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 Mapped9926099.26%
Wrongly Mapped7400.74%
Not Mapped00.0%
Total100000100.0%
Read Failure Statistics
Not mapped00.0%
Missing in mapper output00.0%
Mapped to wrong chromosome5380.538%
Mapped to wrong position2020.202%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.996300
Precision0.992600
Recall1.000000
Timing
Raw Mapping Time21.624s
Effective Mapping Time21.576s
Effective Init Time0.048s
Effective Time MeasureCPU
Mapping Time (Wall)9.391s
Mapping Time (CPU)21.624s
Mapping Time (CPU User)21.068s
Mapping Time (CPU System)0.556s
Init Time (Wall)0.111s
Init Time (CPU)0.048s
Init Time (CPU User)0.004s
Init Time (CPU System)0.044s
Additional Information
Mapper Memory Usage114 MB
Total Test Runtime (Wall)30.324s
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
memory24120000
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/Saccharomyces_cerevisiae.fasta reads_base.fastq
[main] Real time: 0.064 sec; CPU: 0.040 sec
systime0.04
time0.0862820148468
usrtime0.008
working_directory/project/teaser/genometeaser/tests_generated/bc5e667ff41f75be5690d71ac8911c05

/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
memory23928000
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/Saccharomyces_cerevisiae.fasta reads_base.fastq
[main] Real time: 0.071 sec; CPU: 0.040 sec
systime0.044
time0.111264944077
usrtime0.004
working_directory/project/teaser/genometeaser/tests_generated/bc5e667ff41f75be5690d71ac8911c05

/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
memory114376000
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, 48399, 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: (377, 399, 422)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (287, 512)
[M::mem_pestat] mean and std.dev: (399.17, 33.06)
[M::mem_pestat] low and high boundaries for proper pairs: (242, 557)
[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 100000 reads in 21.080 CPU sec, 5.288 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: 9.359 sec; CPU: 21.604 sec
systime0.556
time9.39092302322
usrtime21.068
working_directory/project/teaser/genometeaser/tests_generated/bc5e667ff41f75be5690d71ac8911c05