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 Mapped14620497.469%
Wrongly Mapped37962.531%
Not Mapped00.0%
Total150000100.0%
Read Failure Statistics
Not mapped00.0%
Missing in mapper output00.0%
Mapped to wrong chromosome18271.218%
Mapped to wrong position19691.313%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.987200
Precision0.974700
Recall1.000000
Timing
Raw Mapping Time14.842s
Effective Mapping Time11.818s
Effective Init Time3.024s
Effective Time MeasureCPU
Mapping Time (Wall)6.771s
Mapping Time (CPU)14.842s
Mapping Time (CPU User)13.776s
Mapping Time (CPU System)1.066s
Init Time (Wall)2.581s
Init Time (CPU)3.024s
Init Time (CPU User)2.032s
Init Time (CPU System)0.992s
Additional Information
Mapper Memory Usage1791 MB
Total Test Runtime (Wall)37.514s
Mapper Command Line: 
/project/teaser/genometeaser/software/ngm/ngm --output out_ngm.sam --ref /project/teaser/genometeaser/references/Schizosaccharomyces_pombe.fa -t 4 --qry reads.fastq --no-progress
Errors and Warnings
No problems were encountered.
Subprocess Log

/project/teaser/genometeaser/software/ngm/ngm --ref /project/teaser/genometeaser/references/Schizosaccharomyces_pombe.fa

command/project/teaser/genometeaser/software/ngm/ngm --ref /project/teaser/genometeaser/references/Schizosaccharomyces_pombe.fa
return1
status1
stderr
None
stdout
[MAIN] NextGenMap 0.5.3
[MAIN] Startup : x64 (build Jan 31 2017 16:20:45)
[MAIN] Starting time: 2017-05-17.23:35:42
[CONFIG] Parameter: --affine 0 --argos_min_score 0 --bin_size 2 --block_multiplier 2 --bs_cutoff 6 --bs_mapping 0 --cpu_threads 1 --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 0 --no_unal 0 --ocl_threads 1 --overwrite 1 --pair_score_cutoff 0.900000 --paired 0 --parse_all 1 --pe_delimiter / --qry_count -1 --qry_start 0 --ref /project/teaser/genometeaser/references/Schizosaccharomyces_pombe.fa --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] Wrinting output (SAM) to stdout
[SEQPROV] Encoding reference sequence.
[SEQPROV] Size of reference genome 12 Mbp (max. 17179 Mbp)
[SEQPROV] Allocating 6319196 (12842237) bytes for the reference.
[SEQPROV] BinRef length: 6319191ll (elapsed 0.158402)
[SEQPROV] 0 reference sequences were skipped (length < 10).
[SEQPROV] Writing encoded reference to /project/teaser/genometeaser/references/Schizosaccharomyces_pombe.fa-enc.2.ngm
[SEQPROV] Writing to disk took 0.19s
[PREPROCESS] Building reference table
[PREPROCESS] Allocated 1 hashtable units (tableLocMax=2^32.000000, genomeSize=2^23.591308)
[PREPROCESS] Building RefTable #0 (kmer length: 13, reference skip: 2)
[PREPROCESS] Number of k-mers: 67108865
[PREPROCESS] Counting kmers took 0.75s
[PREPROCESS] Average number of positions per prefix: 1.126804
[PREPROCESS] Index size: 335544325 byte (67108865 x 5)
[PREPROCESS] Generating index took 7.63s
[PREPROCESS] Allocating and initializing prefix Table took 0.01s
[PREPROCESS] Number of prefix positions is 4210172 (4)
[PREPROCESS] Size of RefTable is 16840688
[PREPROCESS] Number of repetitive k-mers ignored: 109
[PREPROCESS] Overall time for creating RefTable: 9.57s
[PREPROCESS] Writing RefTable to /project/teaser/genometeaser/references/Schizosaccharomyces_pombe.fa-ht-13-2.3.ngm
[PREPROCESS] Writing to disk took 5.30s
[PREPROCESS] Max. k-mer frequency set so 100!
[MAIN] Finished building hash table.
[MAIN] No qry file specified. If you want to map single-end data use -q/--qry. If you want to map paired-end data, either use -q/--qry and -p or --qry1 and --qry2.
systime0
time15.8164930344
usrtime0
working_directory/project/teaser/genometeaser/tests_generated/78245a202e759eede079b41dad2c7157

