#!/usr/bin/env bash
# Bulk download script for GSE69889
# Generated from Yeo Lab Publications Database
# Total files: 132

OUTDIR="GSE69889"
mkdir -p "$OUTDIR"
cd "$OUTDIR"

# --- GEO supplementary files ---
wget -nc "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE69nnn/GSE69889/suppl/GSE69889_Cycling_Human_Islet_Genes.txt.gz" -O "GSE69889_Cycling_Human_Islet_Genes.txt.gz"
wget -nc "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE69nnn/GSE69889/suppl/GSE69889_Cycling_Mouse_Islet_Genes.txt.gz" -O "GSE69889_Cycling_Mouse_Islet_Genes.txt.gz"

# --- SRA run files ---
# Tip: use 'fasterq-dump' from SRA Toolkit for FASTQ conversion
#      with optional renaming to original submitted FASTQ names.
# Set to 1 to rename SRR outputs (e.g. SRR_1.fastq.gz -> sample_R1.fastq.gz)
RENAME_SRA_TO_ORIGINAL=1

_compress_if_exists() {
  local stem="$1"
  if [ -f "${stem}.fastq" ]; then
    gzip -f "${stem}.fastq"
    echo "${stem}.fastq.gz"
    return 0
  fi
  if [ -f "${stem}.fq" ]; then
    gzip -f "${stem}.fq"
    echo "${stem}.fq.gz"
    return 0
  fi
  return 1
}

# Option A: Download via SRA Toolkit (recommended)
fasterq-dump --split-files "SRR2063284"
gz1="$(_compress_if_exists 'SRR2063284_1' || true)"
gz2="$(_compress_if_exists 'SRR2063284_2' || true)"
gzs="$(_compress_if_exists 'SRR2063284' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "M1CT00_1.fq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "M1CT00_2.fq.gz"
fi

fasterq-dump --split-files "SRR2063285"
gz1="$(_compress_if_exists 'SRR2063285_1' || true)"
gz2="$(_compress_if_exists 'SRR2063285_2' || true)"
gzs="$(_compress_if_exists 'SRR2063285' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "M1CT04_1.fq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "M1CT04_2.fq.gz"
fi

fasterq-dump --split-files "SRR2063286"
gz1="$(_compress_if_exists 'SRR2063286_1' || true)"
gz2="$(_compress_if_exists 'SRR2063286_2' || true)"
gzs="$(_compress_if_exists 'SRR2063286' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "M1CT08_1.fq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "M1CT08_2.fq.gz"
fi

fasterq-dump --split-files "SRR2063287"
gz1="$(_compress_if_exists 'SRR2063287_1' || true)"
gz2="$(_compress_if_exists 'SRR2063287_2' || true)"
gzs="$(_compress_if_exists 'SRR2063287' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "M1CT12_1.fq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "M1CT12_2.fq.gz"
fi

fasterq-dump --split-files "SRR2063288"
gz1="$(_compress_if_exists 'SRR2063288_1' || true)"
gz2="$(_compress_if_exists 'SRR2063288_2' || true)"
gzs="$(_compress_if_exists 'SRR2063288' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "M1CT16_1.fq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "M1CT16_2.fq.gz"
fi

fasterq-dump --split-files "SRR2063289"
gz1="$(_compress_if_exists 'SRR2063289_1' || true)"
gz2="$(_compress_if_exists 'SRR2063289_2' || true)"
gzs="$(_compress_if_exists 'SRR2063289' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "M1CT20_1.fq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "M1CT20_2.fq.gz"
fi

fasterq-dump --split-files "SRR2063290"
gz1="$(_compress_if_exists 'SRR2063290_1' || true)"
gz2="$(_compress_if_exists 'SRR2063290_2' || true)"
gzs="$(_compress_if_exists 'SRR2063290' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "M1CT24_1.fq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "M1CT24_2.fq.gz"
fi

fasterq-dump --split-files "SRR2063291"
gz1="$(_compress_if_exists 'SRR2063291_1' || true)"
gz2="$(_compress_if_exists 'SRR2063291_2' || true)"
gzs="$(_compress_if_exists 'SRR2063291' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "M1CT28_1.fq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "M1CT28_2.fq.gz"
fi

