Allelotyping : Cannot find system Renviron, unable to open base package

[syikin]

Hi Mellisa,

I hope you can bear with me:)

After a few trial to run lobSTR and some issues has been fixed. I find myself stuck with allelotyping step. The error details is quite simple, as you can see from below;

#command

allelotype --command classify --bam test.aligned.bam --noise_model PATH/models/illumina.noisemodel.txt --out test --sex M

#error

can not find system Renviron

Fatal error: unable to open base package

I've tried to change the permission for R_HOME/etc/* and add it to the environment variables, but still the same error appear. Do you have this kind of problem last time? Can you help me with this as well? 

My next question is whether the illumina.noisemodel.txt provided is universal? I'm currently running data from illumina sequencing technologies, so does the provided ones is enuff? or i need to specify my own noisemodel?if need, how i get that?

lastly, can i ignore --sex parameter? 

Thanks!

Syikin

[Melissa Gymrek]

Hello,

The Renviron issue has come up before. This message in the README pertains to this issue:

========

R environment: Some users have reported the error "cannot find system Renviron" after running the allelotype step. This issue is due to the environment variable $R_HOME not being set correctly. To fix this issue, set $R_HOME to a path where the Renviron file can be found. 

For example in tcsh:

setenv R_HOME /usr/lib/R

In bash:

export R_HOME=/usr/lib/R

You may need to replace /usr/lib/R to where R is installed in your system if it is not in the default path.

========

Let me know if that doesn't do the trick.

For the stutter model, I would recommend using the provided model for now. Training is not incredibly robust right now, and is something we're working on improving.

Lastly, if --sex is not relevant, just specify --sex U.

Cheers,

~Melissa

[Gareth Highnam]

I am trying to use that --bampair parameter in this command line:

lobSTR -f human.bam --bampair -p 6 -v -o LOBSTR_.july23 --index-prefix index-lobstr/index_trf_hg19_extend1000/lobSTR_

It doesn't work, and I'm not sure why... other than "Warning, multithreading on small files (< several million reads) may fail to produce BAM output", there isn't any other error message. It returns the --help dialogue after about 1 second.

[Gareth Highnam]

I also wanted to add that I did name sort the BAM with "samtools sort -n"

[Melissa Gymrek]

Hi Gareth,

Although it is redundant, you should also specify the --bam flag. Try:

lobSTR -f human.bam --bampair --bam -p 6 -v -o LOBSTR_.july23 --index-prefix index-lobstr/index_trf_hg19_extend1000/lobSTR_

Cheers,

~M