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training_data_nonCG.txt does not exist #14

Closed Papareddy closed 6 years ago

Papareddy commented 6 years ago

Hello There,

Fairly new informatics.. sorry if it as naive question eating up a bit of your time. I tried running home on both pairwise and time series mode for my sample at CHH and CHG context its giving me no DMrs while giving a note stating non_CG data not trained.

Am I missing something obvious. Please find the error below

cheers and many thanks, Ranj. ranjith.papareddy@dmn3 [~/HOME/tspool]> HOME-pairwise -t CHG -i ~/HOME/tspool/timeseries.tsv -o ~/HOME/tspool/ -npp 32 Preparing the DMRs from HOME..... GOOD LUCK ! /net/gmi.oeaw.ac.at/software/mendel/29_04_2013/software/statsmodels/0.8.0-foss-2017a-Python-2.7.13/lib/python2.7/site-packages/statsmodels-0.8.0-py2.7-linux-x86_64.egg/statsmodels/stats/weightstats.py:670: RuntimeWarning: invalid value encountered in double_scalars zstat = value / std_diff /net/gmi.oeaw.ac.at/software/mendel/29_04_2013/software/statsmodels/0.8.0-foss-2017a-Python-2.7.13/lib/python2.7/site-packages/statsmodels-0.8.0-py2.7-linux-x86_64.egg/statsmodels/stats/weightstats.py:670: RuntimeWarning: invalid value encountered in double_scalars zstat = value / std_diff /net/gmi.oeaw.ac.at/software/mendel/29_04_2013/software/statsmodels/0.8.0-foss-2017a-Python-2.7.13/lib/python2.7/site-packages/statsmodels-0.8.0-py2.7-linux-x86_64.egg/statsmodels/stats/weightstats.py:670: RuntimeWarning: invalid value encountered in double_scalars zstat = value / std_diff /net/gmi.oeaw.ac.at/software/mendel/29_04_2013/software/statsmodels/0.8.0-foss-2017a-Python-2.7.13/lib/python2.7/site-packages/statsmodels-0.8.0-py2.7-linux-x86_64.egg/statsmodels/stats/weightstats.py:670: RuntimeWarning: invalid value encountered in double_scalars zstat = value / std_diff /net/gmi.oeaw.ac.at/software/mendel/29_04_2013/software/statsmodels/0.8.0-foss-2017a-Python-2.7.13/lib/python2.7/site-packages/statsmodels-0.8.0-py2.7-linux-x86_64.egg/statsmodels/stats/weightstats.py:670: RuntimeWarning: invalid value encountered in double_scalars zstat = value / std_diff File /home/GMI/ranjith.papareddy/HOME/tspool/training_data/training_data_nonCG.txt does not exist

Akanksha2511 commented 6 years ago

Hi, Please run it from within the HOME directory, not tspool. Also please make sure the versions of python packages match as required by the tool.

Thanks, Akanksha

Papareddy commented 6 years ago

Hi thanks for the response,

I did so but if no avail. I thought knits an issue with our HPC most probably ...

Cheers and thanks again Ranj