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 Mapped24902091.366%
Wrongly Mapped211657.765%
Not Mapped23680.869%
Total272553100.0%
Read Failure Statistics
Not mapped23680.869%
Missing in mapper output00.0%
Mapped to wrong chromosome97073.562%
Mapped to wrong position114584.204%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.954900
Precision0.921700
Recall0.990600
Timing
Raw Mapping Time181.376s
Effective Mapping Time157.376s
Effective Init Time24.000s
Effective Time MeasureCPU
Mapping Time (Wall)68.806s
Mapping Time (CPU)181.376s
Mapping Time (CPU User)153.144s
Mapping Time (CPU System)28.232s
Init Time (Wall)16.944s
Init Time (CPU)24.000s
Init Time (CPU User)2.672s
Init Time (CPU System)21.328s
Additional Information
Mapper Memory Usage6559 MB
Total Test Runtime (Wall)1337.061s
Mapper Command Line: 
/project/teaser/genometeaser/software/ngm/ngm --output out_ngm.sam --ref /project/teaser/genometeaser/references/M_musculus_cutf.fasta -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/M_musculus_cutf.fasta

command/project/teaser/genometeaser/software/ngm/ngm --ref /project/teaser/genometeaser/references/M_musculus_cutf.fasta
return1
status1
stderr
None
stdout
[MAIN] NextGenMap 0.5.3
[MAIN] Startup : x64 (build Jan 31 2017 16:20:45)
[MAIN] Starting time: 2017-08-19.08:53:47
[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/M_musculus_cutf.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] Wrinting output (SAM) to stdout
[SEQPROV] Encoding reference sequence.
[SEQPROV] Size of reference genome 2725 Mbp (max. 17179 Mbp)
[SEQPROV] Allocating 1362780352 (2770964555) bytes for the reference.
[SEQPROV] BinRef length: 1362780340ll (elapsed 42.631275)
[SEQPROV] 0 reference sequences were skipped (length < 10).
[SEQPROV] Writing encoded reference to /project/teaser/genometeaser/references/M_musculus_cutf.fasta-enc.2.ngm
[SEQPROV] Writing to disk took 118.26s
[PREPROCESS] Building reference table
[PREPROCESS] Allocated 1 hashtable units (tableLocMax=2^32.000000, genomeSize=2^31.343906)
[PREPROCESS] Building RefTable #0 (kmer length: 13, reference skip: 2)
[PREPROCESS] Number of k-mers: 67108865
[PREPROCESS] Counting kmers took 106.59s
[PREPROCESS] Average number of positions per prefix: 16.251629
[PREPROCESS] Index size: 335544325 byte (67108865 x 5)
[PREPROCESS] Generating index took 8.35s
[PREPROCESS] Allocating and initializing prefix Table took 3.87s
[PREPROCESS] Number of prefix positions is 882323331 (4)
[PREPROCESS] Size of RefTable is 3529293324
[PREPROCESS] Number of repetitive k-mers ignored: 187434
[PREPROCESS] Overall time for creating RefTable: 678.95s
[PREPROCESS] Writing RefTable to /project/teaser/genometeaser/references/M_musculus_cutf.fasta-ht-13-2.3.ngm
[PREPROCESS] Writing to disk took 333.87s
[PREPROCESS] Max. k-mer frequency set so 1003!
[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
time1188.61051106
usrtime0
working_directory/project/teaser/genometeaser/tests_generated/ef84d4ed82d0fef31ff0765d0f19324d

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

command/project/teaser/genometeaser/software/ngm/ngm --output out_ngm.sam --ref /project/teaser/genometeaser/references/M_musculus_cutf.fasta -t 4 --qry reads_base.fastq --no-progress
memory5862384000
return0
status1
stderr
None
stdout
[MAIN] NextGenMap 0.5.3
[MAIN] Startup : x64 (build Jan 31 2017 16:20:45)
[MAIN] Starting time: 2017-08-19.09:13:36
[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/M_musculus_cutf.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.sam
[SEQPROV] Reading encoded reference from /project/teaser/genometeaser/references/M_musculus_cutf.fasta-enc.2.ngm
[SEQPROV] Reading 2725 Mbp from disk took 1.67s
[PREPROCESS] Reading RefTable from /project/teaser/genometeaser/references/M_musculus_cutf.fasta-ht-13-2.3.ngm
[PREPROCESS] Reading from disk took 7.87s
[PREPROCESS] Max. k-mer frequency set so 1003!
[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 (1 reads mapped (100.00%), 0 reads not mapped, 1 lines written)(elapsed: 20.424398s)
[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)
systime21.428
time20.7636861801
usrtime2.828
working_directory/project/teaser/genometeaser/tests_generated/ef84d4ed82d0fef31ff0765d0f19324d

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

command/project/teaser/genometeaser/software/ngm/ngm --output out_ngm.sam --ref /project/teaser/genometeaser/references/M_musculus_cutf.fasta -t 4 --qry reads_base.fastq --no-progress
memory5923060000
return0
status1
stderr
None
stdout
[MAIN] NextGenMap 0.5.3
[MAIN] Startup : x64 (build Jan 31 2017 16:20:45)
[MAIN] Starting time: 2017-08-19.09:13:57
[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/M_musculus_cutf.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.sam
[SEQPROV] Reading encoded reference from /project/teaser/genometeaser/references/M_musculus_cutf.fasta-enc.2.ngm
[SEQPROV] Reading 2725 Mbp from disk took 1.50s
[PREPROCESS] Reading RefTable from /project/teaser/genometeaser/references/M_musculus_cutf.fasta-ht-13-2.3.ngm
[PREPROCESS] Reading from disk took 6.87s
[PREPROCESS] Max. k-mer frequency set so 1003!
[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 (1 reads mapped (100.00%), 0 reads not mapped, 1 lines written)(elapsed: 16.750744s)
[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)
systime21.328
time16.9442379475
usrtime2.672
working_directory/project/teaser/genometeaser/tests_generated/ef84d4ed82d0fef31ff0765d0f19324d

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

command/project/teaser/genometeaser/software/ngm/ngm --output out_ngm.sam --ref /project/teaser/genometeaser/references/M_musculus_cutf.fasta -t 4 --qry reads.fastq --no-progress
memory6559176000
return0
status1
stderr
None
stdout
[MAIN] NextGenMap 0.5.3
[MAIN] Startup : x64 (build Jan 31 2017 16:20:45)
[MAIN] Starting time: 2017-08-19.09:14:14
[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/M_musculus_cutf.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.sam
[SEQPROV] Reading encoded reference from /project/teaser/genometeaser/references/M_musculus_cutf.fasta-enc.2.ngm
[SEQPROV] Reading 2725 Mbp from disk took 1.48s
[PREPROCESS] Reading RefTable from /project/teaser/genometeaser/references/M_musculus_cutf.fasta-ht-13-2.3.ngm
[PREPROCESS] Reading from disk took 5.80s
[PREPROCESS] Max. k-mer frequency set so 1003!
[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: 272553
[INPUT] Average read length: 100 (min: 100, max: 102)
[INPUT] Corridor width: 20
[INPUT] Average kmer hits pro read: 23.318550
[INPUT] Max possible kmer hit: 29
[INPUT] Estimated sensitivity: 0.804088
[INPUT] Estimating parameter took 2.255s
[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: 270431
[MAIN] Done (270185 reads mapped (99.13%), 2368 reads not mapped, 272553 lines written)(elapsed: 61.352821s)
[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)
systime28.232
time68.8059051037
usrtime153.144
working_directory/project/teaser/genometeaser/tests_generated/ef84d4ed82d0fef31ff0765d0f19324d