AmpliconSuite

[Anne Van Arsdale]

Is it possible to use single strand long range sequencing with the pipeline? 

My input is a sorted bam, but it keeps giving me an error message

Thanks!

[Jens Luebeck]

Hi Anne,

Thanks for this great question. Unfortunately, AmpliconSuite only supports paired-end WGS data, and will result in an error otherwise.

We are working on a complementary method that will work on single-end long reads (Nanopore), however it is still a couple months from being released. We'll make a note of it on the AmpliconSuite GitHub as soon as a beta version is available for testing!

Thanks,

Jens

[Anne Van Arsdale]

Hi-

Have there been errors running the Amplicon Suite/AA command? 

It immediately gives me an error message when I submit the command. 

[Ted Liefeld]

Anne

The computer system that the genepattern.ucsd.edu server uses just went down for maintenance.  Try running at https://cloud.genepattern.org/gp instead for the rest of today.  You may need to register your account again there as they do not share user login (unless you login using globus/google/sso)

Ted

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Ted Liefeld                                      UC San Diego

Mesirov Lab                                    lie...@ucsd.edu                                
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[Ted Liefeld]

The SDSC Expanse maintenance completed last night at out GenePattern server at https://genepattern.ucsd.edu/gp is once again operating normally.

Ted

[Anne Van Arsdale]

Hi-

Sorry...another issue...I am trying to run a WGS sorted bam file on Amplicon Suite, however I keep getting the error message that the MOSEK file is not found. Any troubleshooting for this? 

thanks!

[edh...@cloud.ucsd.edu]

Hi, 

From the job results, I think your job result ID is 21657. I've recently replaced the mosek file on the server, that error message will be removed in the next patch but should not affect the module running. 

I noticed you uploaded your inputs as .fq files. Can you rename those files to .fastq and try running again? In the upcoming patch, I'll include .fq as one of the allowed file extensions. 

Thanks, 

Edwin