Dear all:
### realloc Extra_Ref_Space max_extra_ref_ct = 13463849
Too many skip kmer strings for hash table.
Try skipping hopeless check (-z option)
Anybody can tell me how shoud I deal with?
If you search the bug system for "Too many skip kmer strings", you will see that we have addressed this before. For instance, bug 3081448.
If you are using CA 6.1, then try using the latest from CVS. Search for instructions on check out and compile.
The error was printed by the overlap program. You can run 'overlap' by itself to see that -z is a valid option. That option is not supported by runCA, but you can set it directly in the generated shell script called overlap.sh in your 0-overlap directory. However, you can probably do better than that. Most likely, you are sending too much data to each overlap job. Try adjusting the OVL overlapper parameters that affect batch size. These are documented for the runCA command. Note the overlapper spits out logs that sometimes help diagnose the problem.
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
For the record, this was officially resolved (by side effect) on 2011/12/13 by increasing a data element size. The penalty was a doubling in memory usage for the same parameters.
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
If you search the bug system for "Too many skip kmer strings", you will see that we have addressed this before. For instance, bug 3081448.
If you are using CA 6.1, then try using the latest from CVS. Search for instructions on check out and compile.
The error was printed by the overlap program. You can run 'overlap' by itself to see that -z is a valid option. That option is not supported by runCA, but you can set it directly in the generated shell script called overlap.sh in your 0-overlap directory. However, you can probably do better than that. Most likely, you are sending too much data to each overlap job. Try adjusting the OVL overlapper parameters that affect batch size. These are documented for the runCA command. Note the overlapper spits out logs that sometimes help diagnose the problem.
For the record, this was officially resolved (by side effect) on 2011/12/13 by increasing a data element size. The penalty was a doubling in memory usage for the same parameters.