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novoalab / EpiNano

Detection of RNA modifications from Oxford Nanopore direct RNA sequencing reads (Liu*, Begik* et al., Nature Comm 2019)
GNU General Public License v2.0
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Epinano_Current is really slow #107

Closed margot701 closed 2 years ago

margot701 commented 2 years ago

Dear Epinano team, we are trying to use the Epinano 1.2 tool and we are struggling with the Epinano_Current step because it is incredibly slow. We are running with t=6. It is running for 2 days now and it is still in chunk 0 (each chunk has around 2GB data). When doing top we observe that processes are mainly in "S" status (see attachment). We also did top -H to explore the subprocesses and only 4 to 8 are running while the other are consuming CPU though being in "S" status (see attachment). We are running in Intel i9-7920X computer with 12 core and 64 GB of ram. The data are in Samsung 860 SATA SSD. Is it suppose to be as slow or is there tools compatibility issue or anything else? for the fisrt step (Epinano_Variant) we used the transcriptome option using the ensembl reference. Thank you a lot by advance for your advice,

printscreen top printscreen top -H

Huanle commented 2 years ago

Hi @margot701 , sorry for the delayed response. have you finished it? I will look into the scripts and see if there is a way to improve it.