[mira_talk] Solexa Mapping Runtime
- From: Christian Schleberger <Christian.Schleberger@xxxxxxxxxxxxxxxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Thu, 05 Aug 2010 13:17:11 +0200
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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