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 Mapped00.0%
Wrongly Mapped00.0%
Not Mapped313713100.0%
Total313713100.0%
Read Failure Statistics
Not mapped00.0%
Missing in mapper output313713100.0%
Mapped to wrong chromosome00.0%
Mapped to wrong position00.0%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.000000
Precision0.000000
Recall0.000000
Timing
Raw Mapping Time6.967s
Effective Mapping Time0.466s
Effective Init Time6.501s
Effective Time MeasureCPU
Mapping Time (Wall)27.064s
Mapping Time (CPU)6.967s
Mapping Time (CPU User)2.538s
Mapping Time (CPU System)4.429s
Init Time (Wall)49.236s
Init Time (CPU)6.501s
Init Time (CPU User)1.377s
Init Time (CPU System)5.124s
Additional Information
Mapper Memory Usage6338 MB
Total Test Runtime (Wall)134.370s
Mapper Command Line: 
/project/teaser/genometeaser/software/ngm/ngm --qry2 reads2.fastq --output out_ngm.sam --qry1 reads1.fastq --ref /project/teaser/genometeaser/references/H_sapiens.fa -t 4 --no-progress
Errors and Warnings
TypeMessageFilePosition
Unexpectedly reached end of mapper outputsorted_out_ngm.samY29udGlnXzc0MDA4OTJfNzQwMDk3Ml8wXzFfMF8wXzI6MDowXzA6MDowXzczMmQ=
Subprocess Log

/project/teaser/genometeaser/software/ngm/ngm --output out_ngm.sam --ref /project/teaser/genometeaser/references/H_sapiens.fa -t 4 --qry reads_base.fastq --no-progress

command/project/teaser/genometeaser/software/ngm/ngm --output out_ngm.sam --ref /project/teaser/genometeaser/references/H_sapiens.fa -t 4 --qry reads_base.fastq --no-progress
memory5992864000
return0
status1
stderr
None
stdout
[MAIN] NextGenMap 0.5.3
[MAIN] Startup : x64 (build Jan 31 2017 16:20:45)
[MAIN] Starting time: 2017-05-11.03:43:51
[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.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 /project/teaser/genometeaser/references/H_sapiens.fa --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.sam
[SEQPROV] Reading encoded reference from /project/teaser/genometeaser/references/H_sapiens.fa-enc.2.ngm
[SEQPROV] Reading 3137 Mbp from disk took 14.44s
[PREPROCESS] Reading RefTable from /project/teaser/genometeaser/references/H_sapiens.fa-ht-13-2.3.ngm
[PREPROCESS] Reading from disk took 34.57s
[PREPROCESS] Max. k-mer frequency set so 879!
[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
[OPENCL] Available platforms: 2
[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) Xeon(R) CPU X5650 @ 2.67GHz (Driver: 1214.3 (sse2))
[OPENCL] 24 CPU cores available.
[MAIN] Alignments computed: 1
[MAIN] Done (1 reads mapped (100.00%), 0 reads not mapped, 1 lines written)(elapsed: 51.024586s)
systime5.469168
time51.3831830025
usrtime1.333797
working_directory/project/teaser/genometeaser/tests_generated/cc90747119948fac5bcca0e53c33f3a3

/project/teaser/genometeaser/software/ngm/ngm --output out_ngm.sam --ref /project/teaser/genometeaser/references/H_sapiens.fa -t 4 --qry reads_base.fastq --no-progress

command/project/teaser/genometeaser/software/ngm/ngm --output out_ngm.sam --ref /project/teaser/genometeaser/references/H_sapiens.fa -t 4 --qry reads_base.fastq --no-progress
memory5992816000
return0
status1
stderr
None
stdout
[MAIN] NextGenMap 0.5.3
[MAIN] Startup : x64 (build Jan 31 2017 16:20:45)
[MAIN] Starting time: 2017-05-11.03:44:43
[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.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 /project/teaser/genometeaser/references/H_sapiens.fa --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.sam
[SEQPROV] Reading encoded reference from /project/teaser/genometeaser/references/H_sapiens.fa-enc.2.ngm
[SEQPROV] Reading 3137 Mbp from disk took 13.33s
[PREPROCESS] Reading RefTable from /project/teaser/genometeaser/references/H_sapiens.fa-ht-13-2.3.ngm
[PREPROCESS] Reading from disk took 33.70s
[PREPROCESS] Max. k-mer frequency set so 879!
