Error with processsamples.py

[lucacozzuto]

Dear authors, I'm using processsamples.py and I got this error:

Rscript /opt/trax//newcoverageplots.R --cov=tRNA/tRNA-coverage.txt --locicov=tRNA/pretRNAs/tRNA-pretRNAcoverage.t
xt --trna=../anno/db-trnatable.txt --samples=samplefile.txt --allcov=tRNA/tRNA-coverage.pdf --runname=tRNA --modo
mics=../anno/db-modomics.txt --combinecov=tRNA/tRNA-combinecoverage.pdf --directory=tRNA
Rscript /opt/trax//boxplotmismatches.R --runname=tRNA --mismatch=tRNA/tRNA-coverage.txt --trna=../anno/db-trnatab
le.txt --samples=samplefile.txt --directory=tRNA/mismatch/
Traceback (most recent call last):
  File "/opt/trax/processsamples.py", line 580, in <module>
    gettraxqc(samplefilename, trnainfo, expinfo, tgirtmode = nofrag)
  File "/opt/trax/processsamples.py", line 262, in gettraxqc
    traxqc.main(samplefile=samplefile,databasename=trnainfo.dbname,experimentname=expinfo.expname,tgirt = tgirtmo
de, output=expinfo.qaoutputname)
  File "/opt/trax/traxqc.py", line 724, in main
    prepresults = checkreadprep(runnames,sampleinfo)
  File "/opt/trax/traxqc.py", line 212, in checkreadprep
    prepdict.update({currsample : prepresults.getmergedpercent(currsample) for currsample in samples}) 
  File "/opt/trax/traxqc.py", line 212, in <dictcomp>
    prepdict.update({currsample : prepresults.getmergedpercent(currsample) for currsample in samples}) 
  File "/opt/trax/traxqc.py", line 130, in getmergedpercent
    return self.merged[sample] / (1.*self.gettotal(sample))
ZeroDivisionError: float division by zero

I'm not sure where is the problem, I'm using the hg38 database.

Best,

Luca

[andrewdholmes]

OK it looks like that's a problem that can occur with some edge cases in the data, I'll take a look at it but you should still have access to the analysis results, the only thing that should be missing is the QC report summary

On Fri, Jun 18, 2021 at 2:35 AM Luca Cozzuto @.***> wrote:

Dear authors, I'm using processsamples.py and I got this error:

Rscript /opt/trax//newcoverageplots.R --cov=tRNA/tRNA-coverage.txt --locicov=tRNA/pretRNAs/tRNA-pretRNAcoverage.t xt --trna=../anno/db-trnatable.txt --samples=samplefile.txt --allcov=tRNA/tRNA-coverage.pdf --runname=tRNA --modo mics=../anno/db-modomics.txt --combinecov=tRNA/tRNA-combinecoverage.pdf --directory=tRNA Rscript /opt/trax//boxplotmismatches.R --runname=tRNA --mismatch=tRNA/tRNA-coverage.txt --trna=../anno/db-trnatab le.txt --samples=samplefile.txt --directory=tRNA/mismatch/ Traceback (most recent call last): File "/opt/trax/processsamples.py", line 580, in gettraxqc(samplefilename, trnainfo, expinfo, tgirtmode = nofrag) File "/opt/trax/processsamples.py", line 262, in gettraxqc traxqc.main(samplefile=samplefile,databasename=trnainfo.dbname,experimentname=expinfo.expname,tgirt = tgirtmo de, output=expinfo.qaoutputname) File "/opt/trax/traxqc.py", line 724, in main prepresults = checkreadprep(runnames,sampleinfo) File "/opt/trax/traxqc.py", line 212, in checkreadprep prepdict.update({currsample : prepresults.getmergedpercent(currsample) for currsample in samples}) File "/opt/trax/traxqc.py", line 212, in prepdict.update({currsample : prepresults.getmergedpercent(currsample) for currsample in samples}) File "/opt/trax/traxqc.py", line 130, in getmergedpercent return self.merged[sample] / (1.*self.gettotal(sample)) ZeroDivisionError: float division by zero

I'm not sure where is the problem, I'm using the hg38 database.

Best,

Luca

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[lucacozzuto]

Hi! I'm wondering if we have any news about this issue. I also got niether volcano nor typescatter plots.

Thanks!

[andrewdholmes]

Alright I've pushed an update to github that should prevent that error message. That shouldn't relate to the volcano or typescatter plots though, are you using a pair file? If you don't supply a list of pairs then those files wouldn't be generated

On Mon, Jul 5, 2021 at 4:41 AM Luca Cozzuto @.***> wrote:

Hi! I'm wondering if we have any news about this issue. I also got niether volcano nor typescatter plots.

Thanks!

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