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 Mapped26701389.004%
Wrongly Mapped47431.581%
Not Mapped282449.415%
Total300000100.0%
Read Failure Statistics
Not mapped282449.415%
Missing in mapper output00.0%
Mapped to wrong chromosome38491.283%
Mapped to wrong position8940.298%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.941800
Precision0.982500
Recall0.904300
Timing
Raw Mapping Time25.076s
Effective Mapping Time25.024s
Effective Init Time0.052s
Effective Time MeasureCPU
Mapping Time (Wall)15.277s
Mapping Time (CPU)25.076s
Mapping Time (CPU User)24.584s
Mapping Time (CPU System)0.492s
Init Time (Wall)0.702s
Init Time (CPU)0.052s
Init Time (CPU User)0.000s
Init Time (CPU System)0.052s
Additional Information
Mapper Memory Usage48 MB
Total Test Runtime (Wall)134.815s
Mapper Command Line: 
/project/teaser/genometeaser/software/bowtie --threads 4 -S /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta_bo reads.fastq out_bowtie.sam
Errors and Warnings
No problems were encountered.
Subprocess Log

/project/teaser/genometeaser/software/bowtie-build /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta_bo

command/project/teaser/genometeaser/software/bowtie-build /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta_bo
return1
status1
stderr
None
stdout
Settings:
Output files: "/project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta_bo.*.ebwt"
Line rate: 6 (line is 64 bytes)
Lines per side: 1 (side is 64 bytes)
Offset rate: 5 (one in 32)
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/Saccharomyces_cerevisiae.fasta
Reading reference sizes
Time reading reference sizes: 00:00:02
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
Time to join reference sequences: 00:00:00
bmax according to bmaxDivN setting: 2844529
Using parameters --bmax 2133397 --dcv 1024
Doing ahead-of-time memory usage test
Passed! Constructing with these parameters: --bmax 2133397 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
Building sPrime
Building sPrimeOrder
V-Sorting samples
V-Sorting samples time: 00:00:00
Allocating rank array
Ranking v-sort output
Ranking v-sort output time: 00:00:00
Invoking Larsson-Sadakane on ranks
Invoking Larsson-Sadakane on ranks time: 00:00:00
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: 00:00:01
Splitting and merging
Splitting and merging time: 00:00:00
Split 2, merged 7; iterating...
Binary sorting into buckets
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Binary sorting into buckets time: 00:00:01
Splitting and merging
Splitting and merging time: 00:00:00
Split 1, merged 0; iterating...
Binary sorting into buckets
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Binary sorting into buckets time: 00:00:01
Splitting and merging
Splitting and merging time: 00:00:00
Avg bucket size: 1.62544e+06 (target: 2133396)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 7
Reserving size (2133397) for bucket
Calculating Z arrays
Calculating Z arrays time: 00:00:00
Entering block accumulator loop:
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Block accumulator loop time: 00:00:01
Sorting block of length 1844367
(Using difference cover)
Sorting block time: 00:00:01
Returning block of 1844368
Getting block 2 of 7
Reserving size (2133397) for bucket
Calculating Z arrays
Calculating Z arrays time: 00:00:00
Entering block accumulator loop:
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Block accumulator loop time: 00:00:01
Sorting block of length 2042707
(Using difference cover)
Sorting block time: 00:00:02
Returning block of 2042708
Getting block 3 of 7
Reserving size (2133397) for bucket
Calculating Z arrays
Calculating Z arrays time: 00:00:00
Entering block accumulator loop:
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Block accumulator loop time: 00:00:00
Sorting block of length 1266532
(Using difference cover)
Sorting block time: 00:00:01
Returning block of 1266533
Getting block 4 of 7
Reserving size (2133397) for bucket
Calculating Z arrays
Calculating Z arrays time: 00:00:00
Entering block accumulator loop:
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Block accumulator loop time: 00:00:00
Sorting block of length 1648897
(Using difference cover)
Sorting block time: 00:00:02
Returning block of 1648898
Getting block 5 of 7
Reserving size (2133397) for bucket
Calculating Z arrays
Calculating Z arrays time: 00:00:00
Entering block accumulator loop:
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Block accumulator loop time: 00:00:00
Sorting block of length 1490647
(Using difference cover)
Sorting block time: 00:00:02
Returning block of 1490648
Getting block 6 of 7
Reserving size (2133397) for bucket
Calculating Z arrays
Calculating Z arrays time: 00:00:00
Entering block accumulator loop:
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Block accumulator loop time: 00:00:01
Sorting block of length 1779685
(Using difference cover)
Sorting block time: 00:00:01
Returning block of 1779686
Getting block 7 of 7
Reserving size (2133397) for bucket
Calculating Z arrays
Calculating Z arrays time: 00:00:00
Entering block accumulator loop:
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Block accumulator loop time: 00:00:00
Sorting block of length 1305275
(Using difference cover)
Sorting block time: 00:00:01
Returning block of 1305276
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 3492643
fchr[G]: 5693324
fchr[T]: 7892488
fchr[$]: 11378116
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 7564570 bytes to primary EBWT file: /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta_bo.1.ebwt
