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 Mapped44157291.264%
Wrongly Mapped415178.581%
Not Mapped7530.156%
Total483842100.0%
Read Failure Statistics
Not mapped7530.156%
Missing in mapper output00.0%
Mapped to wrong chromosome214244.428%
Mapped to wrong position200934.153%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment36
Secondary Alignments0
F-Measure0.954300
Precision0.914100
Recall0.998300
Timing
Raw Mapping Time1321.008s
Effective Mapping Time1243.528s
Effective Init Time77.480s
Effective Time MeasureCPU
Mapping Time (Wall)413.863s
Mapping Time (CPU)1321.008s
Mapping Time (CPU User)1119.960s
Mapping Time (CPU System)201.048s
Init Time (Wall)78.563s
Init Time (CPU)77.480s
Init Time (CPU User)0.192s
Init Time (CPU System)77.288s
Additional Information
Mapper Memory Usage8701 MB
Total Test Runtime (Wall)645.667s
Mapper Command Line: 
/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/M_musculus.fasta reads.fastq -t 4 > out_bwasw.sam
Errors and Warnings
No problems were encountered.
Subprocess Log

/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/M_musculus.fasta reads_base.fastq -t 4 > out_bwasw.sam

command/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/M_musculus.fasta reads_base.fastq -t 4 > out_bwasw.sam
memory8272220000
return0
status1
stderr
None
stdout
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[bsw2_aln] read 1 sequences/pairs (60 bp) ...
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa bwasw -t 4 /project/teaser/genometeaser/references/M_musculus.fasta reads_base.fastq
[main] Real time: 76.622 sec; CPU: 74.960 sec
systime74.872
time76.6466460228
usrtime0.104
working_directory/project/teaser/genometeaser/tests_generated/0c6bc0fb80fb6958e0d82aa8c71411b8

/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/M_musculus.fasta reads_base.fastq -t 4 > out_bwasw.sam

command/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/M_musculus.fasta reads_base.fastq -t 4 > out_bwasw.sam
memory8272120000
return0
status1
stderr
None
stdout
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[bsw2_aln] read 1 sequences/pairs (60 bp) ...
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa bwasw -t 4 /project/teaser/genometeaser/references/M_musculus.fasta reads_base.fastq
[main] Real time: 78.521 sec; CPU: 77.460 sec
systime77.288
time78.5626308918
usrtime0.192
working_directory/project/teaser/genometeaser/tests_generated/0c6bc0fb80fb6958e0d82aa8c71411b8

/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/M_musculus.fasta reads.fastq -t 4 > out_bwasw.sam

command/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/M_musculus.fasta reads.fastq -t 4 > out_bwasw.sam
memory8701580000
return0
status1
stderr
None
stdout
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[bsw2_aln] read 400000 sequences/pairs (40000000 bp) ...
[bsw2_aln] read 83842 sequences/pairs (8384200 bp) ...
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa bwasw -t 4 /project/teaser/genometeaser/references/M_musculus.fasta reads.fastq
[main] Real time: 413.785 sec; CPU: 1320.940 sec
systime201.048
time413.863471031
usrtime1119.96
working_directory/project/teaser/genometeaser/tests_generated/0c6bc0fb80fb6958e0d82aa8c71411b8