colindaven
commented
8 months ago You're probably adding special characters to the file. Try checking with
dos2unix
dos2unix *.fasta
show non-printing chars
cat -e file.txt
grep non-printing characters
grep -P -n "[\x00-\x1F\x7F-\xFF]"
vim view special characters
Re: How to view special characters in text files ?
well, VI has some options for this:set list
lh3
Hi. I'm trying to generate a graph from 3 fasta files (reference + 2 samples).
If I run the command with the test files, all is going well. I tried the command with my dataset (1 chromosome for each fasta file ~26Mbp):
minigraph -xggs -t20 reference_chr01.fasta sample1_chr01.fasta sample2_chr01.fasta > out.gfabut i get this error: _*[M::main::0.0021.68] loaded the graph from "reference_chr01.fasta" [M::mg_index::0.0182.09] indexed the graph [M::mg_opt_update::0.0201.95] occ_max1=26; lc_max_occ=2 [M::ggen_map::0.0221.82] loaded file "sample1_chr01.fasta" [M::ggen_map::0.0771.25] mapped 1 sequence(s) to the graph Illegal instruction**_
I noticed that, giving just the first 59940bp, the command is working. Instead, by giving one more row in each fasta (60bp more), the program is not working anymore.
P.S. I get the same error by using the -c option, as suggested in the usage example, even with the test dataset.
Best Mario