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 Mapped58834395.646%
Wrongly Mapped254094.131%
Not Mapped13760.224%
Total615128100.0%
Read Failure Statistics
Not mapped13760.224%
Missing in mapper output00.0%
Mapped to wrong chromosome178462.901%
Mapped to wrong position75631.23%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.977700
Precision0.958600
Recall0.997700
Timing
Raw Mapping Time1127.316s
Effective Mapping Time1067.504s
Effective Init Time59.812s
Effective Time MeasureCPU
Mapping Time (Wall)729.492s
Mapping Time (CPU)1127.316s
Mapping Time (CPU User)898.312s
Mapping Time (CPU System)229.004s
Init Time (Wall)64.808s
Init Time (CPU)59.812s
Init Time (CPU User)0.448s
Init Time (CPU System)59.364s
Additional Information
Mapper Memory Usage4871 MB
Total Test Runtime (Wall)1510.496s
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
memory4598848000
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/H_sapiens.fa reads_base.fastq
[main] Real time: 337.567 sec; CPU: 23.940 sec
[bwa_aln_core] convert to sequence coordinate... 37.95 sec
[bwa_aln_core] refine gapped alignments... 2.77 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: 283.464 sec; CPU: 40.720 sec
systime64.416
time621.266322136
usrtime0.252
working_directory/project/teaser/genometeaser/tests_generated/4ff0769a44d529563c64b75a1aaf552d

/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
memory4598860000
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/H_sapiens.fa reads_base.fastq
[main] Real time: 24.830 sec; CPU: 22.164 sec
[bwa_aln_core] convert to sequence coordinate... 35.39 sec
[bwa_aln_core] refine gapped alignments... 2.24 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: 39.876 sec; CPU: 37.628 sec
systime59.364
time64.8083109856
usrtime0.448
working_directory/project/teaser/genometeaser/tests_generated/4ff0769a44d529563c64b75a1aaf552d

/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
memory4871000000
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... 237.65 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... 41.97 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 307564 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: 117.385 sec; CPU: 299.552 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... 332.11 sec
[bwa_aln_core] write to the disk... 0.15 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_aln_core] calculate SA coordinate... 56.56 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 307564 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: 173.283 sec; CPU: 407.040 sec
[bwa_sai2sam_pe_core] convert to sequence coordinate...
[infer_isize] (25, 50, 75) percentile: (78, 99, 121)
[infer_isize] low and high boundaries: 51 and 207 for estimating avg and std
[infer_isize] inferred external isize from 218797 pairs: 101.048 +/- 29.627
[infer_isize] skewness: 0.410; kurtosis: -0.347; ap_prior: 1.00e-05
[infer_isize] inferred maximum insert size: 310 (7.04 sigma)
[bwa_sai2sam_pe_core] time elapses: 347.55 sec
[bwa_sai2sam_pe_core] changing coordinates of 12458 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 2868 out of 3596 Q17 singletons are mated.
[bwa_paired_sw] 1009 out of 18017 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 3.50 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 2.84 sec
[bwa_sai2sam_pe_core] print alignments... 2.38 sec
[bwa_sai2sam_pe_core] 262144 sequences have been processed.
[bwa_sai2sam_pe_core] convert to sequence coordinate...
[infer_isize] (25, 50, 75) percentile: (78, 99, 121)
[infer_isize] low and high boundaries: 51 and 207 for estimating avg and std
[infer_isize] inferred external isize from 37832 pairs: 101.172 +/- 29.616
[infer_isize] skewness: 0.423; kurtosis: -0.317; ap_prior: 1.00e-05
[infer_isize] inferred maximum insert size: 310 (7.04 sigma)
[bwa_sai2sam_pe_core] time elapses: 60.73 sec
[bwa_sai2sam_pe_core] changing coordinates of 2167 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 473 out of 609 Q17 singletons are mated.
[bwa_paired_sw] 146 out of 3106 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.18 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.30 sec
[bwa_sai2sam_pe_core] print alignments... 0.40 sec
[bwa_sai2sam_pe_core] 307564 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: 436.564 sec; CPU: 420.644 sec
systime229.004
time729.492473841
usrtime898.312
working_directory/project/teaser/genometeaser/tests_generated/4ff0769a44d529563c64b75a1aaf552d