Starting /dee2/code/volunteer_pipeline.sh SRR12682224 current disk space = 1547644407808 free memory = 1600648944 SRR12682224 SRAfilesize 919cba1b407222d5a883f06afa687f45 SRR12682224.sra SRR12682224.sra file validated SRR12682224 is single end SRR12682224 is conventional basespace SRR12682224 read1 length is 35-150 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12682224_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 35-150 %GC 51 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 31.45 32.0 32.0 32.0 32.0 32.0 2 31.52275 32.0 32.0 32.0 32.0 32.0 3 31.582 32.0 32.0 32.0 32.0 32.0 4 31.599 32.0 32.0 32.0 32.0 32.0 5 31.65425 32.0 32.0 32.0 32.0 32.0 6 34.917 36.0 36.0 36.0 36.0 36.0 7 35.24775 36.0 36.0 36.0 36.0 36.0 8 35.06225 36.0 36.0 36.0 36.0 36.0 9 35.2055 36.0 36.0 36.0 36.0 36.0 10-14 35.1536 36.0 36.0 36.0 36.0 36.0 15-19 35.0977 36.0 36.0 36.0 36.0 36.0 20-24 35.02625 36.0 36.0 36.0 35.2 36.0 25-29 34.87525 36.0 36.0 36.0 35.2 36.0 30-34 34.877300000000005 36.0 36.0 36.0 34.4 36.0 35-39 34.84724855147003 36.0 36.0 36.0 34.4 36.0 40-44 34.82161621215912 36.0 36.0 36.0 35.2 36.0 45-49 34.650467768243594 36.0 36.0 36.0 32.8 36.0 50-54 34.644394394394396 36.0 36.0 36.0 32.8 36.0 55-59 34.475493202839885 36.0 36.0 36.0 32.0 36.0 60-64 34.29268083694192 36.0 36.0 36.0 32.0 36.0 65-69 34.2248611039949 36.0 36.0 36.0 32.0 36.0 70-74 34.22863801107221 36.0 36.0 36.0 32.0 36.0 75-79 34.14450594397364 36.0 36.0 36.0 32.0 36.0 80-84 34.06695161055866 36.0 36.0 36.0 32.0 36.0 85-89 33.96512225176775 36.0 36.0 36.0 31.0 36.0 90-94 33.95794203120388 36.0 36.0 36.0 32.0 36.0 95-99 33.89225689995134 36.0 36.0 36.0 29.0 36.0 100-104 33.77387358230824 36.0 36.0 36.0 28.0 36.0 105-109 33.4298203478604 36.0 32.8 36.0 27.0 36.0 110-114 33.31766590033435 36.0 32.8 36.0 27.0 36.0 115-119 32.96735441937504 36.0 32.0 36.0 27.0 36.0 120-124 32.42485329854697 34.4 32.0 36.0 25.8 36.0 125-129 32.242286433522295 34.4 32.0 36.0 24.6 36.0 130-134 31.746397555815786 33.6 32.0 36.0 22.2 36.0 135-139 31.783047344217515 33.6 32.0 36.0 22.2 36.0 140-144 31.869671919418845 35.2 32.0 36.0 21.0 36.0 145-149 31.58935063146459 32.0 32.0 36.0 21.0 36.0 150 26.27289156626506 27.0 14.0 32.0 14.0 36.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 1.0 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 1.0 18 0.0 19 2.0 20 2.0 21 3.0 22 8.0 23 11.0 24 17.0 25 36.0 26 36.0 27 47.0 28 74.0 29 87.0 30 139.0 31 177.0 32 219.0 33 364.0 34 944.0 35 1832.