The path to the index. For partitioned indices, the suffix _x, where x is a number, must be omitted.
--query
File containing query sequences.
Many file types and compressions are supported. Click to show a list.
Supported file extensions are (possibly followed by bz2, gz, or bgzf):
embl
fasta
fa
fna
ffn
faa
frn
fas
fastq
fq
genbank
gb
gbk
sam
--output
The output file name.
###<text> | Meta-information
##<text> | Meta-information
#<number><tab><filepaths> | Assigns each input file a number. Multiple filepaths are separated by a whitespace
#QUERY_NAME<tab>USER_BINS | Header for the results
<query_id><tab>[<number>...] | A line for each query, listing matches in input files, if any. Multiple hits are separated by a comma.
### Minimiser parameters
## Window size = 19
## Shape = 1111111111111111111
## Shape size (length) = 19
## Shape count (number of 1s) = 19
### Search parameters
## Query file = "/data/query.fq"
## Pattern size = 65
## Output file = "search.out"
## Threads = 1
## tau = 0.9999
## p_max = 0.4
## Percentage threshold = nan
## Errors = 0
## Cache thresholds = false
### Index parameters
## Index = "/data/index.hibf"
## Index hashes = 2
## Index parts = 1
## False positive rate = 0.05
## Index is HIBF = true
#0 /data/bin1.fa
#1 /data/bin2.fa
#2 /data/bin3.fa
#3 /data/bin4.fa
#QUERY_NAME USER_BINS
query1
query2 1
query3 0,1,2
--threads
The number of threads to use. Sequences in the query file will be processed in parallel. Negligible effect on RAM usage for unpartitioned indices. Moderate effect for partitioned indices.
--quiet
By default, runtime and memory statistics are printed to stderr at the end.
This flag disables this behaviour.
--error
The number of allowed errors.
Note
Mutually exclusive with –threshold.
--threshold
Ratio of k-mers that need to be found for a hit to occur.
Note
Mutually exclusive with –error.
--query_length
The sequence length of a query. Used to determine thresholds. The sequence lengths should have little to no variance.
If not provided:
the median of sequence lengths in the query file is used.
a warning is emitted if there is a high variance in sequence lengths.
an error occurs if any sequence is shorter than the window size.
--tau
The higher tau, the lower the threshold.
Note
Has no effect when using --threshold or w == k.
--p_max
The higher p_max, the higher the threshold.
Note
Has no effect when using --threshold or w == k.
--cache-thresholds
Stores the computed thresholds with a unique name next to the index. In the next search call using this option, the stored thresholds are re-used. Two files are stored:
threshold_*.bin: Depends on query_length, window, kmer/shape, errors, and tau.
correction_*.bin: Depends on query_length, window, kmer/shape, p_max, and fpr.
1.10.0