Problem with EMBL flat file (ERROR: Invalid {0} line format)
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4.1 years ago
nadal-t ▴ 20

Dear Biostars,

I prepared an EMBL flat file for my fungal genome using EMBLmyGFF3. I am now checking the flat file with embl-api-validator-1.1.263 and below are what it pointed out:


Compressed messages (occurring more than 5 times)

WARNING: "{0}" usually expected to be at least "{1}" nt long. Please check the accuracy. (593 occurrences) (FeatureLengthCheck-1)

WARNING: check qualifier "{0}" values "{1}" for Unmatched left parenthesis of type"{2}". (174 occurrences) (UnbalancedParenthesesCheck_2)

WARNING: check qualifier "{0}" values "{1}"for Unmatched right parenthesis of type"{2}". (25 occurrences) (UnbalancedParenthesesCheck_1)

ERROR: Abutting features cannot be adjacent between neighbouring exons. (19 occurrences) (ExonFeaturesIntervalCheck)

ERROR: Invalid {0} line format (743 occurrences) (FF.1)

While I think I can probably remove the offending exon to correct the Abutting problem, I have absolutely no idea how to fix "Invalid {0} line format" .

Thank you very much for your advice in advance!

Assembly genome • 482 views

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