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 Mapped52916088.362%
Wrongly Mapped6961111.624%
Not Mapped870.015%
Total598858100.0%
Read Failure Statistics
Not mapped870.015%
Missing in mapper output00.0%
Mapped to wrong chromosome411966.879%
Mapped to wrong position284154.745%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.938200
Precision0.883700
Recall0.999800
Timing
Raw Mapping Time121.832s
Effective Mapping Time118.164s
Effective Init Time3.668s
Effective Time MeasureCPU
Mapping Time (Wall)45.233s
Mapping Time (CPU)121.832s
Mapping Time (CPU User)111.512s
Mapping Time (CPU System)10.320s
Init Time (Wall)3.779s
Init Time (CPU)3.668s
Init Time (CPU User)0.016s
Init Time (CPU System)3.652s
Additional Information
Mapper Memory Usage892 MB
Total Test Runtime (Wall)125.142s
Mapper Command Line: 
/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/D_melanogaster.fasta 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/D_melanogaster.fasta reads_base.fastq -t 4 > out_bwamem.sam

command/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/D_melanogaster.fasta reads_base.fastq -t 4 > out_bwamem.sam
memory248852000
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, 0.003 real sec
[main] Version: 0.7.12-r1039
[main] CMD: /project/teaser/genometeaser/software/bwa mem -t 4 /project/teaser/genometeaser/references/D_melanogaster.fasta reads_base.fastq
[main] Real time: 3.383 sec; CPU: 3.304 sec
systime3.316
time3.40553283691
usrtime0.008
working_directory/project/teaser/genometeaser/tests_generated/370d4fd7160225b686abe184c6e4adf0

/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/D_melanogaster.fasta reads_base.fastq -t 4 > out_bwamem.sam

command/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/D_melanogaster.fasta reads_base.fastq -t 4 > out_bwamem.sam
memory248852000
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, 0.004 real sec
[main] Version: 0.7.12-r1039
[main] CMD: /project/teaser/genometeaser/software/bwa mem -t 4 /project/teaser/genometeaser/references/D_melanogaster.fasta reads_base.fastq
[main] Real time: 3.748 sec; CPU: 3.652 sec
systime3.652
time3.77928996086
usrtime0.016
working_directory/project/teaser/genometeaser/tests_generated/370d4fd7160225b686abe184c6e4adf0

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

command/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/D_melanogaster.fasta reads.fastq -t 4 > out_bwamem.sam
memory892568000
return0
status1
stderr
None
stdout
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 598858 sequences (35931480 bp)...
[M::mem_process_seqs] Processed 598858 reads in 116.480 CPU sec, 29.654 real sec
[main] Version: 0.7.12-r1039
[main] CMD: /project/teaser/genometeaser/software/bwa mem -t 4 /project/teaser/genometeaser/references/D_melanogaster.fasta reads.fastq
[main] Real time: 45.186 sec; CPU: 121.784 sec
systime10.32
time45.233314991
usrtime111.512
working_directory/project/teaser/genometeaser/tests_generated/370d4fd7160225b686abe184c6e4adf0