Illegal instruction error

[drs357]

Hello I tried using Racon 1.3.2 and I received the error message illegal instruction. I used bbmap to generate the sam file with merged illumina reads. If there is more information that would be helpful to provide, please let me know.

Thanks, Dave

[rvaser]

Which g++ version do you have?

[drs357]

(assembly) [drs4001@hippocampus build]$ g++ --version
g++ (GCC) 4.4.7 20120313 (Red Hat 4.4.7-23)
Copyright (C) 2010 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

[rvaser]

You will need to update that too. I'll emulate your distribution in VirtualBox, try to make racon run and get back to you.

[ptrebert]

Just to confirm this error - same "Illegal Instruction" here with Racon v1.3.2 (installed from bioconda). If your suggestion is still to use the current master and compile from source, that is no problem, but I can try not sooner than, say, tomorrow afternoon or so. For the record, OS is Debian 9.4, environment is an isolated Conda env

[rvaser]

@ptrebert can you check if your CPU supports sse4.1+?

[ptrebert]

Yes, it does - it's a Intel Xeon E7-8857 v2

[rvaser]

@drs357, I have installed CentOS6 in VirtualBox, installed cmake3.6 as described above, updated gcc compiler to 7.2 (minimum required is 4.8) and was able to build and run racon/racon_test. I would advise you to update your compiler with either devtools-2 or locally without sudo (download the source and compile, when running cmake add flags -DCMAKE_CXX_COMPILER=<path_to_new_g++> and -DCMAKE_C_COMPILER=<path_to_new_gcc>).

[drs357]

Thank you, will give that a try

[ptrebert]

@rvaser For the record, I just successfully built racon inside a Conda environment following your instructions w/o any issues (how nice!). The Conda env is minimal:

name: racon
channels:
  - conda-forge
dependencies:
  - Python=3.6.*
  - cmake=3.14.4
  - gxx_linux-64=7.3.0  

All tests run fine, I am going to test my BAM file now with this version (same Xeon machine as mentioned above).

[rvaser]

Great to hear that! Unfortunately, racon does not support BAM files (only SAM):/

[ptrebert]

@rvaser :-) apparently, it's too early for me - anyway, Racon is running, let's see what happens...

[ptrebert]

@rvaser In my case, the "illegal instruction" error did not occur with the Racon version that I built from source on Friday (same data and same everything otherwise)

[ptrebert]

@rvaser Bad news: with the new racon release version 1.3.3 (installed via bioconda), I get the "illegal instruction" error again. Same compute server as before. If it helps: last entry in the log is [racon::Polisher::initialize] transformed data into windows 191.728 s. Same error with two different datasets. I am testing the same data with the racon version built from source...

[rvaser]

@ptrebert it is probably due to some CPU/OS mismatch. Cloning and compiling from source should still work.

[EdHarry]

Error also occurs in v1.4.3 (from bioconda). Seems to happen on AMD cpus. I compiled from source (on an Intel cpu, with the -march=x86-64 flag) and got the same error (on an AMD cpu). Pretty weird, and annoying on clusters with a mix of Intel and AMD hardware.