Starting /dee2/code/volunteer_pipeline.sh SRR12682226 current disk space = 1547657068544 free memory = 1603730232 SRR12682226 SRAfilesize 4a976aa38d3ae1dc2a24823c02bda51e SRR12682226.sra SRR12682226.sra file validated SRR12682226 is single end SRR12682226 is conventional basespace SRR12682226 read1 length is 40-150 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12682226_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 40-150 %GC 52 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 31.4475 32.0 32.0 32.0 32.0 32.0 2 31.462 32.0 32.0 32.0 32.0 32.0 3 31.46775 32.0 32.0 32.0 32.0 32.0 4 31.5175 32.0 32.0 32.0 32.0 32.0 5 31.584 32.0 32.0 32.0 32.0 32.0 6 34.75475 36.0 36.0 36.0 32.0 36.0 7 35.07975 36.0 36.0 36.0 36.0 36.0 8 35.028 36.0 36.0 36.0 36.0 36.0 9 34.963 36.0 36.0 36.0 36.0 36.0 10-14 35.0204 36.0 36.0 36.0 35.2 36.0 15-19 34.94565 36.0 36.0 36.0 34.4 36.0 20-24 34.87835 36.0 36.0 36.0 34.4 36.0 25-29 34.68055 36.0 36.0 36.0 32.0 36.0 30-34 34.6909 36.0 36.0 36.0 32.0 36.0 35-39 34.64790000000001 36.0 36.0 36.0 32.0 36.0 40-44 34.53898101020738 36.0 36.0 36.0 32.0 36.0 45-49 34.34639310786547 36.0 36.0 36.0 32.0 36.0 50-54 34.329474787901496 36.0 36.0 36.0 32.0 36.0 55-59 34.21203058836289 36.0 36.0 36.0 32.0 36.0 60-64 34.015711273037596 36.0 36.0 36.0 32.0 36.0 65-69 33.93351683189708 36.0 36.0 36.0 29.0 36.0 70-74 33.94789737872869 36.0 36.0 36.0 29.0 36.0 75-79 33.82914209776404 36.0 36.0 36.0 29.0 36.0 80-84 33.817655820609836 36.0 36.0 36.0 28.0 36.0 85-89 33.65759236519328 36.0 36.0 36.0 27.0 36.0 90-94 33.597874150603644 36.0 36.0 36.0 27.0 36.0 95-99 33.47755377646903 36.0 36.0 36.0 27.0 36.0 100-104 33.47678515237645 36.0 36.0 36.0 27.0 36.0 105-109 33.175048780014265 36.0 32.8 36.0 27.0 36.0 110-114 33.0388421180964 36.0 32.0 36.0 27.0 36.0 115-119 32.67682649627152 36.0 32.0 36.0 27.0 36.0 120-124 32.02554993627924 34.4 32.0 36.0 23.4 36.0 125-129 31.898832318860478 33.6 32.0 36.0 23.4 36.0 130-134 31.439327294380455 32.0 32.0 36.0 21.0 36.0 135-139 31.483632454695385 32.8 32.0 36.0 21.0 36.0 140-144 31.628727096778277 35.2 32.0 36.0 21.0 36.0 145-149 31.448497882021123 32.8 32.0 36.0 21.0 36.0 150 26.257677902621722 27.0 14.0 32.0 14.0 36.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 17 1.0 18 3.0 19 2.0 20 2.0 21 5.0 22 8.0 23 12.0 24 11.0 25 38.0 26 61.0 27 77.0 28 85.0 29 99.0 30 145.0 31 177.0 32 249.0 33 409.0 34 935.0 35 1681.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 29.525000000000002 10.4 8.649999999999999 51.425 2 22.675 13.975000000000001 31.624999999999996 31.724999999999998 3 21.0 15.85 20.200000000000003 42.95 4 27.875 22.825 17.599999999999998 31.7 5 26.924999999999997 27.675 21.349999999999998 24.05 6 23.91851106639839 31.136820925553323 22.962776659959758 21.98189134808853 7 18.625 22.525000000000002 37.675 21.175 8 19.775000000000002 20.4 29.525000000000002 30.3 9 20.3 19.950000000000003 33.225 26.525 10-14 22.88 25.135 24.895 27.089999999999996 15-19 23.655 23.630000000000003 25.380000000000003 27.334999999999997 20-24 24.635 23.72 24.665 26.979999999999997 25-29 23.965 23.615 24.11 28.310000000000002 30-34 23.625 23.330000000000002 25.06 27.985 35-39 23.925 23.695 24.635 27.744999999999997 40-44 24.55473283970382 23.454072443466078 24.109465679407645 27.881729037422453 45-49 24.644573488185824 23.51822186623949 24.264116940328396 27.573087705246298 50-54 23.2860934448395 23.656667835144475 24.943662677149582 28.113576042866445 55-59 24.117882919005613 23.336006415396955 25.0 27.546110665597435 60-64 23.9375846671015 22.402287893231648 25.678591139431038 27.981536300235817 65-69 23.601486391483377 23.01396002812092 25.479562117103544 27.904991463292156 70-74 24.127160058441234 23.280769812081214 25.215376089475537 27.376694040002015 75-79 24.710463763718202 23.613007636676276 23.901279522581298 27.77524907702422 80-84 24.426121036290528 22.67012775487352 24.13600040718685 28.767750801649107 85-89 24.06711616655515 23.145812960008236 24.242112306346183 28.544958567090433 90-94 24.136673785092974 22.829314026772227 24.813792385020054 28.220219803114745 95-99 22.93057763645999 23.683094859565447 25.246422893481718 28.139904610492845 100-104 24.169480448752857 23.14018080819083 23.918963075917656 28.771375667138656 105-109 24.026010743567998 23.160870794458578 24.828951088493074 27.98416737348035 110-114 25.09465215333649 22.929484145764317 24.597728348319926 27.37813535257927 115-119 24.670621292538243 23.103340618170463 25.22010615048392 27.00593193880737 120-124 25.382059800664454 23.036544850498338 23.993355481727573 27.588039867109636 125-129 24.91663710535651 23.206810925860232 22.937211777225965 28.93934019155729 130-134 25.689760882893932 22.0570202329859 24.01900674432863 28.234212139791538 135-139 24.88822652757079 23.174366616989566 24.225865209471767 27.711541645967873 140-144 25.64859545535874 23.42100554660941 23.295759527643586 27.63463947038826 145-149 25.993459518382718 22.059260727380835 24.041224853830144 27.906054900406303 150 26.06741573033708 0.0 34.6816479400749 39.250936329588015 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 0.0 1 0.0 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10 0.0 11 0.0 12 0.0 13 0.0 14 0.0 15 0.0 16 0.0 17 0.0 18 0.5 19 0.5 20 0.0 21 0.5 22 0.5 23 0.0 24 0.0 25 0.5 26 1.5 27 1.5 28 1.0 29 1.0 30 1.5 31 1.5 32 3.5 33 7.5 34 12.5 35 22.0 36 45.5 37 52.5 38 44.5 39 61.5 40 75.0 41 84.5 42 98.0 43 110.5 44 117.0 45 133.5 46 155.0 47 171.5 48 187.0 49 196.5 50 206.0 51 212.0 52 193.5 53 166.0 54 156.5 55 165.0 56 168.0 57 140.0 58 120.0 59 105.0 60 91.0 61 84.0 62 69.5 63 69.0 64 67.0 65 54.5 66 47.0 67 46.5 68 53.0 69 47.0 70 47.0 71 41.0 72 27.0 73 20.5 74 13.0 75 15.5 76 14.5 77 10.0 78 9.0 79 3.5 80 1.0 81 1.0 82 0.0 83 0.0 84 0.0 85 0.0 86 0.0 87 0.0 88 0.0 89 0.0 90 0.0 91 0.0 92 0.0 93 0.0 94 0.0 95 0.0 96 0.0 97 0.5 98 0.5 99 0.0 100 0.0 >>END_MODULE >>Per base N content pass #Base N-Count 1 0.0 2 0.0 3 0.0 4 0.0 5 0.0 6 0.6 7 0.0 8 0.0 9 0.0 10-14 0.0 15-19 0.0 20-24 0.0 25-29 0.0 30-34 0.0 35-39 0.0 40-44 0.005002751513332333 45-49 0.02002002002002002 50-54 0.01001452105553052 55-59 0.030063132578414673 60-64 0.04012237323837705 65-69 0.025101661730006525 70-74 0.030219088390833544 75-79 0.010113780025284451 80-84 0.020355198208742556 85-89 0.025728105382319642 90-94 0.03644694366343851 95-99 0.05296610169491525 100-104 0.043549265106151334 105-109 0.045215621997400104 110-114 0.017744129650440643 115-119 0.031210986267166042 120-124 0.013287270794578792 125-129 0.04963834917033045 130-134 0.01532567049808429 135-139 0.016556291390728478 140-144 0.017889087656529516 145-149 0.0396235760277365 150 0.0 >>END_MODULE >>Sequence Length Distribution warn #Length Count 40-44 3.0 45-49 2.0 50-54 3.0 55-59 3.0 60-64 4.0 65-69 7.0 70-74 15.0 75-79 21.0 80-84 35.0 85-89 45.0 90-94 50.0 95-99 91.0 100-104 122.0 105-109 160.0 110-114 163.0 115-119 189.0 120-124 195.0 125-129 207.0 130-134 197.0 135-139 183.0 140-144 172.0 145-149 798.0 150-151 1335.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 81.89999999999999 #Duplication Level Percentage of deduplicated Percentage of total 1 89.1941391941392 73.05 2 5.616605616605617 9.2 3 2.6862026862026864 6.6000000000000005 4 1.0683760683760684 3.5000000000000004 5 0.4884004884004884 2.0 6 0.3968253968253968 1.95 7 0.2442002442002442 1.4000000000000001 8 0.09157509157509157 0.6 9 0.1221001221001221 0.8999999999999999 >10 0.09157509157509157 0.8 >50 0.0 0.0 >100 0.0 0.0 >500 0.0 0.0 >1k 0.0 0.0 >5k 0.0 0.0 >10k+ 0.0 0.0 >>END_MODULE >>Overrepresented sequences warn #Sequence Count Percentage Possible Source CCCGACTGTCCCTATTAATCATTACTCCGATCCCGAAGGCCAACACAATA 12 0.3 No Hit CCCGTGTCAGGATTGGGTAATTTGCGCGCCTGCTGCCTTCCTTGGATGTG 10 0.25 No Hit CCGACATCGAAGGATCAAAAAGCAACGTCGCTATGAACGCTTGGCTGCCA 10 0.25 No Hit CTTCCGTCAATTCCTTTAAGTTTCAGCCTTGCGACCATACTCCCCCCGGA 9 0.22499999999999998 No Hit GTCGGCATCGTTTATGGTTGAGACTAGGACGGTATCTGATCGTCTTCGAG 9 0.22499999999999998 No Hit CTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATT 9 0.22499999999999998 No Hit CCTCGCGGTACTTGTTCGCTATCGGTCTCTCGCCTGTATTTAGCCTTGGA 9 0.22499999999999998 No Hit CTTGTTACGACTTCTCCTTCCTCTAAATGATAAGGTTCAATGGACTTCTC 8 0.2 No Hit CTAGAATTACTACGGTTATCCGAGTAGCACGTACCATCAAACAAACTATA 8 0.2 No Hit CTCAAACTTCCGTCGCCTAAACGGCGATAGTCCCTCTAAGAAGCTAGCTG 8 0.2 No Hit CCTAATTCTCCGTCACCCGTCACCACCATGGTAGGCCCCTATCCTACCAT 7 0.17500000000000002 No Hit GGCAGAAATTTGAATGATGCGTCGCCGGCACGAGGGCCGTGCGATCCGTC 7 0.17500000000000002 No Hit CTCAGAGCCAATCCTTTTCCCGAAGTTACGGATCCGTTTTGCCGACTTCC 7 0.17500000000000002 No Hit CCCGAAGTTACGGATCCGTTTTGCCGACTTCCCTTGCCTACATTGTTCCA 7 0.17500000000000002 No Hit CTTTTATCTAATAAATGCGCCCCTCCCAGAAGTCGGGGTTTGTTGCACGT 7 0.17500000000000002 No Hit GTCGGGGCAGGCGGCGGGCGCAGGCGCCGCTTGCTAGCTTGGATTCTGAC 7 0.17500000000000002 No Hit CCCATCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCT 7 0.17500000000000002 No Hit CGGCATCGTTTATGGTTGAGACTAGGACGGTATCTGATCGTCTTCGAGCC 7 0.17500000000000002 No Hit GTCACTACCTCCCCGTGTCAGGATTGGGTAATTTGCGCGCCTGCTGCCTT 6 0.15 No Hit CTGACTATGAAATACGAATGCCCCCGACTGTCCCTATTAATCATTACTCC 6 0.15 No Hit CCCGGAACCCAAAGACTTTGATTTCTCATAAGGTGCCGGCGGAGTCCTAT 6 0.15 No Hit GCACGTACCATCAAACAAACTATAACTGATTTAATGAGCCATTCGCAGTT 6 0.15 No Hit CCACGCTTTCACGGTTCGTATTCGTACTGGAAATCAGAATCAAACGAGCT 6 0.15 No Hit CTGCAAAGGATTCAGCCCGCCGCCCGTGGGGAAGGGAGCTTCGAGGCGGC 6 0.15 No Hit CCTCTAAGAAGCTAGCTGCGGAGGGATGGCTCCGCATAGCTAGTTAGCAG 6 0.15 No Hit CCCAACTTTCGTTCTTGATTAATGAAAACATCCTTGGCAAATGCTTTCGC 6 0.15 No Hit CTTTTGTTCCACACGAGATTTCTGTTCTCGTTGAGCTCATCTTAGGACAC 6 0.15 No Hit CCCCCATCCGCTTCCCTCCCGGCAATTTCAAGCACTCTTTGACTCTCTTT 6 0.15 No Hit GCCACGCTTTCACGGTTCGTATTCGTACTGGAAATCAGAATCAAACGAGC 6 0.15 No Hit CCCACTTATCCTACACCTCTCAAGTCATTTCACAAAGTCGGACTAGAGTC 6 0.15 No Hit CTATTAATCATTACTCCGATCCCGAAGGCCAACACAATAGGACCGGAATC 6 0.15 No Hit GCTTTACCTGATAGAACTCGTAATGGGCTCCAGCTATCCTGAGGGAAACT 5 0.125 No Hit CCGCCGTTTACCCGCGCTTGGTTGAATTTCTTCACTTTGACATTCAGAGC 5 0.125 No Hit GCCCAGTCCTCAGAGCCAATCCTTTTCCCGAAGTTACGGATCCGTTTTGC 5 0.125 No Hit CGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACT 5 0.125 No Hit CGCTATTGGAGCTGGAATTACCGCGGCTGCTGGCACCAGACTTGCCCTCC 5 0.125 No Hit CCGAAGGCCAACACAATAGGACCGGAATCCTATGATGTTATCCCATGCTA 5 0.125 No Hit CTCTGACTATGAAATACGAATGCCCCCGACTGTCCCTATTAATCATTACT 5 0.125 No Hit CCCTAATTCTCCGTCACCCGTCACCACCATGGTAGGCCCCTATCCTACCA 5 0.125 No Hit GCATCGTTTATGGTTGAGACTAGGACGGTATCTGATCGTCTTCGAGCCCC 5 0.125 No Hit CCCATGCTAATGTATCCAGAGCGATGGCTTGCTTTGAGCACTCTAATTTC 5 0.125 No Hit CGAAGATCTAAAGGATCGATAGGCCACGCTTTCACGGTTCGTATTCGTAC 5 0.125 No Hit ATCCAGAGCGATGGCTTGCTTTGAGCACTCTAATTTCTTCAAAGTAACGA 5 0.125 No Hit CCGCAGGCTCCACGCCTGGTGGTGCCCTTCCGTCAATTCCTTTAAGTTTC 5 0.125 No Hit ATCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCTATA 5 0.125 No Hit GTCCCGACAGGCGTGCTCCAACTCGAACCCTTCACAGAAGATCAGGGTCG 5 0.125 No Hit GTTCAGTCATAATCCGGCACACGGTAGCTTCGCGCCACTGGCTTTTCAAC 5 0.125 No Hit >>END_MODULE >>Adapter Content pass #Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence SOLID Small RNA Adapter 1 0.0 0.0 0.0 0.0 0.0 2 0.0 0.0 0.0 0.0 0.0 3 0.0 0.0 0.0 0.0 0.0 4 0.0 0.0 0.0 0.0 0.0 5 0.0 0.0 0.0 0.0 0.0 6 0.0 0.0 0.0 0.0 0.0 7 0.0 0.0 0.0 0.0 0.0 8 0.0 0.0 0.0 0.0 0.0 9 0.0 0.0 0.0 0.0 0.0 10-11 0.0 0.0 0.0 0.0 0.0 12-13 0.0 0.0 0.0 0.0 0.0 14-15 0.0 0.0 0.0 0.0 0.0 16-17 0.0 0.0 0.0 0.0 0.0 18-19 0.0 0.0 0.0 0.0 0.0 20-21 0.0 0.0 0.0 0.0 0.0 22-23 0.0 0.0 0.0 0.0 0.0 24-25 0.0 0.0 0.0 0.0 0.0 26-27 0.0 0.0 0.0 0.0 0.0 28-29 0.0 0.0 0.0 0.0 0.0 30-31 0.0 0.0 0.0 0.0 0.0 32-33 0.0 0.0 0.0 0.0 0.0 34-35 0.0 0.0 0.0 0.0 0.0 36-37 0.0 0.0 0.0 0.0 0.0 38-39 0.0 0.0 0.0 0.0 0.0 40-41 0.0 0.0 0.0 0.0 0.0 42-43 0.0 0.0 0.0 0.0 0.0 44-45 0.0 0.0 0.0 0.0 0.0 46-47 0.0 0.0 0.0 0.0 0.0 48-49 0.0 0.0 0.0 0.0 0.0 50-51 0.0 0.0 0.0 0.0 0.0 52-53 0.0 0.0 0.0 0.0 0.0 54-55 0.0 0.0 0.0 0.0 0.0 56-57 0.0 0.0 0.0 0.0 0.0 58-59 0.0 0.0 0.0 0.0 0.0 60-61 0.0 0.0 0.0 0.0 0.0 62-63 0.0 0.0 0.0 0.0 0.0 64-65 0.0 0.0 0.0 0.0 0.0 66-67 0.0 0.0 0.0 0.0 0.0 68-69 0.0 0.0 0.0 0.0 0.0 70-71 0.0 0.0 0.0 0.0 0.0 72-73 0.0 0.0 0.0 0.0 0.0 74-75 0.0 0.0 0.0 0.0 0.0 76-77 0.0 0.0 0.0 0.0 0.0 78-79 0.0 0.0 0.0 0.0 0.0 80-81 0.0 0.0 0.0 0.0 0.0 82-83 0.0 0.0 0.0 0.0 0.0 84-85 0.0 0.0 0.0 0.0 0.0 86-87 0.0 0.0 0.0 0.0 0.0 88-89 0.0 0.0 0.0 0.0 0.0 90-91 0.0 0.0 0.0 0.0 0.0 92-93 0.0 0.0 0.0 0.0 0.0 94-95 0.0 0.0 0.0 0.0 0.0 96-97 0.0 0.0 0.0 0.0 0.0 98-99 0.0125 0.0 0.0 0.0 0.0 100-101 0.025 0.0 0.0 0.0 0.0 102-103 0.025 0.0 0.0 0.0 0.0 104-105 0.025 0.0 0.0 0.0 0.0 106-107 0.025 0.0 0.0 0.0 0.0 108-109 0.025 0.0 0.0 0.0 0.0 110-111 0.025 0.0 0.0 0.0 0.0 112-113 0.025 0.0 0.0 0.0 0.0 114-115 0.025 0.0 0.0 0.0 0.0 116-117 0.025 0.0 0.0 0.0 0.0 118-119 0.037500000000000006 0.0 0.0 0.0 0.0 120-121 0.0625 0.0 0.0 0.0 0.0 122-123 0.075 0.0 0.0 0.0 0.0 124-125 0.075 0.0 0.0 0.0 0.0 126-127 0.075 0.0 0.0 0.0 0.0 128-129 0.075 0.0 0.0 0.0 0.0 130-131 0.075 0.0 0.0 0.0 0.0 132-133 0.075 0.0 0.0 0.0 0.0 134-135 0.075 0.0 0.0 0.0 0.0 136-137 0.075 0.0 0.0 0.0 0.0 138 0.075 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Rejected 1412724 READS because READLEN < 1 Read 1412724 spots for SRR12682226.sra Written 1412724 spots for SRR12682226.sra Rejected 1412724 READS because READLEN < 1 Read 1412724 spots for SRR12682226.sra Written 1412724 spots for SRR12682226.sra Rejected 1412724 READS because READLEN < 1 Read 1412724 spots for SRR12682226.sra Written 1412724 spots for SRR12682226.sra Rejected 1412724 READS because READLEN < 1 Read 1412724 spots for SRR12682226.sra Written 1412724 spots for SRR12682226.sra Rejected 1412724 READS because READLEN < 1 Read 1412724 spots for SRR12682226.sra Written 1412724 spots for SRR12682226.sra Rejected 1412742 READS because READLEN < 1 Read 1412742 spots for SRR12682226.sra Written 1412742 spots for SRR12682226.sra Rejected 1412724 READS because READLEN < 1 Read 1412724 spots for SRR12682226.sra Written 1412724 spots for SRR12682226.sra Rejected 1412724 READS because READLEN < 1 Read 1412724 spots for SRR12682226.sra Written 1412724 spots for SRR12682226.sra Rejected 1412724 READS because READLEN < 1 Read 1412724 spots for SRR12682226.sra Written 1412724 spots for SRR12682226.sra Rejected 1412724 READS because READLEN < 1 Read 1412724 spots for SRR12682226.sra Written 1412724 spots for SRR12682226.sra Rejected 1412724 READS because READLEN < 1 Read 1412724 spots for SRR12682226.sra Written 1412724 spots for SRR12682226.sra Rejected 1412724 READS because READLEN < 1 Read 1412724 spots for SRR12682226.sra Written 1412724 spots for SRR12682226.sra Rejected 1412724 READS because READLEN < 1 Read 1412724 spots for SRR12682226.sra Written 1412724 spots for SRR12682226.sra Rejected 1412724 READS because READLEN < 1 Read 1412724 spots for SRR12682226.sra Written 1412724 spots for SRR12682226.sra Rejected 1412724 READS because READLEN < 1 Read 1412724 spots for SRR12682226.sra Written 1412724 spots for SRR12682226.sra Rejected 1412724 READS because READLEN < 1 Read 1412724 spots for SRR12682226.sra Written 1412724 spots for SRR12682226.sra Rejected 1412724 READS because READLEN < 1 Read 1412724 spots for SRR12682226.sra Written 1412724 spots for SRR12682226.sra Rejected 1412724 READS because READLEN < 1 Read 1412724 spots for SRR12682226.sra Written 1412724 spots for SRR12682226.sra Rejected 1412724 READS because READLEN < 1 Read 1412724 spots for SRR12682226.sra Written 1412724 spots for SRR12682226.sra Rejected 1412724 READS because READLEN < 1 Read 1412724 spots for SRR12682226.sra Written 1412724 spots for SRR12682226.sra SRR ids: ['SRR12682226.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_l4p5th6g SRR12682226.sra spots: 28254498 blocks: [[1, 1412724], [1412725, 2825448], [2825449, 4238172], [4238173, 5650896], [5650897, 7063620], [7063621, 8476344], [8476345, 9889068], [9889069, 11301792], [11301793, 12714516], [12714517, 14127240], [14127241, 15539964], [15539965, 16952688], [16952689, 18365412], [18365413, 19778136], [19778137, 21190860], [21190861, 22603584], [22603585, 24016308], [24016309, 25429032], [25429033, 26841756], [26841757, 28254498]] SRR12682226 file size 8632433 SRR12682226 completed basic pipeline successfully skewer v0.2.2 [April 4, 2016] COMMAND LINE: skewer -f sanger -l 18 -q 10 -k inf -t 20 -o SRR12682226 SRR12682226_1.fastq Input file: SRR12682226_1.fastq trimmed: SRR12682226-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -- maximum error ratio allowed (-r): 0.100 -- maximum indel error ratio allowed (-d): 0.030 -- end quality threshold (-q): 10 -- minimum read length allowed after trimming (-l): 18 -- file format (-f): Sanger/Illumina 1.8+ FASTQ -- minimum overlap length for adapter detection (-k): inf -- number of concurrent threads (-t): 20 Sat Dec 7 03:18:13 2024 >> started Sat Dec 7 03:18:29 2024 >> done (15.554s) 28254498 reads processed; of these: 