ERROR: Invalid inference value tRNAscan-SE

[MonicaSteffi]

I am trying Cenote-take. Everything was fine until running tbl2asn step. Kindly check the following logfile

[tbl2asn] ERROR: Invalid inference value tRNAscan-SE score:33.8
[tbl2asn] ERROR: Invalid inference value tRNAscan-SE score:44.2
[tbl2asn] Flatfile x10

[tbl2asn] Validating x10

[tbl2asn] Flatfile x1

[tbl2asn] Validating x1

[tbl2asn] Flatfile x2

[tbl2asn] Validating x2

[tbl2asn] ERROR: Invalid inference value tRNAscan-SE score:44.5
[tbl2asn] ERROR: Invalid inference value tRNAscan-SE score:37.9
[tbl2asn] ERROR: Invalid inference value tRNAscan-SE score:37.9
[tbl2asn] Flatfile x3

[tbl2asn] Validating x3

[tbl2asn] ERROR: Invalid inference value tRNAscan-SE score:47.6
[tbl2asn] Flatfile x4

[tbl2asn] Validating x4

[tbl2asn] Flatfile x5

[tbl2asn] Validating x5

[tbl2asn] Flatfile x6

[tbl2asn] Validating x6

[tbl2asn] ERROR: Invalid inference value tRNAscan-SE score:44.5
[tbl2asn] ERROR: Invalid inference value tRNAscan-SE score:37.9
[tbl2asn] ERROR: Invalid inference value tRNAscan-SE score:37.9
[tbl2asn] Flatfile x7

[tbl2asn] Validating x7

[tbl2asn] Flatfile x8

[tbl2asn] Validating x8

[tbl2asn] Flatfile x9

[tbl2asn] Validating x9

Making gtf tables from final feature tables

kindly let me know how to resolve this

[mtisza1]

Hi,

Thanks for opening this issue. I'm nearly sure that, despite the error message, this is actually not a problem. The tbl2asn program doesn't recognize the "score" field, and flags that the system may throw an error if you were to submit the .sqn files of the virus genomes to GenBank. However, I've submitted many phage genomes encoding tRNAs annotated by Cenote-Taker 2 to GenBank with the "score" field, and I haven't had an issue.

Just to be sure, can you please open the genome maps (.gbf files) for the genomes with tRNAs to be sure that the tRNA annotations look OK? If there is something wrong with those, I'll look into the issue further.

Best,

Mike