Issue with ENC calculation

[mgshapiro100]

I have been getting an issue while trying to run the program (copy + pasted here): Calculating ENC Traceback (most recent call last): File "CodonShuffle.py", line 1664, in <module> call(["./lib/codonW/codonw", filename, "-enc", "-nomenu", "-nowarn", "-silent"]) #Insert path before codonw in this line (ENC) File "/usr/lib/python2.7/subprocess.py", line 523, in call return Popen(*popenargs, **kwargs).wait() File "/usr/lib/python2.7/subprocess.py", line 711, in __init__ errread, errwrite) File "/usr/lib/python2.7/subprocess.py", line 1343, in _execute_child raise child_exception OSError: [Errno 8] Exec format error And the program exits. Any help I can get with this?

[alauring]

Thanks for using codon shuffle.

We are looking into this issue now and will let you know what we can figure out for you soon.

• Adam

Adam Lauring, MD, PhD Assistant Professor Department of Medicine, Division of Infectious Diseases Department of Microbiology & Immunology University of Michigan Medical School

5510B MSRB I, SPC 5680 1150 W. Medical Center Dr. Ann Arbor, MI 48109-5680 (734) 764-7731 alauring@med.umich.edumailto:alauring@med.umich.edu

On Nov 13, 2016, at 6:55 PM, mgshapiro100 notifications@github.com<mailto:notifications@github.com> wrote:

I have been getting an issue while trying to run the program (copy + pasted here): Calculating ENC Traceback (most recent call last): File "CodonShuffle.py", line 1664, in call(["./lib/codonW/codonw", filename, "-enc", "-nomenu", "-nowarn", "-silent"]) #Insert path before codonw in this line (ENC) File "/usr/lib/python2.7/subprocess.py", line 523, in call return Popen(_popenargs, *_kwargs).wait() File "/usr/lib/python2.7/subprocess.py", line 711, in init errread, errwrite) File "/usr/lib/python2.7/subprocess.py", line 1343, in _execute_child raise child_exception OSError: [Errno 8] Exec format error And the program exits. Any help I can get with this?

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[danielmjorge]

Hi, Thanks for using CodonShuffle. Is the script working with the example that we add in the package? Please, could you double check if exists any space in the fasta file between the name and sequence, please? Because, if there are any space the script could stop. Or could you send me the fasta file, so I can try to run here? Thank you.

[mgshapiro100]

The issue arose with the example sequence that was provided with codon shuffle.

On Nov 17, 2016 4:47 PM, "danielmjorge" notifications@github.com wrote:

Hi, Thanks for using CodonShuffle. Is the script working with the example that we add in the package? Please, could you double check if exists any space in the fasta file between the name and sequence, please? Because, if there are any space the script could stop. Or could you send me the fasta file, so I can try to run here? Thank you.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/lauringlab/CodonShuffle/issues/4#issuecomment-261380034, or mute the thread https://github.com/notifications/unsubscribe-auth/APLZ1Nj-DorGhLBzSSFgluNaf0B6TK9Qks5q_MtkgaJpZM4Kw2Uo .

[danielmjorge]

Ok, thanks for letting know. Some questions: Are you using mac, linux or PC? If you are using mac, did you updated PIP installer? Do you have installed in your mac the software Xcode? When you are running the install_dependencies.py, did you get any error in the command line? Thank you

[mgshapiro100]

I am using Ubuntu, and had no problems with the installation.

On Nov 18, 2016 7:41 AM, "danielmjorge" notifications@github.com wrote:

Ok, thanks for letting know. Some questions: Are you using mac, linux or PC? If you are using mac, did you updated PIP installer? Do you have installed in your mac the software Xcode? When you are running the install_dependencies.py, did you get any error in the command line? Thank you

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[danielmjorge]

Ok. Please, could you check if the Codonw is working well? Since is getting an error running it. Could you run the command: # ./lib/codonW/codonw . If the codonw is running well, you will get a initial menu with some option. Please use the item 1 in the menu to load the file "Poliovirus_1_Mahoney_P1.fas". It will ask you to create two new files a "out" and "blk" files. After that, you could run the analysis typing "4" and "4" again to select Effective number of codons. Finally, please could you run the analysis typing "R". The out file will have the results from ENC. Second question, since the program is stopping in the ENC step, are you getting the results from shuffle part of the script? Are you getting fasta file, hamming distance and CAI results? Third question, which is the version of the python ( I am using version 2.7.10) that you have in your computer? Sorry about so many questions, I am trying to figure out what is causing this problem. Thanks for your patience.

[mgshapiro100]

So it may be an issue with codonW. When trying to execute codonw, I get an error:

bash: ./lib/codonW/codonw: cannot execute binary file: Exec format error

Otherwise, I am getting results from the hamming distance, CAI, and shuffle portion of the script, and I use python 2.7.10 as well.

Please don't apologize for asking questions. I understand debugging and programming come without a crystal ball. If you need any other info, please let me know.

Max

Maxwell Shapiro Department of Applied Mathematics & Statistics http://www.ams.stonybrook.edu maxwell.shapiro@stonybrook.edu

"If I have seen further than others, it is by standing upon the shoulders of giants." - Sir Isaac Newton

On Fri, Nov 18, 2016 at 12:12 PM, danielmjorge notifications@github.com wrote:

Ok. Please, could you check if the Codonw is working well? Since is getting an error running it. Could you run the command: # ./lib/codonW/codonw . If the codonw is running well, you will get a initial menu with some option. Please use the item 1 in the menu to load the file "Poliovirus_1_Mahoney_P1.fas". It will ask you to create two new files a "out" and "blk" files. After that, you could run the analysis typing "4" and "4" again to select Effective number of codons. Finally, please could you run the analysis typing "R". The out file will have the results from ENC. Second question, since the program is stopping in the ENC step, are you getting the results from shuffle part of the script? Are you getting fasta file, hamming distance and CAI results? Third question, which is the version of the python ( I am using version 2.7.10) that you have in your computer? Sorry about so many questions, I am trying to figure out what is causing this problem. Thanks for your patience.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/lauringlab/CodonShuffle/issues/4#issuecomment-261586605, or mute the thread https://github.com/notifications/unsubscribe-auth/APLZ1LbDTcFttUqgrX2ytqumtZRVHZQ6ks5q_dxqgaJpZM4Kw2Uo .

[danielmjorge]

Thanks for your feedback. Did you try to change the permission for the codonw executable file?