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kundajelab / 3DChromatin_ReplicateQC

Software to compute reproducibility and quality scores for Hi-C data
MIT License
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Rscript: command not found #10

Open Phlya opened 5 years ago

Phlya commented 5 years ago

Hi, I am trying to run HiCRep using your setup, but can't figure out why I keep getting this error in the .e files (I am running it on the cluster):

/var/spool/gridscheduler/execd/node2c19/job_scripts/1028343: line 3: Rscript: command not found
cat: /gpfs/igmmfs01/eddie/wendy-lab/ilia/coolers/QCRep/output/results/reproducibility/HiCRep/chr1.WT-1.vs.KO-2.scores.txt: No such file or directory

I can use Rscript normally in the conda environment I am using, but for some reason it doesn't work in the jobs submitted by 3DChromatin_ReplicateQC concordance... Any thought will be appreciated.

oursu commented 5 years ago

Hi @Phlya

Can you try running "3DChromatin_ReplicateQC" without the job submission (i.e. --running_mode NA)? If the Rscript command works when you don't submit a job, then it means there is some problem with finding R when the job gets run on a new node compared to when you run the code interactively.

let me know how that goes and I will try to help further.