Issue 20# Home run doesn’t end about home HOT 6 CLOSED

Hi Ranj, yes it does work for single replicate data. In fact, it should be much quicker with single replicate data. It's tested on HPC and works fine. If you can share the files, I will be happy to look into what's causing the issue.

Cheers,
Akanksha

from home.

Here is the header of an example file i am using for your perusal

1 34 - CHG 5 8
1 80 - CHH 2 15
1 84 + CHH 0 4
1 85 + CHH 1 4
1 100 + CHH 1 4
1 101 + CHH 0 4
1 102 + CHH 2 4
1 110 - CG 11 11
1 116 - CG 10 10
1 117 - CHG 2 10
1 121 + CHH 1 4
1 123 + CHG 3 4
1 125 - CHG 7 7
1 126 - CHH 0 5
1 129 - CHH 2 4

I dont see anything peculiar with this.

And the error was basically PBS ending after reaching wall time maxima.
for example:

Preparing the DMRs from HOME.....
GOOD LUCK !
/net/gmi.oeaw.ac.at/software/mendel/29_04_2013/software/statsmodels/0.6.1-foss-2017a-Python-2.7.13/lib/python2.7/site-packages/statsmodels-0.6.1-py2.7-linux-x86_64.egg/statsmodels/stats/weightstats.py:575: RuntimeWarning: invalid value encountered in double_scalars
zstat = value / std_diff
=>> PBS: job killed: walltime 172825 exceeded limit 172800

from home.

input files were tab seperated BTW

from home.

Hi, the input file format seems ok. Which context are you running it for? ..how big are the files? Can you try it on some other system and see how much time it takes to complete? Also, may be good to try on small input files first. If its running fine in case of multiple replicates as you mentioned (on the same system ?), there is no reason why won't it run for the single replicate dataset.

from home.

I am running for CG and arabidopsis genome (fairly small)..Yeah it was running nicely for timeseries with same conditions for multi rep exeriments.Only change atm was all comparisions are single replicates. Will have to trying some thing.

Cheers,
Ranj

from home.

Yes, try it on the small test case and see if it finishes. Sorry, for the issue but will have to try a few things to resolve it.

from home.