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alekseyzimin / masurca

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Not in-off RAM #172

Open aureliendejode opened 4 years ago

aureliendejode commented 4 years ago

Hello,

I am trying to assemble a mollusc genome (1.35 Gb) using Masurca with Illumina and PacBio reads. I manage to get the mr_pass2 folder with all the job on the grid successful. After this step when I relaunch Masurca I get RAM issues on my cluster. The limit is 1T0 of RAM and this is not in-off. I think I know why: I used to many Illumina data in the first place (500X coverage).

Is there a way a this stage to continue the assembly with a subset of the data ? or is the only solution to restart everything but using only a subset of the Illumnia raw data (to get to 100X) ?

alekseyzimin commented 3 years ago

If you are through with pass one, you can use MEGA_READS_ONE_PASS=1 option, it will skip the second pass.