sh: R: command not found

Dear ROSE developers:

This is the first time that I use ROSE, Could you please help me with the following error:

python2.7 ROSE_main.py -g hg38 -i callpeak_002_peaks.narrowPeak.gff -r sort_002.bam -o /home/vpsilos/His -c sort_001.bam -s 12500 -t 2000

USING callpeak_002_peaks.narrowPeak.gff AS THE INPUT GFF

USING hg38 AS THE GENOME

MAKING START DICT

LOADING IN GFF REGIONS

CHECKING INPUT TO MAKE SURE EACH REGION HAS A UNIQUE IDENTIFIER

REFERENCE COLLECTION PASSES QC

STITCHING REGIONS TOGETHER

PERFORMING REGION STITCHING

REMOVED 609 LOCI BECAUSE THEY WERE CONTAINED BY A TSS

REMOVED 1 STITCHED LOCI BECAUSE THEY OVERLAPPED MULTIPLE TSSs

ADDED BACK 32 ORIGINAL LOCI

MAKING GFF FROM STITCHED COLLECTION

WRITING STITCHED GFF TO DISK AS /home/vpsilos/His/gff/callpeak_002_peaks_12KB_STITCHED_TSS_DISTAL.gff

OUTPUT WILL BE WRITTEN TO /home/vpsilos/His/callpeak_002_peaks_12KB_STITCHED_TSS_DISTAL_ENHANCER_REGION_MAP.txt

python ROSE_bamToGFF.py -f 1 -e 200 -r -m 1 -b sort_002.bam -i /home/vpsilos/His/gff/callpeak_002_peaks_12KB_STITCHED_TSS_DISTAL.gff -o /home/vpsilos/His/mappedGFF/callpeak_002_peaks_12KB_STITCHED_TSS_DISTAL_sort_002.bam_MAPPED.gff &

python ROSE_bamToGFF.py -f 1 -e 200 -r -m 1 -b sort_002.bam -i callpeak_002_peaks.narrowPeak.gff -o /home/vpsilos/His/mappedGFF/callpeak_002_peaks_sort_002.bam_MAPPED.gff &

python ROSE_bamToGFF.py -f 1 -e 200 -r -m 1 -b sort_001.bam -i /home/vpsilos/His/gff/callpeak_002_peaks_12KB_STITCHED_TSS_DISTAL.gff -o /home/vpsilos/His/mappedGFF/callpeak_002_peaks_12KB_STITCHED_TSS_DISTAL_sort_001.bam_MAPPED.gff &

python ROSE_bamToGFF.py -f 1 -e 200 -r -m 1 -b sort_001.bam -i callpeak_002_peaks.narrowPeak.gff -o /home/vpsilos/His/mappedGFF/callpeak_002_peaks_sort_001.bam_MAPPED.gff &

PAUSING TO MAP

{'matrix': '1', 'extension': '200', 'floor': '1', 'sense': 'both', 'output': '/home/vpsilos/His/mappedGFF/callpeak_002_peaks_sort_002.bam_MAPPED.gff', 'bam': 'sort_002.bam', 'rpm': True, 'input': 'callpeak_002_peaks.narrowPeak.gff'}

[]

{'matrix': '1', 'extension': '200', 'floor': '1', 'sense': 'both', 'output': '/home/vpsilos/His/mappedGFF/callpeak_002_peaks_12KB_STITCHED_TSS_DISTAL_sort_002.bam_MAPPED.gff', 'bam': 'sort_002.bam', 'rpm': True, 'input': '/home/vpsilos/His/gff/callpeak_002_peaks_12KB_STITCHED_TSS_DISTAL.gff'}

[]

{'matrix': '1', 'extension': '200', 'floor': '1', 'sense': 'both', 'output': '/home/vpsilos/His/mappedGFF/callpeak_002_peaks_sort_001.bam_MAPPED.gff', 'bam': 'sort_001.bam', 'rpm': True, 'input': 'callpeak_002_peaks.narrowPeak.gff'}

[]

mapping to GFF and making a matrix with fixed bin number

{'matrix': '1', 'extension': '200', 'floor': '1', 'sense': 'both', 'output': '/home/vpsilos/His/mappedGFF/callpeak_002_peaks_12KB_STITCHED_TSS_DISTAL_sort_001.bam_MAPPED.gff', 'bam': 'sort_001.bam', 'rpm': True, 'input': '/home/vpsilos/His/gff/callpeak_002_peaks_12KB_STITCHED_TSS_DISTAL.gff'}

[]

mapping to GFF and making a matrix with fixed bin number

WAITING FOR MAPPING TO COMPLETE. ELAPSED TIME (MIN):

0

using a MMR value of 43.5701

has chr

Number lines processed

0

using a MMR value of 43.5701

has chr

Number lines processed

0

using a MMR value of 51.0726

has chr

Number lines processed

0

using a MMR value of 51.0726

has chr

Number lines processed

0

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MAPPING TOOK 10 MINUTES

BAM MAPPING COMPLETED NOW MAPPING DATA TO REGIONS

FORMATTING TABLE

GETTING MAPPED DATA

GETTING MAPPING DATA FOR sort_002.bam

OPENING /home/vpsilos/His/mappedGFF/callpeak_002_peaks_12KB_STITCHED_TSS_DISTAL_sort_002.bam_MAPPED.gff

MAKING SIGNAL DICT FOR sort_002.bam

GETTING MAPPING DATA FOR sort_001.bam

OPENING /home/vpsilos/His/mappedGFF/callpeak_002_peaks_12KB_STITCHED_TSS_DISTAL_sort_001.bam_MAPPED.gff

MAKING SIGNAL DICT FOR sort_001.bam

CALLING AND PLOTTING SUPER-ENHANCERS

R --no-save /home/vpsilos/His/ /home/vpsilos/His/callpeak_002_peaks_12KB_STITCHED_TSS_DISTAL_ENHANCER_REGION_MAP.txt callpeak_002_peaks sort_001.bam < ROSE_callSuper.R

sh: R: command not found

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