7 ( 0.00%) short reads filtered out after trimming by size control 6460 ( 0.02%) empty reads filtered out after trimming by size control 28248031 (99.98%) reads available; of these: 19571 ( 0.07%) trimmed reads available after processing 28228460 (99.93%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 1 0.00% 19 0 0.00% 20 0 0.00% 21 0 0.00% 22 16 0.00% 23 34 0.00% 24 48 0.00% 25 57 0.00% 26 112 0.00% 27 139 0.00% 28 204 0.00% 29 226 0.00% 30 256 0.00% 31 292 0.00% 32 305 0.00% 33 364 0.00% 34 437 0.00% 35 554 0.00% 36 632 0.00% 37 716 0.00% 38 992 0.00% 39 1222 0.00% 40 1295 0.00% 41 1575 0.01% 42 1537 0.01% 43 1544 0.01% 44 1635 0.01% 45 1763 0.01% 46 2005 0.01% 47 2329 0.01% 48 2843 0.01% 49 3444 0.01% 50 3853 0.01% 51 4291 0.02% 52 4648 0.02% 53 4598 0.02% 54 4686 0.02% 55 5145 0.02% 56 5457 0.02% 57 6228 0.02% 58 7303 0.03% 59 8073 0.03% 60 8920 0.03% 61 9887 0.04% 62 10690 0.04% 63 11318 0.04% 64 11838 0.04% 65 12391 0.04% 66 13649 0.05% 67 14877 0.05% 68 16067 0.06% 69 17104 0.06% 70 18264 0.06% 71 21334 0.08% 72 23019 0.08% 73 25528 0.09% 74 26677 0.09% 75 28181 0.10% 76 31106 0.11% 77 32450 0.11% 78 34453 0.12% 79 38857 0.14% 80 41407 0.15% 81 44587 0.16% 82 48841 0.17% 83 51261 0.18% 84 55888 0.20% 85 63334 0.22% 86 70590 0.25% 87 73063 0.26% 88 78176 0.28% 89 81217 0.29% 90 86590 0.31% 91 90172 0.32% 92 101078 0.36% 93 108470 0.38% 94 111870 0.40% 95 122841 0.43% 96 132384 0.47% 97 136679 0.48% 98 152002 0.54% 99 153263 0.54% 100 156344 0.55% 101 160710 0.57% 102 170006 0.60% 103 180238 0.64% 104 188293 0.67% 105 189165 0.67% 106 196489 0.70% 107 209756 0.74% 108 201161 0.71% 109 217870 0.77% 110 218039 0.77% 111 229806 0.81% 112 245908 0.87% 113 240484 0.85% 114 254399 0.90% 115 268201 0.95% 116 271861 0.96% 117 261316 0.93% 118 259865 0.92% 119 272725 0.97% 120 285550 1.01% 121 274298 0.97% 122 295062 1.04% 123 301835 1.07% 124 290827 1.03% 125 287703 1.02% 126 293586 1.04% 127 283860 1.00% 128 287076 1.02% 129 301777 1.07% 130 290105 1.03% 131 286984 1.02% 132 286943 1.02% 133 289531 1.02% 134 280295 0.99% 135 282159 1.00% 136 287587 1.02% 137 285320 1.01% 138 271482 0.96% 139 277783 0.98% 140 270119 0.96% 141 261370 0.93% 142 257011 0.91% 143 254571 0.90% 144 263271 0.93% 145 249969 0.88% 146 297176 1.05% 147 462840 1.64% 148 991587 3.51% 149 3187558 11.28% 150 9328978 33.03% 28248031 reads passed initial QC criterion=sequence-density sequence-density=0.61 sequence-density-rank=1 fanout-score=2.73 fanout-score-rank=33 prefix-density=1.66 prefix-fanout=1.0 sequence=CTTGGATGTGGCAGCCGTTTCTC criterion=fanout-score sequence-density=0.03 sequence-density-rank=37 fanout-score=55.67 fanout-score-rank=1 prefix-density=1.40 prefix-fanout=1.1 