blanks in the files: couldn't find the reason

Hi, I am a newbie to mothur.
I am trying to replicate the Costello stool analysis example using mothur v 1.17.3 in suse linux.
It shows the following error.

mothur> align.seqs(candidate=stool.trim.unique.fasta, template=silva.bacteria/silva.bacteria.fasta, processors=2)

Reading in the silva.bacteria/silva.bacteria.fasta template sequences...        DONE.
Aligning sequences from stool.trim.unique.fasta ...

[ERROR]: stool.trim.unique.align11024.num.temp is blank. Please correct.
[ERROR]: stool.trim.unique.align11025.num.temp is blank. Please correct.
It took 103 secs to align 0 sequences.

I looked for the spaces, but couldn’t find and moreover its running fine with the same files in the windows system.
I would appreciate any information about the error and its cause?