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 Mapped3764915.717%
Wrongly Mapped34721.449%
Not Mapped19842282.834%
Total239543100.0%
Read Failure Statistics
Not mapped19842282.834%
Missing in mapper output00.0%
Mapped to wrong chromosome18490.772%
Mapped to wrong position16230.678%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.271600
Precision0.915600
Recall0.159500
Timing
Raw Mapping Time12.822s
Effective Mapping Time12.682s
Effective Init Time0.139s
Effective Time MeasureWall clock
Mapping Time (Wall)12.822s
Mapping Time (CPU)36.338s
Mapping Time (CPU User)36.074s
Mapping Time (CPU System)0.265s
Init Time (Wall)0.139s
Init Time (CPU)0.092s
Init Time (CPU User)0.007s
Init Time (CPU System)0.085s
Additional Information
Mapper Memory Usage381 MB
Total Test Runtime (Wall)25.623s
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: 0.037 sec; CPU: 0.034 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: 0.069 sec; CPU: 0.062 sec
systime0.090986
time0.114233016968
usrtime0.008998
working_directory/project2/NextGenMapTest/Teaser/tests_generated/D2_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
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: 0.036 sec; CPU: 0.035 sec

[bwa_aln_core] convert to sequence coordinate... 0.04 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: /project2/NextGenMapTest/Teaser/software/bwa samse /project2/NextGenMapTest/Teaser/references/d_melanogaster.fasta out_bwa.sam.bwa reads_base.fastq

[main] Real time: 0.061 sec; CPU: 0.054 sec
systime0.084987
time0.139225959778
usrtime0.006998
working_directory/project2/NextGenMapTest/Teaser/tests_generated/D2_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
memory381784000
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... 33.88 sec

[bwa_aln_core] write to the disk... 0.02 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: 9.548 sec; CPU: 34.190 sec

[bwa_aln_core] convert to sequence coordinate... 0.21 sec

[bwa_aln_core] refine gapped alignments... 1.46 sec

[bwa_aln_core] print alignments... 0.18 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: 3.258 sec; CPU: 2.140 sec
systime0.264959
time12.8216571808
usrtime36.073515
working_directory/project2/NextGenMapTest/Teaser/tests_generated/D2_n