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Forum: Bioinformatics 10-09-2013, 06:17 AM
Replies: 1
Views: 2,453
Posted By ashNZ
Exclamation SOAPsnpZ error : 'std::out_of_range'

Gday all,

I am attempting to use SOAPsnpZ to call SNPs from SOLiD data that I aligned using SOAP2. After conducting the alignment I 'sorted' the output .txt file and when I try to feed it into the...
Forum: Pacific Biosciences 05-24-2013, 04:23 AM
Replies: 55
Views: 24,463
Posted By ashNZ
I tried various.... turns out it was a...

I tried various.... turns out it was a compatibility issue. All running fine now! Thanks a heap for all your help!
Forum: Pacific Biosciences 05-22-2013, 11:35 AM
Replies: 55
Views: 24,463
Posted By ashNZ
Yep, I was most definitely doing that! Cheers for...

Yep, I was most definitely doing that! Cheers for the help.... now when it gets to the novoindex bit its saying:

===novoindex pseudochr:===
/home/ash/Bioinformatics/novocraft/novoindex: 1:...
Forum: Pacific Biosciences 05-22-2013, 11:26 AM
Replies: 55
Views: 24,463
Posted By ashNZ
When I run the program, it goes through the first...

When I run the program, it goes through the first few steps all good and then when it gets to these steps I have errors with not finding novoalign:

===novoindex pseudochr:===
sh: 1: novoindex:...
Forum: Pacific Biosciences 05-22-2013, 11:19 AM
Replies: 55
Views: 24,463
Posted By ashNZ
yep, got it. Where do I add that code?

yep, got it. Where do I add that code?
Forum: Pacific Biosciences 05-22-2013, 11:16 AM
Replies: 55
Views: 24,463
Posted By ashNZ
OK... cheers first problem solved. I am now...

OK... cheers first problem solved. I am now getting through the first few steps but am running into problems when the program is trying to find novoalign. I don't understand where to put that 'which...
Forum: Pacific Biosciences 05-22-2013, 04:34 AM
Replies: 55
Views: 24,463
Posted By ashNZ
I guess that this may be contributing to the...

I guess that this may be contributing to the problem also... as I am running ubuntu 12.04 which comes with Python 2.7, so I am using a local copy of Python 2.6. Can you tell me where I need to edit...
Forum: Pacific Biosciences 05-21-2013, 04:38 AM
Replies: 55
Views: 24,463
Posted By ashNZ
Cheers! Had a look and the permissions are...

Cheers! Had a look and the permissions are definitely fine, files are -rwxrwxrwx.... any other ideas on what it could be? I might try start from scratch, uninstall everything and then rebuild it all....
Forum: Pacific Biosciences 05-20-2013, 10:46 AM
Replies: 55
Views: 24,463
Posted By ashNZ
Not sure....

I'm not sure... how can I check that? I am just using the example package from the 'tutorial' section of the LSC website
Forum: Pacific Biosciences 05-20-2013, 08:17 AM
Replies: 55
Views: 24,463
Posted By ashNZ
Cheers for your answer, it was very helpful. I've...

Cheers for your answer, it was very helpful. I've run into another problem I haven't been able to work out. After checking the parameters of my config file to make sure that all of the file paths are...
Forum: Pacific Biosciences 05-17-2013, 05:35 AM
Replies: 55
Views: 24,463
Posted By ashNZ
Question Gday all, I am trying to run LSC to improve...

Gday all,

I am trying to run LSC to improve my PacBio data to use for a hybrid de novo assembly of a cattle genome, however I am having trouble getting the program to run!
I am running Ubuntu...
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