Says "If neither -t or -s specified, just saves output statistics." but -t is threads and -s doesn't exist?
usage: mccortex63 clean [options] <in.ctx> [in2.ctx ...]
Clean a cortex graph. Joins graphs first, if multiple inputs given.
If neither -t or -s specified, just saves output statistics.
-h, --help This help message
-q, --quiet Silence status output normally printed to STDERR
-f, --force Overwrite output files
-o, --out <out.ctx> Save output graph file [required]
-m, --memory <mem> Memory to use
-n, --nkmers <kmers> Number of hash table entries (e.g. 1G ~ 1 billion)
-t, --threads <T> Number of threads to use [default: 2]
-N, --ncols <N> Number of graph colours to use
Cleaning:
-T[L], --tips[=L] Clip tips shorter than <L> kmers [default: auto]
-U[X], --unitigs[=X] Remove low coverage unitigs with median cov < X [default: auto]
-B, --fallback <T> Fall back threshold if we can't pick
Statistics:
-c, --covg-before <out.csv> Save kmer coverage histogram before cleaning
-C, --covg-after <out.csv> Save kmer coverage histogram after cleaning
-l, --len-before <out.csv> Save unitig length histogram before cleaning
-L, --len-after <out.csv> Save unitig length histogram after cleaning
--unitigs without a threshold, causes a calculated threshold to be used
Default: --tips 2*kmer_size --unitigs
Set thresholds to zero to turn-off cleaning
Says "If neither -t or -s specified, just saves output statistics." but
-t
is threads and-s
doesn't exist?