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 Mapped14444896.299%
Wrongly Mapped55523.701%
Not Mapped00.0%
Total150000100.0%
Read Failure Statistics
Not mapped00.0%
Missing in mapper output00.0%
Mapped to wrong chromosome00.0%
Mapped to wrong position55523.701%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.981100
Precision0.963000
Recall1.000000
Timing
Raw Mapping Time3.475s
Effective Mapping Time2.362s
Effective Init Time1.112s
Effective Time MeasureWall clock
Mapping Time (Wall)3.475s
Mapping Time (CPU)7.964s
Mapping Time (CPU User)7.222s
Mapping Time (CPU System)0.742s
Init Time (Wall)1.112s
Init Time (CPU)1.239s
Init Time (CPU User)1.001s
Init Time (CPU System)0.238s
Additional Information
Mapper Memory Usage1767 MB
Total Test Runtime (Wall)20.674s
Mapper Command Line: 
/project2/NextGenMapTest/Teaser/software/ngm/ngm --output out_ngm.sam --ref /project2/NextGenMapTest/Teaser/references/E_coli.fasta -t 4 --qry reads.fastq --no-progress
Errors and Warnings
No problems were encountered.
Subprocess Log

/project2/NextGenMapTest/Teaser/software/ngm/ngm --ref /project2/NextGenMapTest/Teaser/references/E_coli.fasta

command/project2/NextGenMapTest/Teaser/software/ngm/ngm --ref /project2/NextGenMapTest/Teaser/references/E_coli.fasta
return1
status1
stderr

None
stdout

[MAIN] NextGenMap 0.4.13

[MAIN] Startup : x64 (build Jan 20 2017 17:23:16)

[MAIN] Starting time: 2017-01-20.17:33:19

[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_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 4 --match_bonus_tt 4 --max_cmrs 2147483647 --max_equal 1 --max_insert_size 1000 --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 /project2/NextGenMapTest/Teaser/references/E_coli.fasta --ref_mode -1 --silent_clip 0 --skip_mate_check 0 --skip_save 0 --step_count 4 --strata 0 --topn 1 --update_check 0

[NGM] Wrinting output (SAM) to stdout

[SEQPROV] Encoding reference sequence.

[SEQPROV] Size of reference genome 5 Mbp (max. 17179 Mbp)

[SEQPROV] Allocating 2567036 (5205467) bytes for the reference.

[SEQPROV] BinRef length: 2567034ll (elapsed 0.022885)

[SEQPROV] 0 reference sequences were skipped (length < 10).

[SEQPROV] Writing encoded reference to /project2/NextGenMapTest/Teaser/references/E_coli.fasta-enc.2.ngm

[SEQPROV] Writing to disk took 0.34s

[PREPROCESS] Building reference table

[PREPROCESS] Allocated 1 hashtable units (tableLocMax=2^32.000000, genomeSize=2^22.291671)

[PREPROCESS] Building RefTable #0 (kmer length: 13, reference skip: 2)

[PREPROCESS] 	Number of k-mers: 67108865

[PREPROCESS] 	Counting kmers took 0.11s

[PREPROCESS] 	Average number of positions per prefix: 1.060443

[PREPROCESS] 	0 prefixes are ignored due to the frequency cutoff (1000)

[PREPROCESS] 	Index size: 335544325 byte (67108865 x 5)

[PREPROCESS] 	Generating index took 2.59s

[PREPROCESS] 	Allocating and initializing prefix Table took 0.00s

[PREPROCESS] 	Number of prefix positions is 1710686 (4)

[PREPROCESS] 	Size of RefTable is 6842744

[PREPROCESS] 	Number of repetitive k-mers ignored: 0

[PREPROCESS] 	Overall time for creating RefTable: 2.92s

[PREPROCESS] Writing RefTable to /project2/NextGenMapTest/Teaser/references/E_coli.fasta-ht-13-2.2.ngm

[PREPROCESS] Writing to disk took 4.01s

[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
time7.35129785538
usrtime0
working_directory/project2/NextGenMapTest/Teaser/tests_generated/ecoli_test

/project2/NextGenMapTest/Teaser/software/ngm/ngm --output out_ngm.sam --ref /project2/NextGenMapTest/Teaser/references/E_coli.fasta -t 4 --qry reads_base.fastq --no-progress

command/project2/NextGenMapTest/Teaser/software/ngm/ngm --output out_ngm.sam --ref /project2/NextGenMapTest/Teaser/references/E_coli.fasta -t 4 --qry reads_base.fastq --no-progress
memory709960000
return0
status1
stderr

None
stdout

[MAIN] NextGenMap 0.4.13

[MAIN] Startup : x64 (build Jan 20 2017 17:23:16)

[MAIN] Starting time: 2017-01-20.17:33:27

[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_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 4 --match_bonus_tt 4 --max_cmrs 2147483647 --max_equal 1 --max_insert_size 1000 --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 /project2/NextGenMapTest/Teaser/references/E_coli.fasta --ref_mode -1 --silent_clip 0 --skip_mate_check 0 --skip_save 0 --step_count 4 --strata 0 --topn 1 --update_check 0

[NGM] Opening for output (SAM): out_ngm.sam

[SEQPROV] Reading encoded reference from /project2/NextGenMapTest/Teaser/references/E_coli.fasta-enc.2.ngm

[SEQPROV] Reading 5 Mbp from disk took 0.00s

[PREPROCESS] Reading RefTable from /project2/NextGenMapTest/Teaser/references/E_coli.fasta-ht-13-2.2.ngm

[PREPROCESS] Reading from disk took 0.14s

[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 0.002s

[INPUT] Input is Fastq

Setting of real/effective user Id to 0/0 failed

FATAL: Module fglrx not found.

