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 Mapped71351888.481%
Wrongly Mapped9275111.502%
Not Mapped1350.017%
Total806404100.0%
Read Failure Statistics
Not mapped1350.017%
Missing in mapper output00.0%
Mapped to wrong chromosome548236.798%
Mapped to wrong position379284.703%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments7
F-Measure0.938900
Precision0.885000
Recall0.999800
Timing
Raw Mapping Time731.988s
Effective Mapping Time469.856s
Effective Init Time262.132s
Effective Time MeasureCPU
Mapping Time (Wall)338.868s
Mapping Time (CPU)731.988s
Mapping Time (CPU User)459.600s
Mapping Time (CPU System)272.388s
Init Time (Wall)265.181s
Init Time (CPU)262.132s
Init Time (CPU User)0.100s
Init Time (CPU System)262.032s
Additional Information
Mapper Memory Usage10273 MB
Total Test Runtime (Wall)985.010s
Mapper Command Line: 
/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/M_musculus.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/M_musculus.fasta reads_base.fastq -t 4 > out_bwamem.sam

command/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/M_musculus.fasta reads_base.fastq -t 4 > out_bwamem.sam
memory8271708000
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 0.048 CPU sec, 0.048 real sec
[main] Version: 0.7.12-r1039
[main] CMD: /project/teaser/genometeaser/software/bwa mem -t 4 /project/teaser/genometeaser/references/M_musculus.fasta reads_base.fastq
[main] Real time: 274.684 sec; CPU: 271.376 sec
systime271.336
time274.709550142
usrtime0.064
working_directory/project/teaser/genometeaser/tests_generated/a720be7d510db33409606fe9fee515f7

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

command/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/M_musculus.fasta reads_base.fastq -t 4 > out_bwamem.sam
memory8271708000
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, 0.010 real sec
[main] Version: 0.7.12-r1039
[main] CMD: /project/teaser/genometeaser/software/bwa mem -t 4 /project/teaser/genometeaser/references/M_musculus.fasta reads_base.fastq
[main] Real time: 265.149 sec; CPU: 262.112 sec
systime262.032
time265.181059122
usrtime0.1
working_directory/project/teaser/genometeaser/tests_generated/a720be7d510db33409606fe9fee515f7

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

command/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/M_musculus.fasta reads.fastq -t 4 > out_bwamem.sam
memory10273208000
return0
status1
stderr
None
stdout
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 666668 sequences (40000080 bp)...
[M::process] read 139736 sequences (8384160 bp)...
[M::mem_process_seqs] Processed 666668 reads in 419.124 CPU sec, 107.460 real sec
[M::mem_process_seqs] Processed 139736 reads in 114.680 CPU sec, 28.383 real sec
[main] Version: 0.7.12-r1039
[main] CMD: /project/teaser/genometeaser/software/bwa mem -t 4 /project/teaser/genometeaser/references/M_musculus.fasta reads.fastq
[main] Real time: 338.569 sec; CPU: 731.720 sec
systime272.388
time338.86785388
usrtime459.6
working_directory/project/teaser/genometeaser/tests_generated/a720be7d510db33409606fe9fee515f7