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 Mapped2199284100.0%
Total2199284100.0%
Read Failure Statistics
Not mapped00.0%
Missing in mapper output2199284100.0%
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 Time658.372s
Effective Mapping Time650.664s
Effective Init Time7.708s
Effective Time MeasureCPU
Mapping Time (Wall)178.947s
Mapping Time (CPU)658.372s
Mapping Time (CPU User)618.864s
Mapping Time (CPU System)39.508s
Init Time (Wall)7.811s
Init Time (CPU)7.708s
Init Time (CPU User)0.164s
Init Time (CPU System)7.544s
Additional Information
Mapper Memory Usage13679 MB
Total Test Runtime (Wall)289.725s
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
memory8273272000
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, 0.004 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: 7.770 sec; CPU: 7.704 sec
systime7.58
time7.79236793518
usrtime0.156
working_directory/project/teaser/genometeaser/tests_generated/3f55d5f326042c6d121b7048b0ae8ccd

/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
memory8273272000
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, 0.003 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: 7.789 sec; CPU: 7.684 sec
systime7.544
time7.81102490425
usrtime0.164
working_directory/project/teaser/genometeaser/tests_generated/3f55d5f326042c6d121b7048b0ae8ccd

/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
memory13679104000
return1
status1
stderr
None
stdout
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 1818182 sequences (40000004 bp)...
[M::process] read 381102 sequences (8384244 bp)...
[mem_chain2aln] Failed to allocate 45056 bytes at bwamem.c line 708: Cannot allocate memory
systime39.508
time178.946852922
usrtime618.864
working_directory/project/teaser/genometeaser/tests_generated/3f55d5f326042c6d121b7048b0ae8ccd