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CSU-KangHu / HiTE

High-precision TE Annotator
GNU General Public License v3.0
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Skip benchmarking of RepeatModeler2，EDTA and HiTE #12

Closed xupoding closed 2 months ago

xupoding commented 3 months ago

Hi Kang，

In the last step of Start conduct benchmarking of RepeatModeler2, EDTA, and HiTE, these three pipeline were always skipped, is it standard？How modified in step if it were bugs？

Regards

xupoding commented 3 months ago

Please refer the following information： 2024-07-28 13:39:40,424 - /HiTE/module/benchmarking.py[line:131] - DEBUG: Skip benchmarking of RepeatModeler2 2024-07-28 13:39:40,424 - /HiTE/module/benchmarking.py[line:168] - DEBUG: Skip benchmarking of EDTA 2024-07-28 13:39:40,424 - /HiTE/module/benchmarking.py[line:184] - DEBUG: Skip benchmarking of HiTE 2024-07-28 13:39:40,437 - main.py[line:634] - INFO: Running time of step6: 0.295043 s 2024-07-28 13:39:41,074 - main.py[line:644] - INFO: Running time of the whole pipeline: 193.4811 s

RepeatModeler2 and HiTE have been installed, EDTA was not installed in the environment of HiTE

CSU-KangHu commented 3 months ago

Hi @xupoding,

This is not a bug. In the default HiTE workflow, the benchmarking of RepeatModeler2, EDTA, and HiTE is not performed unless explicitly specified by the user. Skipping these benchmarking steps does not affect the HiTE workflow. These steps are included solely for the purpose of reproducing the quantitative results from the HiTE paper. For more details, please refer to this link.

Best regards,

Kang