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 Mapped70555687.494%
Wrongly Mapped9288511.518%
Not Mapped79630.987%
Total806404100.0%
Read Failure Statistics
Not mapped79630.987%
Missing in mapper output00.0%
Mapped to wrong chromosome542916.732%
Mapped to wrong position385934.786%
Mapped to wrong strand10.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.933300
Precision0.883700
Recall0.988800
Timing
Raw Mapping Time284.720s
Effective Mapping Time272.452s
Effective Init Time12.268s
Effective Time MeasureCPU
Mapping Time (Wall)144.788s
Mapping Time (CPU)284.720s
Mapping Time (CPU User)247.312s
Mapping Time (CPU System)37.408s
Init Time (Wall)12.439s
Init Time (CPU)12.268s
Init Time (CPU User)0.384s
Init Time (CPU System)11.884s
Additional Information
Mapper Memory Usage7221 MB
Total Test Runtime (Wall)986.821s
Mapper Command Line: 
/project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/M_musculus.fasta reads.fastq -t 4 > out_bwa.sam.bwa; /project/teaser/genometeaser/software/bwa samse /project/teaser/genometeaser/references/M_musculus.fasta out_bwa.sam.bwa reads.fastq > out_bwa.sam
Errors and Warnings
No problems were encountered.
Subprocess Log

/project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/M_musculus.fasta reads_base.fastq -t 4 > out_bwa.sam.bwa; /project/teaser/genometeaser/software/bwa samse /project/teaser/genometeaser/references/M_musculus.fasta out_bwa.sam.bwa reads_base.fastq > out_bwa.sam

command/project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/M_musculus.fasta reads_base.fastq -t 4 > out_bwa.sam.bwa; /project/teaser/genometeaser/software/bwa samse /project/teaser/genometeaser/references/M_musculus.fasta out_bwa.sam.bwa reads_base.fastq > out_bwa.sam
memory7090952000
return0
status1
stderr
None
stdout
[bwa_aln] 17bp reads: max_diff = 2
[bwa_aln] 38bp reads: max_diff = 3
[bwa_aln] 64bp reads: max_diff = 4
[bwa_aln] 93bp reads: max_diff = 5
[bwa_aln] 124bp reads: max_diff = 6
[bwa_aln] 157bp reads: max_diff = 7
[bwa_aln] 190bp reads: max_diff = 8
[bwa_aln] 225bp reads: max_diff = 9
[bwa_aln_core] calculate SA coordinate... 0.00 sec
[bwa_aln_core] write to the disk... 0.00 sec
[bwa_aln_core] 1 sequences have been processed.
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa aln -t 4 /project/teaser/genometeaser/references/M_musculus.fasta reads_base.fastq
[main] Real time: 411.567 sec; CPU: 7.056 sec
[bwa_aln_core] convert to sequence coordinate... 9.32 sec
[bwa_aln_core] refine gapped alignments... 2.13 sec
[bwa_aln_core] print alignments... 0.00 sec
[bwa_aln_core] 1 sequences have been processed.
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa samse /project/teaser/genometeaser/references/M_musculus.fasta out_bwa.sam.bwa reads_base.fastq
[main] Real time: 313.758 sec; CPU: 11.460 sec
systime18.292
time725.390964031
usrtime0.24
working_directory/project/teaser/genometeaser/tests_generated/023be73dabd493f04945e37217bf7c31

/project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/M_musculus.fasta reads_base.fastq -t 4 > out_bwa.sam.bwa; /project/teaser/genometeaser/software/bwa samse /project/teaser/genometeaser/references/M_musculus.fasta out_bwa.sam.bwa reads_base.fastq > out_bwa.sam

