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 Mapped7510.125%
Wrongly Mapped59673899.646%
Not Mapped13690.229%
Total598858100.0%
Read Failure Statistics
Not mapped13690.229%
Missing in mapper output00.0%
Mapped to wrong chromosome49022581.86%
Mapped to wrong position10651317.786%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.002500
Precision0.001300
Recall0.354200
Timing
Raw Mapping Time75.204s
Effective Mapping Time75.061s
Effective Init Time0.143s
Effective Time MeasureCPU
Mapping Time (Wall)21.626s
Mapping Time (CPU)75.204s
Mapping Time (CPU User)74.473s
Mapping Time (CPU System)0.731s
Init Time (Wall)0.179s
Init Time (CPU)0.143s
Init Time (CPU User)0.006s
Init Time (CPU System)0.137s
Additional Information
Mapper Memory Usage960 MB
Total Test Runtime (Wall)48.058s
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
memory247124000
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, 0.002 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: 0.173 sec; CPU: 0.140 sec
systime0.141978
time0.177906036377
usrtime0.002999
working_directory/project/teaser/genometeaser/tests_generated/3d3edd8a6a451905ff28f5063d73cc4e

/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
memory247124000
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 0.001 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/D_melanogaster.fasta reads_base.fastq
[main] Real time: 0.174 sec; CPU: 0.139 sec
systime0.136979
time0.178997993469
usrtime0.005999
working_directory/project/teaser/genometeaser/tests_generated/3d3edd8a6a451905ff28f5063d73cc4e

/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
memory960224000
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 74.340 CPU sec, 18.925 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: 21.614 sec; CPU: 75.193 sec
systime0.730888
time21.6257688999
usrtime74.472678
working_directory/project/teaser/genometeaser/tests_generated/3d3edd8a6a451905ff28f5063d73cc4e