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 Mapped9891398.913%
Wrongly Mapped10871.087%
Not Mapped00.0%
Total100000100.0%
Read Failure Statistics
Not mapped00.0%
Missing in mapper output00.0%
Mapped to wrong chromosome8690.869%
Mapped to wrong position2180.218%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.994500
Precision0.989100
Recall1.000000
Timing
Raw Mapping Time31.716s
Effective Mapping Time31.680s
Effective Init Time0.036s
Effective Time MeasureCPU
Mapping Time (Wall)20.529s
Mapping Time (CPU)31.716s
Mapping Time (CPU User)31.152s
Mapping Time (CPU System)0.564s
Init Time (Wall)0.148s
Init Time (CPU)0.036s
Init Time (CPU User)0.012s
Init Time (CPU System)0.024s
Additional Information
Mapper Memory Usage114 MB
Total Test Runtime (Wall)43.087s
Mapper Command Line: 
/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta 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/Saccharomyces_cerevisiae.fasta reads_base.fastq -t 4 > out_bwamem.sam

command/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta reads_base.fastq -t 4 > out_bwamem.sam
memory25640000
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 0.004 CPU sec, 0.048 real sec
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa mem -t 4 /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta reads_base.fastq
[main] Real time: 0.166 sec; CPU: 0.052 sec
systime0.044
time0.19435095787
usrtime0.012
working_directory/project/teaser/genometeaser/tests_generated/b0bfc21db96b7744c4389e9b4b565dc9

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

command/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta reads_base.fastq -t 4 > out_bwamem.sam
memory24808000
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 0.004 CPU sec, 0.048 real sec
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa mem -t 4 /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta reads_base.fastq
[main] Real time: 0.121 sec; CPU: 0.032 sec
systime0.024
time0.14816403389
usrtime0.012
working_directory/project/teaser/genometeaser/tests_generated/b0bfc21db96b7744c4389e9b4b565dc9

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

command/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta reads1.fastq reads2.fastq -t 4 > out_bwamem.sam
memory114224000
return0
status1
stderr
None
stdout
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 100000 sequences (15000000 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 48197, 43, 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: (80, 103, 125)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 215)
[M::mem_pestat] mean and std.dev: (102.33, 32.42)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 260)
[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 100000 reads in 31.316 CPU sec, 14.096 real sec
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa mem -t 4 /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta reads1.fastq reads2.fastq
[main] Real time: 20.482 sec; CPU: 31.696 sec
systime0.564
time20.5292310715
usrtime31.152
working_directory/project/teaser/genometeaser/tests_generated/b0bfc21db96b7744c4389e9b4b565dc9