TypeError and png error

[hwick]

Hello,
I am using python 2.7 to and R 3.3.1 run Rose, and getting the following type error:

PAUSING TO MAP
{'matrix': '1', 'extension': '200', 'floor': '1', 'sense': 'both', 'output': 'example/mappedGFF/HG18_MM1S_MED1_12KB_STITCHED_TSS_DISTAL_MM1S_MED1.hg18.bwt.sorted.bam_MAPPED.gff', 'bam': './data/MM1S_MED1.hg18.bwt.sorted.bam', 'rpm': True, 'input': 'example/gff/HG18_MM1S_MED1_12KB_STITCHED_TSS_DISTAL.gff'}
[]
mapping to GFF and making a matrix with fixed bin number
Traceback (most recent call last):
  File "ROSE_bamToGFF.py", line 247, in <module>
    main()
  File "ROSE_bamToGFF.py", line 238, in main
    newGFF = mapBamToGFF(bamFile,gffFile,options.sense,int(options.extension),options.floor,options.rpm,options.matrix)
  File "ROSE_bamToGFF.py", line 40, in mapBamToGFF
    MMR= round(float(bam.getTotalReads('mapped'))/1000000,4)
TypeError: float() argument must be a string or a number
{'matrix': '1', 'extension': '200', 'floor': '1', 'sense': 'both', 'output': 'example/mappedGFF/HG18_MM1S_MED1_MM1S_MED1.hg18.bwt.sorted.bam_MAPPED.gff', 'bam': './data/MM1S_MED1.hg18.bwt.sorted.bam', 'rpm': True, 'input': './data/HG18_MM1S_MED1.gff'}
[]
mapping to GFF and making a matrix with fixed bin number
Traceback (most recent call last):
  File "ROSE_bamToGFF.py", line 247, in <module>
    main()
  File "ROSE_bamToGFF.py", line 238, in main
    newGFF = mapBamToGFF(bamFile,gffFile,options.sense,int(options.extension),options.floor,options.rpm,options.matrix)
  File "ROSE_bamToGFF.py", line 40, in mapBamToGFF
    MMR= round(float(bam.getTotalReads('mapped'))/1000000,4)
TypeError: float() argument must be a string or a number
{'matrix': '1', 'extension': '200', 'floor': '1', 'sense': 'both', 'output': 'example/mappedGFF/HG18_MM1S_MED1_12KB_STITCHED_TSS_DISTAL_MM1S_WCE.hg18.bwt.sorted.bam_MAPPED.gff', 'bam': './data/MM1S_WCE.hg18.bwt.sorted.bam', 'rpm': True, 'input': 'example/gff/HG18_MM1S_MED1_12KB_STITCHED_TSS_DISTAL.gff'}
[]
mapping to GFF and making a matrix with fixed bin number
Traceback (most recent call last):
  File "ROSE_bamToGFF.py", line 247, in <module>
    main()
  File "ROSE_bamToGFF.py", line 238, in main
    newGFF = mapBamToGFF(bamFile,gffFile,options.sense,int(options.extension),options.floor,options.rpm,options.matrix)
  File "ROSE_bamToGFF.py", line 40, in mapBamToGFF
    MMR= round(float(bam.getTotalReads('mapped'))/1000000,4)
TypeError: float() argument must be a string or a number
{'matrix': '1', 'extension': '200', 'floor': '1', 'sense': 'both', 'output': 'example/mappedGFF/HG18_MM1S_MED1_MM1S_WCE.hg18.bwt.sorted.bam_MAPPED.gff', 'bam': './data/MM1S_WCE.hg18.bwt.sorted.bam', 'rpm': True, 'input': './data/HG18_MM1S_MED1.gff'}
[]
mapping to GFF and making a matrix with fixed bin number
Traceback (most recent call last):
  File "ROSE_bamToGFF.py", line 247, in <module>
    main()
  File "ROSE_bamToGFF.py", line 238, in main
    newGFF = mapBamToGFF(bamFile,gffFile,options.sense,int(options.extension),options.floor,options.rpm,options.matrix)
  File "ROSE_bamToGFF.py", line 40, in mapBamToGFF
    MMR= round(float(bam.getTotalReads('mapped'))/1000000,4)
TypeError: float() argument must be a string or a number
WAITING FOR MAPPING TO COMPLETE. ELAPSED TIME (MIN):
0
MAPPING TOOK 5 MINUTES

And then the following R error when the R script is called:

> png(filename=plotFileName,height=600,width=600)
Error in .External2(C_X11, paste("png::", filename, sep = ""), g$width,  : 
  unable to start device PNG
Calls: png
In addition: Warning message:
In png(filename = plotFileName, height = 600, width = 600) :
  unable to open connection to X11 display ''
Execution halted

I have XQuartz installed.
Is there a suggested workaround for these issues? I downloaded ROSE and example data from the bitbucket website.
Thank you,
Heather

[rakarnik]

