Rosetta3.10 on macOS segmentation fault 11

[Anonymous]

 

I have tried several times to install Rosetta3.10 for macOS version 10.14.2. My system info is:

Model Name: MacBook Pro

  Model Identifier: MacBookPro15,2

  Processor Name: Intel Core i7

  Processor Speed: 2,7 GHz

  Number of Processors: 1

  Total Number of Cores: 4

  L2 Cache (per Core): 256 KB

  L3 Cache: 8 MB

  Memory: 8 GB

 I have used both Rosetta 3.10 source + binaries for Mac or Rosetta 3.10 source. and have the latest clang compiled using Xcode:

Apple LLVM version 10.0.0 (clang-1000.11.45.5)

Target: x86_64-apple-darwin18.2.0

Thread model: posix

InstalledDir: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin

I run a simple command:

> ./scon.py -j 4 mode=release bin

I don’t see any problem during installation.

However, when I perform first antibody prediction step like grafting using following command:

> antibody.macosclangrelease -fasta antibody_human_test.fast

I get following output and program ends with segmentation fault 11:

protocols.antibody.grafting: Setting antibody grafting database path from command line-options to: /Users/mustafa/Documents/Install/rosetta_src_2018.33.60351_bundle//tools/antibody

protocols.antibody.grafting: Setting output prefix from command line-options to: grafting/

protocols.antibody.grafting: Setting path to NCBI-Blast+ executable from command line-options to: blastp

basic.execute: Running blast+ for frh… blastp -db /Users/mustafa/Documents/Install/rosetta_src_2018.33.60351_bundle//tools/antibody/blast_database/database.FRH -query grafting/frh.fasta -out grafting/frh.align -word_size 2 -outfmt 7 -max_target_seqs 1024 -evalue 0.00001 -matrix BLOSUM62

basic.execute: Running blast+ for h1… blastp -db /Users/mustafa/Documents/Install/rosetta_src_2018.33.60351_bundle//tools/antibody/blast_database/database.H1.10 -query grafting/h1.fasta -out grafting/h1.align -word_size 2 -outfmt 7 -max_target_seqs 1024 -evalue 2000 -matrix PAM30

basic.execute: Running blast+ for h2… blastp -db /Users/mustafa/Documents/Install/rosetta_src_2018.33.60351_bundle//tools/antibody/blast_database/database.H2.16 -query grafting/h2.fasta -out grafting/h2.align -word_size 2 -outfmt 7 -max_target_seqs 1024 -evalue 2000 -matrix PAM30

basic.execute: Running blast+ for h3… blastp -db /Users/mustafa/Documents/Install/rosetta_src_2018.33.60351_bundle//tools/antibody/blast_database/database.H3.13 -query grafting/h3.fasta -out grafting/h3.align -word_size 2 -outfmt 7 -max_target_seqs 1024 -evalue 2000 -matrix PAM30

basic.execute: Running blast+ for frl… blastp -db /Users/mustafa/Documents/Install/rosetta_src_2018.33.60351_bundle//tools/antibody/blast_database/database.FRL -query grafting/frl.fasta -out grafting/frl.align -word_size 2 -outfmt 7 -max_target_seqs 1024 -evalue 0.00001 -matrix BLOSUM62

basic.execute: Running blast+ for l1… blastp -db /Users/mustafa/Documents/Install/rosetta_src_2018.33.60351_bundle//tools/antibody/blast_database/database.L1.12 -query grafting/l1.fasta -out grafting/l1.align -word_size 2 -outfmt 7 -max_target_seqs 1024 -evalue 2000 -matrix PAM30

basic.execute: Running blast+ for l2… blastp -db /Users/mustafa/Documents/Install/rosetta_src_2018.33.60351_bundle//tools/antibody/blast_database/database.L2.7 -query grafting/l2.fasta -out grafting/l2.align -word_size 2 -outfmt 7 -max_target_seqs 1024 -evalue 2000 -matrix PAM30

basic.execute: Running blast+ for l3… blastp -db /Users/mustafa/Documents/Install/rosetta_src_2018.33.60351_bundle//tools/antibody/blast_database/database.L3.9 -query grafting/l3.fasta -out grafting/l3.align -word_size 2 -outfmt 7 -max_target_seqs 1024 -evalue 2000 -matrix PAM30

basic.execute: Running blast+ for orientation… blastp -db /Users/mustafa/Documents/Install/rosetta_src_2018.33.60351_bundle//tools/antibody/blast_database/database.light_heavy -query grafting/orientation.fasta -out grafting/orientation.align -word_size 2 -outfmt 7 -max_target_seqs 1024 -evalue 0.00001 -matrix BLOSUM62

Segmentation fault: 11

 

Is there anything I am doing wrong or something is missing that cause this error? Looking for help!

with kind regards

Mustafa

[Anonymous]

Segmentation faults are difficult to debug, in part because of the limited amount of information that is availible. (But you can take scant solace in the fact that segfaults are totally the fault of Rosetta developers – at the very least we should be providing you an error message, rather than a segfault.)

The first step in debugging a segfault is to double-check all your inputs. Segfaults are normally caused by conditions which the programmer didn’t anticipate. If there’s something “off” about your inputs – if there’s formatting issues, or you’re not matching the way the program expects things to be formatted – that can often be the cause of the segfault.

The next step, if there’s nothing obviously wrong with the inputs, is to compile the debug mode of Rosetta (add “mode=debug” to the scons command line, rather than “mode=release”, and use the “antibody.macosclangdebug” executable rather than “antibody.macosclangrelease” one). This has extra checking which slows the run down, but can give you better diagnostics. Often this can give a better indication of what went wrong.

If that doesn’t help, you may need to run things under a debugger to get a backtrace of where the segfault is happening.

Feel free to post what additional information you have here. If you can bundle up enough of your inputs such that we can try the run on our own machines, that can sometimes help. It’s not always easy to see what might be going on without a better understanding of Rosetta internals. (Though unfortunately we can be slow about it, which is why the self-investigation above can sometimes give quicker results.)

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