Closed myliu221 closed 1 year ago
Hi, I encountered the same issue long ago. So I check the the input file which are the *SuperStitched.table.txt
and *AllStitched.table.txt
. And it turns out the column CHROM
have unsaual format like chr6_Nw12...
. After I remove this kind of row manually, It goes well.
Thanks to Gemma-Zhang.The same problem has been solved in your way
Hi, I encountered the same issue long ago. So I check the the input file which are the
*SuperStitched.table.txt
and*AllStitched.table.txt
. And it turns out the columnCHROM
have unsaual format likechr6_Nw12...
. After I remove this kind of row manually, It goes well.
Hi, I encountered this problem when running ROSE, do you know how to solve it?
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
Thanks to Gemma-Zhang.The same problem has been solved in your way
Hi, I encountered this problem when running ROSE, do you know how to solve it?
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
@taolin1988 Hello,I encountered the same problem, after running ROSE_main,I didn't get the SuperEnhancers.table.txt file, and got the error:IndexError: list index out of range. Did you solve the problem?
Hi,
I am currently working on SE analysis for a set of samples. For all samples, the analysis went well in the ROSE_callSuper step. However, in the ROSE_geneMapper step, I got _SuperStitched_GENE_TO_REGION.txt, _SuperStitched_REGION_TO_GENE.txt, _AllStitched_GENE_TO_REGION.txt and _AllStitched_REGION_TO_GENE.txt outputs for fewer samples. I got only _SuperStitched_GENE_TO_REGION.txt and _SuperStitched_REGION_TO_GENE.txt outputs for most samples, while I got no outputs for some samples with index error. The errors are shown as follows, Warning message: In write.table(file = outputFile, superEnhancer, sep = "\t", quote = FALSE, : appending column names to file Warning message: In write.table(file = outputFile, superEnhancer, sep = "\t", quote = FALSE, : appending column names to file Traceback (most recent call last): File "/hpcstor6/scratch01/m/mingyu.liu001/Super_Enhancer/ROSE-1.3.0/bin/ROSE_geneMapper.py", line 291, in
main()
File "/hpcstor6/scratch01/m/mingyu.liu001/Super_Enhancer/ROSE-1.3.0/bin/ROSE_geneMapper.py", line 277, in main
enhancerToGeneTable,geneToEnhancerTable = mapEnhancerToGene(annotFile,enhancerFile,uniqueGenes=True,byRefseq=options.refseq, transcribedFile=transcribedFile)
File "/hpcstor6/scratch01/m/mingyu.liu001/Super_Enhancer/ROSE-1.3.0/bin/ROSE_geneMapper.py", line 145, in mapEnhancerToGene
closestGene = allEnhancerGenes[distList.index(min(distList))]
IndexError: list index out of range
Traceback (most recent call last):
File "/hpcstor6/scratch01/m/mingyu.liu001/Super_Enhancer/ROSE-1.3.0/bin/ROSE_geneMapper.py", line 291, in
main()
File "/hpcstor6/scratch01/m/mingyu.liu001/Super_Enhancer/ROSE-1.3.0/bin/ROSE_geneMapper.py", line 277, in main
enhancerToGeneTable,geneToEnhancerTable = mapEnhancerToGene(annotFile,enhancerFile,uniqueGenes=True,byRefseq=options.refseq, transcribedFile=transcribedFile)
File "/hpcstor6/scratch01/m/mingyu.liu001/Super_Enhancer/ROSE-1.3.0/bin/ROSE_geneMapper.py", line 145, in mapEnhancerToGene
closestGene = allEnhancerGenes[distList.index(min(distList))]
IndexError: list index out of range
Can you help or provide some suggestions? Thank you.
Best, Mingyu