Populus trichocarpa Genome

patricksis commented 5 years ago

Publication and Data Information

https://phytozome.jgi.doe.gov/pz/portal.html#!info?alias=Org_Ptrichocarpa

Additional Information

This organism has been added to the site before, but it is missing some features so we may want to update it.

Checklist

See New Genome Documentation for detailed instructions.

[x] Create Organism
[x] Create Publication
[x] Create Reference Genome
[x] Create InterProScan Annotation
[x] Create BLAST Annotation
[x] Run Chado FASTA Loader for CDS
[x] Run Chado FASTA Loader for Polypeptides
[x] Publish Tripal content
[x] Create KEGG Annotation
[x] Run Chado KEGG Loader
[x] Run Chado BLAST XML results loader
[x] Run Chado InterProScan XML results loader
[x] Create Blast Database

patricksis commented 5 years ago

patricksis commented 5 years ago

patricksis commented 5 years ago

@almasaeed2010 I think we may be running low on memory? I got this error when uploading IPS results:


Error: Allowed memory size of 134217728 bytes exhausted (tried to
allocate 18874368 bytes) in phar:///usr/bin/drush/includes/drush.inc,
line 78```

patricksis commented 5 years ago

Blast data base: Transcripts: https://www.hardwoodgenomics.org/content/populus-trichocarpa-transcripts Peptides: https://www.hardwoodgenomics.org/content/populus-trichocarpa-peptides

almasaeed2010 commented 5 years ago

@patricksis could you retry loading IPS? I changed the setting to allow for more memory.

patricksis commented 5 years ago

Thanks @almasaeed2010 that worked, It's strange though, it still shows an error on the job page, but the job logs in terminal seems normal and the results show up on the website.

almasaeed2010 commented 5 years ago

are you sure you are looking at the latest job page not the previous one?

almasaeed2010 commented 5 years ago

Yeah the latest one shows an error: https://hardwoodgenomics.org/admin/tripal/tripal_jobs/view/750289 you are right. Something must've gone wrong in that case.

patricksis commented 5 years ago

Here's the results for one feature: https://www.hardwoodgenomics.org/feature/Potri001G0078001?tripal_pane=group_interpro I'm not sure why results would show up if there was an error.

almasaeed2010 commented 5 years ago

So what could’ve happened is that the transaction was committed even though the job failed. That would cause some of the results to exist and some not to. So for now I need to investigate the issue a little more. I'll probably ask you to rerun later.

patricksis commented 5 years ago

Scaffolds: https://www.hardwoodgenomics.org/content/populus-trichocarpa-scaffolds KEGG annotation: https://www.hardwoodgenomics.org/KEGGresults/3032842 KEGG loader: https://www.hardwoodgenomics.org/admin/tripal/tripal_jobs/view/751090

patricksis commented 5 years ago

Jbrowse track added: https://www.hardwoodgenomics.org/admin/tripal/extension/tripal_jbrowse/management/instances/6

CaseyRichards92 commented 5 years ago

@patricksis

[x] I dont think your BLAST swissprot or trembl loaded correctly https://www.hardwoodgenomics.org/feature/Potri001G2412501?tripal_pane=group_homology

patricksis commented 5 years ago

@cricha59 Really it looks fine on this one and a few others: https://www.hardwoodgenomics.org/feature/Potri001G0007002?tripal_pane=group_homology

almasaeed2010 commented 5 years ago

The blast results that @cricha59 found are ok. An empty chart just means that we ran Blast for this feature but found no results (which is helpful info).

patricksis commented 5 years ago

Yeah that's what I figured

statonlab / hardwoods_site