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 Mapped30560697.416%
Wrongly Mapped69832.226%
Not Mapped11230.358%
Total313712100.0%
Read Failure Statistics
Not mapped11230.358%
Missing in mapper output00.0%
Mapped to wrong chromosome41461.322%
Mapped to wrong position28370.904%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment4
Secondary Alignments0
F-Measure0.986900
Precision0.977700
Recall0.996300
Timing
Raw Mapping Time50.581s
Effective Mapping Time48.798s
Effective Init Time1.783s
Effective Time MeasureWall clock
Mapping Time (Wall)50.581s
Mapping Time (CPU)162.423s
Mapping Time (CPU User)159.888s
Mapping Time (CPU System)2.536s
Init Time (Wall)1.783s
Init Time (CPU)1.700s
Init Time (CPU User)0.031s
Init Time (CPU System)1.669s
Additional Information
Mapper Memory Usage4816 MB
Total Test Runtime (Wall)119.260s
Mapper Command Line: 
/project2/NextGenMapTest/Teaser/software/bwa aln /project2/NextGenMapTest/Teaser/references/GRCh37.fa reads1.fastq -t 4 > out_bwa.sam_1.sai; /project2/NextGenMapTest/Teaser/software/bwa aln /project2/NextGenMapTest/Teaser/references/GRCh37.fa reads2.fastq -t 4 > out_bwa.sam_2.sai; /project2/NextGenMapTest/Teaser/software/bwa sampe /project2/NextGenMapTest/Teaser/references/GRCh37.fa out_bwa.sam_1.sai out_bwa.sam_2.sai reads1.fastq reads2.fastq > out_bwa.sam
Errors and Warnings
No problems were encountered.
Subprocess Log

/project2/NextGenMapTest/Teaser/software/bwa aln /project2/NextGenMapTest/Teaser/references/GRCh37.fa reads_base.fastq -t 4 > out_bwa.sam.bwa; /project2/NextGenMapTest/Teaser/software/bwa samse /project2/NextGenMapTest/Teaser/references/GRCh37.fa out_bwa.sam.bwa reads_base.fastq > out_bwa.sam

command/project2/NextGenMapTest/Teaser/software/bwa aln /project2/NextGenMapTest/Teaser/references/GRCh37.fa reads_base.fastq -t 4 > out_bwa.sam.bwa; /project2/NextGenMapTest/Teaser/software/bwa samse /project2/NextGenMapTest/Teaser/references/GRCh37.fa out_bwa.sam.bwa reads_base.fastq > out_bwa.sam
memory4597376000
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/GRCh37.fa reads_base.fastq

[main] Real time: 30.925 sec; CPU: 1.189 sec

[bwa_aln_core] convert to sequence coordinate... 1.24 sec

[bwa_aln_core] refine gapped alignments... 0.29 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/GRCh37.fa out_bwa.sam.bwa reads_base.fastq

[main] Real time: 24.377 sec; CPU: 1.543 sec
systime2.69159
time55.3185880184
usrtime0.042993
working_directory/project2/NextGenMapTest/Teaser/tests_generated/H1_n

/project2/NextGenMapTest/Teaser/software/bwa aln /project2/NextGenMapTest/Teaser/references/GRCh37.fa reads_base.fastq -t 4 > out_bwa.sam.bwa; /project2/NextGenMapTest/Teaser/software/bwa samse /project2/NextGenMapTest/Teaser/references/GRCh37.fa out_bwa.sam.bwa reads_base.fastq > out_bwa.sam

command/project2/NextGenMapTest/Teaser/software/bwa aln /project2/NextGenMapTest/Teaser/references/GRCh37.fa reads_base.fastq -t 4 > out_bwa.sam.bwa; /project2/NextGenMapTest/Teaser/software/bwa samse /project2/NextGenMapTest/Teaser/references/GRCh37.fa out_bwa.sam.bwa reads_base.fastq > out_bwa.sam
memory4597380000
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/GRCh37.fa reads_base.fastq

[main] Real time: 0.612 sec; CPU: 0.610 sec

[bwa_aln_core] convert to sequence coordinate... 0.92 sec

[bwa_aln_core] refine gapped alignments... 0.16 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/GRCh37.fa out_bwa.sam.bwa reads_base.fastq

