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 Mapped21932291.559%
Wrongly Mapped201728.421%
Not Mapped490.02%
Total239543100.0%
Read Failure Statistics
Not mapped490.02%
Missing in mapper output00.0%
Mapped to wrong chromosome105874.42%
Mapped to wrong position95854.001%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.955900
Precision0.915800
Recall0.999800
Timing
Raw Mapping Time9.400s
Effective Mapping Time8.054s
Effective Init Time1.346s
Effective Time MeasureWall clock
Mapping Time (Wall)9.400s
Mapping Time (CPU)26.754s
Mapping Time (CPU User)24.922s
Mapping Time (CPU System)1.832s
Init Time (Wall)1.346s
Init Time (CPU)1.442s
Init Time (CPU User)1.141s
Init Time (CPU System)0.301s
Additional Information
Mapper Memory Usage2038 MB
Total Test Runtime (Wall)29.759s
Mapper Command Line: 
/software/ngm/dev/ngm-0.5.3/ngm --output out_ngm-0.5.3.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/dev/ngm-0.5.3/ngm --output out_ngm-0.5.3.sam --ref /project2/NextGenMapTest/Teaser/references/d_melanogaster.fasta -t 4 --qry reads_base.fastq --no-progress

command/software/ngm/dev/ngm-0.5.3/ngm --output out_ngm-0.5.3.sam --ref /project2/NextGenMapTest/Teaser/references/d_melanogaster.fasta -t 4 --qry reads_base.fastq --no-progress
memory959928000
return0
status1
stderr

None
stdout

[MAIN] NextGenMap 0.5.3

[MAIN] Startup : x64 (build Feb  2 2017 12:01:29)

[MAIN] Starting time: 2017-02-06.14:54:15

[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-0.5.3.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 --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-0.5.3.sam

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

[SEQPROV] Reading 145 Mbp from disk took 0.66s

[PREPROCESS] Reading RefTable from /project2/NextGenMapTest/Teaser/references/d_melanogaster.fasta-ht-13-2.3.ngm

[PREPROCESS] Reading from disk took 4.75s

[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 0.002s

[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: 6.914377s)
systime0.387941
time7.15442585945
usrtime1.158823
working_directory/project2/NextGenMapTest/Teaser/tests_generated/D1_n

/software/ngm/dev/ngm-0.5.3/ngm --output out_ngm-0.5.3.sam --ref /project2/NextGenMapTest/Teaser/references/d_melanogaster.fasta -t 4 --qry reads_base.fastq --no-progress

command/software/ngm/dev/ngm-0.5.3/ngm --output out_ngm-0.5.3.sam --ref /project2/NextGenMapTest/Teaser/references/d_melanogaster.fasta -t 4 --qry reads_base.fastq --no-progress
memory957972000
return0
status1
stderr

None
stdout

[MAIN] NextGenMap 0.5.3

[MAIN] Startup : x64 (build Feb  2 2017 12:01:29)

[MAIN] Starting time: 2017-02-06.14:54:23

[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-0.5.3.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 --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-0.5.3.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-13-2.3.ngm

[PREPROCESS] Reading from disk took 0.18s

[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

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: 1.256277s)
systime0.300954
time1.34558296204
usrtime1.140826
working_directory/project2/NextGenMapTest/Teaser/tests_generated/D1_n

/software/ngm/dev/ngm-0.5.3/ngm --output out_ngm-0.5.3.sam --ref /project2/NextGenMapTest/Teaser/references/d_melanogaster.fasta -t 4 --qry reads.fastq --no-progress

command/software/ngm/dev/ngm-0.5.3/ngm --output out_ngm-0.5.3.sam --ref /project2/NextGenMapTest/Teaser/references/d_melanogaster.fasta -t 4 --qry reads.fastq --no-progress
memory2038084000
return0
status1
stderr

None
stdout

[MAIN] NextGenMap 0.5.3

[MAIN] Startup : x64 (build Feb  2 2017 12:01:29)

[MAIN] Starting time: 2017-02-06.14:54:25

[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-0.5.3.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 --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-0.5.3.sam

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

[SEQPROV] Reading 145 Mbp from disk took 0.01s

[PREPROCESS] Reading RefTable from /project2/NextGenMapTest/Teaser/references/d_melanogaster.fasta-ht-13-2.3.ngm

[PREPROCESS] Reading from disk took 0.17s

[PREPROCESS] Max. k-mer frequency set so 100!

[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: 239543

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

[INPUT] Corridor width: 27

[INPUT] Average kmer hits pro read: 40.405861

[INPUT] Max possible kmer hit: 46

[INPUT] Estimated sensitivity: 0.878388

[INPUT] Estimating parameter took 0.729s

[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: 239520

[MAIN] Done (239494 reads mapped (99.98%), 49 reads not mapped, 239543 lines written)(elapsed: 8.245819s)
systime1.831721
time9.39999103546
usrtime24.922211
working_directory/project2/NextGenMapTest/Teaser/tests_generated/D1_n