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/Dataformwhich as Lionel said and I also felt earlier is cause ofmira 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, SharmisthaOn 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, BastienPS: 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)
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