16s功能注释--PICRUST2的安装及使用

安装

本地安装

在github网址下载压缩包：https://github.com/picrust/picrust2/releases/tag/v2.5.2
解压后将bin目录设置到环境变量

conda安装

利用bioconda安装

conda create -n picrust2 -c bioconda -c conda-forge picrust2=2.5.2
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安装成功：

使用

picrust2_pipeline.py -s asv-sequences.fasta -i asv_table.txt -o picrust2_result -p 10
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得到的结果：

结果注释：
详见：
https://blog.csdn.net/woodcorpse/article/details/118618094?spm=1001.2014.3001.5506

一些报错

全部ASV和ASV前10000注释时都报错，暂未找到解决方法
但使用ASV前1000则能运行成功


运行命令：

(picrust2) yangzy@DESKTOP-1J86A3B:/mnt/d/WSL/799F/yunyan87$ picrust2_pipeline.py -s asv-sequences.fasta -i step2.even.14615.asv_table.rename.txt -o picrust2_result -p 10
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报错信息：

Error running this command:
place_seqs.py --study_fasta asv-sequences.fasta --ref_dir /home/yangzy/anaconda3/envs/picrust2/lib/python3.8/site-packages/picrust2/default_files/prokaryotic/pro_ref --out_tree picrust2_result/out.tre --processes 10 --intermediate picrust2_result/intermediate/place_seqs --min_align 0.8 --chunk_size 5000 --placement_tool epa-ng

Standard error of the above failed command:
Warning - 70 input sequences aligned poorly to reference sequences (--min_align option specified a minimum proportion of 0.8 aligning to reference sequences). These input sequences will not be placed and will be excluded from downstream steps.

This is the set of poorly aligned input sequences to be excluded: ASV62839, ASV93483, ASV26791, ASV102682, ASV97176, ASV59758, ASV85125, ASV38932, ASV90242, ASV32757, ASV91755, ASV80919, ASV79359, ASV99099, ASV48371, ASV92728, ASV56198, ASV94807, ASV38419, ASV32421, ASV65544, ASV43259, ASV74887, ASV71270, ASV94630, ASV59930, ASV110098, ASV68072, ASV107416, ASV56326, ASV109445, ASV98991, ASV72629, ASV90196, ASV84467, ASV101288, ASV100585, ASV99664, ASV70821, ASV62940, ASV85563, ASV84512, ASV110740, ASV55046, ASV102543, ASV44147, ASV72670, ASV63978, ASV38842, ASV55069, ASV103868, ASV97565, ASV111824, ASV87304, ASV52082, ASV97688, ASV95257, ASV111042, ASV99079, ASV91731, ASV57867, ASV72833, ASV111128, ASV112709, ASV43327, ASV85200, ASV73620, ASV97864, ASV106479, ASV102761


Error running this command:
epa-ng --tree /home/yangzy/anaconda3/envs/picrust2/lib/python3.8/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.tre --ref-msa picrust2_result/intermediate/place_seqs/ref_seqs_hmmalign.fasta --query picrust2_result/intermediate/place_seqs/study_seqs_hmmalign.fasta --chunk-size 5000 -T 10 -m /home/yangzy/anaconda3/envs/picrust2/lib/python3.8/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.model -w picrust2_result/intermediate/place_seqs/epa_out --filter-acc-lwr 0.99 --filter-max 100

Standard output of the above failed command:
INFO Selected: Output dir: picrust2_result/intermediate/place_seqs/epa_out/
INFO Selected: Query file: picrust2_result/intermediate/place_seqs/study_seqs_hmmalign.fasta
INFO Selected: Tree file: /home/yangzy/anaconda3/envs/picrust2/lib/python3.8/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.tre
INFO Selected: Reference MSA: picrust2_result/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/yangzy/anaconda3/envs/picrust2/lib/python3.8/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.model
INFO Selected: Reading queries in chunks of: 5000
INFO Selected: Using threads: 10
INFO     ______ ____   ___           _   __ ______
        / ____// __ \ /   |         / | / // ____/
       / __/  / /_/ // /| | ______ /  |/ // / __
      / /___ / ____// ___ |/_____// /|  // /_/ /
     /_____//_/    /_/  |_|      /_/ |_/ \____/ (v0.3.8)
INFO Using model parameters:
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 Output file: picrust2_result/intermediate/place_seqs/epa_out/epa_result.jplace
INFO 5000 Sequences done!
INFO 10000 Sequences done!
INFO 15000 Sequences done!
INFO 20000 Sequences done!
INFO 25000 Sequences done!
INFO 30000 Sequences done!
INFO 35000 Sequences done!
INFO 40000 Sequences done!
INFO 45000 Sequences done!
INFO 50000 Sequences done!
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参考：
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