strange bowtie index building and mapping problem

[Gangcai]

Hello everyone,
I have met a quite strange problem when running bowtie for my SOLID sequencing result.
I have succeeded to build bowtie colorspace index for chimpanzee whole genome, but when I run bowtie , it showed the error like:
"run_bowtie.sh: line 32: 1898 Segmentation fault $bowtie -C --phred33-quals -n 3 -a -m 3 --best --strata -p 4 -S $index -q $infile $out_dir/$out_name
"
Then I checked the output, the output just contain sam header and a few line of alignment result. The strange thing is that the sam header is like this(chromosome name is incorrect):
@HD VN:1.0 SO:unsorted
@SQ SN:IB<8D><EA>^RP<F3>{<<FD><FA><93>ދ<FC>^X%^M<C3>^R^V<DA>A LN:135001995
@SQ SN:1 LN:8402541
@SQ SN:2 LN:134204764
@SQ SN:3 LN:8412303
@SQ SN:4 LN:135371336
@SQ SN:5 LN:2259969
@SQ SN:6 LN:115868456
@SQ SN:7 LN:9231045
@SQ SN:8 LN:107349158
@SQ SN:9 LN:2108736
@SQ SN:10 LN:100063422
@SQ SN:11 LN:3087076
@SQ SN:12 LN:90682376
@SQ SN:13 LN:6370548
@SQ SN:14 LN:83384210
@SQ SN:15 LN:5078517
@SQ SN:16 LN:77261746
@SQ SN:17 LN:1841920
@SQ SN:18 LN:64473437
@SQ SN:19 LN:2407237
......

I have done same procedure for human, the sam header is :
@HD VN:1.0 SO:unsorted
@SQ SN:chr10 LN:135534747
@SQ SN:chr11 LN:135006516
@SQ SN:chr11_gl000202_random LN:40103
@SQ SN:chr12 LN:133851895
@SQ SN:chr13 LN:115169878
@SQ SN:chr14 LN:107349540
@SQ SN:chr15 LN:102531392
@SQ SN:chr16 LN:90354753
@SQ SN:chr17_ctg5_hap1 LN:1680828
.....

So it seems bowtie either didn't build a correct colorspace index or read the index incorrectly. By the way, I have checked the chimpanzee genome I used, it seems OK(the chromosome name is chr1,chr2a, .....chrX, ...).

Have anybody met the same problem before? I am quite precious to hear your suggestion.