fasterq-dump --split-files "SRR2063292"
gz1="$(_compress_if_exists 'SRR2063292_1' || true)"
gz2="$(_compress_if_exists 'SRR2063292_2' || true)"
gzs="$(_compress_if_exists 'SRR2063292' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "M1CT32_1.fq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "M1CT32_2.fq.gz"
fi

fasterq-dump --split-files "SRR2063293"
gz1="$(_compress_if_exists 'SRR2063293_1' || true)"
gz2="$(_compress_if_exists 'SRR2063293_2' || true)"
gzs="$(_compress_if_exists 'SRR2063293' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "M1CT36_1.fq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "M1CT36_2.fq.gz"
fi

fasterq-dump --split-files "SRR2063294"
gz1="$(_compress_if_exists 'SRR2063294_1' || true)"
gz2="$(_compress_if_exists 'SRR2063294_2' || true)"
gzs="$(_compress_if_exists 'SRR2063294' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "M1CT40_1.fq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "M1CT40_2.fq.gz"
fi

fasterq-dump --split-files "SRR2063295"
gz1="$(_compress_if_exists 'SRR2063295_1' || true)"
gz2="$(_compress_if_exists 'SRR2063295_2' || true)"
gzs="$(_compress_if_exists 'SRR2063295' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "M1CT44_1.fq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "M1CT44_2.fq.gz"
fi

fasterq-dump --split-files "SRR2063296"
gz1="$(_compress_if_exists 'SRR2063296_1' || true)"
gz2="$(_compress_if_exists 'SRR2063296_2' || true)"
gzs="$(_compress_if_exists 'SRR2063296' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "M2CT00_1.fq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "M2CT00_2.fq.gz"
fi

fasterq-dump --split-files "SRR2063297"
gz1="$(_compress_if_exists 'SRR2063297_1' || true)"
gz2="$(_compress_if_exists 'SRR2063297_2' || true)"
gzs="$(_compress_if_exists 'SRR2063297' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "M2CT04_1.fq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "M2CT04_2.fq.gz"
fi

fasterq-dump --split-files "SRR2063298"
gz1="$(_compress_if_exists 'SRR2063298_1' || true)"
gz2="$(_compress_if_exists 'SRR2063298_2' || true)"
gzs="$(_compress_if_exists 'SRR2063298' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "M2CT08_1.fq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "M2CT08_2.fq.gz"
fi

fasterq-dump --split-files "SRR2063299"
gz1="$(_compress_if_exists 'SRR2063299_1' || true)"
gz2="$(_compress_if_exists 'SRR2063299_2' || true)"
gzs="$(_compress_if_exists 'SRR2063299' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "M2CT12_1.fq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "M2CT12_2.fq.gz"
fi

fasterq-dump --split-files "SRR2063300"
gz1="$(_compress_if_exists 'SRR2063300_1' || true)"
gz2="$(_compress_if_exists 'SRR2063300_2' || true)"
gzs="$(_compress_if_exists 'SRR2063300' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "M2CT16_1.fq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "M2CT16_2.fq.gz"
fi

fasterq-dump --split-files "SRR2063301"
gz1="$(_compress_if_exists 'SRR2063301_1' || true)"
gz2="$(_compress_if_exists 'SRR2063301_2' || true)"
gzs="$(_compress_if_exists 'SRR2063301' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "M2CT20_1.fq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "M2CT20_2.fq.gz"
fi

fasterq-dump --split-files "SRR2063302"
gz1="$(_compress_if_exists 'SRR2063302_1' || true)"
gz2="$(_compress_if_exists 'SRR2063302_2' || true)"
gzs="$(_compress_if_exists 'SRR2063302' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "M2CT24_1.fq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "M2CT24_2.fq.gz"
fi

fasterq-dump --split-files "SRR2063303"
gz1="$(_compress_if_exists 'SRR2063303_1' || true)"
gz2="$(_compress_if_exists 'SRR2063303_2' || true)"
gzs="$(_compress_if_exists 'SRR2063303' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "M2CT28_1.fq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "M2CT28_2.fq.gz"
fi

fasterq-dump --split-files "SRR2063304"
gz1="$(_compress_if_exists 'SRR2063304_1' || true)"
gz2="$(_compress_if_exists 'SRR2063304_2' || true)"
gzs="$(_compress_if_exists 'SRR2063304' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "M2CT32_1.fq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "M2CT32_2.fq.gz"
fi

