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 Mapped71316888.438%
Wrongly Mapped9308311.543%
Not Mapped1530.019%
Total806404100.0%
Read Failure Statistics
Not mapped1530.019%
Missing in mapper output00.0%
Mapped to wrong chromosome541656.717%
Mapped to wrong position389174.826%
Mapped to wrong strand10.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments6
F-Measure0.938600
Precision0.884500
Recall0.999800
Timing
Raw Mapping Time346.280s
Effective Mapping Time338.724s
Effective Init Time7.556s
Effective Time MeasureCPU
Mapping Time (Wall)108.306s
Mapping Time (CPU)346.280s
Mapping Time (CPU User)325.168s
Mapping Time (CPU System)21.112s
Init Time (Wall)7.650s
Init Time (CPU)7.556s
Init Time (CPU User)0.132s
Init Time (CPU System)7.424s
Additional Information
Mapper Memory Usage10266 MB
Total Test Runtime (Wall)221.886s
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
memory8271652000
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 0.076 CPU sec, 0.076 real sec
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa mem -t 4 /project/teaser/genometeaser/references/M_musculus.fasta reads_base.fastq
[main] Real time: 7.596 sec; CPU: 7.528 sec
systime7.38
time7.61875104904
usrtime0.164
working_directory/project/teaser/genometeaser/tests_generated/023be73dabd493f04945e37217bf7c31

/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
memory8271640000
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 0.084 CPU sec, 0.080 real sec
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa mem -t 4 /project/teaser/genometeaser/references/M_musculus.fasta reads_base.fastq
[main] Real time: 7.627 sec; CPU: 7.540 sec
systime7.424
time7.65015912056
usrtime0.132
working_directory/project/teaser/genometeaser/tests_generated/023be73dabd493f04945e37217bf7c31

/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
memory10266008000
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 274.008 CPU sec, 69.574 real sec
[M::mem_process_seqs] Processed 139736 reads in 62.620 CPU sec, 15.394 real sec
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa mem -t 4 /project/teaser/genometeaser/references/M_musculus.fasta reads.fastq
[main] Real time: 108.155 sec; CPU: 346.144 sec
systime21.112
time108.305787802
usrtime325.168
working_directory/project/teaser/genometeaser/tests_generated/023be73dabd493f04945e37217bf7c31