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 31.407851962990748 9.377344336084022 7.95198799699925 51.26281570392598 2 22.05551387846962 14.378594648662165 33.80845211302826 29.75743935983996 3 22.18054513628407 15.353838459614904 21.155288822205552 41.31032758189547 4 27.631907976994246 24.281070267566893 17.60440110027507 30.48262065516379 5 25.906476619154787 28.257064266066518 22.58064516129032 23.25581395348837 6 21.547379032258064 30.065524193548388 25.05040322580645 23.336693548387096 7 17.20430107526882 22.755688922230558 38.284571142785694 21.75543885971493 8 20.40510127531883 19.779944986246562 30.55763940985246 29.257314328582147 9 19.204801200300075 21.205301325331334 32.733183295823956 26.85671417854464 10-14 22.875718929732432 25.496374093523382 24.971242810702677 26.65666416604151 15-19 23.01575393848462 24.33108277069267 26.246561640410103 26.406601650412604 20-24 23.775943985996502 25.121280320080018 24.896224056014006 26.206551637909474 25-29 23.400850212553138 24.276069017254315 24.691172793198298 27.631907976994246 30-34 23.20080020005001 23.460865216304075 25.0112528132033 28.327081770442607 35-39 23.684473789515806 24.56482593037215 24.93497398959584 26.815726290516206 40-44 23.472604453340004 24.513385038779084 24.808606454841133 27.20540405303978 45-49 23.698959167333868 24.184347477982385 25.185148118494794 26.931545236188953 50-54 23.428428428428425 24.624624624624623 24.464464464464463 27.482482482482485 55-59 23.69343211854225 24.44933920704846 24.909891870244294 26.947336804165 60-64 23.029118428306518 23.50523730767303 25.224277051070015 28.241367212950436 65-69 23.38503237464237 23.540631431009388 25.171911860663553 27.902424333684685 70-74 24.48723104765735 23.723104765734966 24.819022722702595 26.97064146390509 75-79 24.82602118003026 24.009077155824507 24.503277861825516 26.661623802319717 80-84 23.595505617977526 23.68154671525458 24.622937544285858 28.100010122482033 85-89 23.532401524777637 23.532401524777637 25.209656925031766 27.725540025412958 90-94 24.253769617396657 23.946045748281875 24.858959893322393 26.941224740999075 95-99 23.152196543826776 23.714345200916096 24.932333957942955 28.201124297314177 100-104 23.63617066440246 23.917427297813628 25.05306728932286 27.39333474846105 105-109 23.501953973078592 23.843899261832394 24.78831958315241 27.865827181936602 110-114 24.585050685084102 24.33441015929598 23.86097805502952 27.2195611005904 115-119 24.846625766871167 23.619631901840492 24.534089593702976 26.999652737585368 120-124 24.423321426409153 23.472785614821092 24.992432039716654 27.111460919053098 125-129 24.504447268106734 24.263024142312577 23.106734434561627 28.125794155019058 130-134 24.98824793499429 23.013901014035323 23.987643543079713 28.010207507890673 135-139 25.405520774046668 23.826124075128057 23.669607285145133 27.098747865680135 140-144 24.608551641071966 23.434206564287866 23.99126769045468 27.965974104185488 145-149 25.460952224862737 22.8796197656314 23.985905105301974 27.673522904203885 150 29.277108433734938 0.0 32.7710843373494 37.95180722891566 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 3.0 1 1.5 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 0.0 19 0.0 20 0.0 21 0.0 22 0.0 23 0.5 24 1.0 25 0.5 26 0.5 27 2.5 28 2.5 29 2.0 30 2.0 31 2.5 32 9.0 33 13.5 34 16.5 35 25.5 36 41.5 37 58.0 38 63.0 39 70.0 40 84.0 41 93.5 42 107.5 43 117.0 44 121.5 45 148.0 46 173.5 47 179.0 48 197.5 49 220.5 50 218.5 51 191.5 52 170.0 53 162.0 54 155.5 55 166.5 56 161.0 57 137.5 58 118.0 59 87.5 60 78.0 61 76.0 62 64.5 63 59.5 64 55.0 65 49.5 66 42.5 67 44.5 68 47.0 69 36.5 70 27.5 71 24.0 72 22.0 73 18.0 74 14.0 75 14.0 76 10.0 77 6.5 78 4.5 79 4.0 80 3.0 81 1.0 82 1.0 83 0.5 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 1.0 99 0.5 100 0.5 >>END_MODULE >>Per base N content pass #Base N-Count 1 0.025 2 0.025 3 0.025 4 0.025 5 0.025 6 0.8 7 0.025 8 0.025 9 0.025 10-14 0.025 15-19 0.025 20-24 0.025 25-29 0.025 30-34 0.025 35-39 0.00500175061271445 40-44 0.0 45-49 0.0 50-54 0.0 55-59 0.00500575662011313 60-64 0.01503307276007216 65-69 0.005019072475406545 70-74 0.02512941649494899 75-79 0.0 80-84 0.0050609848676552455 85-89 0.005082333807684488 90-94 0.015383826470437414 95-99 0.0156128024980484 100-104 0.026526606186004564 105-109 0.00542740841248304 110-114 0.0 115-119 0.005787371954395509 120-124 0.006054001695120475 125-129 0.006352836541515787 130-134 0.0 135-139 0.0 140-144 0.0 145-149 0.0 150 0.0 >>END_MODULE >>Sequence Length Distribution warn #Length Count 35-39 3.0 40-44 0.0 45-49 1.0 50-54 0.0 55-59 2.0 60-64 8.0 65-69 3.0 70-74 11.0 75-79 13.0 80-84 16.0 85-89 28.0 90-94 43.0 95-99 72.0 100-104 80.0 105-109 84.0 110-114 118.0 115-119 150.0 120-124 160.0 125-129 166.0 130-134 165.0 135-139 160.0 140-144 160.0 145-149 897.0 150-151 1660.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 85.2 #Duplication Level Percentage of deduplicated Percentage of total 1 91.4906103286385 77.95 2 4.694835680751173 8.0 3 1.7018779342723005 4.35 4 0.8215962441314555 2.8000000000000003 5 0.5868544600938966 2.5 6 0.35211267605633806 1.7999999999999998 7 0.11737089201877934 0.7000000000000001 8 0.11737089201877934 0.8 9 0.05868544600938967 0.44999999999999996 >10 0.05868544600938967 0.65 >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 CCGACATCGAAGGATCAAAAAGCAACGTCGCTATGAACGCTTGGCTGCCA 15 0.375 No Hit CCCGACTGTCCCTATTAATCATTACTCCGATCCCGAAGGCCAACACAATA 11 0.27499999999999997 No Hit CTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATT 9 0.22499999999999998 No Hit CTTTTATCTAATAAATGCGCCCCTCCCAGAAGTCGGGGTTTGTTGCACGT 9 0.22499999999999998 No Hit CTGACTATGAAATACGAATGCCCCCGACTGTCCCTATTAATCATTACTCC 8 0.2 No Hit CCTAATTCTCCGTCACCCGTCACCACCATGGTAGGCCCCTATCCTACCAT 8 0.2 No Hit CTAGAATTACTACGGTTATCCGAGTAGCACGTACCATCAAACAAACTATA 8 0.2 No Hit CTCAAACTTCCGTCGCCTAAACGGCGATAGTCCCTCTAAGAAGCTAGCTG 8 0.2 No Hit CCGGAACCCAAAGACTTTGATTTCTCATAAGGTGCCGGCGGAGTCCTATA 7 0.17500000000000002 No Hit GTCCTTTTCATCTTTCCCTCGCGGTACTTGTTCGCTATCGGTCTCTCGCC 7 0.17500000000000002 No Hit CATGAATCATCGGATCAGCGAGCAAAGCCCGCGTCAGCCTTTTATCTAAT 7 0.17500000000000002 No Hit GTCGAGTTATCATGAATCATCGGATCAGCGAGCAAAGCCCGCGTCAGCCT 7 0.17500000000000002 No