ROSE Algorithm: index out of range
Hi, Everyone.
I encountered this problem when running ROSE, Does anyone know how to solve it? Thanks very much for your help.
python2.7) rose % python ROSE_main.py -g /Users/ROSE/hg19 -i /Users/ROSE/HG19_MM1S_MED1.gff -r /Users/ROSE/MM1S_MED1.hg19. bwt.sorted.bam -o /Users//ROSE -s 12500 -t 2000
USING /Users/ROSE/HG19_MM1S_MED1.gff AS THE INPUT GFF
USING /Users/ROSE/hg19 AS THE GENOME
MAKING START DICT
Traceback (most recent call last):
File "ROSE_main.py", line 484, in
main()
File "ROSE_main.py", line 336, in main
startDict = ROSE_utils.makeStartDict(annotFile)
File "/Users/liurui/ROSE/ROSE_utils.py", line 168, in makeStartDict
refseqTable,refseqDict = importRefseq(annotFile)
File "/Users/liurui/ROSE/ROSE_utils.py", line 230, in importRefseq
if refseqDict.has_key(line[1]):
IndexError: list index out of range
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Do you need the space here:
-r /Users/ROSE/MM1S_MED1.hg19. bwt.sorted.bamor should it be-r /Users/ROSE/MM1S_MED1.hg19.bwt.sorted.bam?