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 Mapped32123689.575%
Wrongly Mapped331239.236%
Not Mapped42641.189%
Total358623100.0%
Read Failure Statistics
Not mapped42641.189%
Missing in mapper output00.0%
Mapped to wrong chromosome174194.857%
Mapped to wrong position157044.379%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.945000
Precision0.906500
Recall0.986900
Timing
Raw Mapping Time395.448s
Effective Mapping Time280.616s
Effective Init Time114.832s
Effective Time MeasureCPU
Mapping Time (Wall)243.631s
Mapping Time (CPU)395.448s
Mapping Time (CPU User)197.276s
Mapping Time (CPU System)198.172s
Init Time (Wall)116.338s
Init Time (CPU)114.832s
Init Time (CPU User)0.044s
Init Time (CPU System)114.788s
Additional Information
Mapper Memory Usage4137 MB
Total Test Runtime (Wall)865.501s
Mapper Command Line: 
/project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/M_musculus_cutf.fasta reads.fastq -t 4 > out_bwa.sam.bwa; /project/teaser/genometeaser/software/bwa samse /project/teaser/genometeaser/references/M_musculus_cutf.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_cutf.fasta reads_base.fastq -t 4 > out_bwa.sam.bwa; /project/teaser/genometeaser/software/bwa samse /project/teaser/genometeaser/references/M_musculus_cutf.fasta out_bwa.sam.bwa reads_base.fastq > out_bwa.sam

command/project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/M_musculus_cutf.fasta reads_base.fastq -t 4 > out_bwa.sam.bwa; /project/teaser/genometeaser/software/bwa samse /project/teaser/genometeaser/references/M_musculus_cutf.fasta out_bwa.sam.bwa reads_base.fastq > out_bwa.sam
memory3995844000
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_cutf.fasta reads_base.fastq
[main] Real time: 232.367 sec; CPU: 33.768 sec
[bwa_aln_core] convert to sequence coordinate... 68.54 sec
[bwa_aln_core] refine gapped alignments... 9.32 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_cutf.fasta out_bwa.sam.bwa reads_base.fastq
[main] Real time: 227.365 sec; CPU: 77.868 sec
systime111.584
time459.797324181
usrtime0.068
working_directory/project/teaser/genometeaser/tests_generated/9616eba5217c671aa1e17d118aefe3c9

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

command/project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/M_musculus_cutf.fasta reads_base.fastq -t 4 > out_bwa.sam.bwa; /project/teaser/genometeaser/software/bwa samse /project/teaser/genometeaser/references/M_musculus_cutf.fasta out_bwa.sam.bwa reads_base.fastq > out_bwa.sam
memory3995812000
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_cutf.fasta reads_base.fastq
[main] Real time: 31.323 sec; CPU: 30.644 sec
[bwa_aln_core] convert to sequence coordinate... 69.22 sec
[bwa_aln_core] refine gapped alignments... 14.95 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_cutf.fasta out_bwa.sam.bwa reads_base.fastq
[main] Real time: 84.947 sec; CPU: 84.172 sec
systime114.788
time116.338224888
usrtime0.044
working_directory/project/teaser/genometeaser/tests_generated/9616eba5217c671aa1e17d118aefe3c9

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

command/project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/M_musculus_cutf.fasta reads.fastq -t 4 > out_bwa.sam.bwa; /project/teaser/genometeaser/software/bwa samse /project/teaser/genometeaser/references/M_musculus_cutf.fasta out_bwa.sam.bwa reads.fastq > out_bwa.sam
memory4137808000
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... 160.14 sec
[bwa_aln_core] write to the disk... 0.18 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_aln_core] calculate SA coordinate... 65.40 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 358623 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_cutf.fasta reads.fastq
[main] Real time: 101.954 sec; CPU: 257.232 sec
[bwa_aln_core] convert to sequence coordinate... 64.36 sec
[bwa_aln_core] refine gapped alignments... 10.68 sec
[bwa_aln_core] print alignments... 1.32 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_aln_core] convert to sequence coordinate... 51.67 sec
[bwa_aln_core] refine gapped alignments... 8.31 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 358623 sequences have been processed.
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa samse /project/teaser/genometeaser/references/M_musculus_cutf.fasta out_bwa.sam.bwa reads.fastq
[main] Real time: 141.567 sec; CPU: 138.168 sec
systime198.172
time243.631393194
usrtime197.276
working_directory/project/teaser/genometeaser/tests_generated/9616eba5217c671aa1e17d118aefe3c9