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 Mapped40035195.81%
Wrongly Mapped172294.123%
Not Mapped2800.067%
Total417860100.0%
Read Failure Statistics
Not mapped2800.067%
Missing in mapper output00.0%
Mapped to wrong chromosome68561.641%
Mapped to wrong position103722.482%
Mapped to wrong strand10.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.978600
Precision0.958700
Recall0.999300
Timing
Raw Mapping Time35.356s
Effective Mapping Time32.116s
Effective Init Time3.240s
Effective Time MeasureCPU
Mapping Time (Wall)21.118s
Mapping Time (CPU)35.356s
Mapping Time (CPU User)33.316s
Mapping Time (CPU System)2.040s
Init Time (Wall)3.092s
Init Time (CPU)3.240s
Init Time (CPU User)2.372s
Init Time (CPU System)0.868s
Additional Information
Mapper Memory Usage1977 MB
Total Test Runtime (Wall)157.827s
Mapper Command Line: 
/project/teaser/genometeaser/software/ngm/ngm --output out_ngm.sam --ref /project/teaser/genometeaser/references/C_elegans.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/C_elegans.fa

command/project/teaser/genometeaser/software/ngm/ngm --ref /project/teaser/genometeaser/references/C_elegans.fa
return1
status1
stderr
None
stdout
[MAIN] NextGenMap 0.5.3
[MAIN] Startup : x64 (build Jan 31 2017 16:20:45)
[MAIN] Starting time: 2018-07-13.14:26:24
[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/C_elegans.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 100 Mbp (max. 17179 Mbp)
[SEQPROV] Allocating 50147208 (101958257) bytes for the reference.
[SEQPROV] BinRef length: 50147202ll (elapsed 1.452121)
[SEQPROV] 0 reference sequences were skipped (length < 10).
[SEQPROV] Writing encoded reference to /project/teaser/genometeaser/references/C_elegans.fa-enc.2.ngm
[SEQPROV] Writing to disk took 4.44s
[PREPROCESS] Building reference table
[PREPROCESS] Allocated 1 hashtable units (tableLocMax=2^32.000000, genomeSize=2^26.579666)
[PREPROCESS] Building RefTable #0 (kmer length: 13, reference skip: 2)
[PREPROCESS] Number of k-mers: 67108865
[PREPROCESS] Counting kmers took 5.21s
[PREPROCESS] Average number of positions per prefix: 1.956028
[PREPROCESS] Index size: 335544325 byte (67108865 x 5)
[PREPROCESS] Generating index took 10.18s
[PREPROCESS] Allocating and initializing prefix Table took 0.06s
[PREPROCESS] Number of prefix positions is 33428428 (4)
[PREPROCESS] Size of RefTable is 133713712
[PREPROCESS] Number of repetitive k-mers ignored: 347
[PREPROCESS] Overall time for creating RefTable: 28.08s
[PREPROCESS] Writing RefTable to /project/teaser/genometeaser/references/C_elegans.fa-ht-13-2.3.ngm
[PREPROCESS] Writing to disk took 40.83s
[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.
[UPDATE_CHECK] Your version of NGM is more than 6 months old - a newer version may be available. (For performing an automatic check use --update-check)
systime0
time75.9418079853
usrtime0
working_directory/project/teaser/genometeaser/tests_generated/0b75acea7debea0665280a94869c22a6

