Warning: gene is missing from Notes file. Please inform curator

[Former user]

Dear Resfinder Team,

I find the below warnings from resfinder version:4.1.3:

Resistance gene Identity Alignment Length/Gene Length Coverage Position in reference Contig Position in contig Phenotype Accession no. blaOXA-193 99.61 774/774 100.0 1..774 fiar-1656_S5_L001_NODE_5_length_132472_cov_90.259874_pilon 121884..122657 Beta-lactam resistance CP013032 blaOXA-450 99.61 774/774 100.0 1..774 fiar-1656_S5_L001_NODE_5_length_132472_cov_90.259874_pilon 121884..122657 Warning: gene is missing from Notes file. Please inform curator. KR061502 blaOXA-453 99.61 774/774 100.0 1..774 fiar-1656_S5_L001_NODE_5_length_132472_cov_90.259874_pilon 121884..122657 Warning: gene is missing from Notes file. Please inform curator. KR061507 blaOXA-452 99.61 774/774 100.0 1..774 fiar-1656_S5_L001_NODE_5_length_132472_cov_90.259874_pilon 121884..122657 Warning: gene is missing from Notes file. Please inform curator. KR061505 blaOXA-61 99.61 774/774 100.0 1..774 fiar-1656_S5_L001_NODE_5_length_132472_cov_90.259874_pilon 121884..122657 Beta-lactam resistance Alternate name; Cam-1 AY587956 blaOXA-489 99.61 774/774 100.0 1..774 fiar-1656_S5_L001_NODE_5_length_132472_cov_90.259874_pilon 121884..122657 Warning: gene is missing from Notes file. Please inform curator. CP013733 blaOXA-451 99.61 774/774 100.0 1..774 fiar-1656_S5_L001_NODE_5_length_132472_cov_90.259874_pilon 121884..122657 Warning: gene is missing from Notes file. Please inform curator. KR061504 tet(O) 99.90 1920/1920 100.0 1..1920 fiar-1656_S5_L001_NODE_18_length_30931_cov_79.152935_pilon 23904..25823 Tetracycline resistance M18896

Could you kindly let me know how to solve this issue?

Best Regards, Bala

[Alfred Ferrer Florensa]

Dear Bala,

It is a warning that will be solved in the next update. But it does not affect the results.

‌

Best,

Alfred Ferrer Florensa

[Peter Cock]

I’m seeing this on resfinder 4.1.3, lots of cases like this all for mdf(A) in assorted E. coli samples:

mdf(A)  97.97   1233/1233   100.0   1..1234 NA  NA..NA  Warning: gene is missing from Notes file. Please inform curator.    Y08743

‌

[Peter Cock]

Edit is not working for me, I meant to say version 4.1.6 (but perhaps the DB version is more relevant?)

[Alfred Ferrer Florensa]

Dear Peter,

The warnings from the Notes file are currently irrelevant. However, we have not been able yet to make ResFinder work without the Notes file. We hope in the next versions we will be able to make ResFinder not need the Notes file.

[Peter Cock]

In that case perhaps remove the “Please inform curator” part of the warning?

[Alfred Ferrer Florensa]

True, thank you, the v4.2 out next week will have it