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 Mapped13352389.015%
Wrongly Mapped33992.266%
Not Mapped130788.719%
Total150000100.0%
Read Failure Statistics
Not mapped130788.719%
Missing in mapper output00.0%
Mapped to wrong chromosome16211.081%
Mapped to wrong position17781.185%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.941900
Precision0.975200
Recall0.910800
Timing
Raw Mapping Time40.901s
Effective Mapping Time40.872s
Effective Init Time0.029s
Effective Time MeasureCPU
Mapping Time (Wall)44.493s
Mapping Time (CPU)40.901s
Mapping Time (CPU User)40.659s
Mapping Time (CPU System)0.242s
Init Time (Wall)0.099s
Init Time (CPU)0.029s
Init Time (CPU User)0.002s
Init Time (CPU System)0.027s
Additional Information
Mapper Memory Usage108 MB
Total Test Runtime (Wall)54.033s
Mapper Command Line: 
/project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/Schizosaccharomyces_pombe.fa reads.fastq -t 4 > out_bwa.sam.bwa; /project/teaser/genometeaser/software/bwa samse /project/teaser/genometeaser/references/Schizosaccharomyces_pombe.fa out_bwa.sam.bwa reads.fastq > out_bwa.sam
Errors and Warnings
No problems were encountered.
Subprocess Log

/project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/Schizosaccharomyces_pombe.fa reads_base.fastq -t 4 > out_bwa.sam.bwa; /project/teaser/genometeaser/software/bwa samse /project/teaser/genometeaser/references/Schizosaccharomyces_pombe.fa out_bwa.sam.bwa reads_base.fastq > out_bwa.sam

command/project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/Schizosaccharomyces_pombe.fa reads_base.fastq -t 4 > out_bwa.sam.bwa; /project/teaser/genometeaser/software/bwa samse /project/teaser/genometeaser/references/Schizosaccharomyces_pombe.fa out_bwa.sam.bwa reads_base.fastq > out_bwa.sam
memory22264000
return0
status1
stderr
None
stdout
[bwa_aln] 17bp reads: max_diff = 2
[bwa_aln] 38bp reads: max_diff = 3
[bwa_aln] 64bp reads: max_diff = 4
[bwa_aln] 93bp reads: max_diff = 5
[bwa_aln] 124bp reads: max_diff = 6
[bwa_aln] 157bp reads: max_diff = 7
[bwa_aln] 190bp reads: max_diff = 8
[bwa_aln] 225bp reads: max_diff = 9
[bwa_aln_core] calculate SA coordinate... 0.00 sec
[bwa_aln_core] write to the disk... 0.00 sec
[bwa_aln_core] 1 sequences have been processed.
[main] Version: 0.7.12-r1039
[main] CMD: /project/teaser/genometeaser/software/bwa aln -t 4 /project/teaser/genometeaser/references/Schizosaccharomyces_pombe.fa reads_base.fastq
[main] Real time: 0.196 sec; CPU: 0.010 sec
[bwa_aln_core] convert to sequence coordinate... 0.01 sec
[bwa_aln_core] refine gapped alignments... 0.00 sec
[bwa_aln_core] print alignments... 0.00 sec
[bwa_aln_core] 1 sequences have been processed.
[main] Version: 0.7.12-r1039
[main] CMD: /project/teaser/genometeaser/software/bwa samse /project/teaser/genometeaser/references/Schizosaccharomyces_pombe.fa out_bwa.sam.bwa reads_base.fastq
[main] Real time: 0.172 sec; CPU: 0.015 sec
systime0.028995
time0.377753019333
usrtime0.0
working_directory/project/teaser/genometeaser/tests_generated/78245a202e759eede079b41dad2c7157

