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 Mapped24978391.646%
Wrongly Mapped226188.299%
Not Mapped1520.056%
Total272553100.0%
Read Failure Statistics
Not mapped1520.056%
Missing in mapper output00.0%
Mapped to wrong chromosome110334.048%
Mapped to wrong position115854.251%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.956400
Precision0.917000
Recall0.999400
Timing
Raw Mapping Time264.260s
Effective Mapping Time260.668s
Effective Init Time3.592s
Effective Time MeasureCPU
Mapping Time (Wall)71.137s
Mapping Time (CPU)264.260s
Mapping Time (CPU User)256.960s
Mapping Time (CPU System)7.300s
Init Time (Wall)3.546s
Init Time (CPU)3.592s
Init Time (CPU User)0.164s
Init Time (CPU System)3.428s
Additional Information
Mapper Memory Usage3139 MB
Total Test Runtime (Wall)13951.373s
Mapper Command Line: 
/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/M_musculus_cutf.fasta_bt -U reads.fastq -S out_bowtie2.sam
Errors and Warnings
No problems were encountered.
Subprocess Log

/project/teaser/genometeaser/software/bowtie2/bowtie2-build /project/teaser/genometeaser/references/M_musculus_cutf.fasta /project/teaser/genometeaser/references/M_musculus_cutf.fasta_bt

