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 Mapped1935370100.0%
Total1935370100.0%
Read Failure Statistics
Not mapped1935370100.0%
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 Time123.872s
Effective Mapping Time31.484s
Effective Init Time92.388s
Effective Time MeasureCPU
Mapping Time (Wall)127.673s
Mapping Time (CPU)123.872s
Mapping Time (CPU User)25.200s
Mapping Time (CPU System)98.672s
Init Time (Wall)92.839s
Init Time (CPU)92.388s
Init Time (CPU User)0.036s
Init Time (CPU System)92.352s
Additional Information
Mapper Memory Usage8953 MB
Total Test Runtime (Wall)479.901s
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
memory8272156000
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: 94.596 sec; CPU: 92.972 sec
systime93.004
time94.6091630459
usrtime0.02
working_directory/project/teaser/genometeaser/tests_generated/43bdd5cc22aa7c6d1994fe8ebc8d72d4

/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
memory8272144000
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: 92.814 sec; CPU: 92.336 sec
systime92.352
time92.8385660648
usrtime0.036
working_directory/project/teaser/genometeaser/tests_generated/43bdd5cc22aa7c6d1994fe8ebc8d72d4

/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
memory8953256000
return0
status1
stderr
None
stdout
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[bsw2_aln] read 1600000 sequences/pairs (40000000 bp) ...
[bsw2_aln] read 335370 sequences/pairs (8384250 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: 127.601 sec; CPU: 123.776 sec
systime98.672
time127.672791958
usrtime25.2
working_directory/project/teaser/genometeaser/tests_generated/43bdd5cc22aa7c6d1994fe8ebc8d72d4