Mapping Quality Thresholds

The plot below shows the percentages of correctly and wrongly mapped reads for all mapping quality thresholds for this mapper. The values at threshold 0 therefore correspond to the unfiltered results.

Basic Statistics
Correctly Mapped16669193.711%
Wrongly Mapped111876.289%
Not Mapped00.0%
Total177878100.0%
Read Failure Statistics
Not mapped00.0%
Missing in mapper output00.0%
Mapped to wrong chromosome57583.237%
Mapped to wrong position54293.052%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.967500
Precision0.937100
Recall1.000000
Timing
Raw Mapping Time134.788s
Effective Mapping Time131.212s
Effective Init Time3.576s
Effective Time MeasureCPU
Mapping Time (Wall)43.375s
Mapping Time (CPU)134.788s
Mapping Time (CPU User)130.560s
Mapping Time (CPU System)4.228s
Init Time (Wall)3.688s
Init Time (CPU)3.576s
Init Time (CPU User)0.012s
Init Time (CPU System)3.564s
Additional Information
Mapper Memory Usage452 MB
Total Test Runtime (Wall)87.986s
Mapper Command Line: 
/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/D_melanogaster.fasta reads1.fastq reads2.fastq -t 4 > out_bwamem.sam
Errors and Warnings
No problems were encountered.
Subprocess Log

/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/D_melanogaster.fasta reads_base.fastq -t 4 > out_bwamem.sam

command/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/D_melanogaster.fasta reads_base.fastq -t 4 > out_bwamem.sam
memory248860000
return0
status1
stderr
None
stdout
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 1 sequences (60 bp)...
[M::mem_process_seqs] Processed 1 reads in 0.000 CPU sec, 0.002 real sec
[main] Version: 0.7.12-r1039
[main] CMD: /project/teaser/genometeaser/software/bwa mem -t 4 /project/teaser/genometeaser/references/D_melanogaster.fasta reads_base.fastq
[main] Real time: 5.128 sec; CPU: 5.008 sec
systime4.992
time5.17856407166
usrtime0.028
working_directory/project/teaser/genometeaser/tests_generated/e06f9a576d69697f7ad166f2c53eac4f

/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/D_melanogaster.fasta reads_base.fastq -t 4 > out_bwamem.sam

command/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/D_melanogaster.fasta reads_base.fastq -t 4 > out_bwamem.sam
memory250752000
return0
status1
stderr
None
stdout
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 1 sequences (60 bp)...
[M::mem_process_seqs] Processed 1 reads in 0.024 CPU sec, 0.024 real sec
[main] Version: 0.7.12-r1039
[main] CMD: /project/teaser/genometeaser/software/bwa mem -t 4 /project/teaser/genometeaser/references/D_melanogaster.fasta reads_base.fastq
[main] Real time: 3.656 sec; CPU: 3.568 sec
systime3.564
time3.68784308434
usrtime0.012
working_directory/project/teaser/genometeaser/tests_generated/e06f9a576d69697f7ad166f2c53eac4f

/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/D_melanogaster.fasta reads1.fastq reads2.fastq -t 4 > out_bwamem.sam

command/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/D_melanogaster.fasta reads1.fastq reads2.fastq -t 4 > out_bwamem.sam
memory452076000
return0
status1
stderr
None
stdout
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 177878 sequences (35931356 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 74359, 58, 0)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (79, 101, 123)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 211)
[M::mem_pestat] mean and std.dev: (100.96, 32.67)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 255)
[M::mem_pestat] analyzing insert size distribution for orientation RF...
[M::mem_pestat] (25, 50, 75) percentile: (1, 1, 1)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1)
[M::mem_pestat] mean and std.dev: (1.00, 0.00)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1)
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_pestat] skip orientation RF
[M::mem_process_seqs] Processed 177878 reads in 132.376 CPU sec, 33.319 real sec
[main] Version: 0.7.12-r1039
[main] CMD: /project/teaser/genometeaser/software/bwa mem -t 4 /project/teaser/genometeaser/references/D_melanogaster.fasta reads1.fastq reads2.fastq
[main] Real time: 43.288 sec; CPU: 134.748 sec
systime4.228
time43.3752119541
usrtime130.56
working_directory/project/teaser/genometeaser/tests_generated/e06f9a576d69697f7ad166f2c53eac4f