Hit CCCGGAACCCAAAGACTTTGATTTCTCATAAGGTGCCGGCGGAGTCCTAT 6 0.15 No Hit CCCGTGTCAGGATTGGGTAATTTGCGCGCCTGCTGCCTTCCTTGGATGTG 6 0.15 No Hit CCCAACTTTCGTTCTTGATTAATGAAAACATCCTTGGCAAATGCTTTCGC 6 0.15 No Hit CTGAGGTCTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAAC 6 0.15 No Hit CGCCCCTATACCCAAGTCAGACGAACGATTTGCACGTCAGTATCGCTTCG 6 0.15 No Hit CTCAGAGCCAATCCTTTTCCCGAAGTTACGGATCCGTTTTGCCGACTTCC 6 0.15 No Hit CTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGG 6 0.15 No Hit CCCGAAGTTACGGATCCGTTTTGCCGACTTCCCTTGCCTACATTGTTCCA 6 0.15 No Hit CGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCAT 6 0.15 No Hit CACGCTTTCACGGTTCGTATTCGTACTGGAAATCAGAATCAAACGAGCTT 6 0.15 No Hit GTGCGACGTGGGGCTGGATCTCAGTGGATCGTGGCAGCAAGGCCACTCTG 6 0.15 No Hit CCGCAGGCTCCACGCCTGGTGGTGCCCTTCCGTCAATTCCTTTAAGTTTC 6 0.15 No Hit CCCGCGTCAGCCTTTTATCTAATAAATGCGCCCCTCCCAGAAGTCGGGGT 5 0.125 No Hit CGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTC 5 0.125 No Hit CTTCCGTCAATTCCTTTAAGTTTCAGCCTTGCGACCATACTCCCCCCGGA 5 0.125 No Hit GTCGGCATCGTTTATGGTTGAGACTAGGACGGTATCTGATCGTCTTCGAG 5 0.125 No Hit GCACGTACCATCAAACAAACTATAACTGATTTAATGAGCCATTCGCAGTT 5 0.125 No Hit CCTCTAAGAAGCTAGCTGCGGAGGGATGGCTCCGCATAGCTAGTTAGCAG 5 0.125 No Hit GTCAGGATTGGGTAATTTGCGCGCCTGCTGCCTTCCTTGGATGTGGTAGC 5 0.125 No Hit CACGTTCCCTATTGGTGGGTGAACAATCCAACACTTGGTGAATTCTGCTT 5 0.125 No Hit CGCTATTGGAGCTGGAATTACCGCGGCTGCTGGCACCAGACTTGCCCTCC 5 0.125 No Hit GCTTGCTTTGAGCACTCTAATTTCTTCAAAGTAACGATGCCGGAGGCACG 5 0.125 No Hit CCCTTTTGTTCCACACGAGATTTCTGTTCTCGTTGAGCTCATCTTAGGAC 5 0.125 No Hit CTTTTGTTCCACACGAGATTTCTGTTCTCGTTGAGCTCATCTTAGGACAC 5 0.125 No Hit GCCCGTTCCCTTGGCTGTGGTTTCGCTGGATAGTAGACAGGGACAGTGGG 5 0.125 No Hit GTCGGGGCAGGCGGCGGGCGCAGGCGCCGCTTGCTAGCTTGGATTCTGAC 5 0.125 No Hit CGGCAATTTCAAGCACTCTTTGACTCTCTTTTCAAAGTCCTTTTCATCTT 5 0.125 No Hit CTCATTCCAATTACCAGACACTAATGTGCCCGGTATTGTTATTTATTGTC 5 0.125 No Hit ATCCCATGCTAATGTATCCAGAGCGATGGCTTGCTTTGAGCACTCTAATT 5 0.125 No Hit CGCGGCACGGTCATCAGTAGGGTAAAACTAACCTGTCTCACGACGGTCTA 5 0.125 No Hit TGCACGTATTAGCTCTAGAATTACTACGGTTATCCGAGTAGCACGTACCA 5 0.125 No Hit CAATGATCTATCCCCATCACGATGAAATTTCCCAAGATTACCCGGGCCTG 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 0.0 0.0 0.0 0.0 0.0 100-101 0.0 0.0 0.0 0.0 0.0 102-103 0.0 0.0 0.0 0.0 0.0 104-105 0.0 0.0 0.0 0.0 0.0 106-107 0.0 0.0 0.0 0.0 0.0 108-109 0.0 0.0 0.0 0.0 0.0 110-111 0.0 0.0 0.0 0.0 0.0 112-113 0.0 0.0 0.0 0.0 0.0 114-115 0.0 0.0 0.0 0.0 0.0 116-117 0.0 0.0 0.0 0.0 0.0 118-119 0.0125 0.0 0.0 0.0 0.0 120-121 0.025 0.0 0.0 0.0 0.0 122-123 0.025 0.0 0.0 0.0 0.0 124-125 0.025 0.0 0.0 0.0 0.0 126-127 0.025 0.0 0.0 0.0 0.0 128-129 0.037500000000000006 0.0 0.0 0.0 0.0 130-131 0.05 0.0 0.0 0.0 0.0 132-133 0.05 0.0 0.0 0.0 0.0 134-135 0.05 0.0 0.0 0.0 0.0 136-137 0.05 0.0 0.0 0.0 0.0 138 0.05 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position AATCTGT 10 0.008961475 132.4125 5 AGGATTG 20 5.1488186E-4 