fasterq-dump --split-files "SRR2063305"
gz1="$(_compress_if_exists 'SRR2063305_1' || true)"
gz2="$(_compress_if_exists 'SRR2063305_2' || true)"
gzs="$(_compress_if_exists 'SRR2063305' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "M2CT36_1.fq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "M2CT36_2.fq.gz"
fi

fasterq-dump --split-files "SRR2063306"
gz1="$(_compress_if_exists 'SRR2063306_1' || true)"
gz2="$(_compress_if_exists 'SRR2063306_2' || true)"
gzs="$(_compress_if_exists 'SRR2063306' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "M2CT40_1.fq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "M2CT40_2.fq.gz"
fi

fasterq-dump --split-files "SRR2063307"
gz1="$(_compress_if_exists 'SRR2063307_1' || true)"
gz2="$(_compress_if_exists 'SRR2063307_2' || true)"
gzs="$(_compress_if_exists 'SRR2063307' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "M2CT44_1.fq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "M2CT44_2.fq.gz"
fi

fasterq-dump --split-files "SRR2063308"
gz1="$(_compress_if_exists 'SRR2063308_1' || true)"
gz2="$(_compress_if_exists 'SRR2063308_2' || true)"
gzs="$(_compress_if_exists 'SRR2063308' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "M3CT00_1.fq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "M3CT00_2.fq.gz"
fi

fasterq-dump --split-files "SRR2063309"
gz1="$(_compress_if_exists 'SRR2063309_1' || true)"
gz2="$(_compress_if_exists 'SRR2063309_2' || true)"
gzs="$(_compress_if_exists 'SRR2063309' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "M3CT04_1.fq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "M3CT04_2.fq.gz"
fi

fasterq-dump --split-files "SRR2063310"
gz1="$(_compress_if_exists 'SRR2063310_1' || true)"
gz2="$(_compress_if_exists 'SRR2063310_2' || true)"
gzs="$(_compress_if_exists 'SRR2063310' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "M3CT08_1.fq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "M3CT08_2.fq.gz"
fi

fasterq-dump --split-files "SRR2063311"
gz1="$(_compress_if_exists 'SRR2063311_1' || true)"
gz2="$(_compress_if_exists 'SRR2063311_2' || true)"
gzs="$(_compress_if_exists 'SRR2063311' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "M3CT12_1.fq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "M3CT12_2.fq.gz"
fi

fasterq-dump --split-files "SRR2063312"
gz1="$(_compress_if_exists 'SRR2063312_1' || true)"
gz2="$(_compress_if_exists 'SRR2063312_2' || true)"
gzs="$(_compress_if_exists 'SRR2063312' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "M3CT16_1.fq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "M3CT16_2.fq.gz"
fi

fasterq-dump --split-files "SRR2063313"
gz1="$(_compress_if_exists 'SRR2063313_1' || true)"
gz2="$(_compress_if_exists 'SRR2063313_2' || true)"
gzs="$(_compress_if_exists 'SRR2063313' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "M3CT20_1.fq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "M3CT20_2.fq.gz"
fi

fasterq-dump --split-files "SRR2063314"
gz1="$(_compress_if_exists 'SRR2063314_1' || true)"
gz2="$(_compress_if_exists 'SRR2063314_2' || true)"
gzs="$(_compress_if_exists 'SRR2063314' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "M3CT24_1.fq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "M3CT24_2.fq.gz"
fi

fasterq-dump --split-files "SRR2063315"
gz1="$(_compress_if_exists 'SRR2063315_1' || true)"
gz2="$(_compress_if_exists 'SRR2063315_2' || true)"
gzs="$(_compress_if_exists 'SRR2063315' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "M3CT28_1.fq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "M3CT28_2.fq.gz"
fi

fasterq-dump --split-files "SRR2063316"
gz1="$(_compress_if_exists 'SRR2063316_1' || true)"
gz2="$(_compress_if_exists 'SRR2063316_2' || true)"
gzs="$(_compress_if_exists 'SRR2063316' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "M3CT32_1.fq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "M3CT32_2.fq.gz"
fi

fasterq-dump --split-files "SRR2063317"
gz1="$(_compress_if_exists 'SRR2063317_1' || true)"
gz2="$(_compress_if_exists 'SRR2063317_2' || true)"
gzs="$(_compress_if_exists 'SRR2063317' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "M3CT36_1.fq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "M3CT36_2.fq.gz"
fi

