-------------------------------------------------------------------------------- gmapper: COLOUR SPACE (AB SOLiD). SHRiMP 2.2.3 [ICC Intel(R) C++ g++ 4.1 mode; CXXFLAGS="-O3 -DNDEBUG -Kc++ -wd383,981,1572 -axP -ipo -openmp -static-intel -D__STDC_FORMAT_MACROS -D__STDC_LIMIT_MACROS -DGIT_VERSION=04238a0"] -------------------------------------------------------------------------------- note: mapping qualities are not available in local alignment mode; disabling them Loading genome from /data/results/reference/mmu/mm9/shrimp/ref/shrimp/mm9-cs.genome Loading seed from /data/results/reference/mmu/mm9/shrimp/ref/shrimp/mm9-cs.seed.0 Loading seed from /data/results/reference/mmu/mm9/shrimp/ref/shrimp/mm9-cs.seed.1 Loading seed from /data/results/reference/mmu/mm9/shrimp/ref/shrimp/mm9-cs.seed.2 Loading seed from /data/results/reference/mmu/mm9/shrimp/ref/shrimp/mm9-cs.seed.3 Loading seed from /data/results/reference/mmu/mm9/shrimp/ref/shrimp/mm9-cs.seed.4 Loading seed from /data/results/reference/mmu/mm9/shrimp/ref/shrimp/mm9-cs.seed.5 Loading seed from /data/results/reference/mmu/mm9/shrimp/ref/shrimp/mm9-cs.seed.6 Loading seed from /data/results/reference/mmu/mm9/shrimp/ref/shrimp/mm9-cs.seed.7 Loading seed from /data/results/reference/mmu/mm9/shrimp/ref/shrimp/mm9-cs.seed.8 Loading seed from /data/results/reference/mmu/mm9/shrimp/ref/shrimp/mm9-cs.seed.9 Loading seed from /data/results/reference/mmu/mm9/shrimp/ref/shrimp/mm9-cs.seed.10 Loading seed from /data/results/reference/mmu/mm9/shrimp/ref/shrimp/mm9-cs.seed.11 Loading seed from /data/results/reference/mmu/mm9/shrimp/ref/shrimp/mm9-cs.seed.12 Loading seed from /data/results/reference/mmu/mm9/shrimp/ref/shrimp/mm9-cs.seed.13 Loading seed from /data/results/reference/mmu/mm9/shrimp/ref/shrimp/mm9-cs.seed.14 Settings: Spaced Seeds (weight/span) 010111111111111 (13/15) 101011111111111 (13/15) 110101111111111 (13/15) 111010111111111 (13/15) 111101011111111 (13/15) 111110101111111 (13/15) 111111010111111 (13/15) 111111101011111 (13/15) 111111110101111 (13/15) 111111111010111 (13/15) 111111111101011 (13/15) 111111111110101 (13/15) 111111111111010 (13/15) 111111111111101 (14/15) 111111111111111 (15/15) Number of threads: 20 Thread chunk size: 1000 Window length: 150.00% Hash filter calls: yes Anchor width: 8 Indel taboo Len: 0 (disabled) Index list cutoff length: 15824 Gapless mode: no Global alignment: no Region filter: yes Region size: 2048 Region overlap: 50 Ignore QVs: no Minimum average qv: 10 Compute mapping qualities: no SW Match Score: 10 SW Mismatch Score [Prob]: -24 [1.2e-03] SW Del Open Score [Prob]: -33 [5.0e-04] SW Ins Open Score [Prob]: -33 [5.0e-04] SW Del Extend Score [Prob]: -255 [3.2e-26] SW Ins Extend Score [Prob]: -255 [1.3e-26] SW Crossover Score [Prob]: -20 [3.0e-02] Unpaired mapping options, set [0] [ regions: recompute:false anchor_list: recompute:true collapse:true use_region_counts:false use_mp_region_counts:0 hit_list: recompute:true gapless:false match_mode:1 threshold:30.00% pass1: recompute:true threshold:20.00% window_overlap:90.00% min_matches:1 gapless:false num_outputs:30 pass2: threshold:20.00% strata:false save_outputs:false num_outputs:10 stop: stop_count:0 ] note: detected fasta format in input file [/data/images/proton/DKlab/mr/parclip/raw/IGG-q20-m15.fa] - Processing read file [/data/images/proton/DKlab/mr/parclip/raw/IGG-q20-m15.fa] done r/hr r/core-hr [samopen] SAM header is present: 22 sequences. 