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 Mapped17668099.243%
Wrongly Mapped13480.757%
Not Mapped00.0%
Total178028100.0%
Read Failure Statistics
Not mapped00.0%
Missing in mapper output00.0%
Mapped to wrong chromosome8000.449%
Mapped to wrong position5480.308%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.996200
Precision0.992400
Recall1.000000
Timing
Raw Mapping Time137.480s
Effective Mapping Time133.996s
Effective Init Time3.484s
Effective Time MeasureCPU
Mapping Time (Wall)43.977s
Mapping Time (CPU)137.480s
Mapping Time (CPU User)130.244s
Mapping Time (CPU System)7.236s
Init Time (Wall)5.895s
Init Time (CPU)3.484s
Init Time (CPU User)0.068s
Init Time (CPU System)3.416s
Additional Information
Mapper Memory Usage4813 MB
Total Test Runtime (Wall)83.609s
Mapper Command Line: 
/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/Bos_taurus.fa 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/Bos_taurus.fa reads_base.fastq -t 4 > out_bwamem.sam

command/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/Bos_taurus.fa reads_base.fastq -t 4 > out_bwamem.sam
memory4568220000
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 0.008 CPU sec, 0.007 real sec
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa mem -t 4 /project/teaser/genometeaser/references/Bos_taurus.fa reads_base.fastq
[main] Real time: 3.486 sec; CPU: 3.368 sec
systime3.324
time3.50685787201
usrtime0.056
working_directory/project/teaser/genometeaser/tests_generated/14e5e97d9d3c2238f7310baab576d567

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

command/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/Bos_taurus.fa reads_base.fastq -t 4 > out_bwamem.sam
memory4570024000
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, 0.003 real sec
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa mem -t 4 /project/teaser/genometeaser/references/Bos_taurus.fa reads_base.fastq
[main] Real time: 5.864 sec; CPU: 3.472 sec
systime3.416
time5.89456796646
usrtime0.068
working_directory/project/teaser/genometeaser/tests_generated/14e5e97d9d3c2238f7310baab576d567

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

command/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/Bos_taurus.fa reads1.fastq reads2.fastq -t 4 > out_bwamem.sam
memory4813252000
return0
status1
stderr
None
stdout
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 178028 sequences (26704200 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 79086, 108, 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: (78, 100, 122)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 210)
[M::mem_pestat] mean and std.dev: (100.24, 32.54)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 254)
[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 178028 reads in 133.252 CPU sec, 33.530 real sec
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa mem -t 4 /project/teaser/genometeaser/references/Bos_taurus.fa reads1.fastq reads2.fastq
[main] Real time: 43.937 sec; CPU: 137.468 sec
systime7.236
time43.9769229889
usrtime130.244
working_directory/project/teaser/genometeaser/tests_generated/14e5e97d9d3c2238f7310baab576d567