fasterq-dump --split-files "SRR2063318"
gz1="$(_compress_if_exists 'SRR2063318_1' || true)"
gz2="$(_compress_if_exists 'SRR2063318_2' || true)"
gzs="$(_compress_if_exists 'SRR2063318' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "M3CT40_1.fq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "M3CT40_2.fq.gz"
fi

fasterq-dump --split-files "SRR2063319"
gz1="$(_compress_if_exists 'SRR2063319_1' || true)"
gz2="$(_compress_if_exists 'SRR2063319_2' || true)"
gzs="$(_compress_if_exists 'SRR2063319' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "M3CT44_1.fq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "M3CT44_2.fq.gz"
fi

fasterq-dump --split-files "SRR2063320"
gz1="$(_compress_if_exists 'SRR2063320_1' || true)"
gz2="$(_compress_if_exists 'SRR2063320_2' || true)"
gzs="$(_compress_if_exists 'SRR2063320' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "FloxControl01_B_1.fq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "FloxControl01_B_2.fq.gz"
fi

fasterq-dump --split-files "SRR2063321"
gz1="$(_compress_if_exists 'SRR2063321_1' || true)"
gz2="$(_compress_if_exists 'SRR2063321_2' || true)"
gzs="$(_compress_if_exists 'SRR2063321' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "FloxControl02_B_1.fq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "FloxControl02_B_2.fq.gz"
fi

fasterq-dump --split-files "SRR2063322"
gz1="$(_compress_if_exists 'SRR2063322_1' || true)"
gz2="$(_compress_if_exists 'SRR2063322_2' || true)"
gzs="$(_compress_if_exists 'SRR2063322' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "FloxControl03_B_1.fq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "FloxControl03_B_2.fq.gz"
fi

fasterq-dump --split-files "SRR2063323"
gz1="$(_compress_if_exists 'SRR2063323_1' || true)"
gz2="$(_compress_if_exists 'SRR2063323_2' || true)"
gzs="$(_compress_if_exists 'SRR2063323' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "Bmal1KO01_B_1.fq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "Bmal1KO01_B_2.fq.gz"
fi

fasterq-dump --split-files "SRR2063324"
gz1="$(_compress_if_exists 'SRR2063324_1' || true)"
gz2="$(_compress_if_exists 'SRR2063324_2' || true)"
gzs="$(_compress_if_exists 'SRR2063324' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "Bmal1KO02_B_1.fq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "Bmal1KO02_B_2.fq.gz"
fi

fasterq-dump --split-files "SRR2063325"
gz1="$(_compress_if_exists 'SRR2063325_1' || true)"
gz2="$(_compress_if_exists 'SRR2063325_2' || true)"
gzs="$(_compress_if_exists 'SRR2063325' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "Bmal1KO03_2_B.fq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "Bmal1KO03_1_B.fq.gz"
fi

fasterq-dump --split-files "SRR2063326"
gz1="$(_compress_if_exists 'SRR2063326_1' || true)"
gz2="$(_compress_if_exists 'SRR2063326_2' || true)"
gzs="$(_compress_if_exists 'SRR2063326' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "D1CT00_1.fq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "D1CT00_2.fq.gz"
fi

fasterq-dump --split-files "SRR2063327"
gz1="$(_compress_if_exists 'SRR2063327_1' || true)"
gz2="$(_compress_if_exists 'SRR2063327_2' || true)"
gzs="$(_compress_if_exists 'SRR2063327' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "D1CT04_1.fq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "D1CT04_2.fq.gz"
fi

fasterq-dump --split-files "SRR2063328"
gz1="$(_compress_if_exists 'SRR2063328_1' || true)"
gz2="$(_compress_if_exists 'SRR2063328_2' || true)"
gzs="$(_compress_if_exists 'SRR2063328' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "D1CT08_1.fq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "D1CT08_2.fq.gz"
fi

fasterq-dump --split-files "SRR2063329"
gz1="$(_compress_if_exists 'SRR2063329_1' || true)"
gz2="$(_compress_if_exists 'SRR2063329_2' || true)"
gzs="$(_compress_if_exists 'SRR2063329' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "D1CT12_1.fq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "D1CT12_2.fq.gz"
fi

