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 Mapped52930788.386%
Wrongly Mapped6944511.596%
Not Mapped1060.018%
Total598858100.0%
Read Failure Statistics
Not mapped1060.018%
Missing in mapper output00.0%
Mapped to wrong chromosome409856.844%
Mapped to wrong position284604.752%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.938400
Precision0.884000
Recall0.999800
Timing
Raw Mapping Time180.552s
Effective Mapping Time166.536s
Effective Init Time14.016s
Effective Time MeasureCPU
Mapping Time (Wall)74.832s
Mapping Time (CPU)180.552s
Mapping Time (CPU User)155.456s
Mapping Time (CPU System)25.096s
Init Time (Wall)14.391s
Init Time (CPU)14.016s
Init Time (CPU User)0.024s
Init Time (CPU System)13.992s
Additional Information
Mapper Memory Usage887 MB
Total Test Runtime (Wall)184.474s
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
memory248852000
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 0.112 CPU sec, 0.113 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: 7.635 sec; CPU: 7.320 sec
systime7.312
time7.78863310814
usrtime0.028
working_directory/project/teaser/genometeaser/tests_generated/f2a6f25cabc55338e734f1adbe44516b

/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 0.128 CPU sec, 0.127 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: 14.330 sec; CPU: 14.000 sec
systime13.992
time14.3914070129
usrtime0.024
working_directory/project/teaser/genometeaser/tests_generated/f2a6f25cabc55338e734f1adbe44516b

/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
memory887604000
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 165.020 CPU sec, 48.788 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: 74.779 sec; CPU: 180.508 sec
systime25.096
time74.8315939903
usrtime155.456
working_directory/project/teaser/genometeaser/tests_generated/f2a6f25cabc55338e734f1adbe44516b