RSeQC GeneBody_coverage.py function error. Stops at R Script Step RScript
1
1
Entering edit mode
17 months ago
592809957 ▴ 10

my geneBody_coverage.py script:

geneBody_coverage.py -r hg19.housekeeping.bed  -i s1TR_soorted.bam -o output

but the result was error:

@ 2019-11-06 16:04:21: Read BED file (reference gene model) ...
@ 2019-11-06 16:05:52: Total 159322 transcripts loaded
@ 2019-11-06 16:05:53: Get BAM file(s) ...
    ../s1TR_FRAS190103124-1a_soorted.bam
@ 2019-11-06 16:05:53: Processing s1TR_soorted.bam ...

Cannot get coverage signal from s1TR_soorted.bam ! Skip
    Sample  Skewness
@ 2019-11-06 16:06:01: Running R script ...
/bin/sh: Rscript: command not found`

AND then i vi geneBody_coverage.py , i found that

 printlog("Running R script ...")
    try:
            subprocess.call("Rscript " + options.output_prefix + '.geneBodyCoverage.r',shell=True)
    except:
            print >>sys.stderr, "Cannot generate pdf file from " + options.output_prefix + '.geneBodyCoverage.r'
            pass


    if __name__ == '__main__':
    main()

the one of the output of the script is "output.geneBodyCoverage.r",

 lesss -S output.geneBodyCoverage.r
pdf("output.geneBodyCoverage.curves.pdf")
x=1:100
icolor = colorRampPalette(c("#7fc97f","#beaed4","#fdc086","#ffff99","#386cb0","#f0027f"))(0)
dev.off()

i used conda to install RSeQC

conda install -c bioconda RSeQC

i have install R

which R
/cluster/home/miniconda3/envs/rna/bin/R
which Rscript
/cluster/home/miniconda3/envs/rna/bin/Rscript
echo$PATH

/cluster/home/miniconda3/envs/rna/bin/R

R is in my PATH; before i ran the script

source activate rna

but the error still was

/bin/sh: Rscript: command not found`

why did geneBody_coverage.py script go to the /bin/sh to find Rscript????

my R is not in the /bin/sh:,

why didn't go to the "/cluster/home/miniconda3/envs/rna/bin/R" to use R ?

i don't know what's wrong,

Is there something wrong with running R ? or the output file "output.geneBodyCoverage.r"?

please help me thanks a lot!

RNA-Seq R bioconda • 814 views
ADD COMMENT
0
Entering edit mode

Before getting ahead of yourself. Is R installed and in your PATH variable?

ADD REPLY
0
Entering edit mode

i have installe R ,and R is in my PATH variable, thanks for your reply

ADD REPLY
0
Entering edit mode
17 months ago
592809957 ▴ 10

i have install R

which R
/cluster/home/miniconda3/envs/rna/bin/R
which Rscript
/cluster/home/miniconda3/envs/rna/bin/Rscript
echo$PATH
/cluster/home/miniconda3/envs/rna/bin/R:

R is in my PATH; before i ran the script

source activate rna

but the error still was

/bin/sh: Rscript: command not found`

why did geneBody_coverage.py script go to the /bin/sh to find Rscript???? my R is not in the /bin/sh: , i even don't have sh in /bin/

ADD COMMENT
0
Entering edit mode

I think the issue is that Rscript is not installed on the node you are submitting the job to. You should contact your administrator and ask how to install/access Rscript in the node. If your admins use module then you might need to module load R or similar.

ADD REPLY

Login before adding your answer.

Traffic: 1606 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6