command/project/teaser/genometeaser/software/bowtie2/bowtie2-build /project/teaser/genometeaser/references/M_musculus_cutf.fasta /project/teaser/genometeaser/references/M_musculus_cutf.fasta_bt
return1
status1
stderr
None
stdout
Settings:
Output files: "/project/teaser/genometeaser/references/M_musculus_cutf.fasta_bt.*.bt2"
Line rate: 6 (line is 64 bytes)
Lines per side: 1 (side is 64 bytes)
Offset rate: 4 (one in 16)
FTable chars: 10
Strings: unpacked
Max bucket size: default
Max bucket size, sqrt multiplier: default
Max bucket size, len divisor: 4
Difference-cover sample period: 1024
Endianness: little
Actual local endianness: little
Sanity checking: disabled
Assertions: disabled
Random seed: 0
Sizeofs: void*:8, int:4, long:8, size_t:8
Input files DNA, FASTA:
/project/teaser/genometeaser/references/M_musculus_cutf.fasta
Building a SMALL index
Reading reference sizes
Time reading reference sizes: 00:01:29
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
Time to join reference sequences: 00:00:59
bmax according to bmaxDivN setting: 661884432
Using parameters --bmax 496413324 --dcv 1024
Doing ahead-of-time memory usage test
Passed! Constructing with these parameters: --bmax 496413324 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
Building sPrime
Building sPrimeOrder
V-Sorting samples
V-Sorting samples time: 00:02:56
Allocating rank array
Ranking v-sort output
Ranking v-sort output time: 00:00:36
Invoking Larsson-Sadakane on ranks
Invoking Larsson-Sadakane on ranks time: 00:00:48
Sanity-checking and returning
Building samples
Reserving space for 12 sample suffixes
Generating random suffixes
QSorting 12 sample offsets, eliminating duplicates
QSorting sample offsets, eliminating duplicates time: 00:00:00
Multikey QSorting 12 samples
(Using difference cover)
Multikey QSorting samples time: 00:00:00
Calculating bucket sizes
Binary sorting into buckets
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Binary sorting into buckets time: 00:02:56
Splitting and merging
Splitting and merging time: 00:00:00
Split 1, merged 6; iterating...
Binary sorting into buckets
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Binary sorting into buckets time: 00:02:42
Splitting and merging
Splitting and merging time: 00:00:00
Avg bucket size: 3.7822e+08 (target: 496413323)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 7
Reserving size (496413324) for bucket
Calculating Z arrays
Calculating Z arrays time: 00:00:00
Entering block accumulator loop:
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Block accumulator loop time: 00:01:35
Sorting block of length 469251159
(Using difference cover)
Sorting block time: 00:09:11
Returning block of 469251160
Getting block 2 of 7
Reserving size (496413324) for bucket
Calculating Z arrays
Calculating Z arrays time: 00:00:00
Entering block accumulator loop:
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Block accumulator loop time: 00:01:04
Sorting block of length 353948707
(Using difference cover)
Sorting block time: 00:11:41
Returning block of 353948708
Getting block 3 of 7
Reserving size (496413324) for bucket
Calculating Z arrays
Calculating Z arrays time: 00:00:00
Entering block accumulator loop:
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Block accumulator loop time: 00:01:21
Sorting block of length 486679537
(Using difference cover)
Sorting block time: 00:09:36
Returning block of 486679538
Getting block 4 of 7
Reserving size (496413324) for bucket
Calculating Z arrays
Calculating Z arrays time: 00:00:00
Entering block accumulator loop:
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Block accumulator loop time: 00:01:23
Sorting block of length 105711784
(Using difference cover)
Sorting block time: 00:01:47
Returning block of 105711785
Getting block 5 of 7
Reserving size (496413324) for bucket
Calculating Z arrays
Calculating Z arrays time: 00:00:00
Entering block accumulator loop:
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Block accumulator loop time: 00:01:07
Sorting block of length 443963514
(Using difference cover)
Sorting block time: 00:14:06
Returning block of 443963515
Getting block 6 of 7
Reserving size (496413324) for bucket
Calculating Z arrays
Calculating Z arrays time: 00:00:00
Entering block accumulator loop:
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Block accumulator loop time: 00:01:26
Sorting block of length 348920483
(Using difference cover)
Sorting block time: 00:08:19
Returning block of 348920484
Getting block 7 of 7
Reserving size (496413324) for bucket
Calculating Z arrays
Calculating Z arrays time: 00:00:00
Entering block accumulator loop:
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Block accumulator loop time: 00:00:47
Sorting block of length 439062540
(Using difference cover)
Sorting block time: 00:08:24
Returning block of 439062541
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 771762840
fchr[G]: 1323322411
fchr[T]: 1874920620
fchr[$]: 2647537730
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 886714424 bytes to primary EBWT file: /project/teaser/genometeaser/references/M_musculus_cutf.fasta_bt.1.bt2
Wrote 661884440 bytes to secondary EBWT file: /project/teaser/genometeaser/references/M_musculus_cutf.fasta_bt.2.bt2
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
len: 2647537730
bwtLen: 2647537731
sz: 661884433
bwtSz: 661884433
lineRate: 6
offRate: 4
offMask: 0xfffffff0
ftabChars: 10
eftabLen: 20
eftabSz: 80
ftabLen: 1048577
ftabSz: 4194308
offsLen: 165471109
offsSz: 661884436
lineSz: 64
sideSz: 64
sideBwtSz: 48
sideBwtLen: 192
numSides: 13789260
numLines: 13789260
ebwtTotLen: 882512640
ebwtTotSz: 882512640
color: 0
reverse: 0
Total time for call to driver() for forward index: 01:42:25
Reading reference sizes
Time reading reference sizes: 00:01:05
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
Time to join reference sequences: 00:01:45
Time to reverse reference sequence: 00:00:08
bmax according to bmaxDivN setting: 661884432
Using parameters --bmax 496413324 --dcv 1024
Doing ahead-of-time memory usage test
Passed! Constructing with these parameters: --bmax 496413324 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
Building sPrime
Building sPrimeOrder
V-Sorting samples
V-Sorting samples time: 00:04:32
Allocating rank array
Ranking v-sort output
Ranking v-sort output time: 00:00:55
Invoking Larsson-Sadakane on ranks
Invoking Larsson-Sadakane on ranks time: 00:01:31
Sanity-checking and returning
Building samples
Reserving space for 12 sample suffixes
Generating random suffixes
QSorting 12 sample offsets, eliminating duplicates
QSorting sample offsets, eliminating duplicates time: 00:00:00
Multikey QSorting 12 samples
(Using difference cover)
Multikey QSorting samples time: 00:00:00
Calculating bucket sizes
Binary sorting into buckets
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100%
Binary sorting into buckets time: 00:06:35
Splitting and merging
Splitting and merging time: 00:00:00
Avg bucket size: 3.7822e+08 (target: 496413323)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 7
Reserving size (496413324) for bucket
Calculating Z arrays
Calculating Z arrays time: 00:00:00
Entering block accumulator loop:
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Block accumulator loop time: 00:02:04
Sorting block of length 328616319
(Using difference cover)
Sorting block time: 00:09:45
Returning block of 328616320
Getting block 2 of 7
Reserving size (496413324) for bucket
Calculating Z arrays
Calculating Z arrays time: 00:00:00
Entering block accumulator loop:
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Block accumulator loop time: 00:02:16
Sorting block of length 460468899
(Using difference cover)
Sorting block time: 00:16:15
Returning block of 460468900
Getting block 3 of 7
Reserving size (496413324) for bucket
Calculating Z arrays
Calculating Z arrays time: 00:00:00
Entering block accumulator loop:
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Block accumulator loop time: 00:01:04
Sorting block of length 143612630
(Using difference cover)
Sorting block time: 00:02:26
Returning block of 143612631
Getting block 4 of 7
Reserving size (496413324) for bucket
Calculating Z arrays
Calculating Z arrays time: 00:00:00
Entering block accumulator loop:
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Block accumulator loop time: 00:02:25
Sorting block of length 492748577
(Using difference cover)
Sorting block time: 00:14:45
Returning block of 492748578
Getting block 5 of 7
Reserving size (496413324) for bucket
Calculating Z arrays
Calculating Z arrays time: 00:00:00
Entering block accumulator loop:
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Block accumulator loop time: 00:02:49
Sorting block of length 476395330
(Using difference cover)
Sorting block time: 00:14:00
Returning block of 476395331
Getting block 6 of 7
Reserving size (496413324) for bucket
Calculating Z arrays
Calculating Z arrays time: 00:00:00
Entering block accumulator loop:
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Block accumulator loop time: 00:02:20
Sorting block of length 304120551
(Using difference cover)
Sorting block time: 00:08:02
Returning block of 304120552
Getting block 7 of 7
Reserving size (496413324) for bucket
Calculating Z arrays
Calculating Z arrays time: 00:00:00
Entering block accumulator loop:
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Block accumulator loop time: 00:01:41
Sorting block of length 441575418
(Using difference cover)
Sorting block time: 00:12:19
Returning block of 441575419
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 771762840
fchr[G]: 1323322411
fchr[T]: 1874920620
fchr[$]: 2647537730
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 886714424 bytes to primary EBWT file: /project/teaser/genometeaser/references/M_musculus_cutf.fasta_bt.rev.1.bt2
Wrote 661884440 bytes to secondary EBWT file: /project/teaser/genometeaser/references/M_musculus_cutf.fasta_bt.rev.2.bt2
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
len: 2647537730
bwtLen: 2647537731
sz: 661884433
bwtSz: 661884433
lineRate: 6
offRate: 4
offMask: 0xfffffff0
ftabChars: 10
eftabLen: 20
eftabSz: 80
ftabLen: 1048577
ftabSz: 4194308
offsLen: 165471109
offsSz: 661884436
lineSz: 64
sideSz: 64
sideBwtSz: 48
sideBwtLen: 192
numSides: 13789260
numLines: 13789260
ebwtTotLen: 882512640
ebwtTotSz: 882512640
color: 0
reverse: 1
Total time for backward call to driver() for mirror index: 02:07:45
systime0
time13811.384845
usrtime0
working_directory/project/teaser/genometeaser/tests_generated/ef84d4ed82d0fef31ff0765d0f19324d