/project/teaser/genometeaser/software/ngm/ngm --output out_ngm.sam --ref /project/teaser/genometeaser/references/C_elegans.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/C_elegans.fa -t 4 --qry reads_base.fastq --no-progress
memory892100000
return0
status1
stderr
None
stdout
[MAIN] NextGenMap 0.5.3
[MAIN] Startup : x64 (build Jan 31 2017 16:20:45)
[MAIN] Starting time: 2018-07-13.14:27:40
[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/C_elegans.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/C_elegans.fa-enc.2.ngm
[SEQPROV] Reading 100 Mbp from disk took 0.05s
[PREPROCESS] Reading RefTable from /project/teaser/genometeaser/references/C_elegans.fa-ht-13-2.3.ngm
[PREPROCESS] Reading from disk took 0.62s
[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 0.003s
[INPUT] Input is Fastq
No protocol specified
[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: AMD Opteron(tm) Processor 6348 (Driver: 1214.3 (sse2,avx,fma4))
[OPENCL] 48 CPU cores available.
[MAIN] Alignments computed: 1
[MAIN] Done (0 reads mapped (0.00%), 1 reads not mapped, 1 lines written)(elapsed: 6.037254s)
[UPDATE_CHECK] Your version of NGM is more than 6 months old - a newer version may be available. (For performing an automatic check use --update-check)
systime0.908
time6.12196993828
usrtime2.412
working_directory/project/teaser/genometeaser/tests_generated/0b75acea7debea0665280a94869c22a6

/project/teaser/genometeaser/software/ngm/ngm --output out_ngm.sam --ref /project/teaser/genometeaser/references/C_elegans.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/C_elegans.fa -t 4 --qry reads_base.fastq --no-progress
memory892128000
return0
status1
stderr
None
stdout
[MAIN] NextGenMap 0.5.3
[MAIN] Startup : x64 (build Jan 31 2017 16:20:45)
[MAIN] Starting time: 2018-07-13.14:27:47
[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/C_elegans.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/C_elegans.fa-enc.2.ngm
[SEQPROV] Reading 100 Mbp from disk took 0.05s
[PREPROCESS] Reading RefTable from /project/teaser/genometeaser/references/C_elegans.fa-ht-13-2.3.ngm
[PREPROCESS] Reading from disk took 0.57s
[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 0.004s
[INPUT] Input is Fastq
No protocol specified
[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: AMD Opteron(tm) Processor 6348 (Driver: 1214.3 (sse2,avx,fma4))
[OPENCL] 48 CPU cores available.
[MAIN] Alignments computed: 1
[MAIN] Done (0 reads mapped (0.00%), 1 reads not mapped, 1 lines written)(elapsed: 3.026274s)
[UPDATE_CHECK] Your version of NGM is more than 6 months old - a newer version may be available. (For performing an automatic check use --update-check)
systime0.868
time3.09150600433
usrtime2.372
working_directory/project/teaser/genometeaser/tests_generated/0b75acea7debea0665280a94869c22a6

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

command/project/teaser/genometeaser/software/ngm/ngm --output out_ngm.sam --ref /project/teaser/genometeaser/references/C_elegans.fa -t 4 --qry reads.fastq --no-progress
memory1977860000
return0
status1
stderr
None
stdout
[MAIN] NextGenMap 0.5.3
[MAIN] Startup : x64 (build Jan 31 2017 16:20:45)
[MAIN] Starting time: 2018-07-13.14:27:51
[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/C_elegans.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/C_elegans.fa-enc.2.ngm
[SEQPROV] Reading 100 Mbp from disk took 0.04s
[PREPROCESS] Reading RefTable from /project/teaser/genometeaser/references/C_elegans.fa-ht-13-2.3.ngm
[PREPROCESS] Reading from disk took 0.57s
[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: 417860
[INPUT] Average read length: 60 (min: 60, max: 62)
[INPUT] Corridor width: 14
[INPUT] Average kmer hits pro read: 14.031250
[INPUT] Max possible kmer hit: 16
[INPUT] Estimated sensitivity: 0.876953
[INPUT] Estimating parameter took 1.932s
[INPUT] Input is Fastq
No protocol specified
[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: AMD Opteron(tm) Processor 6348 (Driver: 1214.3 (sse2,avx,fma4))
[OPENCL] 48 CPU cores available.
[MAIN] Alignments computed: 417650
[MAIN] Done (417580 reads mapped (99.93%), 280 reads not mapped, 417860 lines written)(elapsed: 12.854363s)
[UPDATE_CHECK] Your version of NGM is more than 6 months old - a newer version may be available. (For performing an automatic check use --update-check)
systime2.04
time21.1178469658
usrtime33.316
working_directory/project/teaser/genometeaser/tests_generated/0b75acea7debea0665280a94869c22a6