User: petinho86

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petinho860
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Posts by petinho86

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Answer: A: Setup PHG with Singularity
... Hi, I'll add the CreateHaplotypesFromGVCF log in the next days. It did work in the end. And I probably had some mismatching bed files. The out of memory problem seems very odd. I have a 430mb genome (rice) and 4 Taxons. And I only added 1000 x 1000bp ranges. Nothing spectacular. I found the probl ...
written 17 days ago by petinho860
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Answer: A: Setup PHG with Singularity
... **Update** Hi again. Turns out having multiple config files makes this a lot easier to grasp. It would be probably good to show that in the description of each step, eg: makeinitialDB_config.txt Here is the way it works for me: **Make working directory using singularity:** $ singularit ...
written 20 days ago by petinho860
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Answer: A: Setup PHG with Singularity
... Hi Zack, Yes singularity has nothing to do with this. It looks like it all stands and falls with a proper config file. I hacked the config file a lot and got some steps further into the pipeline. I replaced the #required parameters section with the part you wrote and I added the sql db config sect ...
written 28 days ago by petinho860
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Comment: A: Setup PHG with Singularity
... Hi Zack, Thanks a lot. I started to fill in the gaps, but there are still plenty of spaces / UNASSIGED sections to fill. I figured that for the initial run I mainly need to setup the required parameters: (this is how my config.txt looks now): ######################################## #Req ...
written 4 weeks ago by petinho860
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Setup PHG with Singularity
... Hi, I am trying to setup PHG. I am using Singularity as I am working on a cluster. The installation sis pretty simple as described on : https://bitbucket.org/bucklerlab/practicalhaplotypegraph/wiki/UserInstructions/CreatePHG_step0_singularity.md So I ran: $ cd phg_singularity $ module l ...
phg written 4 weeks ago by petinho860

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