Anton Korobeynikov
Anton Korobeynikov
Hello Will you please attach the proper complete spades.log file?
Your SPAdes job was killed. Likely you can find more information in the system log, but I'd suspect you're running out of RAM
As far as I can see, SPAdes did produce the output files. I would suggest you to inspect SPAdes output directory to see what is going there. Note that since...
Looks like it crashed straight at the launch. I suspect there is incompatibility between your system and conda pre-built binaries. We do not maintain these packages, I would suggest you...
Likely the problem is around I/O on your server if it stuck at this moment. Try moving temporary directory location from some network shared storage to local / scratch.
> Thanks for the suggestion. My temporary directory is already located on local storage. It doesn't seem so. You `spades.log` reads: ``` Other parameters: Dir for temp files: /public/home/xzh/south/11-JRT-2/assembly_0.1/tmp ```...
> The default tmp-dir is already set to the output directory. Right. And if it on some kind of NFS shared storage, it could easily cause problems as these systems...
> The file system in use is ParaStor, a distributed file system. If it is ok? You'd better ask your system administrator. We cannot know the specifics of every NAS...
@mrmckain Just curious: have you also taught in class how to read manuals, logs and error messages? :)
Does the problem reproduce with the latest SPAdes 4.0?