CNV3 (CNVseq) summary issues

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-CNV3 (CNVseq):

The last discussion we made was:

"(3) CNV3 (CNVseq path): I searched for the Rexe (bc I wanted to avoid bugging 
you anymore but I couldn't find it), so just to keep in mind when you have time.

·        I’m sorry I confused you yesterday! I think Rexe is just a pointer 
to the /uci/fgene location of the R executable. I believe (on fgene1) this 
location may be: /raid/programs/linux/R-2.8.1/bin/R"

I run the attached pipe, having an error in the cnvseq module, no error stream 
but if I run the command line I have an error about the Rexe:


/projects1/test_pipeline/NEW_ORGANIZATION/scripts/cnv-seq.pl --test 
/usr/pl_cache/pipeline/2011August04_16h10m56s535ms/ExtractHits_2.OutputHits-1.hi
ts --ref 
/usr/pl_cache/pipeline/2011August04_16h10m56s535ms/ExtractHits_1.OutputHits-1.hi
ts --genome human --Rexe /applications/R-2.11.1/bin/exec/R 
/usr/pl_cache/pipeline/2011August04_16h10m56s535ms/CNV-Seq_1.OutputCountFile-1.c
ount 
/usr/pl_cache/pipeline/2011August04_16h10m56s535ms/CNV-Seq_1.OutputCNVFile-1.cnv
genome size used for calculation is 3253037807
/usr/pl_cache/pipeline/2011August04_16h10m56s535ms/ExtractHits_2.OutputHits-1.hi
ts: 48477750 reads
/usr/pl_cache/pipeline/2011August04_16h10m56s535ms/ExtractHits_1.OutputHits-1.hi
ts: 34426365 reads
/applications/R-2.11.1/bin/exec/R: error while loading shared libraries: 
libRblas.so: cannot open shared object file: No such file or directory

 Error: can not find program /applications/R-2.11.1/bin/exec/R at /projects1/test_pipeline/NEW_ORGANIZATION/scripts/cnv-seq.pl line 123.

...so the problem is always the path to Rexe, even if I put the path that also 
you suggested and that make more sense also to me.

I don't find any issue about CNV3 on the tracker, so hopefully I anot misisng 
any piece of info.

Original issue reported on code.google.com by [email protected] on 4 Aug 2011 at 11:30

Attachments:

• CNV3_070711_UCI.pipe