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 Mapped00.0%
Wrongly Mapped00.0%
Not Mapped2199284100.0%
Total2199284100.0%
Read Failure Statistics
Not mapped2199284100.0%
Missing in mapper output00.0%
Mapped to wrong chromosome00.0%
Mapped to wrong position00.0%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.000000
Precision0.000000
Recall0.000000
Timing
Raw Mapping Time26.232s
Effective Mapping Time18.456s
Effective Init Time7.776s
Effective Time MeasureCPU
Mapping Time (Wall)31.724s
Mapping Time (CPU)26.232s
Mapping Time (CPU User)16.304s
Mapping Time (CPU System)9.928s
Init Time (Wall)7.861s
Init Time (CPU)7.776s
Init Time (CPU User)0.160s
Init Time (CPU System)7.616s
Additional Information
Mapper Memory Usage8987 MB
Total Test Runtime (Wall)228.210s
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
memory8271996000
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: 7.836 sec; CPU: 7.748 sec
systime7.604
time7.85786604881
usrtime0.176
working_directory/project/teaser/genometeaser/tests_generated/3f55d5f326042c6d121b7048b0ae8ccd

/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
memory8272128000
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: 7.830 sec; CPU: 7.752 sec
systime7.616
time7.86128520966
usrtime0.16
working_directory/project/teaser/genometeaser/tests_generated/3f55d5f326042c6d121b7048b0ae8ccd

/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
memory8987012000
return0
status1
stderr
None
stdout
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[bsw2_aln] read 1818182 sequences/pairs (40000004 bp) ...
[bsw2_aln] read 381102 sequences/pairs (8384244 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: 31.635 sec; CPU: 26.152 sec
systime9.928
time31.7243888378
usrtime16.304
working_directory/project/teaser/genometeaser/tests_generated/3f55d5f326042c6d121b7048b0ae8ccd