ubuntu运行生信分析细菌功能预测picrust2失败

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ubuntu运行生信分析细菌功能预测picrust2失败

#1

帖子 Risk超 » 2019-10-12 15:43

ubuntu18.04.3LTS安装了生信分析细菌功能预测picrust2,可是运行起来总是失败,终端提示里会出现大写的EPA-NG,运行的源文件都没有问题
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astolia
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Re: ubuntu运行生信分析细菌功能预测picrust2失败

#2

帖子 astolia » 2019-10-13 1:31

软件是从哪里获取的?你是怎么运行的?运行后的完整输出信息是什么?
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Re: ubuntu运行生信分析细菌功能预测picrust2失败

#3

帖子 九天星 » 2019-10-13 1:34

错误代码呢?
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Re: ubuntu运行生信分析细菌功能预测picrust2失败

#4

帖子 Risk超 » 2019-10-13 21:37

astolia 写了:
2019-10-13 1:31
软件是从哪里获取的?你是怎么运行的?运行后的完整输出信息是什么?
软件是从GitHub上下载的,安装命令是conda create -n picrust2 -c bioconda -c conda-forge picrust2=2.2.0_b,安装成功,源文件就是OTU表格和fasta文件,运行命令是picrust2_pipeline.py -s otus.fa -i otutab.txt \-o picrust2_out,错误代码是
Error running this command:
place_seqs.py --study_fasta otus.fa --ref_dir /home/liuchao/miniconda3/envs/picrust2/lib/python3.6/site-packages/picrust2/default_files/prokaryotic/pro_ref --out_tree picrust2_out/out.tre --processes 1 --intermediate picrust2_out/intermediate/place_seqs --chunk_size 5000

Standard output of failed command:
""

Standard error of failed command:
"
Error running this command:
epa-ng --tree /home/liuchao/miniconda3/envs/picrust2/lib/python3.6/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.tre --ref-msa picrust2_out/intermediate/place_seqs/ref_seqs_hmmalign.fasta --query picrust2_out/intermediate/place_seqs/study_seqs_hmmalign.fasta --chunk-size 5000 -T 1 -m /home/liuchao/miniconda3/envs/picrust2/lib/python3.6/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.model -w picrust2_out/intermediate/place_seqs/epa_out --filter-acc-lwr 0.99 --filter-max 100

Standard output of failed command:
"INFO Selected: Output dir: picrust2_out/intermediate/place_seqs/epa_out/
INFO Selected: Query file: picrust2_out/intermediate/place_seqs/study_seqs_hmmalign.fasta
INFO Selected: Tree file: /home/liuchao/miniconda3/envs/picrust2/lib/python3.6/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.tre
INFO Selected: Reference MSA: picrust2_out/intermediate/place_seqs/ref_seqs_hmmalign.fasta
INFO Selected: Filtering by accumulated threshold: 0.99
INFO Selected: Maximum number of placements per query: 100
INFO Selected: Automatic switching of use of per rate scalers
INFO Selected: Preserving the root of the input tree
INFO Selected: Specified model file: /home/liuchao/miniconda3/envs/picrust2/lib/python3.6/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.model
INFO Rate heterogeneity: GAMMA (4 cats, mean), alpha: 0.453141 (user), weights&rates: (0.25,0.0250674) (0.25,0.220229) (0.25,0.782933) (0.25,2.97177)
Base frequencies (user): 0.229585 0.22008 0.298596 0.251739
Substitution rates (user): 1.00319 2.79077 1.5301 0.87441 3.83966 1
INFO Selected: Reading queries in chunks of: 5000
INFO Selected: Using threads: 1
INFO ______ ____ ___ _ __ ______
/ ____// __ \ / | / | / // ____/
/ __/ / /_/ // /| | ______ / |/ // / __
/ /___ / ____// ___ |/_____// /| // /_/ /
/_____//_/ /_/ |_| /_/ |_/ \____/ (v0.3.5)
INFO Output file: picrust2_out/intermediate/place_seqs/epa_out/epa_result.jplace
"

