construct whole genome reference for HG19

[foxyg]

I download HG19 from ucsc, after unzip it is many files seperated by chr.

I did
cat chr1.fa chr2.fa chr3.fa chr4.fa chr5.fa chr6.fa chr7.fa chr8.fa chr9.fa chr10.fa chr11.fa chr12.fa chr13.fa chr14.fa chr15.fa chr16.fa chr17.fa chr18.fa chr19.fa chr20.fa chr21.fa chr22.fa chrX.fa chrY.f
a chrM.fa >hg19.fa

to create the hg19.fa

then I used bwa to build the index,
./bwa index hg19.fa
This step has no error either.

Then I run bwa like this

./bwa aln -q 15 hg19.fa sample.txt>sample.sai

I get this error

[bwa_aln] 17bp reads: max_diff = 2
[bwa_aln] 38bp reads: max_diff = 3
[bwa_aln] 64bp reads: max_diff = 4
[bwa_aln] 93bp reads: max_diff = 5
[bwa_aln] 124bp reads: max_diff = 6
[bwa_aln] 157bp reads: max_diff = 7
[bwa_aln] 190bp reads: max_diff = 8
[bwa_aln] 225bp reads: max_diff = 9
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... Segmentation fault


Does anyone know what could have caused this error?

[dawe]

I download HG19 from ucsc, after unzip it is many files seperated by chr.
[…]

Does anyone know what could have caused this error?

If you run

$ bwa index

you'll see this note:

Warning: `-a bwtsw' does not work for short genomes, while `-a is' and
         `-a div' do not work not for long genomes. Please choose `-a'
         according to the length of the genome.

hence you can fix it indexing like this:

$ bwa index -a bwtsw hg19.fa

d

[foxyg]

Thanks I am trying this. But I have built index for single chr before without using -a option and it worked out fine.

[dawe]

Thanks I am trying this. But I have built index for single chr before without using -a option and it worked out fine.

A single chrom is probably small enough for default "is" algorithm