ROSE Algorithm: list index out of range

I am trying to run the ROSE algorithm created by the young lab. However, I got the problem posted below. Any help is appreciated. Thank you!

MAKING TSS COLLECTION
Traceback (most recent call last):
File "/media/wangxiaohan/software/lib/ROSE-1.3.1/ROSE_geneMapper.py", line 291, in <modute>
  main()
File "/media/wangxiaohan/software/lib/ROSE-1.3.1/ROSE_geneMapper.py", line 277, in 
  mainenhancerToGeneTable,geneToEnhancerTable = mapEnhancerToGene
(annotFile, enhancerFile, uniqueGene.True, byRefseg=options.refseq, transcribedFile=transcribedFile)
File "/media/wangxiaohan/software/lib/ROSE-1.3.1/ROSE_geneMapper.py", line 145, in mapEnhancerToGene
  closestGene = allEnhancerGenesldistList.index(min(distlist))]
IndexError: list index out of range

rose super-enhancer

• 1,568 views • link

updated 2.8 years ago by Ram

• written 3.0 years ago by Bradley •

Hi, Everyone.

I encountered this problem when running ROSE, Does you know how to solve it? Thanks very much for your help.

python2.7) liurui@dhcp651-233 rose % python ROSE_main.py -g /Users/liurui/ROSE/hg19 -i /Users/liurui/ROSE/HG18_MM1S_MED1.gff -r /Users/liurui/ROSE/MM1S_MED1.hg18. bwt.sorted.bam -o /Users/liurui/ROSE -s 12500 -t 2000
folder /Users/liurui/ROSE/mappedGFF/ does not exist
USING /Users/liurui/ROSE/HG18_MM1S_MED1.gff AS THE INPUT GFF
USING /Users/liurui/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

• 0 views • link

updated 2.8 years ago by Ram

• written 2.8 years ago by Tao •

0 answers

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