trinity运行原理及常见报错(四)
2017-05-27 15:18
239 查看
6.运行butterfly
Butterfly consists of two parts. 分为两步:
第一步:graph simplification
During the first part, called graph simplification, Butterfly iterates between (i) merging consecutive nodes in linear paths in the de Bruijn graph to form nodes that represent longer sequences and (ii) pruning edges that represent minor deviations (supported
by comparatively few reads), which likely correspond to sequencing errors. Diploid polymorphisms are expected to be more frequent than sequencing errors and will likely be maintained.
(i)合并在de Bruijn graph中有线性节点的路径,以形成更长的路径
(ii)剔除可能由于测序错误导致的分岔路径,使得路径的边缘平滑均匀,这些分岔路径一般都有极少的reads支持。此外,多倍体多态性比测序错误更为常见,这种情况对分支进行保留。
第二步:plausible path scoring
In the second part, called plausible path scoring, Butterfly identifies those paths that are supported by actual reads and read pairs, using a dynamic programming procedure that traverses potential paths in the graph while maintaining the reads (and pairs)
that support them.
用动态规划算法进行打分,鉴定出被reads和read pairs支持的路径,剔除reads支持较少的路径。
--------------------------------------------------------------------------------
------------ Trinity Phase 2: Assembling Clusters of Reads ---------------------
--------------------------------------------------------------------------------
因为这是之前已经得到的文件,就会显示:successfully completed from a previous run. Skipping it here.
Wednesday, May 17, 2017: 23:01:34 CMD: /lustre/02.work/liufei/tools/trinityrnaseq-Trinity-v2.4.0/trinity-plugins/parafly/bin/ParaFly -c recursive_trinity.cmds -CPU 4 -v
warning, command: /lustre/02.work/liufei/tools/trinityrnaseq-Trinity-v2.4.0/util/support_scripts/../../Trinity --single "/lustre/02.work/liufei/denovo/trinity_test/All_Combination_Trinity/read_partitions/Fb_0/CBin_0/c0.trinity.reads.fa" --output "/lustre/02.work/liufei/denovo/trinity_test/All_Combination_Trinity/read_partitions/Fb_0/CBin_0/c0.trinity.reads.fa.out"
--CPU 1 --max_memory 1G --run_as_paired --seqType fa --trinity_complete --no_cleanup --min_kmer_cov 1 --bflyHeapSpaceMax 20G --bflyGCThreads 5 has successfully completed from a previous run. Skipping it here.
warning, command: /lustre/02.work/liufei/tools/trinityrnaseq-Trinity-v2.4.0/util/support_scripts/../../Trinity --single "/lustre/02.work/liufei/denovo/trinity_test/All_Combination_Trinity/read_partitions/Fb_0/CBin_0/c1.trinity.reads.fa" --output "/lustre/02.work/liufei/denovo/trinity_test/All_Combination_Trinity/read_partitions/Fb_0/CBin_0/c1.trinity.reads.fa.out"
--CPU 1 --max_memory 1G --run_as_paired --seqType fa --trinity_complete --no_cleanup --min_kmer_cov 1 --bflyHeapSpaceMax 20G --bflyGCThreads 5 has successfully completed from a previous run. Skipping it here.
...
...
warning, command: /lustre/02.work/liufei/tools/trinityrnaseq-Trinity-v2.4.0/util/support_scripts/../../Trinity --single "/lustre/02.work/liufei/denovo/trinity_test/All_Combination_Trinity/read_partitions/Fb_0/CBin_213/c21303.trinity.reads.fa" --output "/lustre/02.work/liufei/denovo/trinity_test/All_Combination_Trinity/read_partitions/Fb_0/CBin_213/c21303.trinity.reads.fa.out"
--CPU 1 --max_memory 1G --run_as_paired --seqType fa --trinity_complete --no_cleanup --min_kmer_cov 1 --bflyHeapSpaceMax 20G --bflyGCThreads 5 has successfully completed from a previous run. Skipping it here.
