I also had a problem with the second step about ervcaller HOT 10 OPEN

Prof. Chen, I successfully ran the software by modifying the reference genome. For other species, chromosome number modification is a must. ERVcaller works great!！！

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nice, let me know if you have further questions.

Xun

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Hi, I think you forgot to put the number of CPUs for "-t", like "-t 10". Also "-I" is for the folder containing the FASTQ files and "-O" for your output folder.

Thanks,
Xun

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Prof. Chen, thank you very much for your reply. However I still have the same problem when running the code. Then how can I solve it?

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Hi,

Have you run the test data yet? Btw, have you installed SEI-MEI successfully? if not, you could follow the steps in README. could you also show a list of files under the output folder?

Thanks,
Xun

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yeah，SEI-MEI should be installed successfully.like this:


I tried the test data, but the same error was reported. Then ran my own data.
the output/ file is as follows：

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from ervcaller.

Hi,

I would suggest you run it with the test data first and then apply it to your datasets.

Few suggestions and tips for testing the tools:

1. please export the paths of all included tools, including SEI-MEI (see README file).

2. all references should be indexed with bwa, including the human reference genome and TE reference genome (see README file too).

3. ERVcaller would support human chromosome IDs, such as "chr1", "chr2" and so on. If you are working on other species, you could try rename them.

Best,
Xun

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Okay, thanks again for your reply. I will try it again. Best wishes to you!!

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yeah！Thank you！

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