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problem at step Strain clustering and assembly: Invalid version format (non-numeric data) #57
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Hi Davila, thanks for using OPERA-MS ! Top help you I will need to look at your species coverage file. To do that, you can locate which species is problematic with : Regards, |
Hi Jean, Thanks a lot for your answer and valuable help. Acutalibacter_muris.log:Invalid version format (non-numeric data) at /beegfs/group_dv/home/DDavila/.perl/5.24.1/lib/perl5/Statistics/R.pm line 369. I will send to you the contigs_window_cov of this single file to "jsgounot+github" jsgounot+github@gmail.com. Please let me know if you do not receive the file. Thanks a lot for your help!!! Best, |
I'm able to read and process your file without issues. Can you check your perl, R module and R version ?
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Hi Jean, This is the output that I got: Loading rlang/3.6.3 This is perl 5, version 24, subversion 1 (v5.24.1) built for x86_64-linux Statistics::R
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Hi Jean, I re-run the pipeline and still have the problem in line 369 on Statistics::R. The problem is in this part:
Do you have any idea on how to solve this? Thanks a lot for the valuable help! Best, Daniel Davila |
Hi Jean, Besides the problem above, I also have another error in nucmer.error which is: 20210413|122427|196763| ERROR: The following critical files could not be used Is this could the problem with line 369 in Statistics::R? |
Hi Daniel, the problem is linked to the perl module and maybe your version of perl. I'm using the same version of the R::Statistics module than you so I don't really know what's happening here. So first you can try to update / reinstall your module, I don't think it will work but cost nothing to try and should be fast : But I think that you should try Opera-MS with a new fresh perl installation (I'm using Before running the whole opera pipeline, you can check if libraries are able to be loaded. For this you can run an interactive sessions with
I hope this will work, |
I'm having the same issue. My perl version is 5.26.2, and I have all perl dependencies installed, running the perl debugger above and loading the statistics modules does not produce any errors or warnings. |
I've figured out the NUCMER error. Seems like Opera-ms assumes you are running your analysis within the folder you have opera-ms installed. For me that is in my home directory: This produces the nucmer error, and the following strain analysis error I assume. Even if I run everything from within my home directory, inside where I've download the OPERA-MS files it still does the same thing... Is there a particular file setup that oepra-ms is demandning or are we missing something? |
Concerning the issue relative to nucmer, please see the answer in the dedicated thread #63. |
Dear all,
I ran the test files and work perfectly. When I ran my own data, I have a problem with the Strain clustering and assembly step. I have this problem
*** End window construction
Invalid version format (non-numeric data) at /beegfs/group_dv/home/DDavila/.perl/5.24.1/lib/perl5/Statistics/R.pm line 369
Could you please help me on this problem?
Thanks you so much in advance for your time!
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