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 Mapped50314796.23%
Wrongly Mapped197133.77%
Not Mapped00.0%
Total522860100.0%
Read Failure Statistics
Not mapped00.0%
Missing in mapper output00.0%
Mapped to wrong chromosome128962.466%
Mapped to wrong position68171.304%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.980800
Precision0.962300
Recall1.000000
Timing
Raw Mapping Time178.644s
Effective Mapping Time173.920s
Effective Init Time4.724s
Effective Time MeasureCPU
Mapping Time (Wall)59.913s
Mapping Time (CPU)178.644s
Mapping Time (CPU User)168.312s
Mapping Time (CPU System)10.332s
Init Time (Wall)4.791s
Init Time (CPU)4.724s
Init Time (CPU User)0.112s
Init Time (CPU System)4.612s
Additional Information
Mapper Memory Usage6193 MB
Total Test Runtime (Wall)123.017s
Mapper Command Line: 
/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/H_sapiens.fa 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/H_sapiens.fa reads_base.fastq -t 4 > out_bwamem.sam

command/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/H_sapiens.fa reads_base.fastq -t 4 > out_bwamem.sam
memory5367872000
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 0.012 CPU sec, 0.008 real sec
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa mem -t 4 /project/teaser/genometeaser/references/H_sapiens.fa reads_base.fastq
[main] Real time: 4.798 sec; CPU: 4.748 sec
systime4.656
time4.82061004639
usrtime0.104
working_directory/project/teaser/genometeaser/tests_generated/293e14569a4a233bf507f46e325e460e

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

command/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/H_sapiens.fa reads_base.fastq -t 4 > out_bwamem.sam
memory5364628000
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 0.008 CPU sec, 0.005 real sec
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa mem -t 4 /project/teaser/genometeaser/references/H_sapiens.fa reads_base.fastq
[main] Real time: 4.770 sec; CPU: 4.716 sec
systime4.612
time4.79088592529
usrtime0.112
working_directory/project/teaser/genometeaser/tests_generated/293e14569a4a233bf507f46e325e460e

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

command/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/H_sapiens.fa reads1.fastq reads2.fastq -t 4 > out_bwamem.sam
memory6193372000
return0
status1
stderr
None
stdout
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 522860 sequences (31371600 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 210531, 271, 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: (76, 98, 120)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 208)
[M::mem_pestat] mean and std.dev: (98.05, 32.37)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 252)
[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 522860 reads in 172.756 CPU sec, 44.000 real sec
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa mem -t 4 /project/teaser/genometeaser/references/H_sapiens.fa reads1.fastq reads2.fastq
[main] Real time: 59.867 sec; CPU: 178.612 sec
systime10.332
time59.9133601189
usrtime168.312
working_directory/project/teaser/genometeaser/tests_generated/293e14569a4a233bf507f46e325e460e