Error when using Krona to generate hierarchical representation of Tax4Fun output??

[emankhalaf]

Hello everyone,

I would like to use krona to display Tax4Fun output: 0.008833584 Metabolism carbohydrate metabolism Glycolysis / Gluconeogenesis 0.006236372 Metabolism carbohydrate metabolism Citrate cycle (TCA cycle) 0.008593556 Metabolism carbohydrate metabolism Pentose phosphate pathway 0.005395773 Metabolism carbohydrate metabolism Pentose and glucuronate interconversions

I installed Krona as following: curl -LOk https://github.com/marbl/Krona/releases/download/v2.7/KronaTools-2.7.tar sudo ./install.pl sudo ./updateTaxonomy.sh sudo ./updateAccessions.sh

However, I am going to use krona with only regular data stored in text files (as above) not taxonomy files.

I copied the files in kronaTools-2.7 folder and then use this command: ktImportText control.text -o ctrl_krona.html I got this error: No such file or directory at /usr/local/bin/ktImportText line 71.

May you please help me in solving this issue. Is there any mistake in the above steps?

Thanks

[emankhalaf]

I tried this command; module load kronaTools
and got this error; module: command not found (I don't know the correct order for using krona) Then tried: KtImportText control.txt -o control.html

got this: KtImportText: command not found

How to load/activate krona before using arguments??

Help please Thanks

[ashishdamania]

Please follow this link on how to install Krona:

https://github.com/marbl/Krona/wiki/Installing

or you can also see my comment on this issue. (You can start following just after the "curl" command)

https://github.com/marbl/Krona/issues/46#issuecomment-293116180

[emankhalaf]

Hello deep, I created a new environment to install krona, however it was successfully installed in the first time (based on the resulting messages). I followed the link, install complete and updates of taxonomy and accession were finished. Then I changed the directory to script folder to run ./ImportText.pl and I got this error: No such file or directory at ./ImportText.pl line 71. Should I change 71 line in the ImportText.pl file? Please, help, I am stuck for couple of days after a long unsuccessful trial to install STAMP Thanks

On Tue, Jul 17, 2018 at 11:38 AM deepthoughts [email protected] wrote:

Please follow this link on how to install Krona:

https://github.com/marbl/Krona/wiki/Installing

or you can also see my comment on this issue. (You can start following just after the "curl" command)

#46 (comment) https://github.com/marbl/Krona/issues/46#issuecomment-293116180

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/marbl/Krona/issues/95#issuecomment-405647358, or mute the thread https://github.com/notifications/unsubscribe-auth/AZOrV0gD-om3WvEKcvudR6rT9ZwSxb4Hks5uHhL8gaJpZM4VRV2t .

-- Eman M Khalaf (PhD) Lecturer of Microbiology Faculty of Pharmacy Damanhour University e.mail: [email protected] Cell Phone: 002-01005043084

[ashishdamania]

The line 71 in ImportText.pl script checks for the input file. If you have installed it correctly then you should see the instructions on how to use that script once you execute this line:

./ImportText.pl

Also, where is your input file? Are you correctly pointing to the right input file?

[emankhalaf]

I removed all krona files and folders, and re-start from scratch. Then cd scripts then $./ImportText.pl /Home/Documents/files-circos/control.txt -o control_results.html

No such file or directory at ./ImportText.pl line 71.

$ sudo ./ImportText.pl /Home/Documents/files-circos/control.txt -o control_results.html [sudo] password for eman: No such file or directory at ./ImportText.pl line 71.

What is wrong in my steps. I believe something wrong in ImportText.pl Please let me know Eman

On Tue, Jul 17, 2018 at 1:58 PM deepthoughts [email protected] wrote:

The particular line 71 in ImportText.pl script checks for the input file. If you have installed it correctly then you should see the instructions on how to use that script once you execute this line:

./ImportText.pl

Also, where is your input file? Are you correctly pointing to the right input file?

