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 Mapped	1363902	83.509%
Wrongly Mapped	263064	16.107%
Not Mapped	6283	0.385%
Total	1633249	100.0%

Read Failure Statistics

Not mapped	6283	0.385%
Missing in mapper output	0	0.0%
Mapped to wrong chromosome	178021	10.9%
Mapped to wrong position	85034	5.206%
Mapped to wrong strand	9	0.001%

Advanced Statistics

Missing in comparison alignment	0
Secondary Alignments	0
F-Measure	0.910100
Precision	0.838300
Recall	0.995400

Timing

Raw Mapping Time	47.364s
Effective Mapping Time	47.205s
Effective Init Time	0.159s
Effective Time Measure	Wall clock
Mapping Time (Wall)	47.364s
Mapping Time (CPU)	140.766s
Mapping Time (CPU User)	139.967s
Mapping Time (CPU System)	0.799s
Init Time (Wall)	0.159s
Init Time (CPU)	0.095s
Init Time (CPU User)	0.007s
Init Time (CPU System)	0.088s

Additional Information

Mapper Memory Usage	306 MB
Total Test Runtime (Wall)	94.726s
Mapper Command Line:
/project2/NextGenMapTest/Teaser/software/bwa aln /project2/NextGenMapTest/Teaser/references/d_melanogaster.fasta reads.fastq -t 4 > out_bwa.sam.bwa; /project2/NextGenMapTest/Teaser/software/bwa samse /project2/NextGenMapTest/Teaser/references/d_melanogaster.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/d_melanogaster.fasta reads_base.fastq -t 4 > out_bwa.sam.bwa; /project2/NextGenMapTest/Teaser/software/bwa samse /project2/NextGenMapTest/Teaser/references/d_melanogaster.fasta out_bwa.sam.bwa reads_base.fastq > out_bwa.sam

command	/project2/NextGenMapTest/Teaser/software/bwa aln /project2/NextGenMapTest/Teaser/references/d_melanogaster.fasta reads_base.fastq -t 4 > out_bwa.sam.bwa; /project2/NextGenMapTest/Teaser/software/bwa samse /project2/NextGenMapTest/Teaser/references/d_melanogaster.fasta out_bwa.sam.bwa reads_base.fastq > out_bwa.sam
memory	212892000
return	0
status	1
stderr	stderr None
stdout	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/d_melanogaster.fasta reads_base.fastq [main] Real time: 0.126 sec; CPU: 0.032 sec [bwa_aln_core] convert to sequence coordinate... 0.04 sec [bwa_aln_core] refine gapped alignments... 0.01 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/d_melanogaster.fasta out_bwa.sam.bwa reads_base.fastq [main] Real time: 0.063 sec; CPU: 0.057 sec
systime	0.087986
time	0.379452943802
usrtime	0.003999
working_directory	/project2/NextGenMapTest/Teaser/tests_generated/D4_n

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

command	/project2/NextGenMapTest/Teaser/software/bwa aln /project2/NextGenMapTest/Teaser/references/d_melanogaster.fasta reads_base.fastq -t 4 > out_bwa.sam.bwa; /project2/NextGenMapTest/Teaser/software/bwa samse /project2/NextGenMapTest/Teaser/references/d_melanogaster.fasta out_bwa.sam.bwa reads_base.fastq > out_bwa.sam
memory	212892000
return	0
status	1
stderr	stderr None
stdout	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/d_melanogaster.fasta reads_base.fastq [main] Real time: 0.037 sec; CPU: 0.036 sec [bwa_aln_core] convert to sequence coordinate... 0.04 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/d_melanogaster.fasta out_bwa.sam.bwa reads_base.fastq [main] Real time: 0.113 sec; CPU: 0.055 sec
systime	0.087986
time	0.159321069717
usrtime	0.006998
working_directory	/project2/NextGenMapTest/Teaser/tests_generated/D4_n

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

command	/project2/NextGenMapTest/Teaser/software/bwa aln /project2/NextGenMapTest/Teaser/references/d_melanogaster.fasta reads.fastq -t 4 > out_bwa.sam.bwa; /project2/NextGenMapTest/Teaser/software/bwa samse /project2/NextGenMapTest/Teaser/references/d_melanogaster.fasta out_bwa.sam.bwa reads.fastq > out_bwa.sam
memory	306700000
return	0
status	1
stderr	stderr None
stdout	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... 21.07 sec [bwa_aln_core] write to the disk... 0.01 sec [bwa_aln_core] 262144 sequences have been processed. [bwa_aln_core] calculate SA coordinate... 20.87 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... 20.79 sec [bwa_aln_core] write to the disk... 0.01 sec [bwa_aln_core] 786432 sequences have been processed. [bwa_aln_core] calculate SA coordinate... 20.77 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... 20.80 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 1310720 sequences have been processed. [bwa_aln_core] calculate SA coordinate... 20.78 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... 4.83 sec [bwa_aln_core] write to the disk... 0.01 sec [bwa_aln_core] 1633249 sequences have been processed. [main] Version: 0.7.12-r1039 [main] CMD: /project2/NextGenMapTest/Teaser/software/bwa aln -t 4 /project2/NextGenMapTest/Teaser/references/d_melanogaster.fasta reads.fastq [main] Real time: 34.553 sec; CPU: 130.751 sec [bwa_aln_core] convert to sequence coordinate... 1.05 sec [bwa_aln_core] refine gapped alignments... 0.10 sec [bwa_aln_core] print alignments... 0.32 sec [bwa_aln_core] 262144 sequences have been processed. [bwa_aln_core] convert to sequence coordinate... 1.05 sec [bwa_aln_core] refine gapped alignments... 0.11 sec [bwa_aln_core] print alignments... 0.32 sec [bwa_aln_core] 524288 sequences have been processed. [bwa_aln_core] convert to sequence coordinate... 1.04 sec [bwa_aln_core] refine gapped alignments... 0.12 sec [bwa_aln_core] print alignments... 0.32 sec [bwa_aln_core] 786432 sequences have been processed. [bwa_aln_core] convert to sequence coordinate... 1.05 sec [bwa_aln_core] refine gapped alignments... 0.10 sec [bwa_aln_core] print alignments... 0.31 sec [bwa_aln_core] 1048576 sequences have been processed. [bwa_aln_core] convert to sequence coordinate... 1.04 sec [bwa_aln_core] refine gapped alignments... 0.11 sec [bwa_aln_core] print alignments... 0.31 sec [bwa_aln_core] 1310720 sequences have been processed. [bwa_aln_core] convert to sequence coordinate... 1.04 sec [bwa_aln_core] refine gapped alignments... 0.11 sec [bwa_aln_core] print alignments... 0.32 sec [bwa_aln_core] 1572864 sequences have been processed. [bwa_aln_core] convert to sequence coordinate... 0.28 sec [bwa_aln_core] refine gapped alignments... 0.02 sec [bwa_aln_core] print alignments... 0.09 sec [bwa_aln_core] 1633249 sequences have been processed. [main] Version: 0.7.12-r1039 [main] CMD: /project2/NextGenMapTest/Teaser/software/bwa samse /project2/NextGenMapTest/Teaser/references/d_melanogaster.fasta out_bwa.sam.bwa reads.fastq [main] Real time: 12.792 sec; CPU: 10.009 sec
systime	0.798878
time	47.3642048836
usrtime	139.966721
working_directory	/project2/NextGenMapTest/Teaser/tests_generated/D4_n

stderr

stdout

stderr

stdout

stderr

stdout