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Old 12-21-2009, 09:08 PM   #1
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Location: india

Join Date: Nov 2009
Posts: 7
Default SOAPdenovo assembler

i am trynig to use SOAPdenovo assembler but it is not working..
the command i type is ./SOAPdenovo all –s mydata.config -K:31 -p:8 -M:1 -L:K+2 -o:contig.fastq , and in the conf. file i gave the path like.q1=/home/shailesh/Desktop/softwares/SOAP/SOAPdenovo_Release1.03/SRR015342.fastq
why it is not working??? plese suggest me some easy way to use this software. its urgent..
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Old 12-21-2009, 09:20 PM   #2
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Try to keep things on target next time!

The error messages you receive may be helpful to anyone trying to help you with your urgent question.
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Old 12-22-2009, 03:28 AM   #3
Location: China

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try the follows:
./SOAPdenovo all –s mydata.config -K 31 -p 8 -M 1 -L 2 -o contig.fastq
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Old 12-23-2009, 12:16 AM   #4
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Use:./SOAPdenovo all –s mydata.config -K 31 -L -o contig.fastq
No need to insert -p and -M option as you are using default setting. I never use -L before but the manual said -L doesn't require integer or string.
Use q = /path for single FASTQ reads.
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Old 12-23-2009, 11:33 AM   #5
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Location: Davis, CA

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I had this message when I used SOAPdenovo
avt$ ./SOAPdenovo all -s file.config -K 25 -L -o contig.fastq
-bash: ./SOAPdenovo: cannot execute binary file
How to solve this problem? I run it on MAC OS X v10.6
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Old 09-30-2010, 06:08 AM   #6
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Location: Japan

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I had same error message as avt
Can anyone tell me what is wrong?
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Old 10-04-2010, 06:35 PM   #7
Location: Singapore

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Usually in this case, the binary program is not the correct version for your machine. Make sure you got the right version for your OS/32/64-bit.
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