error: your ngs.plot database may be corrupted.

[Denis Seyres]

Hi,

I would to use dm3 genome; I found it, I downloaded it but I have this error when I want to install it, or just list installed genomes.
Could you help me?
I have already re-re-downloaded files..

thanks

best

Denis

[ningyi shao]

Hi Denis,

Would you mind pasting the command you used and the exact output in the installation?

And could you paste the output of the following command?

ngsplotdb.py list

Thank you,

Ning-Yi

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[Denis Seyres]

Hi,

here is the command and the output

> ./bin/ngsplotdb.py install ngsplotdb_dm3_71_1.11.tar.gz
Extracting information from package... contains 42 tables.
Open ~/software/ngsplot/database/gn_list.txt error: your ngs.plot database may be corrupted.

> ngsplotdb.py list
Open ~/software/ngsplot/database/gn_list.txt error: your ngs.plot database may be corrupted.

Thanks

Denis

[Li Shen]

Denis,

Can you make sure this "~/software/ngsplot/database/gn_list.txt" actually exists? If it is somehow corrupted, a re-installation might just solve the problem. 

Li

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--

Li Shen, Ph.D. Computer Science
Assistant Professor
Department of Neuroscience
Icahn School of Medicine at Mount Sinai
New York, NY 10029
#################
ngs.plot - the coolest NGS plotting tool: https://code.google.com/p/ngsplot/

Want ChIP-seq differential analysis? Use: https://code.google.com/p/diffreps/

[Denis Seyres]

ok it was a problem with my ./bash_profile and the NGSPLOT variable.
thanks. Now, let's try!

Denis

[Federico Gaiti]

Hi Denis,

I am actually encountering the same issue. Could you be more specific in explaining what was your problem with bash_profile and NGSPLOT variable? And how did you solve it? 

I have the feeling it can be the same issue because I have successfully installed all the packages and ngs.plot.r command is working. I just can't make the ngsplotdb.py works. I did this: 

 

[federico@ago-qris ~]$ ngsplotdb.py install ngsplotdb_Aqu21_0_3.00.tar.gz
File "/opsin/u/federico/TOOLS/ngsplot/bin/ngsplotdb.py", line 74
print "Open {0} error: your ngs.plot database may be corrupted.".\
                                                                   ^
 SyntaxError: invalid syntax

 

Thanks

Federico

[Li Shen]

Where does your NGSPLOT point to?

Li

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[Federico Gaiti]

Hi Li,

it is pointing to the folder ngsplot is installed in. 

# User specific environment and startup programs

PATH=$PATH:$HOME/bin

export PATH

export PATH=~/TOOLS/ngsplot/bin:$PATH

export NGSPLOT=~/TOOLS/ngsplot

Cheers

Federico

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[Li Shen]

Is the error specific to this genome file? What about "ngsplotdb.py list"?

Li

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[Federico Gaiti]

It seems the error is not specific to the genome. I also reinstalled everything and re-downloaded the genome file. Using “ngsplotdb.py list” I get the same. 

[federico@ago-qris ~]$ ngsplotdb.py list 

 File "/opsin/u/federico/TOOLS/ngsplot/bin/ngsplotdb.py", line 74

    print "Open {0} error: your ngs.plot database may be corrupted.".\

                                                                   ^

SyntaxError: invalid syntax

Any idea? 

Thanks

Federico

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[Li Shen]

Would you provide more details regarding your machine and system? Such as Linux version, Python version, etc.

Li

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[Federico Gaiti]

Hi Li,

I am using CentOS x86_64 6.4, R 3.1.2 and python 2.7.6. 

I reinstalled python and it seems it’s now working. I was able to install the genome. 

Thanks for help

Federico

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[Li Shen]

Great. You either reinstall ngs.plot or some other part of your system and it works out just fine...

Li

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[shimeng...@u.northwestern.edu]

Dear Li,

When installing NGSplot, I have also encountered this problem. 

After installation step and adding the ngsplot file to my path, I ran command: ngsplotdb.py list

Output is as following: 

 File "/Users/slu403/ngsplot/bin/ngsplotdb.py", line 74

    print "Open {0} error: your ngs.plot database may be corrupted.".\

                                                                   ^

SyntaxError: Missing parentheses in call to 'print'

Do you know what this problem mean? 

Thank you so much!

Best,

Shimeng Liu

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-- 

Li Shen, Ph.D. Computer Science
Assistant Professor
Department of Neuroscience
Icahn School of Medicine at Mount Sinai
New York, NY 10029
#################
ngs.plot - the coolest NGS plotting tool: https://code.google.com/p/ngsplot/

Want ChIP-seq differential analysis? Use: https://code.google.com/p/diffreps/

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[Talon Trecek]

Hey Shimeng,

The reason for me was that this python script has the shebang  #!/usr/bin/env python

This means python will be called from here

Check the python version the script is calling on by typing:

/usr/bin/env python -V

If its python 3, thats the reason it failing.

Refer to jjlin's answer on https://stackoverflow.com/questions/22671764/shebang-usr-bin-env-python-invoking-the-wrong-python-interpreter

In summary adding the bellow line to ~/.bashrc or ~/.bash_profile then sourcing or restarting terminal worked for me.

export -n PATH

I don't know how this PATH problem arose in the first place..

Thanks,

Talon