fasterq-dump --split-files "SRR2063330"
gz1="$(_compress_if_exists 'SRR2063330_1' || true)"
gz2="$(_compress_if_exists 'SRR2063330_2' || true)"
gzs="$(_compress_if_exists 'SRR2063330' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "D1CT16_1.fq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "D1CT16_2.fq.gz"
fi

fasterq-dump --split-files "SRR2063331"
gz1="$(_compress_if_exists 'SRR2063331_1' || true)"
gz2="$(_compress_if_exists 'SRR2063331_2' || true)"
gzs="$(_compress_if_exists 'SRR2063331' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "D1CT20_1.fq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "D1CT20_2.fq.gz"
fi

fasterq-dump --split-files "SRR2063332"
gz1="$(_compress_if_exists 'SRR2063332_1' || true)"
gz2="$(_compress_if_exists 'SRR2063332_2' || true)"
gzs="$(_compress_if_exists 'SRR2063332' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "D2CT00_1.fq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "D2CT00_2.fq.gz"
fi

fasterq-dump --split-files "SRR2063333"
gz1="$(_compress_if_exists 'SRR2063333_1' || true)"
gz2="$(_compress_if_exists 'SRR2063333_2' || true)"
gzs="$(_compress_if_exists 'SRR2063333' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "D2CT04_1.fq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "D2CT04_2.fq.gz"
fi

fasterq-dump --split-files "SRR2063334"
gz1="$(_compress_if_exists 'SRR2063334_1' || true)"
gz2="$(_compress_if_exists 'SRR2063334_2' || true)"
gzs="$(_compress_if_exists 'SRR2063334' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "D2CT08_1.fq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "D2CT08_2.fq.gz"
fi

fasterq-dump --split-files "SRR2063335"
gz1="$(_compress_if_exists 'SRR2063335_1' || true)"
gz2="$(_compress_if_exists 'SRR2063335_2' || true)"
gzs="$(_compress_if_exists 'SRR2063335' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "D2CT12_1.fq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "D2CT12_2.fq.gz"
fi

fasterq-dump --split-files "SRR2063336"
gz1="$(_compress_if_exists 'SRR2063336_1' || true)"
gz2="$(_compress_if_exists 'SRR2063336_2' || true)"
gzs="$(_compress_if_exists 'SRR2063336' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "D2CT16_1.fq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "D2CT16_2.fq.gz"
fi

fasterq-dump --split-files "SRR2063337"
gz1="$(_compress_if_exists 'SRR2063337_1' || true)"
gz2="$(_compress_if_exists 'SRR2063337_2' || true)"
gzs="$(_compress_if_exists 'SRR2063337' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "D2CT20_1.fq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "D2CT20_2.fq.gz"
fi

fasterq-dump --split-files "SRR2063338"
gz1="$(_compress_if_exists 'SRR2063338_1' || true)"
gz2="$(_compress_if_exists 'SRR2063338_2' || true)"
gzs="$(_compress_if_exists 'SRR2063338' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "D3CT00_1.fq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "D3CT00_2.fq.gz"
fi

fasterq-dump --split-files "SRR2063339"
gz1="$(_compress_if_exists 'SRR2063339_1' || true)"
gz2="$(_compress_if_exists 'SRR2063339_2' || true)"
gzs="$(_compress_if_exists 'SRR2063339' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "D3CT04_1.fq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "D3CT04_2.fq.gz"
fi

fasterq-dump --split-files "SRR2063340"
gz1="$(_compress_if_exists 'SRR2063340_1' || true)"
gz2="$(_compress_if_exists 'SRR2063340_2' || true)"
gzs="$(_compress_if_exists 'SRR2063340' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "D3CT08_1.fq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "D3CT08_2.fq.gz"
fi

fasterq-dump --split-files "SRR2063341"
gz1="$(_compress_if_exists 'SRR2063341_1' || true)"
gz2="$(_compress_if_exists 'SRR2063341_2' || true)"
gzs="$(_compress_if_exists 'SRR2063341' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "D3CT12_1.fq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "D3CT12_2.fq.gz"
fi

