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 Mapped14181394.542%
Wrongly Mapped53573.571%
Not Mapped28301.887%
Total150000100.0%
Read Failure Statistics
Not mapped28301.887%
Missing in mapper output00.0%
Mapped to wrong chromosome00.0%
Mapped to wrong position53573.571%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.971900
Precision0.963600
Recall0.980400
Timing
Raw Mapping Time4.345s
Effective Mapping Time4.305s
Effective Init Time0.040s
Effective Time MeasureWall clock
Mapping Time (Wall)4.345s
Mapping Time (CPU)8.990s
Mapping Time (CPU User)8.884s
Mapping Time (CPU System)0.106s
Init Time (Wall)0.040s
Init Time (CPU)0.017s
Init Time (CPU User)0.001s
Init Time (CPU System)0.016s
Additional Information
Mapper Memory Usage107 MB
Total Test Runtime (Wall)14.421s
Mapper Command Line: 
/project2/NextGenMapTest/Teaser/software/bwa aln /project2/NextGenMapTest/Teaser/references/E_coli.fasta reads.fastq -t 4 > out_bwa.sam.bwa; /project2/NextGenMapTest/Teaser/software/bwa samse /project2/NextGenMapTest/Teaser/references/E_coli.fasta out_bwa.sam.bwa reads.fastq > out_bwa.sam
Errors and Warnings
No problems were encountered.
Subprocess Log

/project2/NextGenMapTest/Teaser/software/bwa index /project2/NextGenMapTest/Teaser/references/E_coli.fasta

command/project2/NextGenMapTest/Teaser/software/bwa index /project2/NextGenMapTest/Teaser/references/E_coli.fasta
return1
status1
stderr

None
stdout

[bwa_index] Pack FASTA... 0.04 sec

[bwa_index] Construct BWT for the packed sequence...

[bwa_index] 1.21 seconds elapse.

[bwa_index] Update BWT... 0.03 sec

[bwa_index] Pack forward-only FASTA... 0.02 sec

[bwa_index] Construct SA from BWT and Occ... 0.50 sec

[main] Version: 0.7.12-r1039

[main] CMD: /project2/NextGenMapTest/Teaser/software/bwa index /project2/NextGenMapTest/Teaser/references/E_coli.fasta

[main] Real time: 2.227 sec; CPU: 1.815 sec
systime0
time2.23200798035
usrtime0
working_directory/project2/NextGenMapTest/Teaser/tests_generated/ecoli_test

/project2/NextGenMapTest/Teaser/software/bwa aln /project2/NextGenMapTest/Teaser/references/E_coli.fasta reads_base.fastq -t 4 > out_bwa.sam.bwa; /project2/NextGenMapTest/Teaser/software/bwa samse /project2/NextGenMapTest/Teaser/references/E_coli.fasta out_bwa.sam.bwa reads_base.fastq > out_bwa.sam

command/project2/NextGenMapTest/Teaser/software/bwa aln /project2/NextGenMapTest/Teaser/references/E_coli.fasta reads_base.fastq -t 4 > out_bwa.sam.bwa; /project2/NextGenMapTest/Teaser/software/bwa samse /project2/NextGenMapTest/Teaser/references/E_coli.fasta out_bwa.sam.bwa reads_base.fastq > out_bwa.sam
memory19292000
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: /project2/NextGenMapTest/Teaser/software/bwa aln -t 4 /project2/NextGenMapTest/Teaser/references/E_coli.fasta reads_base.fastq

[main] Real time: 0.011 sec; CPU: 0.005 sec

[bwa_aln_core] convert to sequence coordinate... 0.00 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: /project2/NextGenMapTest/Teaser/software/bwa samse /project2/NextGenMapTest/Teaser/references/E_coli.fasta out_bwa.sam.bwa reads_base.fastq

[main] Real time: 0.131 sec; CPU: 0.009 sec
systime0.011998
time0.149211883545
usrtime0.003999
working_directory/project2/NextGenMapTest/Teaser/tests_generated/ecoli_test

/project2/NextGenMapTest/Teaser/software/bwa aln /project2/NextGenMapTest/Teaser/references/E_coli.fasta reads_base.fastq -t 4 > out_bwa.sam.bwa; /project2/NextGenMapTest/Teaser/software/bwa samse /project2/NextGenMapTest/Teaser/references/E_coli.fasta out_bwa.sam.bwa reads_base.fastq > out_bwa.sam

command/project2/NextGenMapTest/Teaser/software/bwa aln /project2/NextGenMapTest/Teaser/references/E_coli.fasta reads_base.fastq -t 4 > out_bwa.sam.bwa; /project2/NextGenMapTest/Teaser/software/bwa samse /project2/NextGenMapTest/Teaser/references/E_coli.fasta out_bwa.sam.bwa reads_base.fastq > out_bwa.sam
memory19292000
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: /project2/NextGenMapTest/Teaser/software/bwa aln -t 4 /project2/NextGenMapTest/Teaser/references/E_coli.fasta reads_base.fastq

[main] Real time: 0.007 sec; CPU: 0.006 sec

[bwa_aln_core] convert to sequence coordinate... 0.00 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: /project2/NextGenMapTest/Teaser/software/bwa samse /project2/NextGenMapTest/Teaser/references/E_coli.fasta out_bwa.sam.bwa reads_base.fastq

[main] Real time: 0.017 sec; CPU: 0.008 sec
systime0.015997
time0.0399270057678
usrtime0.000999
working_directory/project2/NextGenMapTest/Teaser/tests_generated/ecoli_test

/project2/NextGenMapTest/Teaser/software/bwa aln /project2/NextGenMapTest/Teaser/references/E_coli.fasta reads.fastq -t 4 > out_bwa.sam.bwa; /project2/NextGenMapTest/Teaser/software/bwa samse /project2/NextGenMapTest/Teaser/references/E_coli.fasta out_bwa.sam.bwa reads.fastq > out_bwa.sam

command/project2/NextGenMapTest/Teaser/software/bwa aln /project2/NextGenMapTest/Teaser/references/E_coli.fasta reads.fastq -t 4 > out_bwa.sam.bwa; /project2/NextGenMapTest/Teaser/software/bwa samse /project2/NextGenMapTest/Teaser/references/E_coli.fasta out_bwa.sam.bwa reads.fastq > out_bwa.sam
memory107716000
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... 7.15 sec

[bwa_aln_core] write to the disk... 0.01 sec

[bwa_aln_core] 150000 sequences have been processed.

[main] Version: 0.7.12-r1039

[main] CMD: /project2/NextGenMapTest/Teaser/software/bwa aln -t 4 /project2/NextGenMapTest/Teaser/references/E_coli.fasta reads.fastq

[main] Real time: 2.021 sec; CPU: 7.317 sec

[bwa_aln_core] convert to sequence coordinate... 0.31 sec

[bwa_aln_core] refine gapped alignments... 0.99 sec

[bwa_aln_core] print alignments... 0.20 sec

[bwa_aln_core] 150000 sequences have been processed.

[main] Version: 0.7.12-r1039

[main] CMD: /project2/NextGenMapTest/Teaser/software/bwa samse /project2/NextGenMapTest/Teaser/references/E_coli.fasta out_bwa.sam.bwa reads.fastq

[main] Real time: 2.311 sec; CPU: 1.665 sec
systime0.105983
time4.34469294548
usrtime8.883649
working_directory/project2/NextGenMapTest/Teaser/tests_generated/ecoli_test