warning, command: /lustre/02.work/liufei/tools/trinityrnaseq-Trinity-v2.4.0/util/support_scripts/../../Trinity --single "/lustre/02.work/liufei/denovo/trinity_test/All_Combination_Trinity/read_partitions/Fb_0/CBin_213/c21304.trinity.reads.fa" --output "/lustre/02.work/liufei/denovo/trinity_test/All_Combination_Trinity/read_partitions/Fb_0/CBin_213/c21304.trinity.reads.fa.out"
--CPU 1 --max_memory 1G --run_as_paired --seqType fa --trinity_complete --no_cleanup --min_kmer_cov 1 --bflyHeapSpaceMax 20G --bflyGCThreads 5 has successfully completed from a previous run. Skipping it here.
warning, command: /lustre/02.work/liufei/tools/trinityrnaseq-Trinity-v2.4.0/util/support_scripts/../../Trinity --single "/lustre/02.work/liufei/denovo/trinity_test/All_Combination_Trinity/read_partitions/Fb_0/CBin_213/c21305.trinity.reads.fa" --output "/lustre/02.work/liufei/denovo/trinity_test/All_Combination_Trinity/read_partitions/Fb_0/CBin_213/c21305.trinity.reads.fa.out"
--CPU 1 --max_memory 1G --run_as_paired --seqType fa --trinity_complete --no_cleanup --min_kmer_cov 1 --bflyHeapSpaceMax 20G --bflyGCThreads 5 has successfully completed from a previous run. Skipping it here.
Number of Commands: 27523
succeeded(1) 0.00363332% completed.
succeeded(2) 0.00726665% completed.
succeeded(3) 0.0109% completed.
succeeded(4) 0.0145333% completed.
succeeded(5) 0.0181666% completed.
succeeded(6) 0.0217999% completed.
...
...
succeeded(27521) 99.9927% completed.
succeeded(27522) 99.9964% completed.
succeeded(27523) 100% completed.
All commands completed successfully. :-)
#有时候会出现报错:We are sorry, commands in file: [FailedCommands] failed.这种情况,检查FailedCommands文件,把出现的reads在recursive_trinity.cmds文件中整行删除掉,然后执行下面两步:
#doqsub "/data/tools/trinityrnaseq-2.2.0/trinity-plugins/parafly/bin/ParaFly -c recursive_trinity.cmds -CPU 20 -v" ##如果成功显示All commands completed successfully. :-)
#doqsub "find read_partitions/ -name '*inity.fasta' | /data/tools/trinityrnaseq-2.2.0/util/support_scripts/partitioned_trinity_aggregator.pl TRINITY_DN > Trinity.fasta.tmp"
#得到Trinity.fasta后保留Trinity.fasta外,尽快把trinity目录删掉
#报错
'''
We are sorry, commands in file: [failed_butterfly_commands.5819.txt] failed. :-(
We are sorry, commands in file: [failed_butterfly_commands.5818.txt] failed. :-(
We are sorry, commands in file: [FailedCommands] failed. :-(
'''
** Harvesting all assembled transcripts into a single multi-fasta file...
Thursday, May 18, 2017: 08:12:59 CMD: find read_partitions/ -name '*inity.fasta' | /lustre/02.work/liufei/tools/trinityrnaseq-Trinity-v2.4.0/util/support_scripts/partitioned_trinity_aggregator.pl TRINITY_DN > Trinity.fasta.tmp
###################################################################
Butterfly assemblies are written to /lustre/02.work/liufei/denovo/trinity_test/All_Combination_Trinity/Trinity.fasta
###################################################################
This-Work-is-Completed!
Butterfly consists of two parts. 分为两步:
第一步:graph simplification
During the first part, called graph simplification, Butterfly iterates between (i) merging consecutive nodes in linear paths in the de Bruijn graph to form nodes that represent longer sequences and (ii) pruning edges that represent minor deviations (supported
by comparatively few reads), which likely correspond to sequencing errors. Diploid polymorphisms are expected to be more frequent than sequencing errors and will likely be maintained.
