Fix athalia_rosae: correct assembly GCF_917208135.1 (iyAthRosa1.1) — old accession GCF_000515845.1 was invalid (404)

Author: AI Agent

config/amalgkit/amalgkit_athalia_rosae.yaml

@@ -1,12 +1,12 @@
 # METAINFORMANT Amalgkit Configuration
 # Species: Athalia rosae (Turnip sawfly)
 # NCBI Taxonomy ID: 37344
-# Assembly: GCF_000515845.1
+# Assembly: GCF_917208135.1 (iyAthRosa1.1, chromosome-level)
 # Note: Added for Hymenoptera cross-species tissue comparisons (antenna, brain, ovary, tubules)
 
 work_dir: projects/hymenoptera_amalgkit/data/athalia_rosae/work
 log_dir: projects/hymenoptera_amalgkit/data/athalia_rosae/logs
-threads: 4
+threads: 16
 
 auto_install_amalgkit: true
 
@@ -19,7 +19,7 @@ species_list:
 taxon_id: 37344
 
 genome:
-  accession: GCF_000515845.1
+  accession: GCF_917208135.1
   dest_dir: projects/hymenoptera_amalgkit/data/athalia_rosae/genome
 
   include:
@@ -29,13 +29,13 @@ genome:
     - cds             
     - protein         
 
-  ftp_url: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/515/845/GCF_000515845.1/
+  ftp_url: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/917/208/135/GCF_917208135.1_iyAthRosa1.1/
   files:
-    genomic_fasta: GCF_000515845.1_genomic.fna.gz
-    transcriptome_fasta: GCF_000515845.1_rna_from_genomic.fna.gz
-    cds_fasta: GCF_000515845.1_cds_from_genomic.fna.gz
-    protein_fasta: GCF_000515845.1_protein.faa.gz
-    annotation_gff: GCF_000515845.1_genomic.gff.gz
+    genomic_fasta: GCF_917208135.1_iyAthRosa1.1_genomic.fna.gz
+    transcriptome_fasta: GCF_917208135.1_iyAthRosa1.1_rna_from_genomic.fna.gz
+    cds_fasta: GCF_917208135.1_iyAthRosa1.1_cds_from_genomic.fna.gz
+    protein_fasta: GCF_917208135.1_iyAthRosa1.1_protein.faa.gz
+    annotation_gff: GCF_917208135.1_iyAthRosa1.1_genomic.gff.gz
 
 steps:
   metadata:
@@ -50,13 +50,13 @@ steps:
     max_bp: 10000000000
     out_dir: projects/hymenoptera_amalgkit/data/athalia_rosae/fastq
     remove_sra: yes
-    threads: 4
+    threads: 16
     pfd: yes
     redo: no
   quant:
     jobs: 1
     out_dir: projects/hymenoptera_amalgkit/data/athalia_rosae/quant
-    threads: 4
+    threads: 16
     redo: no
     keep_fastq: no
   merge: