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 Mapped28987692.402%
Wrongly Mapped106143.383%
Not Mapped132234.215%
Total313713100.0%
Read Failure Statistics
Not mapped132234.215%
Missing in mapper output00.0%
Mapped to wrong chromosome69622.219%
Mapped to wrong position36521.164%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment3
Secondary Alignments0
F-Measure0.960500
Precision0.964700
Recall0.956400
Timing
Raw Mapping Time47.684s
Effective Mapping Time46.004s
Effective Init Time1.680s
Effective Time MeasureWall clock
Mapping Time (Wall)47.684s
Mapping Time (CPU)163.458s
Mapping Time (CPU User)160.542s
Mapping Time (CPU System)2.917s
Init Time (Wall)1.680s
Init Time (CPU)1.659s
Init Time (CPU User)0.035s
Init Time (CPU System)1.624s
Additional Information
Mapper Memory Usage4764 MB
Total Test Runtime (Wall)61.899s
Mapper Command Line: 
/project2/NextGenMapTest/Teaser/software/bwa aln /project2/NextGenMapTest/Teaser/references/GRCh37.fa reads.fastq -t 4 > out_bwa.sam.bwa; /project2/NextGenMapTest/Teaser/software/bwa samse /project2/NextGenMapTest/Teaser/references/GRCh37.fa 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/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: 0.610 sec; CPU: 0.606 sec

[bwa_aln_core] convert to sequence coordinate... 0.90 sec

[bwa_aln_core] refine gapped alignments... 0.14 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: 1.055 sec; CPU: 1.050 sec
systime1.622753
time1.67485308647
usrtime0.035994
working_directory/project2/NextGenMapTest/Teaser/tests_generated/H2_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
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: 0.611 sec; CPU: 0.609 sec

[bwa_aln_core] convert to sequence coordinate... 0.89 sec

[bwa_aln_core] refine gapped alignments... 0.15 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: 1.059 sec; CPU: 1.047 sec
systime1.623753
time1.67985606194
usrtime0.034994
working_directory/project2/NextGenMapTest/Teaser/tests_generated/H2_n

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

command/project2/NextGenMapTest/Teaser/software/bwa aln /project2/NextGenMapTest/Teaser/references/GRCh37.fa reads.fastq -t 4 > out_bwa.sam.bwa; /project2/NextGenMapTest/Teaser/software/bwa samse /project2/NextGenMapTest/Teaser/references/GRCh37.fa out_bwa.sam.bwa reads.fastq > out_bwa.sam
memory4764096000
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... 131.29 sec

[bwa_aln_core] write to the disk... 0.03 sec

[bwa_aln_core] 262144 sequences have been processed.

[bwa_aln_core] calculate SA coordinate... 26.45 sec

[bwa_aln_core] write to the disk... 0.02 sec

[bwa_aln_core] 313716 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.fastq

[main] Real time: 41.589 sec; CPU: 158.720 sec

[bwa_aln_core] convert to sequence coordinate... 1.93 sec

[bwa_aln_core] refine gapped alignments... 0.65 sec

[bwa_aln_core] print alignments... 0.37 sec

[bwa_aln_core] 262144 sequences have been processed.

[bwa_aln_core] convert to sequence coordinate... 1.12 sec

[bwa_aln_core] refine gapped alignments... 0.24 sec

[bwa_aln_core] print alignments... 0.07 sec

[bwa_aln_core] 313716 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.fastq

[main] Real time: 6.072 sec; CPU: 4.730 sec
systime2.916556
time47.6837940216
usrtime160.541593
working_directory/project2/NextGenMapTest/Teaser/tests_generated/H2_n