Bowtie mapping error on color space data [Read is less than 4 charact?]

[SF_mallish]

Hi,

I am using bowtie-0.12.7 to map genomic sequencing data of NCI-H209 cell line into human hg19 genome. The data is from this paper, and the color space .csfasta file is like that:

# Title: S0020_20080602_1_2_3kb_4_
>1_65_78_F3
T0110200122031310012203232
>1_65_110_F3
T0300212221202330222130212
>1_65_167_F3
T0300010011322223223000011
>1_65_188_F3
T0100000032100011213033102
>1_65_305_F3
T0200012011300201011021211
>1_65_560_F3
T0110310212122001103001112
>1_65_621_F3
T3032102121011220311021112

And the setting I use is as following:

bowtie-0.12.7/bowtie -f -p 8 -S -v 2 -m 1 -t hg19_c -C sample.csfasta sample.sam >> sample.log 2>&1

After aligning ~4E8 reads, which is about 1/3 of total reads, bowtie report an error below:

Error: Read (1_122_1720_F3) is less than 4 characters long
terminate called after throwing an instance of 'int'
Aborted

But when I look into the csfasta file, that read is intact with 25bp

>1_122_1605_F3
T0000230330110303213113211
>1_122_1666_F3
T0030121112113303000031132
>1_122_1720_F3
T3021210332111212021021211
>1_122_1796_F3
T0201302031033230230331311
>1_122_1832_F3
T0023102022001211001001111

Does anyone know what might be the reason for this problem and how to fix it?

Thanks in advance!