(i)合并在de Bruijn graph中有线性节点的路径,以形成更长的路径
(ii)剔除可能由于测序错误导致的分岔路径,使得路径的边缘平滑均匀,这些分岔路径一般都有极少的reads支持。此外,多倍体多态性比测序错误更为常见,这种情况对分支进行保留。
第二步:plausible path scoring
In the second part, called plausible path scoring, Butterfly identifies those paths that are supported by actual reads and read pairs, using a dynamic programming procedure that traverses potential paths in the graph while maintaining the reads (and pairs)
that support them.
用动态规划算法进行打分,鉴定出被reads和read pairs支持的路径,剔除reads支持较少的路径。
--------------------------------------------------------------------------------
------------ Trinity Phase 2: Assembling Clusters of Reads ---------------------
--------------------------------------------------------------------------------
因为这是之前已经得到的文件,就会显示:successfully completed from a previous run. Skipping it here.
Wednesday, May 17, 2017: 23:01:34 CMD: /lustre/02.work/liufei/tools/trinityrnaseq-Trinity-v2.4.0/trinity-plugins/parafly/bin/ParaFly -c recursive_trinity.cmds -CPU 4 -v
warning, command: /lustre/02.work/liufei/tools/trinityrnaseq-Trinity-v2.4.0/util/support_scripts/../../Trinity --single "/lustre/02.work/liufei/denovo/trinity_test/All_Combination_Trinity/read_partitions/Fb_0/CBin_0/c0.trinity.reads.fa" --output "/lustre/02.work/liufei/denovo/trinity_test/All_Combination_Trinity/read_partitions/Fb_0/CBin_0/c0.trinity.reads.fa.out"
--CPU 1 --max_memory 1G --run_as_paired --seqType fa --trinity_complete --no_cleanup --min_kmer_cov 1 --bflyHeapSpaceMax 20G --bflyGCThreads 5 has successfully completed from a previous run. Skipping it here.
warning, command: /lustre/02.work/liufei/tools/trinityrnaseq-Trinity-v2.4.0/util/support_scripts/../../Trinity --single "/lustre/02.work/liufei/denovo/trinity_test/All_Combination_Trinity/read_partitions/Fb_0/CBin_0/c1.trinity.reads.fa" --output "/lustre/02.work/liufei/denovo/trinity_test/All_Combination_Trinity/read_partitions/Fb_0/CBin_0/c1.trinity.reads.fa.out"
--CPU 1 --max_memory 1G --run_as_paired --seqType fa --trinity_complete --no_cleanup --min_kmer_cov 1 --bflyHeapSpaceMax 20G --bflyGCThreads 5 has successfully completed from a previous run. Skipping it here.
...
...
warning, command: /lustre/02.work/liufei/tools/trinityrnaseq-Trinity-v2.4.0/util/support_scripts/../../Trinity --single "/lustre/02.work/liufei/denovo/trinity_test/All_Combination_Trinity/read_partitions/Fb_0/CBin_213/c21303.trinity.reads.fa" --output "/lustre/02.work/liufei/denovo/trinity_test/All_Combination_Trinity/read_partitions/Fb_0/CBin_213/c21303.trinity.reads.fa.out"
--CPU 1 --max_memory 1G --run_as_paired --seqType fa --trinity_complete --no_cleanup --min_kmer_cov 1 --bflyHeapSpaceMax 20G --bflyGCThreads 5 has successfully completed from a previous run. Skipping it here.
warning, command: /lustre/02.work/liufei/tools/trinityrnaseq-Trinity-v2.4.0/util/support_scripts/../../Trinity --single "/lustre/02.work/liufei/denovo/trinity_test/All_Combination_Trinity/read_partitions/Fb_0/CBin_213/c21304.trinity.reads.fa" --output "/lustre/02.work/liufei/denovo/trinity_test/All_Combination_Trinity/read_partitions/Fb_0/CBin_213/c21304.trinity.reads.fa.out"
--CPU 1 --max_memory 1G --run_as_paired --seqType fa --trinity_complete --no_cleanup --min_kmer_cov 1 --bflyHeapSpaceMax 20G --bflyGCThreads 5 has successfully completed from a previous run. Skipping it here.
