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 Mapped32545090.75%
Wrongly Mapped331689.249%
Not Mapped50.001%
Total358623100.0%
Read Failure Statistics
Not mapped50.001%
Missing in mapper output00.0%
Mapped to wrong chromosome173064.826%
Mapped to wrong position158624.423%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments2
F-Measure0.951500
Precision0.907500
Recall1.000000
Timing
Raw Mapping Time290.056s
Effective Mapping Time201.764s
Effective Init Time88.292s
Effective Time MeasureCPU
Mapping Time (Wall)160.218s
Mapping Time (CPU)290.056s
Mapping Time (CPU User)156.260s
Mapping Time (CPU System)133.796s
Init Time (Wall)89.092s
Init Time (CPU)88.292s
Init Time (CPU User)0.016s
Init Time (CPU System)88.276s
Additional Information
Mapper Memory Usage5524 MB
Total Test Runtime (Wall)351.060s
Mapper Command Line: 
/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/M_musculus_cutf.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/M_musculus_cutf.fasta reads_base.fastq -t 4 > out_bwamem.sam

command/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/M_musculus_cutf.fasta reads_base.fastq -t 4 > out_bwamem.sam
memory4660860000
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, 0.010 real sec
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa mem -t 4 /project/teaser/genometeaser/references/M_musculus_cutf.fasta reads_base.fastq
[main] Real time: 54.110 sec; CPU: 53.760 sec
systime53.748
time54.133551836
usrtime0.024
working_directory/project/teaser/genometeaser/tests_generated/9616eba5217c671aa1e17d118aefe3c9

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

command/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/M_musculus_cutf.fasta reads_base.fastq -t 4 > out_bwamem.sam
memory4660860000
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 0.048 CPU sec, 0.040 real sec
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa mem -t 4 /project/teaser/genometeaser/references/M_musculus_cutf.fasta reads_base.fastq
[main] Real time: 89.063 sec; CPU: 88.276 sec
systime88.276
time89.0921339989
usrtime0.016
working_directory/project/teaser/genometeaser/tests_generated/9616eba5217c671aa1e17d118aefe3c9

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

command/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/M_musculus_cutf.fasta reads.fastq -t 4 > out_bwamem.sam
memory5524224000
return0
status1
stderr
None
stdout
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 358623 sequences (27255348 bp)...
[M::mem_process_seqs] Processed 358623 reads in 185.096 CPU sec, 47.090 real sec
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa mem -t 4 /project/teaser/genometeaser/references/M_musculus_cutf.fasta reads.fastq
[main] Real time: 160.172 sec; CPU: 290.040 sec
systime133.796
time160.217917919
usrtime156.26
working_directory/project/teaser/genometeaser/tests_generated/9616eba5217c671aa1e17d118aefe3c9