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 Mapped69336588.407%
Wrongly Mapped8157310.401%
Not Mapped93521.192%
Total784290100.0%
Read Failure Statistics
Not mapped93521.192%
Missing in mapper output00.0%
Mapped to wrong chromosome666058.492%
Mapped to wrong position149641.908%
Mapped to wrong strand40.001%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.938500
Precision0.894700
Recall0.986700
Timing
Raw Mapping Time221.212s
Effective Mapping Time216.864s
Effective Init Time4.348s
Effective Time MeasureCPU
Mapping Time (Wall)71.646s
Mapping Time (CPU)221.212s
Mapping Time (CPU User)209.436s
Mapping Time (CPU System)11.776s
Init Time (Wall)4.419s
Init Time (CPU)4.348s
Init Time (CPU User)0.092s
Init Time (CPU System)4.256s
Additional Information
Mapper Memory Usage7081 MB
Total Test Runtime (Wall)164.602s
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
memory5364632000
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 0.068 CPU sec, 0.065 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: 4.470 sec; CPU: 4.408 sec
systime4.316
time4.58320999146
usrtime0.116
working_directory/project/teaser/genometeaser/tests_generated/d355779ac9fa0c29904cf2683bc616bd

/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 0.064 CPU sec, 0.061 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: 4.387 sec; CPU: 4.332 sec
systime4.256
time4.41873788834
usrtime0.092
working_directory/project/teaser/genometeaser/tests_generated/d355779ac9fa0c29904cf2683bc616bd

/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
memory7081784000
return0
status1
stderr
None
stdout
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 784290 sequences (31371600 bp)...
[M::mem_process_seqs] Processed 784290 reads in 215.276 CPU sec, 54.743 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: 71.587 sec; CPU: 221.192 sec
systime11.776
time71.645802021
usrtime209.436
working_directory/project/teaser/genometeaser/tests_generated/d355779ac9fa0c29904cf2683bc616bd