warning, command: /lustre/02.work/liufei/tools/trinityrnaseq-Trinity-v2.4.0/util/support_scripts/../../Trinity --single "/lustre/02.work/liufei/denovo/trinity_test/All_Combination_Trinity/read_partitions/Fb_0/CBin_213/c21305.trinity.reads.fa" --output "/lustre/02.work/liufei/denovo/trinity_test/All_Combination_Trinity/read_partitions/Fb_0/CBin_213/c21305.trinity.reads.fa.out"
--CPU 1 --max_memory 1G --run_as_paired --seqType fa --trinity_complete --no_cleanup --min_kmer_cov 1 --bflyHeapSpaceMax 20G --bflyGCThreads 5 has successfully completed from a previous run. Skipping it here.
Number of Commands: 27523
succeeded(1) 0.00363332% completed.
succeeded(2) 0.00726665% completed.
succeeded(3) 0.0109% completed.
succeeded(4) 0.0145333% completed.
succeeded(5) 0.0181666% completed.
succeeded(6) 0.0217999% completed.
...
...
succeeded(27521) 99.9927% completed.
succeeded(27522) 99.9964% completed.
succeeded(27523) 100% completed.
All commands completed successfully. :-)
#有时候会出现报错:We are sorry, commands in file: [FailedCommands] failed.这种情况,检查FailedCommands文件,把出现的reads在recursive_trinity.cmds文件中整行删除掉,然后执行下面两步:
#doqsub "/data/tools/trinityrnaseq-2.2.0/trinity-plugins/parafly/bin/ParaFly -c recursive_trinity.cmds -CPU 20 -v" ##如果成功显示All commands completed successfully. :-)
#doqsub "find read_partitions/ -name '*inity.fasta' | /data/tools/trinityrnaseq-2.2.0/util/support_scripts/partitioned_trinity_aggregator.pl TRINITY_DN > Trinity.fasta.tmp"
#得到Trinity.fasta后保留Trinity.fasta外,尽快把trinity目录删掉
#报错
'''
We are sorry, commands in file: [failed_butterfly_commands.5819.txt] failed. :-(
We are sorry, commands in file: [failed_butterfly_commands.5818.txt] failed. :-(
We are sorry, commands in file: [FailedCommands] failed. :-(
'''
** Harvesting all assembled transcripts into a single multi-fasta file...
Thursday, May 18, 2017: 08:12:59 CMD: find read_partitions/ -name '*inity.fasta' | /lustre/02.work/liufei/tools/trinityrnaseq-Trinity-v2.4.0/util/support_scripts/partitioned_trinity_aggregator.pl TRINITY_DN > Trinity.fasta.tmp
###################################################################
Butterfly assemblies are written to /lustre/02.work/liufei/denovo/trinity_test/All_Combination_Trinity/Trinity.fasta
###################################################################
This-Work-is-Completed!
相关文章推荐
- trinity运行原理及常见报错(三)
- trinity运行原理及常见报错(二)
- trinity运行原理及常见报错(一)
- 常见的几种语言C,C#,JAVA,Python的运行原理
- 通过MSIL了解CLR的运行原理
- [读书笔记][深入剖析ASP.NET组件设计]一书第三章关于ASP.NET运行原理讲述的补白
- 学习笔记——windows程序运行原理
- 第二章 Win32程序运行原理
- Visual Fortran 常见运行错误信息
- CLR 中类型字段的运行时内存布局 (Layout) 原理浅析 [2]
- 通过避免下列 10 个常见 ASP.NET 缺陷使网站平稳运行
- 打印机结构、原理及常见故障
- Lesson1 Windows程序内部运行原理 ---孙鑫VC++教程
- 通过避免下列 10 个常见 ASP.NET 缺陷使网站平稳运行(转载)
- 通过避免下列 10 个常见 ASP.NET 缺陷使网站平稳运行(转载)
- 通过避免下列 10 个常见 ASP.NET 缺陷使网站平稳运行(转载)
- BT运行原理分析及内网提速方法(转)
- DoS攻击原理以及常见方法介绍(三)
- 孙鑫VC讲座笔记--WINDOWS程序内部运行原理
- 通过避免下列 10 个常见 ASP.NET 缺陷使网站平稳运行