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CSU-KangHu / HiTE

High-precision TE Annotator
GNU General Public License v3.0
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My doubts when I run HiTE #13

Closed chenxuming-0330 closed 2 months ago

chenxuming-0330 commented 3 months ago

Dear Author,

Thank you for developing such an excellent software.I get some problems when I use HiTE to run my project. Would you give me some help？ I set my order like “nohup python main.py --genome genome.fasta --thread 10 --outdir outdir/ --domain 1 --intact_anno 1 > HiTE.log 2>&1 &”to run HiTE. When the program got finished, I found there're no file named " HiTE_intact.sorted.gff3" as the output file for the parameter "--intact_anno 1". What's wrong with this result? And when I check the HiTE.log,I found error "cp: cannot stat ‘/storage/chenxuming/HiTE/20century/NeuralTE_all/classified_TE.fa’: No such file or directory cp: cannot stat ‘/storage/chenxuming/HiTE/20century/TE_merge_tmp.fa.classified’: No such file or directory" in step3: generate non-redundant library another error : Traceback (most recent call last): File "/storage/zhangyunqi/HiTE/./module/get_full_length_annotation.py", line 97, in classification = TE_classifications[query_name] KeyError: 'TIR_584' in step4: get full-length TE annotation Did those errors above cause HiTE_intact.sorted.gff3 non-existent？

chenxuming-0330 commented 3 months ago

and I I mainly study in TIRs.I also want to know which file can show the detail of TIRs ( such as superfamily,start,end,TIR,TSD)

CSU-KangHu commented 3 months ago

Hi @chenxuming-0330,

I apologize for the late response. Based on your error message, it seems there might be an issue with the classification module. But I have redownloaded the code and ran it without encountering any errors. Please try setting both the --genome and --outdir parameters to absolute paths.

Using --intact_anno 1 will provide full-length annotation information for all TEs, including TIRs.

Best, Kang