100000 175790 8789. 200000 138373 6918. 300000 147029 7351. 400000 156832 7841. 500000 157332 7866. 600000 150236 7511. 700000 136501 6825. 800000 138937 6946. 900000 167257 8362. 1000000 149651 7482. 1100000 211618 10580. 1200000 183361 9168. 1300000 153877 7693. 1400000 151634 7581. 1500000 189276 9463. 1600000 164654 8232. 1700000 164925 8246. 1800000 145828 7291. 1900000 162892 8144. 2000000 159549 7977. 2100000 174673 8733. 2200000 141563 7078. 2300000 134497 6724. 2400000 142331 7116. 2500000 144646 7232. 2600000 149044 7452. 2700000 206144 10307. 2800000 178755 8937. 2900000 237894 11894. 3000000 239753 11987. 3100000 209752 10487. 3200000 204093 10204. 3300000 225693 11284. 3400000 232371 11618. 3500000 205307 10265. 3600000 203859 10192. 3700000 206280 10314. 3800000 205362 10268. 3900000 210290 10514. 4000000 242449 12122. 4100000 237636 11881. Statistics: Overall: Load Genome Time: 1786.00 seconds Read Mapping Time: 87019.16 seconds Reads per hour: 173,730 Reads per core-hour: 8,686 Spaced Seed Scan: Run-time: 340824.74 seconds Vector Smith-Waterman: Run-time: 1373804.84 seconds Invocations: 379,208,425,055 Bypassed Calls: 39,884,520,753 Cells Computed: 942366316.54 million Cells per Second: 685.95 million Scalar Smith-Waterman: Run-time: 18302.27 seconds Invocations: 125,617,250 Cells Computed: 109082.88 million Cells per Second: 5.96 million Forward-Backward: Run-time: 0.00 seconds Invocations: 0 Cells Computed: 0.00 million Cells per Second: 0.00 million Miscellaneous Totals: Fasta Lib Time: 23.14 seconds Read Load Time: 7448.36 seconds Wait Time: 2.98 seconds General: Reads Matched: 4,187,242 (99.7102%) ... with QV >= 10: 4,187,242 (99.7102%) Reads Dropped: 0 (0.0000%) Total Matches: 41,872,278 Avg Hits/Matched Read: 10.00 Duplicate Hits Pruned: 32,855 Memory usage: Genomemap: 0 -------------------------------------------------------------------------------- gmapper: COLOUR SPACE (AB SOLiD). SHRiMP 2.2.3 [ICC Intel(R) C++ g++ 4.1 mode; CXXFLAGS="-O3 -DNDEBUG -Kc++ -wd383,981,1572 -axP -ipo -openmp -static-intel -D__STDC_FORMAT_MACROS -D__STDC_LIMIT_MACROS -DGIT_VERSION=04238a0"] -------------------------------------------------------------------------------- note: mapping qualities are not available in local alignment mode; disabling them Loading genome from /data/results/reference/mmu/mm9/shrimp/ref/shrimp/mm9-cs.genome Loading seed from /data/results/reference/mmu/mm9/shrimp/ref/shrimp/mm9-cs.seed.0 Loading seed from /data/results/reference/mmu/mm9/shrimp/ref/shrimp/mm9-cs.seed.1 Loading seed from /data/results/reference/mmu/mm9/shrimp/ref/shrimp/mm9-cs.seed.2 Loading seed from /data/results/reference/mmu/mm9/shrimp/ref/shrimp/mm9-cs.seed.3 Loading seed from /data/results/reference/mmu/mm9/shrimp/ref/shrimp/mm9-cs.seed.4 Loading seed from /data/results/reference/mmu/mm9/shrimp/ref/shrimp/mm9-cs.seed.5 Loading seed