Wrote 1422272 bytes to secondary EBWT file: /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta_bo.2.ebwt
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
len: 11378116
bwtLen: 11378117
sz: 2844529
bwtSz: 2844530
lineRate: 6
linesPerSide: 1
offRate: 5
offMask: 0xffffffe0
isaRate: -1
isaMask: 0xffffffff
ftabChars: 10
eftabLen: 20
eftabSz: 80
ftabLen: 1048577
ftabSz: 4194308
offsLen: 355567
offsSz: 1422268
isaLen: 0
isaSz: 0
lineSz: 64
sideSz: 64
sideBwtSz: 56
sideBwtLen: 224
numSidePairs: 25398
numSides: 50796
numLines: 50796
ebwtTotLen: 3250944
ebwtTotSz: 3250944
reverse: 0
Total time for call to driver() for forward index: 00:00:25
Reading reference sizes
Time reading reference sizes: 00:00:01
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
Time to join reference sequences: 00:00:00
bmax according to bmaxDivN setting: 2844529
Using parameters --bmax 2133397 --dcv 1024
Doing ahead-of-time memory usage test
Passed! Constructing with these parameters: --bmax 2133397 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
Building sPrime
Building sPrimeOrder
V-Sorting samples
V-Sorting samples time: 00:00:01
Allocating rank array
Ranking v-sort output
Ranking v-sort output time: 00:00:00
Invoking Larsson-Sadakane on ranks
Invoking Larsson-Sadakane on ranks time: 00:00:00
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: 00:00:01
Splitting and merging
Splitting and merging time: 00:00:00
Split 2, merged 6; iterating...
Binary sorting into buckets
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Binary sorting into buckets time: 00:00:01
Splitting and merging
Splitting and merging time: 00:00:00
Avg bucket size: 1.42226e+06 (target: 2133396)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 8
Reserving size (2133397) for bucket
Calculating Z arrays
Calculating Z arrays time: 00:00:00
Entering block accumulator loop:
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Block accumulator loop time: 00:00:00
Sorting block of length 1991463
(Using difference cover)
Sorting block time: 00:00:02
Returning block of 1991464
Getting block 2 of 8
Reserving size (2133397) for bucket
Calculating Z arrays
Calculating Z arrays time: 00:00:00
Entering block accumulator loop:
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Block accumulator loop time: 00:00:00
Sorting block of length 1244235
(Using difference cover)
Sorting block time: 00:00:02
Returning block of 1244236
Getting block 3 of 8
Reserving size (2133397) for bucket
Calculating Z arrays
Calculating Z arrays time: 00:00:00
Entering block accumulator loop:
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Block accumulator loop time: 00:00:01
Sorting block of length 1198558
(Using difference cover)
Sorting block time: 00:00:01
Returning block of 1198559
Getting block 4 of 8
Reserving size (2133397) for bucket
Calculating Z arrays
Calculating Z arrays time: 00:00:00
Entering block accumulator loop:
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Block accumulator loop time: 00:00:00
Sorting block of length 1802656
(Using difference cover)
Sorting block time: 00:00:02
Returning block of 1802657
Getting block 5 of 8
Reserving size (2133397) for bucket
Calculating Z arrays
Calculating Z arrays time: 00:00:00
Entering block accumulator loop:
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Block accumulator loop time: 00:00:00
Sorting block of length 1582033
(Using difference cover)
Sorting block time: 00:00:02
Returning block of 1582034
Getting block 6 of 8
Reserving size (2133397) for bucket
Calculating Z arrays
Calculating Z arrays time: 00:00:00
Entering block accumulator loop:
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Block accumulator loop time: 00:00:00
Sorting block of length 814481
(Using difference cover)
Sorting block time: 00:00:01
Returning block of 814482
Getting block 7 of 8
Reserving size (2133397) for bucket
Calculating Z arrays
Calculating Z arrays time: 00:00:00
Entering block accumulator loop:
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Block accumulator loop time: 00:00:00
Sorting block of length 1788176
(Using difference cover)
Sorting block time: 00:00:02
Returning block of 1788177
Getting block 8 of 8
Reserving size (2133397) for bucket
Calculating Z arrays
Calculating Z arrays time: 00:00:00
Entering block accumulator loop:
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Block accumulator loop time: 00:00:00
Sorting block of length 956507
(Using difference cover)
Sorting block time: 00:00:01
Returning block of 956508
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 3492643
fchr[G]: 5693324
fchr[T]: 7892488
fchr[$]: 11378116
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 7564570 bytes to primary EBWT file: /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta_bo.rev.1.ebwt
Wrote 1422272 bytes to secondary EBWT file: /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta_bo.rev.2.ebwt
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
len: 11378116
bwtLen: 11378117
sz: 2844529
bwtSz: 2844530
lineRate: 6
linesPerSide: 1
offRate: 5
offMask: 0xffffffe0
isaRate: -1
isaMask: 0xffffffff
ftabChars: 10
eftabLen: 20
eftabSz: 80
ftabLen: 1048577
ftabSz: 4194308
offsLen: 355567
offsSz: 1422268
isaLen: 0
isaSz: 0
lineSz: 64
sideSz: 64
sideBwtSz: 56
sideBwtLen: 224
numSidePairs: 25398
numSides: 50796
numLines: 50796
ebwtTotLen: 3250944
ebwtTotSz: 3250944
reverse: 0
Total time for backward call to driver() for mirror index: 00:00:24
systime0
time48.8773081303
usrtime0
working_directory/project/teaser/genometeaser/tests_generated/37932f46d81271bed2cae5ca41c9d972