99.30937 9 TCAGGAT 20 5.1488186E-4 99.30937 7 TGTCAGG 20 5.1488186E-4 99.30937 5 CCCGTGT 20 5.1488186E-4 99.30937 1 CGTGTCA 20 5.1488186E-4 99.30937 3 CAGGATT 20 5.1488186E-4 99.30937 8 GTCAGGA 20 5.1488186E-4 99.30937 6 CCGTGTC 25 0.0012498469 79.447495 2 GTGTCAG 30 0.0025768625 66.20625 4 >>END_MODULE Rejected 1344248 READS because READLEN < 1 Read 1344248 spots for SRR12682224.sra Written 1344248 spots for SRR12682224.sra Rejected 1344248 READS because READLEN < 1 Read 1344248 spots for SRR12682224.sra Written 1344248 spots for SRR12682224.sra Rejected 1344248 READS because READLEN < 1 Read 1344248 spots for SRR12682224.sra Written 1344248 spots for SRR12682224.sra Rejected 1344248 READS because READLEN < 1 Read 1344248 spots for SRR12682224.sra Written 1344248 spots for SRR12682224.sra Rejected 1344248 READS because READLEN < 1 Read 1344248 spots for SRR12682224.sra Written 1344248 spots for SRR12682224.sra Rejected 1344248 READS because READLEN < 1 Read 1344248 spots for SRR12682224.sra Written 1344248 spots for SRR12682224.sra Rejected 1344248 READS because READLEN < 1 Read 1344248 spots for SRR12682224.sra Written 1344248 spots for SRR12682224.sra Rejected 1344248 READS because READLEN < 1 Read 1344248 spots for SRR12682224.sra Written 1344248 spots for SRR12682224.sra Rejected 1344248 READS because READLEN < 1 Read 1344248 spots for SRR12682224.sra Written 1344248 spots for SRR12682224.sra Rejected 1344248 READS because READLEN < 1 Read 1344248 spots for SRR12682224.sra Written 1344248 spots for SRR12682224.sra Rejected 1344248 READS because READLEN < 1 Read 1344248 spots for SRR12682224.sra Written 1344248 spots for SRR12682224.sra Rejected 1344258 READS because READLEN < 1 Read 1344258 spots for SRR12682224.sra Written 1344258 spots for SRR12682224.sra Rejected 1344248 READS because READLEN < 1 Read 1344248 spots for SRR12682224.sra Written 1344248 spots for SRR12682224.sra Rejected 1344248 READS because READLEN < 1 Read 1344248 spots for SRR12682224.sra Written 1344248 spots for SRR12682224.sra Rejected 1344248 READS because READLEN < 1 Read 1344248 spots for SRR12682224.sra Written 1344248 spots for SRR12682224.sra Rejected 1344248 READS because READLEN < 1 Read 1344248 spots for SRR12682224.sra Written 1344248 spots for SRR12682224.sra Rejected 1344248 READS because READLEN < 1 Read 1344248 spots for SRR12682224.sra Written 1344248 spots for SRR12682224.sra Rejected 1344248 READS because READLEN < 1 Read 1344248 spots for SRR12682224.sra Written 1344248 spots for SRR12682224.sra Rejected 1344248 READS because READLEN < 1 Read 1344248 spots for SRR12682224.sra Written 1344248 spots for SRR12682224.sra Rejected 1344248 READS because READLEN < 1 Read 1344248 spots for SRR12682224.sra Written 1344248 spots for SRR12682224.sra SRR ids: ['SRR12682224.