SOAPDeNovo question

[francism]

working on soapdenovo but having run the analysis for more than 60hrs. Still not able to get any result from the analysis. Have 5 pair reads making up 10 fastq files. Below is the details of my config file. Please kindly help out to check if there are things that am not getting right.#maximal read length
max_rd_len=201
[LIB]
#average insert size
avg_ins=300
#if sequence needs to be reversed
reverse_seq=0
#in which part(s) the reads are used
asm_flags=3
#use only first 100 bps of each read
rd_len_cutoff=100
#in which order the reads are used while scaffolding
rank=1
# cutoff of pair number for a reliable connection (at least 3 for short insert size)
pair_num_cutoff=3
#minimum aligned length to contigs for a reliable read location (at least 32 for short insert size)
map_len=32
#a pair of fastq file, read 1 file should always be followed by read 2 file
q1=/syn02iscsi/agisel/Cassava/Ismail/WGS/raw_data/3422_7332_10694_H9WVUADXX_I961089A_CTTGTA_R1.fastq.gz
q2=/syn02iscsi/agisel/Cassava/Ismail/WGS/raw_data/3422_7332_10694_H9WVUADXX_I961089A_CTTGTA_R2.fastq.gz
#another pair of fastq file, read 1 file should always be followed by read 2 file
q1=/syn02iscsi/agisel/Cassava/Ismail/WGS/raw_data/3422_7332_10694_HA63NADXX_I961089A_CTTGTA_R1.fastq.gz
q2=/syn02iscsi/agisel/Cassava/Ismail/WGS/raw_data/3422_7332_10694_HA63NADXX_I961089A_CTTGTA_R2.fastq.gz
#a pair of fasta file, read 1 file should always be followed by read 2 file
[LIB]
avg_ins=500
reverse_seq=o
asm_flags=3
rank=2
# cutoff of pair number for a reliable connection (at least 5 for large insert size)
pair_num_cutoff=5
#minimum aligned length to contigs for a reliable read location (at least 35 for large insert size)
map_len=35
q1=/syn02iscsi/agisel/Cassava/Ismail/WGS/raw_data/3423_7332_10706_H9WVUADXX_I961089A_500_ATTCCT_R1.fastq.gz
q2=/syn02iscsi/agisel/Cassava/Ismail/WGS/raw_data/3423_7332_10706_H9WVUADXX_I961089A_500_ATTCCT_R2.fastq.gz
#a pair of fastq file, read 1 file should always be followed by read 2 file
q1=/syn02iscsi/agisel/Cassava/Ismail/WGS/raw_data/3423_7332_10706_HA63NADXX_I961089A_500_ATTCCT_R1.fastq.gz
q2=/syn02iscsi/agisel/Cassava/Ismail/WGS/raw_data/3423_7332_10706_HA63NADXX_I961089A_500_ATTCCT_R2.fastq.gz
#a pair of fastq file, read 1 file should always be followed by read 2 file
q1=/syn02iscsi/agisel/Cassava/Ismail/WGS/raw_data/3423_7332_10706_HAK9RADXX_I961089A_500_ATTCCT_R1.fastq.gz
q2=/syn02iscsi/agisel/Cassava/Ismail/WGS/raw_data/3423_7332_10706_HAK9RADXX_I961089A_500_ATTCCT_R2.fastq.gz

[GenoMax]

@francism: I moved your post to a new thread.

Depending on the hardware you are using (and the size of the data) it is not unreasonable to have a de novo assembly run for 5 days (or longer).

Are you getting an error? Do you see files being written? Is the process running actively ("top" or a similar command)?

[francism]

I'm not getting an error . The files are not written in the specified output. The top shows S.

[GenoMax]

S means that the process is sleeping. But that alone is not enough to tell us if this is working.

Can you provide some additional information about how large is this dataset and how much memory you have available? Have you tested the SOAPdenovo install with a test dataset to ensure that the program is correctly installed and working?

[francism]

pls, how do i test if the install SOAPdenovo is working?do you have a dataset sample. Will appreciate if you can help.

[francism]

Version 2.04: released on July 13th, 2012
Compile Jul 9 2013 11:57:30

Usage: SOAPdenovo <command> [option]
pregraph construct kmer-graph
sparse_pregraph construct sparse kmer-graph
contig eliminate errors and output contigs
map map reads to contigs
scaff construct scaffolds
all do pregraph-contig-map-scaff in turn.
It shows that SOAPdenovo installation was properly done.

[GenoMax]

Test data is available on the SOAP download page: http://soap.genomics.org.cn/down/test.tar.gz

[anita]

I want to run soapdenovo for genome assembly of Oryza sativa cultivar. Need help to figure out where I did wrong in config file. this is my config file

#maximal read length
max_rd_len=90
[LIB]
#average insert size
avg_ins= 130
#if sequence needs to be reversed
reverse_seq=0
#in which part(s) the reads are used
asm_flags=3
#use only first 90 bps of each read
rd_len_cutoff=90
#in which order the reads are used while scaffolding
rank=1
# cutoff of pair number for a reliable connection (at least 3 for short insert size)
pair_num_cutoff=3
#minimum aligned length to contigs for a reliable read location (at least 32 for short insert size)
map_len=32
#a pair of fastq file, read 1 file should always be followed by read 2 file
q1=/path/read1.fastq_filtered
q2=/path/read2.fastq_filtered
#bam file for single or paired reads, reads 1 in paired reads file should always be followed by reads 2
#NOTE: If a read in bam file fails platform/vendor quality checks(the flag field 0x0200 is set), itself and it's paired read would be ignored.
b=/path to bam file created with read1 with the reference/aln-se1.bam
#another bam file for single or paired reads
b=/path to bam file created with read2 with the reference/aln-se2.bam

Regards..