/project/teaser/genometeaser/software/bowtie --threads 4 -S /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta_bo reads_base.fastq out_bowtie.sam

command/project/teaser/genometeaser/software/bowtie --threads 4 -S /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta_bo reads_base.fastq out_bowtie.sam
memory48820000
return0
status1
stderr
None
stdout
# reads processed: 1
# reads with at least one reported alignment: 0 (0.00%)
# reads that failed to align: 1 (100.00%)
No alignments
systime0.048
time0.13185095787
usrtime0.004
working_directory/project/teaser/genometeaser/tests_generated/37932f46d81271bed2cae5ca41c9d972

/project/teaser/genometeaser/software/bowtie --threads 4 -S /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta_bo reads_base.fastq out_bowtie.sam

command/project/teaser/genometeaser/software/bowtie --threads 4 -S /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta_bo reads_base.fastq out_bowtie.sam
memory48820000
return0
status1
stderr
None
stdout
# reads processed: 1
# reads with at least one reported alignment: 0 (0.00%)
# reads that failed to align: 1 (100.00%)
No alignments
systime0.052
time0.70153594017
usrtime0.0
working_directory/project/teaser/genometeaser/tests_generated/37932f46d81271bed2cae5ca41c9d972

/project/teaser/genometeaser/software/bowtie --threads 4 -S /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta_bo reads.fastq out_bowtie.sam

command/project/teaser/genometeaser/software/bowtie --threads 4 -S /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta_bo reads.fastq out_bowtie.sam
memory48820000
return0
status1
stderr
None
stdout
# reads processed: 300000
# reads with at least one reported alignment: 271756 (90.59%)
# reads that failed to align: 28244 (9.41%)
Reported 271756 alignments to 1 output stream(s)
systime0.492
time15.2774319649
usrtime24.584
working_directory/project/teaser/genometeaser/tests_generated/37932f46d81271bed2cae5ca41c9d972