Hi
There was an option in "old" MosaikAligner to load the keys-file, and/or positions-file into the memory by using "-km" and "-pm" from a reference jump database. I was never able to load both into memory due to lack of sufficient RAM, (loaded just the keys-file). This features are now removed in "new" MosaikAligner, and I am not able to aligne with my new jump-database.
Are there any tricks besides upgrading the hardware to get around this problem?
Error message:
Server:
Linux 2.6.25-gentoo-r7 #1 SMP x86_64 Intel(R) Xeon(R) CPU E5440 @ 2.83GHz GenuineIntel GNU/Linux
cat /proc/meminfo gives "MemTotal: 16430836 kB"
cat /proc/cpuinfo gives "8 times Intel(R) Xeon(R) CPU E5440 @ 2.83GHz"
There was an option in "old" MosaikAligner to load the keys-file, and/or positions-file into the memory by using "-km" and "-pm" from a reference jump database. I was never able to load both into memory due to lack of sufficient RAM, (loaded just the keys-file). This features are now removed in "new" MosaikAligner, and I am not able to aligne with my new jump-database.
Are there any tricks besides upgrading the hardware to get around this problem?
Error message:
Code:
------------------------------------------------------------------------------ MosaikAligner 1.0.1307 2009-10-14 Michael Stromberg & Wan-Ping Lee Marth Lab, Boston College Biology Department ------------------------------------------------------------------------------ - Using the following alignment algorithm: all positions - Using the following alignment mode: aligning reads to all possible locations - Using a maximum mismatch threshold of 6 - Using a hash size of 15 - Aligning in colorspace (SOLiD) - Using 4 processors - Using an alignment candidate threshold of 25bp. - Setting hash position threshold to 100 - Using a jump database for hashing. Storing keys & positions in memory. - loading basespace reference sequences... finished. terminate called after throwing an instance of 'std::bad_alloc' what(): std::bad_alloc Aborted
Linux 2.6.25-gentoo-r7 #1 SMP x86_64 Intel(R) Xeon(R) CPU E5440 @ 2.83GHz GenuineIntel GNU/Linux
cat /proc/meminfo gives "MemTotal: 16430836 kB"
cat /proc/cpuinfo gives "8 times Intel(R) Xeon(R) CPU E5440 @ 2.83GHz"