[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 0.001s
[INPUT] Input is Fastq
[OPENCL] Available platforms: 2
[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) Xeon(R) CPU X5650 @ 2.67GHz (Driver: 1214.3 (sse2))
[OPENCL] 24 CPU cores available.
[MAIN] Alignments computed: 1
[MAIN] Done (1 reads mapped (100.00%), 0 reads not mapped, 1 lines written)(elapsed: 48.895580s)
systime5.124221
time49.2363688946
usrtime1.37679
working_directory/project/teaser/genometeaser/tests_generated/cc90747119948fac5bcca0e53c33f3a3

/project/teaser/genometeaser/software/ngm/ngm --qry2 reads2.fastq --output out_ngm.sam --qry1 reads1.fastq --ref /project/teaser/genometeaser/references/H_sapiens.fa -t 4 --no-progress

command/project/teaser/genometeaser/software/ngm/ngm --qry2 reads2.fastq --output out_ngm.sam --qry1 reads1.fastq --ref /project/teaser/genometeaser/references/H_sapiens.fa -t 4 --no-progress
memory6338952000
return134
status1
stderr
None
stdout
[MAIN] NextGenMap 0.5.3
[MAIN] Startup : x64 (build Jan 31 2017 16:20:45)
[MAIN] Starting time: 2017-05-11.03:45:33
[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 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.sam --overwrite 1 --pair_score_cutoff 0.900000 --paired 1 --parse_all 1 --pe_delimiter / --qry1 reads1.fastq --qry2 reads2.fastq --qry_count -1 --qry_start 0 --ref /project/teaser/genometeaser/references/H_sapiens.fa --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.sam
[SEQPROV] Reading encoded reference from /project/teaser/genometeaser/references/H_sapiens.fa-enc.2.ngm
[SEQPROV] Reading 3137 Mbp from disk took 12.90s
[PREPROCESS] Reading RefTable from /project/teaser/genometeaser/references/H_sapiens.fa-ht-13-2.3.ngm
[PREPROCESS] Reading from disk took 11.59s
[PREPROCESS] Max. k-mer frequency set so 879!
[INPUT] Input is paired end data.
[INPUT] Opening file reads1.fastq for reading
[INPUT] Opening file reads2.fastq for reading
[INPUT] Input is Fastq
[INPUT] Estimating parameter from data
[INPUT] Reads found in files: 156858
[INPUT] Average read length: 100 (min: 100, max: 102)
[INPUT] Corridor width: 20
[INPUT] Average kmer hits pro read: 18.844152
[INPUT] Max possible kmer hit: 29
[INPUT] Estimated sensitivity: 0.649798
[INPUT] Estimating parameter took 0.694s
[INPUT] Input is Fastq
[INPUT] Input is Fastq
[OPENCL] Available platforms: 2
[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) Xeon(R) CPU X5650 @ 2.67GHz (Driver: 1214.3 (sse2))
[OPENCL] 24 CPU cores available.
Exception bad_alloc occured in thread 2. This usually means you ran out of physical or virtual memory (try ulimit -v)
*** glibc detected *** /project/teaser/genometeaser/software/ngm/ngm-core: free(): invalid pointer: 0x0000000000791470 ***
======= Backtrace: =========
/lib64/libc.so.6(+0x733b6)[0x7f26cb4343b6]
/lib64/libc.so.6(cfree+0x6c)[0x7f26cb4392dc]
/project/teaser/genometeaser/software/ngm/ngm-core(_ZN2CSD1Ev+0x4d)[0x44aded]
/project/teaser/genometeaser/software/ngm/ngm-core(_ZN2CSD0Ev+0x9)[0x44ae29]
/project/teaser/genometeaser/software/ngm/ngm-core(_ZN4_NGM10ThreadFuncEPv+0x72)[0x4504b2]
