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 Mapped52870588.286%
Wrongly Mapped7006111.699%
Not Mapped920.015%
Total598858100.0%
Read Failure Statistics
Not mapped920.015%
Missing in mapper output00.0%
Mapped to wrong chromosome416396.953%
Mapped to wrong position284224.746%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.937800
Precision0.883000
Recall0.999800
Timing
Raw Mapping Time90.524s
Effective Mapping Time89.260s
Effective Init Time1.264s
Effective Time MeasureCPU
Mapping Time (Wall)35.648s
Mapping Time (CPU)90.524s
Mapping Time (CPU User)84.788s
Mapping Time (CPU System)5.736s
Init Time (Wall)1.343s
Init Time (CPU)1.264s
Init Time (CPU User)0.024s
Init Time (CPU System)1.240s
Additional Information
Mapper Memory Usage897 MB
Total Test Runtime (Wall)86.563s
Mapper Command Line: 
/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/D_melanogaster.fasta reads.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
memory248856000
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, 0.001 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: 1.300 sec; CPU: 1.232 sec
systime1.248
time1.33453202248
usrtime0.012
working_directory/project/teaser/genometeaser/tests_generated/36c0b9ed4ca2236f8f8f48f19e427ab8

/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
memory248848000
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: 0.7.12-r1039
[main] CMD: /project/teaser/genometeaser/software/bwa mem -t 4 /project/teaser/genometeaser/references/D_melanogaster.fasta reads_base.fastq
[main] Real time: 1.303 sec; CPU: 1.248 sec
systime1.24
time1.34279799461
usrtime0.024
working_directory/project/teaser/genometeaser/tests_generated/36c0b9ed4ca2236f8f8f48f19e427ab8

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

command/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/D_melanogaster.fasta reads.fastq -t 4 > out_bwamem.sam
memory897404000
return0
status1
stderr
None
stdout
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 598858 sequences (35931480 bp)...
[M::mem_process_seqs] Processed 598858 reads in 87.220 CPU sec, 22.177 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.fastq
[main] Real time: 35.586 sec; CPU: 90.464 sec
systime5.736
time35.6483938694
usrtime84.788
working_directory/project/teaser/genometeaser/tests_generated/36c0b9ed4ca2236f8f8f48f19e427ab8