[mira_talk] Solexa Mapping Runtime

Dear all,

I have started a mapping job with mira a couple of days ago and until
now it is not finished. I am wondering how long it will take. From the
manual I understood that a job like this would be finished in max two days.


Here are the details:

The computer is a Intel Xeon 2.13 GHz with 8 cores and 12 GB RAM. The
mira version is 3.2.0rc2 64 bit.

the job was started with:
./mira --project=K12mut --fastq --job=mapping,genome,accurate,solexa
-AS:nop=1 -SB:lsd=yes:bsn=K12_wt:bft=gbf:bbq=30 >&log_assembly.txt &


#####part of the log file for the detailed data of the reads and the
backbone:

Loading backbone from GBF file: K12mut_backbone_in.gbf
Done.
Adding sequences as backbones ...  done.
Postprocessing backbone (this may take a while)
1 to process
U00096_bb       4639675
Localtime: Fri Jul 30 14:14:51 2010

Seeing strain 1: "K12_wt"
Generated 1 unique strain ids for 1 reads.
Strain "default" has 0 reads.
Strain "K12_wt" has 1 reads.
Loading data (Solexa) from FASTQ files,
Counting sequences in FASTQ file: found 6826967 sequences.
Solexa will load 6826967 reads.
Longest Sanger: 0
Longest 454: 0
Longest PacBio: 0
Longest Solexa: 38
Longest Solid: 0
Longest overall: 38
Total reads to load: 6826967

#### the last statistics:
Contig id: 1
Contig length: 4640360

                      Sanger         454      PacBio      Solexa       Solid
Num. reads                 1           0           0       82089           0
100% merged reads          -           -           -     5399486           0
Avg. read len        4639675           0           0          36           0
Max. coverage              1           0           0         122           0
Avg. coverage          1.000       0.000       0.000      43.031       0.000

Max. contig coverage: 123
Avg. contig coverage: 44.031

Consensus contains:     A: 1142233      C: 1179561      G: 1176933     
T: 1140987      N: 0
                        IUPAC: 0        Funny: 0        *: 646
GC content: 50.790%

#### This is the last step:
Gogo: mapping all 4 errors
Localtime: Wed Aug  4 13:03:29 2010

Gogo: mapping all 5 errors
Localtime: Thu Aug  5 06:39:02 2010

So it needed ~17h for this step.


Is there something wrong with the data? How many steps should still come?

best regards


Christian

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