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 Mapped30548797.378%
Wrongly Mapped82262.622%
Not Mapped00.0%
Total313713100.0%
Read Failure Statistics
Not mapped00.0%
Missing in mapper output00.0%
Mapped to wrong chromosome51791.651%
Mapped to wrong position30470.971%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment3
Secondary Alignments3
F-Measure0.986700
Precision0.973800
Recall1.000000
Timing
Raw Mapping Time161.859s
Effective Mapping Time158.982s
Effective Init Time2.878s
Effective Time MeasureCPU
Mapping Time (Wall)44.368s
Mapping Time (CPU)161.859s
Mapping Time (CPU User)158.625s
Mapping Time (CPU System)3.235s
Init Time (Wall)2.922s
Init Time (CPU)2.878s
Init Time (CPU User)0.062s
Init Time (CPU System)2.816s
Additional Information
Mapper Memory Usage5823 MB
Total Test Runtime (Wall)63.073s
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
memory5362944000
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 0.002 CPU sec, 0.011 real sec
[main] Version: 0.7.12-r1039
[main] CMD: /project/teaser/genometeaser/software/bwa mem -t 4 /project/teaser/genometeaser/references/H_sapiens.fa reads_base.fastq
[main] Real time: 2.921 sec; CPU: 2.865 sec
systime2.82257
time2.92810893059
usrtime0.048992
working_directory/project/teaser/genometeaser/tests_generated/cc90747119948fac5bcca0e53c33f3a3

/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
memory5362944000
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 0.002 CPU sec, 0.001 real sec
[main] Version: 0.7.12-r1039
[main] CMD: /project/teaser/genometeaser/software/bwa mem -t 4 /project/teaser/genometeaser/references/H_sapiens.fa reads_base.fastq
[main] Real time: 2.916 sec; CPU: 2.871 sec
systime2.815571
time2.92200398445
usrtime0.06199
working_directory/project/teaser/genometeaser/tests_generated/cc90747119948fac5bcca0e53c33f3a3

/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
memory5823536000
return0
status1
stderr
None
stdout
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 313716 sequences (31371600 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 137345, 0, 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: (148, 178, 210)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (24, 334)
[M::mem_pestat] mean and std.dev: (180.87, 43.49)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 396)
[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 313716 reads in 158.572 CPU sec, 39.833 real sec
[main] Version: 0.7.12-r1039
[main] CMD: /project/teaser/genometeaser/software/bwa mem -t 4 /project/teaser/genometeaser/references/H_sapiens.fa reads1.fastq reads2.fastq
[main] Real time: 44.356 sec; CPU: 161.848 sec
systime3.234508
time44.3682911396
usrtime158.624885
working_directory/project/teaser/genometeaser/tests_generated/cc90747119948fac5bcca0e53c33f3a3