Welcome, Guest. Please Login or Register
UGENE Bulletin Board
  Welcome to our forum.
  HomeHelpSearchLoginRegister  
 
 
Pages: 1 2 3 4 5
Newbie: Facing problem on CMD Tools (Read 75792 times)
Reply #15 - Jan 30th, 2012 at 7:20pm

German   Offline
Full Member

Posts: 118
***
 
PEH wrote on Jan 30th, 2012 at 4:43pm:
Since i had granted full right to "/tmp/ugene_tmp/". It should not an issue right? Hmmm... something weird happen but i am not sure where it's. Sad


Oh! I found! Smiley

Look at your fofn.txt file. It contains:
"/home/kenson/
Download
/ABI/forward/...."

But your folder is named "Download
s
", not "Download".
Change it and try again Smiley
 
IP Logged
 
Reply #16 - Jan 31st, 2012 at 10:43am

PEH   Offline
YaBB Newbies

Posts: 11
*
 
Dear Sir,

Ops, thanks for correct me. Smiley
Erm... After try it again and its still giving the same error saying "Error opening URL for read:"  Sad
 
IP Logged
 
Reply #17 - Jan 31st, 2012 at 12:05pm

German   Offline
Full Member

Posts: 118
***
 
PEH wrote on Jan 31st, 2012 at 10:43am:
Dear Sir,

Ops, thanks for correct me. Smiley
Erm... After try it again and its still giving the same error saying "Error opening URL for read:" Sad


Have you tried just to run:
./ttuner -if /home/kenson/Downloads/ABI/forward/fofn.txt -if /tmp/ugene_tmp/tmp_file.fa
?

If tmp_file.fa will be not created then it is some problem of environment, but if it will be then it is our work and we will work with it...
 
IP Logged
 
Reply #18 - Jan 31st, 2012 at 12:51pm

German   Offline
Full Member

Posts: 118
***
 
I have tried this task on Ubuntu with the last snaphot of UGENE (that you have too).

How have I created the new element? You can see it in attachments.
I haven't set environment variable for "ttuner", so I have typed the full path to "ttuner".
Maybe you should do it too?
 

1.JPG (26 KB | )
1.JPG
2.JPG (45 KB | )
2.JPG
3.JPG (32 KB | )
3.JPG
IP Logged
 
Reply #19 - Jan 31st, 2012 at 12:52pm

German   Offline
Full Member

Posts: 118
***
 
And another part of creating of the new element.
 

4.JPG (47 KB | )
4.JPG
IP Logged
 
Reply #20 - Jan 31st, 2012 at 12:53pm

German   Offline
Full Member

Posts: 118
***
 
Then I created a schema and run it.
 

5.JPG (40 KB | )
5.JPG
6.JPG (16 KB | )
6.JPG
7.JPG (117 KB | )
7.JPG
IP Logged
 
Reply #21 - Jan 31st, 2012 at 3:23pm

PEH   Offline
YaBB Newbies

Posts: 11
*
 
Hmm... i got it run nicely now.

What i did is I just remove fof URL parameter and hardcode fof file path in Execution String:
ttuner -if /home/kenson/Downloads/ABI/forward/fofn.txt -sa $outfile

instead of:
ttuner -if $fof -sa $outfile

It's Ugene has issue on URL parameter?
 
IP Logged
 
Reply #22 - Jan 31st, 2012 at 4:43pm

German   Offline
Full Member

Posts: 118
***
 
PEH wrote on Jan 31st, 2012 at 3:23pm:
Hmm... i got it run nicely now.

What i did is I just remove fof URL parameter and hardcode fof file path in Execution String:
ttuner -if /home/kenson/Downloads/ABI/forward/fofn.txt -sa $outfile

instead of:
ttuner -if $fof -sa $outfile

It's Ugene has issue on URL parameter?


It is very good that we finally found a decision! Congratulations! Smiley

Sorry, but I didn't understand clear your last question.

Yes, UGENE provides setting up parameters when you are creating a cmdline element. I have already wrote about it:
http://ugene.unipro.ru/forum/YaBB.pl?num=1326766085/0#6

Maybe those problem was because you set incorrect URL to the created "fof" parameter?

By the way, this mechanism (creating external CMDLine workers) provides running some external programs from UGENE and we have no any way for controlling and retrieving errors from these programs.

I think, TraceTuner prints something into stdout about its problems when you launch your broken example, but we can not catch these messages. UGENE just runs ttuner and waits while the last one is finished up.

Thanks for your feedback. It is very necessary for us to get error reports from users Smiley
 
IP Logged
 
Reply #23 - Jan 31st, 2012 at 5:54pm

PEH   Offline
YaBB Newbies

Posts: 11
*
 
Sorry that i that i didn't not explain clearly on my last question. Actually i had created $fof as URL in Parameter and in execution string i enter: ttuner -if $fof -sa $outfile then i get error.

P/S: $fof browse and selected fofn.txt

After that i just remove $fof parameter and i enter execution string:
ttuner -if /home/kenson/Downloads/ABI/forward/fofn.txt -sa $outfile

Just want to know why $fof doesn't retrieve the correct path.

---------

I will check more info about ttuner whether there is log created or not.

