pdbs_to_vall: chain: _ cleanup: 1 csbuild_profile: 0 exclude_homologs_by_pdb_date: 0 f: myfasta.fasta fastafile: t001_.fasta frags: 1 homs: 1 id: t001 n_candidates: 1000 n_frags: 200 old_name_format: 0 porter: 0 porterfile: psipred: 1 psipredfile: rundir: /rosetta/rosetta-abintio-prediction runid: t001_ sam: 0 samfile: torsion_bin: 0 verbose: 1 -------------------------------------------------------------------------------- FILENAME: t001_.fasta Sequence: MAVGEIQISALPQAALPIDLSDIFHLKQGIEDKRCTLEQLLAPHSSLKNNPHGVTKTQIGLDNVINALQLVAANNLSDIVNVAEARANLQIMSSEEVNSLIQQHINDKSNPHNTTKAQVGLSNVQNWTTSNLYNEDADKYATARAVNNLYKAVQASYPVGTIHLSMNPANPSTYLICGGTWELVSKGRALVGYDSDSRPVGSTFGSQTTALTVNNIPAHTHSVYVTGGGHTHGATASISAFDYGTKGTTTFDYGTKTVSTYDYGNRTTSAAGLTQTTFINRGYADGGWRGLSVEGASYDPRATLTTANNHTHSVAIGAHNHTVGIGAHSHTVAIGSHNHSATVTVTGAGEHSHSGTTGPTGSGQAFSVEQPSFVLYVWQRTA Running sparks for phi, psi, and solvent accessibility predictions t001_.fasta.pssm exists At line 239 of file phipsi_ss0.f (unit = 77, file = '/media/Deepak/NPRP10/softwares/rosetta/rosetta_src_2019.31.60840_bundle/tools/fragment_tools/sparks-x/SPINE-X/weights/ss') Fortran runtime error: End of file Aborting: Can't run first SS0 predictor Error in file: t001_.fasta.phipsi Traceback (most recent call last): File "/media/Deepak/NPRP10/softwares/rosetta/rosetta_src_2019.31.60840_bundle/tools/fragment_tools/sparks-x/bin/buildinp.py", line 255, in run1 buildinp(fphipsiss, fmat, finp) File "/media/Deepak/NPRP10/softwares/rosetta/rosetta_src_2019.31.60840_bundle/tools/fragment_tools/sparks-x/bin/buildinp.py", line 238, in buildinp seq1, ssec1, phipsi1, Fphipsi = rdphipsi(fphipsiss) File "/media/Deepak/NPRP10/softwares/rosetta/rosetta_src_2019.31.60840_bundle/tools/fragment_tools/sparks-x/bin/buildinp.py", line 9, in rdphipsi for line in file(fn): IOError: [Errno 2] No such file or directory: 't001_.fasta.phipsi' sparks path length > 100 characters, which may cause internal errors. Try moving to a shorter path prefix. sparks failed!
the above error comes when running "make_fragments.pl". Can you please let me know how this can be solved?
as the error says:
the poblem is that sparksX is hardcoded to look at only the first 100 or so characters of a file path.
so if you can, make a smylink to the tools folder much higher up in directory space.
ie something like:
or just move the tools folder 'higher up' and it will work.
make sure you run from /media/Deepka/rosetta_tools if you use that method though.it has to 'think' it's a shorter path.
thanks! I did this:
ln -s /media/Deepak/NPRP10/softwares/rosetta/rosetta_src_2019.31.60840_bundle/tools/ /media/Deepak/NPRP10/rosetta_tools
It still takes the old path for some reason. Can you please let me know what am I doing wrong? thanks!
Hrm that's odd... unfortunately it seems like you will have to remove the symlink and mv the folder there completely. sorry : (
thanks! do I need to move only the "spaks-x" folder up the path or all folders; database (657 GB), psipred, csblast, blast. I mean all the folders generated by "install_dependencies.pl"? thanks for your suggestions!
Ok, it works now, I just played around with sym linking appropriate folders and finally it works. thanks!
I am currently facing the exact problem you did. Would you be able to share exactly how you set up your symlinks? I tried the initial one suggested by danpf and it also failed for me as well. It would be extremley helpful and appreciated. Thanks!