/lib64/libpthread.so.0(+0x6a3f)[0x7f26cc0b0a3f]
/lib64/libc.so.6(clone+0x6d)[0x7f26cb49467d]
======= Memory map: ========
00400000-0051f000 r-xp 00000000 00:1d 165787820 /project/teaser/genometeaser/software/ngm/ngm-core
0071f000-00720000 r--p 0011f000 00:1d 165787820 /project/teaser/genometeaser/software/ngm/ngm-core
00720000-00721000 rw-p 00120000 00:1d 165787820 /project/teaser/genometeaser/software/ngm/ngm-core
00721000-01154000 rw-p 00000000 00:00 0 [heap]
200000000-3ab3f0000 ---p 00000000 00:00 0
7f250ff9b000-7f250ff9c000 ---p 00000000 00:00 0
7f250ff9c000-7f250ffdc000 rwxp 00000000 00:00 0
7f252c000000-7f252c544000 rw-p 00000000 00:00 0
7f252c544000-7f2530000000 ---p 00000000 00:00 0
7f2533dfa000-7f2533dff000 r-xp 00000000 09:01 2252476 /tmp/OCL9QYkQ8.so
7f2533dff000-7f2533ffe000 ---p 00005000 09:01 2252476 /tmp/OCL9QYkQ8.so
7f2533ffe000-7f2533fff000 r--p 00004000 09:01 2252476 /tmp/OCL9QYkQ8.so
7f2533fff000-7f2534000000 rw-p 00005000 09:01 2252476 /tmp/OCL9QYkQ8.so
7f2534000000-7f253428f000 rw-p 00000000 00:00 0
7f253428f000-7f2538000000 ---p 00000000 00:00 0
7f253b7aa000-7f253b7ab000 ---p 00000000 00:00 0
7f253b7ab000-7f253bfbd000 rwxp 00000000 00:00 0
7f253bfbd000-7f253bfbe000 ---p 00000000 00:00 0
7f253bfbe000-7f253bffe000 rwxp 00000000 00:00 0
7f253bffe000-7f2550000000 rw-p 00000000 00:00 0
7f2550000000-7f2550a57000 rw-p 00000000 00:00 0
7f2550a57000-7f2554000000 ---p 00000000 00:00 0
7f25540b9000-7f25540ba000 ---p 00000000 00:00 0
7f25540ba000-7f25548cc000 rwxp 00000000 00:00 0
7f25548cc000-7f2556ef2000 rw-p 00000000 00:00 0
7f2556ef2000-7f2556ef7000 r-xp 00000000 09:01 2252475 /tmp/OCL4h77sT.so
7f2556ef7000-7f25570f6000 ---p 00005000 09:01 2252475 /tmp/OCL4h77sT.so
7f25570f6000-7f25570f7000 r--p 00004000 09:01 2252475 /tmp/OCL4h77sT.so
7f25570f7000-7f25570f8000 rw-p 00005000 09:01 2252475 /tmp/OCL4h77sT.so
7f25570f8000-7f25570f9000 ---p 00000000 00:00 0
7f25570f9000-7f255790b000 rwxp 00000000 00:00 0
7f255790b000-7f255790c000 ---p 00000000 00:00 0
7f255790c000-7f255794c000 rwxp 00000000 00:00 0
7f255794c000-7f256cd61000 rw-p 00000000 00:00 0
7f256cd61000-7f256cd66000 r-xp 00000000 09:01 2252474 /tmp/OCLuwLSeH.so
7f256cd66000-7f256cf65000 ---p 00005000 09:01 2252474 /tmp/OCLuwLSeH.so
7f256cf65000-7f256cf66000 r--p 00004000 09:01 2252474 /tmp/OCLuwLSeH.so
7f256cf66000-7f256cf67000 rw-p 00005000 09:01 2252474 /tmp/OCLuwLSeH.so
7f256cf67000-7f256cf68000 ---p 00000000 00:00 0
7f256cf68000-7f256d77a000 rwxp 00000000 00:00 0
7f256d77a000-7f256d790000 r-xp 00000000 09:01 2354794 /lib64/libz.so.1.2.5
7f256d790000-7f256d990000 ---p 00016000 09:01 2354794 /lib64/libz.so.1.2.5
7f256d990000-7f256d991000 r--p 00016000 09:01 2354794 /lib64/libz.so.1.2.5
7f256d991000-7f256d992000 rw-p 00017000 09:01 2354794 /lib64/libz.so.1.2.5
7f256d992000-7f256e0d4000 r-xp 00000000 09:02 1860035 /usr/lib64/libcuda.so.295.41
7f256e0d4000-7f256e2d3000 ---p 00742000 09:02 1860035 /usr/lib64/libcuda.so.295.41
7f256e2d3000-7f256e3c8000 rw-p 00741000 09:02 1860035 /usr/lib64/libcuda.so.295.41
