trinity运行原理及常见报错（四）

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!