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 Mapped14493696.624%
Wrongly Mapped28251.883%
Not Mapped22391.493%
Total150000100.0%
Read Failure Statistics
Not mapped22391.493%
Missing in mapper output00.0%
Mapped to wrong chromosome20971.398%
Mapped to wrong position7280.485%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.982800
Precision0.980900
Recall0.984800
Timing
Raw Mapping Time23.074s
Effective Mapping Time23.032s
Effective Init Time0.042s
Effective Time MeasureCPU
Mapping Time (Wall)16.913s
Mapping Time (CPU)23.074s
Mapping Time (CPU User)22.871s
Mapping Time (CPU System)0.204s
Init Time (Wall)0.111s
Init Time (CPU)0.042s
Init Time (CPU User)0.001s
Init Time (CPU System)0.041s
Additional Information
Mapper Memory Usage126 MB
Total Test Runtime (Wall)40.407s
Mapper Command Line: 
/project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/Cryptosporidium.fasta reads1.fastq -t 4 > out_bwa.sam_1.sai; /project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/Cryptosporidium.fasta reads2.fastq -t 4 > out_bwa.sam_2.sai; /project/teaser/genometeaser/software/bwa sampe /project/teaser/genometeaser/references/Cryptosporidium.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 index /project/teaser/genometeaser/references/Cryptosporidium.fasta

command/project/teaser/genometeaser/software/bwa index /project/teaser/genometeaser/references/Cryptosporidium.fasta
return1
status1
stderr
None
stdout
[bwa_index] Pack FASTA... 0.17 sec
[bwa_index] Construct BWT for the packed sequence...
[bwa_index] 9.84 seconds elapse.
[bwa_index] Update BWT... 0.11 sec
[bwa_index] Pack forward-only FASTA... 0.11 sec
[bwa_index] Construct SA from BWT and Occ... 3.04 sec
[main] Version: 0.7.12-r1039
[main] CMD: /project/teaser/genometeaser/software/bwa index /project/teaser/genometeaser/references/Cryptosporidium.fasta
[main] Real time: 14.789 sec; CPU: 13.273 sec
systime0
time14.795678854
usrtime0
working_directory/project/teaser/genometeaser/tests_generated/f23fe16b99420742b88a981972af6aae

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

command/project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/Cryptosporidium.fasta reads_base.fastq -t 4 > out_bwa.sam.bwa; /project/teaser/genometeaser/software/bwa samse /project/teaser/genometeaser/references/Cryptosporidium.fasta out_bwa.sam.bwa reads_base.fastq > out_bwa.sam
memory29400000
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: 0.7.12-r1039
[main] CMD: /project/teaser/genometeaser/software/bwa aln -t 4 /project/teaser/genometeaser/references/Cryptosporidium.fasta reads_base.fastq
[main] Real time: 0.048 sec; CPU: 0.014 sec
[bwa_aln_core] convert to sequence coordinate... 0.01 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: 0.7.12-r1039
[main] CMD: /project/teaser/genometeaser/software/bwa samse /project/teaser/genometeaser/references/Cryptosporidium.fasta out_bwa.sam.bwa reads_base.fastq
[main] Real time: 0.085 sec; CPU: 0.024 sec
systime0.043993
time0.143939971924
usrtime0.000999
working_directory/project/teaser/genometeaser/tests_generated/f23fe16b99420742b88a981972af6aae

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

command/project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/Cryptosporidium.fasta reads_base.fastq -t 4 > out_bwa.sam.bwa; /project/teaser/genometeaser/software/bwa samse /project/teaser/genometeaser/references/Cryptosporidium.fasta out_bwa.sam.bwa reads_base.fastq > out_bwa.sam
memory29400000
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... 0.01 sec
[bwa_aln_core] write to the disk... 0.00 sec
[bwa_aln_core] 1 sequences have been processed.
[main] Version: 0.7.12-r1039
[main] CMD: /project/teaser/genometeaser/software/bwa aln -t 4 /project/teaser/genometeaser/references/Cryptosporidium.fasta reads_base.fastq
[main] Real time: 0.043 sec; CPU: 0.012 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: 0.7.12-r1039
[main] CMD: /project/teaser/genometeaser/software/bwa samse /project/teaser/genometeaser/references/Cryptosporidium.fasta out_bwa.sam.bwa reads_base.fastq
[main] Real time: 0.058 sec; CPU: 0.025 sec
systime0.040993
time0.110502004623
usrtime0.000999
working_directory/project/teaser/genometeaser/tests_generated/f23fe16b99420742b88a981972af6aae

/project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/Cryptosporidium.fasta reads1.fastq -t 4 > out_bwa.sam_1.sai; /project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/Cryptosporidium.fasta reads2.fastq -t 4 > out_bwa.sam_2.sai; /project/teaser/genometeaser/software/bwa sampe /project/teaser/genometeaser/references/Cryptosporidium.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/Cryptosporidium.fasta reads1.fastq -t 4 > out_bwa.sam_1.sai; /project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/Cryptosporidium.fasta reads2.fastq -t 4 > out_bwa.sam_2.sai; /project/teaser/genometeaser/software/bwa sampe /project/teaser/genometeaser/references/Cryptosporidium.fasta out_bwa.sam_1.sai out_bwa.sam_2.sai reads1.fastq reads2.fastq > out_bwa.sam
memory126968000
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... 9.04 sec
[bwa_aln_core] write to the disk... 0.00 sec
[bwa_aln_core] 75000 sequences have been processed.
[main] Version: 0.7.12-r1039
[main] CMD: /project/teaser/genometeaser/software/bwa aln -t 4 /project/teaser/genometeaser/references/Cryptosporidium.fasta reads1.fastq
[main] Real time: 6.205 sec; CPU: 9.154 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... 9.57 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 75000 sequences have been processed.
[main] Version: 0.7.12-r1039
[main] CMD: /project/teaser/genometeaser/software/bwa aln -t 4 /project/teaser/genometeaser/references/Cryptosporidium.fasta reads2.fastq
[main] Real time: 5.930 sec; CPU: 9.700 sec
[bwa_sai2sam_pe_core] convert to sequence coordinate...
[infer_isize] (25, 50, 75) percentile: (110, 122, 137)
[infer_isize] low and high boundaries: 100 and 191 for estimating avg and std
[infer_isize] inferred external isize from 69604 pairs: 125.598 +/- 19.033
[infer_isize] skewness: 0.855; kurtosis: 0.197; ap_prior: 1.00e-05
[infer_isize] inferred maximum insert size: 246 (6.33 sigma)
[bwa_sai2sam_pe_core] time elapses: 1.07 sec
[bwa_sai2sam_pe_core] changing coordinates of 80 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 691 out of 2662 Q17 singletons are mated.
[bwa_paired_sw] 1 out of 35597 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 0.70 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 1.80 sec
[bwa_sai2sam_pe_core] print alignments... 0.41 sec
[bwa_sai2sam_pe_core] 75000 sequences have been processed.
[main] Version: 0.7.12-r1039
[main] CMD: /project/teaser/genometeaser/software/bwa sampe /project/teaser/genometeaser/references/Cryptosporidium.fasta out_bwa.sam_1.sai out_bwa.sam_2.sai reads1.fastq reads2.fastq
[main] Real time: 4.757 sec; CPU: 4.207 sec
systime0.203968
time16.912815094
usrtime22.870523
working_directory/project/teaser/genometeaser/tests_generated/f23fe16b99420742b88a981972af6aae