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SunPengChuan / wgdi

WGDI: A user-friendly toolkit for evolutionary analyses of whole-genome duplications and ancestral karyotypes
https://wgdi.readthedocs.io/en/latest/
BSD 2-Clause "Simplified" License
114 stars 22 forks source link

wgdi -icl error #20

Closed 123123456abc closed 2 years ago

123123456abc commented 2 years ago

When using wgdi, I encountered the following question. Can you help me answer it? thanks.

gff1 = mgly.gff gff2 = tyun.chr.gene.gff lens1 = mgly.len lens2 = tyun.len blast = tyun_mgly.txt blast_reverse = false multiple = 1 process = 20 evalue = 1e-5 score = 100 grading = 50,40,25 mg = 25,25 pvalue = 1 repeat_number = 2 positon = order savefile = tyun_mgly.collinearity.txt Traceback (most recent call last): File "/home/appl/anaconda3/envs/wgdi/lib/python3.10/site-packages/pandas/core/indexes/base.py", line 3621, in get_loc return self._engine.get_loc(casted_key) File "pandas/_libs/index.pyx", line 136, in pandas._libs.index.IndexEngine.get_loc File "pandas/_libs/index.pyx", line 163, in pandas._libs.index.IndexEngine.get_loc File "pandas/_libs/hashtable_class_helper.pxi", line 2131, in pandas._libs.hashtable.Int64HashTable.get_item File "pandas/_libs/hashtable_class_helper.pxi", line 2140, in pandas._libs.hashtable.Int64HashTable.get_item KeyError: 2

The above exception was the direct cause of the following exception:

Traceback (most recent call last): File "/home/appl/anaconda3/envs/wgdi/bin/wgdi", line 10, in sys.exit(main()) File "/home/appl/anaconda3/envs/wgdi/lib/python3.10/site-packages/wgdi/run.py", line 158, in main module_to_run(arg, value) File "/home/appl/anaconda3/envs/wgdi/lib/python3.10/site-packages/wgdi/run.py", line 118, in module_to_run run_subprogram(program, conf, name) File "/home/appl/anaconda3/envs/wgdi/lib/python3.10/site-packages/wgdi/run.py", line 84, in run_subprogram r.run() File "/home/appl/anaconda3/envs/wgdi/lib/python3.10/site-packages/wgdi/run_colliearity.py", line 65, in run lens2 = base.newlens(self.lens2, 'order') File "/home/appl/anaconda3/envs/wgdi/lib/python3.10/site-packages/wgdi/base.py", line 187, in newlens lens = lens[2] File "/home/appl/anaconda3/envs/wgdi/lib/python3.10/site-packages/pandas/core/frame.py", line 3505, in getitem indexer = self.columns.get_loc(key) File "/home/appl/anaconda3/envs/wgdi/lib/python3.10/site-packages/pandas/core/indexes/base.py", line 3623, in get_loc raise KeyError(key) from err KeyError: 2

SunPengChuan commented 2 years ago

Check this file carefully, lens2 = tyun.len