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 Mapped32322590.129%
Wrongly Mapped306848.556%
Not Mapped47141.314%
Total358623100.0%
Read Failure Statistics
Not mapped47141.314%
Missing in mapper output00.0%
Mapped to wrong chromosome148934.153%
Mapped to wrong position157914.403%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.948100
Precision0.913300
Recall0.985600
Timing
Raw Mapping Time285.252s
Effective Mapping Time202.256s
Effective Init Time82.996s
Effective Time MeasureCPU
Mapping Time (Wall)162.293s
Mapping Time (CPU)285.252s
Mapping Time (CPU User)123.576s
Mapping Time (CPU System)161.676s
Init Time (Wall)70.132s
Init Time (CPU)82.996s
Init Time (CPU User)1.792s
Init Time (CPU System)81.204s
Additional Information
Mapper Memory Usage6563 MB
Total Test Runtime (Wall)814.516s
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: 2017-09-13.10:47:46
[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] Reading encoded reference from /project/teaser/genometeaser/references/M_musculus_cutf.fasta-enc.2.ngm
[SEQPROV] Reading 2725 Mbp from disk took 116.01s
[PREPROCESS] Reading RefTable from /project/teaser/genometeaser/references/M_musculus_cutf.fasta-ht-13-2.3.ngm
[PREPROCESS] Reading from disk took 340.78s
[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
time458.662736893
usrtime0
working_directory/project/teaser/genometeaser/tests_generated/9616eba5217c671aa1e17d118aefe3c9

/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
memory5848568000
return0
status1
stderr
None
stdout
[MAIN] NextGenMap 0.5.3
[MAIN] Startup : x64 (build Jan 31 2017 16:20:45)
[MAIN] Starting time: 2017-09-13.10:55:25
[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 14.97s
[PREPROCESS] Reading RefTable from /project/teaser/genometeaser/references/M_musculus_cutf.fasta-ht-13-2.3.ngm
[PREPROCESS] Reading from disk took 46.46s
[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: 74.301270s)
[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)
systime76.216
time75.1298089027
usrtime1.68
working_directory/project/teaser/genometeaser/tests_generated/9616eba5217c671aa1e17d118aefe3c9

/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
memory6028944000
return0
status1
stderr
None
stdout
[MAIN] NextGenMap 0.5.3
[MAIN] Startup : x64 (build Jan 31 2017 16:20:45)
[MAIN] Starting time: 2017-09-13.10:56:41
[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 12.77s
[PREPROCESS] Reading RefTable from /project/teaser/genometeaser/references/M_musculus_cutf.fasta-ht-13-2.3.ngm
[PREPROCESS] Reading from disk took 43.92s
[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 0.005s
[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: 68.659912s)
[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)
systime81.204
time70.1322059631
usrtime1.792
working_directory/project/teaser/genometeaser/tests_generated/9616eba5217c671aa1e17d118aefe3c9

/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
memory6563632000
return0
status1
stderr
None
stdout
[MAIN] NextGenMap 0.5.3
[MAIN] Startup : x64 (build Jan 31 2017 16:20:45)
[MAIN] Starting time: 2017-09-13.10:57:52
[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 13.61s
[PREPROCESS] Reading RefTable from /project/teaser/genometeaser/references/M_musculus_cutf.fasta-ht-13-2.3.ngm
[PREPROCESS] Reading from disk took 84.15s
[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: 358623
[INPUT] Average read length: 76 (min: 76, max: 78)
[INPUT] Corridor width: 16
[INPUT] Average kmer hits pro read: 17.108545
[INPUT] Max possible kmer hit: 21
[INPUT] Estimated sensitivity: 0.814693
[INPUT] Estimating parameter took 1.714s
[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: 354277
[MAIN] Done (353909 reads mapped (98.69%), 4714 reads not mapped, 358623 lines written)(elapsed: 158.682693s)
[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)
systime161.676
time162.292915106
usrtime123.576
working_directory/project/teaser/genometeaser/tests_generated/9616eba5217c671aa1e17d118aefe3c9