SEA-PHAGES | HHPred not updating in PECAAN

Link to this post \| posted 26 Apr, 2024 16:15
ejyoon	Hello, We are finishing up annotation of a phage (UBSmoodge) and we are finalizing putative function assignments. There are a handful of genes in which HHPred is not updating and providing any results. It keeps queueing repeatedly, and it has been doing so for two days now. Is there anything that I can do to resolve this issue? I just don't know what to do other than keep waiting (and hoping). Thank you for your time and help.

Link to this post | posted 26 Apr, 2024 16:15

Hello,

We are finishing up annotation of a phage (UBSmoodge) and we are finalizing putative function assignments. There are a handful of genes in which HHPred is not updating and providing any results. It keeps queueing repeatedly, and it has been doing so for two days now. Is there anything that I can do to resolve this issue? I just don't know what to do other than keep waiting (and hoping). Thank you for your time and help.

Link to this post \| posted 26 Apr, 2024 17:26
cdshaffer	You can always run the search manually: 1. In PECAAN go to the sequence tab and select the amino acid sequence go to the HHPRED web server: https://toolkit.tuebingen.mpg.de/tools/hhp 2. Paste in your sequence, 3. Select databases: For the typical search, I have students add two databases {Unitrot and Pfam] to search in addition the the default PDB database. You add these by selecting them in the "Select structural/domain databases" menu. 4. click submit 5. wait. Time varies but usually takes 1 to 3 minutes. Results are kept for a few days (links will be in the left column if you come back later from the same computer). Most of the scores you see in PECAAN are in the "Hitlist" section of the results. As a bonus, at the top you will see a graphical representation of the locations of the hits which can help you see the overall domain structure of your protein. And at the bottom you get full alignments which can be helpful in a deep dive into exactly what does and does not match between your protein and the hit.

Link to this post | posted 26 Apr, 2024 17:26

cdshaffer

You can always run the search manually:

1. In PECAAN go to the sequence tab and select the amino acid sequence
go to the HHPRED web server: https://toolkit.tuebingen.mpg.de/tools/hhp
2. Paste in your sequence,
3. Select databases: For the typical search, I have students add two databases {Unitrot and Pfam] to search in addition the the default PDB database. You add these by selecting them in the "Select structural/domain databases" menu.
4. click submit
5. wait. Time varies but usually takes 1 to 3 minutes.
Results are kept for a few days (links will be in the left column if you come back later from the same computer). Most of the scores you see in PECAAN are in the "Hitlist" section of the results.
As a bonus, at the top you will see a graphical representation of the locations of the hits which can help you see the overall domain structure of your protein. And at the bottom you get full alignments which can be helpful in a deep dive into exactly what does and does not match between your protein and the hit.

Link to this post \| posted 26 Apr, 2024 19:29
ejyoon	Thank you for the prompt response. I'm glad that there are people monitoring the forum. I am aware that I can run HHPred manually, and we have done that to collect data for putative function assignment during the semester. We use PECAAN to finalize the annotation and export it to create the required files for QC. We just found the process is easier without having to worry about manually inputting all the data in DNAM for this step. However, if we need to add this information manually into the final DNAM files for QC submission, then we will certainly do that. I was just hoping to avoid that manual work out of convenience.

Link to this post | posted 26 Apr, 2024 19:29

ejyoon

Thank you for the prompt response. I'm glad that there are people monitoring the forum. I am aware that I can run HHPred manually, and we have done that to collect data for putative function assignment during the semester.

We use PECAAN to finalize the annotation and export it to create the required files for QC. We just found the process is easier without having to worry about manually inputting all the data in DNAM for this step.

However, if we need to add this information manually into the final DNAM files for QC submission, then we will certainly do that. I was just hoping to avoid that manual work out of convenience.

Link to this post \| posted 29 Apr, 2024 15:22
jawsWPI	It's possible that HHPred was choked–I setup a manual query around the time you were having issues in PECAAN that was also queued up for a long time and was still 'running' just now but had reached an error stage. Just deleted the request and resent–it ran and came back in a couple of minutes even with a 4-database search. So, if you are still having issues try again.

Link to this post \| posted 29 Apr, 2024 20:39
ejyoon	Thank you for the reply. I just re-ran the HHPred in PECAAN earlier this afternoon. I appreciate your time and help.

Link to this post \| posted 30 Apr, 2024 18:39
jawsWPI	2:38PM 4-30-24. Just tried HHPred again with job grayed out and queued: "We are addressing a Denial of Service attack by a user who is continually changing IP addresses to submit an excessively high number of jobs, significantly impacting our system’s performance. We regret any inconvenience caused and are actively working to resolve this issue.".

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