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 Mapped57783292.095%
Wrongly Mapped488317.783%
Not Mapped7690.123%
Total627432100.0%
Read Failure Statistics
Not mapped7690.123%
Missing in mapper output00.0%
Mapped to wrong chromosome380306.061%
Mapped to wrong position108001.721%
Mapped to wrong strand10.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments1
F-Measure0.958800
Precision0.922100
Recall0.998700
Timing
Raw Mapping Time184.988s
Effective Mapping Time180.464s
Effective Init Time4.524s
Effective Time MeasureCPU
Mapping Time (Wall)60.756s
Mapping Time (CPU)184.988s
Mapping Time (CPU User)173.480s
Mapping Time (CPU System)11.508s
Init Time (Wall)4.587s
Init Time (CPU)4.524s
Init Time (CPU User)0.080s
Init Time (CPU System)4.444s
Additional Information
Mapper Memory Usage6565 MB
Total Test Runtime (Wall)138.945s
Mapper Command Line: 
/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/H_sapiens.fa reads.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
memory5365816000
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 0.068 CPU sec, 0.066 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: 4.542 sec; CPU: 4.484 sec
systime4.42
time4.57152605057
usrtime0.088
working_directory/project/teaser/genometeaser/tests_generated/0ae17b2547a4a7bf1a0dbd8dcfe180bb

/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, 0.065 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: 4.558 sec; CPU: 4.508 sec
systime4.444
time4.58704900742
usrtime0.08
working_directory/project/teaser/genometeaser/tests_generated/0ae17b2547a4a7bf1a0dbd8dcfe180bb

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

command/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/H_sapiens.fa reads.fastq -t 4 > out_bwamem.sam
memory6565224000
return0
status1
stderr
None
stdout
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 627432 sequences (31371600 bp)...
[M::mem_process_seqs] Processed 627432 reads in 180.000 CPU sec, 45.929 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.fastq
[main] Real time: 60.703 sec; CPU: 184.968 sec
systime11.508
time60.7560679913
usrtime173.48
working_directory/project/teaser/genometeaser/tests_generated/0ae17b2547a4a7bf1a0dbd8dcfe180bb