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I run step2 script Run_DeepMSA2.py, but such issue occurred. I don't know how to solve it.

Dear user,

You can ignore this warning, this is may be you run the program two times, and the first time those links are created, the program should run without a problem when you see this message. Let us know if you have any other trouble.

Best Regards
Wei Zheng

Thank you for your reply.
After deleting all the result files, I re-ran the Run_DeepMSA2.py script. After trying many times, this issue always appears. Importantly, after this prompt appears, no new result files continue to be generated in the folder for a quite long time, and the program does not display a termination message. It shows running and this "ln " prompt keeps appearing every so often.
so, I don't know if the program has finished running or not.

jlspzw wrote: ↑Tue Jan 16, 2024 9:54 am Dear user,

You can ignore this warning, this is may be you run the program two times, and the first time those links are created, the program should run without a problem when you see this message. Let us know if you have any other trouble.

Best Regards
Wei Zheng

Thank you for your reply.
After deleting all the result files, I re-ran the Run_DeepMSA2.py script. After trying many times, this issue always appears. Importantly, after this prompt appears, no new result files continue to be generated in the folder for a quite long time, and the program does not display a termination message. It shows running and this "ln " prompt keeps appearing every so often.
so, I don't know if the program has finished running or not.

Dear user,

Please do the following and I will check if the files are correctly generated.

1. check what files exist in your MSA and JGI folder.

2. check if DeepJGI.aln/a3m q3JGI.aln/a3m q4JGI.aln/a3m exists in the JGI folder? (those files should be the results of this step)

3. when running the program, check the background jobs by 'ps -aux|grep your_use_name' to see if any hmmer or hhblits jobs.

4. please give me your FASTA format sequence (you can upload it by the attached files), I will see if anything is not correct.

Best Regards
Wei Zheng

jlspzw wrote: ↑Wed Jan 17, 2024 1:20 am Dear user,

Please do the following and I will check if the files are correctly generated.

1. check what files exist in your MSA and JGI folder.

2. check if DeepJGI.aln/a3m q3JGI.aln/a3m q4JGI.aln/a3m exists in the JGI folder? (those files should be the results of this step)

3. when running the program, check the background jobs by 'ps -aux|grep your_use_name' to see if any hmmer or hhblits jobs.

4. please give me your FASTA format sequence (you can upload it by the attached files), I will see if anything is not correct.

Best Regards
Wei Zheng

Thank you for your reply
I checked the MSA and JGI folders. The results for protein-A are complete, but the some results for protein-B are missing, shown by attached file.
I submitted the task using the slurm platform, and the sq command shows that the program is still running, but no new results continue to be generated, and the 'ln ' prompt still be generated.

Dear user,

This is interesting, could you send me your input sequences, I will test with your case.

Best
Wei

jlspzw wrote: ↑Wed Jan 17, 2024 3:55 am Dear user,

This is interesting, could you send me your input sequences, I will test with your case.

Best
Wei

Thank you.
The prediction for this sequence has been done in your online server. The result is no problem. but after following your installation instruction, I want to conduct the prediction in our server to test whether the program can also work well. However, above mentioned issue occurred.

>protein-A
MSWKRHHLIPETFGVKRRRKRGPVESDPLRGEPGSARAAVSELMQLFPRGLFEDALPPIVLRSQVYSLVPDRTVADRQLKELQEQGEIRIVQLGFDLDAHGIIFTEDYRTRVLKACDGRPYAGAVQKFLASVLPACGDLSFQQDQMTQTFGFRDSEITHLVNAGVLTVRDAGSWWLAVPGAGRFIKYFVKGRQAVLSMVRKAKYRELLLSELLGRRAPVVVRLGLTYHVHDLIGAQLVDCISTTSGTLLRLPET
>protein-B
MLGFLSARQTGLEDPLRLRRAESTRRVLGLELNKDRDVERIHGGGINTLDIEPVEGRYMLSGGSDGVIVLYDLENSSRQSYYTCKAVCSIGRDHPDVHRYSVETVQWYPHDTGMFTSSSFDKTLKVWDTNTLQTADVFNFEETVYSHHMSPVSTKHCLVAVGTRGPKVQLCDLKSGSCSHILQGHRQEILAVSWSPRYDYILATASADSRVKLWDVRRASGCLITLDQHNGKKSQAVESANTAHNGKVNGLCFTSDGLHLLTVGTDNRMRLWNSSNGENTLVNYGKVCNNSKKGLKFTVSCGCSSEFVFVPYGSTIAVYTVYSGEQITMLKGHYKTVDCCVFQSNFQELYSGSRDCNILAWVPSLYEPVPDDDETTTKSQLNPAFEDAWSSSDEEG

Dear user,

Thank you for your sequence, we will test the case and let you know the answer soon.

Best Regards
Wei Zheng

Dear user,

Sorry for the late reply, we have tested your sequences and found the issue. Now new versions of DeepMSA2 (v2.1) and DMFold (v1.1) have been online, we have fixed a couple of issues including the one you find. Thank you.

https://zhanggroup.org/DMFold/download
https://zhanggroup.org/DeepMSA2/download

Best Regards
Wei Zheng