ERROR: OPERATION TIME OUT. MAPPING OUTPUT NOT DETECTED

[Former user]

Hi,

trying to run ROSE on H3K27ac bam files with peaks called. the peaks were in bed format but i converted them to gff using galaxy and removed the unneeded columns. I have the gff and bam files within the rose file where the ROSE_main.py script is. Not sure what else I'm doing wrong, but would love any ideas you have! heres my code:

$python2.7 ROSE_main.py -g hg38 -i LT1_27ac_0_V1.gff -r LT1_27ac_0.bam -o output cp: LT1_27ac_0_V1.gff: No such file or directory USING LT1_27ac_0_V1.gff AS THE INPUT GFF USING hg38 AS THE GENOME MAKING START DICT LOADING IN GFF REGIONS Traceback (most recent call last): File "ROSE_main.py", line 497, in <module> main() File "ROSE_main.py", line 354, in main referenceCollection = ROSE_utils.gffToLocusCollection(inputGFFFile) File "/Users/nur/young_ROSE/ROSE_utils.py", line 506, in gffToLocusCollection gff = parseTable(gff,'\t') File "/Users/nur/young_ROSE/ROSE_utils.py", line 45, in parseTable fh = open(fn) IOError: [Errno 2] No such file or directory: 'LT1_27ac_0_V1.gff' (base) Nurs-MacBook-Pro:young_Rose nur$ python2.7 ROSE_main.py -g hg38 -i gff.gff -r LT1_27ac_0.bam -o output USING gff.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 MAKING GFF FROM STITCHED COLLECTION WRITING STITCHED GFF TO DISK AS output/gff/gff_12KB_STITCHED.gff OUTPUT WILL BE WRITTEN TO output/gff_12KB_STITCHED_ENHANCER_REGION_MAP.txt python ROSE_bamToGFF.py -f 1 -e 200 -r -m 1 -b LT1_27ac_0.bam -i output/gff/gff_12KB_STITCHED.gff -o output/mappedGFF/gff_12KB_STITCHED_LT1_27ac_0.bam_MAPPED.gff & python ROSE_bamToGFF.py -f 1 -e 200 -r -m 1 -b LT1_27ac_0.bam -i gff.gff -o output/mappedGFF/gff_LT1_27ac_0.bam_MAPPED.gff & PAUSING TO MAP File "ROSE_bamToGFF.py", line 49 File "ROSE_bamToGFF.py", line 49 print "has chr" print "has chr" ^ ^ SyntaxError: Missing parentheses in call to 'print'. Did you mean print("has chr")? SyntaxError: Missing parentheses in call to 'print'. Did you mean print("has chr")? WAITING FOR MAPPING TO COMPLETE. ELAPSED TIME (MIN): 0 30 60 90 120 150 180 210 240 270 300 330 360 390 420 450 480 510 540 570 600 630 660 690 ERROR: OPERATION TIME OUT. MAPPING OUTPUT NOT DETECTED