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 Mapped83313595.605%
Wrongly Mapped377154.328%
Not Mapped5820.067%
Total871432100.0%
Read Failure Statistics
Not mapped5820.067%
Missing in mapper output00.0%
Mapped to wrong chromosome254822.924%
Mapped to wrong position122331.404%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.977500
Precision0.956700
Recall0.999300
Timing
Raw Mapping Time448.232s
Effective Mapping Time443.676s
Effective Init Time4.556s
Effective Time MeasureCPU
Mapping Time (Wall)131.173s
Mapping Time (CPU)448.232s
Mapping Time (CPU User)432.824s
Mapping Time (CPU System)15.408s
Init Time (Wall)4.634s
Init Time (CPU)4.556s
Init Time (CPU User)0.196s
Init Time (CPU System)4.360s
Additional Information
Mapper Memory Usage7438 MB
Total Test Runtime (Wall)239.373s
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
memory5365820000
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 0.064 CPU sec, 0.063 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: 4.605 sec; CPU: 4.544 sec
systime4.46
time4.62772297859
usrtime0.092
working_directory/project/teaser/genometeaser/tests_generated/ab0014cf05e86cd590ae0b3283410abf

/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 0.064 CPU sec, 0.060 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: 4.604 sec; CPU: 4.544 sec
systime4.36
time4.63436412811
usrtime0.196
working_directory/project/teaser/genometeaser/tests_generated/ab0014cf05e86cd590ae0b3283410abf

/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
memory7438300000
return0
status1
stderr
None
stdout
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 871432 sequences (31371552 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 286425, 0, 1)
[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: (176, 198, 220)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (88, 308)
[M::mem_pestat] mean and std.dev: (198.05, 32.78)
[M::mem_pestat] low and high boundaries for proper pairs: (44, 352)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 871432 reads in 441.724 CPU sec, 111.517 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: 131.115 sec; CPU: 448.224 sec
systime15.408
time131.172626019
usrtime432.824
working_directory/project/teaser/genometeaser/tests_generated/ab0014cf05e86cd590ae0b3283410abf