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 Mapped16588592.334%
Wrongly Mapped137627.66%
Not Mapped100.006%
Total179657100.0%
Read Failure Statistics
Not mapped100.006%
Missing in mapper output00.0%
Mapped to wrong chromosome71183.962%
Mapped to wrong position66443.698%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.960100
Precision0.923400
Recall0.999900
Timing
Raw Mapping Time23.715s
Effective Mapping Time22.438s
Effective Init Time1.277s
Effective Time MeasureWall clock
Mapping Time (Wall)23.715s
Mapping Time (CPU)76.903s
Mapping Time (CPU User)68.545s
Mapping Time (CPU System)8.359s
Init Time (Wall)1.277s
Init Time (CPU)1.433s
Init Time (CPU User)1.131s
Init Time (CPU System)0.302s
Additional Information
Mapper Memory Usage2056 MB
Total Test Runtime (Wall)35.624s
Mapper Command Line: 
/software/ngm/dev/ngm-0.5.3/ngm --output out_ngm-0.5.3.sam --ref /project2/NextGenMapTest/Teaser/references/d_melanogaster.fasta -t 4 --qry reads.fastq --no-progress
Errors and Warnings
No problems were encountered.
Subprocess Log

/software/ngm/dev/ngm-0.5.3/ngm --output out_ngm-0.5.3.sam --ref /project2/NextGenMapTest/Teaser/references/d_melanogaster.fasta -t 4 --qry reads_base.fastq --no-progress

command/software/ngm/dev/ngm-0.5.3/ngm --output out_ngm-0.5.3.sam --ref /project2/NextGenMapTest/Teaser/references/d_melanogaster.fasta -t 4 --qry reads_base.fastq --no-progress
memory957972000
return0
status1
stderr

None
stdout

[MAIN] NextGenMap 0.5.3

[MAIN] Startup : x64 (build Feb  2 2017 12:01:29)

[MAIN] Starting time: 2017-02-06.14:55:18

[CONFIG] Parameter:  --affine 0 --argos_min_score 0 --bin_size 2 --block_multiplier 2 --bs_cutoff 6 --bs_mapping 0 --cpu_threads 4 --dualstrand 1 --fast 0 --fast_pairing 0 --force_rlength_check 0 --format 1 --gap_extend_penalty 5 --gap_read_penalty 20 --gap_ref_penalty 20 --hard_clip 0 --keep_tags 0 --kmer 13 --kmer_min 0 --kmer_skip 2 --match_bonus 10 --match_bonus_tc 2 --match_bonus_tt 10 --max_cmrs 2147483647 --max_equal 1 --max_insert_size 1000 --max_polya -1 --max_read_length 0 --min_identity 0.650000 --min_insert_size 0 --min_mq 0 --min_residues 0.500000 --min_score 0.000000 --mismatch_penalty 15 --mode 0 --no_progress 1 --no_unal 0 --ocl_threads 1 --output out_ngm-0.5.3.sam --overwrite 1 --pair_score_cutoff 0.900000 --paired 0 --parse_all 1 --pe_delimiter / --qry reads_base.fastq --qry_count -1 --qry_start 0 --ref /project2/NextGenMapTest/Teaser/references/d_melanogaster.fasta --ref_mode -1 --sensitive 0 --silent_clip 0 --skip_mate_check 0 --skip_save 0 --slam_seq 0 --step_count 4 --strata 0 --topn 1 --trim5 0 --update_check 0 --very_fast 0 --very_sensitive 0

[NGM] Opening for output (SAM): out_ngm-0.5.3.sam

[SEQPROV] Reading encoded reference from /project2/NextGenMapTest/Teaser/references/d_melanogaster.fasta-enc.2.ngm

[SEQPROV] Reading 145 Mbp from disk took 0.02s

[PREPROCESS] Reading RefTable from /project2/NextGenMapTest/Teaser/references/d_melanogaster.fasta-ht-13-2.3.ngm

[PREPROCESS] Reading from disk took 0.17s

[PREPROCESS] Max. k-mer frequency set so 100!

[INPUT] Input is single end data.

[INPUT] Opening file reads_base.fastq for reading

[INPUT] Input is Fastq

[INPUT] Estimating parameter from data

[INPUT] Reads found in files: 1

[INPUT] Average read length: 60 (min: 60, max: 62)

[INPUT] Corridor width: 14

[INPUT] Not enough reads to estimate parameter

[INPUT] Sensitivity parameter neither set nor estimated. Falling back to default.

[INPUT] Estimating parameter took 0.002s

[INPUT] Input is Fastq

Setting of real/effective user Id to 0/0 failed

FATAL: Module fglrx not found.

Error! Fail to load fglrx kernel module! Maybe you can switch to root user to load kernel module directly

Setting of real/effective user Id to 0/0 failed

FATAL: Module fglrx not found.

