Nucleotide sequences of genes in 'genome_genes' directory all have identical sequences

[rhysnewell]

Hey Joel,

Hope you are doing well! Found a funky bug in the nucleotide sequence output from enrichm annotate. Here's an example:

>contig_112_pilon_1 TATTTAGTTAATATGTCATTTATATCTTTTGCATTTAGAGAAGAGTATGAGAAGGTAAAGCTTTTGGGAGACAAATTGAACGAGATTGACTCATTGATCAACTGGGAATCATTTAGACCGATAGTGAAAGATATGTTTGACAACAAAAGTGAAAAGGGTGGACGTCCTAATATCGATGAAGTTGTAATGATCAAAACCCTGATTTTACAGGAGTGGCATGGTCTTTCTGATCCAGAACTTGAGCGACAAATCACCGACAGGATATCCTTCCGCAAGTTTTTAGGTTTTCCTGAAAACATACCTGATTTCACAACAGTCTGGACTTTTCGAGAGCGGTTAAGCAAAAAAGGTAAGGACAAAGAAATCTGGAAAGAATTACAGAGACAGCTTGATTCAAAGGGATTGAAGGTAAAAAAGGGGGTTATACAGGATGCAACATTTATCACATCTGATCCAGGACATGCAAAAGCAGATAAACCAAGAGGTGATGAGGCAAAAACACGAAGAAGTAAAGATGGTACCTGGGTAAAAAAGAACAGTAAGTCATACTTCGGGTATAAGTTTCACTCAAAGGAAGATGTTGATTACGGTCTTATAAGGAAGATCGAGACTACAACGGCATCAGTACACGATAGTCAGATTGATCTCTCTGAACCAGGAGAAGTCGTGTACAAGGATAAAGGATATTTTGGAGCGTCATCAAAAGGATACAGTGCGACTATGAGAAGATCTGTTCGTGGTCATCCGATTGGTATCAAAGATATTCTGCGTAACAAACGAATTAGCAAGAAAAGAGCACCTGGAGAAAGACCCTATGCAGTGATTAAAAATGTATTCAAATCAGGGCATATTATGGTTACAACCGTTGCCAGGGCAGCAGTCAAAACGGTATTTACAGCATTTGGATTCAATCTATATCAACTCTTAACTTTGAAGAAACAAGGAATTGTATAG >contig_112_pilon_2 K20155 TATTTAGTTAATATGTCATTTATATCTTTTGCATTTAGAGAAGAGTATGAGAAGGTAAAGCTTTTGGGAGACAAATTGAACGAGATTGACTCATTGATCAACTGGGAATCATTTAGACCGATAGTGAAAGATATGTTTGACAACAAAAGTGAAAAGGGTGGACGTCCTAATATCGATGAAGTTGTAATGATCAAAACCCTGATTTTACAGGAGTGGCATGGTCTTTCTGATCCAGAACTTGAGCGACAAATCACCGACAGGATATCCTTCCGCAAGTTTTTAGGTTTTCCTGAAAACATACCTGATTTCACAACAGTCTGGACTTTTCGAGAGCGGTTAAGCAAAAAAGGTAAGGACAAAGAAATCTGGAAAGAATTACAGAGACAGCTTGATTCAAAGGGATTGAAGGTAAAAAAGGGGGTTATACAGGATGCAACATTTATCACATCTGATCCAGGACATGCAAAAGCAGATAAACCAAGAGGTGATGAGGCAAAAACACGAAGAAGTAAAGATGGTACCTGGGTAAAAAAGAACAGTAAGTCATACTTCGGGTATAAGTTTCACTCAAAGGAAGATGTTGATTACGGTCTTATAAGGAAGATCGAGACTACAACGGCATCAGTACACGATAGTCAGATTGATCTCTCTGAACCAGGAGAAGTCGTGTACAAGGATAAAGGATATTTTGGAGCGTCATCAAAAGGATACAGTGCGACTATGAGAAGATCTGTTCGTGGTCATCCGATTGGTATCAAAGATATTCTGCGTAACAAACGAATTAGCAAGAAAAGAGCACCTGGAGAAAGACCCTATGCAGTGATTAAAAATGTATTCAAATCAGGGCATATTATGGTTACAACCGTTGCCAGGGCAGCAGTCAAAACGGTATTTACAGCATTTGGATTCAATCTATATCAACTCTTAACTTTGAAGAAACAAGGAATTGTATAG >contig_112_pilon_3 TATTTAGTTAATATGTCATTTATATCTTTTGCATTTAGAGAAGAGTATGAGAAGGTAAAGCTTTTGGGAGACAAATTGAACGAGATTGACTCATTGATCAACTGGGAATCATTTAGACCGATAGTGAAAGATATGTTTGACAACAAAAGTGAAAAGGGTGGACGTCCTAATATCGATGAAGTTGTAATGATCAAAACCCTGATTTTACAGGAGTGGCATGGTCTTTCTGATCCAGAACTTGAGCGACAAATCACCGACAGGATATCCTTCCGCAAGTTTTTAGGTTTTCCTGAAAACATACCTGATTTCACAACAGTCTGGACTTTTCGAGAGCGGTTAAGCAAAAAAGGTAAGGACAAAGAAATCTGGAAAGAATTACAGAGACAGCTTGATTCAAAGGGATTGAAGGTAAAAAAGGGGGTTATACAGGATGCAACATTTATCACATCTGATCCAGGACATGCAAAAGCAGATAAACCAAGAGGTGATGAGGCAAAAACACGAAGAAGTAAAGATGGTACCTGGGTAAAAAAGAACAGTAAGTCATACTTCGGGTATAAGTTTCACTCAAAGGAAGATGTTGATTACGGTCTTATAAGGAAGATCGAGACTACAACGGCATCAGTACACGATAGTCAGATTGATCTCTCTGAACCAGGAGAAGTCGTGTACAAGGATAAAGGATATTTTGGAGCGTCATCAAAAGGATACAGTGCGACTATGAGAAGATCTGTTCGTGGTCATCCGATTGGTATCAAAGATATTCTGCGTAACAAACGAATTAGCAAGAAAAGAGCACCTGGAGAAAGACCCTATGCAGTGATTAAAAATGTATTCAAATCAGGGCATATTATGGTTACAACCGTTGCCAGGGCAGCAGTCAAAACGGTATTTACAGCATTTGGATTCAATCTATATCAACTCTTAACTTTGAAGAAACAAGGAATTGTATAG

As you can see, these are all the same sequence.

Thanks,

Rhys

[geronimp]

Hey Rhys,

Thanks for the bug report! Is this just running the default enrichm enrichment pipeline?

[rhysnewell]

This is running enrichm annotate on two genomes, using ko_hmm and then everything else as default. Also, the release version is 0.5.0rc1

[danielkim617]

I got the same error