Error! Fail to load fglrx kernel module! Maybe you can switch to root user to load kernel module directly

Setting of real/effective user Id to 0/0 failed

FATAL: Module fglrx not found.

Error! Fail to load fglrx kernel module! Maybe you can switch to root user to load kernel module directly

[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: Intel(R) Core(TM) i5-2500K CPU @ 3.30GHz (Driver: 1214.3 (sse2,avx))

[OPENCL] 4 CPU cores available.

[MAIN] Alignments computed: 1

[MAIN] Done (0 reads mapped (0.00%), 1 reads not mapped, 1 lines written)(elapsed: 1.609392s)
systime0.246962
time1.62781596184
usrtime0.993848
working_directory/project2/NextGenMapTest/Teaser/tests_generated/ecoli_test

/project2/NextGenMapTest/Teaser/software/ngm/ngm --output out_ngm.sam --ref /project2/NextGenMapTest/Teaser/references/E_coli.fasta -t 4 --qry reads_base.fastq --no-progress

command/project2/NextGenMapTest/Teaser/software/ngm/ngm --output out_ngm.sam --ref /project2/NextGenMapTest/Teaser/references/E_coli.fasta -t 4 --qry reads_base.fastq --no-progress
memory711916000
return0
status1
stderr

None
stdout

[MAIN] NextGenMap 0.4.13

[MAIN] Startup : x64 (build Jan 20 2017 17:23:16)

[MAIN] Starting time: 2017-01-20.17:33:29

[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_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 4 --match_bonus_tt 4 --max_cmrs 2147483647 --max_equal 1 --max_insert_size 1000 --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 /project2/NextGenMapTest/Teaser/references/E_coli.fasta --ref_mode -1 --silent_clip 0 --skip_mate_check 0 --skip_save 0 --step_count 4 --strata 0 --topn 1 --update_check 0

[NGM] Opening for output (SAM): out_ngm.sam

[SEQPROV] Reading encoded reference from /project2/NextGenMapTest/Teaser/references/E_coli.fasta-enc.2.ngm

[SEQPROV] Reading 5 Mbp from disk took 0.00s

[PREPROCESS] Reading RefTable from /project2/NextGenMapTest/Teaser/references/E_coli.fasta-ht-13-2.2.ngm

[PREPROCESS] Reading from disk took 0.14s

[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

Setting of real/effective user Id to 0/0 failed

FATAL: Module fglrx not found.

Error! Fail to load fglrx kernel module! Maybe you can switch to root user to load kernel module directly

Setting of real/effective user Id to 0/0 failed

FATAL: Module fglrx not found.

Error! Fail to load fglrx kernel module! Maybe you can switch to root user to load kernel module directly

[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: Intel(R) Core(TM) i5-2500K CPU @ 3.30GHz (Driver: 1214.3 (sse2,avx))

[OPENCL] 4 CPU cores available.

[MAIN] Alignments computed: 1

[MAIN] Done (0 reads mapped (0.00%), 1 reads not mapped, 1 lines written)(elapsed: 1.042739s)
systime0.237963
time1.11248707771
usrtime1.000847
working_directory/project2/NextGenMapTest/Teaser/tests_generated/ecoli_test

/project2/NextGenMapTest/Teaser/software/ngm/ngm --output out_ngm.sam --ref /project2/NextGenMapTest/Teaser/references/E_coli.fasta -t 4 --qry reads.fastq --no-progress

command/project2/NextGenMapTest/Teaser/software/ngm/ngm --output out_ngm.sam --ref /project2/NextGenMapTest/Teaser/references/E_coli.fasta -t 4 --qry reads.fastq --no-progress
memory1767324000
return0
status1
stderr

None
stdout

[MAIN] NextGenMap 0.4.13

[MAIN] Startup : x64 (build Jan 20 2017 17:23:16)

[MAIN] Starting time: 2017-01-20.17:33:31

[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_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 4 --match_bonus_tt 4 --max_cmrs 2147483647 --max_equal 1 --max_insert_size 1000 --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 /project2/NextGenMapTest/Teaser/references/E_coli.fasta --ref_mode -1 --silent_clip 0 --skip_mate_check 0 --skip_save 0 --step_count 4 --strata 0 --topn 1 --update_check 0

[NGM] Opening for output (SAM): out_ngm.sam

[SEQPROV] Reading encoded reference from /project2/NextGenMapTest/Teaser/references/E_coli.fasta-enc.2.ngm

[SEQPROV] Reading 5 Mbp from disk took 0.00s

[PREPROCESS] Reading RefTable from /project2/NextGenMapTest/Teaser/references/E_coli.fasta-ht-13-2.2.ngm

[PREPROCESS] Reading from disk took 0.14s

[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: 26.236219

[INPUT] Max possible kmer hit: 29

[INPUT] Estimated sensitivity: 0.900000

[INPUT] Estimating parameter took 0.199s

[INPUT] Input is Fastq

Setting of real/effective user Id to 0/0 failed

FATAL: Module fglrx not found.

Error! Fail to load fglrx kernel module! Maybe you can switch to root user to load kernel module directly

Setting of real/effective user Id to 0/0 failed

FATAL: Module fglrx not found.

Error! Fail to load fglrx kernel module! Maybe you can switch to root user to load kernel module directly

[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: Intel(R) Core(TM) i5-2500K CPU @ 3.30GHz (Driver: 1214.3 (sse2,avx))

[OPENCL] 4 CPU cores available.

[MAIN] Alignments computed: 150000

[MAIN] Done (150000 reads mapped (100.00%), 0 reads not mapped, 150000 lines written)(elapsed: 2.895484s)
systime0.741887
time3.47476005554
usrtime7.221902
working_directory/project2/NextGenMapTest/Teaser/tests_generated/ecoli_test