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Old 06-14-2012, 05:04 AM   #1
Lspoor
Member
 
Location: Fife, Scotland

Join Date: Mar 2010
Posts: 18
Default SOAPddenovo v1.05 error-Cannot open output_prefix.kmerFreq.

Hello,

We are using SOAPdenovov1.05 on paired end 36bp Illumina reads with this command:
[s0977659@ris-lx03 bin]$ ./SOAPdenovo-31mer all -p 4 -s /LBEP/Laura/JUNE_2012/14_june_2012/SOAPdenovo_140612/Inputs/AB10.config -o AB10

The Error I get is:
Cannot open AB10.kmerFreq. Now exit to system...

Prior to this output looks ok:
Version 1.05: released on July 29th, 2010

pregraph -s /LBEP/Laura/JUNE_2012/14_june_2012/SOAPdenovo_140612/Inputs/AB10b.config -p 4 -o AB10
In /LBEP/Laura/JUNE_2012/14_june_2012/SOAPdenovo_140612/Inputs/AB10b.config, 1 libs, max seq len 100, max name len 256

4 thread created
read from file:
/LBEP/Laura/Genome_assemblies/ILLUMINARUN3/concat_files/correct_heads/Paired_Filtered_2012-05-18/3_2008/3_2008_1.fq
read from file:
/LBEP/Laura/Genome_assemblies/ILLUMINARUN3/concat_files/correct_heads/Paired_Filtered_2012-05-18/3_2008/3_2008_2.fq
time spent on hash reads: 6s, 1827824 reads processed
[LIB] 0, avg_ins 500, reverse 0
3017193 nodes allocated, 20004683 kmer in reads, 20004683 kmer processed
2924786 linear nodes


Config file is:
#maximal read length
# Lines start with '#' are ignored by the assembler
max_rd_len=100
[LIB]
#average insert size
avg_ins=500
#if sequence needs to be reversed
reverse_seq=0
#in which part(s) the reads are used
asm_flags=3
#in which order the reads are used while scaffolding
rank=1
#fastq file for read 1
q1=/path/to/3_2008_1.fq
#fastq file for read 2 always follows fastq file for read 1
q2=/path/to/3_2008_2.fq
#fastq file for single reads
#q=/path/to/3_2008_single.fq

#87 scaffolds from 2858 contigs sum up 2802411bp, with average length 32211, 1 gaps filled
#188 scaffolds&singleton sum up 2881315bp, with average length 15326
#the longest is 233637bp,scaffold N50 is 65253 bp, scaffold N90 is 19282 bp

I am new to SOAPdenvo, but has anyone had similar problems?

Thanks,

Laura
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Old 06-17-2015, 06:41 AM   #2
Anandi
Junior Member
 
Location: Stellenbosch

Join Date: Jun 2015
Posts: 2
Default You don't have admin rights or something

Hi Laura

I actually had this same problem today!
It's because I did not have administrator's rights to the folder that I wanted to save my output (-o) file in!
As soon as I changed my output file location, and tried again, the run worked just fine.

Hope this helps!
Have fun
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