MIRA question

[kmkocot]

Hi all,

I'm trying to make contigs out of Illumina transcriptome data using MIRA but I keep getting an error.

Command used:

mira -fastq=SRR016565_1.fastq -project=Project --job=denovo,est,normal,solid -lowqualitydata -LR:external_quality=none -LR:load_sequence_data=yes

Error:

Internal logic/programming/debugging error (*sigh* this should not have happened).
Please contact the author: [email protected]
"No input to load or no sequences in input files? Did you provide data to load?"
->Thrown: void Assembly::loadSequenceData()
->Caught: main
Program aborted.
CWD: /home/labgroup/Desktop/Project_Illumina_transcriptome_data
Aborted

Can anyone tell me what I'm doing wrong? My intput files are fastq formatted like this:

@SRR016565.84 BI:081230_SL-XAQ_0001_FC30M3RAAXX:2:1:1:1475 length=76
NTAANGCTTAGGGCGTGGCNNTTGNTTTTTTGTAGTTAATGTGAACAGTTTTAACTCATTGANNACTCANNTNCCG
+SRR016565.84 BI:081230_SL-XAQ_0001_FC30M3RAAXX:2:1:1:1475 length=76
!)99!//3//;3+#3%I6)!!8.A!0&9(0)(0.5%,&041+/0)+*-'&1,-1*2'*+%*.!!+*,+%!!&!'(%

Thanks!
Kevin

[maubp]

I'd have asked on the MIRA mailing list - the author seems very responsive:

http://chevreux.org/mira_mailinglists.html

You should also give the precise version of MIRA you are using, and other details like the OS could be important.

[kmkocot]

Thanks,

I'll try the mailing list. I was hoping it was something really silly I was forgetting.

FWIW, I'm using Ubuntu 9.10 and I have the most recent version of MIRA as of yesterday.

Thanks,
Kevin