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 Mapped9903899.038%
Wrongly Mapped7390.739%
Not Mapped2230.223%
Total100000100.0%
Read Failure Statistics
Not mapped2230.223%
Missing in mapper output00.0%
Mapped to wrong chromosome5070.507%
Mapped to wrong position2320.232%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.995200
Precision0.992600
Recall0.997800
Timing
Raw Mapping Time24.124s
Effective Mapping Time24.064s
Effective Init Time0.060s
Effective Time MeasureCPU
Mapping Time (Wall)17.069s
Mapping Time (CPU)24.124s
Mapping Time (CPU User)23.496s
Mapping Time (CPU System)0.628s
Init Time (Wall)0.150s
Init Time (CPU)0.060s
Init Time (CPU User)0.000s
Init Time (CPU System)0.060s
Additional Information
Mapper Memory Usage104 MB
Total Test Runtime (Wall)35.893s
Mapper Command Line: 
/project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta reads1.fastq -t 4 > out_bwa.sam_1.sai; /project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta reads2.fastq -t 4 > out_bwa.sam_2.sai; /project/teaser/genometeaser/software/bwa sampe /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta out_bwa.sam_1.sai out_bwa.sam_2.sai reads1.fastq reads2.fastq > out_bwa.sam
Errors and Warnings
No problems were encountered.
Subprocess Log

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

command/project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta reads_base.fastq -t 4 > out_bwa.sam.bwa; /project/teaser/genometeaser/software/bwa samse /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta out_bwa.sam.bwa reads_base.fastq > out_bwa.sam
memory21196000
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/Saccharomyces_cerevisiae.fasta reads_base.fastq
[main] Real time: 0.034 sec; CPU: 0.016 sec
[bwa_aln_core] convert to sequence coordinate... 0.02 sec
[bwa_aln_core] refine gapped alignments... 0.01 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/Saccharomyces_cerevisiae.fasta out_bwa.sam.bwa reads_base.fastq
[main] Real time: 0.064 sec; CPU: 0.036 sec
systime0.044
time0.134696960449
usrtime0.02
working_directory/project/teaser/genometeaser/tests_generated/fea6b65881b1ab0892566fb478a26e05

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

command/project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta reads_base.fastq -t 4 > out_bwa.sam.bwa; /project/teaser/genometeaser/software/bwa samse /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta out_bwa.sam.bwa reads_base.fastq > out_bwa.sam
memory21272000
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/Saccharomyces_cerevisiae.fasta reads_base.fastq
[main] Real time: 0.039 sec; CPU: 0.016 sec
[bwa_aln_core] convert to sequence coordinate... 0.02 sec
[bwa_aln_core] refine gapped alignments... 0.00 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/Saccharomyces_cerevisiae.fasta out_bwa.sam.bwa reads_base.fastq
[main] Real time: 0.062 sec; CPU: 0.036 sec
systime0.06
time0.150223016739
usrtime0.0
working_directory/project/teaser/genometeaser/tests_generated/fea6b65881b1ab0892566fb478a26e05

/project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta reads1.fastq -t 4 > out_bwa.sam_1.sai; /project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta reads2.fastq -t 4 > out_bwa.sam_2.sai; /project/teaser/genometeaser/software/bwa sampe /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta out_bwa.sam_1.sai out_bwa.sam_2.sai reads1.fastq reads2.fastq > out_bwa.sam

command/project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta reads1.fastq -t 4 > out_bwa.sam_1.sai; /project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta reads2.fastq -t 4 > out_bwa.sam_2.sai; /project/teaser/genometeaser/software/bwa sampe /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta out_bwa.sam_1.sai out_bwa.sam_2.sai reads1.fastq reads2.fastq > out_bwa.sam
memory104476000
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... 9.42 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 50000 sequences have been processed.
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa aln -t 4 /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta reads1.fastq
[main] Real time: 4.190 sec; CPU: 9.680 sec
[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... 9.41 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 50000 sequences have been processed.
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa aln -t 4 /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta reads2.fastq
[main] Real time: 4.268 sec; CPU: 9.672 sec
[bwa_sai2sam_pe_core] convert to sequence coordinate...
[infer_isize] (25, 50, 75) percentile: (427, 450, 472)
[infer_isize] low and high boundaries: 337 and 562 for estimating avg and std
[infer_isize] inferred external isize from 45078 pairs: 449.561 +/- 32.890
[infer_isize] skewness: -0.000; kurtosis: -0.062; ap_prior: 1.00e-05
[infer_isize] inferred maximum insert size: 650 (6.10 sigma)
[bwa_sai2sam_pe_core] time elapses: 1.15 sec
[bwa_sai2sam_pe_core] changing coordinates of 185 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 3795 out of 3795 Q17 singletons are mated.
[bwa_paired_sw] 0 out of 0 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 0.55 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 2.23 sec
[bwa_sai2sam_pe_core] print alignments... 0.33 sec
[bwa_sai2sam_pe_core] 50000 sequences have been processed.
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa sampe /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta out_bwa.sam_1.sai out_bwa.sam_2.sai reads1.fastq reads2.fastq
[main] Real time: 8.527 sec; CPU: 4.744 sec
systime0.628
time17.0687789917
usrtime23.496
working_directory/project/teaser/genometeaser/tests_generated/fea6b65881b1ab0892566fb478a26e05