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 Mapped71765882.354%
Wrongly Mapped9998711.474%
Not Mapped537886.172%
Total871433100.0%
Read Failure Statistics
Not mapped537886.172%
Missing in mapper output00.0%
Mapped to wrong chromosome832629.555%
Mapped to wrong position167231.919%
Mapped to wrong strand20.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.903200
Precision0.877700
Recall0.930300
Timing
Raw Mapping Time313.064s
Effective Mapping Time268.264s
Effective Init Time44.800s
Effective Time MeasureCPU
Mapping Time (Wall)113.289s
Mapping Time (CPU)313.064s
Mapping Time (CPU User)248.388s
Mapping Time (CPU System)64.676s
Init Time (Wall)44.923s
Init Time (CPU)44.800s
Init Time (CPU User)0.048s
Init Time (CPU System)44.752s
Additional Information
Mapper Memory Usage7441 MB
Total Test Runtime (Wall)244.539s
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
memory5364432000
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 0.004 CPU sec, 0.004 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: 48.157 sec; CPU: 48.044 sec
systime48.044
time48.1779658794
usrtime0.012
working_directory/project/teaser/genometeaser/tests_generated/dbe9c301671e3f72d169833f77afc52d

/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
memory5364592000
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, 0.010 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: 44.894 sec; CPU: 44.788 sec
systime44.752
time44.9228022099
usrtime0.048
working_directory/project/teaser/genometeaser/tests_generated/dbe9c301671e3f72d169833f77afc52d

/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
memory7441768000
return0
status1
stderr
None
stdout
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 871433 sequences (31371588 bp)...
[M::mem_process_seqs] Processed 871433 reads in 269.988 CPU sec, 68.696 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: 113.246 sec; CPU: 313.024 sec
systime64.676
time113.288691998
usrtime248.388
working_directory/project/teaser/genometeaser/tests_generated/dbe9c301671e3f72d169833f77afc52d