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 Mapped30657797.726%
Wrongly Mapped71352.274%
Not Mapped00.0%
Total313712100.0%
Read Failure Statistics
Not mapped00.0%
Missing in mapper output00.0%
Mapped to wrong chromosome42661.36%
Mapped to wrong position28690.915%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment4
Secondary Alignments1
F-Measure0.988500
Precision0.977300
Recall1.000000
Timing
Raw Mapping Time35.004s
Effective Mapping Time5.235s
Effective Init Time29.769s
Effective Time MeasureWall clock
Mapping Time (Wall)35.004s
Mapping Time (CPU)115.359s
Mapping Time (CPU User)112.788s
Mapping Time (CPU System)2.572s
Init Time (Wall)29.769s
Init Time (CPU)5.470s
Init Time (CPU User)0.033s
Init Time (CPU System)5.437s
Additional Information
Mapper Memory Usage5827 MB
Total Test Runtime (Wall)136.581s
Mapper Command Line: 
/project2/NextGenMapTest/Teaser/software/bwa mem /project2/NextGenMapTest/Teaser/references/GRCh37.fa reads1.fastq reads2.fastq -t 4 > out_bwamem.sam
Errors and Warnings
No problems were encountered.
Subprocess Log

/project2/NextGenMapTest/Teaser/software/bwa mem /project2/NextGenMapTest/Teaser/references/GRCh37.fa reads_base.fastq -t 4 > out_bwamem.sam

command/project2/NextGenMapTest/Teaser/software/bwa mem /project2/NextGenMapTest/Teaser/references/GRCh37.fa reads_base.fastq -t 4 > out_bwamem.sam
memory5363224000
return0
status1
stderr

None
stdout

[M::bwa_idx_load_from_disk] read 0 ALT contigs

[M::process] read 1 sequences (60 bp)...

[M::mem_process_seqs] Processed 1 reads in 0.003 CPU sec, 0.012 real sec

[main] Version: 0.7.12-r1039

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

[main] Real time: 59.324 sec; CPU: 10.789 sec
systime10.763363
time59.3314521313
usrtime0.028995
working_directory/project2/NextGenMapTest/Teaser/tests_generated/H1_n

/project2/NextGenMapTest/Teaser/software/bwa mem /project2/NextGenMapTest/Teaser/references/GRCh37.fa reads_base.fastq -t 4 > out_bwamem.sam

command/project2/NextGenMapTest/Teaser/software/bwa mem /project2/NextGenMapTest/Teaser/references/GRCh37.fa reads_base.fastq -t 4 > out_bwamem.sam
memory5357520000
return0
status1
stderr

None
stdout

[M::bwa_idx_load_from_disk] read 0 ALT contigs

[M::process] read 1 sequences (60 bp)...

[M::mem_process_seqs] Processed 1 reads in 0.002 CPU sec, 0.001 real sec

[main] Version: 0.7.12-r1039

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

[main] Real time: 29.714 sec; CPU: 5.466 sec
systime5.437173
time29.7686021328
usrtime0.032994
working_directory/project2/NextGenMapTest/Teaser/tests_generated/H1_n

/project2/NextGenMapTest/Teaser/software/bwa mem /project2/NextGenMapTest/Teaser/references/GRCh37.fa reads1.fastq reads2.fastq -t 4 > out_bwamem.sam

command/project2/NextGenMapTest/Teaser/software/bwa mem /project2/NextGenMapTest/Teaser/references/GRCh37.fa reads1.fastq reads2.fastq -t 4 > out_bwamem.sam
memory5827592000
return0
status1
stderr

None
stdout

[M::bwa_idx_load_from_disk] read 0 ALT contigs

[M::process] read 313716 sequences (31371600 bp)...

[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 135133, 0, 0)

[M::mem_pestat] skip orientation FF as there are not enough pairs

[M::mem_pestat] analyzing insert size distribution for orientation FR...

[M::mem_pestat] (25, 50, 75) percentile: (465, 499, 533)

[M::mem_pestat] low and high boundaries for computing mean and std.dev: (329, 669)

[M::mem_pestat] mean and std.dev: (499.52, 49.87)

[M::mem_pestat] low and high boundaries for proper pairs: (261, 737)

[M::mem_pestat] skip orientation RF as there are not enough pairs

[M::mem_pestat] skip orientation RR as there are not enough pairs

[M::mem_process_seqs] Processed 313716 reads in 112.804 CPU sec, 28.623 real sec

[main] Version: 0.7.12-r1039

[main] CMD: /project2/NextGenMapTest/Teaser/software/bwa mem -t 4 /project2/NextGenMapTest/Teaser/references/GRCh37.fa reads1.fastq reads2.fastq

[main] Real time: 34.899 sec; CPU: 115.347 sec
systime2.571609
time35.0039031506
usrtime112.787853
working_directory/project2/NextGenMapTest/Teaser/tests_generated/H1_n