/project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/Schizosaccharomyces_pombe.fa reads_base.fastq -t 4 > out_bwa.sam.bwa; /project/teaser/genometeaser/software/bwa samse /project/teaser/genometeaser/references/Schizosaccharomyces_pombe.fa out_bwa.sam.bwa reads_base.fastq > out_bwa.sam

command/project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/Schizosaccharomyces_pombe.fa reads_base.fastq -t 4 > out_bwa.sam.bwa; /project/teaser/genometeaser/software/bwa samse /project/teaser/genometeaser/references/Schizosaccharomyces_pombe.fa out_bwa.sam.bwa reads_base.fastq > out_bwa.sam
memory22260000
return0
status1
stderr
None
stdout
[bwa_aln] 17bp reads: max_diff = 2
[bwa_aln] 38bp reads: max_diff = 3
[bwa_aln] 64bp reads: max_diff = 4
[bwa_aln] 93bp reads: max_diff = 5
[bwa_aln] 124bp reads: max_diff = 6
[bwa_aln] 157bp reads: max_diff = 7
[bwa_aln] 190bp reads: max_diff = 8
[bwa_aln] 225bp reads: max_diff = 9
[bwa_aln_core] calculate SA coordinate... 0.00 sec
[bwa_aln_core] write to the disk... 0.00 sec
[bwa_aln_core] 1 sequences have been processed.
[main] Version: 0.7.12-r1039
[main] CMD: /project/teaser/genometeaser/software/bwa aln -t 4 /project/teaser/genometeaser/references/Schizosaccharomyces_pombe.fa reads_base.fastq
[main] Real time: 0.042 sec; CPU: 0.009 sec
[bwa_aln_core] convert to sequence coordinate... 0.01 sec
[bwa_aln_core] refine gapped alignments... 0.00 sec
[bwa_aln_core] print alignments... 0.00 sec
[bwa_aln_core] 1 sequences have been processed.
[main] Version: 0.7.12-r1039
[main] CMD: /project/teaser/genometeaser/software/bwa samse /project/teaser/genometeaser/references/Schizosaccharomyces_pombe.fa out_bwa.sam.bwa reads_base.fastq
[main] Real time: 0.049 sec; CPU: 0.016 sec
systime0.026995
time0.0994029045105
usrtime0.001999
working_directory/project/teaser/genometeaser/tests_generated/78245a202e759eede079b41dad2c7157

/project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/Schizosaccharomyces_pombe.fa reads.fastq -t 4 > out_bwa.sam.bwa; /project/teaser/genometeaser/software/bwa samse /project/teaser/genometeaser/references/Schizosaccharomyces_pombe.fa out_bwa.sam.bwa reads.fastq > out_bwa.sam

command/project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/Schizosaccharomyces_pombe.fa reads.fastq -t 4 > out_bwa.sam.bwa; /project/teaser/genometeaser/software/bwa samse /project/teaser/genometeaser/references/Schizosaccharomyces_pombe.fa out_bwa.sam.bwa reads.fastq > out_bwa.sam
memory108980000
return0
status1
stderr
None
stdout
[bwa_aln] 17bp reads: max_diff = 2
[bwa_aln] 38bp reads: max_diff = 3
[bwa_aln] 64bp reads: max_diff = 4
[bwa_aln] 93bp reads: max_diff = 5
[bwa_aln] 124bp reads: max_diff = 6
[bwa_aln] 157bp reads: max_diff = 7
[bwa_aln] 190bp reads: max_diff = 8
[bwa_aln] 225bp reads: max_diff = 9
[bwa_aln_core] calculate SA coordinate... 36.77 sec
[bwa_aln_core] write to the disk... 0.01 sec
[bwa_aln_core] 150000 sequences have been processed.
[main] Version: 0.7.12-r1039
[main] CMD: /project/teaser/genometeaser/software/bwa aln -t 4 /project/teaser/genometeaser/references/Schizosaccharomyces_pombe.fa reads.fastq
[main] Real time: 39.967 sec; CPU: 36.985 sec
[bwa_aln_core] convert to sequence coordinate... 0.63 sec
[bwa_aln_core] refine gapped alignments... 2.72 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 150000 sequences have been processed.
[main] Version: 0.7.12-r1039
[main] CMD: /project/teaser/genometeaser/software/bwa samse /project/teaser/genometeaser/references/Schizosaccharomyces_pombe.fa out_bwa.sam.bwa reads.fastq
[main] Real time: 4.454 sec; CPU: 3.910 sec
systime0.241963
time44.4925808907
usrtime40.658818
working_directory/project/teaser/genometeaser/tests_generated/78245a202e759eede079b41dad2c7157