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Issues with installation and usage
1. undefined symbol: Perl_xs_apiversion_bootcheck
Type RepeatMasker
in the conda HiTE virtual environment, and an error similar to the following occurred:
undefined symbol: Perl_xs_apiversion_bootcheck
This error is caused by the incompatibility between the local perl of the system and the perl installed by conda.
The solution is: export PERL5LIB=/
1. High disk I/O
HiTE uses blastn multiple times in different steps, such as generating TE sequences with coarse boundaries, which consumes a lot of disk I/O when the genome contains abundant TE instances.
2. Long running time
The runtime of the program depends on the size of the genome and the complexity of the repetitive regions.
Solution: We suggest increasing the number of CPU processors to reduce the runtime. Alternatively, you can split the genome into smaller batches by setting the --chunk_size
parameter, e.g., --chunk_size 200
. However, you should keep in mind that this may result in the loss of some low-copy TEs.
Hunan Provincial Key Lab on Bioinformatics, Central South University.