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jrgreen7 / miPIE

miRNA Prediction using Integrated lines of Evidence
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ValueError: max() arg is an empty sequence #2

Open sridewi1 opened 5 years ago

sridewi1 commented 5 years ago

Dear James,

I am looking forward to try out miPIE as an additional tool for my de novo microRNA pipeline. Unfortunately I am facing an error, which I could not troubleshoot. I hope you can me further with this problem. here is the error I got after I excecute predict.py as suggested: grafik

Thanks in advance for your help! Dewi

vivekruhela commented 4 years ago

Hi,

I am getting the same issue. have you got any solution/response... [Here is the screenshot] Screenshot (141)

jrgreen7 commented 4 years ago

1) Have you run through the tutorial that is included in the repo? Before trying to run miPIE on your own datasets, I'd complete the tutorial to make sure everything is installed properly.

2) Judging by the error message that you are receiving, I'm guessing that the file that is being parsed to extract the features is empty. Please check that file to make sure that it is being properly created. It looks like libsvm_scale is trying to open a temporary file called tmp.libsvm, then scale all data to fall within [-1,1], then saving these scaled data to a new temporary file called tmp.scale.libsvm. That new scaled SVM file is not being loaded properly by load_svm, so I suspect that it is empty. Look at both the input and output temp files used by libsvm_scale. In turn, tmp.libsvm is created from "data/tmp.csv" (see Predict.py, lines 85-94). And "data/tmp.csv" is created from "data/tmp.fa.hmp"... All of these files are ultimately generated from the mirDeep2 files:

mdOutputPath = mirdeepDir+"/output.mrd" mdStrPath = mirdeepDir+'/tmp/precursors.str' mdFaPath = mirdeepDir+'/tmp/precursors.fa' mdRandPath = mirdeepDir+'/tmp/precursors_for_randfold.rand' expFeatsPath = mirdeepDir+'/tmp/expressionFeatures.csv'

I'd make sure that these files are being created correctly. Unfortunately, there is little-to-no error checking in miPIE, so if you run it using empty or corrupt files, it will die without giving meaningful error messages...

Good luck!