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Downloading sequence data

By default adaptiseq -i <accession> resolves the accession, downloads every Run it contains through the segmented engine, and md5-verifies each file.

adaptiseq -i PRJNA211801          # all Runs in a project
adaptiseq -i SRR7706354           # a single Run
adaptiseq -i accessions.txt       # a file of accessions (batch; see batch.md)

For each Run, adaptiSeq downloads, checks the md5 against the public database, and on mismatch retries up to three rounds before recording the result in success.log / fail.log.

-g, --gzip — direct *.fastq.gz

Download FASTQ directly in gzip format.

adaptiseq -i SRR1178105 -g

For GSA accessions most data is already gzip, so -g is effectively always on. For SRA/ENA/DDBJ/GEO, adaptiSeq first tries ENA's *.fastq.gz mirror; if that is unavailable it falls back to downloading the .sra file and converting it with fasterq-dump + pigz.

Note A pure ENA *.fastq.gz download needs only wget (plus pigz for any conversion). sra-tools is required only if the SRA fallback actually triggers — adaptiSeq then prints a clear "install sra-tools" message rather than failing obscurely.

-q, --fastq — convert SRA to FASTQ

After downloading the .sra file, decompose it into uncompressed FASTQ with fasterq-dump.

adaptiseq -i SRR1178105 -q
adaptiseq -i SRR1178105 -q -t 10      # 10 conversion threads

Note -q is particularly useful for single-cell data: it can decompose a run into I1/R1/R2/R3, whereas a direct -g download may yield only R1/R3. Used together, -q -g downloads the .sra, converts it, then gzips the result.

-t, --threads

Threads for SRA→FASTQ conversion and gzip compression (default 8).

adaptiseq -i SRR1178105 -q -t 10

More is not always better — fasterq-dump is IO-heavy, and too many threads raise CPU/IO load. A ceiling around 15 is a sensible default.

-d, --database — force ENA or SRA

adaptiseq -i SRR1178105 -d sra

By default adaptiSeq auto-detects the best database, so -d is usually unnecessary. Force -d sra when ENA is slow for a given file.

Note If a file is not in ENA, adaptiSeq switches to SRA automatically even with -d ena.

-r, --protocol — ENA transport

adaptiseq -i SRR7706354 -g -r https

For the segmented engine, ENA transport defaults to auto (HTTPS-first): it prefers the HTTPS mirror (confirmed by a cheap per-host range probe), then native segmented FTP, then a single stream inside the segmented engine. Pass -r https or -r ftp to force one.

-p, --parallel — classic-engine parallelism

adaptiseq -i PRJNA211801 --engine classic -p 10

-p sets the axel connection count and applies only to the opt-in classic engine (--engine classic). The default segmented engine already fetches each file in multiple byte-range connections (--max-segments) and runs a batch worker pool (-j), so -p is not needed there. See Method details.

-s, --speed — speed cap

adaptiseq -i SRR7706354 -g -s 50      # cap at 50 MB/s

Token-bucket rate limit in MB/s (default 1000), applied by the engine.

-k, --skip-md5

Skip md5/vdb-validate integrity checks. Remove -k and re-run to verify later.

-Q, --quiet

Suppress the live progress bar and non-essential messages — cleaner logs for batch/CI use.