7f256e3c8000-7f256e3ee000 rw-p 00000000 00:00 0
7f256e3ee000-7f256e400000 r-xp 00000000 09:02 1845222 /usr/lib64/libXext.so.6.4.0
7f256e400000-7f256e5ff000 ---p 00012000 09:02 1845222 /usr/lib64/libXext.so.6.4.0
7f256e5ff000-7f256e600000 r--p 00011000 09:02 1845222 /usr/lib64/libXext.so.6.4.0
7f256e600000-7f256e601000 rw-p 00012000 09:02 1845222 /usr/lib64/libXext.so.6.4.0
7f256e601000-7f256e603000 r-xp 00000000 09:02 1838815 /usr/lib64/libXau.so.6.0.0
7f256e603000-7f256e803000 ---p 00002000 09:02 1838815 /usr/lib64/libXau.so.6.0.0
7f256e803000-7f256e804000 r--p 00002000 09:02 1838815 /usr/lib64/libXau.so.6.0.0
7f256e804000-7f256e805000 rw-p 00003000 09:02 1838815 /usr/lib64/libXau.so.6.0.0
7f256e805000-7f256e821000 r-xp 00000000 09:02 1839031 /usr/lib64/libxcb.so.1.1.0
7f256e821000-7f256ea20000 ---p 0001c000 09:02 1839031 /usr/lib64/libxcb.so.1.1.0
7f256ea20000-7f256ea21000 r--p 0001b000 09:02 1839031 /usr/lib64/libxcb.so.1.1.0
7f256ea21000-7f256ea22000 rw-p 0001c000 09:02 1839031 /usr/lib64/libxcb.so.1.1.0
7f256ea22000-7f256eb5f000 r-xp 00000000 09:02 1844776 /usr/lib64/libX11.so.6.3.0
7f256eb5f000-7f256ed5f000 ---p 0013d000 09:02 1844776 /usr/lib64/libX11.so.6.3.0
7f256ed5f000-7f256ed60000 r--p 0013d000 09:02 1844776 /usr/lib64/libX11.so.6.3.0
7f256ed60000-7f256ed65000 rw-p 0013e000 09:02 1844776 /usr/lib64/libX11.so.6.3.0
7f256ed65000-7f256ed6d000 r-xp 00000000 09:01 2354727 /lib64/librt-2.11.3.so
7f256ed6d000-7f256ef6c000 ---p 00008000 09:01 2354727 /lib64/librt-2.11.3.so
7f256ef6c000-7f256ef6d000 r--p 00007000 09:01 2354727 /lib64/librt-2.11.3.so
7f256ef6d000-7f256ef6e000 rw-p 00008000 09:01 2354727 /lib64/librt-2.11.3.so
7f256ef6e000-7f2571094000 r-xp 00000000 00:1d 165787791 /project/teaser/genometeaser/software/ngm/opencl/lib/libamdocl64.so
7f2571094000-7f2571293000 ---p 02126000 00:1d 165787791 /project/teaser/genometeaser/software/ngm/opencl/lib/libamdocl64.so
7f2571293000-7f25714ff000 rw-p 02125000 00:1d 165787791 /project/teaser/genometeaser/software/ngm/opencl/lib/libamdocl64.so
7f25714ff000-7f2571614000 rw-p 00000000 00:00 0
7f2571614000-7f2571615000 ---p 00000000 00:00 0
7f2571615000-7f2571e15000 rwxp 00000000 00:00 0
7f2571e15000-7f2571e16000 ---p 00000000 00:00 0
7f2571e16000-7f2572616000 rwxp 00000000 00:00 0
7f2572616000-7f2572617000 ---p 00000000 00:00 0
7f2572617000-7f2572e17000 rwxp 00000000 00:00 0
7f2572e17000-7f2572e18000 ---p 00000000 00:00 0
7f2572e18000-7f2573618000 rwxp 00000000 00:00 0
7f2573618000-7f26cb1bd000 rw-p 00000000 00:00 0
7f26cb1bd000-7f26cb1bf000 r-xp 00000000 09:01 2354703 /lib64/libdl-2.11.3.so
7f26cb1bf000-7f26cb3bf000 ---p 00002000 09:01 2354703 /lib64/libdl-2.11.3.so
7f26cb3bf000-7f26cb3c0000 r--p 00002000 09:01 2354703 /lib64/libdl-2.11.3.so
7f26cb3c0000-7f26cb3c1000 rw-p 00003000 09:01 2354703 /lib64/libdl-2.11.3.so
7f26cb3c1000-7f26cb525000 r-xp 00000000 09:01 2354697 /lib64/libc-2.11.3.so
systime4.429326
time27.0641160011
usrtime2.537614
working_directory/project/teaser/genometeaser/tests_generated/cc90747119948fac5bcca0e53c33f3a3