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 Mapped14748098.32%
Wrongly Mapped25201.68%
Not Mapped00.0%
Total150000100.0%
Read Failure Statistics
Not mapped00.0%
Missing in mapper output00.0%
Mapped to wrong chromosome20481.365%
Mapped to wrong position4720.315%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.991500
Precision0.983200
Recall1.000000
Timing
Raw Mapping Time11.489s
Effective Mapping Time9.301s
Effective Init Time2.189s
Effective Time MeasureCPU
Mapping Time (Wall)4.771s
Mapping Time (CPU)11.489s
Mapping Time (CPU User)10.412s
Mapping Time (CPU System)1.077s
Init Time (Wall)1.813s
Init Time (CPU)2.189s
Init Time (CPU User)1.418s
Init Time (CPU System)0.771s
Additional Information
Mapper Memory Usage1794 MB
Total Test Runtime (Wall)25.564s
Mapper Command Line: 
/project/teaser/genometeaser/software/ngm/ngm --qry2 reads2.fastq --output out_ngm.sam --qry1 reads1.fastq --ref /project/teaser/genometeaser/references/Cryptosporidium.fasta -t 4 --no-progress
Errors and Warnings
No problems were encountered.
Subprocess Log

/project/teaser/genometeaser/software/ngm/ngm --ref /project/teaser/genometeaser/references/Cryptosporidium.fasta

command/project/teaser/genometeaser/software/ngm/ngm --ref /project/teaser/genometeaser/references/Cryptosporidium.fasta
return1
status1
stderr
None
stdout
[MAIN] NextGenMap 0.5.3
[MAIN] Startup : x64 (build Jan 31 2017 16:20:45)
[MAIN] Starting time: 2017-05-18.00:30:15
[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/Cryptosporidium.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 18 Mbp (max. 17179 Mbp)
[SEQPROV] Allocating 9468444 (19549631) bytes for the reference.
[SEQPROV] BinRef length: 9468436ll (elapsed 0.104762)
[SEQPROV] 0 reference sequences were skipped (length < 10).
[SEQPROV] Writing encoded reference to /project/teaser/genometeaser/references/Cryptosporidium.fasta-enc.2.ngm
[SEQPROV] Writing to disk took 0.22s
[PREPROCESS] Building reference table
[PREPROCESS] Allocated 1 hashtable units (tableLocMax=2^32.000000, genomeSize=2^24.174695)
[PREPROCESS] Building RefTable #0 (kmer length: 13, reference skip: 2)
[PREPROCESS] Number of k-mers: 67108865
[PREPROCESS] Counting kmers took 0.59s
[PREPROCESS] Average number of positions per prefix: 1.101484
[PREPROCESS] Index size: 335544325 byte (67108865 x 5)
[PREPROCESS] Generating index took 3.61s
[PREPROCESS] Allocating and initializing prefix Table took 0.01s
[PREPROCESS] Number of prefix positions is 6305703 (4)
[PREPROCESS] Size of RefTable is 25222812
[PREPROCESS] Number of repetitive k-mers ignored: 117
[PREPROCESS] Overall time for creating RefTable: 5.10s
[PREPROCESS] Writing RefTable to /project/teaser/genometeaser/references/Cryptosporidium.fasta-ht-13-2.3.ngm
[PREPROCESS] Writing to disk took 4.44s
[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
time10.1514918804
usrtime0
working_directory/project/teaser/genometeaser/tests_generated/f23fe16b99420742b88a981972af6aae

/project/teaser/genometeaser/software/ngm/ngm --output out_ngm.sam --ref /project/teaser/genometeaser/references/Cryptosporidium.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/Cryptosporidium.fasta -t 4 --qry reads_base.fastq --no-progress
memory723444000
return0
status1
stderr
None
stdout
[MAIN] NextGenMap 0.5.3
[MAIN] Startup : x64 (build Jan 31 2017 16:20:45)
[MAIN] Starting time: 2017-05-18.00:30:25
[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/Cryptosporidium.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/Cryptosporidium.fasta-enc.2.ngm
[SEQPROV] Reading 18 Mbp from disk took 0.01s
[PREPROCESS] Reading RefTable from /project/teaser/genometeaser/references/Cryptosporidium.fasta-ht-13-2.3.ngm
[PREPROCESS] Reading from disk took 0.27s
[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 (0 reads mapped (0.00%), 1 reads not mapped, 1 lines written)(elapsed: 1.788625s)
systime0.780881
time1.87257504463
usrtime1.424783
working_directory/project/teaser/genometeaser/tests_generated/f23fe16b99420742b88a981972af6aae

