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FAQ

wget can not be found in your PATH ...

adaptiSeq needs wget for metadata/discovery. Install it (e.g. conda install -c conda-forge wget) and re-run. The same message appears for any other required tool the run actually needs.

srapath can not be found in your PATH ... on a -g run

A direct ENA *.fastq.gz download needs only wget. You see this only when the run fell back to the SRA path (the file was not on ENA). Install sra-tools:

conda install -c bioconda 'sra-tools>=2.11.0'

adaptiSeq checks srapath / fasterq-dump lazily — only when the SRA fallback is actually taken — so a pure-ENA workflow stays tool-light. (A missing srapath used to be mis-reported as "not available in all databases"; it now gives this clear message instead.)

fasterq-dump can not be found ... during conversion

The run downloaded a .sra file and needs to convert it (-q, -e, or -g falling back to SRA). Install sra-tools (as above).

A download is slow

  • Try forcing the SRA database: -d sra (or -d ena).
  • Try a different ENA transport: -r https or -r ftp.
  • For ENA/GSA, try Aspera: -a (needs a real ascp + key).
  • Raise/lower batch concurrency: -j N, or pin it with --no-adaptive.

NCBI rate limit / slow metadata for big batches

NCBI E-utilities allows 3 req/s without a key, 10 with one. Export a key:

export NCBI_API_KEY=your_key_here
export NCBI_EMAIL=you@example.com    # optional

Aspera (-a) transfers nothing / authentication fails

  • Ensure a real IBM ascp is on PATH (a no-op stub passes startup checks but transfers nothing).
  • Ensure a key file exists (adaptiSeq searches the conda env and ~/.aspera).
  • ENA migrated DSA→RSA Aspera keys; the legacy asperaweb_id_dsa.openssh is rejected. adaptiSeq's RSA fallback covers this automatically.

A file failed its md5 check

adaptiSeq retries up to three rounds, then records the Run in fail.log and deletes the corrupt partial. Re-run the command to retry. To skip checks entirely use -k/--skip-md5 (then re-run without -k to verify later).

How do I re-download something already in success.log?

Remove its line and re-run:

sed -i '/SRR7706354/d' success.log

Does -p work with the default engine?

No. -p (axel connection count) applies only to --engine classic. The default segmented engine uses --max-segments (per-file ranges) and -j (batch pool) instead.

Can I use adaptiSeq as a library?

Yes — from adaptiseq import fetch, resolve, get_metadata. See the Python API.

Is the output correct?

Resolution, metadata, integrity, logs, and merge are covered by a differential test suite that checks adaptiSeq's output against stored reference fixtures. The engine changes only how bytes are transferred, never which bytes are written. One deliberate improvement over iseq: 3-file runs (orphan/barcode + _1 + _2) that it mishandles are downloaded correctly.