/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/M_musculus_cutf.fasta_bt -U reads_base.fastq -S out_bowtie2.sam

command/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/M_musculus_cutf.fasta_bt -U reads_base.fastq -S out_bowtie2.sam
memory3076928000
return0
status1
stderr
None
stdout
1 reads; of these:
1 (100.00%) were unpaired; of these:
1 (100.00%) aligned 0 times
0 (0.00%) aligned exactly 1 time
0 (0.00%) aligned >1 times
0.00% overall alignment rate
systime3.692
time4.23288297653
usrtime0.128
working_directory/project/teaser/genometeaser/tests_generated/ef84d4ed82d0fef31ff0765d0f19324d

/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/M_musculus_cutf.fasta_bt -U reads_base.fastq -S out_bowtie2.sam

command/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/M_musculus_cutf.fasta_bt -U reads_base.fastq -S out_bowtie2.sam
memory3074800000
return0
status1
stderr
None
stdout
1 reads; of these:
1 (100.00%) were unpaired; of these:
1 (100.00%) aligned 0 times
0 (0.00%) aligned exactly 1 time
0 (0.00%) aligned >1 times
0.00% overall alignment rate
systime3.428
time3.54594802856
usrtime0.164
working_directory/project/teaser/genometeaser/tests_generated/ef84d4ed82d0fef31ff0765d0f19324d

/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/M_musculus_cutf.fasta_bt -U reads.fastq -S out_bowtie2.sam

command/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/M_musculus_cutf.fasta_bt -U reads.fastq -S out_bowtie2.sam
memory3139376000
return0
status1
stderr
None
stdout
272553 reads; of these:
272553 (100.00%) were unpaired; of these:
152 (0.06%) aligned 0 times
216591 (79.47%) aligned exactly 1 time
55810 (20.48%) aligned >1 times
99.94% overall alignment rate
systime7.3
time71.1371831894
usrtime256.96
working_directory/project/teaser/genometeaser/tests_generated/ef84d4ed82d0fef31ff0765d0f19324d