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

[hengyou zhang]

 Hi, all, 

I am trying to use soapdenovo2 to assemble contigs using paired-end reads (100 bp length), when I setup all files and start to run, just got nothing with some empty files, please see the setup file and an output error (log?), and please help me out. Thanks so much. 

PBS file:

#!/bin/bash

#==== PBS OPTIONS ====

#PBS -N QH_kmer_37

#PBS -q copperhead

#PBS -l procs=10

#PBS -l walltime=720:00:00

## cd $PBS_O_WORKDIR

/users/hzhang37/Applications/SOAPdenovo2-bin-LINUX-generic-r240/SOAPdenovo-63mer all -s /scratch/hzhang37/bfecunda/finalass/soap/config_file -K 37 -o /scratch/hzhang37/bfecunda/finalass/soap/QH_kmer_57

Config_file

max_rd_len=98

[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

Here is the output error file:

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 47 -o /scratch/hzhang37/bfecunda/finalass/soap/QH_kmer_57

In /scratch/hzhang37/bfecunda/finalass/soap/config_file, 1 lib(s), maximum read length 98, 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: 0s.

Start to remove frequency-one-kmer tips shorter than 94.

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 98, 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

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

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

Contig

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

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

s/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.

.... a lot here................