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 Mapped8840288.402%
Wrongly Mapped5910.591%
Not Mapped1100711.007%
Total100000100.0%
Read Failure Statistics
Not mapped1100711.007%
Missing in mapper output00.0%
Mapped to wrong chromosome4430.443%
Mapped to wrong position1480.148%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.938400
Precision0.993400
Recall0.889300
Timing
Raw Mapping Time48.752s
Effective Mapping Time48.692s
Effective Init Time0.060s
Effective Time MeasureCPU
Mapping Time (Wall)34.006s
Mapping Time (CPU)48.752s
Mapping Time (CPU User)48.032s
Mapping Time (CPU System)0.720s
Init Time (Wall)0.176s
Init Time (CPU)0.060s
Init Time (CPU User)0.012s
Init Time (CPU System)0.048s
Additional Information
Mapper Memory Usage102 MB
Total Test Runtime (Wall)54.858s
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
memory21268000
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: 0.181 sec; CPU: 0.040 sec
systime0.04
time0.251888990402
usrtime0.024
working_directory/project/teaser/genometeaser/tests_generated/bc5e667ff41f75be5690d71ac8911c05

/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
memory21320000
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: 0.086 sec; CPU: 0.036 sec
systime0.048
time0.176258087158
usrtime0.012
working_directory/project/teaser/genometeaser/tests_generated/bc5e667ff41f75be5690d71ac8911c05

/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
memory102728000
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... 15.87 sec
[bwa_aln_core] write to the disk... 0.03 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: 6.914 sec; CPU: 16.136 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... 16.04 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: 7.069 sec; CPU: 16.308 sec
[bwa_sai2sam_pe_core] convert to sequence coordinate...
[infer_isize] (25, 50, 75) percentile: (378, 400, 422)
[infer_isize] low and high boundaries: 290 and 510 for estimating avg and std
[infer_isize] inferred external isize from 22307 pairs: 399.753 +/- 32.705
[infer_isize] skewness: -0.012; kurtosis: -0.091; ap_prior: 1.00e-05
[infer_isize] inferred maximum insert size: 600 (6.12 sigma)
[bwa_sai2sam_pe_core] time elapses: 0.90 sec
[bwa_sai2sam_pe_core] changing coordinates of 77 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 21514 out of 21514 Q17 singletons are mated.
[bwa_paired_sw] 0 out of 0 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 7.14 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 7.00 sec
[bwa_sai2sam_pe_core] print alignments... 0.73 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: 19.934 sec; CPU: 16.284 sec
systime0.72
time34.0064439774
usrtime48.032
working_directory/project/teaser/genometeaser/tests_generated/bc5e667ff41f75be5690d71ac8911c05