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 Mapped22312196.686%
Wrongly Mapped76473.314%
Not Mapped00.0%
Total230768100.0%
Read Failure Statistics
Not mapped00.0%
Missing in mapper output00.0%
Mapped to wrong chromosome00.0%
Mapped to wrong position76473.314%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.983200
Precision0.966900
Recall1.000000
Timing
Raw Mapping Time51.272s
Effective Mapping Time51.208s
Effective Init Time0.064s
Effective Time MeasureCPU
Mapping Time (Wall)33.404s
Mapping Time (CPU)51.272s
Mapping Time (CPU User)49.904s
Mapping Time (CPU System)1.368s
Init Time (Wall)0.199s
Init Time (CPU)0.064s
Init Time (CPU User)0.008s
Init Time (CPU System)0.056s
Additional Information
Mapper Memory Usage150 MB
Total Test Runtime (Wall)67.905s
Mapper Command Line: 
/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/E_coli.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/E_coli.fasta reads_base.fastq -t 4 > out_bwamem.sam

command/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/E_coli.fasta reads_base.fastq -t 4 > out_bwamem.sam
memory16080000
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, 0.020 real sec
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa mem -t 4 /project/teaser/genometeaser/references/E_coli.fasta reads_base.fastq
[main] Real time: 0.102 sec; CPU: 0.040 sec
systime0.036
time0.140085935593
usrtime0.016
working_directory/project/teaser/genometeaser/tests_generated/f3cfc70a77888b8626def783d24d0e80

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

command/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/E_coli.fasta reads_base.fastq -t 4 > out_bwamem.sam
memory16080000
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, 0.047 real sec
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa mem -t 4 /project/teaser/genometeaser/references/E_coli.fasta reads_base.fastq
[main] Real time: 0.167 sec; CPU: 0.052 sec
systime0.056
time0.198652029037
usrtime0.008
working_directory/project/teaser/genometeaser/tests_generated/f3cfc70a77888b8626def783d24d0e80

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

command/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/E_coli.fasta reads1.fastq reads2.fastq -t 4 > out_bwamem.sam
memory150724000
return0
status1
stderr
None
stdout
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 230768 sequences (14999920 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 108212, 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: (126, 148, 171)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (36, 261)
[M::mem_pestat] mean and std.dev: (148.33, 32.76)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 306)
[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 230768 reads in 50.316 CPU sec, 22.551 real sec
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa mem -t 4 /project/teaser/genometeaser/references/E_coli.fasta reads1.fastq reads2.fastq
[main] Real time: 33.332 sec; CPU: 51.240 sec
systime1.368
time33.4039838314
usrtime49.904
working_directory/project/teaser/genometeaser/tests_generated/f3cfc70a77888b8626def783d24d0e80