Mikado pick does't add the CDS

[francicco]

Hi,

For some reason mikado pick doesn't add CDS to the final annotation although in the serialise step all the CDS and Blastp hits are correctly added to the db.

2024-05-24 14:43:23,462 - serialise - serialise.py:321 - INFO - setup - MainProcess - Mikado version: 2.3.3
2024-05-24 14:43:23,463 - serialise - serialise.py:322 - INFO - setup - MainProcess - Command line: /user/work/tk19812/software/mikado-v.2.3.3/venv/bin/mikado serialise --blast-loading-debug --transcripts mikado_prepared.fasta --blast-targets /user/work/tk19812/Databases/SwissProt/uniprot_sprot.fasta --genome_fai /user/work/tk19812/HeliconiniiProject/CompleteAssemblies/AssembledGenomes/Hmel.assembly.v2.5.fasta.fai --genome /user/work/tk19812/HeliconiniiProject/CompleteAssemblies/AssembledGenomes/Hmel.assembly.v2.5.fasta -p 10 --json-conf configuration.yaml --xml mikado.diamond.xml.gz --orfs mikado_prepared.fasta.transdecoder.bed
2024-05-24 14:43:23,478 - serialise - serialise.py:332 - INFO - setup - MainProcess - Random seed: 0
2024-05-24 14:43:23,479 - serialise - serialise.py:345 - INFO - setup - MainProcess - Using a sqlite database (location: mikado.db)
2024-05-24 14:43:23,479 - serialise - serialise.py:348 - INFO - setup - MainProcess - Requested 10 threads, forcing single thread: False
2024-05-24 14:43:23,480 - serialise - serialise.py:176 - INFO - load_orfs - MainProcess - Starting to load ORF data
2024-05-24 14:43:24,077 - Bed12ParseWrapper-3 - bed12.py:1846 - INFO - run - Bed12ParseWrapper-3 - Started 0
2024-05-24 14:43:24,085 - Bed12ParseWrapper-4 - bed12.py:1846 - INFO - run - Bed12ParseWrapper-4 - Started 1
2024-05-24 14:43:24,088 - Bed12ParseWrapper-5 - bed12.py:1846 - INFO - run - Bed12ParseWrapper-5 - Started 2
2024-05-24 14:43:24,093 - Bed12ParseWrapper-6 - bed12.py:1846 - INFO - run - Bed12ParseWrapper-6 - Started 3
2024-05-24 14:43:24,100 - Bed12ParseWrapper-7 - bed12.py:1846 - INFO - run - Bed12ParseWrapper-7 - Started 4
2024-05-24 14:43:24,106 - Bed12ParseWrapper-8 - bed12.py:1846 - INFO - run - Bed12ParseWrapper-8 - Started 5
2024-05-24 14:43:24,113 - Bed12ParseWrapper-9 - bed12.py:1846 - INFO - run - Bed12ParseWrapper-9 - Started 6
2024-05-24 14:43:24,121 - Bed12ParseWrapper-10 - bed12.py:1846 - INFO - run - Bed12ParseWrapper-10 - Started 7
2024-05-24 14:43:24,130 - Bed12ParseWrapper-11 - bed12.py:1846 - INFO - run - Bed12ParseWrapper-11 - Started 8
2024-05-24 14:43:24,137 - Bed12ParseWrapper-12 - bed12.py:1846 - INFO - run - Bed12ParseWrapper-12 - Started 9
2024-05-24 14:43:44,486 - serialise - orf.py:448 - INFO - __serialize_multiple_threads - MainProcess - Finished loading 39657 ORFs into the database
2024-05-24 14:43:44,860 - serialise - serialise.py:187 - INFO - load_orfs - MainProcess - Finished loading ORF data
2024-05-24 14:43:44,876 - serialise - serialise.py:142 - INFO - load_blast - MainProcess - Starting to load BLAST data
2024-05-24 14:43:44,876 - serialise - blast_serialiser.py:82 - INFO - __init__ - MainProcess - Number of dedicated workers: 10
2024-05-24 14:43:44,891 - serialise - blast_serialiser.py:106 - WARNING - __init__ - MainProcess - Activating the XML debug mode
2024-05-24 14:43:48,004 - serialise - blast_serialiser.py:249 - INFO - __serialize_targets - MainProcess - Started to serialise the targets
2024-05-24 14:43:51,492 - serialise - blast_serialiser.py:283 - INFO - __serialize_targets - MainProcess - Loaded 569213 objects into the "target" table
2024-05-24 14:43:53,474 - serialise - blast_serialiser.py:174 - INFO - __serialize_queries - MainProcess - Started to serialise the queries
2024-05-24 14:43:53,508 - serialise - blast_serialiser.py:226 - INFO - __serialize_queries - MainProcess - Loaded 0 objects into the "query" table
2024-05-24 14:43:53,605 - serialise - blast_serialiser.py:233 - INFO - __serialize_queries - MainProcess - 44941 in queries
2024-05-24 14:43:53,616 - serialise - xml_serialiser.py:132 - WARNING - _serialise_xmls - MainProcess - Creating a pool with 1 processes
2024-05-24 14:49:52,013 - serialise - xml_serialiser.py:168 - INFO - _serialise_xmls - MainProcess - Loaded 535638 alignments for 0 queries
2024-05-24 14:49:52,017 - serialise - xml_serialiser.py:171 - INFO - _serialise_xmls - MainProcess - Finished loading blast hits
2024-05-24 14:49:54,881 - serialise - serialise.py:160 - INFO - load_blast - MainProcess - Finished to load BLAST data
2024-05-24 14:49:54,885 - serialise - serialise.py:115 - INFO - load_junctions - MainProcess - Starting to load junctions: ['../Hmel.portcullis_filter.0.5/portcullis.ONT.pass.junctions.bed']
2024-05-24 14:51:21,587 - serialise - serialise.py:127 - INFO - load_junctions - MainProcess - Loaded junctions
2024-05-24 14:51:21,591 - serialise - serialise.py:405 - INFO - serialise - MainProcess - Finished
2024-05-24 14:51:21,591 - serialise - serialise.py:408 - INFO - serialise - MainProcess - Copying from the temporary database /tmp/tmpti493a3f.db back to disk mikado.db.
2024-05-24 14:51:21,972 - serialise - serialise.py:411 - INFO - serialise - MainProcess - Copied from the temporary database /tmp/tmpti493a3f.db back to disk mikado.db.

Any explanation as to why this is happening?
Cheers
F