I need to make a kmer.fa for a custom reference genome (in our genome chrmosome 3 is a bit different from your GRCh37.) I'm running FlagUniqueKmers.dll in dotnet on Linux and I get "Unhandled Exception: OutOfMemoryException." soon after it starts. The details:
$ dotnet --version
1.1.5
$ cat /etc/os-release
NAME="Scientific Linux"
VERSION="7.3 (Nitrogen)"
ID="rhel"
ID_LIKE="fedora"
VERSION_ID="7.3"
...
Working node has 32 cores and 192GB memory.
The command I run is
$ dotnet ../../Canvas-1.32.0.918.master_x64/Tools/FlagUniqueKmers/FlagUniqueKmers.dll genome.fa kmer.fa
It fails after ">>>1 1 52000000 dict 47331105 incomplete 0", the exit code is 134.
I also tried to run FlagUniqueKmers.dll in mono, it ran for a week and then failed with "[ERROR] FATAL UNHANDLED EXCEPTION: System.NullReferenceException: Object reference not set to an instance of an object" after outputting ">>>1 1 103000000 dict 95491538 incomplete 0" line.
eroller
commented
6 years ago
I need to make a kmer.fa for a custom reference genome (in our genome chrmosome 3 is a bit different from your GRCh37.) I'm running FlagUniqueKmers.dll in dotnet on Linux and I get "Unhandled Exception: OutOfMemoryException." soon after it starts. The details: $ dotnet --version 1.1.5 $ cat /etc/os-release NAME="Scientific Linux" VERSION="7.3 (Nitrogen)" ID="rhel" ID_LIKE="fedora" VERSION_ID="7.3" ...
Working node has 32 cores and 192GB memory.
The command I run is $ dotnet ../../Canvas-1.32.0.918.master_x64/Tools/FlagUniqueKmers/FlagUniqueKmers.dll genome.fa kmer.fa
It fails after ">>>1 1 52000000 dict 47331105 incomplete 0", the exit code is 134.
I also tried to run FlagUniqueKmers.dll in mono, it ran for a week and then failed with "[ERROR] FATAL UNHANDLED EXCEPTION: System.NullReferenceException: Object reference not set to an instance of an object" after outputting ">>>1 1 103000000 dict 95491538 incomplete 0" line.
Thank you!