fasterq-dump --split-files "SRR2063342"
gz1="$(_compress_if_exists 'SRR2063342_1' || true)"
gz2="$(_compress_if_exists 'SRR2063342_2' || true)"
gzs="$(_compress_if_exists 'SRR2063342' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "D3CT16_1.fq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "D3CT16_2.fq.gz"
fi

fasterq-dump --split-files "SRR2063343"
gz1="$(_compress_if_exists 'SRR2063343_1' || true)"
gz2="$(_compress_if_exists 'SRR2063343_2' || true)"
gzs="$(_compress_if_exists 'SRR2063343' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "D3CT20_1.fq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "D3CT20_2.fq.gz"
fi

fasterq-dump --split-files "SRR2479474"
gz1="$(_compress_if_exists 'SRR2479474_1' || true)"
gz2="$(_compress_if_exists 'SRR2479474_2' || true)"
gzs="$(_compress_if_exists 'SRR2479474' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "FloxControl01_C_1.fq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "FloxControl01_C_2.fq.gz"
fi

fasterq-dump --split-files "SRR2479475"
gz1="$(_compress_if_exists 'SRR2479475_1' || true)"
gz2="$(_compress_if_exists 'SRR2479475_2' || true)"
gzs="$(_compress_if_exists 'SRR2479475' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "FloxControl02_C_1.fq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "FloxControl02_C_2.fq.gz"
fi

fasterq-dump --split-files "SRR2479478"
gz1="$(_compress_if_exists 'SRR2479478_1' || true)"
gz2="$(_compress_if_exists 'SRR2479478_2' || true)"
gzs="$(_compress_if_exists 'SRR2479478' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "Bmal1KO01_C_1.fq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "Bmal1KO01_C_2.fq.gz"
fi

fasterq-dump --split-files "SRR2479480"
gz1="$(_compress_if_exists 'SRR2479480_1' || true)"
gz2="$(_compress_if_exists 'SRR2479480_2' || true)"
gzs="$(_compress_if_exists 'SRR2479480' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "Bmal1KO02_C_1.fq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "Bmal1KO02_C_2.fq.gz"
fi

fasterq-dump --split-files "SRR2479481"
gz1="$(_compress_if_exists 'SRR2479481_1' || true)"
gz2="$(_compress_if_exists 'SRR2479481_2' || true)"
gzs="$(_compress_if_exists 'SRR2479481' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "Bmal1KO03_2_C.fq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "Bmal1KO03_1_C.fq.gz"
fi


# Option B: Direct download (larger .sra files)
curl -L -O -C - "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-11/SRR002/063/SRR2063284/SRR2063284.sralite.1"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR2063285/SRR2063285"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR2063286/SRR2063286"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR2063287/SRR2063287"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR2063288/SRR2063288"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR2063289/SRR2063289"
curl -L -O -C - "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-11/SRR002/063/SRR2063290/SRR2063290.sralite.1"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR2063291/SRR2063291"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR2063292/SRR2063292"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR2063293/SRR2063293"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR2063294/SRR2063294"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR2063295/SRR2063295"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR2063296/SRR2063296"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR2063297/SRR2063297"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR2063298/SRR2063298"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR2063299/SRR2063299"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR2063300/SRR2063300"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR2063301/SRR2063301"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR2063302/SRR2063302"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR2063303/SRR2063303"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR2063304/SRR2063304"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR2063305/SRR2063305"
curl -L -O -C - "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-11/SRR002/063/SRR2063306/SRR2063306.sralite.1"
curl -L -O -C - "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-11/SRR002/063/SRR2063307/SRR2063307.sralite.1"
curl -L -O -C - "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-11/SRR002/063/SRR2063308/SRR2063308.sralite.1"
curl -L -O -C - "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-11/SRR002/063/SRR2063309/SRR2063309.sralite.1"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR2063310/SRR2063310"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR2063311/SRR2063311"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR2063312/SRR2063312"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR2063313/SRR2063313"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR2063314/SRR2063314"
curl -L -O -C - "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-11/SRR002/063/SRR2063315/SRR2063315.sralite.1"
curl -L -O -C - "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-11/SRR002/063/SRR2063316/SRR2063316.sralite.1"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR2063317/SRR2063317"
curl -L -O -C - "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-11/SRR002/063/SRR2063318/SRR2063318.sralite.1"
curl -L -O -C - "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-11/SRR002/063/SRR2063319/SRR2063319.sralite.1"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR2063320/SRR2063320"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR2063321/SRR2063321"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR2063322/SRR2063322"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR2063323/SRR2063323"
curl -L -O -C - "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-11/SRR002/063/SRR2063324/SRR2063324.sralite.1"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR2063325/SRR2063325"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR2063326/SRR2063326"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR2063327/SRR2063327"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR2063328/SRR2063328"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR2063329/SRR2063329"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR2063330/SRR2063330"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR2063331/SRR2063331"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR2063332/SRR2063332"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR2063333/SRR2063333"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR2063334/SRR2063334"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR2063335/SRR2063335"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR2063336/SRR2063336"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR2063337/SRR2063337"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR2063338/SRR2063338"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR2063339/SRR2063339"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR2063340/SRR2063340"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR2063341/SRR2063341"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR2063342/SRR2063342"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR2063343/SRR2063343"
curl -L -O -C - "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-11/SRR002/479/SRR2479474/SRR2479474.sralite.1"
curl -L -O -C - "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-11/SRR002/479/SRR2479475/SRR2479475.sralite.1"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR2479478/SRR2479478"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR2479480/SRR2479480"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR2479481/SRR2479481"

