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 Mapped52977888.465%
Wrongly Mapped6898311.519%
Not Mapped970.016%
Total598858100.0%
Read Failure Statistics
Not mapped970.016%
Missing in mapper output00.0%
Mapped to wrong chromosome412236.884%
Mapped to wrong position277604.635%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.938800
Precision0.884800
Recall0.999800
Timing
Raw Mapping Time116.292s
Effective Mapping Time113.796s
Effective Init Time2.496s
Effective Time MeasureCPU
Mapping Time (Wall)43.426s
Mapping Time (CPU)116.292s
Mapping Time (CPU User)107.520s
Mapping Time (CPU System)8.772s
Init Time (Wall)2.553s
Init Time (CPU)2.496s
Init Time (CPU User)0.016s
Init Time (CPU System)2.480s
Additional Information
Mapper Memory Usage895 MB
Total Test Runtime (Wall)140.184s
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, 0.009 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: 2.651 sec; CPU: 2.568 sec
systime2.572
time2.6728990078
usrtime0.012
working_directory/project/teaser/genometeaser/tests_generated/0bc744fc434e081e5d0279784d2334f3

/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
memory248880000
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 0.000 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: 2.521 sec; CPU: 2.472 sec
systime2.48
time2.55346608162
usrtime0.016
working_directory/project/teaser/genometeaser/tests_generated/0bc744fc434e081e5d0279784d2334f3

/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
memory895032000
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 111.436 CPU sec, 28.337 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: 43.362 sec; CPU: 116.276 sec
systime8.772
time43.4262878895
usrtime107.52
working_directory/project/teaser/genometeaser/tests_generated/0bc744fc434e081e5d0279784d2334f3