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 Mapped72487183.181%
Wrongly Mapped9990811.465%
Not Mapped466545.354%
Total871433100.0%
Read Failure Statistics
Not mapped466545.354%
Missing in mapper output00.0%
Mapped to wrong chromosome834749.579%
Mapped to wrong position164301.885%
Mapped to wrong strand40.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.908200
Precision0.878900
Recall0.939500
Timing
Raw Mapping Time278.484s
Effective Mapping Time273.444s
Effective Init Time5.040s
Effective Time MeasureCPU
Mapping Time (Wall)88.719s
Mapping Time (CPU)278.484s
Mapping Time (CPU User)264.616s
Mapping Time (CPU System)13.868s
Init Time (Wall)5.118s
Init Time (CPU)5.040s
Init Time (CPU User)0.076s
Init Time (CPU System)4.964s
Additional Information
Mapper Memory Usage7471 MB
Total Test Runtime (Wall)180.245s
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
memory5364616000
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, 0.002 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: 5.112 sec; CPU: 5.028 sec
systime4.884
time5.15224099159
usrtime0.164
working_directory/project/teaser/genometeaser/tests_generated/913dd6b6c8f0bd5901b65d962c7cd698

/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
memory5365820000
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: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa mem -t 4 /project/teaser/genometeaser/references/H_sapiens.fa reads_base.fastq
[main] Real time: 5.088 sec; CPU: 5.016 sec
systime4.964
time5.11829590797
usrtime0.076
working_directory/project/teaser/genometeaser/tests_generated/913dd6b6c8f0bd5901b65d962c7cd698

/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
memory7471808000
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 271.840 CPU sec, 69.059 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: 88.345 sec; CPU: 278.468 sec
systime13.868
time88.7188689709
usrtime264.616
working_directory/project/teaser/genometeaser/tests_generated/913dd6b6c8f0bd5901b65d962c7cd698