UGENE Forum - Newbie: Facing problem on CMD Tools

Jan 17^th, 2012 at 9:08am

PEH Offline
YaBB Newbies

Posts: 11

Dear Sir,

I am a newbie for using this great software. I am installed UGENE 1.10.1 into my CENTos box. Also, i have installed TraceTuner as external tools to help me on output fasta and qual files.

If i running TraceTuner manually on terminal it was successfully output some data.

So, now i am trying to apply into UGENE CMD Tools:
First, i create custom elements with CMD Tools and Write to FASTA.

Next, i run the schema and get an error below:
"Unknown type of abi2fasta element"

Question:
1. Can UGENE Execute any tools from outside of UGENE?
2. Any method to solve above issue?

Thanks in advanced. Wink

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Reply #1 - Jan 17^th, 2012 at 10:20pm

Mikhail Fursov Offline
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Posts: 162

Hi!

Could you please attach here or send us via email fofn.txt file, so we can reproduce the issue?

---
UGENE team

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Reply #2 - Jan 18^th, 2012 at 8:55am

PEH Offline
YaBB Newbies

Posts: 11

Dear Sir,

Attached file is some files for your reference:
fofn.txt
ITS_GA00285.1.a1.ab1 (sample)
ITS_GA00284.1.a1.ab1 (sample)

Thanks.

fofn.txt (0 KB | )

ITS_GA00284_1_a1_ab1.zip (165 KB | )

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Reply #3 - Jan 18^th, 2012 at 8:56am

PEH Offline
YaBB Newbies

Posts: 11

ITS_GA00285.1.a1.ab1

ITS_GA00285_1_a1_ab1.zip (178 KB | )

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Reply #4 - Jan 20^th, 2012 at 5:00pm

German Offline
Full Member

Posts: 118

PEH wrote on Jan 18^th, 2012 at 8:55am:

Dear Sir,

Attached file is some files for your reference:
fofn.txt
ITS_GA00285.1.a1.ab1 (sample)
ITS_GA00284.1.a1.ab1 (sample)

Thanks.

Thanks for your feedback. We have accepted your request and the corresponded issue has been created at our tracker. The problem will be resolved as soon as possible.

You can watch the progress at our tracker. The name of the issue is https://ugene.unipro.ru/tracker/browse/UGENE-780.

« Last Edit: Jan 20^th, 2012 at 7:19pm by Mikhail Fursov »

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Reply #5 - Jan 23^rd, 2012 at 3:04pm

German Offline
Full Member

Posts: 118

PEH wrote on Jan 18^th, 2012 at 8:55am:

Dear Sir,

Attached file is some files for your reference:
fofn.txt
ITS_GA00285.1.a1.ab1 (sample)
ITS_GA00284.1.a1.ab1 (sample)

Thanks.

Dear user. I have researched the problem and found the reasons of it. We have refactored recently the UGENE infrastructure for achieving a good performance, but this part of the system (workers with external tools) was not modified good. So, we will fix this problem and you could use this schema with UGENE 1.10.2 in couple of weeks.

But, I don't know if your work consists only of this schema? If it is true, then you don't need to use some external tool workers. Use can convert the format of files using standard tools of UGENE. Just make a schema: "Read sequence" -> "Write sequence".

The "Read sequence" worker can get a list of files, but not only one file. And if you put "ITS_GA00285.1.a1.ab1" and "ITS_GA00284.1.a1.ab1" to the "Read sequence" then you can convert them well.

schema.JPG (28 KB | )

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Reply #6 - Jan 24^th, 2012 at 11:15am

German Offline
Full Member

Posts: 118

PEH wrote on Jan 18^th, 2012 at 8:55am:

Dear Sir,

Attached file is some files for your reference:
fofn.txt
ITS_GA00285.1.a1.ab1 (sample)
ITS_GA00284.1.a1.ab1 (sample)

Thanks.

We have resolved your issue. You can try it downloading the latest snapshot on our website or wait for the 1.10.2 version.

Also I should tell you some things about your workflow.
1) The file fofn.txt contains relative paths to ABI files. So, when you use ttuner from UGENE like an external tool these paths become not correct. So, you need to write absolute paths into this file.

