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I want -a sw_scan_16 -e 1 -o 11, however, -O EMOBOSS also not work when -a sw_stats_striped_16 (defulat setting)
[lihuilin@login01 bin]$ ls
myseqs.fasta mytrace parasail1.csv parasail_aligner parasail.csv parasail_stats tb
[lihuilin@login01 bin]$ ./parasail_aligner -h
usage: parasail_aligner [-a funcname] [-c cutoff] [-x] [-e gap_extend] [-o gap_open] [-m matrix] [-t threads] [-d] [-M match] [-X mismatch] [-k band size (for nw_banded)] [-l AOL] [-s SIM] [-i OS] [-v] [-V] -f file [-q query_file] [-g output_file] [-O output_format {EMBOSS,SAM,SAMH,SSW}] [-b batch_size] [-r memory_budget] [-C] [-A alphabet_aliases]
Defaults:
funcname: sw_stats_striped_16
cutoff: 7, must be >= 1, exact match length cutoff
-x: if present, don't use suffix array filter
gap_extend: 1, must be >= 0
gap_open: 10, must be >= 0
matrix: blosum62
-d: if present, assume DNA alphabet ACGT
match: 1, must be >= 0
mismatch: 0, must be >= 0
threads: system-specific default, must be >= 1
AOL: 80, must be 0 <= AOL <= 100, percent alignment length
SIM: 40, must be 0 <= SIM <= 100, percent exact matches
OS: 30, must be 0 <= OS <= 100, percent optimal score
over self score
-v: verbose output, report input parameters and timing
-V: verbose memory output, report memory use
file: no default, must be in FASTA format
query_file: no default, must be in FASTA format
output_file: parasail.csv
output_format: no default, must be one of {EMBOSS,SAM,SAMH,SSW}
batch_size: 0 (calculate based on memory budget),
how many alignments before writing output
memory_budget: 2GB or half available from system query (100.970 GB)
-C: if present, use case sensitive alignments, matrices, etc.
alphabet_aliases: traceback will treat these pairs of characters as matches,
for example, 'TU' for one pair, or multiple pairs as 'XYab'
[lihuilin@login01 bin]$ ./parasail_aligner -f myseqs.fasta -a sw_stats_striped_16 -O EMBOSS
The selected output format 'EMBOSS' requires an alignment function that returns a traceback.
[lihuilin@login01 bin]$
./parasail_aligner -f myseqs.fasta works well, and the output file is
0,1,348,332,678,340,325,142,209,326
The text was updated successfully, but these errors were encountered:
parasail was designed to be performant and as a fallout of that we have (too) many alignment routines. For example, if you only need a score it is wasteful to calculate a traceback. The alignment routine you need is sw_trace_scan_16, note the "trace" in the name.
I want
-a sw_scan_16 -e 1 -o 11
, however,-O EMOBOSS
also not work when-a sw_stats_striped_16
(defulat setting)./parasail_aligner -f myseqs.fasta
works well, and the output file isThe text was updated successfully, but these errors were encountered: