Dear fellows,
I would like to generate fragments for protein sequence structure prediction ab initio locally, on my laptop, without involving any server, such as Robetta. I carry out it with a help of make_fragments.pl script. And I met with several problems with make_fragment.pl dependencies. I want to solve these problems. Could you advise me, if you can, how to solve them, please?
My first problem consists in follows:
Firstly, during run such bash-terminal command "~/rosetta_bin_linux_2019.22.60749_bundle/tools/fragment_tools/make_fragments.pl name.fasta >& make_fragments.local" install_dependencies.pl script couldn't install all necessary dependencies, or install it incorrectly. For example, it can not install correctly psipred:
"Can't exec "make": No such file or directory at ~/rosetta_bin_linux_2019.22.60749_bundle/tools/fragment_tools/install_dependencies.pl line 138.
Can't exec "make": No such file or directory at ~/rosetta_bin_linux_2019.22.60749_bundle/tools/fragment_tools/install_dependencies.pl line 144.
ERROR! psipred installation failed!"
Should I (re)install these dependencies on ~/fragment_tools directory on my own through bash-terminal?
Other problem 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?
For better clarity I attach make_fragments_local.pdf (log-file, where all problems and features are displayed) and a screenshot of ~/fragment_tools directory.
I will be sincerely grateful for your response and help and I am looking forward to it.
Best regards,
Corvin.
| Attachment | Size |
|---|---|
 A log file of make_fragments.pl run | 49.85 KB |
 make_fragments.pl directory | 46.73 KB |
it looks like you're missing 'make'
it looks like you're using linux.
so run the command:
Dear danpf,
I am really thankful for your response and sorry for my slow reply.
I fixed that problem with make, but I met with such problems:
"Resolving www.ncbi.nlm.nih.gov (www.ncbi.nlm.nih.gov)... 130.14.29.110, 2607:f220:41e:4290::110
Connecting to www.ncbi.nlm.nih.gov (www.ncbi.nlm.nih.gov)|130.14.29.110|: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)|130.14.29.110|: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.
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."
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?
Regards,
Corvin.