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 Mapped21939391.588%
Wrongly Mapped201448.409%
Not Mapped60.003%
Total239543100.0%
Read Failure Statistics
Not mapped60.003%
Missing in mapper output00.0%
Mapped to wrong chromosome104814.375%
Mapped to wrong position96634.034%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.956100
Precision0.915900
Recall1.000000
Timing
Raw Mapping Time9.541s
Effective Mapping Time8.397s
Effective Init Time1.144s
Effective Time MeasureWall clock
Mapping Time (Wall)9.541s
Mapping Time (CPU)28.060s
Mapping Time (CPU User)26.276s
Mapping Time (CPU System)1.784s
Init Time (Wall)1.144s
Init Time (CPU)1.307s
Init Time (CPU User)0.999s
Init Time (CPU System)0.308s
Additional Information
Mapper Memory Usage2037 MB
Total Test Runtime (Wall)32.018s
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
memory957448000
return0
status1
stderr

None
stdout

[MAIN] NextGenMap 0.4.13

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

[MAIN] Starting time: 2017-01-21.04:26:21

[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 0.79s

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

[PREPROCESS] Reading from disk took 5.68s

[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: 8.308729s)

[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)
systime0.407937
time9.22728395462
usrtime1.007846
working_directory/project2/NextGenMapTest/Teaser/tests_generated/D1_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: 2017-01-21.04:26:31

[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-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 0.18s

[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: 1.107740s)

[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)
systime0.307953
time1.14412403107
usrtime0.998848
working_directory/project2/NextGenMapTest/Teaser/tests_generated/D1_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
memory2037616000
return0
status1
stderr

None
stdout

[MAIN] NextGenMap 0.4.13

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

[MAIN] Starting time: 2017-01-21.04:26:33

[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: 239543

[INPUT] Average read length: 150 (min: 150, max: 152)

[INPUT] Corridor width: 27

[INPUT] Average kmer hits pro read: 41.368202

[INPUT] Max possible kmer hit: 46

[INPUT] Estimated sensitivity: 0.899309

[INPUT] Estimating parameter took 0.803s

[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: 239537

[MAIN] Done (239537 reads mapped (100.00%), 6 reads not mapped, 239543 lines written)(elapsed: 8.480159s)

[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)
systime1.783728
time9.54071784019
usrtime26.276005
working_directory/project2/NextGenMapTest/Teaser/tests_generated/D1_n