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 Mapped44365691.694%
Wrongly Mapped401868.306%
Not Mapped00.0%
Total483842100.0%
Read Failure Statistics
Not mapped00.0%
Missing in mapper output00.0%
Mapped to wrong chromosome204174.22%
Mapped to wrong position197694.086%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments4
F-Measure0.956700
Precision0.916900
Recall1.000000
Timing
Raw Mapping Time769.492s
Effective Mapping Time685.236s
Effective Init Time84.256s
Effective Time MeasureCPU
Mapping Time (Wall)325.461s
Mapping Time (CPU)769.492s
Mapping Time (CPU User)508.364s
Mapping Time (CPU System)261.128s
Init Time (Wall)87.073s
Init Time (CPU)84.256s
Init Time (CPU User)0.052s
Init Time (CPU System)84.204s
Additional Information
Mapper Memory Usage9167 MB
Total Test Runtime (Wall)599.347s
Mapper Command Line: 
/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/M_musculus.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.fasta reads_base.fastq -t 4 > out_bwamem.sam

command/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/M_musculus.fasta reads_base.fastq -t 4 > out_bwamem.sam
memory8271704000
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, 0.020 real sec
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa mem -t 4 /project/teaser/genometeaser/references/M_musculus.fasta reads_base.fastq
[main] Real time: 103.911 sec; CPU: 85.152 sec
systime85.084
time103.965396881
usrtime0.084
working_directory/project/teaser/genometeaser/tests_generated/0c6bc0fb80fb6958e0d82aa8c71411b8

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

command/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/M_musculus.fasta reads_base.fastq -t 4 > out_bwamem.sam
memory8271732000
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 0.020 CPU sec, 0.010 real sec
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa mem -t 4 /project/teaser/genometeaser/references/M_musculus.fasta reads_base.fastq
[main] Real time: 87.018 sec; CPU: 84.236 sec
systime84.204
time87.072685957
usrtime0.052
working_directory/project/teaser/genometeaser/tests_generated/0c6bc0fb80fb6958e0d82aa8c71411b8

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

command/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/M_musculus.fasta reads.fastq -t 4 > out_bwamem.sam
memory9167464000
return0
status1
stderr
None
stdout
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 400000 sequences (40000000 bp)...
[M::process] read 83842 sequences (8384200 bp)...
[M::mem_process_seqs] Processed 400000 reads in 552.264 CPU sec, 191.659 real sec
[M::mem_process_seqs] Processed 83842 reads in 127.208 CPU sec, 36.011 real sec
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa mem -t 4 /project/teaser/genometeaser/references/M_musculus.fasta reads.fastq
[main] Real time: 325.197 sec; CPU: 769.476 sec
systime261.128
time325.460940838
usrtime508.364
working_directory/project/teaser/genometeaser/tests_generated/0c6bc0fb80fb6958e0d82aa8c71411b8