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-- Eman M Khalaf (PhD) Lecturer of Microbiology Faculty of Pharmacy Damanhour University e.mail: [email protected] Cell Phone: 002-01005043084

[ashishdamania]

Can you try the included example with Krona? https://github.com/marbl/Krona/wiki/Importing-text-and-XML-data

[emankhalaf]

Hello deep, I already did all what is posted on kronaTools' web and I changed the order of columns to fit their requirements, but still have the same error as follow: sudo ./ImportText.pl /home/Documents/files-circos/control.text -o control_results.html [sudo] password for eman: No such file or directory at ./ImportText.pl line 71. I attached a sample of my data in this e.mail. If you don't mind, please try it in your computer and let me know Your help is greatly appreciated Eman

On Tue, Jul 17, 2018 at 10:32 PM deepthoughts [email protected] wrote:

Can you try the included example with Krona? https://github.com/marbl/Krona/wiki/Importing-text-and-XML-data

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/marbl/Krona/issues/95#issuecomment-405798027, or mute the thread https://github.com/notifications/unsubscribe-auth/AZOrV7cYm_Rbwuijfbe34qb7Mc9SIPbcks5uHqxOgaJpZM4VRV2t .

-- Eman M Khalaf (PhD) Lecturer of Microbiology Faculty of Pharmacy Damanhour University e.mail: [email protected] Cell Phone: 002-01005043084

[ashishdamania]

Hi @emankhalaf It works for me. I was able to run both the "ktImportText" and "ImportText.pl " on this example file attached here. text.txt

./ImportText.pl /Users/deepthoughts/Desktop/text.txt -q

and

ktImportText /Users/deepthoughts/Desktop/text.txt

Both gave me the expected results as shown in the wiki.

I suggest you try on a different computer. Can you mention the Operating System of your computer?

deepthoughts

[emankhalaf]

Great. My OS is Ubuntu 16.4. Is there any requirements for Ubuntu. I created an environment to install krona and prevent any interference with other installed programs and I used to do so. Also, I did it without creating an environment?? Please let me know. Much thanks Eman

On Wed, Jul 18, 2018 at 8:59 AM deepthoughts [email protected] wrote:

Hi @emankhalaf https://github.com/emankhalaf It works for me. I was able to run both the "ktImportText" and "ImportText.pl " on this example file attached here. text.txt https://github.com/marbl/Krona/files/2206027/text.txt

./ImportText.pl /Users/deepthoughts/Desktop/text.txt -q

and

ktImportText /Users/ashishdamania/Desktop/text.txt

Both gave me the expected results as shown in the wiki.

I suggest you try on a different computer. Can you mention the Operating System of your computer?

deepthoughts

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/marbl/Krona/issues/95#issuecomment-405940994, or mute the thread https://github.com/notifications/unsubscribe-auth/AZOrV-aB0j6xLEprMnwYlDTnqS_Dm8Dyks5uHz9CgaJpZM4VRV2t .

-- Eman M Khalaf (PhD) Lecturer of Microbiology Faculty of Pharmacy Damanhour University e.mail: [email protected] Cell Phone: 002-01005043084

[emankhalaf]

Good news, it is working now. You are right, I missed something in the path, that is why it can not see the file. Much thanks for your support, really appreciated. Eman

On Wed, Jul 18, 2018 at 9:43 AM Eman Khalaf [email protected] wrote:

Great. My OS is Ubuntu 16.4. Is there any requirements for Ubuntu. I created an environment to install krona and prevent any interference with other installed programs and I used to do so. Also, I did it without creating an environment?? Please let me know. Much thanks Eman

On Wed, Jul 18, 2018 at 8:59 AM deepthoughts [email protected] wrote:

Hi @emankhalaf https://github.com/emankhalaf It works for me. I was able to run both the "ktImportText" and "ImportText.pl " on this example file attached here. text.txt https://github.com/marbl/Krona/files/2206027/text.txt

./ImportText.pl /Users/deepthoughts/Desktop/text.txt -q

and

ktImportText /Users/ashishdamania/Desktop/text.txt

Both gave me the expected results as shown in the wiki.

I suggest you try on a different computer. Can you mention the Operating System of your computer?

deepthoughts

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/marbl/Krona/issues/95#issuecomment-405940994, or mute the thread https://github.com/notifications/unsubscribe-auth/AZOrV-aB0j6xLEprMnwYlDTnqS_Dm8Dyks5uHz9CgaJpZM4VRV2t .

-- Eman M Khalaf (PhD) Lecturer of Microbiology Faculty of Pharmacy Damanhour University e.mail: [email protected] Cell Phone: 002-01005043084

-- Eman M Khalaf (PhD) Lecturer of Microbiology Faculty of Pharmacy Damanhour University e.mail: [email protected] Cell Phone: 002-01005043084