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 Mapped52963688.441%
Wrongly Mapped6913411.544%
Not Mapped880.015%
Total598858100.0%
Read Failure Statistics
Not mapped880.015%
Missing in mapper output00.0%
Mapped to wrong chromosome407796.809%
Mapped to wrong position283554.735%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.938700
Precision0.884500
Recall0.999800
Timing
Raw Mapping Time74.560s
Effective Mapping Time74.308s
Effective Init Time0.252s
Effective Time MeasureCPU
Mapping Time (Wall)30.345s
Mapping Time (CPU)74.560s
Mapping Time (CPU User)71.184s
Mapping Time (CPU System)3.376s
Init Time (Wall)0.300s
Init Time (CPU)0.252s
Init Time (CPU User)0.012s
Init Time (CPU System)0.240s
Additional Information
Mapper Memory Usage892 MB
Total Test Runtime (Wall)101.792s
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
memory250616000
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: 0.277 sec; CPU: 0.244 sec
systime0.232
time0.299506187439
usrtime0.028
working_directory/project/teaser/genometeaser/tests_generated/940d34bf07c6143b2e6e8116a29b2b51

/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
memory250620000
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: 0.271 sec; CPU: 0.236 sec
systime0.24
time0.300132036209
usrtime0.012
working_directory/project/teaser/genometeaser/tests_generated/940d34bf07c6143b2e6e8116a29b2b51

/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
memory892924000
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 72.816 CPU sec, 18.443 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: 30.293 sec; CPU: 74.512 sec
systime3.376
time30.3446550369
usrtime71.184
working_directory/project/teaser/genometeaser/tests_generated/940d34bf07c6143b2e6e8116a29b2b51