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
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!