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 Mapped52408887.515%
Wrongly Mapped6852911.443%
Not Mapped62411.042%
Total598858100.0%
Read Failure Statistics
Not mapped62411.042%
Missing in mapper output00.0%
Mapped to wrong chromosome405446.77%
Mapped to wrong position279844.673%
Mapped to wrong strand10.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.933400
Precision0.884400
Recall0.988200
Timing
Raw Mapping Time112.520s
Effective Mapping Time112.136s
Effective Init Time0.384s
Effective Time MeasureCPU
Mapping Time (Wall)61.584s
Mapping Time (CPU)112.520s
Mapping Time (CPU User)109.704s
Mapping Time (CPU System)2.816s
Init Time (Wall)0.599s
Init Time (CPU)0.384s
Init Time (CPU User)0.020s
Init Time (CPU System)0.364s
Additional Information
Mapper Memory Usage345 MB
Total Test Runtime (Wall)157.851s
Mapper Command Line: 
/project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/D_melanogaster.fasta reads.fastq -t 4 > out_bwa.sam.bwa; /project/teaser/genometeaser/software/bwa samse /project/teaser/genometeaser/references/D_melanogaster.fasta out_bwa.sam.bwa reads.fastq > out_bwa.sam
Errors and Warnings
No problems were encountered.
Subprocess Log

/project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/D_melanogaster.fasta reads_base.fastq -t 4 > out_bwa.sam.bwa; /project/teaser/genometeaser/software/bwa samse /project/teaser/genometeaser/references/D_melanogaster.fasta out_bwa.sam.bwa reads_base.fastq > out_bwa.sam

command/project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/D_melanogaster.fasta reads_base.fastq -t 4 > out_bwa.sam.bwa; /project/teaser/genometeaser/software/bwa samse /project/teaser/genometeaser/references/D_melanogaster.fasta out_bwa.sam.bwa reads_base.fastq > out_bwa.sam
memory220160000
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: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa aln -t 4 /project/teaser/genometeaser/references/D_melanogaster.fasta reads_base.fastq
[main] Real time: 12.367 sec; CPU: 0.180 sec
[bwa_aln_core] convert to sequence coordinate... 0.23 sec
[bwa_aln_core] refine gapped alignments... 0.04 sec
[bwa_aln_core] print alignments... 0.00 sec
[bwa_aln_core] 1 sequences have been processed.
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa samse /project/teaser/genometeaser/references/D_melanogaster.fasta out_bwa.sam.bwa reads_base.fastq
[main] Real time: 9.648 sec; CPU: 0.284 sec
systime0.452
time22.0635750294
usrtime0.024
working_directory/project/teaser/genometeaser/tests_generated/940d34bf07c6143b2e6e8116a29b2b51

/project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/D_melanogaster.fasta reads_base.fastq -t 4 > out_bwa.sam.bwa; /project/teaser/genometeaser/software/bwa samse /project/teaser/genometeaser/references/D_melanogaster.fasta out_bwa.sam.bwa reads_base.fastq > out_bwa.sam

command/project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/D_melanogaster.fasta reads_base.fastq -t 4 > out_bwa.sam.bwa; /project/teaser/genometeaser/software/bwa samse /project/teaser/genometeaser/references/D_melanogaster.fasta out_bwa.sam.bwa reads_base.fastq > out_bwa.sam
memory220160000
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: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa aln -t 4 /project/teaser/genometeaser/references/D_melanogaster.fasta reads_base.fastq
[main] Real time: 0.238 sec; CPU: 0.128 sec
[bwa_aln_core] convert to sequence coordinate... 0.19 sec
[bwa_aln_core] refine gapped alignments... 0.03 sec
[bwa_aln_core] print alignments... 0.00 sec
[bwa_aln_core] 1 sequences have been processed.
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa samse /project/teaser/genometeaser/references/D_melanogaster.fasta out_bwa.sam.bwa reads_base.fastq
[main] Real time: 0.299 sec; CPU: 0.240 sec
systime0.364
time0.59873509407
usrtime0.02
working_directory/project/teaser/genometeaser/tests_generated/940d34bf07c6143b2e6e8116a29b2b51

/project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/D_melanogaster.fasta reads.fastq -t 4 > out_bwa.sam.bwa; /project/teaser/genometeaser/software/bwa samse /project/teaser/genometeaser/references/D_melanogaster.fasta out_bwa.sam.bwa reads.fastq > out_bwa.sam

command/project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/D_melanogaster.fasta reads.fastq -t 4 > out_bwa.sam.bwa; /project/teaser/genometeaser/software/bwa samse /project/teaser/genometeaser/references/D_melanogaster.fasta out_bwa.sam.bwa reads.fastq > out_bwa.sam
memory345228000
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... 42.04 sec
[bwa_aln_core] write to the disk... 0.13 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_aln_core] calculate SA coordinate... 40.92 sec
[bwa_aln_core] write to the disk... 0.13 sec
[bwa_aln_core] 524288 sequences have been processed.
[bwa_aln_core] calculate SA coordinate... 10.57 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 598858 sequences have been processed.
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa aln -t 4 /project/teaser/genometeaser/references/D_melanogaster.fasta reads.fastq
[main] Real time: 33.428 sec; CPU: 95.760 sec
[bwa_aln_core] convert to sequence coordinate... 2.95 sec
[bwa_aln_core] refine gapped alignments... 2.18 sec
[bwa_aln_core] print alignments... 1.31 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_aln_core] convert to sequence coordinate... 2.96 sec
[bwa_aln_core] refine gapped alignments... 2.20 sec
[bwa_aln_core] print alignments... 1.35 sec
[bwa_aln_core] 524288 sequences have been processed.
[bwa_aln_core] convert to sequence coordinate... 0.97 sec
[bwa_aln_core] refine gapped alignments... 0.64 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 598858 sequences have been processed.
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa samse /project/teaser/genometeaser/references/D_melanogaster.fasta out_bwa.sam.bwa reads.fastq
[main] Real time: 28.086 sec; CPU: 16.716 sec
systime2.816
time61.5838429928
usrtime109.704
working_directory/project/teaser/genometeaser/tests_generated/940d34bf07c6143b2e6e8116a29b2b51