younglab / rose Goto Github PK

Hi @abraham2, @chlazaris,

I ran into the IndexError:list index out of range at ROSE_geneMapper.py step.
I tried to address it by manually removing all chr*_ nomenclature from mm10_AllStitched.table.txt. (stjude/ROSE#24)
However, I do not know what to expect in terms of output files at the end of this step.

There are the files in my output folder.

Can you explain/list the output files from running this command.
ROSE_geneMapper.py -g mm10 -i /FILEPATH/ROSE/bin/output/mm10_SuperStitched.table.txt -r TRUE -c
ROSE_geneMapper.py -g mm10 -i /FILEPATH/ROSE/bin/output/mm10_AllStitched.table.txt -r TRUE -c

Traceback (most recent call last):
File "/PATH/ROSE/bin/ROSE_geneMapper.py", line 298, in
main()
File "/PATH/ROSE/bin/ROSE_geneMapper.py", line 281, in main
enhancerToGeneTable,geneToEnhancerTable,withGenesTable = mapEnhancerToGene(annotFile,enhancerFile, uniqueGenes=True, byRefseq=options.refseq, subtractInput=options.control, transcribedFile=transcribedFile)
File "/PATH/ROSE/bin/ROSE_geneMapper.py", line 140, in mapEnhancerToGene
closestGene = allEnhancerGenes[distList.index(min(distList))]
IndexError: list index out of range

Error still persists!

Many thanks!

Hello,
I'm trying to use ROSE_main.py to identify super-enhancers, but I'm encountering the following error.

I have provided the required GFF format file and indexed BAM file as requested.However, when I run this command, the script throws an error.

My command line parameters are:
python ROSE_main.py -g HG38 -i xx.gff -r xx.bam -o xx -s 12500 -t 2500

The error message reads:
ERROR: OPERATION TIME OUT. MAPPING OUTPUT NOT DETECTED

I've tried rerunning the command, but the issue persists. What could be causing this error, and how can I resolve it?
Thanks!