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 Mapped52405387.509%
Wrongly Mapped6852811.443%
Not Mapped62771.048%
Total598858100.0%
Read Failure Statistics
Not mapped62771.048%
Missing in mapper output00.0%
Mapped to wrong chromosome406266.784%
Mapped to wrong position279024.659%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.933400
Precision0.884400
Recall0.988200
Timing
Raw Mapping Time206.048s
Effective Mapping Time186.476s
Effective Init Time19.572s
Effective Time MeasureCPU
Mapping Time (Wall)108.689s
Mapping Time (CPU)206.048s
Mapping Time (CPU User)166.588s
Mapping Time (CPU System)39.460s
Init Time (Wall)20.149s
Init Time (CPU)19.572s
Init Time (CPU User)0.008s
Init Time (CPU System)19.564s
Additional Information
Mapper Memory Usage345 MB
Total Test Runtime (Wall)246.636s
Mapper Command Line: 
/project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/D_melanogaster.fasta reads.fastq -t 4 > out_bwa.sam.bwa; /project/teaser/genometeaser/software/bwa samse /project/teaser/genometeaser/references/D_melanogaster.fasta 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/D_melanogaster.fasta reads_base.fastq -t 4 > out_bwa.sam.bwa; /project/teaser/genometeaser/software/bwa samse /project/teaser/genometeaser/references/D_melanogaster.fasta out_bwa.sam.bwa reads_base.fastq > out_bwa.sam

command/project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/D_melanogaster.fasta reads_base.fastq -t 4 > out_bwa.sam.bwa; /project/teaser/genometeaser/software/bwa samse /project/teaser/genometeaser/references/D_melanogaster.fasta out_bwa.sam.bwa reads_base.fastq > out_bwa.sam
memory214312000
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/D_melanogaster.fasta reads_base.fastq
[main] Real time: 12.307 sec; CPU: 7.400 sec
[bwa_aln_core] convert to sequence coordinate... 11.05 sec
[bwa_aln_core] refine gapped alignments... 1.84 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/D_melanogaster.fasta out_bwa.sam.bwa reads_base.fastq
[main] Real time: 16.984 sec; CPU: 12.904 sec
systime20.304
time29.3347010612
usrtime0.016
working_directory/project/teaser/genometeaser/tests_generated/f2a6f25cabc55338e734f1adbe44516b

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

command/project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/D_melanogaster.fasta reads_base.fastq -t 4 > out_bwa.sam.bwa; /project/teaser/genometeaser/software/bwa samse /project/teaser/genometeaser/references/D_melanogaster.fasta out_bwa.sam.bwa reads_base.fastq > out_bwa.sam
memory214332000
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/D_melanogaster.fasta reads_base.fastq
[main] Real time: 7.757 sec; CPU: 7.516 sec
[bwa_aln_core] convert to sequence coordinate... 10.51 sec
[bwa_aln_core] refine gapped alignments... 1.52 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/D_melanogaster.fasta out_bwa.sam.bwa reads_base.fastq
[main] Real time: 12.307 sec; CPU: 12.044 sec
systime19.564
time20.1488080025
usrtime0.008
working_directory/project/teaser/genometeaser/tests_generated/f2a6f25cabc55338e734f1adbe44516b

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

command/project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/D_melanogaster.fasta reads.fastq -t 4 > out_bwa.sam.bwa; /project/teaser/genometeaser/software/bwa samse /project/teaser/genometeaser/references/D_melanogaster.fasta out_bwa.sam.bwa reads.fastq > out_bwa.sam
memory345156000
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... 64.36 sec
[bwa_aln_core] write to the disk... 0.18 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_aln_core] calculate SA coordinate... 67.28 sec
[bwa_aln_core] write to the disk... 0.16 sec
[bwa_aln_core] 524288 sequences have been processed.
[bwa_aln_core] calculate SA coordinate... 18.93 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 598858 sequences have been processed.
[main] Version: 0.7.12-r1039
[main] CMD: /project/teaser/genometeaser/software/bwa aln -t 4 /project/teaser/genometeaser/references/D_melanogaster.fasta reads.fastq
[main] Real time: 52.834 sec; CPU: 162.168 sec
[bwa_aln_core] convert to sequence coordinate... 13.79 sec
[bwa_aln_core] refine gapped alignments... 4.40 sec
[bwa_aln_core] print alignments... 1.66 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_aln_core] convert to sequence coordinate... 7.87 sec
[bwa_aln_core] refine gapped alignments... 4.41 sec
[bwa_aln_core] print alignments... 1.69 sec
[bwa_aln_core] 524288 sequences have been processed.
[bwa_aln_core] convert to sequence coordinate... 6.04 sec
[bwa_aln_core] refine gapped alignments... 0.75 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 598858 sequences have been processed.
[main] Version: 0.7.12-r1039
[main] CMD: /project/teaser/genometeaser/software/bwa samse /project/teaser/genometeaser/references/D_melanogaster.fasta out_bwa.sam.bwa reads.fastq
[main] Real time: 55.754 sec; CPU: 43.820 sec
systime39.46
time108.689218998
usrtime166.588
working_directory/project/teaser/genometeaser/tests_generated/f2a6f25cabc55338e734f1adbe44516b