I went through it, the solution is to add the index file. Create the index files with

samtools faidx sequence.fa

This creates the index file *.fai. The final command for conversion is

samtools view -bt sequence.fa.fai -S bowtie.glob.sam -o bowtie.glob.sam

Cheers,
Rohit

I know you have got the solution but here is what is mentioned in the samtools manual:

Import SAM to BAM when @SQ lines are present in the header:

samtools view -bS aln.sam > aln.bam

If @SQ lines are absent:

samtools faidx ref.fa 
samtools view -bt ref.fa.fai aln.sam > aln.bam

where ref.fa.fai is generated automatically by the faidx command.