[maker-devel] Dashes in transcript predictions

[Sujai]

Dear Maker Team

On a recent run with maker 2.31, I noticed that a couple of the transcripts
had dashes/hyphens in them.

Example:
>snap_masked-nGt.0.3.035610-processed-gene-0.2-mRNA-1 transcript offset:261
AED:0.25 eAED:0.25 QI:261|0.4|0.83|0.83|0.8|0.83|6|0|240
TTTGATTATTAATTATTTTTGTCTTTATTAA-------AAAATAATTTTGGTACAAACAATCGAATTAATAT-TAATTAAAGTTTTTATCAGCCTTATAAAATCTACGACACCGGCTTTTACCAATGTTTAGCG
AGTGATTCTCTCAACAGAAGTATCTCCAAATCAATATTCGTTGAATGTAAATGAACCCAAACACCTTATTCTCATTCCTCCGGAAGAAGCTCCTGAATCAACTTTTGATCTCTACAGTAATGTATCTATGAATT
GCGAAGGAAGAAGTTATTTTCCGAATCAACCAATCATTGTTAATTGGATGTTTAAACATAAAGACTCATATACGACCATAACAAGAGATCACAAAATGGCTACAAGAATAATCACTGCATCAAACAGATCAAAG
GAAACTAATCTTGATTTGGTCAATATATTTTCTTACCTTACCATAAATGATATCCGCGAAGAAGATGGTGGAGTTTACAAATGTGTGATGACTCAAGGAAGTGTTGACGAAGAACAAGAATTTCTAGTAACTAT
AAACAATCAAAGTGAAAAGGAAATTGATGTATCCATTTTTTACCAAGATGATGACTTTGTAAGTGTTCGAGCAGCCTTAGAAACAGTCAAGATTTTAGAGAATTACCAGTTTCGATGTTGGTTGTACGACCGGG
ATAAGACGTATGGTCAAGACGCCGGGAAGCCGACGAAATCGACAGAAAACCGTATAGGTCGTTATTATCAGTCAAAATATTCTGATTGTTCTCAATTTCGCATAGAAAGTTTCTATCAGCTGCCAATTTCTGTT
AACCGATGGCTGAAAAAAGAACTCAGTTTACAGTCTTTCTTTCAGCCATTTAGCTTTAATTGGGACCCTCAAAAAACCCCTAAAAACAAGAAAATGGTAGTATGGGTTGTTTCTTCCCTACCCTCAGCGGCGAT
TCGTAATGCAAAGAGAAGAATCAATGAACAATCTTCTCATGTATAA

The protein prediction for this transcript is ok:

>snap_masked-nGt.0.3.035610-processed-gene-0.2-mRNA-1 protein AED:0.25
eAED:0.25 QI:261|0.4|0.83|0.83|0.8|0.83|6|0|240
MNCEGRSYFPNQPIIVNWMFKHKDSYTTITRDHKMATRIITASNRSKETNLDLVNIFSYLTINDIREEDGGVYKCVMTQGSVDEEQEFLVTINNQSEKEIDVSIFYQDDDFVSVRAALETVKILENYQFRCWLY
DRDKTYGQDAGKPTKSTENRIGRYYQSKYSDCSQFRIESFYQLPISVNRWLKKELSLQSFFQPFSFNWDPQKTPKNKKMVVWVVSSLPSAAIRNAKRRINEQSSHV

Is this a known bug? I tried searching for "dash|hyphen" in the email list
but couldn't find anything else.

Best wishes,

- Sujai

ps. I pulled out just this one contig and ran maker on it. all the
.maker.output files are attached.
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