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 Mapped59176196.201%
Wrongly Mapped233653.798%
Not Mapped20.0%
Total615128100.0%
Read Failure Statistics
Not mapped20.0%
Missing in mapper output00.0%
Mapped to wrong chromosome159262.589%
Mapped to wrong position74391.209%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments1
F-Measure0.980600
Precision0.962000
Recall1.000000
Timing
Raw Mapping Time962.304s
Effective Mapping Time936.548s
Effective Init Time25.756s
Effective Time MeasureCPU
Mapping Time (Wall)548.264s
Mapping Time (CPU)962.304s
Mapping Time (CPU User)853.064s
Mapping Time (CPU System)109.240s
Init Time (Wall)26.372s
Init Time (CPU)25.756s
Init Time (CPU User)0.208s
Init Time (CPU System)25.548s
Additional Information
Mapper Memory Usage6531 MB
Total Test Runtime (Wall)677.279s
Mapper Command Line: 
/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/H_sapiens.fa reads1.fastq reads2.fastq -M -t 4 > out_bwamem_01.sam
Errors and Warnings
No problems were encountered.
Subprocess Log

/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/H_sapiens.fa reads_base.fastq -M -t 4 > out_bwamem_01.sam

command/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/H_sapiens.fa reads_base.fastq -M -t 4 > out_bwamem_01.sam
memory5364576000
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 0.020 CPU sec, 0.072 real sec
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa mem -M -t 4 /project/teaser/genometeaser/references/H_sapiens.fa reads_base.fastq
[main] Real time: 27.228 sec; CPU: 24.648 sec
systime24.38
time27.2488241196
usrtime0.284
working_directory/project/teaser/genometeaser/tests_generated/4ff0769a44d529563c64b75a1aaf552d

/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/H_sapiens.fa reads_base.fastq -M -t 4 > out_bwamem_01.sam

command/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/H_sapiens.fa reads_base.fastq -M -t 4 > out_bwamem_01.sam
memory5364384000
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, 0.002 real sec
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa mem -M -t 4 /project/teaser/genometeaser/references/H_sapiens.fa reads_base.fastq
[main] Real time: 26.339 sec; CPU: 25.740 sec
systime25.548
time26.3722350597
usrtime0.208
working_directory/project/teaser/genometeaser/tests_generated/4ff0769a44d529563c64b75a1aaf552d

/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/H_sapiens.fa reads1.fastq reads2.fastq -M -t 4 > out_bwamem_01.sam

command/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/H_sapiens.fa reads1.fastq reads2.fastq -M -t 4 > out_bwamem_01.sam
memory6531900000
return0
status1
stderr
None
stdout
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 615128 sequences (31371528 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 237439, 282, 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: (76, 98, 120)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 208)
[M::mem_pestat] mean and std.dev: (98.09, 32.64)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 252)
[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 615128 reads in 934.172 CPU sec, 495.887 real sec
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa mem -M -t 4 /project/teaser/genometeaser/references/H_sapiens.fa reads1.fastq reads2.fastq
[main] Real time: 548.084 sec; CPU: 962.296 sec
systime109.24
time548.264080048
usrtime853.064
working_directory/project/teaser/genometeaser/tests_generated/4ff0769a44d529563c64b75a1aaf552d