etraining --species=generic --stopCodonExcludedFromCDS=true gene.raw.gb 1>generic_train.out 2>generic_train.err
And the error are:
GBProcessor::getGeneList(): Stop codon out of sequence bounds. Ignoring sequence.
Encountered error after reading 1401 annotations.
GBProcessor::getGeneList(): Stop codon out of sequence bounds. Ignoring sequence.
Encountered error after reading 4795 annotations.
Error: In sequence p9_sc00477_896517-901421: One CDS exon does not begin properly after the previous CDS exon.3359 >= 3360
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 5728 annotations.
GBProcessor::getGeneList(): Stop codon out of sequence bounds. Ignoring sequence.
Encountered error after reading 6580 annotations.
GBProcessor::getGeneList(): Stop codon out of sequence bounds. Ignoring sequence.
Encountered error after reading 10454 annotations.
GBProcessor::getGeneList(): Stop codon out of sequence bounds. Ignoring sequence.
Encountered error after reading 11045 annotations.
GBProcessor::getGeneList(): Stop codon out of sequence bounds. Ignoring sequence.
Encountered error after reading 11695 annotations.
Error: In sequence p9_sc02138_221160-230971: One CDS exon does not begin properly after the previous CDS exon.1967 >= 1968
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 11711 annotations.
Error: In sequence p9_sc02293_5716-12857: One CDS exon does not begin properly after the previous CDS exon.1667 >= 1668
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 11983 annotations.
Error: In sequence p9_sc04279_39522-44156: One CDS exon does not begin properly after the previous CDS exon.2501 >= 2502
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 13786 annotations.
Error: In sequence p9_sc04869_20574-31091: One CDS exon does not begin properly after the previous CDS exon.1595 >= 1596
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 14009 annotations.