Cleaning up

A build stages its external-memory intermediates under --work-dir and unlinks them as it consumes them, so a successful run leaves the working directory empty. A run that is killed, fills the disk, or fails partway leaves them behind, and they are large: hundreds of gigabytes for a collection-scale graph. cuttlefish cleanup reclaims that space safely.

Usage:
  cuttlefish cleanup -w DIR [OPTION...]

 options:
  -w, --work-dir <arg>   the --work-dir the build was given
  -p, --prefix <arg>     only this build's artifacts, by output name
  -n, --dry-run          report what would be removed, remove nothing
      --include-repository
                         also remove <name>.cf3rs.color-repository, which a
                         completed colored build needs to interpret its FASTA
  -h, --help             print this help

cuttlefish cleanup -w /path/to/work-dir --dry-run   # report, remove nothing
cuttlefish cleanup -w /path/to/work-dir             # remove them

What it will and will not touch

A working directory is usually shared scratch, so “delete everything” is not an option. Cleanup removes only what cuttlefish itself produces: names matching the exact <name>.cf3rs.<suffix> shape, against a fixed suffix table, and storage-probe files (below). Anything else in the directory is reported and left alone. Removals are listed largest-first with human-readable sizes. Use -p/--prefix to restrict it to one build’s artifacts when several builds share a directory.

It also removes .scratch-probe-* files, left by a storage measurement (--compress-intermediates auto or cuttlefish probe) that was interrupted. One modified in the last minute is skipped and reported: it may belong to a build starting in the same directory, whose measurement it would break. Probe files carry no output name, so -p/--prefix does not narrow them: every stale probe file in the directory is removed.

Two things are never removed by default:

• The output FASTA. After a bailed run it is partial, and whether to keep it is yours to decide.
• The color repository (<name>.cf3rs.color-repository/). It is durable output, not an intermediate: a completed colored build’s FASTA cannot be interpreted without it. Cleanup prints a keeping dir … line instead; pass --include-repository if you really mean to remove one. (The repository is written beside the output prefix, so it only appears here at all when the output prefix points into the working directory.)

Inspecting a run instead

Setting the CF3_RS_KEEP_INTERMEDIATES environment variable makes a build retain all of its intermediates — the thing to use when inspecting a run rather than cleaning up after one. See the working-directory table for what each .cf3rs.* file holds.