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 Mapped9874898.748%
Wrongly Mapped12481.248%
Not Mapped40.004%
Total100000100.0%
Read Failure Statistics
Not mapped40.004%
Missing in mapper output00.0%
Mapped to wrong chromosome10101.01%
Mapped to wrong position2380.238%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment4
Secondary Alignments0
F-Measure0.993700
Precision0.987500
Recall1.000000
Timing
Raw Mapping Time94.112s
Effective Mapping Time94.076s
Effective Init Time0.036s
Effective Time MeasureCPU
Mapping Time (Wall)37.480s
Mapping Time (CPU)94.112s
Mapping Time (CPU User)92.144s
Mapping Time (CPU System)1.968s
Init Time (Wall)0.105s
Init Time (CPU)0.036s
Init Time (CPU User)0.008s
Init Time (CPU System)0.028s
Additional Information
Mapper Memory Usage144 MB
Total Test Runtime (Wall)62.402s
Mapper Command Line: 
/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta reads1.fastq reads2.fastq -t 4 > out_bwasw.sam
Errors and Warnings
No problems were encountered.
Subprocess Log

/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta reads_base.fastq -t 4 > out_bwasw.sam

command/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta reads_base.fastq -t 4 > out_bwasw.sam
memory24808000
return0
status1
stderr
None
stdout
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[bsw2_aln] read 1 sequences/pairs (60 bp) ...
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa bwasw -t 4 /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta reads_base.fastq
[main] Real time: 0.086 sec; CPU: 0.032 sec
systime0.028
time0.109189033508
usrtime0.008
working_directory/project/teaser/genometeaser/tests_generated/b0bfc21db96b7744c4389e9b4b565dc9

/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta reads_base.fastq -t 4 > out_bwasw.sam

command/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta reads_base.fastq -t 4 > out_bwasw.sam
memory24808000
return0
status1
stderr
None
stdout
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[bsw2_aln] read 1 sequences/pairs (60 bp) ...
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa bwasw -t 4 /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta reads_base.fastq
[main] Real time: 0.075 sec; CPU: 0.028 sec
systime0.028
time0.105373859406
usrtime0.008
working_directory/project/teaser/genometeaser/tests_generated/b0bfc21db96b7744c4389e9b4b565dc9

/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta reads1.fastq reads2.fastq -t 4 > out_bwasw.sam

command/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta reads1.fastq reads2.fastq -t 4 > out_bwasw.sam
memory144788000
return0
status1
stderr
None
stdout
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[bsw2_aln] read 100000 sequences/pairs (15000000 bp) ...
[bsw2_stat] infer the insert size distribution from 12051 high-quality pairs.
[bsw2_stat] (25, 50, 75) percentile: (175, 196, 218)
[bsw2_stat] low and high boundaries for computing mean and std.dev: (150, 304)
[bsw2_stat] mean and std.dev: (198.79, 29.56)
[bsw2_stat] low and high boundaries for proper pairs: (150, 347)
[bsw2_pair] #fixed=252, #rescued=20, #moved=0
[bsw2_stat] infer the insert size distribution from 12019 high-quality pairs.
[bsw2_stat] (25, 50, 75) percentile: (175, 196, 219)
[bsw2_stat] low and high boundaries for computing mean and std.dev: (150, 307)
[bsw2_stat] mean and std.dev: (198.99, 29.57)
[bsw2_stat] low and high boundaries for proper pairs: (150, 351)
[bsw2_pair] #fixed=237, #rescued=17, #moved=1
[bsw2_stat] infer the insert size distribution from 12006 high-quality pairs.
[bsw2_stat] (25, 50, 75) percentile: (174, 195, 218)
[bsw2_stat] low and high boundaries for computing mean and std.dev: (150, 306)
[bsw2_stat] mean and std.dev: (198.50, 29.18)
[bsw2_stat] low and high boundaries for proper pairs: (150, 350)
[bsw2_pair] #fixed=237, #rescued=18, #moved=3
[bsw2_stat] infer the insert size distribution from 12038 high-quality pairs.
[bsw2_stat] (25, 50, 75) percentile: (174, 195, 218)
[bsw2_stat] low and high boundaries for computing mean and std.dev: (150, 306)
[bsw2_stat] mean and std.dev: (198.37, 29.36)
[bsw2_stat] low and high boundaries for proper pairs: (150, 350)
[bsw2_pair] #fixed=244, #rescued=23, #moved=2
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa bwasw -t 4 /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta reads1.fastq reads2.fastq
[main] Real time: 37.441 sec; CPU: 94.092 sec
systime1.968
time37.4798939228
usrtime92.144
working_directory/project/teaser/genometeaser/tests_generated/b0bfc21db96b7744c4389e9b4b565dc9