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 Mapped28635095.715%
Wrongly Mapped70912.37%
Not Mapped57281.915%
Total299169100.0%
Read Failure Statistics
Not mapped57281.915%
Missing in mapper output00.0%
Mapped to wrong chromosome26240.877%
Mapped to wrong position44671.493%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.978100
Precision0.975800
Recall0.980400
Timing
Raw Mapping Time80.736s
Effective Mapping Time80.388s
Effective Init Time0.348s
Effective Time MeasureCPU
Mapping Time (Wall)44.181s
Mapping Time (CPU)80.736s
Mapping Time (CPU User)78.928s
Mapping Time (CPU System)1.808s
Init Time (Wall)0.435s
Init Time (CPU)0.348s
Init Time (CPU User)0.016s
Init Time (CPU System)0.332s
Additional Information
Mapper Memory Usage333 MB
Total Test Runtime (Wall)89.509s
Mapper Command Line: 
/project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas reads.fastq -t 4 > out_bwa.sam.bwa; /project/teaser/genometeaser/software/bwa samse /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas 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/Arabidopsis_thaliana.fas reads_base.fastq -t 4 > out_bwa.sam.bwa; /project/teaser/genometeaser/software/bwa samse /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas out_bwa.sam.bwa reads_base.fastq > out_bwa.sam

command/project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas reads_base.fastq -t 4 > out_bwa.sam.bwa; /project/teaser/genometeaser/software/bwa samse /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas out_bwa.sam.bwa reads_base.fastq > out_bwa.sam
memory178828000
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: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa aln -t 4 /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas reads_base.fastq
[main] Real time: 10.300 sec; CPU: 0.168 sec
[bwa_aln_core] convert to sequence coordinate... 0.21 sec
[bwa_aln_core] refine gapped alignments... 0.04 sec
[bwa_aln_core] print alignments... 0.00 sec
[bwa_aln_core] 1 sequences have been processed.
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa samse /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas out_bwa.sam.bwa reads_base.fastq
[main] Real time: 7.905 sec; CPU: 0.256 sec
systime0.428
time18.2769899368
usrtime0.008
working_directory/project/teaser/genometeaser/tests_generated/85176433619c96b494ede3b93198c48c

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

command/project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas reads_base.fastq -t 4 > out_bwa.sam.bwa; /project/teaser/genometeaser/software/bwa samse /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas out_bwa.sam.bwa reads_base.fastq > out_bwa.sam
memory178760000
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: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa aln -t 4 /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas reads_base.fastq
[main] Real time: 0.143 sec; CPU: 0.120 sec
[bwa_aln_core] convert to sequence coordinate... 0.18 sec
[bwa_aln_core] refine gapped alignments... 0.03 sec
[bwa_aln_core] print alignments... 0.00 sec
[bwa_aln_core] 1 sequences have been processed.
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa samse /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas out_bwa.sam.bwa reads_base.fastq
[main] Real time: 0.243 sec; CPU: 0.216 sec
systime0.332
time0.435199975967
usrtime0.016
working_directory/project/teaser/genometeaser/tests_generated/85176433619c96b494ede3b93198c48c

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

command/project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas reads.fastq -t 4 > out_bwa.sam.bwa; /project/teaser/genometeaser/software/bwa samse /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas out_bwa.sam.bwa reads.fastq > out_bwa.sam
memory333664000
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... 57.58 sec
[bwa_aln_core] write to the disk... 0.14 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_aln_core] calculate SA coordinate... 7.87 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 299169 sequences have been processed.
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa aln -t 4 /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas reads.fastq
[main] Real time: 22.438 sec; CPU: 66.908 sec
[bwa_aln_core] convert to sequence coordinate... 2.94 sec
[bwa_aln_core] refine gapped alignments... 6.49 sec
[bwa_aln_core] print alignments... 1.41 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_aln_core] convert to sequence coordinate... 0.56 sec
[bwa_aln_core] refine gapped alignments... 0.92 sec
[bwa_aln_core] print alignments... 0.20 sec
[bwa_aln_core] 299169 sequences have been processed.
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa samse /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas out_bwa.sam.bwa reads.fastq
[main] Real time: 21.622 sec; CPU: 13.788 sec
systime1.808
time44.1808869839
usrtime78.928
working_directory/project/teaser/genometeaser/tests_generated/85176433619c96b494ede3b93198c48c