command/project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/M_musculus.fasta reads_base.fastq -t 4 > out_bwa.sam.bwa; /project/teaser/genometeaser/software/bwa samse /project/teaser/genometeaser/references/M_musculus.fasta out_bwa.sam.bwa reads_base.fastq > out_bwa.sam
memory7091016000
return0
status1
stderr
None
stdout
[bwa_aln] 17bp reads: max_diff = 2
[bwa_aln] 38bp reads: max_diff = 3
[bwa_aln] 64bp reads: max_diff = 4
[bwa_aln] 93bp reads: max_diff = 5
[bwa_aln] 124bp reads: max_diff = 6
[bwa_aln] 157bp reads: max_diff = 7
[bwa_aln] 190bp reads: max_diff = 8
[bwa_aln] 225bp reads: max_diff = 9
[bwa_aln_core] calculate SA coordinate... 0.00 sec
[bwa_aln_core] write to the disk... 0.00 sec
[bwa_aln_core] 1 sequences have been processed.
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa aln -t 4 /project/teaser/genometeaser/references/M_musculus.fasta reads_base.fastq
[main] Real time: 4.452 sec; CPU: 4.404 sec
[bwa_aln_core] convert to sequence coordinate... 6.69 sec
[bwa_aln_core] refine gapped alignments... 1.15 sec
[bwa_aln_core] print alignments... 0.00 sec
[bwa_aln_core] 1 sequences have been processed.
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa samse /project/teaser/genometeaser/references/M_musculus.fasta out_bwa.sam.bwa reads_base.fastq
[main] Real time: 7.924 sec; CPU: 7.844 sec
systime11.884
time12.4391520023
usrtime0.384
working_directory/project/teaser/genometeaser/tests_generated/023be73dabd493f04945e37217bf7c31

/project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/M_musculus.fasta reads.fastq -t 4 > out_bwa.sam.bwa; /project/teaser/genometeaser/software/bwa samse /project/teaser/genometeaser/references/M_musculus.fasta out_bwa.sam.bwa reads.fastq > out_bwa.sam

command/project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/M_musculus.fasta reads.fastq -t 4 > out_bwa.sam.bwa; /project/teaser/genometeaser/software/bwa samse /project/teaser/genometeaser/references/M_musculus.fasta out_bwa.sam.bwa reads.fastq > out_bwa.sam
memory7221892000
return0
status1
stderr
None
stdout
[bwa_aln] 17bp reads: max_diff = 2
[bwa_aln] 38bp reads: max_diff = 3
[bwa_aln] 64bp reads: max_diff = 4
[bwa_aln] 93bp reads: max_diff = 5
[bwa_aln] 124bp reads: max_diff = 6
[bwa_aln] 157bp reads: max_diff = 7
[bwa_aln] 190bp reads: max_diff = 8
[bwa_aln] 225bp reads: max_diff = 9
[bwa_aln_core] calculate SA coordinate... 63.23 sec
[bwa_aln_core] write to the disk... 0.14 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_aln_core] calculate SA coordinate... 78.20 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 524288 sequences have been processed.
[bwa_aln_core] calculate SA coordinate... 78.01 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 786432 sequences have been processed.
[bwa_aln_core] calculate SA coordinate... 5.88 sec
[bwa_aln_core] write to the disk... 0.01 sec
[bwa_aln_core] 806404 sequences have been processed.
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa aln -t 4 /project/teaser/genometeaser/references/M_musculus.fasta reads.fastq
[main] Real time: 82.303 sec; CPU: 232.064 sec
[bwa_aln_core] convert to sequence coordinate... 9.37 sec
[bwa_aln_core] refine gapped alignments... 3.15 sec
[bwa_aln_core] print alignments... 1.40 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_aln_core] convert to sequence coordinate... 9.51 sec
[bwa_aln_core] refine gapped alignments... 3.07 sec
[bwa_aln_core] print alignments... 1.37 sec
[bwa_aln_core] 524288 sequences have been processed.
[bwa_aln_core] convert to sequence coordinate... 9.69 sec
[bwa_aln_core] refine gapped alignments... 3.10 sec
[bwa_aln_core] print alignments... 1.37 sec
[bwa_aln_core] 786432 sequences have been processed.
[bwa_aln_core] convert to sequence coordinate... 6.82 sec
[bwa_aln_core] refine gapped alignments... 1.22 sec
[bwa_aln_core] print alignments... 0.11 sec
[bwa_aln_core] 806404 sequences have been processed.
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa samse /project/teaser/genometeaser/references/M_musculus.fasta out_bwa.sam.bwa reads.fastq
[main] Real time: 62.407 sec; CPU: 52.616 sec
systime37.408
time144.787616968
usrtime247.312
working_directory/project/teaser/genometeaser/tests_generated/023be73dabd493f04945e37217bf7c31