Starting /dee2/code/volunteer_pipeline.sh ERR6133543 current disk space = 1544503644160 free memory = 1604571624 ERR6133543 SRAfilesize 420ee77eb63edf51eb95335e567c0522 ERR6133543.sra ERR6133543.sra file validated ERR6133543 is single end ERR6133543 is conventional basespace ERR6133543 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133543_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 70-93 %GC 46 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 33.899 37.0 33.0 37.0 33.0 37.0 2 35.99025 37.0 37.0 37.0 33.0 37.0 3 35.01875 37.0 33.0 37.0 33.0 37.0 4 35.14025 37.0 37.0 37.0 33.0 37.0 5 35.05625 37.0 37.0 37.0 33.0 37.0 6 35.355 37.0 37.0 37.0 33.0 37.0 7 37.06525 37.0 37.0 40.0 33.0 40.0 8 37.20525 37.0 37.0 40.0 33.0 40.0 9 37.24525 37.0 37.0 40.0 33.0 40.0 10-11 37.305625 37.0 37.0 40.0 33.0 40.0 12-13 37.255624999999995 37.0 37.0 40.0 33.0 40.0 14-15 37.2175 37.0 37.0 40.0 33.0 40.0 16-17 37.111374999999995 37.0 37.0 40.0 33.0 40.0 18-19 37.038624999999996 37.0 37.0 40.0 33.0 40.0 20-21 36.894375 37.0 37.0 40.0 33.0 40.0 22-23 36.874875 37.0 37.0 40.0 33.0 40.0 24-25 36.946124999999995 37.0 37.0 40.0 33.0 40.0 26-27 36.99375 37.0 37.0 40.0 33.0 40.0 28-29 36.850875 37.0 37.0 40.0 33.0 40.0 30-31 36.81225 37.0 37.0 40.0 33.0 40.0 32-33 36.675625 37.0 37.0 40.0 33.0 40.0 34-35 36.547250000000005 37.0 37.0 40.0 33.0 40.0 36-37 36.303375 37.0 37.0 40.0 33.0 40.0 38-39 36.208625 37.0 37.0 40.0 33.0 40.0 40-41 35.877750000000006 37.0 37.0 40.0 33.0 40.0 42-43 35.916375 37.0 37.0 40.0 33.0 40.0 44-45 35.641375 37.0 33.0 38.5 33.0 40.0 46-47 35.234125 37.0 33.0 37.0 30.0 40.0 48-49 35.348 37.0 33.0 37.0 33.0 40.0 50-51 35.265625 37.0 33.0 37.0 33.0 40.0 52-53 35.027625 37.0 33.0 37.0 30.0 40.0 54-55 35.032250000000005 37.0 33.0 37.0 33.0 38.5 56-57 34.835625 37.0 33.0 37.0 30.0 37.0 58-59 34.118875 37.0 33.0 37.0 27.0 37.0 60-61 34.340374999999995 37.0 33.0 37.0 27.0 37.0 62-63 34.3245 37.0 33.0 37.0 27.0 37.0 64-65 34.365875 37.0 33.0 37.0 27.0 37.0 66-67 34.432375 37.0 33.0 37.0 27.0 37.0 68-69 33.476625 35.0 33.0 37.0 27.0 37.0 70-71 33.578419919919924 35.0 33.0 37.0 27.0 37.0 72-73 33.94718431709751 37.0 33.0 37.0 27.0 37.0 74-75 33.906179663363176 37.0 33.0 37.0 27.0 37.0 76-77 33.975891390903975 37.0 33.0 37.0 27.0 37.0 78-79 34.01564643543968 37.0 33.0 37.0 27.0 37.0 80-81 33.96045101249594 37.0 33.0 37.0 27.0 37.0 82-83 33.84164903064888 37.0 33.0 37.0 27.0 37.0 84-85 33.669546532425805 37.0 33.0 37.0 27.0 37.0 86-87 33.69643312101911 37.0 33.0 37.0 27.0 37.0 88-89 33.73490445859873 37.0 33.0 37.0 27.0 37.0 90-91 33.49044585987261 37.0 33.0 37.0 27.0 37.0 92-93 33.49821656050955 37.0 33.0 37.0 27.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 16.0 21 13.0 22 19.0 23 25.0 24 21.0 25 44.0 26 44.0 27 49.0 28 61.0 29 63.0 30 101.0 31 105.0 32 139.0 33 170.0 34 260.0 35 447.0 36 946.0 37 895.0 38 574.0 39 8.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 89.14999999999999 2.25 2.7 5.8999999999999995 2 76.325 13.850000000000001 5.975 3.85 3 40.075 37.8 11.799999999999999 10.325 4 32.525 29.95 17.65 19.875 5 27.400000000000002 31.924999999999997 24.099999999999998 16.575 6 19.85 41.5 22.975 15.675 7 38.675 29.4 16.975 14.95 8 31.525 30.049999999999997 20.45 17.974999999999998 9 26.825 30.4 24.65 18.125 10-11 25.874999999999996 28.9 27.237499999999997 17.9875 12-13 28.3375 26.75 25.874999999999996 