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 Mapped6685666.856%
Wrongly Mapped9500.95%
Not Mapped3219432.194%
Total100000100.0%
Read Failure Statistics
Not mapped3219432.194%
Missing in mapper output00.0%
Mapped to wrong chromosome6850.685%
Mapped to wrong position2650.265%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.801400
Precision0.986000
Recall0.675000
Timing
Raw Mapping Time64.012s
Effective Mapping Time63.960s
Effective Init Time0.052s
Effective Time MeasureCPU
Mapping Time (Wall)38.495s
Mapping Time (CPU)64.012s
Mapping Time (CPU User)63.200s
Mapping Time (CPU System)0.812s
Init Time (Wall)0.977s
Init Time (CPU)0.052s
Init Time (CPU User)0.008s
Init Time (CPU System)0.044s
Additional Information
Mapper Memory Usage101 MB
Total Test Runtime (Wall)61.147s
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
memory24808000
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: 1.163 sec; CPU: 0.020 sec
[bwa_aln_core] convert to sequence coordinate... 0.04 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: 0.952 sec; CPU: 0.052 sec
systime0.064
time2.16477608681
usrtime0.016
working_directory/project/teaser/genometeaser/tests_generated/b0bfc21db96b7744c4389e9b4b565dc9

/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
memory24808000
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: 0.060 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: 0.866 sec; CPU: 0.032 sec
systime0.044
time0.977411985397
usrtime0.008
working_directory/project/teaser/genometeaser/tests_generated/b0bfc21db96b7744c4389e9b4b565dc9

/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
memory101464000
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... 25.90 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: 10.961 sec; CPU: 26.216 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... 24.85 sec
[bwa_aln_core] write to the disk... 0.01 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: 8.621 sec; CPU: 25.020 sec
[bwa_sai2sam_pe_core] convert to sequence coordinate...
[infer_isize] (25, 50, 75) percentile: (174, 195, 217)
[infer_isize] low and high boundaries: 150 and 303 for estimating avg and std
[infer_isize] inferred external isize from 26338 pairs: 197.426 +/- 29.146
[infer_isize] skewness: 0.474; kurtosis: -0.307; ap_prior: 1.00e-05
[infer_isize] inferred maximum insert size: 378 (6.19 sigma)
[bwa_sai2sam_pe_core] time elapses: 1.00 sec
[bwa_sai2sam_pe_core] changing coordinates of 2 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 173 out of 13477 Q17 singletons are mated.
[bwa_paired_sw] 0 out of 24468 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 2.85 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 7.67 sec
[bwa_sai2sam_pe_core] print alignments... 0.84 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: 18.811 sec; CPU: 12.748 sec
systime0.812
time38.4949128628
usrtime63.2
working_directory/project/teaser/genometeaser/tests_generated/b0bfc21db96b7744c4389e9b4b565dc9