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 Mapped25053191.92%
Wrongly Mapped220228.08%
Not Mapped00.0%
Total272553100.0%
Read Failure Statistics
Not mapped00.0%
Missing in mapper output00.0%
Mapped to wrong chromosome105833.883%
Mapped to wrong position114394.197%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments5
F-Measure0.957900
Precision0.919200
Recall1.000000
Timing
Raw Mapping Time175.756s
Effective Mapping Time171.300s
Effective Init Time4.456s
Effective Time MeasureCPU
Mapping Time (Wall)55.811s
Mapping Time (CPU)175.756s
Mapping Time (CPU User)166.956s
Mapping Time (CPU System)8.800s
Init Time (Wall)4.581s
Init Time (CPU)4.456s
Init Time (CPU User)0.088s
Init Time (CPU System)4.368s
Additional Information
Mapper Memory Usage5257 MB
Total Test Runtime (Wall)107.734s
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
memory4662712000
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/M_musculus_cutf.fasta reads_base.fastq
[main] Real time: 5.653 sec; CPU: 5.548 sec
systime5.424
time5.67800402641
usrtime0.14
working_directory/project/teaser/genometeaser/tests_generated/ef84d4ed82d0fef31ff0765d0f19324d

/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
memory4661000000
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/M_musculus_cutf.fasta reads_base.fastq
[main] Real time: 4.511 sec; CPU: 4.444 sec
systime4.368
time4.58065986633
usrtime0.088
working_directory/project/teaser/genometeaser/tests_generated/ef84d4ed82d0fef31ff0765d0f19324d

/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
memory5257612000
return0
status1
stderr
None
stdout
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 272553 sequences (27255300 bp)...
[M::mem_process_seqs] Processed 272553 reads in 169.252 CPU sec, 42.662 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: 55.764 sec; CPU: 175.720 sec
systime8.8
time55.8114211559
usrtime166.956
working_directory/project/teaser/genometeaser/tests_generated/ef84d4ed82d0fef31ff0765d0f19324d