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

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Kenneth, how to use your script? What input parameters does it have? What is the format of used input/output files?

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

Kenneth, I have tried your script and it works very strange.
When I run "./zapping.awk human_T1.fa > out.fa" from command line then the content of out.fa is:
">human_T1
"
Is it correct?

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

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kenkl wrote on Apr 16^th, 2012 at 3:46pm:

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

I guess that the execution string of the lucy element is not correct. Could you show it please?

Also, I should tell you about the zapping element. Why do you use some output port? "Zapping" doesn't produce any data that can be used in UGENE. I think the scheme should look like:

[some workers...] -> [lucy] -> [Write FASTA]
                                    |
                                    v
                            [zapping]

Am I right?

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

Hi German,

I realizes that the zapping.awk does not recognizes Fasta sequence from LUCY in UGENE as when I obtain the LUCY resulting sequence from UGENE workflow and uses zapping.awk on the resulting FASTA file in the command line, the output file that I obtained looks like this:

>ITS_GA00108.1.a1.ab1

Can you look into it?

Thanks!

Kenneth