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EI-CoreBioinformatics / reat

Robust Eukaryotic Annotation Toolkit
https://reat.readthedocs.io/en/latest/
MIT License
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bug call-SubdivideSequence (minor bug, major effect) #20

Closed swarbred closed 2 years ago

swarbred commented 2 years ago

There is a bug with the chunking for augustus (call-SubdivideSequence)

should be start = end + 1 - ~{overlap}

i.e. remove the +

Before the fix This sequence generates the following chunks:

Calendula_officinalis_EIV1.2_Contig_0000001:1-3000001 Calendula_officinalis_EIV1.2_Contig_0000001:2900003-5900003 Calendula_officinalis_EIV1.2_Contig_0000001:8700007-11700007 Calendula_officinalis_EIV1.2_Contig_0000001:20300015-23300015 Calendula_officinalis_EIV1.2_Contig_0000001:43500031-46500031 Calendula_officinalis_EIV1.2_Contig_0000001:89900063-92900063 Calendula_officinalis_EIV1.2_Contig_0000001:182700127-104728146

With the fix

Calendula_officinalis_EIV1.2_Contig_0000001:1-3000001 Calendula_officinalis_EIV1.2_Contig_0000001:2900002-5900002 Calendula_officinalis_EIV1.2_Contig_0000001:5800003-8800003 Calendula_officinalis_EIV1.2_Contig_0000001:8700004-11700004 Calendula_officinalis_EIV1.2_Contig_0000001:11600005-14600005 Calendula_officinalis_EIV1.2_Contig_0000001:14500006-17500006 Calendula_officinalis_EIV1.2_Contig_0000001:17400007-20400007 Calendula_officinalis_EIV1.2_Contig_0000001:20300008-23300008 Calendula_officinalis_EIV1.2_Contig_0000001:23200009-26200009 Calendula_officinalis_EIV1.2_Contig_0000001:26100010-29100010 Calendula_officinalis_EIV1.2_Contig_0000001:29000011-32000011 Calendula_officinalis_EIV1.2_Contig_0000001:31900012-34900012 Calendula_officinalis_EIV1.2_Contig_0000001:34800013-37800013 Calendula_officinalis_EIV1.2_Contig_0000001:37700014-40700014 Calendula_officinalis_EIV1.2_Contig_0000001:40600015-43600015 Calendula_officinalis_EIV1.2_Contig_0000001:43500016-46500016 Calendula_officinalis_EIV1.2_Contig_0000001:46400017-49400017 Calendula_officinalis_EIV1.2_Contig_0000001:49300018-52300018 Calendula_officinalis_EIV1.2_Contig_0000001:52200019-55200019 Calendula_officinalis_EIV1.2_Contig_0000001:55100020-58100020 Calendula_officinalis_EIV1.2_Contig_0000001:58000021-61000021 Calendula_officinalis_EIV1.2_Contig_0000001:60900022-63900022 Calendula_officinalis_EIV1.2_Contig_0000001:63800023-66800023 Calendula_officinalis_EIV1.2_Contig_0000001:66700024-69700024 Calendula_officinalis_EIV1.2_Contig_0000001:69600025-72600025 Calendula_officinalis_EIV1.2_Contig_0000001:72500026-75500026 Calendula_officinalis_EIV1.2_Contig_0000001:75400027-78400027 Calendula_officinalis_EIV1.2_Contig_0000001:78300028-81300028 Calendula_officinalis_EIV1.2_Contig_0000001:81200029-84200029 Calendula_officinalis_EIV1.2_Contig_0000001:84100030-87100030 Calendula_officinalis_EIV1.2_Contig_0000001:87000031-90000031 Calendula_officinalis_EIV1.2_Contig_0000001:89900032-92900032 Calendula_officinalis_EIV1.2_Contig_0000001:92800033-95800033 Calendula_officinalis_EIV1.2_Contig_0000001:95700034-98700034 Calendula_officinalis_EIV1.2_Contig_0000001:98600035-101600035 Calendula_officinalis_EIV1.2_Contig_0000001:101500036-104500036 Calendula_officinalis_EIV1.2_Contig_0000001:104400037-104728146

ljyanesm commented 2 years ago

Fixed by 8ffc62b0

To install the changes on the HPC, go to the reat-dev_prediction path and then into the directory called ...prediction_branch... and run:

source reat-dev_prediction; git pull; pip install .