trinity运行原理及常见报错（二）

4.运行Inchworm

Linear contig construction from k-mers

Inchworm：

将RNA-seq的原始reads数据逐碱基打成kmer,根据kmer之间的重叠关系组装成Contig序列。 C++ 

构建k-mer库.

剔除可能包含错误的k-mer。

选择最高频的k-mer作为种子，用完以后从k-mer库中剔除，用于做conting组装

延伸种子，k-1个overlap关系。

延伸至最长，无法延伸，形成一个线性的conting

重复前面三步，直到k-mer库为空

前面jellyfish已经得到k-mer库并去除了可能错误的k-mer

* Running CMD: /lustre/02.work/liufei/tools/trinityrnaseq-Trinity-v2.4.0/Inchworm/bin//inchworm --kmers jellyfish.kmers.fa --run_inchworm -K 25 -L 25 --monitor 1   --DS  --keep_tmp_files  --num_threads 5  --PARALLEL_IWORM  > /lustre/02.work/liufei/denovo/trinity_test/All_Combination_Trinity/inchworm.K25.L25.DS.fa.tmp

* Running CMD: mv /lustre/02.work/liufei/denovo/trinity_test/All_Combination_Trinity/inchworm.K25.L25.DS.fa.tmp /lustre/02.work/liufei/denovo/trinity_test/All_Combination_Trinity/inchworm.K25.L25.DS.fa

Tuesday, May 16, 2017: 23:57:19 CMD: touch /lustre/02.work/liufei/denovo/trinity_test/All_Combination_Trinity/inchworm.K25.L25.DS.fa.finished

得到inchworm.K25.L25.DS.fa 组成的conting

$grep '>' All_Combination_Trinity/inchworm.K25.L25.DS.fa |head -5

>a1;55 total_counts: 158820 Seed: 66 K: 25 length: 2909

>a2;49 total_counts: 151930 Seed: 62 K: 25 length: 3097

>a3;55 total_counts: 73382 Seed: 2 K: 25 length: 1356

>a4;53 total_counts: 69227 Seed: 29 K: 25 length: 1331

>a5;79 total_counts: 89509 Seed: 51 K: 25 length: 1156