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Old 05-15-2014, 08:49 AM   #1
bsp017
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Location: Bangor, UK

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Default SMRT portal errors

Hi,

I'm trying to assemble six SMRT cells de novo on the SMRT portal. I tried HGAP.2 and HGAP.3 but both fail with different errors:

CeleraAssembler/runCaHgap Failed - for HGAP.2
AssembleUnitig/runCaToUnitig Failed - for HGAP.3

I'm running SMRT portal through Amazon Web Services.

On the PacBio github it provides troubleshooting information for the SMRT pipe but I'm unsure how to access this through AWS.

Any information on how to troubleshoot this would be much appreciated.

James
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Old 05-15-2014, 12:56 PM   #2
rhall
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They are both essentially the same failure. What size amazon instance are you running, in particular memory?
This failure will arise if <16gb of memory is available.
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Old 05-15-2014, 01:19 PM   #3
bsp017
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Its an m3.large instance, with 7.5 GB memory. I guess I need a bigger instance.
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Old 05-26-2014, 04:57 AM   #4
bsp017
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Hello rhall and others,

I changed to a m3.2xlarge instance, with 30 GB of RAM and assembled my two genomes into 1 and 3 contigs. They both have a QV score just under 50.

I uploaded the polished assemblies fasta files to use as a reference and I now want to use the reseqeuncing program to wrap up the assemblies, but when I use this tool I get an error saying: 'Failed to submit job'. The error appears usually after several hours.

I also get this error when I try the Modification and Motif analysis.

Is there a way around this?

Thanks,

James
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