# --- Additional data files ---
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR2063323/SRR2063323"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR2479478/SRR2479478"
curl -L -O -C - "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-11/SRR002/063/SRR2063324/SRR2063324.sralite.1"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR2479480/SRR2479480"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR2063326/SRR2063326"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR2063327/SRR2063327"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR2063328/SRR2063328"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR2063329/SRR2063329"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR2063330/SRR2063330"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR2063332/SRR2063332"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR2063335/SRR2063335"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR2063337/SRR2063337"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR2063338/SRR2063338"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR2063340/SRR2063340"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR2063342/SRR2063342"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR2063343/SRR2063343"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR2063320/SRR2063320"
curl -L -O -C - "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-11/SRR002/479/SRR2479474/SRR2479474.sralite.1"
curl -L -O -C - "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-11/SRR002/479/SRR2479475/SRR2479475.sralite.1"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR2063285/SRR2063285"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR2063287/SRR2063287"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR2063289/SRR2063289"
curl -L -O -C - "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-11/SRR002/063/SRR2063290/SRR2063290.sralite.1"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR2063291/SRR2063291"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR2063293/SRR2063293"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR2063294/SRR2063294"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR2063300/SRR2063300"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR2063301/SRR2063301"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR2063304/SRR2063304"
curl -L -O -C - "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-11/SRR002/063/SRR2063306/SRR2063306.sralite.1"
curl -L -O -C - "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-11/SRR002/063/SRR2063307/SRR2063307.sralite.1"
curl -L -O -C - "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-11/SRR002/063/SRR2063308/SRR2063308.sralite.1"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR2063310/SRR2063310"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR2063311/SRR2063311"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR2063312/SRR2063312"
curl -L -O -C - "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-11/SRR002/063/SRR2063316/SRR2063316.sralite.1"
curl -L -O -C - "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-11/SRR002/063/SRR2063319/SRR2063319.sralite.1"
curl -L -O -C - "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-11/SRR002/063/SRR2063284/SRR2063284.sralite.1"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR2063286/SRR2063286"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR2063288/SRR2063288"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR2063292/SRR2063292"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR2063295/SRR2063295"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR2063296/SRR2063296"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR2063297/SRR2063297"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR2063298/SRR2063298"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR2063299/SRR2063299"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR2063302/SRR2063302"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR2063303/SRR2063303"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR2063305/SRR2063305"
curl -L -O -C - "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-11/SRR002/063/SRR2063309/SRR2063309.sralite.1"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR2063313/SRR2063313"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR2063314/SRR2063314"
curl -L -O -C - "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-11/SRR002/063/SRR2063315/SRR2063315.sralite.1"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR2063317/SRR2063317"
curl -L -O -C - "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-11/SRR002/063/SRR2063318/SRR2063318.sralite.1"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR2063321/SRR2063321"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR2063322/SRR2063322"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR2063325/SRR2063325"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR2063331/SRR2063331"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR2063333/SRR2063333"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR2063334/SRR2063334"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR2063336/SRR2063336"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR2063339/SRR2063339"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR2063341/SRR2063341"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR2479481/SRR2479481"

echo "Download complete. Files saved to $OUTDIR"