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Vicky123wzy / RetroScan

MIT License
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Calculate Ka/Ks error #1

Open marcelbioinf opened 3 years ago

marcelbioinf commented 3 years ago

Hi, I have a problem with calculating Ka/Ks. Every time I run the program (with different datasets) it breaks at this point. I took a look into the code and it seems to happen because the kaks_result.txt file is empty every time. Do you have any idea how to repair that?

Vicky123wzy commented 3 years ago

Regarding your problem, it because that we use KaKs_Calculator to calculate Ka/Ks in RetroScan. But this software has strict naming regulations for input files, and errors may be reported if special or illegal characters are contained. If it is convenient for you, can you provide the path of your input file and your protein sequences file. What’s more, we will modify the code in the future to avoid such errors.

thomasfaraut commented 2 years ago

Hello,

We experienced very similar problem, retroscan crashed, most probably due to KaKs_Calculator error, with the following error. ../.. File $PATH_TO_RETROSCAN/retroscan-v1.0.0_env/bin/retroscan.py", line 366, in kaks_des str(kaks_retro[array[0]][0]) + "\t" + KeyError: 'Retrocopy353' And Retrocopy353 is indeed present in best_parent.out but absent from kaks_result.txt.

It worked fine for a large number of other retrocopies.

You mentioned a naming convention issue. We are working with ncbi gff3, would you recommend to use rather ensembl annotation which has another naming convention. Or do you have any suggestions that would enable us to complete the pipeline (avoiding for exemple ka_ks computation which is not mandatory for what we want to do).

Thank you in advance.