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 Mapped19669598.621%
Wrongly Mapped27511.379%
Not Mapped00.0%
Total199446100.0%
Read Failure Statistics
Not mapped00.0%
Missing in mapper output00.0%
Mapped to wrong chromosome7890.396%
Mapped to wrong position19620.984%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.993100
Precision0.986200
Recall1.000000
Timing
Raw Mapping Time55.336s
Effective Mapping Time55.052s
Effective Init Time0.284s
Effective Time MeasureCPU
Mapping Time (Wall)36.837s
Mapping Time (CPU)55.336s
Mapping Time (CPU User)53.720s
Mapping Time (CPU System)1.616s
Init Time (Wall)0.306s
Init Time (CPU)0.284s
Init Time (CPU User)0.004s
Init Time (CPU System)0.280s
Additional Information
Mapper Memory Usage386 MB
Total Test Runtime (Wall)83.300s
Mapper Command Line: 
/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas 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/Arabidopsis_thaliana.fas reads_base.fastq -t 4 > out_bwamem.sam

command/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas reads_base.fastq -t 4 > out_bwamem.sam
memory207328000
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 0.000 CPU sec, 0.002 real sec
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa mem -t 4 /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas reads_base.fastq
[main] Real time: 0.688 sec; CPU: 0.284 sec
systime0.296
time0.723609924316
usrtime0.0
working_directory/project/teaser/genometeaser/tests_generated/e1c9b59d61d1a772598b0749ea6b7508

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

command/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas reads_base.fastq -t 4 > out_bwamem.sam
memory207332000
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 0.000 CPU sec, 0.001 real sec
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa mem -t 4 /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas reads_base.fastq
[main] Real time: 0.296 sec; CPU: 0.276 sec
systime0.28
time0.30557513237
usrtime0.004
working_directory/project/teaser/genometeaser/tests_generated/e1c9b59d61d1a772598b0749ea6b7508

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

command/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas reads1.fastq reads2.fastq -t 4 > out_bwamem.sam
memory386776000
return0
status1
stderr
None
stdout
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 199446 sequences (29916900 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 90026, 98, 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: (78, 101, 123)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 213)
[M::mem_pestat] mean and std.dev: (100.30, 32.55)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 258)
[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 199446 reads in 54.128 CPU sec, 23.225 real sec
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa mem -t 4 /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas reads1.fastq reads2.fastq
[main] Real time: 36.797 sec; CPU: 55.328 sec
systime1.616
time36.8368859291
usrtime53.72
working_directory/project/teaser/genometeaser/tests_generated/e1c9b59d61d1a772598b0749ea6b7508