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 Mapped83149795.417%
Wrongly Mapped387984.452%
Not Mapped11370.13%
Total871432100.0%
Read Failure Statistics
Not mapped11370.13%
Missing in mapper output00.0%
Mapped to wrong chromosome266783.061%
Mapped to wrong position121191.391%
Mapped to wrong strand10.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.976500
Precision0.955400
Recall0.998600
Timing
Raw Mapping Time792.248s
Effective Mapping Time784.824s
Effective Init Time7.424s
Effective Time MeasureCPU
Mapping Time (Wall)672.870s
Mapping Time (CPU)792.248s
Mapping Time (CPU User)773.196s
Mapping Time (CPU System)19.052s
Init Time (Wall)7.585s
Init Time (CPU)7.424s
Init Time (CPU User)0.220s
Init Time (CPU System)7.204s
Additional Information
Mapper Memory Usage4851 MB
Total Test Runtime (Wall)1259.938s
Mapper Command Line: 
/project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/H_sapiens.fa reads1.fastq -t 4 > out_bwa.sam_1.sai; /project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/H_sapiens.fa reads2.fastq -t 4 > out_bwa.sam_2.sai; /project/teaser/genometeaser/software/bwa sampe /project/teaser/genometeaser/references/H_sapiens.fa 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/H_sapiens.fa reads_base.fastq -t 4 > out_bwa.sam.bwa; /project/teaser/genometeaser/software/bwa samse /project/teaser/genometeaser/references/H_sapiens.fa out_bwa.sam.bwa reads_base.fastq > out_bwa.sam

command/project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/H_sapiens.fa reads_base.fastq -t 4 > out_bwa.sam.bwa; /project/teaser/genometeaser/software/bwa samse /project/teaser/genometeaser/references/H_sapiens.fa out_bwa.sam.bwa reads_base.fastq > out_bwa.sam
memory4599048000
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... 0.08 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/H_sapiens.fa reads_base.fastq
[main] Real time: 266.872 sec; CPU: 3.532 sec
[bwa_aln_core] convert to sequence coordinate... 4.97 sec
[bwa_aln_core] refine gapped alignments... 0.87 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/H_sapiens.fa out_bwa.sam.bwa reads_base.fastq
[main] Real time: 202.889 sec; CPU: 5.852 sec
systime9.248
time469.826513052
usrtime0.148
working_directory/project/teaser/genometeaser/tests_generated/ab0014cf05e86cd590ae0b3283410abf

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

command/project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/H_sapiens.fa reads_base.fastq -t 4 > out_bwa.sam.bwa; /project/teaser/genometeaser/software/bwa samse /project/teaser/genometeaser/references/H_sapiens.fa out_bwa.sam.bwa reads_base.fastq > out_bwa.sam
memory4598752000
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... 0.06 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/H_sapiens.fa reads_base.fastq
[main] Real time: 2.728 sec; CPU: 2.688 sec
[bwa_aln_core] convert to sequence coordinate... 4.05 sec
[bwa_aln_core] refine gapped alignments... 0.67 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/H_sapiens.fa out_bwa.sam.bwa reads_base.fastq
[main] Real time: 4.785 sec; CPU: 4.724 sec
systime7.204
time7.58526420593
usrtime0.22
working_directory/project/teaser/genometeaser/tests_generated/ab0014cf05e86cd590ae0b3283410abf

/project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/H_sapiens.fa reads1.fastq -t 4 > out_bwa.sam_1.sai; /project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/H_sapiens.fa reads2.fastq -t 4 > out_bwa.sam_2.sai; /project/teaser/genometeaser/software/bwa sampe /project/teaser/genometeaser/references/H_sapiens.fa 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/H_sapiens.fa reads1.fastq -t 4 > out_bwa.sam_1.sai; /project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/H_sapiens.fa reads2.fastq -t 4 > out_bwa.sam_2.sai; /project/teaser/genometeaser/software/bwa sampe /project/teaser/genometeaser/references/H_sapiens.fa out_bwa.sam_1.sai out_bwa.sam_2.sai reads1.fastq reads2.fastq > out_bwa.sam
memory4851280000
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... 57.98 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... 36.80 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 435716 sequences have been processed.
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa aln -t 4 /project/teaser/genometeaser/references/H_sapiens.fa reads1.fastq
[main] Real time: 33.790 sec; CPU: 98.460 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... 54.27 sec
[bwa_aln_core] write to the disk... 0.17 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_aln_core] calculate SA coordinate... 39.14 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 435716 sequences have been processed.
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa aln -t 4 /project/teaser/genometeaser/references/H_sapiens.fa reads2.fastq
[main] Real time: 33.517 sec; CPU: 97.080 sec
[bwa_sai2sam_pe_core] convert to sequence coordinate...
[infer_isize] (25, 50, 75) percentile: (177, 199, 222)
[infer_isize] low and high boundaries: 87 and 312 for estimating avg and std
[infer_isize] inferred external isize from 193179 pairs: 199.325 +/- 32.779
[infer_isize] skewness: 0.001; kurtosis: -0.064; ap_prior: 1.00e-05
[infer_isize] inferred maximum insert size: 429 (7.00 sigma)
[bwa_sai2sam_pe_core] time elapses: 350.07 sec
[bwa_sai2sam_pe_core] changing coordinates of 30904 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 3471 out of 3542 Q17 singletons are mated.
[bwa_paired_sw] 2192 out of 2284 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.01 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 1.29 sec
[bwa_sai2sam_pe_core] print alignments... 3.11 sec
[bwa_sai2sam_pe_core] 262144 sequences have been processed.
[bwa_sai2sam_pe_core] convert to sequence coordinate...
[infer_isize] (25, 50, 75) percentile: (177, 199, 221)
[infer_isize] low and high boundaries: 89 and 309 for estimating avg and std
[infer_isize] inferred external isize from 127740 pairs: 199.048 +/- 32.784
[infer_isize] skewness: 0.007; kurtosis: -0.080; ap_prior: 1.00e-05
[infer_isize] inferred maximum insert size: 429 (7.00 sigma)
[bwa_sai2sam_pe_core] time elapses: 235.46 sec
[bwa_sai2sam_pe_core] changing coordinates of 20529 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 2302 out of 2331 Q17 singletons are mated.
[bwa_paired_sw] 1447 out of 1499 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 0.91 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.87 sec
[bwa_sai2sam_pe_core] print alignments... 2.06 sec
[bwa_sai2sam_pe_core] 435716 sequences have been processed.
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa sampe /project/teaser/genometeaser/references/H_sapiens.fa out_bwa.sam_1.sai out_bwa.sam_2.sai reads1.fastq reads2.fastq
[main] Real time: 605.450 sec; CPU: 596.668 sec
systime19.052
time672.870496988
usrtime773.196
working_directory/project/teaser/genometeaser/tests_generated/ab0014cf05e86cd590ae0b3283410abf