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 Mapped21950191.633%
Wrongly Mapped200278.361%
Not Mapped150.006%
Total239543100.0%
Read Failure Statistics
Not mapped150.006%
Missing in mapper output00.0%
Mapped to wrong chromosome107644.494%
Mapped to wrong position92633.867%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.956300
Precision0.916400
Recall0.999900
Timing
Raw Mapping Time11.999s
Effective Mapping Time10.548s
Effective Init Time1.451s
Effective Time MeasureWall clock
Mapping Time (Wall)11.999s
Mapping Time (CPU)31.171s
Mapping Time (CPU User)29.389s
Mapping Time (CPU System)1.783s
Init Time (Wall)1.451s
Init Time (CPU)1.440s
Init Time (CPU User)1.162s
Init Time (CPU System)0.278s
Additional Information
Mapper Memory Usage2036 MB
Total Test Runtime (Wall)32.283s
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: 2017-02-06.14:54:45

[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 0.17s

[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: 1.296565s)
systime0.294955
time1.32725596428
usrtime1.150825
working_directory/project2/NextGenMapTest/Teaser/tests_generated/D2_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
memory957968000
return0
status1
stderr

None
stdout

[MAIN] NextGenMap 0.5.3

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

[MAIN] Starting time: 2017-02-06.14:54:47

[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 0.17s

[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: 1.427119s)
systime0.277957
time1.4508690834
usrtime1.161823
working_directory/project2/NextGenMapTest/Teaser/tests_generated/D2_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
memory2036452000
return0
status1
stderr

None
stdout

[MAIN] NextGenMap 0.5.3

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

[MAIN] Starting time: 2017-02-06.14:54:49

[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: 20.259413

[INPUT] Max possible kmer hit: 46

[INPUT] Estimated sensitivity: 0.440422

[INPUT] Estimating parameter took 2.128s

[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: 239543

[MAIN] Done (239528 reads mapped (99.99%), 15 reads not mapped, 239543 lines written)(elapsed: 10.812459s)
systime1.782728
time11.9988780022
usrtime29.388532
working_directory/project2/NextGenMapTest/Teaser/tests_generated/D2_n