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 Mapped59176196.201%
Wrongly Mapped233653.798%
Not Mapped20.0%
Total615128100.0%
Read Failure Statistics
Not mapped20.0%
Missing in mapper output00.0%
Mapped to wrong chromosome159262.589%
Mapped to wrong position74391.209%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments1
F-Measure0.980600
Precision0.962000
Recall1.000000
Timing
Raw Mapping Time729.752s
Effective Mapping Time696.056s
Effective Init Time33.696s
Effective Time MeasureCPU
Mapping Time (Wall)441.278s
Mapping Time (CPU)729.752s
Mapping Time (CPU User)614.732s
Mapping Time (CPU System)115.020s
Init Time (Wall)36.975s
Init Time (CPU)33.696s
Init Time (CPU User)0.280s
Init Time (CPU System)33.416s
Additional Information
Mapper Memory Usage6531 MB
Total Test Runtime (Wall)592.887s
Mapper Command Line: 
/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/H_sapiens.fa reads1.fastq reads2.fastq -t 4 > out_bwamem.sam
Errors and Warnings
No problems were encountered.
Subprocess Log

/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/H_sapiens.fa reads_base.fastq -t 4 > out_bwamem.sam

command/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/H_sapiens.fa reads_base.fastq -t 4 > out_bwamem.sam
memory5364384000
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 0.020 CPU sec, 0.068 real sec
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa mem -t 4 /project/teaser/genometeaser/references/H_sapiens.fa reads_base.fastq
[main] Real time: 34.084 sec; CPU: 32.876 sec
systime32.752
time34.1288671494
usrtime0.136
working_directory/project/teaser/genometeaser/tests_generated/4ff0769a44d529563c64b75a1aaf552d

/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/H_sapiens.fa reads_base.fastq -t 4 > out_bwamem.sam

command/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/H_sapiens.fa reads_base.fastq -t 4 > out_bwamem.sam
memory5364384000
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 0.028 CPU sec, 0.035 real sec
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa mem -t 4 /project/teaser/genometeaser/references/H_sapiens.fa reads_base.fastq
[main] Real time: 36.544 sec; CPU: 33.668 sec
systime33.416
time36.9746630192
usrtime0.28
working_directory/project/teaser/genometeaser/tests_generated/4ff0769a44d529563c64b75a1aaf552d

/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/H_sapiens.fa reads1.fastq reads2.fastq -t 4 > out_bwamem.sam

command/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/H_sapiens.fa reads1.fastq reads2.fastq -t 4 > out_bwamem.sam
memory6531716000
return0
status1
stderr
None
stdout
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 615128 sequences (31371528 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 237439, 282, 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: (76, 98, 120)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 208)
[M::mem_pestat] mean and std.dev: (98.09, 32.64)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 252)
[M::mem_pestat] analyzing insert size distribution for orientation RF...
[M::mem_pestat] (25, 50, 75) percentile: (1, 1, 1)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1)
[M::mem_pestat] mean and std.dev: (1.00, 0.00)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1)
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_pestat] skip orientation RF
[M::mem_process_seqs] Processed 615128 reads in 682.092 CPU sec, 370.741 real sec
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa mem -t 4 /project/teaser/genometeaser/references/H_sapiens.fa reads1.fastq reads2.fastq
[main] Real time: 441.220 sec; CPU: 729.740 sec
systime115.02
time441.278375864
usrtime614.732
working_directory/project/teaser/genometeaser/tests_generated/4ff0769a44d529563c64b75a1aaf552d