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 Mapped77218585.962%
Wrongly Mapped11568512.878%
Not Mapped104171.16%
Total898287100.0%
Read Failure Statistics
Not mapped104171.16%
Missing in mapper output00.0%
Mapped to wrong chromosome727028.093%
Mapped to wrong position429834.785%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.924500
Precision0.869700
Recall0.986700
Timing
Raw Mapping Time90.648s
Effective Mapping Time90.468s
Effective Init Time0.180s
Effective Time MeasureCPU
Mapping Time (Wall)37.095s
Mapping Time (CPU)90.648s
Mapping Time (CPU User)86.580s
Mapping Time (CPU System)4.068s
Init Time (Wall)0.260s
Init Time (CPU)0.180s
Init Time (CPU User)0.016s
Init Time (CPU System)0.164s
Additional Information
Mapper Memory Usage1300 MB
Total Test Runtime (Wall)96.636s
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
memory322468000
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: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa mem -t 4 /project/teaser/genometeaser/references/D_melanogaster.fasta reads_base.fastq
[main] Real time: 0.309 sec; CPU: 0.256 sec
systime0.26
time0.345150947571
usrtime0.016
working_directory/project/teaser/genometeaser/tests_generated/be9adfa40f58b4dfd03b6dd3624949ef

/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
memory322468000
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 -t 4 /project/teaser/genometeaser/references/D_melanogaster.fasta reads_base.fastq
[main] Real time: 0.208 sec; CPU: 0.156 sec
systime0.164
time0.260456085205
usrtime0.016
working_directory/project/teaser/genometeaser/tests_generated/be9adfa40f58b4dfd03b6dd3624949ef

/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
memory1300000000
return0
status1
stderr
None
stdout
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 898287 sequences (35931480 bp)...
[M::mem_process_seqs] Processed 898287 reads in 89.124 CPU sec, 22.708 real sec
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa mem -t 4 /project/teaser/genometeaser/references/D_melanogaster.fasta reads.fastq
[main] Real time: 37.040 sec; CPU: 90.632 sec
systime4.068
time37.094894886
usrtime86.58
working_directory/project/teaser/genometeaser/tests_generated/be9adfa40f58b4dfd03b6dd3624949ef