Samtools faidx errors

[ashwatha]

Hi,

I am new to samtools and bioinformatics in general. I have a quick question about generating a fasta index file from a .fa file. I see a segmentation fault while running samtools faidx on hg19:

$samtools faidx hg19.fa
[fai_build_core] different line length in sequence 'chr1'.
Segmentation fault

This is probably a dumb question, but what could be causing this?

Thanks!

[nilshomer]

You have differing line lengths after chromosome one. Check that each line in chr1 has the same length (except for the last, which should be equal to or shorter).

[ashwatha]

Thanks - I didn't know that every line had to be the same length.

[annrose]

samtools faidx hg19.fa
[fai_build_core] different line length in sequence 'chrY'

hi i have the same problem.....can you tell how can i correct the length?? i am very new to these stuff