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 Mapped39686094.974%
Wrongly Mapped167684.013%
Not Mapped42321.013%
Total417860100.0%
Read Failure Statistics
Not mapped42321.013%
Missing in mapper output00.0%
Mapped to wrong chromosome63931.53%
Mapped to wrong position103752.483%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.974200
Precision0.959500
Recall0.989400
Timing
Raw Mapping Time73.200s
Effective Mapping Time72.936s
Effective Init Time0.264s
Effective Time MeasureCPU
Mapping Time (Wall)41.545s
Mapping Time (CPU)73.200s
Mapping Time (CPU User)71.464s
Mapping Time (CPU System)1.736s
Init Time (Wall)0.506s
Init Time (CPU)0.264s
Init Time (CPU User)0.004s
Init Time (CPU System)0.260s
Additional Information
Mapper Memory Usage280 MB
Total Test Runtime (Wall)107.751s
Mapper Command Line: 
/project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/C_elegans.fa reads.fastq -t 4 > out_bwa.sam.bwa; /project/teaser/genometeaser/software/bwa samse /project/teaser/genometeaser/references/C_elegans.fa 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/C_elegans.fa reads_base.fastq -t 4 > out_bwa.sam.bwa; /project/teaser/genometeaser/software/bwa samse /project/teaser/genometeaser/references/C_elegans.fa out_bwa.sam.bwa reads_base.fastq > out_bwa.sam

command/project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/C_elegans.fa reads_base.fastq -t 4 > out_bwa.sam.bwa; /project/teaser/genometeaser/software/bwa samse /project/teaser/genometeaser/references/C_elegans.fa out_bwa.sam.bwa reads_base.fastq > out_bwa.sam
memory150360000
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/C_elegans.fa reads_base.fastq
[main] Real time: 8.608 sec; CPU: 0.128 sec
[bwa_aln_core] convert to sequence coordinate... 0.16 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/C_elegans.fa out_bwa.sam.bwa reads_base.fastq
[main] Real time: 6.814 sec; CPU: 0.192 sec
systime0.336
time15.4712309837
usrtime0.004
working_directory/project/teaser/genometeaser/tests_generated/0b75acea7debea0665280a94869c22a6

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

command/project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/C_elegans.fa reads_base.fastq -t 4 > out_bwa.sam.bwa; /project/teaser/genometeaser/software/bwa samse /project/teaser/genometeaser/references/C_elegans.fa out_bwa.sam.bwa reads_base.fastq > out_bwa.sam
memory150416000
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/C_elegans.fa reads_base.fastq
[main] Real time: 0.272 sec; CPU: 0.088 sec
[bwa_aln_core] convert to sequence coordinate... 0.13 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/C_elegans.fa out_bwa.sam.bwa reads_base.fastq
[main] Real time: 0.184 sec; CPU: 0.160 sec
systime0.26
time0.505834102631
usrtime0.004
working_directory/project/teaser/genometeaser/tests_generated/0b75acea7debea0665280a94869c22a6

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

command/project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/C_elegans.fa reads.fastq -t 4 > out_bwa.sam.bwa; /project/teaser/genometeaser/software/bwa samse /project/teaser/genometeaser/references/C_elegans.fa out_bwa.sam.bwa reads.fastq > out_bwa.sam
memory280608000
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... 38.39 sec
[bwa_aln_core] write to the disk... 0.14 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_aln_core] calculate SA coordinate... 22.50 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 417860 sequences have been processed.
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa aln -t 4 /project/teaser/genometeaser/references/C_elegans.fa reads.fastq
[main] Real time: 22.871 sec; CPU: 62.488 sec
[bwa_aln_core] convert to sequence coordinate... 2.55 sec
[bwa_aln_core] refine gapped alignments... 2.09 sec
[bwa_aln_core] print alignments... 1.23 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_aln_core] convert to sequence coordinate... 1.56 sec
[bwa_aln_core] refine gapped alignments... 1.27 sec
[bwa_aln_core] print alignments... 0.73 sec
[bwa_aln_core] 417860 sequences have been processed.
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa samse /project/teaser/genometeaser/references/C_elegans.fa out_bwa.sam.bwa reads.fastq
[main] Real time: 18.600 sec; CPU: 10.676 sec
systime1.736
time41.5452001095
usrtime71.464
working_directory/project/teaser/genometeaser/tests_generated/0b75acea7debea0665280a94869c22a6