Dear Friends,
I am trying to perform ab initio structure prediction by following the tutorial:
In this tutorial, there is a "fragment picking" tutorial:: https://www.rosettacommons.org/demos/latest/public/fragment_picking/README
I am following this tutorila to make fragments for de novo structure prediction:
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Put this vall in the flags:
$ <path-to-Rosetta>/main/database/sampling/filtered.vall.dat.2006-05-05.gz
Update the flags with your correct database location
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Run the picker like this:
I installed all dependencies using "install_dependencies.pl", and now trying to make fragmensts using "make_fragments.pl". when running the script it gives me this error:
softwares/rosetta/rosetta_src_2019.31.60840_bundle/tools/fragment_tools/make_fragments.pl -verbose c600m2-tail-fiber-sequence.fasta
Use of uninitialized value $ENV{"FRAGMENT_PICKER_NUM_CPUS"} in int at softwares/rosetta/rosetta_src_2019.31.60840_bundle/tools/fragment_tools/make_fragments.pl line 35.
Use of uninitialized value $ENV{"BLAST_NUM_CPUS"} in int at softwares/rosetta/rosetta_src_2019.31.60840_bundle/tools/fragment_tools/make_fragments.pl line 41.
Use of uninitialized value $ENV{"PSIPRED_USE_weights_dat4"} in int at softwares/rosetta/rosetta_src_2019.31.60840_bundle/tools/fragment_tools/make_fragments.pl line 52.
Use of uninitialized value $ENV{"SLAVE_LAUNCHER_MAX_JOBS"} in int at softwares/rosetta/rosetta_src_2019.31.60840_bundle/tools/fragment_tools/make_fragments.pl line 71.
Use of uninitialized value $ENV{"SLAVE_MAX_WAIT"} in int at softwares/rosetta/rosetta_src_2019.31.60840_bundle/tools/fragment_tools/make_fragments.pl line 73.
Use of uninitialized value $ENV{"SLAVE_MAX_ATTEMPTS"} in int at softwares/rosetta/rosetta_src_2019.31.60840_bundle/tools/fragment_tools/make_fragments.pl line 74.
Use of uninitialized value $ENV{"PDB2VALL_IGNORE_ERRORS"} in int at softwares/rosetta/rosetta_src_2019.31.60840_bundle/tools/fragment_tools/make_fragments.pl line 80.
Only alphanumeric characters, . and _ are allowed in the filename.
Can ypou please let me know what could be the issue here? and how this can be solved? thanks.
This is just some old weird code...
change the name of your fasta file to something stupid and simple
like:
myfasta.fasta
and you shouldn't see this error!
Thanks it worked and the program ran, but then I face this issue of "sparks failed": Can you please let me know how this can be solved? thanks!
I figured out the answer. thanks!