/project/teaser/genometeaser/software/ngm/ngm --output out_ngm.sam --ref /project/teaser/genometeaser/references/Schizosaccharomyces_pombe.fa -t 4 --qry reads_base.fastq --no-progress

command/project/teaser/genometeaser/software/ngm/ngm --output out_ngm.sam --ref /project/teaser/genometeaser/references/Schizosaccharomyces_pombe.fa -t 4 --qry reads_base.fastq --no-progress
memory715540000
return0
status1
stderr
None
stdout
[MAIN] NextGenMap 0.5.3
[MAIN] Startup : x64 (build Jan 31 2017 16:20:45)
[MAIN] Starting time: 2017-05-17.23:35:58
[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.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 /project/teaser/genometeaser/references/Schizosaccharomyces_pombe.fa --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.sam
[SEQPROV] Reading encoded reference from /project/teaser/genometeaser/references/Schizosaccharomyces_pombe.fa-enc.2.ngm
[SEQPROV] Reading 12 Mbp from disk took 0.01s
[PREPROCESS] Reading RefTable from /project/teaser/genometeaser/references/Schizosaccharomyces_pombe.fa-ht-13-2.3.ngm
[PREPROCESS] Reading from disk took 0.39s
[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 0.001s
[INPUT] Input is Fastq
[OPENCL] Available platforms: 2
[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) Xeon(R) CPU X5650 @ 2.67GHz (Driver: 1214.3 (sse2))
[OPENCL] 24 CPU cores available.
[MAIN] Alignments computed: 1
[MAIN] Done (1 reads mapped (100.00%), 0 reads not mapped, 1 lines written)(elapsed: 2.405791s)
systime1.012846
time2.48197412491
usrtime1.915708
working_directory/project/teaser/genometeaser/tests_generated/78245a202e759eede079b41dad2c7157

/project/teaser/genometeaser/software/ngm/ngm --output out_ngm.sam --ref /project/teaser/genometeaser/references/Schizosaccharomyces_pombe.fa -t 4 --qry reads_base.fastq --no-progress

command/project/teaser/genometeaser/software/ngm/ngm --output out_ngm.sam --ref /project/teaser/genometeaser/references/Schizosaccharomyces_pombe.fa -t 4 --qry reads_base.fastq --no-progress
memory715612000
return0
status1
stderr
None
stdout
[MAIN] NextGenMap 0.5.3
[MAIN] Startup : x64 (build Jan 31 2017 16:20:45)
[MAIN] Starting time: 2017-05-17.23:36:01
[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.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 /project/teaser/genometeaser/references/Schizosaccharomyces_pombe.fa --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.sam
[SEQPROV] Reading encoded reference from /project/teaser/genometeaser/references/Schizosaccharomyces_pombe.fa-enc.2.ngm
[SEQPROV] Reading 12 Mbp from disk took 0.01s
[PREPROCESS] Reading RefTable from /project/teaser/genometeaser/references/Schizosaccharomyces_pombe.fa-ht-13-2.3.ngm
[PREPROCESS] Reading from disk took 0.38s
[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
[OPENCL] Available platforms: 2
[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) Xeon(R) CPU X5650 @ 2.67GHz (Driver: 1214.3 (sse2))
[OPENCL] 24 CPU cores available.
[MAIN] Alignments computed: 1
[MAIN] Done (1 reads mapped (100.00%), 0 reads not mapped, 1 lines written)(elapsed: 2.489785s)
systime0.991849
time2.58068585396
usrtime2.031691
working_directory/project/teaser/genometeaser/tests_generated/78245a202e759eede079b41dad2c7157

/project/teaser/genometeaser/software/ngm/ngm --output out_ngm.sam --ref /project/teaser/genometeaser/references/Schizosaccharomyces_pombe.fa -t 4 --qry reads.fastq --no-progress

command/project/teaser/genometeaser/software/ngm/ngm --output out_ngm.sam --ref /project/teaser/genometeaser/references/Schizosaccharomyces_pombe.fa -t 4 --qry reads.fastq --no-progress
memory1791540000
return0
status1
stderr
None
stdout
[MAIN] NextGenMap 0.5.3
[MAIN] Startup : x64 (build Jan 31 2017 16:20:45)
[MAIN] Starting time: 2017-05-17.23:36:05
[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.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 /project/teaser/genometeaser/references/Schizosaccharomyces_pombe.fa --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.sam
[SEQPROV] Reading encoded reference from /project/teaser/genometeaser/references/Schizosaccharomyces_pombe.fa-enc.2.ngm
[SEQPROV] Reading 12 Mbp from disk took 0.00s
[PREPROCESS] Reading RefTable from /project/teaser/genometeaser/references/Schizosaccharomyces_pombe.fa-ht-13-2.3.ngm
[PREPROCESS] Reading from disk took 0.26s
[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: 150000
[INPUT] Average read length: 100 (min: 100, max: 102)
[INPUT] Corridor width: 20
[INPUT] Average kmer hits pro read: 22.970583
[INPUT] Max possible kmer hit: 29
[INPUT] Estimated sensitivity: 0.792089
[INPUT] Estimating parameter took 0.474s
[INPUT] Input is Fastq
[OPENCL] Available platforms: 2
[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) Xeon(R) CPU X5650 @ 2.67GHz (Driver: 1214.3 (sse2))
[OPENCL] 24 CPU cores available.
[MAIN] Alignments computed: 150000
[MAIN] Done (150000 reads mapped (100.00%), 0 reads not mapped, 150000 lines written)(elapsed: 6.079675s)
systime1.065837
time6.77052402496
usrtime13.775905
working_directory/project/teaser/genometeaser/tests_generated/78245a202e759eede079b41dad2c7157