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 Mapped69209788.245%
Wrongly Mapped8281510.559%
Not Mapped93781.196%
Total784290100.0%
Read Failure Statistics
Not mapped93781.196%
Missing in mapper output00.0%
Mapped to wrong chromosome675918.618%
Mapped to wrong position152211.941%
Mapped to wrong strand30.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.937600
Precision0.893100
Recall0.986600
Timing
Raw Mapping Time210.180s
Effective Mapping Time205.368s
Effective Init Time4.812s
Effective Time MeasureCPU
Mapping Time (Wall)67.912s
Mapping Time (CPU)210.180s
Mapping Time (CPU User)199.144s
Mapping Time (CPU System)11.036s
Init Time (Wall)4.878s
Init Time (CPU)4.812s
Init Time (CPU User)0.088s
Init Time (CPU System)4.724s
Additional Information
Mapper Memory Usage7102 MB
Total Test Runtime (Wall)144.753s
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
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 0.068 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: 4.849 sec; CPU: 4.784 sec
systime4.728
time4.97065114975
usrtime0.08
working_directory/project/teaser/genometeaser/tests_generated/550e44394139b4f9ff4d8f5d1ede8a8f

/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 0.060 CPU sec, 0.061 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: 4.841 sec; CPU: 4.792 sec
systime4.724
time4.87830400467
usrtime0.088
working_directory/project/teaser/genometeaser/tests_generated/550e44394139b4f9ff4d8f5d1ede8a8f

/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
memory7102956000
return0
status1
stderr
None
stdout
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 784290 sequences (31371600 bp)...
[M::mem_process_seqs] Processed 784290 reads in 205.352 CPU sec, 52.131 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: 67.855 sec; CPU: 210.164 sec
systime11.036
time67.9118602276
usrtime199.144
working_directory/project/teaser/genometeaser/tests_generated/550e44394139b4f9ff4d8f5d1ede8a8f