macQiime Issue with Amplicon Noise

[Alex Corder]

Hello,

I am an undergraduate researcher trying to set up MacQiime, which per online instructions require the installation of AmpliconNoise.  When I tried to install this, it is showing an error when the make command is used in terminal.  I have been trying to install this program using the directions listed in the presentation found at https://stamps.mbl.edu/images/4/4e/TutorialV1.25.pdf.  I am able to move and extract the file, however once I try the "make" function, the following error comes up.  

I am not sure what this error means, and I was wondering if anyone could potentially assist me.  I am working on an iMac with OS X 10.9.5 and as far as I can tell, I have already installed the prerequisite program listed on the MacQiime installation instruction website: http://www.wernerlab.org/software/macqiime/macqiime-installation

Thanks in advance for any help!

[Daniel McDonald]

Hi Alex,

What sequencing platform were your data generated from? AmpliconNoise is specific to 454, which largely isn't in use anymore. I'd be happy to help debug but just want to make sure it makes sense to pursue first.

Best,
Daniel

[Alex Corder]

Hey Daniel,

Our data was generated from single-ended reads, quality filtered ion-torrent sequencing.  Is this what you mean?

Thanks again!

Alex

[Daniel McDonald]

Yes, thanks! I don't believe AmpliconNoise can be applied to those data, although I'll confess, I've never actually seen ion-torrent data. Do you have flowgrams (.SFF files)?

Best,

Daniel

[Alex Corder]

The only files we have are the .fastq files.  

Best,

Alex

[Daniel McDonald]

Okay, thanks. So you will not be able to use AmpliconNoise on those data.

Best,

Daniel

[Alex Corder]

Do you have any idea what program could be used for this data?

[Daniel McDonald]

You can use QIIME and just pick OTUs :)

If the data were generated by Illumina HiSeq or MiSeq, you may want to look at either Deblur or DADA2 to denoise the data to derive subOTUs. 

Best,

Daniel