MEGAN使用

作者: 蚂蚁爱吃饭 | 来源:发表于2020-12-10 08:53 被阅读0次

MEGAN使用
MEGAN使用报错：Exception in thread "m
2017-05-19
周主题｜随意
2017-05-22
鹤望兰 Megan
加油！Megan！
加油！Megan！
MEGAN LCA
23、April 5,1951

参考：宏基因组注释和可视化神器MEGAN入门_刘永鑫的博客——宏基因组公众号-CSDN博客

对PE数据的两个fq文件分别跑blastx：

/biostack/tools/alignment/diamond-2.0.4/diamond blastx -c 1 --db /biostack/database/nr/db/nr.dmnd -t tmp1 -p 24 -q all_other.R1.fq.gz --daa diamond-C1.1.daa >diamond.log1 &

/biostack/tools/alignment/diamond-2.0.4/diamond blastx -c 1 --db /biostack/database/nr/db/nr.dmnd -t tmp2 -p 24 -q all_other.R2.fq.gz --daa diamond-C1.2.daa >diamond.log2 &

注意:tmp1和tmp2目录要先建立。这一步会跑很久。

对daa文件进行转化为MEGAN需要的rma文件：

/biostack/tools/microbiome/MEGAN_Community-6.19.2/tools/daa2rma -i diamond-C1.1.daa diamond-C1.2.daa --paired -ms 50 -me 0.01 -top 50 -mdb /biostack/database/megan/megan-map-May2020.db -o diamond-C1.rma

输出为以下：
Version MEGAN Community Edition (version 6.19.2, built 17 Jun 2020)

Author(s) Daniel H. Huson

Functional classifications to use: EGGNOG, GTDB, INTERPRO2GO, SEED

Loading ncbi.map: 2,249,459

Loading ncbi.tre: 2,249,463

Loading eggnog.map: 30,875

Loading eggnog.tre: 30,986

Loading gtdb.map: 182,187

Loading gtdb.tre: 182,191

Loading interpro2go.map: 12,738

Loading interpro2go.tre: 28,689

Loading seed.map: 978

Loading seed.tre: 979

In DAA files: diamond-C1.1.daa, diamond-C1.2.daa

Output file: diamond-C1.rma

Classifications: Taxonomy, SEED, EGGNOG, GTDB, INTERPRO2GO

Generating RMA6 file Parsing matches

Annotating RMA6 file using FAST mode (accession database and first accession per line)

Parsing file diamond-C1.1.daa

Parsing file: diamond-C1.1.daa

10% 20% 30% 40% 50% 60% 70% 80% 90% 100% (2397.7s)

Parsing file diamond-C1.2.daa

Parsing file: diamond-C1.2.daa

10% 20% 30% 40% 50% 60% 70% 80% 90% 100% (2336.6s)

Total reads: 18,425,737

Alignments: 389,875,476

100% (0.0s)

Linking paired reads

Number of pairs: 0

Binning reads: Initializing...

Initializing binning...

Using paired reads in taxonomic assignment...

Using 'Naive LCA' algorithm for binning: Taxonomy

Using Best-Hit algorithm for binning: SEED

Using Best-Hit algorithm for binning: EGGNOG

Using 'Naive LCA' algorithm for binning: GTDB

Using Best-Hit algorithm for binning: INTERPRO2GO

Binning reads...

Binning reads: Analyzing alignments

Total reads: 18,425,737

With hits: 18,425,737

Alignments: 389,875,476

Assig. Taxonomy: 18,366,746

Assig. SEED: 11,106,599

Assig. EGGNOG: 11,487,509

Assig. GTDB: 17,662,177

Assig. INTERPRO2GO: 10,358,118

MinSupport set to: 9212

Binning reads: Applying min-support & disabled filter to Taxonomy...

Min-supp. changes: 8,122

Binning reads: Applying min-support & disabled filter to GTDB...

Min-supp. changes: 20,690

Binning reads: Writing classification tables

Numb. Tax. classes: 133

Numb. SEED classes: 750

Numb. EGG. classes: 7,456

Numb. GTDB classes: 104

Numb. INT. classes: 8,954

Binning reads: Syncing

Class. Taxonomy: 133

Class. SEED: 750

Class. EGGNOG: 7,456

Class. GTDB: 104

Class. INTERPRO2GO: 8,954

100% (19792.7s)

Total time: 24,536s

Peak memory: 144.1 of 195.3 G

耗时差不多7个小时。

提取物种注释数据：

/biostack/tools/microbiome/MEGAN_Community-6.19.2/tools/rma2info -i diamond-C1.rma -c2c Taxonomy -r2c Taxonomy -n true --paths true --ranks true --list true --listMore true --bacteriaOnly true -v > C1Taxonomy1.txt

屏幕输出：

RMA2Info - Analyses an RMA file

Options:

Input and Output

--in: diamond-C1.rma

--out: -

Commands

--list: true

--listMore: true

--class2count: Taxonomy

--read2class: Taxonomy

--names: true

--paths: true

--ranks: true

--majorRanksOnly: false

--bacteriaOnly: true

--virusOnly: false

--ignoreUnassigned: true

Other:

--verbose: true

Version MEGAN Community Edition (version 6.19.2, built 17 Jun 2020)

Author(s) Daniel H. Huson

Loading MEGAN File: diamond-C1.rma

Loading ncbi.map: 2,249,459

Loading ncbi.tre: 2,249,463

Total time: 492s

Peak memory: 29.8 of 195.3 G

提取EGGNOG注释：

/biostack/tools/microbiome/MEGAN_Community-6.19.2/tools/rma2info -i diamond-C1.rma -r2c EGGNOG -n true --paths true --ranks true --list true --listMore true -v > C1eggnog.txt

提取SEED注释：

/biostack/tools/microbiome/MEGAN_Community-6.19.2/tools/rma2info -i diamond-C1.rma -r2c SEED -n true --paths true --ranks true --list true --listMore true -v > C1SEED.txt

提取INTERPRO2GO注释：

/biostack/tools/microbiome/MEGAN_Community-6.19.2/tools/rma2info -i diamond-C1.rma -r2c INTERPRO2GO -n true --paths true --ranks true --list true --listMore true -v > C1INTERPRO2GO.txt

下载MEGAN6 Community Edition installers：https://software-ab.informatik.uni-tuebingen.de/download/megan6/welcome.html