/project/teaser/genometeaser/software/ngm/ngm --output out_ngm.sam --ref /project/teaser/genometeaser/references/Cryptosporidium.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/Cryptosporidium.fasta -t 4 --qry reads_base.fastq --no-progress
memory726904000
return0
status1
stderr
None
stdout
[MAIN] NextGenMap 0.5.3
[MAIN] Startup : x64 (build Jan 31 2017 16:20:45)
[MAIN] Starting time: 2017-05-18.00:30:27
[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/Cryptosporidium.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/Cryptosporidium.fasta-enc.2.ngm
[SEQPROV] Reading 18 Mbp from disk took 0.01s
[PREPROCESS] Reading RefTable from /project/teaser/genometeaser/references/Cryptosporidium.fasta-ht-13-2.3.ngm
[PREPROCESS] Reading from disk took 0.25s
[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 (0 reads mapped (0.00%), 1 reads not mapped, 1 lines written)(elapsed: 1.733338s)
systime0.770882
time1.8129491806
usrtime1.417784
working_directory/project/teaser/genometeaser/tests_generated/f23fe16b99420742b88a981972af6aae

/project/teaser/genometeaser/software/ngm/ngm --qry2 reads2.fastq --output out_ngm.sam --qry1 reads1.fastq --ref /project/teaser/genometeaser/references/Cryptosporidium.fasta -t 4 --no-progress

command/project/teaser/genometeaser/software/ngm/ngm --qry2 reads2.fastq --output out_ngm.sam --qry1 reads1.fastq --ref /project/teaser/genometeaser/references/Cryptosporidium.fasta -t 4 --no-progress
memory1794612000
return0
status1
stderr
None
stdout
[MAIN] NextGenMap 0.5.3
[MAIN] Startup : x64 (build Jan 31 2017 16:20:45)
[MAIN] Starting time: 2017-05-18.00:30:29
[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 1 --parse_all 1 --pe_delimiter / --qry1 reads1.fastq --qry2 reads2.fastq --qry_count -1 --qry_start 0 --ref /project/teaser/genometeaser/references/Cryptosporidium.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/Cryptosporidium.fasta-enc.2.ngm
[SEQPROV] Reading 18 Mbp from disk took 0.01s
[PREPROCESS] Reading RefTable from /project/teaser/genometeaser/references/Cryptosporidium.fasta-ht-13-2.3.ngm
[PREPROCESS] Reading from disk took 0.25s
[PREPROCESS] Max. k-mer frequency set so 100!
[INPUT] Input is paired end data.
[INPUT] Opening file reads1.fastq for reading
[INPUT] Opening file reads2.fastq for reading
[INPUT] Input is Fastq
[INPUT] Estimating parameter from data
[INPUT] Reads found in files: 75000
[INPUT] Average read length: 100 (min: 100, max: 102)
[INPUT] Corridor width: 20
[INPUT] Average kmer hits pro read: 26.367645
[INPUT] Max possible kmer hit: 29
[INPUT] Estimated sensitivity: 0.900000
[INPUT] Estimating parameter took 0.154s
[INPUT] Input is Fastq
[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] Valid pairs found: 99.96%
[MAIN] Estimated insert size: 125 bp
[MAIN] Alignments computed: 150000
[MAIN] Done (150000 reads mapped (100.00%), 0 reads not mapped, 150000 lines written)(elapsed: 4.178481s)
systime1.076836
time4.77132296562
usrtime10.412417
working_directory/project/teaser/genometeaser/tests_generated/f23fe16b99420742b88a981972af6aae