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alekseyzimin / masurca

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masurca is restarting from scratch after runnning on the grid ? #164

Open aureliendejode opened 4 years ago

aureliendejode commented 4 years ago

Hi,

I run Masurca, specifying to run the hybrid assembly on the grid. Everything went fine and I obtained no error message and the mr_pass1 folder was created. Then I rerun the assemble.sh, but now it looks like the assembler is starting from scratch. Is this normal ? I am missing something ?

Thanks

mahalel commented 4 years ago

Hi aureliendejode, I seem to have the same problem. First time around, everything went well and I got the sbatch command to run on the SLURM grid:

sbatch -D /mnt/data/00.reads/mr_pass1 -J create_mega_reads -a 1-203 -n 48 -p htc -N 1 mr_pass1/create_mega_reads.sh

Then it says:

Please re-run assemble.sh when all jobs finish. If you get this message again, it means that some jobs failed, simply re-submit again using the above command.

All jobs finished and output was in mr_pass1 directory with mr*.success files

I then ran the assemble.sh script again and it seems that the mr_pass1 folder is now gone and it's trying the Mega-reads pass 1 again.

I'm not sure if that is normal either, seems like all progress was lost?

mahalel commented 4 years ago

Nevermind, it seems that did not restart and it did get to mr_pass2. I just got a bit scared when mr_pass1 folder went missing :)