Issue during adding of default reference genome

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mkniz...@gmail.com

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Apr 21, 2017, 12:08:14 AM4/21/17
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Hi guys,

Nizam here. I encountered the following error message during OpEx installation:

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

Adding default reference genome ...

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


NOTE: the reference genome is being indexed by BWA and Stampy that will take a while.



================================================================================

OpEx: Indexing genome by BWA

================================================================================


./index_genome.sh: line 11: tools/bwa-0.5.10/bwa: No such file or directory



================================================================================

OpEx: Indexing genome by Stampy

================================================================================


Could not import the maptools module -- does the maptools.so library exist?

Traceback (most recent call last):

  File "tools/stampy-1.0.14.1/stampy.py", line 14, in <module>

    import maptools

ImportError: No module named maptools


Could not import the maptools module -- does the maptools.so library exist?

Traceback (most recent call last):

  File "tools/stampy-1.0.14.1/stampy.py", line 14, in <module>

    import maptools

ImportError: No module named map tools




Can anyone help me to solve this issue?I am very new to bioinformatics so I apologize if my question is too basic for all of you. I really appreciate your kind help.


Thanks 


Nizam

Márton Münz

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Apr 21, 2017, 5:31:18 AM4/21/17
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Hi Nizam,

What operation system are you trying to install OpEx on?

Could you remove the current directory, unpackage the original file and re-run installation capturing the whole output of the installation script by

./install.sh -r /path/to/reference/reference.fasta >> output.txt 2>&1

And then please send me the output.txt file so that I can look into the issue in more details. 

Thanks,
Márton

mkniz...@gmail.com

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Apr 24, 2017, 9:08:11 PM4/24/17
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Hi Márton,

I have followed your advice and I attached the output.text file in this email. I am using OS X Yosemite version 10.10.5 on iMac (2.7 GHz Intel Core i5 with 8 GB DDR3 RAM). Thank you so much for your kind help. I really appreciate it.

Best Wishes,

Mohd Khairul Nizam
output.txt

Márton Münz

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Apr 25, 2017, 5:07:00 PM4/25/17
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Hi Nizam,

Thank you very much for sending me the file and providing additional information.

OpEx only has support for Linux, so you won't be able to install/run it on a Mac OS X. 
I hope you can give it a try to install it on a Linux operating system.

Please let me know if you have any further question!

Best wishes,
Márton

Pengchong Ma

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Dec 5, 2022, 3:39:46 PM12/5/22
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Hi Márton,

I also have this issues when I try to run stampy.py scripts, is there any update solution?

Best wishes,
Pengchong Ma

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