Error! Fail to load fglrx kernel module! Maybe you can switch to root user to load kernel module directly

[OPENCL] Available platforms: 1

[OPENCL] AMD Accelerated Parallel Processing

[OPENCL] Selecting OpenCl platform: AMD Accelerated Parallel Processing

[OPENCL] Platform: OpenCL 1.2 AMD-APP (1214.3)

[OPENCL] 1 CPU device found.

[OPENCL] Device 0: Intel(R) Core(TM) i5-2500K CPU @ 3.30GHz (Driver: 1214.3 (sse2,avx))

[OPENCL] 4 CPU cores available.

[MAIN] Alignments computed: 1

[MAIN] Done (0 reads mapped (0.00%), 1 reads not mapped, 1 lines written)(elapsed: 1.244790s)
systime0.294955
time1.2691321373
usrtime1.132827
working_directory/project2/NextGenMapTest/Teaser/tests_generated/D3_n

/software/ngm/dev/ngm-0.5.3/ngm --output out_ngm-0.5.3.sam --ref /project2/NextGenMapTest/Teaser/references/d_melanogaster.fasta -t 4 --qry reads_base.fastq --no-progress

command/software/ngm/dev/ngm-0.5.3/ngm --output out_ngm-0.5.3.sam --ref /project2/NextGenMapTest/Teaser/references/d_melanogaster.fasta -t 4 --qry reads_base.fastq --no-progress
memory959928000
return0
status1
stderr

None
stdout

[MAIN] NextGenMap 0.5.3

[MAIN] Startup : x64 (build Feb  2 2017 12:01:29)

[MAIN] Starting time: 2017-02-06.14:55:20

[CONFIG] Parameter:  --affine 0 --argos_min_score 0 --bin_size 2 --block_multiplier 2 --bs_cutoff 6 --bs_mapping 0 --cpu_threads 4 --dualstrand 1 --fast 0 --fast_pairing 0 --force_rlength_check 0 --format 1 --gap_extend_penalty 5 --gap_read_penalty 20 --gap_ref_penalty 20 --hard_clip 0 --keep_tags 0 --kmer 13 --kmer_min 0 --kmer_skip 2 --match_bonus 10 --match_bonus_tc 2 --match_bonus_tt 10 --max_cmrs 2147483647 --max_equal 1 --max_insert_size 1000 --max_polya -1 --max_read_length 0 --min_identity 0.650000 --min_insert_size 0 --min_mq 0 --min_residues 0.500000 --min_score 0.000000 --mismatch_penalty 15 --mode 0 --no_progress 1 --no_unal 0 --ocl_threads 1 --output out_ngm-0.5.3.sam --overwrite 1 --pair_score_cutoff 0.900000 --paired 0 --parse_all 1 --pe_delimiter / --qry reads_base.fastq --qry_count -1 --qry_start 0 --ref /project2/NextGenMapTest/Teaser/references/d_melanogaster.fasta --ref_mode -1 --sensitive 0 --silent_clip 0 --skip_mate_check 0 --skip_save 0 --slam_seq 0 --step_count 4 --strata 0 --topn 1 --trim5 0 --update_check 0 --very_fast 0 --very_sensitive 0

[NGM] Opening for output (SAM): out_ngm-0.5.3.sam

[SEQPROV] Reading encoded reference from /project2/NextGenMapTest/Teaser/references/d_melanogaster.fasta-enc.2.ngm

[SEQPROV] Reading 145 Mbp from disk took 0.01s

[PREPROCESS] Reading RefTable from /project2/NextGenMapTest/Teaser/references/d_melanogaster.fasta-ht-13-2.3.ngm

[PREPROCESS] Reading from disk took 0.17s

[PREPROCESS] Max. k-mer frequency set so 100!

[INPUT] Input is single end data.

[INPUT] Opening file reads_base.fastq for reading

[INPUT] Input is Fastq

[INPUT] Estimating parameter from data

[INPUT] Reads found in files: 1

[INPUT] Average read length: 60 (min: 60, max: 62)

[INPUT] Corridor width: 14

[INPUT] Not enough reads to estimate parameter

[INPUT] Sensitivity parameter neither set nor estimated. Falling back to default.

[INPUT] Estimating parameter took 0.000s

[INPUT] Input is Fastq

Setting of real/effective user Id to 0/0 failed

FATAL: Module fglrx not found.

Error! Fail to load fglrx kernel module! Maybe you can switch to root user to load kernel module directly

Setting of real/effective user Id to 0/0 failed

FATAL: Module fglrx not found.

Error! Fail to load fglrx kernel module! Maybe you can switch to root user to load kernel module directly

[OPENCL] Available platforms: 1

[OPENCL] AMD Accelerated Parallel Processing

[OPENCL] Selecting OpenCl platform: AMD Accelerated Parallel Processing

[OPENCL] Platform: OpenCL 1.2 AMD-APP (1214.3)

[OPENCL] 1 CPU device found.

[OPENCL] Device 0: Intel(R) Core(TM) i5-2500K CPU @ 3.30GHz (Driver: 1214.3 (sse2,avx))

[OPENCL] 4 CPU cores available.

