Hi,
I am attempting to assemble the transcriptome of Nodipecten subnodosus using SRA and EST data. I have two files, one containing the 454 reads (all_reads.fastq) and one containing the concatenated EST and mRNA data (all_cdna.fasta). I am attempting to assemble these using MIRA 4.
When I attempt the assembly, I get the following error message:
Warning:
*******************************************************************************
* Number of bases in SCF file (contig00001.scf) does not correspond to the *
* number of bases expected in the read (read from fasta, exp, phd or caf *
* file). Read will _not_ be used in assembly! *
*******************************************************************************
The only two files I have given to MIRA are the fastq and fasta file, there is no SCF file. I am assuming MIRA is looking for the SCF file(s) which match with the fasta reads. ('contig00001.scf' is the first sequence header).
I have used -AS:epoq=no and also --noqualities=sanger, although nothing appears to be working. Is there a specific switch to prevent MIRA from looking for SCF file(s)?
Thanks. Below is my manifest.conf file using the --noqualities switch mentioned above (along with the default_qual option recommended in the documentation)
Lewis
project = nodi_test
job = est,denovo,accurate
parameters = -DI:trt:/tmp/mira_lstevens -AS:ugpf=no -HS:mnr=yes
parameters = SANGER_SETTINGS --noqualities
readgroup = 454_reads
data = /exports/projects/mollusc_db/bivalvia/454_EST/nodipecten_subnodosus/raw_data/files/all_reads.fastq
technology = 454
readgroup = est_sequences
data = /exports/projects/mollusc_db/bivalvia/454_EST/nodipecten_subnodosus/raw_data/files/all_cdna.replaced.fna
technology = sanger
default_qual = 30
have you tried the mira mailing list. They usually answer pretty fast...