2) You can insert "attribute" to your worker for keeping path to fofn.txt. See screenshots.

attribute.JPG (34 KB | )

execution_str.JPG (39 KB | )

schema_001.JPG (22 KB | )

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Reply #7 - Jan 30^th, 2012 at 9:58am

PEH Offline
YaBB Newbies

Posts: 11

Dear Sir,

I did the same way as you shown on above. But i get "Fail to create a worflow Context".

I am using:
- Ugene 1.10-0-dev (30-Jan-2012)
- Centos Linux

Attached screenshot of the error.

Thanks.

worflow_context.png (100 KB | )

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Reply #8 - Jan 30^th, 2012 at 12:25pm

German Offline
Full Member

Posts: 118

PEH wrote on Jan 30^th, 2012 at 9:58am:

Dear Sir,

I did the same way as you shown on above. But i get "Fail to create a worflow Context".

I am using:
- Ugene 1.10-0-dev (30-Jan-2012)
- Centos Linux

Attached screenshot of the error.

Thanks.

It very strange. Have you tried to run some simple workflow schema on your computer with this version of UGENE? For example:
Read sequence -> Write sequence
I suppose that this schema would give this error too.

The error you have received occurs if UGENE can not create the special UGENE database for keeping temporary data.
The default path to this database is "/tmp/ugene_tmp/". Maybe you should set rights on writing to this directory and everything would be all right. Try it, please.

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Reply #9 - Jan 30^th, 2012 at 1:22pm

PEH Offline
YaBB Newbies

Posts: 11

Dear Sir,

Yes, the simple schema 'Read sequence -> Write sequence' is work.

I had giving full access for "/tmp/ugene_tmp/" but seems the access error still occur.

Attached is screenshot. Wink

Thanks.

ftp_right.png (36 KB | )

workflow.png (72 KB | )

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Reply #10 - Jan 30^th, 2012 at 1:35pm

German Offline
Full Member

Posts: 118

Also some problems could appear because more than one versions of UGENE are installed. These versions use one configuration file:
~/.config/Unipro/UGENE.ini
You should remove this file before you run new installed version of UGENE. It could reduce amount of problems.

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Reply #11 - Jan 30^th, 2012 at 1:44pm

German Offline
Full Member

Posts: 118

PEH wrote on Jan 30^th, 2012 at 1:22pm:

Dear Sir,

Yes, the simple schema 'Read sequence -> Write sequence' is work.

I had giving full access for "/tmp/ugene_tmp/" but seems the access error still occur.

Attached is screenshot. Wink

Thanks.

Ok, you can see that when you granted UGENE the writing access to this directory, those error had disappeared.

This message tells that the "abi2Fasta" element is working, but no data is coming to "Write sequence" and the last has no documents to write.

Have you set full paths to ABI files in fofn.txt? I told you that when you launch ttuner from UGENE then relative paths don't work. Try to write to fofn.txt absolute paths to ABI files.

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Reply #12 - Jan 30^th, 2012 at 2:36pm

PEH Offline
YaBB Newbies

Posts: 11

Yes, i did set the ABI full path in fofn.txt. But it still happen "Error opening URL for read".

Sorry for disturbing but hope that you can help me on this issue. Wink

abi_path.png (14 KB | )

setting_fofn_abi_path.png (17 KB | )

workflow_001.png (65 KB | )

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Reply #13 - Jan 30^th, 2012 at 4:24pm

German Offline
Full Member

Posts: 118

PEH wrote on Jan 30^th, 2012 at 2:36pm:

Yes, i did set the ABI full path in fofn.txt. But it still happen "Error opening URL for read".

Sorry for disturbing but hope that you can help me on this issue. Wink

The log message is "Error opening URL for read: " and the temp file. So, after ttuner has finished its work, no files were created. Maybe ttuner has no writing access to "/tmp/ugene_tmp/" too, hasn't it?

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Reply #14 - Jan 30^th, 2012 at 4:43pm

PEH Offline
YaBB Newbies

Posts: 11

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

ftp_right_001.png (36 KB | )

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