Hi there,

I'm trying to execute an AWK script to help me to trim sequences, so I created a custom element for that purposes with below execution string:

zapping.awk $infile > $outfile

It works when I execute the script in the command line but when I used it in the UGENE it "hangs" when it status was changed to "Running".

Kindly advice, thanks!

Kenneth

Hi German, the execution sting would be:

zapping.awk $input > $output

where,
$input = FASTA file from LUCY
$output = FASTA sequence file

That's the way!

Kenneth

Yes German, it is correct. I had troubleshoot this problem and it seems that zapping.awk can only process output files from LUCY.

If only a sequence is dump for zapping.awk, it will eliminate all sequences. That I think are something to do with some LUCY labelling I guess. But the problem now I'm facing also is that the LUCY element could not work.

It kept saying that it can't launch LUCY.

Kindly advice.

Kenneth

Hi German, I had used the exact execution string in the commandline and it works well. But for your reference, my execution string looks like this:

lucy -v $vec $splice $in_fa $in_qul -o $out_fa $out_qul -debug $debug

Besides, actually after zapping it will produce a trimmed FASTA sequence, does UGENE support that? The reason being the trimmed sequenced from zapping are the best quality sequence for further downstream analysis such as BLAST and many more other workers.

Kenneth