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 Mapped162918074.078%
Wrongly Mapped56792625.823%
Not Mapped21780.099%
Total2199284100.0%
Read Failure Statistics
Not mapped21780.099%
Missing in mapper output00.0%
Mapped to wrong chromosome43939919.979%
Mapped to wrong position1285205.844%
Mapped to wrong strand70.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.851100
Precision0.741500
Recall0.998700
Timing
Raw Mapping Time113.978s
Effective Mapping Time108.531s
Effective Init Time5.446s
Effective Time MeasureWall clock
Mapping Time (Wall)113.978s
Mapping Time (CPU)310.400s
Mapping Time (CPU User)291.749s
Mapping Time (CPU System)18.651s
Init Time (Wall)5.446s
Init Time (CPU)3.124s
Init Time (CPU User)0.058s
Init Time (CPU System)3.066s
Additional Information
Mapper Memory Usage7183 MB
Total Test Runtime (Wall)191.316s
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
memory7089396000
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: 4.739 sec; CPU: 1.058 sec

[bwa_aln_core] convert to sequence coordinate... 2.41 sec

[bwa_aln_core] refine gapped alignments... 0.26 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: 5.968 sec; CPU: 2.682 sec
systime3.676441
time10.7266058922
usrtime0.065989
working_directory/project2/NextGenMapTest/Teaser/tests_generated/M4_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
memory7089604000
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: 1.279 sec; CPU: 0.976 sec

[bwa_aln_core] convert to sequence coordinate... 1.86 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: 4.139 sec; CPU: 2.144 sec
systime3.065533
time5.44611597061
usrtime0.057991
working_directory/project2/NextGenMapTest/Teaser/tests_generated/M4_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
memory7183628000
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... 32.93 sec

[bwa_aln_core] write to the disk... 0.02 sec

[bwa_aln_core] 262144 sequences have been processed.

[bwa_aln_core] calculate SA coordinate... 32.80 sec

[bwa_aln_core] write to the disk... 0.02 sec

[bwa_aln_core] 524288 sequences have been processed.

[bwa_aln_core] calculate SA coordinate... 33.12 sec

[bwa_aln_core] write to the disk... 0.03 sec

[bwa_aln_core] 786432 sequences have been processed.

[bwa_aln_core] calculate SA coordinate... 33.05 sec

[bwa_aln_core] write to the disk... 0.02 sec

[bwa_aln_core] 1048576 sequences have been processed.

[bwa_aln_core] calculate SA coordinate... 32.94 sec

[bwa_aln_core] write to the disk... 0.03 sec

[bwa_aln_core] 1310720 sequences have been processed.

[bwa_aln_core] calculate SA coordinate... 32.90 sec

[bwa_aln_core] write to the disk... 0.02 sec

[bwa_aln_core] 1572864 sequences have been processed.

[bwa_aln_core] calculate SA coordinate... 33.04 sec

[bwa_aln_core] write to the disk... 0.02 sec

[bwa_aln_core] 1835008 sequences have been processed.

[bwa_aln_core] calculate SA coordinate... 32.78 sec

[bwa_aln_core] write to the disk... 0.02 sec

[bwa_aln_core] 2097152 sequences have been processed.

[bwa_aln_core] calculate SA coordinate... 12.94 sec

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

[bwa_aln_core] 2199284 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: 72.968 sec; CPU: 278.567 sec

[bwa_aln_core] convert to sequence coordinate... 3.80 sec

[bwa_aln_core] refine gapped alignments... 0.36 sec

[bwa_aln_core] print alignments... 0.33 sec

[bwa_aln_core] 262144 sequences have been processed.

[bwa_aln_core] convert to sequence coordinate... 3.14 sec

[bwa_aln_core] refine gapped alignments... 0.32 sec

[bwa_aln_core] print alignments... 0.34 sec

[bwa_aln_core] 524288 sequences have been processed.

[bwa_aln_core] convert to sequence coordinate... 2.83 sec

[bwa_aln_core] refine gapped alignments... 0.33 sec

[bwa_aln_core] print alignments... 0.33 sec

[bwa_aln_core] 786432 sequences have been processed.

[bwa_aln_core] convert to sequence coordinate... 2.79 sec

[bwa_aln_core] refine gapped alignments... 0.32 sec

[bwa_aln_core] print alignments... 0.34 sec

[bwa_aln_core] 1048576 sequences have been processed.

[bwa_aln_core] convert to sequence coordinate... 2.68 sec

[bwa_aln_core] refine gapped alignments... 0.31 sec

[bwa_aln_core] print alignments... 0.34 sec

[bwa_aln_core] 1310720 sequences have been processed.

[bwa_aln_core] convert to sequence coordinate... 2.73 sec

[bwa_aln_core] refine gapped alignments... 0.34 sec

[bwa_aln_core] print alignments... 0.35 sec

[bwa_aln_core] 1572864 sequences have been processed.

[bwa_aln_core] convert to sequence coordinate... 2.62 sec

[bwa_aln_core] refine gapped alignments... 0.31 sec

[bwa_aln_core] print alignments... 0.34 sec

[bwa_aln_core] 1835008 sequences have been processed.

[bwa_aln_core] convert to sequence coordinate... 2.58 sec

[bwa_aln_core] refine gapped alignments... 0.32 sec

[bwa_aln_core] print alignments... 0.33 sec

[bwa_aln_core] 2097152 sequences have been processed.

[bwa_aln_core] convert to sequence coordinate... 1.87 sec

[bwa_aln_core] refine gapped alignments... 0.27 sec

[bwa_aln_core] print alignments... 0.13 sec

[bwa_aln_core] 2199284 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: 40.959 sec; CPU: 31.829 sec
systime18.651164
time113.977607012
usrtime291.748647
working_directory/project2/NextGenMapTest/Teaser/tests_generated/M4_n