[main] Real time: 1.161 sec; CPU: 1.088 sec
systime1.668746
time1.78276014328
usrtime0.030995
working_directory/project2/NextGenMapTest/Teaser/tests_generated/H1_n

/project2/NextGenMapTest/Teaser/software/bwa aln /project2/NextGenMapTest/Teaser/references/GRCh37.fa reads1.fastq -t 4 > out_bwa.sam_1.sai; /project2/NextGenMapTest/Teaser/software/bwa aln /project2/NextGenMapTest/Teaser/references/GRCh37.fa reads2.fastq -t 4 > out_bwa.sam_2.sai; /project2/NextGenMapTest/Teaser/software/bwa sampe /project2/NextGenMapTest/Teaser/references/GRCh37.fa out_bwa.sam_1.sai out_bwa.sam_2.sai reads1.fastq reads2.fastq > out_bwa.sam

command/project2/NextGenMapTest/Teaser/software/bwa aln /project2/NextGenMapTest/Teaser/references/GRCh37.fa reads1.fastq -t 4 > out_bwa.sam_1.sai; /project2/NextGenMapTest/Teaser/software/bwa aln /project2/NextGenMapTest/Teaser/references/GRCh37.fa reads2.fastq -t 4 > out_bwa.sam_2.sai; /project2/NextGenMapTest/Teaser/software/bwa sampe /project2/NextGenMapTest/Teaser/references/GRCh37.fa out_bwa.sam_1.sai out_bwa.sam_2.sai reads1.fastq reads2.fastq > out_bwa.sam
memory4816488000
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... 77.08 sec

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

[bwa_aln_core] 156858 sequences have been processed.

[main] Version: 0.7.12-r1039

[main] CMD: /project2/NextGenMapTest/Teaser/software/bwa aln -t 4 /project2/NextGenMapTest/Teaser/references/GRCh37.fa reads1.fastq

[main] Real time: 21.004 sec; CPU: 77.871 sec

[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... 76.35 sec

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

[bwa_aln_core] 156858 sequences have been processed.

[main] Version: 0.7.12-r1039

[main] CMD: /project2/NextGenMapTest/Teaser/software/bwa aln -t 4 /project2/NextGenMapTest/Teaser/references/GRCh37.fa reads2.fastq

[main] Real time: 20.796 sec; CPU: 77.151 sec

[bwa_sai2sam_pe_core] convert to sequence coordinate... 

[infer_isize] (25, 50, 75) percentile: (467, 500, 534)

[infer_isize] low and high boundaries: 333 and 668 for estimating avg and std

[infer_isize] inferred external isize from 133620 pairs: 500.601 +/- 49.846

[infer_isize] skewness: 0.007; kurtosis: -0.098; ap_prior: 1.00e-05

[infer_isize] inferred maximum insert size: 845 (6.90 sigma)

[bwa_sai2sam_pe_core] time elapses: 5.24 sec

[bwa_sai2sam_pe_core] changing coordinates of 3211 alignments.

[bwa_sai2sam_pe_core] align unmapped mate...

[bwa_paired_sw] 11333 out of 11337 Q17 singletons are mated.

[bwa_paired_sw] 120 out of 120 Q17 discordant pairs are fixed.

[bwa_sai2sam_pe_core] time elapses: 0.85 sec

[bwa_sai2sam_pe_core] refine gapped alignments... 0.38 sec

[bwa_sai2sam_pe_core] print alignments... 0.56 sec

[bwa_sai2sam_pe_core] 156858 sequences have been processed.

[main] Version: 0.7.12-r1039

[main] CMD: /project2/NextGenMapTest/Teaser/software/bwa sampe /project2/NextGenMapTest/Teaser/references/GRCh37.fa out_bwa.sam_1.sai out_bwa.sam_2.sai reads1.fastq reads2.fastq

[main] Real time: 8.758 sec; CPU: 7.391 sec
systime2.535614
time50.5807929039
usrtime159.887693
working_directory/project2/NextGenMapTest/Teaser/tests_generated/H1_n