stjude
ValueError: invalid literal for int() with base 10: '1e+05'
Hello, I had this error after running a long time on 16 core cpu, 384gb ram and python 3.6. How can I solve this? ROSE version is 1.3.1
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
Traceback (most recent call last):
File "/cm/shared/apps/ROSE/bin/ROSE_geneMapper.py", line 291, in <module>
main()
File "/cm/shared/apps/ROSE/bin/ROSE_geneMapper.py", line 277, in main
enhancerToGeneTable,geneToEnhancerTable = mapEnhancerToGene(annotFile,enhancerFile,uniqueGenes=True,byRefseq=options.refseq, transcribedFile=transcribedFile)
File "/cm/shared/apps/ROSE/bin/ROSE_geneMapper.py", line 192, in mapEnhancerToGene
enhancerOrder = ROSE_utils.order([int(line[-2]) for line in enhancerToGeneTable[1:]])
File "/cm/shared/apps/ROSE/bin/ROSE_geneMapper.py", line 192, in <listcomp>
enhancerOrder = ROSE_utils.order([int(line[-2]) for line in enhancerToGeneTable[1:]])
ValueError: invalid literal for int() with base 10: '1e+05'
Hello @madetunj, We use job scheduler Slurm. Here is the slurm file for this job:
#!/bin/bash
#SBATCH -p ulimited3
#SBATCH -J rose_1
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --mail-type=ALL
#SBATCH [email protected]
#SBATCH --output=rose1-output-%j.out
#SBATCH --error=rose1-error-%j.err
PATHTO=/cm/shared/apps/ROSE
PYTHONPATH=$PATHTO/lib
alias python=python3
export PYTHONPATH
export PATH=$PATH:$PATHTO/bin
module load samtools/1.9.0
ROSE_main.py -g MM10 -i /archive/username/Vehicle_broad/Vehicle_K27Ac_IP-S1_R1_broad_peaks.gff -r /archive/username/Vehicle_broad/Vehicle_K27Ac_IP-S1_R1.mLb.clN.sorted.bam -c /archive/username/PT48_broad_pooled/pooled_input_R1.mLb.clN.sorted.bam -o /archive/username/Vehicle_broad/output_2/
The path of ROSE is /cm/shared/apps/ROSE/bin/.
The output file is: rose1-output-10713.out.txt
The error file is: rose1-error-10713.err.txt
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
