Usage overview¶

adaptiseq -i accession [options]

-i/--input takes a single accession or a file with one accession per line. adaptiSeq first retrieves the accession's metadata, then downloads each Run it contains, verifies md5, and (optionally) converts/merges.

Full option list¶

Usage:
  adaptiseq -i accession [options]

Required:
  -i, --input     [text|file]   Single accession or a file of accessions (one per line).

Optional:
  -m, --metadata                Skip downloads; only fetch metadata.
  -g, --gzip                    Download FASTQ files in gzip format directly (*.fastq.gz).
  -q, --fastq                   Convert SRA files to FASTQ format.
  -t, --threads   int           Threads for SRA->FASTQ / compression (default: 8).
  -e, --merge     [ex|sa|st]    Merge fastq files per Experiment / Sample / Study.
  -d, --database  [ena|sra]     Force database for SRA data (default: auto-detect).
  -p, --parallel  int           axel connection count (classic engine only), e.g. -p 10.
  -a, --aspera                  Use Aspera (ascp); GSA/ENA only.
  -s, --speed     int           Download speed limit in MB/s (default: 1000).
  -k, --skip-md5                Skip the md5 check for downloaded files.
  -r, --protocol  [ftp|https]   ENA transport (default: auto, HTTPS-first).
  -Q, --quiet                   Suppress download progress bars.
  -o, --output    text          Output directory (created if missing; default: cwd).

Engine / batch / adaptive:
  --engine        [segmented|classic]   Download engine (default: segmented).
  --segment-size  int           Target segment size in MB (default: 512).
  --max-segments  int           Max connections per file (default: 8).
  --max-conns-per-host int      Global cap on connections to one host (default: 8).
  -j, --jobs      int           Max worker-pool size for batch download (default: 20).
  --adaptive / --no-adaptive    Gradient adaptive-concurrency controller (default: on).
  --probe-window  int           Adaptive probe window, seconds (default: 5).
  --cc-penalty    float         Worker-cost penalty K in score=throughput/K**workers (1.01).
  --meta-jobs     int           Parallelism for metadata/URL resolution (default: 3).
  --aspera-efficiency float     Keep an extra ascp worker only above this efficiency (0.70).

  -h, --help                    Show help.
  -v, --version                 Show version.

Where to go next¶

Downloading sequence data — the default download path, -g, -q, -d, -r, -p
Fetching metadata — -m, and what files you get per database
Merging FASTQ — -e ex|sa|st
Batch & adaptive download — accession lists, -j, --adaptive, --meta-jobs
Aspera — -a and the adaptive ascp pool
Python API — fetch, resolve, get_metadata

Logs and re-runs¶

File	Contents
`success.log`	Runs downloaded and verified
`fail.log`	Runs that failed after 3 retry rounds

A Run already in success.log is skipped on re-run; remove its line (e.g. sed -i '/SRR7706354/d' success.log) to force a re-download. Partial files left by the segmented engine (*.part, *.part.meta) are resumed, not restarted.