Metamos help request

[trexbob]

Has anyone out there used MetAmos with a single read fastq file? I've downloaded the binary with Blast DBs and tried using initPipeline -q -1 myfile.fastq which seems to work, but then when I do runPipeline it errors out at the MapReads step with Bowtie2 giving an error that sounds like it's looking for paired data. Am I missing a parameter somewhere?

[chevrm]

I believe (could be wrong) you're looking for -m. From the man:

-m: interleaved file of paired reads
usage: initPipeline -q -m file.fastq.12 -d projectDir -i 300:500

[trexbob]

I'm using single reads, so the -m is for specifying mate-paired reads, and the -i parameter is for insert size - I can't give an insert size as that only applies to paired reads... right?

I believe my problem has to do with the binary download. I have had *slightly* more luck getting some of the pipeline running with the version 1.3 download, but there are several parts of the pipeline that I cannot get installed and working on my system (Ubuntu 12.04), with Glimmer-MG, Kraken and MetaPhyler all giving me fits, never installing all the way. It seems like to get a lot of this working right you have to be an expert in ALL of the languages used... shell scripting, R, Perl, Python, java, c++.

[clintp]

Are you using the precompiled binary?

[trexbob]

I started off using the binary, but as I mentioned, it seems like it's looking for paired data exclusively, so I switched to using 1.3 (non-binary) version. I am still having trouble getting the whole pipeline to work, but making progress.

[clintp]

Ah, I see now you mentioned that. I've been trying off and on with folks to get the 1.2 binary to work, but it has had several problems, including the one you mentioned. The most recent was that it was referencing a path that didn't exist.

Anyway, I've been a little out of the loop the last few weeks, but I see that a 1.3 frozen binary is now available. This at least will make your set up a little easier...