from /data/results/reference/mmu/mm9/shrimp/ref/shrimp/mm9-cs.seed.6 Loading seed from /data/results/reference/mmu/mm9/shrimp/ref/shrimp/mm9-cs.seed.7 Loading seed from /data/results/reference/mmu/mm9/shrimp/ref/shrimp/mm9-cs.seed.8 Loading seed from /data/results/reference/mmu/mm9/shrimp/ref/shrimp/mm9-cs.seed.9 Loading seed from /data/results/reference/mmu/mm9/shrimp/ref/shrimp/mm9-cs.seed.10 Loading seed from /data/results/reference/mmu/mm9/shrimp/ref/shrimp/mm9-cs.seed.11 Loading seed from /data/results/reference/mmu/mm9/shrimp/ref/shrimp/mm9-cs.seed.12 Loading seed from /data/results/reference/mmu/mm9/shrimp/ref/shrimp/mm9-cs.seed.13 Loading seed from /data/results/reference/mmu/mm9/shrimp/ref/shrimp/mm9-cs.seed.14 Settings: Spaced Seeds (weight/span) 010111111111111 (13/15) 101011111111111 (13/15) 110101111111111 (13/15) 111010111111111 (13/15) 111101011111111 (13/15) 111110101111111 (13/15) 111111010111111 (13/15) 111111101011111 (13/15) 111111110101111 (13/15) 111111111010111 (13/15) 111111111101011 (13/15) 111111111110101 (13/15) 111111111111010 (13/15) 111111111111101 (14/15) 111111111111111 (15/15) Number of threads: 11 Thread chunk size: 1000 Window length: 150.00% Hash filter calls: yes Anchor width: 8 Indel taboo Len: 0 (disabled) Index list cutoff length: 15824 Gapless mode: no Global alignment: no Region filter: yes Region size: 2048 Region overlap: 50 Ignore QVs: no Minimum average qv: 10 Compute mapping qualities: no SW Match Score: 10 SW Mismatch Score [Prob]: -24 [1.2e-03] SW Del Open Score [Prob]: -33 [5.0e-04] SW Ins Open Score [Prob]: -33 [5.0e-04] SW Del Extend Score [Prob]: -255 [3.2e-26] SW Ins Extend Score [Prob]: -255 [1.3e-26] SW Crossover Score [Prob]: -20 [3.0e-02] Unpaired mapping options, set [0] [ regions: recompute:false anchor_list: recompute:true collapse:true use_region_counts:false use_mp_region_counts:0 hit_list: recompute:true gapless:false match_mode:1 threshold:30.00% pass1: recompute:true threshold:20.00% window_overlap:90.00% min_matches:1 gapless:false num_outputs:30 pass2: threshold:20.00% strata:false save_outputs:false num_outputs:10 stop: stop_count:0 ] note: detected fasta format in input file [/data/images/proton/DKlab/mr/parclip/raw/0hrep3-q20-m15.fa] - Processing read file [/data/images/proton/DKlab/mr/parclip/raw/0hrep3-q20-m15.fa] done r/hr r/core-hr [samopen] SAM header is present: 22 sequences. 100000 100154 9104. 200000 104755 9523. 300000 96042 8731. 400000 90419 8219. 500000 88193 8017. 600000 93905 8536. 700000 87978 7998. 800000 94066 8551. 900000 97717 8883. 1000000 98410 8946. 1100000 92169 8379. 1200000 106664 9696. 1300000 97846 8895. 1400000 100848 9168. 1500000 110550 10050. 1600000 98792 8981. 1700000 91502 8318. 1800000 90192 8199. 1900000 88412 8037. 2000000 95734 8703. 2100000 83858 7623. 2200000 94565 8596. 2300000 88579 8052. 2400000 97881 8898. 2500000 105805 9618. 2600000 88868 8078. 2700000 98477 8952. 2800000 119288 10844. 2900000 131914 11992. 3000000 145596 13236. 3100000 108075 9825. 3200000 114622 10420. 3300000 120725 10975. 3400000 100471 9133. 3500000 100160 9105. 3600000 93688 8517. 3700000 88272 8024. 3800000 92972 8452. 3900000 101176 9197. 4000000 135173 12288. 4100000 105416 9583. 4200000 106584 9689. 4300000 104270 9479. 4400000 110281 10025. 4500000 95916 8719. 4600000 99545 9049. 4700000 96081 8734. 4800000 98811 8982. 4900000 99832 9075. 5000000 90043 8185. 5100000 100026 9093. 5200000 104443 9494. 5300000 91872 8352. 5400000 109448 9949. 5500000 98103 8918. 5600000 104656 9514. 5700000 105070 9551. 5800000 108063 9823. 5900000 116956 10632. 6000000 94701 8609. 6100000 97572 8870. 6200000 92970 8451. 6300000 86003 7818. 6400000 95787 8707. 6500000 89356 8123. 6600000 90306 8209. 6700000 88902 8082. 6800000 88181 8016. 6900000 89633 8148. 7000000 91200 8290. 7100000 102105 9282. 7200000 98932 8993. 7300000 93967 8542. 7400000 104854 9532. 7500000 111299 10118. 7600000 141879 12898. 7700000 140024 12729. 7800000 108435 9857. 7900000 124820 11347. 8000000 109808 9982. 8100000 128856 11714. 8200000 154287 14026. 8300000 144667 13151. 8400000 145305 13209. 8500000 160276 14570. 8600000 136330 12393. 8700000 113027 10275. 8800000 159185 14471. 8900000 132646 12058. 9000000 136024 12365. 9100000 125080 11370. 9200000 128459 11678. 9300000 137564 12505. 9400000 136700 12427. 9500000 157889 14353. 9600000 135539 12321. 9700000 132312 12028. 9800000 120360 10941. 9900000 122969 11179. 10000000 126147 11467. 10100000 123665 11242. 10200000 124612 11328. 10300000 138222 12565. 10400000 125587 11417. 10500000 126007 11455. 10600000 130768 11888. 10700000 124374 11306. 10800000 121483 11043. 10900000 133423 12129. 11000000 143697 13063. 11100000 114644 10422. 11200000 122876 11170. 11300000 129955 11814. 11400000 128292 11662. 11500000 124457 11314. 11600000 128544 11685. 11700000 122455 11132. 11800000 157645 14331. 11900000 165707 15064. 12000000 151892 13808. 12100000 148472 13497. 12200000 135328 12302. 12300000 148762 13523. 12400000 159131 14466. 12500000 153007 13909. Statistics: Overall: Load Genome Time: 1676.36 seconds Read Mapping Time: 409556.61 seconds Reads per hour: 110,366 Reads per core-hour: 10,033 Spaced Seed Scan: Run-time: 957559.82 seconds Vector Smith-Waterman: Run-time: 3483650.18 seconds Invocations: 1,089,192,622,036 Bypassed Calls: 112,214,935,856 Cells Computed: 2634099984.11 million Cells per Second: 756.13 million Scalar Smith-Waterman: Run-time: 46322.92 seconds Invocations: 375,707,277 Cells Computed: 315606.04 million Cells per Second: 6.81 million Forward-Backward: Run-time: 0.00 seconds Invocations: 0 Cells Computed: 0.00 million Cells per Second: 0.00 million Miscellaneous Totals: Fasta Lib Time: 44.55 seconds Read Load Time: 17587.96 seconds Wait Time: 1.86 seconds General: Reads Matched: 12,523,583 (99.7422%) ... with QV >= 10: 12,523,583 (99.7422%) Reads Dropped: 0 (0.0000%) Total Matches: 125,235,523 Avg Hits/Matched Read: 10.00 Duplicate Hits Pruned: 88,904 Memory usage: Genomemap: 0 -------------------------------------------------------------------------------- gmapper: COLOUR SPACE (AB SOLiD). SHRiMP 2.2.3 [ICC Intel(R) C++ g++ 4.1 mode; CXXFLAGS="-O3 -DNDEBUG -Kc++ -wd383,981,1572 -axP -ipo -openmp -static-intel -D__STDC_FORMAT_MACROS -D__STDC_LIMIT_MACROS -DGIT_VERSION=04238a0"] -------------------------------------------------------------------------------- note: mapping qualities are not available in local alignment mode; disabling them Loading genome from /data/results/reference/mmu/mm9/shrimp/ref/shrimp/mm9-cs.genome Loading seed from /data/results/reference/mmu/mm9/shrimp/ref/shrimp/mm9-cs.seed.0 Loading seed from /data/results/reference/mmu/mm9/shrimp/ref/shrimp/mm9-cs.seed.1 Loading seed from /data/results/reference/mmu/mm9/shrimp/ref/shrimp/mm9-cs.seed.2 Loading seed from /data/results/reference/mmu/mm9/shrimp/ref/shrimp/mm9-cs.seed.3 Loading seed from /data/results/reference/mmu/mm9/shrimp/ref/shrimp/mm9-cs.seed.4 Loading seed from /data/results/reference/mmu/mm9/shrimp/ref/shrimp/mm9-cs.seed.5 Loading seed from /data/results/reference/mmu/mm9/shrimp/ref/shrimp/mm9-cs.seed.6 Loading seed from /data/results/reference/mmu/mm9/shrimp/ref/shrimp/mm9-cs.seed.7 Loading seed from /data/results/reference/mmu/mm9/shrimp/ref/shrimp/mm9-cs.seed.8 Loading seed from /data/results/reference/mmu/mm9/shrimp/ref/shrimp/mm9-cs.seed.9 Loading seed from /data/results/reference/mmu/mm9/shrimp/ref/shrimp/mm9-cs.seed.10 Loading seed from /data/results/reference/mmu/mm9/shrimp/ref/shrimp/mm9-cs.seed.11 Loading seed from /data/results/reference/mmu/mm9/shrimp/ref/shrimp/mm9-cs.seed.12 Loading seed from /data/results/reference/mmu/mm9/shrimp/ref/shrimp/mm9-cs.seed.13 Loading seed from /data/results/reference/mmu/mm9/shrimp/ref/shrimp/mm9-cs.seed.14 Settings: Spaced Seeds (weight/span) 010111111111111 (13/15) 101011111111111 (13/15) 110101111111111 (13/15) 111010111111111 (13/15) 111101011111111 (13/15) 111110101111111 (13/15) 111111010111111 (13/15) 111111101011111 (13/15) 111111110101111 (13/15) 111111111010111 (13/15) 111111111101011 (13/15) 111111111110101 (13/15) 111111111111010 (13/15) 111111111111101 (14/15) 111111111111111 (15/15) Number of threads: 20 Thread chunk size: 1000 Window length: 150.00% Hash filter calls: yes Anchor width: 8 Indel taboo Len: 0 (disabled) Index list cutoff length: 15824 Gapless mode: no Global alignment: no Region filter: yes Region size: 2048 Region overlap: 50 Ignore QVs: no Minimum average qv: 10 Compute mapping qualities: no SW Match Score: 10 SW Mismatch Score [Prob]: -24 [1.2e-03] SW Del Open Score [Prob]: -33 [5.0e-04] SW Ins Open Score [Prob]: -33 [5.0e-04] SW Del Extend Score [Prob]: -255 [3.2e-26] SW Ins Extend Score [Prob]: -255 [1.3e-26] SW Crossover Score [Prob]: -20 [3.0e-02] Unpaired mapping options, set [0] [ regions: recompute:false anchor_list: recompute:true collapse:true use_region_counts:false use_mp_region_counts:0 hit_list: recompute:true gapless:false match_mode:1 threshold:30.00% pass1: recompute:true threshold:20.00% window_overlap:90.00% min_matches:1 gapless:false num_outputs:30 pass2: threshold:20.00% strata:false save_outputs:false num_outputs:10 stop: stop_count:0 ] error: Syscall stat failed on file "/data/images/proton/DKlab/mr/parclip/raw/IFN-q20-m15.fa"! error: failed to open read file [/data/images/proton/DKlab/mr/parclip/raw/IFN-q20-m15.fa]: No such file or directory [samopen] no @SQ lines in the header. [sam_read1] missing header? Abort!