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 Mapped132199180.942%
Wrongly Mapped30290118.546%
Not Mapped83570.512%
Total1633249100.0%
Read Failure Statistics
Not mapped83570.512%
Missing in mapper output00.0%
Mapped to wrong chromosome21092212.914%
Mapped to wrong position919735.631%
Mapped to wrong strand60.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.894700
Precision0.813600
Recall0.993700
Timing
Raw Mapping Time11.464s
Effective Mapping Time10.203s
Effective Init Time1.261s
Effective Time MeasureWall clock
Mapping Time (Wall)11.464s
Mapping Time (CPU)28.638s
Mapping Time (CPU User)27.951s
Mapping Time (CPU System)0.687s
Init Time (Wall)1.261s
Init Time (CPU)1.282s
Init Time (CPU User)1.004s
Init Time (CPU System)0.278s
Additional Information
Mapper Memory Usage2086 MB
Total Test Runtime (Wall)60.351s
Mapper Command Line: 
/software/ngm/bin-linux/ngm-0.4.13 --output out_ngm-0.4.13.sam --ref /project2/NextGenMapTest/Teaser/references/d_melanogaster.fasta -t 4 --qry reads.fastq --no-progress
Errors and Warnings
No problems were encountered.
Subprocess Log

/software/ngm/bin-linux/ngm-0.4.13 --output out_ngm-0.4.13.sam --ref /project2/NextGenMapTest/Teaser/references/d_melanogaster.fasta -t 4 --qry reads_base.fastq --no-progress

command/software/ngm/bin-linux/ngm-0.4.13 --output out_ngm-0.4.13.sam --ref /project2/NextGenMapTest/Teaser/references/d_melanogaster.fasta -t 4 --qry reads_base.fastq --no-progress
memory959428000
return0
status1
stderr

None
stdout

[MAIN] NextGenMap 0.4.13

[MAIN] Startup : x64 (build Jun 26 2015 16:16:32)

[MAIN] Starting time: 2017-01-21.04:28:03

[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-0.4.13.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/d_melanogaster.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-0.4.13.sam

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

[SEQPROV] Reading 145 Mbp from disk took 0.02s

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

[PREPROCESS] Reading from disk took 0.17s

[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: 1.094500s)

[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)
systime0.275958
time1.20107913017
usrtime1.013845
working_directory/project2/NextGenMapTest/Teaser/tests_generated/D4_n

/software/ngm/bin-linux/ngm-0.4.13 --output out_ngm-0.4.13.sam --ref /project2/NextGenMapTest/Teaser/references/d_melanogaster.fasta -t 4 --qry reads_base.fastq --no-progress

command/software/ngm/bin-linux/ngm-0.4.13 --output out_ngm-0.4.13.sam --ref /project2/NextGenMapTest/Teaser/references/d_melanogaster.fasta -t 4 --qry reads_base.fastq --no-progress
memory957448000
return0
status1
stderr

None
stdout

[MAIN] NextGenMap 0.4.13

[MAIN] Startup : x64 (build Jun 26 2015 16:16:32)

[MAIN] Starting time: 2017-01-21.04:28:05

[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-0.4.13.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/d_melanogaster.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-0.4.13.sam

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

[SEQPROV] Reading 145 Mbp from disk took 0.02s

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

[PREPROCESS] Reading from disk took 0.17s

[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: 1.209258s)

[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)
systime0.277957
time1.26113796234
usrtime1.003847
working_directory/project2/NextGenMapTest/Teaser/tests_generated/D4_n

/software/ngm/bin-linux/ngm-0.4.13 --output out_ngm-0.4.13.sam --ref /project2/NextGenMapTest/Teaser/references/d_melanogaster.fasta -t 4 --qry reads.fastq --no-progress

command/software/ngm/bin-linux/ngm-0.4.13 --output out_ngm-0.4.13.sam --ref /project2/NextGenMapTest/Teaser/references/d_melanogaster.fasta -t 4 --qry reads.fastq --no-progress
memory2086292000
return0
status1
stderr

None
stdout

[MAIN] NextGenMap 0.4.13

[MAIN] Startup : x64 (build Jun 26 2015 16:16:32)

[MAIN] Starting time: 2017-01-21.04:28:07

[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-0.4.13.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/d_melanogaster.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-0.4.13.sam

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

[SEQPROV] Reading 145 Mbp from disk took 0.02s

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

[PREPROCESS] Reading from disk took 0.17s

[INPUT] Input is Fastq

[INPUT] Estimating parameter from data

[INPUT] Reads found in files: 1633249

[INPUT] Average read length: 22 (min: 22, max: 24)

[INPUT] Corridor width: 8

[INPUT] Average kmer hits pro read: 2.763689

[INPUT] Max possible kmer hit: 3

[INPUT] Estimated sensitivity: 0.900000

[INPUT] Estimating parameter took 1.194s

[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: 1624892

[MAIN] Done (1624892 reads mapped (99.49%), 8357 reads not mapped, 1633249 lines written)(elapsed: 8.953648s)

[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)
systime0.686895
time11.4641828537
usrtime27.95075
working_directory/project2/NextGenMapTest/Teaser/tests_generated/D4_n