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 Mapped00.0%
Wrongly Mapped00.0%
Not Mapped1935370100.0%
Total1935370100.0%
Read Failure Statistics
Not mapped00.0%
Missing in mapper output1935370100.0%
Mapped to wrong chromosome00.0%
Mapped to wrong position00.0%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.000000
Precision0.000000
Recall0.000000
Timing
Raw Mapping Time1358.804s
Effective Mapping Time1267.220s
Effective Init Time91.584s
Effective Time MeasureCPU
Mapping Time (Wall)473.092s
Mapping Time (CPU)1358.804s
Mapping Time (CPU User)1020.012s
Mapping Time (CPU System)338.792s
Init Time (Wall)92.215s
Init Time (CPU)91.584s
Init Time (CPU User)0.024s
Init Time (CPU System)91.560s
Additional Information
Mapper Memory Usage13575 MB
Total Test Runtime (Wall)750.473s
Mapper Command Line: 
/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/M_musculus.fasta reads.fastq -t 4 > out_bwamem.sam
Errors and Warnings
TypeMessageFilePosition
Unexpectedly reached end of mapper outputsorted_out_bwamem.samread.000000000
Subprocess Log

/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/M_musculus.fasta reads_base.fastq -t 4 > out_bwamem.sam

command/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/M_musculus.fasta reads_base.fastq -t 4 > out_bwamem.sam
memory8271636000
return0
status1
stderr
None
stdout
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 1 sequences (60 bp)...
[M::mem_process_seqs] Processed 1 reads in 0.004 CPU sec, 0.010 real sec
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa mem -t 4 /project/teaser/genometeaser/references/M_musculus.fasta reads_base.fastq
[main] Real time: 91.963 sec; CPU: 91.444 sec
systime91.452
time91.9739999771
usrtime0.048
working_directory/project/teaser/genometeaser/tests_generated/43bdd5cc22aa7c6d1994fe8ebc8d72d4

/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/M_musculus.fasta reads_base.fastq -t 4 > out_bwamem.sam

command/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/M_musculus.fasta reads_base.fastq -t 4 > out_bwamem.sam
memory8271640000
return0
status1
stderr
None
stdout
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 1 sequences (60 bp)...
[M::mem_process_seqs] Processed 1 reads in 0.004 CPU sec, 0.010 real sec
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa mem -t 4 /project/teaser/genometeaser/references/M_musculus.fasta reads_base.fastq
[main] Real time: 92.198 sec; CPU: 91.524 sec
systime91.56
time92.2148079872
usrtime0.024
working_directory/project/teaser/genometeaser/tests_generated/43bdd5cc22aa7c6d1994fe8ebc8d72d4

/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/M_musculus.fasta reads.fastq -t 4 > out_bwamem.sam

command/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/M_musculus.fasta reads.fastq -t 4 > out_bwamem.sam
memory13575976000
return1
status1
stderr
None
stdout
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 1600000 sequences (40000000 bp)...
[M::process] read 335370 sequences (8384250 bp)...
[mem_chain2aln] Failed to allocate 45056 bytes at bwamem.c line 708: Cannot allocate memory
systime338.792
time473.091850042
usrtime1020.012
working_directory/project/teaser/genometeaser/tests_generated/43bdd5cc22aa7c6d1994fe8ebc8d72d4