Question

我在dada2步骤中运行了QIIME2动画教程，

我在跑步：

qiime dada2 denoise-single \   
--i-demultiplexed-seqs demux.qza \  
--p-trim-left 0 \   
--p-trunc-len 120 \
--o-representative-sequences rep-seqs-dada2.qza \
--o-table table-dada2.qza

并遇到了这个错误：

 Plugin error from dada2:

 An error was encountered while running DADA2 in R (return code 1),  
 please inspect stdout and stderr to learn more.

 Debug info has been saved to /tmp/qiime2-q2cli-err-52fzrvlu.log.

然后我打开文件：/tmp/qiime2-q2cli-err-52fzrvlu.log。这是我发现的：

 Running external command line application(s). This may print messages
 to stdout and/or stderr. The command(s) being run are below. These
 commands cannot be manually re-run as they will depend on temporary
 files that no longer exist.

Command: run_dada_single.R
 /tmp/qiime2-archive-pco6y5vm/fe614b44-775f-41b1-9ee3-04319005e830/data
 /tmp/tmpda8dnyve/output.tsv.biom /tmp/tmpda8dnyve 120 0 2.0 2
 consensus 1.0 1 1000000

 R version 3.3.1 (2016-06-21) Loading required package: Rcpp Error in
 dyn.load(file, DLLpath = DLLpath, ...) :   unable to load shared
 object '/home/cao/lib/R/library/rlang/libs/rlang.so':  
 /home/cao/lib/R/library/rlang/libs/rlang.so: undefined symbol:
 R_ExternalPtrAddrFn In addition: Warning message: package ‘Rcpp’ was
 built under R version 3.4.1 Error: package or namespace load failed
 for ‘dada2’ Execution halted Traceback (most recent call last):   File
 "/home/cao/miniconda3/envs/qiime2-2017.7/lib/python3.5/site-packages/q2_dada2/_denoise.py",
 line 126, in denoise_single
     run_commands([cmd])   File "/home/cao/miniconda3/envs/qiime2-2017.7/lib/python3.5/site-packages/q2_dada2/_denoise.py",
 line 35, in run_commands
     subprocess.run(cmd, check=True)   File "/home/cao/miniconda3/envs/qiime2-2017.7/lib/python3.5/subprocess.py",
 line 398, in run
     output=stdout, stderr=stderr) subprocess.CalledProcessError: Command '['run_dada_single.R',
 '/tmp/qiime2-archive-pco6y5vm/fe614b44-775f-41b1-9ee3-04319005e830/data',
 '/tmp/tmpda8dnyve/output.tsv.biom', '/tmp/tmpda8dnyve', '120', '0',
 '2.0', '2', 'consensus', '1.0', '1', '1000000']' returned non-zero
 exit status 1

 During handling of the above exception, another exception occurred:

 Traceback (most recent call last):   File
"/home/cao/miniconda3/envs/qiime2-2017.7/lib/python3.5/site-packages/q2cli/commands.py",
 line 222, in __call__
     results = action(**arguments)   File "<decorator-gen-252>", line 2, in denoise_single   File
 "/home/cao/miniconda3/envs/qiime2-2017.7/lib/python3.5/site-packages/qiime2/sdk/action.py",
 line 201, in callable_wrapper
     output_types, provenance)   File "/home/cao/miniconda3/envs/qiime2-2017.7/lib/python3.5/site-packages/qiime2/sdk/action.py",
 line 334, in _callable_executor_
     output_views = callable(**view_args)   File "/home/cao/miniconda3/envs/qiime2-2017.7/lib/python3.5/site-packages/q2_dada2/_denoise.py",
 line 137, in denoise_single
     " and stderr to learn more." % e.returncode) Exception: An error was encountered while running DADA2 in R (return code 1), please
 inspect stdout and stderr to learn more.

然后'sudo R'并安装了Rcpp和rlang软件包，但是当我运行与我第一次相同的代码时仍然遇到了同样的错误：

qiime dada2 denoise-single \ --i-demultiplexed-seqs demux.qza \ --p-trim-left 0 \ --p-trunc-len 120 \ --o-representative-sequences rep-seqs-dada2.qza \ --o-table table-dada2.qza

Answer 1

我明白了：这是R版本：我卸载R3.4并安装R 3.3并且每个工作都

Answer 2

我认为这是内存错误。我尝试过该教程。第一次我有输出，但是迟到了。我在办公室使用另一台计算机。它具有32 GB的内存。而且我在r代码1错误中没有像dada2这样的错误。高ram所有者的可能性如果我被告知这个问题与R版本的ram有关，我认为。这是我在qiime2论坛站点enter link description here

中的帖子

QIIME2 dada2 rlang.so错误

2 个答案: