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4.0 years ago
emma7227d
•
0
Good Afternoon I have recently installed SPAdes-3.12.0 on my Mac (running OSX11) and had successfully run the test programme a few times with no issue. I have come back to use it today and I am unable to run anything. When I execute the command I get no error message the cursor just moves to a new line in the terminal. This is for both the test programme and with actual data. I have checked my pwd and can see no obvious issues. I am running the command to the full location pathway as I was previously. If I move to another location then I get the error messages I expect. I am very new to both Mac and command line etc... so it may be that the fix is an obvious one but I just can't see it. Please can anyone assist? Thanks Emma
What is the size of the genome and the amount of data you are working with? How much RAM you have available? Unless you are working with a small genome it would not be useful to try to run SPAdes on a local mac. Having a small test run does not mean that you can use the program with more data than your computer can handle.
Hi Genomax Thanks for your response. Its only a small amount of data, expected genome size is 36kb (viral genome), the fast.gz files are only around 20kb. The Mac I am using has 16GB of RAM installed.
I have managed to get it working now by reinstalling in a different directory. Not sure what the issue was originally but I have managed to run to successful completion for both the test and my desired files. Is it likely my issue was with the directory or looking in the wrong place?
BW Emma
That sounds like a fine application. Good to hear it is working. Consider using
condafor bioinformatics software in future. It should simplify acquiring and running new software.Thanks for the recommendation, I'll take a look at that this afternoon
In addition to Genomax's comments, you may need to provide us with more information about the directory you're trying to run this in. If it works (or at least errors) in the expected way in different directories you might have permission or filepath issues.
Hi Joe Thanks for your comment. As I mentioned above I have managed to get it working by reinstalling in the /usr/local directory instead of in the original location it was in which was in my documents folder. BW Emma