Soapdenovo2

[hengyou zhang]

您好，我最近在使用Soapdenovo2 去装配基因组。我跑了之后出错，请帮忙看看。测序数据是双端100bp。十分感激。

config file：

max_rd_len=100

[LIB]

avg_ins=90

reverse_seq=0

asm_flags=1

rd_len_cuff=90

rank=1

pair_num_cutoff=3

map_len=32

q1 = /scratch/hzhang37/bfecunda/finalass/raw_reads/QH_trim_1.fq

q2 = /scratch/hzhang37/bfecunda/finalass/raw_reads/QH_trim_2.fq

提交的file:

/users/hzhang37/Applications/SOAPdenovo2-bin-LINUX-generic-r240/SOAPdenovo-127mer all -s /scratch/hzhang37/bfecunda/finalass/soap/config_file -K 71 -o /scratch/hzhang37/bfecunda/finalass/soap/QH_kmer_57

出错：

Version 2.04: released on July 13th, 2012

Compile Jul  9 2013     11:57:30

********************

Pregraph

********************

Parameters: pregraph -s /scratch/hzhang37/bfecunda/finalass/soap/config_file -K 71 -o /scratch/hzhang37/bfecunda/finalass/soap/QH_kmer_57

In /scratch/hzhang37/bfecunda/finalass/soap/config_file, 1 lib(s), maximum read length 100, maximum name length 256.

8 thread(s) initialized.

Time spent on hashing reads: 0s, 0 read(s) processed.

LIB(s) information:

 [LIB] 0, avg_ins 90, reverse 0.

0 node(s) allocated, 0 kmer(s) in reads, 0 kmer(s) processed.

done hashing nodes

0 linear node(s) marked.

Time spent on marking linear nodes: 0s.

Time spent on pre-graph construction: 1s.

Start to remove frequency-one-kmer tips shorter than 142.

Total 0 tip(s) removed.

8 thread(s) initialized.

0 linear node(s) marked.

Start to remove tips with minority links.

0 tip(s) removed in cycle 1.

Total 0 tip(s) removed.

8 thread(s) initialized.

0 linear node(s) marked.

Time spent on removing tips: 0s.

0 (0) edge(s) and 0 extra node(s) constructed.

Time spent on constructing edges: 0s.

In file: /scratch/hzhang37/bfecunda/finalass/soap/config_file, max seq len 100, max name len 256.

8 thread(s) initialized.

0 read(s) processed.

Time spent on:

 importing reads: 0s,

 chopping reads to kmers: 0s,

 searching kmers: 0s,

 aligning reads to edges: 0s,

 searching (K+1)mers: 0s,

 adding pre-arcs: 0s,

 recording read paths: 0s.

0 marker(s) output.

Reads alignment done, 0 read(s) deleted, 0 pre-arc(s) added.

LIB(s) information:

 [LIB] 0, avg_ins 90, reverse 0.

Time spent on aligning reads: 0s.

0 vertex(es) output.

Overall time spent on constructing pre-graph: 0m.

********************

Contig

********************

Parameters: contig -g /scratch/hzhang37/bfecunda/finalass/soap/QH_kmer_57 -M 1 -s /scratch/hzhang37/bfecunda/finalass/soap/config_file

There are 0 kmer(s) in vertex file.

There are 0 edge(s) in edge file.

Kmers sorted.

0 edge(s) input.

0 pre-arcs loaded.

0 none-palindrome edge(s) swapped, 0 palindrome edge(s) processed.

0 edge(s) sorted.

Arcs sorted.

Start to pinch bubbles, cutoff 0.100000, MAX NODE NUM 3, MAX DIFF NUM 2.

0 start points, 0 dheap nodes.

0 pair(s) found, 0 pair of path(s) compared, 0 pair(s) merged.

Sequence comparison failed:

 Path crossing deleted edge                         0

 Length difference of two paths greater than two    0

 Mismatch score greater than cutoff (2)             0

 Mismatch score ratio greater than cutoff (0.1)     0

 Path length shorter than (Kmer-1)                  0

DFibHeap: 0 node(s) allocated.

0 edge(s) concatenated in cycle 1.

Time spent on pinching bubbles: 0s.

Start to destroy weak inner edges.

0 weak inner edge(s) destroyed in cycle 1.

0 dead arc(s) removed.

0 inner edge(s) with coverage lower than or equal to 1 destroyed.

0 dead arc(s) removed.

0 edge(s) concatenated in cycle 1.

Before compacting, 0 edge(s) existed.

After compacting, 0 edge(s) left.

Strict: 0, cutoff length: 142.

0 tips cut in cycle 1.

0 dead arc(s) removed.

0 edge(s) concatenated in cycle 1.

Before compacting, 0 edge(s) existed.

After compacting, 0 edge(s) left.

No contig was constructed!

0 contig(s) longer than 72 output.

Time spent on constructing contig: 0m.

********************

Map

********************

Parameters: map -s /scratch/hzhang37/bfecunda/finalass/soap/config_file -g /scratch/hzhang37/bfecunda/finalass/soap/QH_kmer_57 -K 71

Kmer size: 71.

Contig length cutoff: 73.

0 contig(s), maximum sequence length 10, minimum sequence length 0, maximum name length 10.

Time spent on parsing contigs file: 0s.

8 thread(s) initialized.

Time spent on hashing contigs: 0s.

0 node(s) allocated, 0 kmer(s) in contigs, 0 kmer(s) processed.

Time spent on graph construction: 1s.

Time spent on aligning long reads: 0s.

In file: /scratch/hzhang37/bfecunda/finalass/soap/config_file, max seq len 100, max name len 256

8 thread(s) initialized.

0 edge(s) in the graph.

Reads on contigs    0

Ratio               nan%

No paired reads found.

LIB(s) information:

 [LIB] 0, avg_ins 90, reverse 0.

Time spent on aligning reads: 1s.

Overall time spent on alignment: 0m.

********************

Scaff

********************

Parameters: scaff -g /scratch/hzhang37/bfecunda/finalass/soap/QH_kmer_57

/scratch/hzhang37/bfecunda/finalass/soap/QH_kmer_57.Arc: no such file or empty file!

There are 0 grad(s), 0 read(s), max read len 100.

Kmer size: 71

There are 0 edge(s) in edge file.

Mask contigs with coverage lower than 0.0 or higher than 0.0, and strict length 0.

Average contig coverage is 0, 0 contig(s) masked.

Mask contigs shorter than 73, 0 contig(s) masked.

0 arc(s) loaded, average weight is 0.

0 contig(s) loaded.

Done loading updated edges.

Time spent on loading updated edges: 0s.

There are 0 grad(s), 0 read(s), max read len 100.

*****************************************************

Start to load paired-end reads information.

All paired-end reads information loaded.

Time spent on loading paired-end reads information: 0s.

*****************************************************

Start to construct scaffolds.

There are 0 grad(s), 0 read(s), max read len 100.

All links loaded.

Time spent on constructing scaffolds: 0s.

The final rank

No scaffold was constructed.

Done with 0 scaffolds, 0 gaps finished, 0 gaps overall.

Segmentation fault (core dumped)

--

Hengyou Zhang, Ph.D

-----------------------

Postdoctoral Associate

The Song Lab

Department of Biological Sciences

University of North Carolina at Charlotte (UNC-Charlotte)

9201 University Blvd, Charlotte, NC 28223, USA

Tel: (704)-687-0148