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 Mapped5118315.868%
Wrongly Mapped48251.496%
Not Mapped26655382.636%
Total322561100.0%
Read Failure Statistics
Not mapped26655382.636%
Missing in mapper output00.0%
Mapped to wrong chromosome25600.794%
Mapped to wrong position22650.702%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.273900
Precision0.913900
Recall0.161100
Timing
Raw Mapping Time84.916s
Effective Mapping Time74.708s
Effective Init Time10.208s
Effective Time MeasureWall clock
Mapping Time (Wall)84.916s
Mapping Time (CPU)248.140s
Mapping Time (CPU User)240.741s
Mapping Time (CPU System)7.399s
Init Time (Wall)10.208s
Init Time (CPU)3.602s
Init Time (CPU User)0.060s
Init Time (CPU System)3.542s
Additional Information
Mapper Memory Usage7274 MB
Total Test Runtime (Wall)126.091s
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
memory7089616000
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: 1.260 sec; CPU: 0.994 sec

[bwa_aln_core] convert to sequence coordinate... 3.59 sec

[bwa_aln_core] refine gapped alignments... 0.36 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: 13.200 sec; CPU: 3.960 sec
systime4.886257
time14.4863491058
usrtime0.071989
working_directory/project2/NextGenMapTest/Teaser/tests_generated/M2_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
memory7089428000
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: 1.370 sec; CPU: 0.981 sec

[bwa_aln_core] convert to sequence coordinate... 2.28 sec

[bwa_aln_core] refine gapped alignments... 0.33 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: 8.761 sec; CPU: 2.618 sec
systime3.542461
time10.2075259686
usrtime0.05999
working_directory/project2/NextGenMapTest/Teaser/tests_generated/M2_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
memory7274216000
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... 192.67 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... 45.18 sec

[bwa_aln_core] write to the disk... 0.00 sec

[bwa_aln_core] 322561 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: 62.803 sec; CPU: 239.190 sec

[bwa_aln_core] convert to sequence coordinate... 3.10 sec

[bwa_aln_core] refine gapped alignments... 1.89 sec

[bwa_aln_core] print alignments... 0.18 sec

[bwa_aln_core] 262144 sequences have been processed.

[bwa_aln_core] convert to sequence coordinate... 2.67 sec

[bwa_aln_core] refine gapped alignments... 0.67 sec

[bwa_aln_core] print alignments... 0.04 sec

[bwa_aln_core] 322561 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: 22.060 sec; CPU: 8.940 sec
systime7.398875
time84.9157788754
usrtime240.741401
working_directory/project2/NextGenMapTest/Teaser/tests_generated/M2_n