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_ai9yljil SRR12682224.sra spots: 26884970 blocks: [[1, 1344248], [1344249, 2688496], [2688497, 4032744], [4032745, 5376992], [5376993, 6721240], [6721241, 8065488], [8065489, 9409736], [9409737, 10753984], [10753985, 12098232], [12098233, 13442480], [13442481, 14786728], [14786729, 16130976], [16130977, 17475224], [17475225, 18819472], [18819473, 20163720], [20163721, 21507968], [21507969, 22852216], [22852217, 24196464], [24196465, 25540712], [25540713, 26884970]] SRR12682224 file size 8438127 SRR12682224 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 SRR12682224 SRR12682224_1.fastq Input file: SRR12682224_1.fastq trimmed: SRR12682224-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 03:15:32 2024 >> started Sat Dec 7 03:15:47 2024 >> done (14.510s) 26884970 reads processed; of these: 2 ( 0.00%) short reads filtered out after trimming by size control 5780 ( 0.02%) empty reads filtered out after trimming by size control 26879188 (99.98%) reads available; of these: 12556 ( 0.05%) trimmed reads available after processing 26866632 (99.95%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 19 1 0.00% 20 0 0.00% 21 1 0.00% 22 19 0.00% 23 20 0.00% 24 24 0.00% 25 47 0.00% 26 62 0.00% 27 103 0.00% 28 141 0.00% 29 134 0.00% 30 189 0.00% 31 152 0.00% 32 244 0.00% 33 266 0.00% 34 314 0.00% 35 405 0.00% 36 438 0.00% 37 528 0.00% 38 649 0.00% 39 728 0.00% 40 871 0.00% 41 977 0.00% 42 1006 0.00% 43 978 0.00% 44 1022 0.00% 45 1072 0.00% 46 1173 0.00% 47 1572 0.01% 48 1765 0.01% 49 2098 0.01% 50 2401 0.01% 51 2556 0.01% 52 2661 0.01% 53 2672 0.01% 54 2770 0.01% 55 2845 0.01% 56 3158 0.01% 57 3481 0.01% 58 4150 0.02% 59 4533 0.02% 60 5130 0.02% 61 5489 0.02% 62 6013 0.02% 63 5975 0.02% 64 6410 0.02% 65 6486 0.02% 66 7272 0.03% 67 7955 0.03% 68 8484 0.03% 69 9171 0.03% 70 9664 0.04% 71 11257 0.04% 72 12354 0.05% 73 13589 0.05% 74 14257 0.05% 75 15102 0.06% 76 16362 0.06% 77 17095 0.06% 78 18528 0.07% 79 20954 0.08% 80 22454 0.08% 81 24097 0.09% 82 26472 0.10% 83 28375 0.11% 84 31135 0.12% 85 35389 0.13% 86 39471 0.15% 87 41070 0.15% 88 44155 0.16% 89 45940 0.17% 90 50088 0.19% 91 52485 0.20% 92 59435 0.22% 93 64119 0.24% 94 66492 0.25% 95 73613 0.27% 96 80624 0.30% 97 84458 0.31% 98 92991 0.35% 99 96128 0.36% 100 97997 0.36% 101 101920 0.38% 102 110034 0.41% 103 117884 0.44% 104 123667 0.46% 105 124791 0.46% 106 132080 0.49% 107 141690 0.53% 108 139384 0.52% 109 151419 0.56% 110 154232 0.57% 111 162852 0.61% 112 175191 0.65% 113 173460 0.65% 114 184670 0.69% 115 195053 0.73% 116 199834 0.74% 117 194105 0.72% 118 196732 0.73% 119 206422 0.77% 120 217295 0.81% 121 210992 0.78% 122 226677 0.84% 123 230582 0.86% 124 224467 0.84% 125 226543 0.84% 126 234024 0.87% 127 231059 0.86% 128 235382 0.88% 129 247032 0.92% 130 238500 0.89% 131 237194 0.88% 132 237720 0.88% 133 244817 0.91% 134 238650 0.89% 135 241608 0.90% 136 245832 0.91% 137 247223 0.92% 138 238163 0.89% 139 243525 0.91% 