Demo cases?

[BinhongLiu]

Hi, I just test DPAM on my local Linux server using AF-A0A0K2WPR7-F1-model_v4 protein model from Caenorhabditis elegans. It seems to be executed well, but some warnings appeared.

1. • 13:41:05.697 WARNING: Number of hits passing 2nd prefilter (reduced from 70733 to allowed maximum of 20000). You can increase the allowed maximum using the -maxfilt option.
2. • 13:47:09.756 WARNING: Number of hits passing 2nd prefilter (reduced from 87397 to allowed maximum of 20000). You can increase the allowed maximum using the -maxfilt option.
3. • 13:49:14.511 WARNING: Input alignment A0A0K2WPR7.hmm looks like aligned FASTA instead of A2M/A3M format. Consider using '-M first' or '-M 50'
4. cat: /home/liuhongbin/soft/DPAM-main/output_dir2/iterativeDaliA0A0K2WPR7/A0A0K2WPR7*_hits: 没有那个文件或目录

the log file is attached here. log.txt

And the final number of found domains was 4, but in the model_organisms folder it's 3. 4 domains: D1 31-65 D2 141-165 D3 166-260 D4 296-320 3 domains: D1 6-65 D2 156-260 D3 261-335

Has the tool been run well? Should I fix these warnings? And I'm not sure the difference between two results was caused by the update of database or some other reasons. Could you provide some demo AF2 models and results for the test? Many thanks!

[jzhan6]

@BinhongLiu Sorry for the late reply. It seems Dali does not run correctly in your case. So the pipeline only used hhsearch hits. I will put some demos in the following days. Sorry for the confusion.

[BinhongLiu]

I checked the environment and found that the Dali could be performed correctly. I'm not sure which step or tool caused the problem.

the output folder

[CongLabCode]

Sorry for the late reply. Here is my result. You can see that your A0A0K2WPR7_iterativdDali_hits is empty, while mine is 120K. So somehow, your iterative Dali process does not run correctly in your system. I uploaded the demo for this protein in zip file on github.

[BinhongLiu]

Yes. Was this _iterativdDali_hits file created by step 7 or step 6? Is there any method to debug the error? Thanks! Best!

[CongLabCode]

step7. You have already successfully finished the first six steps, you can just run step 7 to see if any error messages are reported.

[BinhongLiu]

Yes. I tested step 7 but nothing was reported. It seemed to be that nothing was done because the script was completed rapidly after I entered the command. And still the size of A0A0K2WPR7_iterativdDali_hits was 0.

python step7_iterative_dali_aug_multi.py A0A0K2WPR7 20 output_dir2 /home/liuhongbin/database/DPAM

Here is the output files: output_dir2.zip

Thank you for your help with this error!

[BinhongLiu]

Hi, Sorry to bother you again. Would you like to help me fix this error? Thanks!

[jzhan6]

Absolutely, I have requested a colleague in the lab to test my GitHub code in their environment to ensure a smooth installation process. Additionally, I discovered a bug in my previous download scripts, which failed to download crucial files such as ECOD_norms, ecod.latest.domains, ECOD_length, and ECOD_pdbmap. Could you please confirm if you have downloaded these files? Meanwhile, please note that the step7 script necessitates a data structure like {data_dir}/ECOD70/{edomain}.pdb. So you have to put ECOD70 under the {data_dir} you provide to the wrapper.

On Mon, Mar 27, 2023 at 12:05 AM Hongbin Liu @.***> wrote:

Hi, Sorry to bother you again. Would you like to help me fix this error? Thanks!

— Reply to this email directly, view it on GitHub https://github.com/CongLabCode/DPAM/issues/9#issuecomment-1484499882, or unsubscribe https://github.com/notifications/unsubscribe-auth/AQHKGOZPCN3B2CK5ECLEYETW6ENZ5ANCNFSM6AAAAAAVFGFQDM . You are receiving this because you commented.Message ID: @.***>

[BinhongLiu]

Yes. I think I've prepared the database properly.

[BinhongLiu]

dd

[BinhongLiu]

Hi, I recently do some new tests, and it seems to be that the error happened at step 7. I test step 7 using the files you've produced (https://github.com/CongLabCode/DPAM/blob/main/A0A0K2WPR7.zip) python /home/liuhongbin/soft/DPAM-main/step7_iterative_dali_aug_multi.py A0A0K2WPR7 20 /home/liuhongbin/soft/DPAM-main/output_dir2 /home/liuhongbin/database/DPAM

The folder iterativeDali_A0A0K2WPR7 was created and some temp folders were created within it.

However, all the temp folders disappeared and no iterativeDaliA0A0K2WPR7/A0A0K2WPR7*_hits was reported when the script completed.

Was this caused by the ECOD70 database?

[jzhan6]

Hi Hongbin,

No. I think it should be deleted by the scripts. Here our scripts have very intensive i/o usage. I do not know if personal computer handle it well.It may be caused by Dali. Dali is very old software although it is still the best for structure alignment and it has limited length allowed for the input filename. The absolute path (/home/liuhongbin/database/ DPAM/ECOD70/000000003.pdb) may be too long for it. Let me check if it is true. Thanks for your details.

Best, Jing Zhang

On Mon, Apr 10, 2023 at 10:56 AM Hongbin Liu @.***> wrote:

Hi, I recently do some new tests, and it seems to be that the error happened at step 7. I test step 7 using the files you've produced ( https://github.com/CongLabCode/DPAM/blob/main/A0A0K2WPR7.zip) python /home/liuhongbin/soft/DPAM-main/step7_iterative_dali_aug_multi.py A0A0K2WPR7 20 /home/liuhongbin/soft/DPAM-main/output_dir2 /home/liuhongbin/database/DPAM

The folder iterativeDali_A0A0K2WPR7 was created and some temp folders were created within it. [image: image] https://user-images.githubusercontent.com/35453307/230939672-a61b7390-2374-40a8-a51d-306a4579320e.png

However, all the temp folders disappeared and no iterativeDaliA0A0K2WPR7/A0A0K2WPR7*_hits was reported when the script completed.

Was this caused by the ECOD70 database?

— Reply to this email directly, view it on GitHub https://github.com/CongLabCode/DPAM/issues/9#issuecomment-1501985032, or unsubscribe https://github.com/notifications/unsubscribe-auth/AQHKGO6XV4WG7IM4GKO56MLXAQUTXANCNFSM6AAAAAAVFGFQDM . You are receiving this because you commented.Message ID: @.***>