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Nextomics / NextDenovo

Fast and accurate de novo assembler for long reads
GNU General Public License v3.0
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the problem of software running in v2.2-beta.0 version #55

Closed lbbobo closed 4 years ago

lbbobo commented 4 years ago

When I ran the test data with nextdenovo v2.2-beta.0 installed, I had a problem！！

Program running parameters： The parameters in the run.cfg file of test data are used without modification.

I found that when I ran the following command, the program did not compute (CPU was not used).

minimap2-nd --step 1 -I 3G -x ava-ont -t 8 ./input.seed.001.2bit ./input.seed.001.2bit -o input.seed.001.2bit.1.ovl

moold commented 4 years ago

What is your system and how about your system memory? Have you checked uisng top -p MINIMAP2_ND_SUBTASK_PID?

lbbobo commented 4 years ago

That's 2,019 Gb of system memory.

the minimap2_nd showed

PID PR NI VIRT RES SHR S %CPU %MEM TIME+ COMMAND 10009 20 0 1346m 1.2g 820 S 0.0 0.1 0:02.09 /vol1/agis/wanfa

moold commented 4 years ago

What is your system version and gcc version? The memory is enough.

lbbobo commented 4 years ago

system version: cLSB Version: :base-4.0-amd64:base-4.0-noarch:core-4.0-amd64:core-4.0-noarch:graphics-4.0-amd64:graphics-4.0-noarch:printing-4.0-amd64:printing-4.0-noarch Distributor ID: CentOS Description: CentOS release 6.5 (Final) Release: 6.5 Codename: Final

gcc version: gcc version 5.4.0 (GCC)

DengHAU commented 4 years ago

This problem has also been encountered in my system. In another linux system(CentOS Linux release 7.6.1810 (Core)，gcc 5.4.0), it works well. Has it been solved?

DengHAU commented 4 years ago

Probably the glibc version problem. Using export LD_PRELOAD=/to/your/path/libc-2.14.so when you runing can works. Good luck!