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 Mapped85523185.686%
Wrongly Mapped13430613.456%
Not Mapped85600.858%
Total998097100.0%
Read Failure Statistics
Not mapped85600.858%
Missing in mapper output00.0%
Mapped to wrong chromosome853608.552%
Mapped to wrong position489454.904%
Mapped to wrong strand10.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.922900
Precision0.864300
Recall0.990100
Timing
Raw Mapping Time135.196s
Effective Mapping Time132.236s
Effective Init Time2.960s
Effective Time MeasureCPU
Mapping Time (Wall)99.037s
Mapping Time (CPU)135.196s
Mapping Time (CPU User)124.788s
Mapping Time (CPU System)10.408s
Init Time (Wall)3.348s
Init Time (CPU)2.960s
Init Time (CPU User)0.020s
Init Time (CPU System)2.940s
Additional Information
Mapper Memory Usage320 MB
Total Test Runtime (Wall)330.085s
Mapper Command Line: 
/project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/D_melanogaster.fasta reads.fastq -t 4 > out_bwa.sam.bwa; /project/teaser/genometeaser/software/bwa samse /project/teaser/genometeaser/references/D_melanogaster.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/D_melanogaster.fasta reads_base.fastq -t 4 > out_bwa.sam.bwa; /project/teaser/genometeaser/software/bwa samse /project/teaser/genometeaser/references/D_melanogaster.fasta out_bwa.sam.bwa reads_base.fastq > out_bwa.sam

command/project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/D_melanogaster.fasta reads_base.fastq -t 4 > out_bwa.sam.bwa; /project/teaser/genometeaser/software/bwa samse /project/teaser/genometeaser/references/D_melanogaster.fasta out_bwa.sam.bwa reads_base.fastq > out_bwa.sam
memory313576000
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/D_melanogaster.fasta reads_base.fastq
[main] Real time: 14.504 sec; CPU: 1.180 sec
[bwa_aln_core] convert to sequence coordinate... 2.03 sec
[bwa_aln_core] refine gapped alignments... 0.06 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/D_melanogaster.fasta out_bwa.sam.bwa reads_base.fastq
[main] Real time: 19.201 sec; CPU: 2.104 sec
systime3.3
time33.7497820854
usrtime0.016
working_directory/project/teaser/genometeaser/tests_generated/47ed064b8a7255de5257058de7620d9c

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

command/project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/D_melanogaster.fasta reads_base.fastq -t 4 > out_bwa.sam.bwa; /project/teaser/genometeaser/software/bwa samse /project/teaser/genometeaser/references/D_melanogaster.fasta out_bwa.sam.bwa reads_base.fastq > out_bwa.sam
memory313576000
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/D_melanogaster.fasta reads_base.fastq
[main] Real time: 1.265 sec; CPU: 1.116 sec
[bwa_aln_core] convert to sequence coordinate... 1.77 sec
[bwa_aln_core] refine gapped alignments... 0.04 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/D_melanogaster.fasta out_bwa.sam.bwa reads_base.fastq
[main] Real time: 1.874 sec; CPU: 1.816 sec
systime2.94
time3.3484480381
usrtime0.02
working_directory/project/teaser/genometeaser/tests_generated/47ed064b8a7255de5257058de7620d9c

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

command/project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/D_melanogaster.fasta reads.fastq -t 4 > out_bwa.sam.bwa; /project/teaser/genometeaser/software/bwa samse /project/teaser/genometeaser/references/D_melanogaster.fasta out_bwa.sam.bwa reads.fastq > out_bwa.sam
memory320656000
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... 28.99 sec
[bwa_aln_core] write to the disk... 0.16 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_aln_core] calculate SA coordinate... 28.73 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 524288 sequences have been processed.
[bwa_aln_core] calculate SA coordinate... 30.98 sec
[bwa_aln_core] write to the disk... 0.13 sec
[bwa_aln_core] 786432 sequences have been processed.
[bwa_aln_core] calculate SA coordinate... 24.02 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 998097 sequences have been processed.
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa aln -t 4 /project/teaser/genometeaser/references/D_melanogaster.fasta reads.fastq
[main] Real time: 53.293 sec; CPU: 117.552 sec
[bwa_aln_core] convert to sequence coordinate... 4.27 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_aln_core] convert to sequence coordinate... 2.72 sec
[bwa_aln_core] refine gapped alignments... 0.35 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 524288 sequences have been processed.
[bwa_aln_core] convert to sequence coordinate... 2.76 sec
[bwa_aln_core] refine gapped alignments... 0.36 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 786432 sequences have been processed.
[bwa_aln_core] convert to sequence coordinate... 3.07 sec
[bwa_aln_core] refine gapped alignments... 0.28 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 998097 sequences have been processed.
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa samse /project/teaser/genometeaser/references/D_melanogaster.fasta out_bwa.sam.bwa reads.fastq
[main] Real time: 41.738 sec; CPU: 17.596 sec
systime10.408
time99.0366508961
usrtime124.788
working_directory/project/teaser/genometeaser/tests_generated/47ed064b8a7255de5257058de7620d9c