I am studying to generate fragments for structure prediction ab initio locally, on my laptop (OS - Linux OpenSUSE), with a help of appropriate script "make_fragments.pl". I met with several problems during its running.
Firstly, "make_fragments.pl" can not connect to dependencies links. When I run such command, as "~/rosetta_bin_linux_2019.22.60749_bundle/tools/fragment_tools/make_fragments.pl name.fasta >& make_fragments.local", it gives me such error:
"Resolving www.ncbi.nlm.nih.gov (www.ncbi.nlm.nih.gov)... 184.108.40.206, 2607:f220:41e:4290::110
Connecting to www.ncbi.nlm.nih.gov (www.ncbi.nlm.nih.gov)|220.127.116.11|:80... connected.
HTTP request sent, awaiting response... 301 Moved Permanently
Location: https://www.ncbi.nlm.nih.gov/blast/docs/update_blastdb.pl [following] --2019-08-26 12:52:03-- https://www.ncbi.nlm.nih.gov/blast/docs/update_blastdb.pl
Connecting to www.ncbi.nlm.nih.gov (www.ncbi.nlm.nih.gov)|18.104.22.168|:443... connected.
HTTP request sent, awaiting response... 404 Not Found
2019-08-26 12:52:03 ERROR 404: Not Found.
ERROR! wget http://www.ncbi.nlm.nih.gov/blast/docs/update_blastdb.pl failed."
How I understood, there are problems about foregoing sites. It is looked like, that these sites are expired, or don't exist more. How I can fix these problems with these sites? Creating or downloading API for such dependencies is a good option for 'make_fragments.pl'? Or I should download appropriate databases at "~/rosetta_bin_linux_2019.22.60749_bundle/main/database" or even create a separated database directory in Rosetta?
Secondly, a next part of my problem with "make_fragments.pl" consists in next:
"WARNING! ~/rosetta_bin_linux_2019.22.60749_bundle/tools/fragment_tools/../../main/source/bin/fragment_picker.boost_thread.linuxgccrelease does not exist. Trying default.
ERROR! ~/rosetta_bin_linux_2019.22.60749_bundle/tools/fragment_tools/../../main/source/bin/fragment_picker.default.linuxgccrelease does not exist."
I downloaded such version of Rosetta with binaries, where all default.scripts are replaced by static.scripts. It means, that I should replace "fragment_picker.default.linuxgccrelease" to "fragment_picker.static.linuxgccrelease", in "make_fragments.pl" script, shouldn't I?
I attach some files to this topic.
I will be sincerely grateful for your response and help and I am looking forward to it.