140 240474 0.89% 141 232344 0.86% 142 233396 0.87% 143 230525 0.86% 144 240618 0.90% 145 234372 0.87% 146 292228 1.09% 147 490499 1.82% 148 1112367 4.14% 149 3797803 14.13% 150 10669096 39.69% 26879188 reads passed initial QC criterion=sequence-density sequence-density=0.59 sequence-density-rank=1 fanout-score=2.70 fanout-score-rank=37 prefix-density=1.58 prefix-fanout=1.0 sequence=CTTGGATGTGGCAGCCGTTTCTC criterion=fanout-score sequence-density=0.06 sequence-density-rank=32 fanout-score=220.59 fanout-score-rank=1 prefix-density=0.47 prefix-fanout=28.0 sequence=CTTCTTCTTGTC Started job on | Dec 07 03:16:11 Started mapping on | Dec 07 03:16:11 Finished on | Dec 07 03:17:22 Mapping speed, Million of reads per hour | 1362.89 Number of input reads | 26879188 Average input read length | 138 UNIQUE READS: Uniquely mapped reads number | 13785146 Uniquely mapped reads % | 51.29% Average mapped length | 138.15 Number of splices: Total | 5613828 Number of splices: Annotated (sjdb) | 5280234 Number of splices: GT/AG | 5539165 Number of splices: GC/AG | 66703 Number of splices: AT/AC | 3750 Number of splices: Non-canonical | 4210 Mismatch rate per base, % | 0.23% Deletion rate per base | 0.01% Deletion average length | 1.57 Insertion rate per base | 0.00% Insertion average length | 1.13 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 1301845 % of reads mapped to multiple loci | 4.84% Number of reads mapped to too many loci | 9947077 % of reads mapped to too many loci | 37.01% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.85% % of reads unmapped: other | 5.02% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 11792197 11792197 11792197 N_multimapping 1301845 1301845 1301845 N_noFeature 801737 13425240 914180 N_ambiguous 292275 1455 46076 UnstrandedReadsAssigned:12691134 PositiveStrandReadsAssigned:358451 NegativeStrandReadsAssigned:12824890 Dataset is classified negative stranded MeadianReadLen=149 20thPercentileLength=124 echo kmer=119 SRR12682224 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: SRR12682224-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 26,879,188 reads, 13,161,631 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,138 rounds 52973 SRR12682224.ke.tsv 35125 SRR12682224.se.tsv 88098 total ==> SRR12682224.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 837 4.32936e-07 6.06155e-08 PNS24247 1044 945 48.9204 6.06657 PNS24249 1928 1829 99.5091 6.37578 PNS24246 1044 945 48.9204 6.06657 PNS24248 1044 945 48.9204 6.06657 PNS24244 1471 1372 101.73 8.68916 PNS24243 293 194 2 1.20813 KQK14069 1603 1504 6292.28 490.281 KQK14071 474 375 611.356 191.05 ==> SRR12682224.se.tsv <== BRADI_1g14170v3 7711 BRADI_1g53295v3 92 BRADI_1g59795v3 392 BRADI_1g07683v3 0 BRADI_1g00485v3 4 BRADI_1g20270v3 568 BRADI_1g74790v3 513 BRADI_1g09890v3 0 BRADI_1g77505v3 158 BRADI_1g48960v3 0 SRR12682224 completed mapping pipeline successfully