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 Mapped28987189.865%
Wrongly Mapped203956.323%
Not Mapped122953.812%
Total322561100.0%
Read Failure Statistics
Not mapped122953.812%
Missing in mapper output00.0%
Mapped to wrong chromosome95522.961%
Mapped to wrong position108433.362%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.946600
Precision0.934300
Recall0.959300
Timing
Raw Mapping Time122.180s
Effective Mapping Time53.038s
Effective Init Time69.141s
Effective Time MeasureWall clock
Mapping Time (Wall)122.180s
Mapping Time (CPU)261.734s
Mapping Time (CPU User)250.831s
Mapping Time (CPU System)10.903s
Init Time (Wall)69.141s
Init Time (CPU)14.199s
Init Time (CPU User)0.081s
Init Time (CPU System)14.118s
Additional Information
Mapper Memory Usage7280 MB
Total Test Runtime (Wall)331.035s
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
memory7089496000
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: 52.747 sec; CPU: 4.029 sec

[bwa_aln_core] convert to sequence coordinate... 11.73 sec

[bwa_aln_core] refine gapped alignments... 0.46 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: 71.210 sec; CPU: 12.202 sec
systime16.128548
time124.101085901
usrtime0.106983
working_directory/project2/NextGenMapTest/Teaser/tests_generated/M1_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... 0.02 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: 28.005 sec; CPU: 4.543 sec

[bwa_aln_core] convert to sequence coordinate... 9.17 sec

[bwa_aln_core] refine gapped alignments... 0.47 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: 40.949 sec; CPU: 9.650 sec
systime14.117853
time69.1413140297
usrtime0.080987
working_directory/project2/NextGenMapTest/Teaser/tests_generated/M1_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
memory7280492000
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... 199.03 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... 44.75 sec

[bwa_aln_core] write to the disk... 0.01 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: 67.659 sec; CPU: 245.172 sec

[bwa_aln_core] convert to sequence coordinate... 6.78 sec

[bwa_aln_core] refine gapped alignments... 4.28 sec

[bwa_aln_core] print alignments... 0.41 sec

[bwa_aln_core] 262144 sequences have been processed.

[bwa_aln_core] convert to sequence coordinate... 3.30 sec

[bwa_aln_core] refine gapped alignments... 1.27 sec

[bwa_aln_core] print alignments... 0.09 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: 54.224 sec; CPU: 16.548 sec
systime10.903342
time122.179671049
usrtime250.830867
working_directory/project2/NextGenMapTest/Teaser/tests_generated/M1_n