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 Mapped32713091.043%
Wrongly Mapped321848.957%
Not Mapped00.0%
Total359314100.0%
Read Failure Statistics
Not mapped00.0%
Missing in mapper output00.0%
Mapped to wrong chromosome173594.831%
Mapped to wrong position148254.126%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.953100
Precision0.910400
Recall1.000000
Timing
Raw Mapping Time76.391s
Effective Mapping Time76.185s
Effective Init Time0.206s
Effective Time MeasureCPU
Mapping Time (Wall)38.317s
Mapping Time (CPU)76.391s
Mapping Time (CPU User)75.779s
Mapping Time (CPU System)0.612s
Init Time (Wall)0.238s
Init Time (CPU)0.206s
Init Time (CPU User)0.010s
Init Time (CPU System)0.196s
Additional Information
Mapper Memory Usage608 MB
Total Test Runtime (Wall)56.839s
Mapper Command Line: 
/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/D_melanogaster.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/D_melanogaster.fasta reads_base.fastq -t 4 > out_bwamem.sam

command/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/D_melanogaster.fasta reads_base.fastq -t 4 > out_bwamem.sam
memory247128000
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, 0.000 real sec
[main] Version: 0.7.12-r1039
[main] CMD: /project/teaser/genometeaser/software/bwa mem -t 4 /project/teaser/genometeaser/references/D_melanogaster.fasta reads_base.fastq
[main] Real time: 0.231 sec; CPU: 0.206 sec
systime0.200969
time0.235604047775
usrtime0.007998
working_directory/project/teaser/genometeaser/tests_generated/6e77d132a218d55fc27515c6d7f3e63e

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

command/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/D_melanogaster.fasta reads_base.fastq -t 4 > out_bwamem.sam
memory247136000
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 0.001 CPU sec, 0.001 real sec
[main] Version: 0.7.12-r1039
[main] CMD: /project/teaser/genometeaser/software/bwa mem -t 4 /project/teaser/genometeaser/references/D_melanogaster.fasta reads_base.fastq
[main] Real time: 0.234 sec; CPU: 0.202 sec
systime0.19597
time0.237806081772
usrtime0.009998
working_directory/project/teaser/genometeaser/tests_generated/6e77d132a218d55fc27515c6d7f3e63e

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

command/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/D_melanogaster.fasta reads1.fastq reads2.fastq -t 4 > out_bwamem.sam
memory608504000
return0
status1
stderr
None
stdout
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 359314 sequences (35931400 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 149279, 150, 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: (77, 99, 121)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 209)
[M::mem_pestat] mean and std.dev: (99.12, 32.19)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 253)
[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 359314 reads in 75.770 CPU sec, 36.298 real sec
[main] Version: 0.7.12-r1039
[main] CMD: /project/teaser/genometeaser/software/bwa mem -t 4 /project/teaser/genometeaser/references/D_melanogaster.fasta reads1.fastq reads2.fastq
[main] Real time: 38.306 sec; CPU: 76.381 sec
systime0.611906
time38.3165400028
usrtime75.779479
working_directory/project/teaser/genometeaser/tests_generated/6e77d132a218d55fc27515c6d7f3e63e