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 Mapped20.001%
Wrongly Mapped00.0%
Not Mapped24191999.999%
Total241921100.0%
Read Failure Statistics
Not mapped24191999.999%
Missing in mapper output00.0%
Mapped to wrong chromosome00.0%
Mapped to wrong position00.0%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.000000
Precision1.000000
Recall0.000000
Timing
Raw Mapping Time14.796s
Effective Mapping Time7.611s
Effective Init Time7.186s
Effective Time MeasureWall clock
Mapping Time (Wall)14.796s
Mapping Time (CPU)22.772s
Mapping Time (CPU User)18.892s
Mapping Time (CPU System)3.879s
Init Time (Wall)7.186s
Init Time (CPU)3.785s
Init Time (CPU User)0.069s
Init Time (CPU System)3.716s
Additional Information
Mapper Memory Usage7320 MB
Total Test Runtime (Wall)40.933s
Mapper Command Line: 
/project2/NextGenMapTest/Teaser/software/bwa aln /project2/NextGenMapTest/Teaser/references/m_musculus.fasta reads.fastq -t 4 > out_bwa.sam.bwa; /project2/NextGenMapTest/Teaser/software/bwa samse /project2/NextGenMapTest/Teaser/references/m_musculus.fasta out_bwa.sam.bwa reads.fastq > out_bwa.sam
Errors and Warnings
No problems were encountered.
Subprocess Log

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

command/project2/NextGenMapTest/Teaser/software/bwa aln /project2/NextGenMapTest/Teaser/references/m_musculus.fasta reads_base.fastq -t 4 > out_bwa.sam.bwa; /project2/NextGenMapTest/Teaser/software/bwa samse /project2/NextGenMapTest/Teaser/references/m_musculus.fasta out_bwa.sam.bwa reads_base.fastq > out_bwa.sam
memory7089572000
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/m_musculus.fasta reads_base.fastq

[main] Real time: 1.242 sec; CPU: 0.976 sec

[bwa_aln_core] convert to sequence coordinate... 2.35 sec

[bwa_aln_core] refine gapped alignments... 0.32 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/m_musculus.fasta out_bwa.sam.bwa reads_base.fastq

[main] Real time: 8.069 sec; CPU: 2.678 sec
systime3.589454
time9.32836413383
usrtime0.066989
working_directory/project2/NextGenMapTest/Teaser/tests_generated/M3_n

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

command/project2/NextGenMapTest/Teaser/software/bwa aln /project2/NextGenMapTest/Teaser/references/m_musculus.fasta reads_base.fastq -t 4 > out_bwa.sam.bwa; /project2/NextGenMapTest/Teaser/software/bwa samse /project2/NextGenMapTest/Teaser/references/m_musculus.fasta out_bwa.sam.bwa reads_base.fastq > out_bwa.sam
memory7089392000
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/m_musculus.fasta reads_base.fastq

[main] Real time: 1.704 sec; CPU: 0.989 sec

[bwa_aln_core] convert to sequence coordinate... 2.51 sec

[bwa_aln_core] refine gapped alignments... 0.27 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/m_musculus.fasta out_bwa.sam.bwa reads_base.fastq

[main] Real time: 5.437 sec; CPU: 2.794 sec
systime3.716435
time7.18560695648
usrtime0.068989
working_directory/project2/NextGenMapTest/Teaser/tests_generated/M3_n

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

command/project2/NextGenMapTest/Teaser/software/bwa aln /project2/NextGenMapTest/Teaser/references/m_musculus.fasta reads.fastq -t 4 > out_bwa.sam.bwa; /project2/NextGenMapTest/Teaser/software/bwa samse /project2/NextGenMapTest/Teaser/references/m_musculus.fasta out_bwa.sam.bwa reads.fastq > out_bwa.sam
memory7320056000
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... 18.09 sec

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

[bwa_aln_core] 241921 sequences have been processed.

[main] Version: 0.7.12-r1039

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

[main] Real time: 7.475 sec; CPU: 19.446 sec

[bwa_aln_core] convert to sequence coordinate... 2.40 sec

[bwa_aln_core] refine gapped alignments... 0.34 sec

[bwa_aln_core] print alignments... 0.16 sec

[bwa_aln_core] 241921 sequences have been processed.

[main] Version: 0.7.12-r1039

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

[main] Real time: 7.203 sec; CPU: 3.305 sec
systime3.87941
time14.7961740494
usrtime18.892127
working_directory/project2/NextGenMapTest/Teaser/tests_generated/M3_n