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ruanjue / wtdbg2

Redbean: A fuzzy Bruijn graph approach to long noisy reads assembly
GNU General Public License v3.0
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wtdbg2 stagnate at the sorting stage? #92

Closed xiaoyezao closed 5 years ago

xiaoyezao commented 5 years ago

Hi, I am rnning wtdbg2 on canu corrected pacbio reads. It takes about two hours to get to the sorting stage and then seems to have stagnated there for 7 hours up to now. Nothing changed in the log file for the past seven hours. Because I submitted the job to cluster, I am not sure whether it's still running, or I should kill the job.

the last lines of the log are: [Fri Mar 29 13:18:55 2019] - indexed 37903968 kmers, 904259273 instances [Fri Mar 29 13:19:03 2019] - masked 3777124 bins as closed [Fri Mar 29 13:19:03 2019] - sorting PROC_STAT(0) : real 5590.962 sec, user 2448.800 sec, sys 3133.670 sec, maxrss 9736684.0 kB, maxvsize 13504296.0 kB [Fri Mar 29 13:24:09 2019] Done

ruanjue commented 5 years ago

The next step of this job should be alignment, please have a look whether .alignments file exists. You'd better to run it again.

xiaoyezao commented 5 years ago

Hi ruanjue, I run it again and this time it finished the alignment, but exited at generating regs step because of memery shortage. I try to allocate more memory and run it again. Is it possible to resume the process from the generating regs step?

ruanjue commented 5 years ago

Have a look at wtdbg2 --help for the option --load-alignments.

xiaoyezao commented 5 years ago

Thanks, that works