`GLIBCXX_3.4.20' not found

[wlaw13]

I'm trying to use NextSV2 to identify SV using Nanopore data, specifically using the sniffles caller. I've installed Sniffles and can run it as a stand alone caller with no issues. However, when I run NextSV2, it goes for ~10 hours before throwing this error:

sniffles: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.21' not found (required by sniffles)

When I go to /usr/lib64/, I can see libstdc++.so.6.0.19, so I'm not sure what the issue is.

Any ideas?

[fangli80]

Hi,

The sniffles in your system requires a higher version of libstdc++. Probably because it was compiled by a newer version of GCC, which is not in you system.

Please use the following commands to download sniffles and re-compile it using the current GCC in your system. If you can succesfully compile the sniffles, you should be OK.

wget https://github.com/fritzsedlazeck/Sniffles/archive/master.tar.gz -O Sniffles.tar.gz
tar xzvf Sniffles.tar.gz
cd Sniffles-master/
mkdir -p build/
cd build/
cmake ..
make

cd ../bin/sniffles*
./sniffles

[wlaw13]

I can try that, but it doesn't make sense the running sniffles by itself works with no problems. I'll give it a chance once the server frees up and let you know.

[fangli80]

Did you test running sniffles itself in the same node? Sometimes the compute nodes have different environmental settings with the login node. You can also find the command of Sniffles used by NextSV in the work.sh file and test if it works.

Best,
Li

[wlaw13]

Ah, yes you're probably right. They recently changed the standard partition to something else. That makes sense. Let me try to reinstall once a few jobs finish and I'll try again. Thanks!

[wlaw13]

Unfortunately I'm still running into the same problem. I ensured I was on the same cluster that the job would ultimately run on, and reinstalled using the commands you posted above. I'd be happy to privately send you the full error file to look at if that would be helpful.