search

Nextomics / NextDenovo

Fast and accurate de novo assembler for long reads
GNU General Public License v3.0
352 stars 52 forks source link

GLIBC2.14 not found #62

Closed Lyang556 closed 3 years ago

Lyang556 commented 4 years ago

Hello,i am really want to use this software to generate the genome，but it always warn glibc 2.14 not found，i am not the administrator,i can not add the glibc 2.14.Can you tell me what should i do to solve this problem. Thank you

moold commented 4 years ago

Hi, what is your system and gcc version?

Lyang556 commented 4 years ago

Hi,its detail is gcc version 4.4.6 20120305 (Red Hat 4.4.6-4) (GCC)

Lyang556 commented 4 years ago

Hi,its detail is gcc version 4.4.6 20120305 (Red Hat 4.4.6-4) (GCC)

------------------ 原始邮件 ------------------ 发件人: "Hu Jiang"<notifications@github.com>; 发送时间: 2020年4月18日(星期六) 下午2:33 收件人: "Nextomics/NextDenovo"<NextDenovo@noreply.github.com>; 抄送: "我家Misssi"<3152680050@qq.com>;"Author"<author@noreply.github.com>; 主题: Re: [Nextomics/NextDenovo] GLIBC2.14 not found (#62)

Hi, what is your system and gcc version?

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or unsubscribe.

moold commented 4 years ago

Could you try to update your gcc version to 4.8.5 or higher?

Lyang556 commented 4 years ago

No,it does not work when i uddate the gcc to 7.+

moold commented 4 years ago

Hi, Could you try to this version, which is the lastest version we are working on and includes some minor changes, any questions are welcome.

Lyang556 commented 4 years ago

Hi，it works,but the false is Traceback (most recent call last):   File "/next/NextDenovo-Pro-dev/lib/nextcorrect.py", line 310, in <module>     main(args)   File "/next/NextDenovo-Pro-dev/lib/nextcorrect.py", line 228, in main     worker, read_seq_data(args, corrected_seeds), chunksize=1):   File "/home/anaconda3/envs/py27/lib/python2.7/multiprocessing/pool.py", line 673, in next     raise value UnicodeDecodeError: 'utf8' codec can't decode byte 0xc8 in position 0: invalid continuation byte

------------------ 原始邮件 ------------------ 发件人: "Hu Jiang"<notifications@github.com>; 发送时间: 2020年4月20日(星期一) 下午3:37 收件人: "Nextomics/NextDenovo"<NextDenovo@noreply.github.com>; 抄送: "我家Misssi"<3152680050@qq.com>;"Author"<author@noreply.github.com>; 主题: Re: [Nextomics/NextDenovo] GLIBC2.14 not found (#62)

Hi, Could you try to this version, which is the lastest version we are working on and includes some minor changes, any questions are welcome.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or unsubscribe.

moold commented 4 years ago

What is your python version? I cannot reproduce this error.

Lyang556 commented 4 years ago

python version is 2.7.17

moold commented 4 years ago

I have tested with python2.7 and python3, it finished without any errors. Could you rerun it with test_data?

Lyang556 commented 4 years ago

ok，i will try it at once

Lyang556 commented 4 years ago

File "/home/wanglei/data/jzw/yl/next/NextDenovo-Pro-dev/lib/ctg_cns.py", line 228, in main(args) File "/home/wanglei/data/jzw/yl/next/NextDenovo-Pro-dev/lib/ctg_cns.py", line 183, in main pool = Pool(args.process, initializer=start) File "/home/wanglei/anaconda3/lib/python3.7/multiprocessing/context.py", line 119, in Pool context=self.get_context()) File "/home/wanglei/anaconda3/lib/python3.7/multiprocessing/pool.py", line 176, in init self._repopulate_pool() File "/home/wanglei/anaconda3/lib/python3.7/multiprocessing/pool.py", line 231, in _repopulate_pool for i in range(self._processes - len(self._pool)): TypeError: 'float' object cannot be interpreted as an integer

Lyang556 commented 4 years ago

this python version is 3.7.3

moold commented 4 years ago

Do you use the default config file? or paste your config file to here.

Lyang556 commented 4 years ago

thank you ，i try python 2.7 and use the test data ，it finish with out err

Lyang556 commented 4 years ago

hi，when i use my data it occur the same err my config file is [General] job_type = local job_prefix = nextDenovo task = all # 'all', 'correct', 'assemble' rewrite = yes # yes/no deltmp = yes rerun = 3 parallel_jobs = 3 input_type = raw input_fofn = /home/wanglei/data/jzw/yl/next/NextDenovo-Pro-dev/test_data/input.fofn workdir = /home/wanglei/data/jzw/yl/next/NextDenovo-Pro-dev/test_data/01_rundir

[correct_option] read_cutoff = 1k seed_cutoff = 4k blocksize = 3g pa_correction = 10 seed_cutfiles = 10 sort_options = -m 2g -t 2 -k 50 minimap2_options_raw = -x ava-ont -t 3 correction_options = -p 15

[assemble_option] minimap2_options_cns = -x ava-ont -t 8 -k17 -w17 nextgraph_options = -a 1

moold commented 4 years ago

you can try to use ctg_cns.zip to replace the same file in the lib directory, and continue to run the unfinished tasks.

Lyang556 commented 4 years ago

it does not work，Thank you for your patient guidance。

------------------ 原始邮件 ------------------ 发件人: "Hu Jiang"<notifications@github.com>; 发送时间: 2020年4月22日(星期三) 下午3:45 收件人: "Nextomics/NextDenovo"<NextDenovo@noreply.github.com>; 抄送: "我家Misssi"<3152680050@qq.com>;"Author"<author@noreply.github.com>; 主题: Re: [Nextomics/NextDenovo] GLIBC2.14 not found (#62)

you can try to use ctg_cns.zip to replace the same file in the lib directory, and continue to run the unfinished tasks.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or unsubscribe.

zhk2017 commented 4 years ago

I also encountered the same problem, solved in the following way: step1: download this version ,and unzip it; step2: download nextdenovo from the github(wget https://github.com/Nextomics/NextDenovo/releases/download/v2.2-beta.0/NextDenovo.tgz), and tar -xzvf step3: cd step2 installed nextdenovo path, and repalce bin directory with step1's Pro version bin; also replace ctg_cns.so and ovlseq.so with NextDenovo-Pro-dev's ctg_cns.so and ovlseq.so.

At last, use step2 NextDenovo will be ok.

Haikuan