[MAIN] Alignments computed: 1

[MAIN] Done (0 reads mapped (0.00%), 1 reads not mapped, 1 lines written)(elapsed: 1.237839s)
systime0.301954
time1.27734303474
usrtime1.130828
working_directory/project2/NextGenMapTest/Teaser/tests_generated/D3_n

/software/ngm/dev/ngm-0.5.3/ngm --output out_ngm-0.5.3.sam --ref /project2/NextGenMapTest/Teaser/references/d_melanogaster.fasta -t 4 --qry reads.fastq --no-progress

command/software/ngm/dev/ngm-0.5.3/ngm --output out_ngm-0.5.3.sam --ref /project2/NextGenMapTest/Teaser/references/d_melanogaster.fasta -t 4 --qry reads.fastq --no-progress
memory2056024000
return0
status1
stderr

None
stdout

[MAIN] NextGenMap 0.5.3

[MAIN] Startup : x64 (build Feb  2 2017 12:01:29)

[MAIN] Starting time: 2017-02-06.14:55:22

[CONFIG] Parameter:  --affine 0 --argos_min_score 0 --bin_size 2 --block_multiplier 2 --bs_cutoff 6 --bs_mapping 0 --cpu_threads 4 --dualstrand 1 --fast 0 --fast_pairing 0 --force_rlength_check 0 --format 1 --gap_extend_penalty 5 --gap_read_penalty 20 --gap_ref_penalty 20 --hard_clip 0 --keep_tags 0 --kmer 13 --kmer_min 0 --kmer_skip 2 --match_bonus 10 --match_bonus_tc 2 --match_bonus_tt 10 --max_cmrs 2147483647 --max_equal 1 --max_insert_size 1000 --max_polya -1 --max_read_length 0 --min_identity 0.650000 --min_insert_size 0 --min_mq 0 --min_residues 0.500000 --min_score 0.000000 --mismatch_penalty 15 --mode 0 --no_progress 1 --no_unal 0 --ocl_threads 1 --output out_ngm-0.5.3.sam --overwrite 1 --pair_score_cutoff 0.900000 --paired 0 --parse_all 1 --pe_delimiter / --qry reads.fastq --qry_count -1 --qry_start 0 --ref /project2/NextGenMapTest/Teaser/references/d_melanogaster.fasta --ref_mode -1 --sensitive 0 --silent_clip 0 --skip_mate_check 0 --skip_save 0 --slam_seq 0 --step_count 4 --strata 0 --topn 1 --trim5 0 --update_check 0 --very_fast 0 --very_sensitive 0

[NGM] Opening for output (SAM): out_ngm-0.5.3.sam

[SEQPROV] Reading encoded reference from /project2/NextGenMapTest/Teaser/references/d_melanogaster.fasta-enc.2.ngm

[SEQPROV] Reading 145 Mbp from disk took 0.01s

[PREPROCESS] Reading RefTable from /project2/NextGenMapTest/Teaser/references/d_melanogaster.fasta-ht-13-2.3.ngm

[PREPROCESS] Reading from disk took 0.17s

[PREPROCESS] Max. k-mer frequency set so 100!

[INPUT] Input is single end data.

[INPUT] Opening file reads.fastq for reading

[INPUT] Input is Fastq

[INPUT] Estimating parameter from data

[INPUT] Reads found in files: 179657

[INPUT] Average read length: 214 (min: 197, max: 240)

[INPUT] Corridor width: 37

[INPUT] Average kmer hits pro read: 13.244768

[INPUT] Max possible kmer hit: 67

[INPUT] Estimated sensitivity: 0.300000

[INPUT] Estimating parameter took 0.877s

[INPUT] Input is Fastq

Setting of real/effective user Id to 0/0 failed

FATAL: Module fglrx not found.

Error! Fail to load fglrx kernel module! Maybe you can switch to root user to load kernel module directly

Setting of real/effective user Id to 0/0 failed

FATAL: Module fglrx not found.

Error! Fail to load fglrx kernel module! Maybe you can switch to root user to load kernel module directly

[OPENCL] Available platforms: 1

[OPENCL] AMD Accelerated Parallel Processing

[OPENCL] Selecting OpenCl platform: AMD Accelerated Parallel Processing

[OPENCL] Platform: OpenCL 1.2 AMD-APP (1214.3)

[OPENCL] 1 CPU device found.

[OPENCL] Device 0: Intel(R) Core(TM) i5-2500K CPU @ 3.30GHz (Driver: 1214.3 (sse2,avx))

[OPENCL] 4 CPU cores available.

[MAIN] Alignments computed: 179657

[MAIN] Done (179647 reads mapped (99.99%), 10 reads not mapped, 179657 lines written)(elapsed: 22.370958s)
systime8.358729
time23.7149739265
usrtime68.544579
working_directory/project2/NextGenMapTest/Teaser/tests_generated/D3_n