Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

modification issues - don't know how to fix (logfiles) #3793

Open
ValWood opened this issue Jan 30, 2025 · 1 comment
Open

modification issues - don't know how to fix (logfiles) #3793

ValWood opened this issue Jan 30, 2025 · 1 comment
Assignees

Comments

@ValWood
Copy link
Member

ValWood commented Jan 30, 2025

loading: /var/pomcur/sources/pombe-embl/external_data/modification_files/PMID_18257517_modifications.tsv
failed to load line 1346:
storing feature_cvterm from SPBC1652.01.1 to O-phospho-L-serine [present_during] cellular response to thiabendazole - failed to store feature_cvterm: that annotation has already been stored in Chado with properties: evidence: "tryptic phosphopeptide mapping assay evidence used in automatic assertion", residue: "S194" from session: UNKNOWN
loading: /var/pomcur/sources/pombe-embl/external_data/modification_files/PMID_30726745_modifications.tsv
can't find modification term "FALSE" in Chado, skipping line 458

@kimrutherford
Copy link
Member

storing feature_cvterm from SPBC1652.01.1 to O-phospho-L-serine [present_during] cellular response to thiabendazole

That warning is probably from these lines in pombe-embl/external_data/modification_files/PMID_18257517_modifications.tsv:

PMID_18257517_modifications.tsv:1345:SPBC1652.01               MOD:00046       ECO:0007464     S194    present_during(GO:0072713)       PMID:18257517   4896    2014-04-30
PMID_18257517_modifications.tsv:1346:SPBC1652.01               MOD:00046       ECO:0007464     S194    present_during(GO:0072713)       PMID:18257517   4896    2014-04-30

can't find modification term "FALSE" in Chado, skipping line 458

That's because of this line in pombe-embl/external_data/modification_files/PMID_30726745_modifications.tsv:

SPCC162.07  ent1    FALSE   ECO:0007464     624     affected_by(Pombase:SPAC821.12) PMID:30726745   4896    2019-02-05

@ValWood ValWood self-assigned this Jan 31, 2025
@ValWood ValWood transferred this issue from pombase/pombase-chado Jan 31, 2025
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

2 participants