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 Mapped71725182.307%
Wrongly Mapped10054511.538%
Not Mapped536376.155%
Total871433100.0%
Read Failure Statistics
Not mapped536376.155%
Missing in mapper output00.0%
Mapped to wrong chromosome840879.649%
Mapped to wrong position164541.888%
Mapped to wrong strand40.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.902900
Precision0.877100
Recall0.930400
Timing
Raw Mapping Time442.664s
Effective Mapping Time348.252s
Effective Init Time94.412s
Effective Time MeasureCPU
Mapping Time (Wall)196.704s
Mapping Time (CPU)442.664s
Mapping Time (CPU User)293.008s
Mapping Time (CPU System)149.656s
Init Time (Wall)95.683s
Init Time (CPU)94.412s
Init Time (CPU User)0.012s
Init Time (CPU System)94.400s
Additional Information
Mapper Memory Usage7443 MB
Total Test Runtime (Wall)460.849s
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
memory5364348000
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 0.024 CPU sec, 0.021 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: 96.456 sec; CPU: 95.276 sec
systime95.236
time96.5083239079
usrtime0.06
working_directory/project/teaser/genometeaser/tests_generated/49efbf792a671892244ba9297cc6202a

/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
memory5364348000
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, 0.010 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: 95.650 sec; CPU: 94.388 sec
systime94.4
time95.6825799942
usrtime0.012
working_directory/project/teaser/genometeaser/tests_generated/49efbf792a671892244ba9297cc6202a

/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
memory7443952000
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 348.184 CPU sec, 89.291 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: 196.544 sec; CPU: 442.640 sec
systime149.656
time196.703746796
usrtime293.008
working_directory/project/teaser/genometeaser/tests_generated/49efbf792a671892244ba9297cc6202a