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ROSE error: IndexError: list index out of range #40

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Krithika-Bhuvan opened this issue Jan 3, 2025 · 0 comments
Open

ROSE error: IndexError: list index out of range #40

Krithika-Bhuvan opened this issue Jan 3, 2025 · 0 comments

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@Krithika-Bhuvan
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I ran ROSE with the following command and got the error. Any idea what is causing the error and how to fix this ?

ROSE_main.py \
	-g hg38 \
	-i $infile \
	-r $samplesortedbam \
	-c $inputsortedbam \
	-o $outfolder \
	-s 12500 -t 2500

ERROR

01_A_Control_RNAPOL
17_A_Control_INPUT
/data/CCRCCDI/analysis/ccrtegs4/06_chipseq_haiyan_pipeline/output/filterbam/
Call function to make gff for pvalue p-5
Function: make GFF file for sample:  01_A_Control_RNAPOL
p-5narrowpeak
calling function rose
[-] Unloading singularity  4.1.5  on cn4247 
[-] Unloading ROSE  1.3.1 
[+] Loading singularity  4.1.5  on cn4247 
[+] Loading ROSE  1.3.1 
Function: Run ROSE to find super enhancer for:  01_A_Control_RNAPOL
/data/CCRCCDI/analysis/ccrtegs4/06_chipseq_haiyan_pipeline/output/ROSE/01_A_Control_RNAPOL_p5_peaks.gff
/data/CCRCCDI/analysis/ccrtegs4/06_chipseq_haiyan_pipeline/output/01_A_Control_RNAPOL/01_A_Control_RNAPOL_sorted.bam
/data/CCRCCDI/analysis/ccrtegs4/06_chipseq_haiyan_pipeline/output/17_A_Control_INPUT/17_A_Control_INPUT_sorted.bam
/data/CCRCCDI/analysis/ccrtegs4/06_chipseq_haiyan_pipeline/output/ROSE/01_A_Control_RNAPOL_p5_rose_12.5kb
{'bam': '/data/CCRCCDI/analysis/ccrtegs4/06_chipseq_haiyan_pipeline/output/17_A_Control_INPUT/17_A_Control_INPUT_sorted.bam', 'input': '/data/CCRCCDI/analysis/ccrtegs4/06_chipseq_haiyan_pipeline/output/ROSE/01_A_Control_RNAPOL_p5_rose_12.5kb/gff/01_A_Control_RNAPOL_p5_peaks_12.5KB_STITCHED_TSS_DISTAL.gff', 'output': '/data/CCRCCDI/analysis/ccrtegs4/06_chipseq_haiyan_pipeline/output/ROSE/01_A_Control_RNAPOL_p5_rose_12.5kb/mappedGFF/01_A_Control_RNAPOL_p5_peaks_12.5KB_STITCHED_TSS_DISTAL_17_A_Control_INPUT_sorted.bam_MAPPED.gff', 'sense': 'both', 'floor': '1', 'extension': '200', 'rpm': True, 'matrix': '1'}
[]
mapping to GFF and making a matrix with fixed bin number
using a MMR value of 13.959
has chr
Number lines processed
0
100
200
300
400
500
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{'bam': '/data/CCRCCDI/analysis/ccrtegs4/06_chipseq_haiyan_pipeline/output/01_A_Control_RNAPOL/01_A_Control_RNAPOL_sorted.bam', 'input': '/data/CCRCCDI/analysis/ccrtegs4/06_chipseq_haiyan_pipeline/output/ROSE/01_A_Control_RNAPOL_p5_rose_12.5kb/gff/01_A_Control_RNAPOL_p5_peaks_12.5KB_STITCHED_TSS_DISTAL.gff', 'output': '/data/CCRCCDI/analysis/ccrtegs4/06_chipseq_haiyan_pipeline/output/ROSE/01_A_Control_RNAPOL_p5_rose_12.5kb/mappedGFF/01_A_Control_RNAPOL_p5_peaks_12.5KB_STITCHED_TSS_DISTAL_01_A_Control_RNAPOL_sorted.bam_MAPPED.gff', 'sense': 'both', 'floor': '1', 'extension': '200', 'rpm': True, 'matrix': '1'}
[]
mapping to GFF and making a matrix with fixed bin number
using a MMR value of 17.4184
has chr
Number lines processed
0
100
200
300
400
500
600
700
800
900
1000
1100
1200
1300
1400
1500
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1700
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{'bam': '/data/CCRCCDI/analysis/ccrtegs4/06_chipseq_haiyan_pipeline/output/17_A_Control_INPUT/17_A_Control_INPUT_sorted.bam', 'input': '/data/CCRCCDI/analysis/ccrtegs4/06_chipseq_haiyan_pipeline/output/ROSE/01_A_Control_RNAPOL_p5_peaks.gff', 'output': '/data/CCRCCDI/analysis/ccrtegs4/06_chipseq_haiyan_pipeline/output/ROSE/01_A_Control_RNAPOL_p5_rose_12.5kb/mappedGFF/01_A_Control_RNAPOL_p5_peaks_17_A_Control_INPUT_sorted.bam_MAPPED.gff', 'sense': 'both', 'floor': '1', 'extension': '200', 'rpm': True, 'matrix': '1'}
[]
mapping to GFF and making a matrix with fixed bin number
using a MMR value of 13.959
has chr
Number lines processed
0
100
200
300
400
500
600
700
800
900
1000
1100
1200
1300
1400
1500
1600
1700
1800
1900
2000
2100
2200
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2400
2500
2600
2700
2800
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3000
3100
3200
3300
3400
3500
3600
3700
3800
3900
4000
4100
4200
4300
4400
4500
4600
4700
4800
4900
5000
5100
5200
5300
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5500
5600
5700
5800
5900
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6300
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6500
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6900
7000
