I was following the antibody modeling tutorial on Nature Protocols paper and I wasn’t successful. I followed the tutorial in the Supplementary Material, and got the following error right after performing blastp query. Blast+ was performed well and produced output alright.
libc++abi.dylib: terminating with uncaught exception of type std::out_of_range: basic_string
 37692 abort $ROSETTA_BIN/antibody.macosclangrelease -fasta antibody.fasta 95 90
Mac OS version: 10.12.3
Rosetta Version: 3.7 (2016.34)
Blast+ version: 2.6.0
LLVM version: 8.0.0 (clang-800.0.42.1)
And, here's the files that I used including log files:
The Antibody team says:
"[You] need the latest weekly [release], as blast changed their output header format"
Thanks, I updated Rosetta to 2016.46 and still have the same error message. Or is there a newer build that I'm supposed to use? I'm a commercial user and 2016.46 is the newest build that I'm seeing.
hmm, that does look like the latest release. We had a hiccup in the release system but it must not have restarted smoothly. 3.8 is in the works and will be out before too long. I'll ping the sysadmin.
Can you let me know what is the latest Rosetta version available?
Are you one of the author of the manuscript (http://www.nature.com/nprot/journal/v12/n2/abs/nprot.2016.180.html)? I'd like to know what version of Rosetta and blastp was used, but unable to find such information in the manuscript.
The problem that's been holding up releases has been resolved. It's looking likely we will process one this Friday. (Well, we'll definitely process one, it has a good chance of passing the automated tests).
A new weekly is up, give it a try.
Thanks, I updated to vesion 2017.8 and the protocol started working.