Between, can you try to use ubuntu run below schema whether ok or not:
1. Read Sequence - select ABI file.
2. abi2fasta - as screen attached
3. Write Sequence

For above schema i got "Error opening URL for read". Just want to know why.  Wink

Thanks for helping me.  Smiley
 
IP Logged
 
Reply #24 - Jan 31st, 2012 at 6:46pm

German   Offline
Full Member

Posts: 118
***
 
PEH wrote on Jan 31st, 2012 at 5:54pm:
Sorry that i that i didn't not explain clearly on my last question. Actually i had created $fof as URL in Parameter and in execution string i enter: ttuner -if $fof -sa $outfile then i get error.

P/S: $fof browse and selected fofn.txt

After that i just remove $fof parameter and i enter execution string:
ttuner -if /home/kenson/Downloads/ABI/forward/fofn.txt -sa $outfile

Just want to know why $fof doesn't retrieve the correct path.

---------

I will check more info about ttuner whether there is log created or not.

Between, can you try to use ubuntu run below schema whether ok or not:
1. Read Sequence - select ABI file.
2. abi2fasta - as screen attached
3. Write Sequence

For above schema i got "Error opening URL for read". Just want to know why. Wink

Thanks for helping me. Smiley


This schema is not so good.
First of all, ABI files are not just for keeping sequences. They keep sequences and chromatograms. As you can see from the Workflow Designer manual, UGENE Wokrflow Designer has 4 datatypes: Sequence, Annotation, MSA, String.
So, when you read an ABI file by the "Read sequence" element, its output port has no any chromatogram, it contains just a sequence from the file.

You set the "infile" parameter format as "FASTA". So, what is happening in UGENE?
1) The "Read sequence" element reads a sequence from your ABI files and sends it to "abi2fasta". The "infile" parameter format is FASTA, so the sequence is saved into tmp file with FASTA format.
2) abi2fasta runs ttuner:
./ttuner created_tmp_file.fa -sa another_tmp_file.fa
because of the "outfile" parameter format is also FASTA.

So, you can see that "./ttuner created_tmp_file.fa -sa another_tmp_file.fa" is not good execution string. You can run simple ttuner with such way and you would see that it will be not working.

-----------------

You should understand, that when you create input/output port with Sequence type and with name "qqqqq", and if you write execution string:
"<your_tool> $qqqqq"
then the real execution string will be:
"<your_tool> temporary_file.<chosen_format>"
 
IP Logged
 
Reply #25 - Feb 3rd, 2012 at 1:09pm

German   Offline
Full Member

Posts: 118
***
 
Dear PEH,
have you got to solve your problem with adding a parameter?
http://ugene.unipro.ru/forum/YaBB.pl?num=1326766085/15#21

If you haven't, could you send us, please, a log of your failed UGENE run? (please, set all of log levels: right click at the log area -> Settings -> check all log levels). We would try to find a solution.

Our team has reviewed the mechanism of external tool elements using in UGENE and decided to improve it at several things.

You can see them through these links:
https://ugene.unipro.ru/tracker/browse/UGENE-807
https://ugene.unipro.ru/tracker/browse/UGENE-812
https://ugene.unipro.ru/tracker/browse/UGENE-815
https://ugene.unipro.ru/tracker/browse/UGENE-816
https://ugene.unipro.ru/tracker/browse/UGENE-817
https://ugene.unipro.ru/tracker/browse/UGENE-819
 
IP Logged
 
Reply #26 - Feb 10th, 2012 at 10:47am

kenkl   Offline
Junior Member

Posts: 73
**
 
Dear Sir,

I'm facing the same stated problem regarding the integration of ttuner into the WD using CMD line elements. I'm using the latest UGENE 1.10.2 and its still not working. Kindly advice.

Regards,
Kenneth
 
IP Logged
 
Reply #27 - Feb 10th, 2012 at 2:33pm

German   Offline
Full Member

Posts: 118
***
 
kenkl wrote on Feb 10th, 2012 at 10:47am:
Dear Sir,

I'm facing the same stated problem regarding the integration of ttuner into the WD using CMD line elements. I'm using the latest UGENE 1.10.2 and its still not working. Kindly advice.

Regards,
Kenneth

Dear Kenneth,

could you describe your problems, please? What things can't you do with ttuner integration?
 
IP Logged
 
Reply #28 - Feb 13th, 2012 at 2:38pm

kenkl   Offline
Junior Member

Posts: 73
**
 
Yes.

I could reproduce the one you had posted earlier in the post, however when I set URL as a parameter to browse for my own input data it failed with an error of "error opening URL to read" and then a statement stating "nothing to write:no document".

I had the snapshots of what I had been doing but could not upload it on my post since yesterday.

Hope you can help. =)

Regards,
Kenneth
 
IP Logged
 
Reply #29 - Feb 13th, 2012 at 4:29pm

German   Offline
Full Member

Posts: 118
***
 
kenkl wrote on Feb 13th, 2012 at 2:38pm:
Yes.

I could reproduce the one you had posted earlier in the post, however when I set URL as a parameter to browse for my own input data it failed with an error of "error opening URL to read" and then a statement stating "nothing to write:no document".

I had the snapshots of what I had been doing but could not upload it on my post since yesterday.

Hope you can help. =)

Regards,
Kenneth


It is very strange, because I can not reproduce this problem. I have tried it on two systems (Windows XP and Ubuntu) using the latest snaphots and it works good. Could you show me in detail, please, how do you create this element (with screenshots)?

Also, it would be good if you send a log of running process (please, set all of log levels: right click at the log area -> Settings -> check all log levels).

Then I could investigate your problem better.
 
IP Logged
 
Pages: 1 2 3 4 5