samtools faidx Segmentation fault

[totalnew]

I had this problem too, my solution was to use unix command to trim and fold the fasta file. You would have to cut the header first, and catenate it with your sorted fasta file. It perfectly solves the problem.

Writing a shell script may be a good idea to make things easlier.

[webbrewer]

This bioperl snippet fixes the fasta:

use Bio::SeqIO;
$in  = Bio::SeqIO->new(-file => "inputfilename",
                       -format => 'Fasta');
$out = Bio::SeqIO->new(-file => ">outputfilename",
                       -format => 'Fasta');
while ( my $seq = $in->next_seq() ) {$out->write_seq($seq); }

[webbrewer]

I am having this same issue. While I have verified that there are lines of different length in the sequence file, however, why should this matter?

[nilshomer]

populus@Rust:~/samtools-0.1.5c_x86_64-linux$ ./samtools faidx /media/Poplar/baohua/genome/poplar_genome.fa
[fai_build_core] different line length in sequence 'scaffold_28'.
Segmentation fault

What's the meaning of defferent line length ?

It's the standard fasta file.

I download it from:
ftp://ftp.jgi-psf.org/pub/JGI_data/P...asked.fasta.gz

Can you verify that every sequence line in the FASTA has the same length?

[baohua100]

populus@Rust:~/samtools-0.1.5c_x86_64-linux$ ./samtools faidx /media/Poplar/baohua/genome/poplar_genome.fa
[fai_build_core] different line length in sequence 'scaffold_28'.
Segmentation fault

What's the meaning of defferent line length ?

It's the standard fasta file.

I download it from:
ftp://ftp.jgi-psf.org/pub/JGI_data/P...asked.fasta.gz