<p>Hi all,</p>

<p>I&#39;m dealing with a fasta file with spaces at the end of line, which caused the problem. I didn&#39;t find a suitable way to remove them. Please kindly tell me the appropriate command for removing them?</p>

Not a bioinformatics questions, you should try <a href="http://stackoverflow.com/" target="_blank">Stack Overflow</a> for this, but here is a quick answer in perl:

    perl -i.bak -pe 's/\h+$//' sequences.fa