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 Mapped52846984.227%
Wrongly Mapped479537.643%
Not Mapped510108.13%
Total627432100.0%
Read Failure Statistics
Not mapped510108.13%
Missing in mapper output00.0%
Mapped to wrong chromosome379916.055%
Mapped to wrong position99621.588%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment14
Secondary Alignments0
F-Measure0.914400
Precision0.916800
Recall0.912000
Timing
Raw Mapping Time242.160s
Effective Mapping Time237.620s
Effective Init Time4.540s
Effective Time MeasureCPU
Mapping Time (Wall)113.065s
Mapping Time (CPU)242.160s
Mapping Time (CPU User)226.612s
Mapping Time (CPU System)15.548s
Init Time (Wall)4.728s
Init Time (CPU)4.540s
Init Time (CPU User)0.112s
Init Time (CPU System)4.428s
Additional Information
Mapper Memory Usage5800 MB
Total Test Runtime (Wall)189.323s
Mapper Command Line: 
/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/H_sapiens.fa reads.fastq -t 4 > out_bwasw.sam
Errors and Warnings
No problems were encountered.
Subprocess Log

/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/H_sapiens.fa reads_base.fastq -t 4 > out_bwasw.sam

command/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/H_sapiens.fa reads_base.fastq -t 4 > out_bwasw.sam
memory5364904000
return0
status1
stderr
None
stdout
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[bsw2_aln] read 1 sequences/pairs (60 bp) ...
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa bwasw -t 4 /project/teaser/genometeaser/references/H_sapiens.fa reads_base.fastq
[main] Real time: 4.574 sec; CPU: 4.516 sec
systime4.428
time4.68843793869
usrtime0.108
working_directory/project/teaser/genometeaser/tests_generated/0ae17b2547a4a7bf1a0dbd8dcfe180bb

/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/H_sapiens.fa reads_base.fastq -t 4 > out_bwasw.sam

command/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/H_sapiens.fa reads_base.fastq -t 4 > out_bwasw.sam
memory5366680000
return0
status1
stderr
None
stdout
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[bsw2_aln] read 1 sequences/pairs (60 bp) ...
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa bwasw -t 4 /project/teaser/genometeaser/references/H_sapiens.fa reads_base.fastq
[main] Real time: 4.580 sec; CPU: 4.524 sec
systime4.428
time4.72786808014
usrtime0.112
working_directory/project/teaser/genometeaser/tests_generated/0ae17b2547a4a7bf1a0dbd8dcfe180bb

/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/H_sapiens.fa reads.fastq -t 4 > out_bwasw.sam

command/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/H_sapiens.fa reads.fastq -t 4 > out_bwasw.sam
memory5800256000
return0
status1
stderr
None
stdout
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[bsw2_aln] read 627432 sequences/pairs (31371600 bp) ...
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa bwasw -t 4 /project/teaser/genometeaser/references/H_sapiens.fa reads.fastq
[main] Real time: 113.021 sec; CPU: 242.140 sec
systime15.548
time113.065080166
usrtime226.612
working_directory/project/teaser/genometeaser/tests_generated/0ae17b2547a4a7bf1a0dbd8dcfe180bb