BaitDesigner ran as expected and generated many baits but the out put fasta files don't have the corresponding gene name in front of the bait number, the SN in dictionary as well as input and out put interval lists look fine and the headers in the input fasta file are fine too. They're just missing from the bait pool fasta files

java -jar $EBROOTPICARD/picard.jar BaitDesigner --TARGETS CryptoDB-62_CparvumIOWA-ATCC_Genome.interval_list --DESIGN_NAME Cparvum_Baits_Transcript --REFERENCE_SEQUENCE CryptoDB-62_CparvumIOWA-ATCC_AnnotatedTranscripts.fasta --BAIT_OFFSET 60 --BAIT_SIZE 120

11:10:14.109 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/flask/apps/eb/software/picard/2.23.8-Java-11/picard.jar!/com/intel/gkl/native/libgkl_compression.so

[Wed Apr 12 11:10:14 BST 2023] BaitDesigner --TARGETS CryptoDB-62_CparvumIOWA-ATCC_Genome.interval_list --DESIGN_NAME Cparvum_Baits_Transcript --BAIT_SIZE 120 --BAIT_OFFSET 60 --REFERENCE_SEQUENCE CryptoDB-62_CparvumIOWA-ATCC_AnnotatedTranscripts.fasta --LEFT_PRIMER ATCGCACCAGCGTGT --RIGHT_PRIMER CACTGCGGCTCCTCA --DESIGN_STRATEGY FixedOffset --MINIMUM_BAITS_PER_TARGET 2 --PADDING 0 --REPEAT_TOLERANCE 50 --POOL_SIZE 55000 --FILL_POOLS true --DESIGN_ON_TARGET_STRAND false --MERGE_NEARBY_TARGETS true --OUTPUT_AGILENT_FILES true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false

[Wed Apr 12 11:10:14 BST 2023] Executing as on Linux 3.10.0-1160.62.1.el7.x86_64 amd64; OpenJDK 64-Bit Server VM 11.0.2+9; Deflater: Intel; Inflater: Intel; Provider GCS is not available; Picard version: Version:2.23.8

INFO    2023-04-12 11:10:14     BaitDesigner    Starting with 4428 targets.

INFO    2023-04-12 11:10:14     BaitDesigner    After uniquing 4428 targets remain.

INFO    2023-04-12 11:10:14     BaitDesigner    After collapsing nearby targets 4428 targets remain.

INFO    2023-04-12 11:10:15     BaitDesigner    Designed and kept 119522 baits, discarded 0

[Wed Apr 12 11:10:15 BST 2023] picard.util.BaitDesigner done. Elapsed time: 0.03 minutes.