ModuleNotFoundError: No module named 'RunCmdsMP'

[2eYu]

Hi, rengang

TEsorter is very cool!!!but I have a problem: I use `conda install -c bioconda tesorter` to install TEsorter in my linux server, I installed it successfully. The output of `TEsorter input_file -db rexdb-plant` is normal, but when I ran `concatenate_domains.py HFgenome.fa.mod.LTR.intact.fa.rexdb-plant.cls.pep GAG PROT RH RT INT > HFgenome.fa.mod.LTR.intact.fa.rexdb-plant.cls.pep.full.aln` command, error occurred: `Traceback (most recent call last):

File "~/miniconda3/envs/TEsorter/bin/concatenate_domains.py", line 7, in from RunCmdsMP import run_cmd ModuleNotFoundError: No module named 'RunCmdsMP'`. Could you kind enough to tell me why this occurs and how to run the command correctly?

best wishes

[zhangrengang]

Hi @2eYu. Please refer to https://github.com/zhangrengang/TEsorter/issues/34 (the last comment). RunCmdsMP.py is in ~/miniconda3/envs/TEsorter/lib/python*/site-packages/TEsorter*/TEsorter/modules/, but is not found from PYTHONPATH. You can link it into PYTHONPATH or ~/miniconda3/envs/TEsorter/bin/. It should work.

[2eYu]

Hi @zhangrengang

Thanks for your quick reply, I used this command ~/miniconda3/pkgs/tesorter-1.3.0-py_0/site-packages/TEsorter/modules/concatenate_domains.py HFgenome.fa.mod.LTR.intact.fa.rexdb-plant.cls.pep GAG PROT RH RT INT > HFgenome.fa.mod.LTR.intact.fa.rexdb-plant.cls.pep.full.aln2 It finally worked. Thank you!!!