Comments (6)
Hi Núria,
That's strange! How many replicates you have ?. Can you please try running it with "-sin" parameter
HOME-pairwise -t CG -sin -i ./sample_file_CG_comparison1.txt -o ./output_comparison1_CG -npp 32
Thanks,
Akanksha
from home.
from home.
Hi Núria,
Its pretty surprising that run is taking so long. Even without -sin parameter, it should finish within 2 hours, roughly (more quickly for plant genome). So, Just a bit of detail, without -sin parameter, HOME runs parallel processes for each chromosome (5 in case of Arabidopsis). With -sin parameter it breaks the single chromosome into chunks (depending on npp parameter) and will run parallel for each chunk. If you don't use -sin parameter and run HOME in default mode, set the npp parameter to max. no. of chromosomes the data have or less if your system does not allow it. Setting it more than that won't help in this case. But, if you run it with -sin parameter, you can set the npp parameter as high as possible. If possible, please share with me the input files, so that I can have a look what's wrong.
Please let me know if you have any further doubts or issues.
Thanks,
Akanksha
from home.
from home.
Closing this issue because of HPC related problem at the user end.
from home.
Hi Akanksha,
Just to be sure, is HOME compatable for single replicate timeseries analysis (or pairwise) ?. I have HOME (>0.7) working well for both timeseries or pairewise when i have multi replicates but never ending job run for single replicates as Nuria mentioned(with or without -sin paramether ). Do you think is there something do with single replicate experiments. And i also see double scalar error in these cases. We use the same HPC.
Cheers,
Ranj
from home.
Related Issues (20)
- training data CG and non-CG for arabidopsis HOT 1
- HOME-timeseries error HOT 2
- sample path HOT 1
- cannot open file './scripts/HOME_R.R': No such file or directory HOT 1
- HOME-pairwise script is missing HOT 1
- Error when finding DMR's with scaffolded genome HOT 4
- multiprocessing range parameter HOT 3
- double scalar error HOT 5
- Issue 20# Home run doesn’t end HOT 6
- HOME-pairwise for different numbers of replicate HOT 4
- HOME ubale to open X server HOT 1
- HOME_DMR error HOT 1
- All Comb1-n "NA" for most DMRs in CHH HOT 8
- Push more
- Nanopore data? HOT 2
- NameError: name 'status' is not defined HOT 2
- HOME-timeseries Exception HOT 4
- Exception: reduce() of empty sequence with no initial value
- Installation Error
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