SEA-PHAGES | Rerun function not updating

Link to this post \| posted 09 May, 2019 13:46
fogartym1	There are some recent published genome additions to Genbank and phagesdb that are very relevant for my annotation of Sixama. However, when I hit the rerun button for phagesdb and NCBI in PECAAN it is not updating. If I change the start site it updates, but for most genes I don't want to change the start site. Is there a way to rerun the databases (ideally for the entire genome at once)? Thanks Marie

Link to this post | posted 09 May, 2019 13:46

There are some recent published genome additions to Genbank and phagesdb that are very relevant for my annotation of Sixama. However, when I hit the rerun button for phagesdb and NCBI in PECAAN it is not updating. If I change the start site it updates, but for most genes I don't want to change the start site. Is there a way to rerun the databases (ideally for the entire genome at once)?
Thanks
Marie

Link to this post \| posted 10 May, 2019 21:44
cdshaffer	there is a button that should do that but if the button on each gene is not working the whole phage might not either. Go to Admin menu -> phages; search for your phage and click the edit button. From there you should get a page which includes button to reblast the whole phage.

Link to this post \| posted 13 May, 2020 00:51
abeyer	I'm having this same issue with PECAAN; if I click on any particular gene's "rerun" button (for BLAST, HHPRED, etc.) it will refresh the page but then show the old data without rerunning. I noticed the same as what Marie said- it will rerun if the start site is changed. I do not necessarily want to rerun everything, but mostly would like to get the fresh PhagesDB data. Anybody else experience this, or know of a way to get it to work?

Link to this post | posted 13 May, 2020 00:51

abeyer

I'm having this same issue with PECAAN; if I click on any particular gene's "rerun" button (for BLAST, HHPRED, etc.) it will refresh the page but then show the old data without rerunning. I noticed the same as what Marie said- it will rerun if the start site is changed. I do not necessarily want to rerun everything, but mostly would like to get the fresh PhagesDB data. Anybody else experience this, or know of a way to get it to work?

Link to this post \| posted 13 May, 2020 15:44
fogartym1	I didn't manage to solve this issue, I addressed it in my cover letter and did my best with what was available, sorry!

Link to this post \| posted 13 May, 2020 23:08
ClaireRinehart	Since PECAAN's BLASTS, HHPred and other queries are run locally in our High Performance Computer Center to avoid overloading NCBI and other services we sometimes get out of sync with them. We check these databases regularly to see when we need to update, but sometimes we get out of sync and simply need to download the latest database. So, if you see this kind of problem again, just drop us a line and we will initiate an additional download from these databases. HPCC administrator has informed me that we should be back in sync. Just a note concerning a global re-run on your whole phage from the Admin - Phages window that Chris mentioned. If you re-BLAST the whole phage genome you will often loose the evidence checkmarks. Therefore, do so with the assumption that the checkmarks will be reset to zero. Thanks, Claire Edited 13 May, 2020 23:10

Link to this post | posted 13 May, 2020 23:08

ClaireRinehart

Since PECAAN's BLASTS, HHPred and other queries are run locally in our High Performance Computer Center to avoid overloading NCBI and other services we sometimes get out of sync with them. We check these databases regularly to see when we need to update, but sometimes we get out of sync and simply need to download the latest database. So, if you see this kind of problem again, just drop us a line and we will initiate an additional download from these databases.

HPCC administrator has informed me that we should be back in sync.

Just a note concerning a global re-run on your whole phage from the Admin - Phages window that Chris mentioned. If you re-BLAST the whole phage genome you will often loose the evidence checkmarks. Therefore, do so with the assumption that the checkmarks will be reset to zero.

Thanks,
Claire

Edited 13 May, 2020 23:10

Link to this post \| posted 14 May, 2020 01:57
abeyer	Thank you Claire!!

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Rerun function not updating