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 Time154.433s
Effective Mapping Time130.175s
Effective Init Time24.258s
Effective Time MeasureWall clock
Mapping Time (Wall)154.433s
Mapping Time (CPU)478.482s
Mapping Time (CPU User)463.132s
Mapping Time (CPU System)15.351s
Init Time (Wall)24.258s
Init Time (CPU)2.345s
Init Time (CPU User)0.041s
Init Time (CPU System)2.304s
Additional Information
Mapper Memory Usage15978 MB
Total Test Runtime (Wall)308.552s
Mapper Command Line: 
/project2/NextGenMapTest/Teaser/software/bwa mem /project2/NextGenMapTest/Teaser/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

/project2/NextGenMapTest/Teaser/software/bwa mem /project2/NextGenMapTest/Teaser/references/m_musculus.fasta reads_base.fastq -t 4 > out_bwamem.sam

command/project2/NextGenMapTest/Teaser/software/bwa mem /project2/NextGenMapTest/Teaser/references/m_musculus.fasta reads_base.fastq -t 4 > out_bwamem.sam
memory8270144000
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 0.002 CPU sec, 0.034 real sec

[main] Version: 0.7.12-r1039

[main] CMD: /project2/NextGenMapTest/Teaser/software/bwa mem -t 4 /project2/NextGenMapTest/Teaser/references/m_musculus.fasta reads_base.fastq

[main] Real time: 99.551 sec; CPU: 3.225 sec
systime3.167518
time99.5586380959
usrtime0.05999
working_directory/project2/NextGenMapTest/Teaser/tests_generated/M4_n

/project2/NextGenMapTest/Teaser/software/bwa mem /project2/NextGenMapTest/Teaser/references/m_musculus.fasta reads_base.fastq -t 4 > out_bwamem.sam

command/project2/NextGenMapTest/Teaser/software/bwa mem /project2/NextGenMapTest/Teaser/references/m_musculus.fasta reads_base.fastq -t 4 > out_bwamem.sam
memory8259576000
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 0.003 CPU sec, 0.022 real sec

[main] Version: 0.7.12-r1039

[main] CMD: /project2/NextGenMapTest/Teaser/software/bwa mem -t 4 /project2/NextGenMapTest/Teaser/references/m_musculus.fasta reads_base.fastq

[main] Real time: 24.185 sec; CPU: 2.341 sec
systime2.303649
time24.2581031322
usrtime0.040993
working_directory/project2/NextGenMapTest/Teaser/tests_generated/M4_n

/project2/NextGenMapTest/Teaser/software/bwa mem /project2/NextGenMapTest/Teaser/references/m_musculus.fasta reads.fastq -t 4 > out_bwamem.sam

command/project2/NextGenMapTest/Teaser/software/bwa mem /project2/NextGenMapTest/Teaser/references/m_musculus.fasta reads.fastq -t 4 > out_bwamem.sam
memory15978168000
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_chain] Failed to allocate 20000 bytes at bwamem.c line 304: Cannot allocate memory

[mem_chain2aln] Failed to allocate 45056 bytes at bwamem.c line 715: Cannot allocate memory
systime15.350666
time154.433423042
usrtime463.131593
working_directory/project2/NextGenMapTest/Teaser/tests_generated/M4_n