[mira_talk] Re: Assembly

  • From: Lionel Guy <guy.lionel@xxxxxxxxx>
  • To: mira_talk@xxxxxxxxxxxxx
  • Date: Fri, 2 Oct 2009 14:51:19 +0200

You don't have fasta and fasta.qual, but a fastq file. Rename your cotton_in.solexa.fasta.qual to fastq:


mv cotton_in.solexa.fasta.qual cotton_in.solexa.fastq

And launch the command I indicated you before (note the -fastq switch), starting mira with fastq data loading mode.

mira -fastq --project=cotton --job=mapping,genome,accurate,solexa - AS:nop=1 -SB:lsd=yes:bsn=cotton_ref:bft=gbf:bbq=30 >&log_assembly.txt

If it still doesn't work, please paste the error message AND the content of your directory AND the exact command you typed.

L.
On 2 Oct 2009, at 14:43 , Sharmista Saha wrote:

Hi,

Following Bastein only, I renamed both the fasta and fastaqual file as it is mentioned in the manual. I did follow thw respective manual from the first.
my mira command can run with the fasta file,
but as it comes to the fasta qual file
it shows me the error which I have written previously, where it stops at (@40 ). since my fasta.qual file in a phred score containing file so, I feel the error lies in there. Loading quality data from FASTA quality file cotton_in.solexa.fasta.qual:

Fatal Error: "Illegal character (@: 40) at begin of fasta integer value sequence in file at byte position 1"
->Thrown: void FASTA::loadNextINTSeq(ifstream & fin, int32 maxvalue)
->Caught: Assembly::loadFASTA(const string & fastafile, const string & fastaqualfile, const uint8 readtype, const uint8 loadaction)
Program aborted.
CWD: /home/sharmistha/Sharmistha/Bioinfo/Project_data/Cotton_data/ mira_3rc2_dev_linux-gnu_i686_32_static/bin/Dataform

Anyhow, since my data set is a confidential one,

I can cite an example of my qual file.
which is similar as below.


+SRR001666.1 07+SRR001666.1 071112_SLXA-EAS1_s_7:5:1:817:345 length=36
IIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IG9IC




Now can you suggest me how to rectify the error? as I get the same error after re running mira, since it is able to take in fasta file,

but while reading fasta.qual file it is facing this error and got aborted.

Thanks and regards,


Sharmistha



















On Fri, Oct 2, 2009 at 5:07 PM, Lionel Guy <guy.lionel@xxxxxxxxx> wrote: From what Bastien said, use the fastq file as input (if if is a true fastq file). Don't forget to rename your qual file (cotton_in.solexa.fasta.qual, now, or cotton.fastq, I don't know) as cotton_in.solexa.fastq
And run:
mira -fastq --project=cotton --job=mapping,genome,accurate,solexa - AS:nop=1 -SB:lsd=yes:bsn=cotton_ref:bft=gbf:bbq=30 >&log_assembly.txt

If that doesn't work again, please copy paste the error message, the command you type, and the first ten lines of your qual file (cotton_in.solexa.fastq).

I would really suggest that you read the different manuals... 
http://chevreux.org/mira_manuals.html

Lionel


On 2 Oct 2009, at 13:18 , Sharmista Saha wrote:

Hi All,

Thanks a lot for your guidance.

As you said, I renamed the respective file and now could proceed, but still the program aborted,

which shows in the log file as follows:
Loading quality data from FASTA quality file cotton_in.solexa.fasta.qual:

Fatal Error: "Illegal character (@: 40) at begin of fasta integer value sequence in file at byte position 1"
->Thrown: void FASTA::loadNextINTSeq(ifstream & fin, int32 maxvalue)
->Caught: Assembly::loadFASTA(const string & fastafile, const string & fastaqualfile, const uint8 readtype, const uint8 loadaction)
Program aborted.
CWD: /home/sharmistha/Sharmistha/Bioinfo/Project_data/Cotton_data/ mira_3rc2_dev_linux-gnu_i686_32_static/bin/Dataform

which as Lionel said and I also felt earlier is cause of
mira expects the quality file to contain Solexa scores (but only one per base), not phred style quality scores. Should you have already the scores already converted to phred style, you will need to set - LR:ssiqf=no.

so, how and where exactly to apply the given -LR:ssiqf=no. so that my phred scores are converted in fasta.qual file into solexa scores? if you can guide me, it will be good.

Thanks and regards,
Sharmistha


On Fri, Oct 2, 2009 at 4:12 PM, Bastien Chevreux <bach@xxxxxxxxxxxx> wrote:
> Fatal Error: "cotton_in.solexa.fasta"

Well, there indeed is no such file in the directory listing you gave, so mira correctly could not find it: your listing shows a "cotton.fasta" and a "cotton.fastq".

Why didn't you name one of the files as shown in the walkthrough?

Regards,
 Bastien

PS: I also notice that there is no FASTA quality file belonging to the FASTA. You should always have a quality file. PPS: Or use the fastq as input (that is, if it contains the same data as the fasta)



============================================
Lionel Guy
Thunmansgatan 25, SE-75421 Uppsala

phone: +46 (0)18 245596
mobile: +46 (0)73 9760618
email: guy.lionel@xxxxxxxxx
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============================================
Lionel Guy
Thunmansgatan 25, SE-75421 Uppsala

phone: +46 (0)18 245596
mobile: +46 (0)73 9760618
email: guy.lionel@xxxxxxxxx
============================================


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