The file "https://zhanggroup.org/ftp/data/JGIclust50/list" not exit.

liujie1993228 · Post by **liujie1993228** » Sat Aug 02, 2025 9:16 pm

Hello,
I encountered an error while attempting to download the D-I-TASSER library using the following command:
./DIT_anaconda3/envs/DIT/bin/python ./download_lib.py -libdir /share/org/YZWL/yzwl_liujie/liujie/workspace/D-I-TASSER/ITLIB -P true -B true -N true -MSA DeepMSA2-IMG -ITmode DIT-AF2
The error message indicates:
subprocess.CalledProcessError: Command 'wget -c https://zhanggroup.org/ftp/data/JGIclust50/list' returned non-zero exit status 8.
It appears the file at https://zhanggroup.org/ftp/data/JGIclust50/list is not accessible (returns "404 Not Found"). Could you please:
Verify if this is the correct URL?
Suggest an alternative download source if available?
Thank you for your assistance.

Best regards

Tianrui · Post by **Tianrui** » Tue Aug 12, 2025 10:57 am

Hello,

Thank you for reporting this issue. The broken link to https://zhanggroup.org/ftp/data/JGIclust50/list has now been fixed.
Please try rerunning the original command — it should download successfully without modification.

We appreciate your feedback and help in improving D-I-TASSER.

Best regards,
Tianrui

liujie1993228 · Post by **liujie1993228** » Tue Aug 12, 2025 11:24 am

Dear Tianrui,
Thanks so much for your reply.
After successfully downloading the file from https://zhanggroup.org/ftp/data/JGIclust50/list, I encountered another error when executing the following command:
./DIT_anaconda3/envs/DIT/bin/python ./download_lib.py -libdir /share/org/YZWL/yzwl_liujie/liujie/workspace/D-I-TASSER/ITLIB -P true -B true -N true -MSA DeepMSA2-IMG -ITmode DIT-AF2.

The error message indicates:
returned non-zero exit status 1.d 'wget -c https://zhanggroup.org/ftp/data/JGIclust50/<html>

I have attached the detailed error log for your reference.

Best,
Jie

Tianrui · Post by **Tianrui** » Wed Aug 13, 2025 2:47 pm

Hi Jie,

Thanks for your update!

I just ran a quick check and found that the issue likely stems from the server rejecting the request made by Python’s requests library when trying to access the JGI file list. Specifically, it returns a 403 Forbidden error because the request doesn’t include a browser-like User-Agent header.

To fix this, we need to modify the script slightly by adding a User-Agent header to the requests.get(...) call so the server doesn’t block it. Here’s a quick patch for that part of the script:

Code: Select all

headers = {
    "User-Agent": "Mozilla/5.0"
}
response = requests.get("https://zhanggroup.org/ftp/data/JGIclust50/list", headers=headers)
JGI_list = response.text.split('\n')

After this change, the request works well and returns:

Code: Select all

['DB.fasta.aa', 'DB.fasta.ab', 'DB.fasta.ac', 'DB.fasta.ad', '']

Let me know if you’d like me to send back a patched version of the script with this fix.

Again, thank you for your continued efforts on the DIT framework — it’s a great contribution to the community.

Best regards,
Tianrui

Tianrui · Post by **Tianrui** » Wed Aug 13, 2025 2:51 pm

Hi Jie,

Small correction — the issue was fixed by adding this User-Agent header:

Code: Select all

headers = {
    "User-Agent": "Mozilla/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/115.0 Safari/537.36"
}

Best,
Tianrui

liujie1993228 · Post by **liujie1993228** » Wed Aug 20, 2025 8:41 am

Dear Tianrui,
Thanks so much for your help.

After resolved the former errors, I encountered another error when executing the following command:
./DIT_anaconda3/envs/DIT/bin/python ./download_lib.py -libdir /share/org/YZWL/yzwl_liujie/liujie/workspace/D-I-TASSER/ITLIB -P true -B true -N true -MSA DeepMSA2-IMG -ITmode DIT-AF2.

The error message indicates:
subprocess.CalledProcessError: Command 'wget -c https://zhanggroup.org/ftp/data/JGIclus ... asta.aa.xz' returned non-zero exit status 8.

I have attached the detailed error log for your reference.

Best,
Jie

The file "https://zhanggroup.org/ftp/data/JGIclust50/list" not exit.

The file "https://zhanggroup.org/ftp/data/JGIclust50/list" not exit.

Re: The file "https://zhanggroup.org/ftp/data/JGIclust50/list" not exit.

Re: The file "https://zhanggroup.org/ftp/data/JGIclust50/list" not exit.

Re: The file "https://zhanggroup.org/ftp/data/JGIclust50/list" not exit.

Re: The file "https://zhanggroup.org/ftp/data/JGIclust50/list" not exit.

Re: The file "https://zhanggroup.org/ftp/data/JGIclust50/list" not exit.