Standard error of failed command:
""
"
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Re: ubuntu运行生信分析细菌功能预测picrust2失败

#5

帖子 Risk超 » 2019-10-13 21:38

九天星 写了:
2019-10-13 1:34
错误代码呢?
错误代码是
Error running this command:
place_seqs.py --study_fasta otus.fa --ref_dir /home/liuchao/miniconda3/envs/picrust2/lib/python3.6/site-packages/picrust2/default_files/prokaryotic/pro_ref --out_tree picrust2_out/out.tre --processes 1 --intermediate picrust2_out/intermediate/place_seqs --chunk_size 5000

Standard output of failed command:
""

Standard error of failed command:
"
Error running this command:
epa-ng --tree /home/liuchao/miniconda3/envs/picrust2/lib/python3.6/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.tre --ref-msa picrust2_out/intermediate/place_seqs/ref_seqs_hmmalign.fasta --query picrust2_out/intermediate/place_seqs/study_seqs_hmmalign.fasta --chunk-size 5000 -T 1 -m /home/liuchao/miniconda3/envs/picrust2/lib/python3.6/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.model -w picrust2_out/intermediate/place_seqs/epa_out --filter-acc-lwr 0.99 --filter-max 100

Standard output of failed command:
"INFO Selected: Output dir: picrust2_out/intermediate/place_seqs/epa_out/
INFO Selected: Query file: picrust2_out/intermediate/place_seqs/study_seqs_hmmalign.fasta
INFO Selected: Tree file: /home/liuchao/miniconda3/envs/picrust2/lib/python3.6/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.tre
INFO Selected: Reference MSA: picrust2_out/intermediate/place_seqs/ref_seqs_hmmalign.fasta
INFO Selected: Filtering by accumulated threshold: 0.99
INFO Selected: Maximum number of placements per query: 100
INFO Selected: Automatic switching of use of per rate scalers
INFO Selected: Preserving the root of the input tree
INFO Selected: Specified model file: /home/liuchao/miniconda3/envs/picrust2/lib/python3.6/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.model
INFO Rate heterogeneity: GAMMA (4 cats, mean), alpha: 0.453141 (user), weights&rates: (0.25,0.0250674) (0.25,0.220229) (0.25,0.782933) (0.25,2.97177)
Base frequencies (user): 0.229585 0.22008 0.298596 0.251739
Substitution rates (user): 1.00319 2.79077 1.5301 0.87441 3.83966 1
INFO Selected: Reading queries in chunks of: 5000
INFO Selected: Using threads: 1
INFO ______ ____ ___ _ __ ______
/ ____// __ \ / | / | / // ____/
/ __/ / /_/ // /| | ______ / |/ // / __
/ /___ / ____// ___ |/_____// /| // /_/ /
/_____//_/ /_/ |_| /_/ |_/ \____/ (v0.3.5)
INFO Output file: picrust2_out/intermediate/place_seqs/epa_out/epa_result.jplace
"

Standard error of failed command:
""
"
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astolia
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Re: ubuntu运行生信分析细菌功能预测picrust2失败

#6

帖子 astolia » 2019-10-13 23:55

我觉得你跟这人遇到的问题相同 https://github.com/picrust/picrust2/iss ... -473521572
他是输入的数据量太大,内存不足导致程序出错。你可以尝试换用那个帖子后里提到的q2插件,或是加内存
Risk超
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Re: ubuntu运行生信分析细菌功能预测picrust2失败

#7

帖子 Risk超 » 2019-10-14 22:56

astolia 写了:
2019-10-13 23:55
我觉得你跟这人遇到的问题相同 https://github.com/picrust/picrust2/iss ... -473521572
他是输入的数据量太大,内存不足导致程序出错。你可以尝试换用那个帖子后里提到的q2插件,或是加内存
好的,我试试,可能还真是这个问题,我用我的另一台windows电脑(16G内存+i7-8750)安装了Ubuntu跑了一遍,就没出错
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