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7300
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7500
7600
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7800
7900
8000
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8200
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8500
8600
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9200
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10700
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10900
{'bam': '/data/CCRCCDI/analysis/ccrtegs4/06_chipseq_haiyan_pipeline/output/01_A_Control_RNAPOL/01_A_Control_RNAPOL_sorted.bam', 'input': '/data/CCRCCDI/analysis/ccrtegs4/06_chipseq_haiyan_pipeline/output/ROSE/01_A_Control_RNAPOL_p5_peaks.gff', 'output': '/data/CCRCCDI/analysis/ccrtegs4/06_chipseq_haiyan_pipeline/output/ROSE/01_A_Control_RNAPOL_p5_rose_12.5kb/mappedGFF/01_A_Control_RNAPOL_p5_peaks_01_A_Control_RNAPOL_sorted.bam_MAPPED.gff', 'sense': 'both', 'floor': '1', 'extension': '200', 'rpm': True, 'matrix': '1'}
[]
mapping to GFF and making a matrix with fixed bin number
using a MMR value of 17.4184
has chr
Number lines processed
0
100
200
300
400
500
600
700
800
900
1000
1100
1200
1300
1400
1500
1600
1700
1800
1900
2000
2100
2200
2300
2400
2500
2600
2700
2800
2900
3000
3100
3200
3300
3400
3500
3600
3700
3800
3900
4000
4100
4200
4300
4400
4500
4600
4700
4800
4900
5000
5100
5200
5300
5400
5500
5600
5700
5800
5900
6000
6100
6200
6300
6400
6500
6600
6700
6800
6900
7000
7100
7200
7300
7400
7500
7600
7700
7800
7900
8000
8100
8200
8300
8400
8500
8600
8700
8800
8900
9000
9100
9200
9300
9400
9500
9600
9700
9800
9900
10000
10100
10200
10300
10400
10500
10600
10700
10800
10900
/bin/bash: /opt/conda/envs/rose/lib/libtinfo.so.6: no version information available (required by /bin/bash)
[1] "THESE ARE THE ARGUMENTS"
[1] "/usr/lib/R/bin/exec/R"                                                                                                                                                           
[2] "--slave"                                                                                                                                                                         
[3] "--no-restore"                                                                                                                                                                    
[4] "--file=/opt/conda/envs/rose/ROSE-1.3.1/bin/ROSE_callSuper.R"                                                                                                                     
[5] "--args"                                                                                                                                                                          
[6] "/data/CCRCCDI/analysis/ccrtegs4/06_chipseq_haiyan_pipeline/output/ROSE/01_A_Control_RNAPOL_p5_rose_12.5kb/"                                                                      
[7] "/data/CCRCCDI/analysis/ccrtegs4/06_chipseq_haiyan_pipeline/output/ROSE/01_A_Control_RNAPOL_p5_rose_12.5kb/01_A_Control_RNAPOL_p5_peaks_12.5KB_STITCHED_TSS_DISTAL_REGION_MAP.txt"
[8] "01_A_Control_RNAPOL_p5_peaks"                                                                                                                                                    
[9] "17_A_Control_INPUT_sorted.bam"                                                                                                                                                   
[1] "HERE IS THE WCE NAME"
[1] "X17_A_Control_INPUT_sorted.bam"
null device 
          1 
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
USING hg38 AS THE GENOME
Herp
Derp
MAKING TRANSCRIPT COLLECTION
1000
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MAKING TSS COLLECTION
USING hg38 AS THE GENOME
Herp
Derp
MAKING TRANSCRIPT COLLECTION
1000
2000
3000
4000
5000
6000
7000
8000
9000
10000
11000
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57000
58000
MAKING TSS COLLECTION
Traceback (most recent call last):
  File "/opt/conda/envs/rose/ROSE-1.3.1/bin/ROSE_geneMapper.py", line 291, in <module>
    main()
  File "/opt/conda/envs/rose/ROSE-1.3.1/bin/ROSE_geneMapper.py", line 277, in main
    enhancerToGeneTable,geneToEnhancerTable = mapEnhancerToGene(annotFile,enhancerFile,uniqueGenes=True,byRefseq=options.refseq, transcribedFile=transcribedFile)
  File "/opt/conda/envs/rose/ROSE-1.3.1/bin/ROSE_geneMapper.py", line 145, in mapEnhancerToGene
    closestGene = allEnhancerGenes[distList.index(min(distList))]
IndexError: list index out of range
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@Krithika-Bhuvan