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:
""
"