search

ogotoh / spaln

Genome mapping and spliced alignment of cDNA or amino acid sequences
GNU General Public License v2.0
94 stars 16 forks source link

Can't open query! #5

Open geycu opened 6 years ago

geycu commented 6 years ago

Hi,

When I ran the new version Spaln 2.3.1 with command:

spaln -dGenome test.fa

It reported "Can't open query !".

Any idea why?

Thanks!

pvanheus commented 5 years ago

I get exactly the same error and had a dive into the code. Turns out (from https://github.com/ogotoh/spaln/blob/master/src/spaln.c#L396) that the -d flag is only used if you set -Q to a number greater than 4.

So in your example spaln -Q4 -dGenome test.fa. And by the way the genome index needs to be in either the current directory, or the one referred to by the ALN_DBS environment variable or the compiled in default for ALN_DBS (the directory called seqdb in the source code).

Unfortunately when I get all the parameters correct the code fails with a segmentation fault. I am still investigating this.

pvanheus commented 5 years ago

I looked at the documentation a bit more clearly and using -Q7 works, for example:

spaln -ospaln_q7.out -Q7 -O0 -dhard_masked_seabass_genome fish_proteins_0.fasta

ogotoh commented 5 years ago

The problem with -Q4 option has been fixed in spaln2.3.3.

Osamu