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 Mapped21121988.176%
Wrongly Mapped191127.979%
Not Mapped92123.846%
Total239543100.0%
Read Failure Statistics
Not mapped92123.846%
Missing in mapper output00.0%
Mapped to wrong chromosome99464.152%
Mapped to wrong position91663.826%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.937200
Precision0.917000
Recall0.958200
Timing
Raw Mapping Time18.992s
Effective Mapping Time18.870s
Effective Init Time0.122s
Effective Time MeasureWall clock
Mapping Time (Wall)18.992s
Mapping Time (CPU)49.824s
Mapping Time (CPU User)49.529s
Mapping Time (CPU System)0.295s
Init Time (Wall)0.122s
Init Time (CPU)0.101s
Init Time (CPU User)0.009s
Init Time (CPU System)0.092s
Additional Information
Mapper Memory Usage389 MB
Total Test Runtime (Wall)32.769s
Mapper Command Line: 
/project2/NextGenMapTest/Teaser/software/bwa aln /project2/NextGenMapTest/Teaser/references/d_melanogaster.fasta reads.fastq -t 4 > out_bwa.sam.bwa; /project2/NextGenMapTest/Teaser/software/bwa samse /project2/NextGenMapTest/Teaser/references/d_melanogaster.fasta out_bwa.sam.bwa reads.fastq > out_bwa.sam
Errors and Warnings
No problems were encountered.
Subprocess Log

/project2/NextGenMapTest/Teaser/software/bwa aln /project2/NextGenMapTest/Teaser/references/d_melanogaster.fasta reads_base.fastq -t 4 > out_bwa.sam.bwa; /project2/NextGenMapTest/Teaser/software/bwa samse /project2/NextGenMapTest/Teaser/references/d_melanogaster.fasta out_bwa.sam.bwa reads_base.fastq > out_bwa.sam

command/project2/NextGenMapTest/Teaser/software/bwa aln /project2/NextGenMapTest/Teaser/references/d_melanogaster.fasta reads_base.fastq -t 4 > out_bwa.sam.bwa; /project2/NextGenMapTest/Teaser/software/bwa samse /project2/NextGenMapTest/Teaser/references/d_melanogaster.fasta out_bwa.sam.bwa reads_base.fastq > out_bwa.sam
memory212896000
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: /project2/NextGenMapTest/Teaser/software/bwa aln -t 4 /project2/NextGenMapTest/Teaser/references/d_melanogaster.fasta reads_base.fastq

[main] Real time: 1.629 sec; CPU: 0.061 sec

[bwa_aln_core] convert to sequence coordinate... 0.07 sec

[bwa_aln_core] refine gapped alignments... 0.01 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: /project2/NextGenMapTest/Teaser/software/bwa samse /project2/NextGenMapTest/Teaser/references/d_melanogaster.fasta out_bwa.sam.bwa reads_base.fastq

[main] Real time: 1.086 sec; CPU: 0.093 sec
systime0.150977
time2.72533488274
usrtime0.005999
working_directory/project2/NextGenMapTest/Teaser/tests_generated/D1_n

/project2/NextGenMapTest/Teaser/software/bwa aln /project2/NextGenMapTest/Teaser/references/d_melanogaster.fasta reads_base.fastq -t 4 > out_bwa.sam.bwa; /project2/NextGenMapTest/Teaser/software/bwa samse /project2/NextGenMapTest/Teaser/references/d_melanogaster.fasta out_bwa.sam.bwa reads_base.fastq > out_bwa.sam

command/project2/NextGenMapTest/Teaser/software/bwa aln /project2/NextGenMapTest/Teaser/references/d_melanogaster.fasta reads_base.fastq -t 4 > out_bwa.sam.bwa; /project2/NextGenMapTest/Teaser/software/bwa samse /project2/NextGenMapTest/Teaser/references/d_melanogaster.fasta out_bwa.sam.bwa reads_base.fastq > out_bwa.sam
memory212892000
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: /project2/NextGenMapTest/Teaser/software/bwa aln -t 4 /project2/NextGenMapTest/Teaser/references/d_melanogaster.fasta reads_base.fastq

[main] Real time: 0.034 sec; CPU: 0.033 sec

[bwa_aln_core] convert to sequence coordinate... 0.04 sec

[bwa_aln_core] refine gapped alignments... 0.01 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: /project2/NextGenMapTest/Teaser/software/bwa samse /project2/NextGenMapTest/Teaser/references/d_melanogaster.fasta out_bwa.sam.bwa reads_base.fastq

[main] Real time: 0.078 sec; CPU: 0.064 sec
systime0.091986
time0.121681928635
usrtime0.008998
working_directory/project2/NextGenMapTest/Teaser/tests_generated/D1_n

/project2/NextGenMapTest/Teaser/software/bwa aln /project2/NextGenMapTest/Teaser/references/d_melanogaster.fasta reads.fastq -t 4 > out_bwa.sam.bwa; /project2/NextGenMapTest/Teaser/software/bwa samse /project2/NextGenMapTest/Teaser/references/d_melanogaster.fasta out_bwa.sam.bwa reads.fastq > out_bwa.sam

command/project2/NextGenMapTest/Teaser/software/bwa aln /project2/NextGenMapTest/Teaser/references/d_melanogaster.fasta reads.fastq -t 4 > out_bwa.sam.bwa; /project2/NextGenMapTest/Teaser/software/bwa samse /project2/NextGenMapTest/Teaser/references/d_melanogaster.fasta out_bwa.sam.bwa reads.fastq > out_bwa.sam
memory389052000
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... 44.18 sec

[bwa_aln_core] write to the disk... 0.01 sec

[bwa_aln_core] 239543 sequences have been processed.

[main] Version: 0.7.12-r1039

[main] CMD: /project2/NextGenMapTest/Teaser/software/bwa aln -t 4 /project2/NextGenMapTest/Teaser/references/d_melanogaster.fasta reads.fastq

[main] Real time: 12.351 sec; CPU: 44.493 sec

[bwa_aln_core] convert to sequence coordinate... 0.94 sec

[bwa_aln_core] refine gapped alignments... 3.71 sec

[bwa_aln_core] print alignments... 0.37 sec

[bwa_aln_core] 239543 sequences have been processed.

[main] Version: 0.7.12-r1039

[main] CMD: /project2/NextGenMapTest/Teaser/software/bwa samse /project2/NextGenMapTest/Teaser/references/d_melanogaster.fasta out_bwa.sam.bwa reads.fastq

[main] Real time: 6.626 sec; CPU: 5.323 sec
systime0.294955
time18.992043972
usrtime49.52947
working_directory/project2/NextGenMapTest/Teaser/tests_generated/D1_n