Hi Heather, Please contact the ROSE developers about this error. This GitHub repo is merely a copy of the bitbucket repo and not an official repository. Good luck! Best, Rahul -- Rahul Karnik rahul@genebrew.com

On Wed, Aug 26, 2020, at 4:20 PM, hwick wrote: Hello, I am using python 2.7 to and R 3.3.1 run Rose, and getting the following type error: `PAUSING TO MAP

{'matrix': '1', 'extension': '200', 'floor': '1', 'sense': 'both', 'output': 'example/mappedGFF/HG18_MM1S_MED1_12KB_STITCHED_TSS_DISTAL_MM1S_MED1.hg18.bwt.sorted.bam_MAPPED.gff', 'bam': './data/MM1S_MED1.hg18.bwt.sorted.bam', 'rpm': True, 'input': 'example/gff/HG18_MM1S_MED1_12KB_STITCHED_TSS_DISTAL.gff'} [] mapping to GFF and making a matrix with fixed bin number Traceback (most recent call last): File "ROSE_bamToGFF.py", line 247, in <module> main() File "ROSE_bamToGFF.py", line 238, in main newGFF = mapBamToGFF(bamFile,gffFile,options.sense,int(options.extension),options.floor,options.rpm,options.matrix) File "ROSE_bamToGFF.py", line 40, in mapBamToGFF MMR= round(float(bam.getTotalReads('mapped'))/1000000,4) TypeError: float() argument must be a string or a number {'matrix': '1', 'extension': '200', 'floor': '1', 'sense': 'both', 'output': 'example/mappedGFF/HG18_MM1S_MED1_MM1S_MED1.hg18.bwt.sorted.bam_MAPPED.gff', 'bam': './data/MM1S_MED1.hg18.bwt.sorted.bam', 'rpm': True, 'input': './data/HG18_MM1S_MED1.gff'} [] mapping to GFF and making a matrix with fixed bin number Traceback (most recent call last): File "ROSE_bamToGFF.py", line 247, in <module> main() File "ROSE_bamToGFF.py", line 238, in main newGFF = mapBamToGFF(bamFile,gffFile,options.sense,int(options.extension),options.floor,options.rpm,options.matrix) File "ROSE_bamToGFF.py", line 40, in mapBamToGFF MMR= round(float(bam.getTotalReads('mapped'))/1000000,4) TypeError: float() argument must be a string or a number {'matrix': '1', 'extension': '200', 'floor': '1', 'sense': 'both', 'output': 'example/mappedGFF/HG18_MM1S_MED1_12KB_STITCHED_TSS_DISTAL_MM1S_WCE.hg18.bwt.sorted.bam_MAPPED.gff', 'bam': './data/MM1S_WCE.hg18.bwt.sorted.bam', 'rpm': True, 'input': 'example/gff/HG18_MM1S_MED1_12KB_STITCHED_TSS_DISTAL.gff'} [] mapping to GFF and making a matrix with fixed bin number Traceback (most recent call last): File "ROSE_bamToGFF.py", line 247, in <module> main() File "ROSE_bamToGFF.py", line 238, in main newGFF = mapBamToGFF(bamFile,gffFile,options.sense,int(options.extension),options.floor,options.rpm,options.matrix) File "ROSE_bamToGFF.py", line 40, in mapBamToGFF MMR= round(float(bam.getTotalReads('mapped'))/1000000,4) TypeError: float() argument must be a string or a number {'matrix': '1', 'extension': '200', 'floor': '1', 'sense': 'both', 'output': 'example/mappedGFF/HG18_MM1S_MED1_MM1S_WCE.hg18.bwt.sorted.bam_MAPPED.gff', 'bam': './data/MM1S_WCE.hg18.bwt.sorted.bam', 'rpm': True, 'input': './data/HG18_MM1S_MED1.gff'} [] mapping to GFF and making a matrix with fixed bin number Traceback (most recent call last): File "ROSE_bamToGFF.py", line 247, in <module> main() File "ROSE_bamToGFF.py", line 238, in main newGFF = mapBamToGFF(bamFile,gffFile,options.sense,int(options.extension),options.floor,options.rpm,options.matrix) File "ROSE_bamToGFF.py", line 40, in mapBamToGFF MMR= round(float(bam.getTotalReads('mapped'))/1000000,4) TypeError: float() argument must be a string or a number WAITING FOR MAPPING TO COMPLETE. ELAPSED TIME (MIN): 0 MAPPING TOOK 5 MINUTES `

And then the following R error when the R script is called: `> png(filename=plotFileName,height=600,width=600)

Error in .External2(C_X11, paste("png::", filename, sep = ""), g$width, : unable to start device PNG Calls: png In addition: Warning message: In png(filename = plotFileName, height = 600, width = 600) : unable to open connection to X11 display '' Execution halted `

…

I have XQuartz installed. Is there a suggested workaround for these issues? I downloaded ROSE and example data from the bitbucket website. Thank you, Heather — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#3>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAH6MNQ2IZLWBWTE6FJGS2DSCVVA3ANCNFSM4QMHBCEQ>.