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 Mapped29493198.584%
Wrongly Mapped39241.312%
Not Mapped3130.105%
Total299168100.0%
Read Failure Statistics
Not mapped3130.105%
Missing in mapper output00.0%
Mapped to wrong chromosome10910.365%
Mapped to wrong position28330.947%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.992900
Precision0.986900
Recall0.998900
Timing
Raw Mapping Time78.400s
Effective Mapping Time78.096s
Effective Init Time0.304s
Effective Time MeasureCPU
Mapping Time (Wall)43.940s
Mapping Time (CPU)78.400s
Mapping Time (CPU User)76.536s
Mapping Time (CPU System)1.864s
Init Time (Wall)0.400s
Init Time (CPU)0.304s
Init Time (CPU User)0.016s
Init Time (CPU System)0.288s
Additional Information
Mapper Memory Usage372 MB
Total Test Runtime (Wall)105.024s
Mapper Command Line: 
/project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas reads1.fastq -t 4 > out_bwa.sam_1.sai; /project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas reads2.fastq -t 4 > out_bwa.sam_2.sai; /project/teaser/genometeaser/software/bwa sampe /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas 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/Arabidopsis_thaliana.fas reads_base.fastq -t 4 > out_bwa.sam.bwa; /project/teaser/genometeaser/software/bwa samse /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas out_bwa.sam.bwa reads_base.fastq > out_bwa.sam

command/project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas reads_base.fastq -t 4 > out_bwa.sam.bwa; /project/teaser/genometeaser/software/bwa samse /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas out_bwa.sam.bwa reads_base.fastq > out_bwa.sam
memory178668000
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/Arabidopsis_thaliana.fas reads_base.fastq
[main] Real time: 10.308 sec; CPU: 0.156 sec
[bwa_aln_core] convert to sequence coordinate... 0.19 sec
[bwa_aln_core] refine gapped alignments... 0.04 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/Arabidopsis_thaliana.fas out_bwa.sam.bwa reads_base.fastq
[main] Real time: 7.905 sec; CPU: 0.232 sec
systime0.388
time18.2591898441
usrtime0.012
working_directory/project/teaser/genometeaser/tests_generated/337f8b971fac4ff7ee4490260598b300

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

command/project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas reads_base.fastq -t 4 > out_bwa.sam.bwa; /project/teaser/genometeaser/software/bwa samse /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas out_bwa.sam.bwa reads_base.fastq > out_bwa.sam
memory178668000
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/Arabidopsis_thaliana.fas reads_base.fastq
[main] Real time: 0.127 sec; CPU: 0.104 sec
[bwa_aln_core] convert to sequence coordinate... 0.16 sec
[bwa_aln_core] refine gapped alignments... 0.03 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/Arabidopsis_thaliana.fas out_bwa.sam.bwa reads_base.fastq
[main] Real time: 0.221 sec; CPU: 0.192 sec
systime0.288
time0.400472164154
usrtime0.016
working_directory/project/teaser/genometeaser/tests_generated/337f8b971fac4ff7ee4490260598b300

/project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas reads1.fastq -t 4 > out_bwa.sam_1.sai; /project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas reads2.fastq -t 4 > out_bwa.sam_2.sai; /project/teaser/genometeaser/software/bwa sampe /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas 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/Arabidopsis_thaliana.fas reads1.fastq -t 4 > out_bwa.sam_1.sai; /project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas reads2.fastq -t 4 > out_bwa.sam_2.sai; /project/teaser/genometeaser/software/bwa sampe /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas out_bwa.sam_1.sai out_bwa.sam_2.sai reads1.fastq reads2.fastq > out_bwa.sam
memory372500000
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... 30.22 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 149584 sequences have been processed.
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa aln -t 4 /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas reads1.fastq
[main] Real time: 9.152 sec; CPU: 30.972 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... 28.94 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 149584 sequences have been processed.
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa aln -t 4 /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas reads2.fastq
[main] Real time: 8.471 sec; CPU: 29.704 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 135914 pairs: 399.686 +/- 32.818
[infer_isize] skewness: 0.002; kurtosis: -0.077; ap_prior: 1.00e-05
[infer_isize] inferred maximum insert size: 612 (6.47 sigma)
[bwa_sai2sam_pe_core] time elapses: 5.95 sec
[bwa_sai2sam_pe_core] changing coordinates of 2260 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 5349 out of 5349 Q17 singletons are mated.
[bwa_paired_sw] 22 out of 22 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.17 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 7.29 sec
[bwa_sai2sam_pe_core] print alignments... 2.01 sec
[bwa_sai2sam_pe_core] 149584 sequences have been processed.
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa sampe /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas out_bwa.sam_1.sai out_bwa.sam_2.sai reads1.fastq reads2.fastq
[main] Real time: 26.158 sec; CPU: 17.672 sec
systime1.864
time43.9404489994
usrtime76.536
working_directory/project/teaser/genometeaser/tests_generated/337f8b971fac4ff7ee4490260598b300