sequence=CAAACTCCCCAGTGCAGAGAGCTTGATCAAATGTACCAATTACACACACAGACACACAGATACATACATACTCACAAGGAAGGATACACCAATTAAGAGCAAGTAAACAACAACACAATCACACCACACGCTCTGACTCGGCGCTTATTTACTAACCACAAGTTCATCATGATTAATGGACTAACAGTTACAAGGGTTGCACTTGCAGTTGTCGCCGCAGCTGCACCCTTCGCCGGACACGCCGGCCATCTCGAACTGCTCCTGTTTCTTCTC Started job on | Dec 07 03:18:50 Started mapping on | Dec 07 03:19:00 Finished on | Dec 07 03:20:23 Mapping speed, Million of reads per hour | 1225.22 Number of input reads | 28248031 Average input read length | 133 UNIQUE READS: Uniquely mapped reads number | 12696341 Uniquely mapped reads % | 44.95% Average mapped length | 133.80 Number of splices: Total | 4898323 Number of splices: Annotated (sjdb) | 4615056 Number of splices: GT/AG | 4832658 Number of splices: GC/AG | 58554 Number of splices: AT/AC | 3438 Number of splices: Non-canonical | 3673 Mismatch rate per base, % | 0.25% Deletion rate per base | 0.01% Deletion average length | 1.61 Insertion rate per base | 0.00% Insertion average length | 1.12 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 1279508 % of reads mapped to multiple loci | 4.53% Number of reads mapped to too many loci | 12025637 % of reads mapped to too many loci | 42.57% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.97% % of reads unmapped: other | 5.98% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 14272182 14272182 14272182 N_multimapping 1279508 1279508 1279508 N_noFeature 711335 12367042 822215 N_ambiguous 258354 1267 41027 UnstrandedReadsAssigned:11726652 PositiveStrandReadsAssigned:328032 NegativeStrandReadsAssigned:11833099 Dataset is classified negative stranded MeadianReadLen=146 20thPercentileLength=116 echo kmer=111 SRR12682226 Starting Kallisto single end mapping to ensembl reference transcriptome. kmer=31 [quant] fragment length distribution is truncated gaussian with mean = 100, sd = 20 [index] k-mer length: 31 [index] number of targets: 52,972 [index] number of k-mers: 66,720,672 [index] number of equivalence classes: 111,837 [quant] running in single-end mode [quant] will process file 1: SRR12682226-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 28,248,031 reads, 12,140,344 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,092 rounds 52973 SRR12682226.ke.tsv 35125 SRR12682226.se.tsv 88098 total ==> SRR12682226.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 837 59.5055 8.85864 PNS24247 1044 945 20.2633 2.67185 PNS24249 1928 1829 122.027 8.31337 PNS24246 1044 945 20.2633 2.67185 PNS24248 1044 945 20.2633 2.67185 PNS24244 1471 1372 99.6778 9.05273 PNS24243 293 194 0 0 KQK14069 1603 1504 6470.71 536.092 KQK14071 474 375 544.334 180.871 ==> SRR12682226.se.tsv <== BRADI_1g14170v3 7662 BRADI_1g53295v3 63 BRADI_1g59795v3 242 BRADI_1g07683v3 0 BRADI_1g00485v3 8 BRADI_1g20270v3 652 BRADI_1g74790v3 400 BRADI_1g09890v3 0 BRADI_1g77505v3 133 BRADI_1g48960v3 0 SRR12682226 completed mapping pipeline successfully