Hi again,
I am trying to run the ROSE algorithm created by the young lab, url here:
http://younglab.wi.mit.edu/super_enhancer_code.html
Specifically, I am running the ROSE_main.py script: http://younglab.wi.mit.edu/super_enhancer_code.html
I created a python 2.7 environment to run the script as it is compatible with python 2.7. When I run the script in ubuntu:
python ROSE_main.py -g hg38.gtf -i 10A_1_H3K.gff3 -r 10A_1_H3K_aligned.bam -o 10A_1_H3K_ROSE
I get the following error
/network/rit/lab/herschkolab/Ali/ChIPseqH3Kdata/data/peakcalls
WARNING: INPUT FILE DOES NOT END IN .gff or .bed. ASSUMING .gff FILE FORMAT
USING 10A_1_H3K.gff3 AS THE INPUT GFF
USING hg38.gtf AS THE GENOME
MAKING START DICT Traceback (most recent call last):
File "ROSE_main.py", line 483, in <module>
main()
File "ROSE_main.py", line 329, in main
startDict = ROSE_utils.makeStartDict(annotFile)
File "/network/rit/lab/herschkolab/Ali/ChIPseqH3Kdata/data/peakcalls/ROSE_utils.py", line 167, in makeStartDict
refseqTable, refseqDict = importRefseq(annotFile)
File "/network/rit/lab/herschkolab/Ali/ChIPseqH3Kdata/data/peakcalls/ROSE_utils.py", line 227, in importRefseq
if refseqDict.has_key(line[1]):
IndexError: list index out of range
So I am guessing the genome build file in gtf is where the indexing is the problem. I was hoping someone could help me understand why I get that error and how to fix it. Any help is appreciated. Thank you!
1 answer
Look in rose/bin/annotation at any of the annotation files and you'll notice the issue. It expects the GENOME file (-g) to be in an odd modified UCSC tableTrack format. You'll have to play around a bit with the table browser to get the appropriate format, particularly if you want gene symbols to be used for the annotation step. I have no idea for how the bin column is generated in their annotation file, so that might take some investigation.
Hi, Everyone.
I encountered this problem when running ROSE, Does anyone 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
And you're mixing hg18 inputs with hg19 reference data. Which may or may not be the root issue, but it's certainly not helping.
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