INIT_CMD cp /.../canu4_assembly/canu4_A_alt.fa.gz data.pre/aatro_alt
INIT_CMD gzip -r data.pre/aatro_alt
INIT_CMD mkdir -p data.pre/aatro_alt
RNA_FILE
LOWER_CS_RANK 4
SPLIT_INTO_CONTIGS 1
KEEP_CTG_SCF_CHR_MAPPING 0
ALT_MAPPING_CMD 'cat GCA_002892825.2_ISE6_asm2.2_deduplicated_assembly_structure/all_alt_scaffold_placement.txt | cut -f 4,7,9,10-12,13-14 | grep -v na'
ASM_SCAF_MAPPING_FILE GCA_004352715.1_Hmi_1.0_assembly_report.txt
HAS_NON_REF 1
HAS_NON_REF_MAPPING 1
NON_REF_IDS_CMD cat GCA_002892825.2_ISE6_asm2.2_deduplicated_assembly_structure/Alts/component_localID2acc | tail -n +2 | cut -f 2
NON_REF_IDS_CMD cat GCA_004136515.2_ASM413651v2_assembly_structure/haplotigs/component_localID2acc | tail -n +2 | cut -f 2
NON_REF_IDS_CMD zcat GCA_003951495.1_AfunF3_assembly_structure/*/unplaced_scaffolds/AGP/unplaced.scaf.agp.gz | grep ^RCWQ | cut -f 1 | sort | uniq
OLD_REGION_SYNS_CMD
OLD_REGION_SYNS_DB drosophila_melanogaster_core_98_7
GFF_LOGIC_NAME
GFF_GENE_SOURCE Ensembl_Metazoa
PREPROCESS_GFF YES
DROP_CD_PFX cds-
DROP_EXON_PFX exon-gnl|WGS:VCGU|
DROP_GENE_PFX gene-
DROP_MRNA_PFX rna-gnl|WGS:VCGU|
ORIG_GENE_PFX AATE
ORIG_GENE_PFX g
ORIG_GENE_PFX gene
APPLY_PROTEIN_SEQEDITS YES
TAXON_ID 7227
COPY_STABLE_IDS_HISTORY YES
ATAC_FROM_CMD
ATAC_FROM_DB anopheles_atroparvus_core_1906_95_3
ATAC_FROM_DB_GENES anopheles_gambiae_core_1904_95_4
PROJ_COMPARA_CMD
PROJ_COMPARA_DB ensembl_compara_master
PROJ_COMPARA_FILTER_SRC YES
PROJ_COMPARA_FROM_CMD
PROJ_COMPARA_FROM_DB anopheles_atroparvus_core_1906_95_3
PROJ_COMPARA_FROM_GENEPFX AATE
COMPARA_PROJ_TO_GFF_OPTS -exon_inflation_max 3 -exons_gained_max 10
COMPARA_PROJ_TO_GFF_OPTS -exon_inflation_max 3 -unplaced_ctg "UNK" -exons_gained_max 10
RUN_VB_XREF NO/YES
REPBASE_SPECIES_NAME Drosophila_melanogaster
RM_CLEAN_PEP_FILE /.../Anopheles-funestus-FUMOZ_PEPTIDES_AfunF1.10.fa.gz
RM_CLEAN_RNA_FILE /.../Ixodes-scapularis-Wikel_TRANSCRIPTS_IscaW1.6.fa.gz