ROSE Algorithm: index out of range

Question

[mropri]

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!

Answer 1

[jared.andrews07]

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.

[mropri]

Thank you, will check that, you are amazing with all the answers you give out. Much appreciated

[Tao]

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

[Ram]

Open a new question instead of adding comments (and worse, "answers") in multiple threads. Reference these threads in your new post if they add context.

[Tao]

Thanks for your suggestion, I've opened a new question. But no one seems to have the answer

[Ram]

What are you talking about? Did you even open a new question where people can answer?

[jared.andrews07]

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.

[Tao]

Hi, Thanks a lot for your reply. This shouldn't be a problem. I tried other data at the same time and this problem still occurs.