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Old 05-03-2011, 06:48 AM   #1
flobpf
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Question SOAPdenovo Config file

Hi
I'm trying to use SOAPdenovo with 14 paired end 500bp Illumina FQ files (7 files of each end). I tried to follow the example.config file on the SOAPdenovo website here

In my config file, I am specifying all my PE files as a single library since all have the same insert size. In that one library though, how do I specify my different PE files? I had specified them as (q1, q2) (q3, q4 ) and so on, but SOAPdenovo only looks at q1 and q2 files.
Code:
#maximal read length
max_rd_len=70
[LIB]
#average insert size
avg_ins=516
#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=s_1_1_sequence.txt.trim70.gz
#fastq file for read 2 always follows fastq file for read 1
q2=s_1_2_sequence.txt.trim70.gz
####
#fastq file for read 1 
q3=s_2_1_sequence.txt.trim70.gz
#fastq file for read 2 always follows fastq file for read 1
q4=s_2_2_sequence.txt.trim70.gz
####
#fastq file for read 1 
q5=s_3_1_sequence.txt.trim70.gz
#fastq file for read 2 always follows fastq file for read 1
q6=s_3_2_sequence.txt.trim70.gz
In the output, SOAPdenovo is looking only at q1 and q2. Is my config file correct?


My questions are:

1) Should I specify each PE set as q1,q2 in the same library? OR
2) Does each PE set need to be specified as a different library, each with its own q1, q2?
3) Any other solution??

I'd appreciate your help!
Thanks
Flobpf
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Old 05-04-2011, 05:53 AM   #2
Malabady
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Default I am having the same problem

Did you find any answers to this question?
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Old 05-04-2011, 05:59 AM   #3
flobpf
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Quote:
Originally Posted by Malabady View Post
Did you find any answers to this question?
I ran it specifying (q1, q2) multiple times in the same library for each pair of FQ files. SOAPdenovo used all the files alright, but i'm not sure if thats the correct way to do it. plus, i'm not sure what all the output lines mean.
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Old 05-04-2011, 06:57 AM   #4
Malabady
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Thanks, it worked. There is a section in the manual of soapdenovo that explains each of the output files.
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Old 05-04-2011, 07:20 AM   #5
flobpf
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Quote:
Originally Posted by Malabady View Post
Thanks, it worked. There is a section in the manual of soapdenovo that explains each of the output files.
I had hoped that there would be a summary file having different values such as N50, Assembly size, number of bases in the assembly, number of reads used in assembly, minimum contig size etc. i have used ABySS and it gives all such values.

There are several lines that are printed out while SOAPdenovo is running and I think some of those lines may be useful. however, there is no explanation in the manual about the on-screen output, just to confirm that they are indeed what I think they are.
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Old 05-04-2011, 07:37 AM   #6
Malabady
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I use the abyss stats script (fac.pl) to get the stats you mentioned from the saopdenovo assembly. This script can be used very much with any fasta file.

I don't think soapdenovo authors are supporting it the same way the abyss authors do. Abyss authors are excellent and continuously upgrading their algorithm.
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Old 05-04-2011, 07:53 AM   #7
flobpf
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Quote:
Originally Posted by Malabady View Post
I don't think soapdenovo authors are supporting it the same way the abyss authors do. Abyss authors are excellent and continuously upgrading their algorithm.
I agree. ABySS support is terrific

Thanks for the note about the stats script. that would be useful.
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Old 11-21-2011, 08:22 PM   #8
tejas
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Hello Everyone...!
I am new to this software and I find it easy to manage the usage of the software. But I am finding it little tricky and difficult to find the analysis of the output files.

Its like I have to find :
1) No. of scaffolds :
2) No. of single contigs :
3)Total length of Scaffolds :
4)Total length of Contigs :
5)Total bases in Contig + Scaffolds


Can anyone please help me with linux commands and SOAPdenovo result analysis.
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Old 09-10-2015, 11:50 AM   #9
mgbfx9
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Thank you for all these answers as I was about to ask these questions.
So,

Q1. Where to look for the output file?

There are several lines that are printed out while SOAPdenovo is running, are these output results?

I tried to see by *.contig (according to the instruction), but, output says:
-bash: graph_prefix.contig: command not found.

Q2. I tested a small configuration file from my SOAPdenovo directory, and it worked.
Now I am making more configuration files, but they are not working. I am running SOAPdenovo from my directory as before only changing with my new.cfgfile, it is not running, output is:

Compile Sep xx 2015 (the same day when I did the first one...)

Cannot open new.cfgfile. Now exit to system......

What am I doing wrong?

Thanks in advance,
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Old 09-10-2015, 01:15 PM   #10
westerman
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Quote:
Originally Posted by mgbfx9 View Post
...
Q2. I tested a small configuration file from my SOAPdenovo directory, and it worked.
Now I am making more configuration files, but they are not working.
...
Cannot open new.cfgfile. Now exit to system......

What am I doing wrong?
It is hard to say what you are doing wrong without seeing what you are doing. That is, the output from 'ls' (to make sure the file exists), the command line you are using, etc. We can not look over your shoulder so you will have to provide screen shots and/or copy-n-paste of the exact commands you are using.

SOAPdenovo works as per the test configuration. But with your config file the program complains about the file not existing. I believe the program. So whatever is going wrong is something that is simple. You must be mis-typing something but, as I said, we can not look over your shoulder so you will need to give us more information.
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Old 09-11-2015, 11:45 AM   #11
mgbfx9
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Hi Westerman,

Thank you for your reply.

I can see my files are there by the command 'ls' at SOAPdenovo2-src-r240 directory. I can see ass.err, ass.log files too.

My command to run my test configuration file is:

[home/mydirrectory/ SOAPdenovo2-src-r240]$ /home/mydirectory/SOAPdenovo2-src-r240/SOAPdenovo-63mer pregraph -s myconfigurationfile.cfg -K 63 -R -o graph_prefix 1>ass.log 2>ass.err

I can view my output results by the following command:

cat ass.err

But after that, I can not run any other configuration files with any other fastq files; I changed the config file accordingly; also if I add different .fq files in the same config file which ran before (definitely I changed the config file accordingly), the program does not run. It says : Cannot open new.cfgfile. Now exit to system......

I need to run my actual file, but I am not sure how can I do that? Any help is really appreciated.

Thank you in advance,
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Old 09-14-2015, 10:07 AM   #12
westerman
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Weekend got in the way of a quick response. I still think that you are probably missing something obvious. But, once again, without being able to see what you are doing it is hard to troubleshoot. For example you say "... I changed the config file accordingly ..." That is ok to do but if you messed something up how can we tell? Screen shots are useful.
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