19.037499999999998 14-15 22.0875 32.425 26.825 18.6625 16-17 25.45 31.35 24.0375 19.162499999999998 18-19 24.90311288911114 25.84073009126141 28.6160770096262 20.64008001000125 20-21 26.569142285571395 25.78144536134033 27.894473618404604 19.754938734683673 22-23 27.6 23.0 27.450000000000003 21.95 24-25 25.387500000000003 24.1125 28.1125 22.3875 26-27 26.387500000000003 24.8 29.45 19.3625 28-29 24.637500000000003 27.537499999999998 27.3875 20.4375 30-31 28.8875 25.7 25.624999999999996 19.787499999999998 32-33 25.275 26.0375 27.025 21.6625 34-35 24.4463905917678 27.624171149756037 26.585762542224444 21.34367571625172 36-37 25.650000000000002 24.175 27.3625 22.8125 38-39 28.287499999999998 24.3125 29.1875 18.212500000000002 40-41 26.550775387693847 24.23711855927964 29.00200100050025 20.210105052526263 42-43 25.807259073842303 28.848560700876096 25.782227784730914 19.56195244055069 44-45 25.062531265632813 24.7623811905953 28.989494747373683 21.1855927963982 46-47 24.95 23.425 27.5875 24.0375 48-49 25.165645705713214 24.315539442430303 29.353669208651077 21.165145643205403 50-51 24.349999999999998 26.375 28.462500000000002 20.8125 52-53 24.690431519699814 26.49155722326454 26.416510318949342 22.401500938086304 54-55 22.8625 26.525 29.875 20.7375 56-57 26.775 25.75 27.237499999999997 20.2375 58-59 24.5625 25.0125 28.8625 21.5625 60-61 26.637499999999996 24.1625 29.15 20.05 62-63 21.762500000000003 26.8 32.3875 19.05 64-65 23.5875 28.375 28.1125 19.925 66-67 24.712500000000002 28.025 28.15 19.112499999999997 68-69 22.0125 25.7125 29.049999999999997 23.225 70-71 24.6248124062031 25.68784392196098 27.351175587793897 22.336168084042022 72-73 25.95840641443247 24.36732648459033 29.4287146078677 20.245552493109496 74-75 24.362677382895896 27.966846665829458 27.703126962200177 19.96734898907447 76-77 22.51163961243236 24.62564489744558 28.903988926638984 23.958726563483076 78-79 24.706772606886116 25.930129902888133 29.322739311388574 20.04035817883718 80-81 23.316062176165804 29.508403892329078 29.040818905598382 18.134715025906736 82-83 24.692609963239953 25.199645075421472 28.482697426796804 21.625047534541768 84-85 23.80407124681934 24.198473282442748 31.00508905852417 20.99236641221374 86-87 21.528662420382165 28.038216560509554 30.420382165605098 20.012738853503183 88-89 21.261146496815286 27.6687898089172 30.980891719745223 20.089171974522294 90-91 27.146496815286625 25.949044585987263 28.878980891719745 18.025477707006367 92-93 21.91082802547771 27.94904458598726 30.40764331210191 19.73248407643312 >>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 0.5 16 0.5 17 5.5 18 7.5 19 2.5 20 0.5 21 2.0 22 3.5 23 6.5 24 8.0 25 5.0 26 9.0 27 12.5 28 16.0 29 22.5 30 22.0 31 26.0 32 37.5 33 58.0 34 73.5 35 75.5 36 87.0 37 120.0 38 165.0 39 175.5 40 177.5 41 189.0 42 195.5 43 202.5 44 192.0 45 185.5 46 199.5 47 187.0 48 167.0 49 165.0 50 157.5 51 149.0 52 141.0 53 159.5 54 191.5 55 152.5 56 78.5 57 56.0 58 57.5 59 51.5 60 44.5 61 40.5 62 33.0 63 35.0 64 36.5 65 25.0 66 18.5 67 19.0 68 17.0 69 12.5 70 7.5 71 6.0 72 4.0 73 2.5 74 2.5 75 1.0 76 1.0 77 1.0 78 0.0 79 0.0 80 0.0 81 0.0 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 0.0 98 0.0 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 0.0 7 0.0 8 0.0 9 0.0 10-11 0.0 12-13 0.0 14-15 0.0 16-17 0.0 18-19 0.0125 20-21 0.025 22-23 0.0 24-25 0.0 26-27 0.0 28-29 0.0 30-31 0.0 32-33 0.0 34-35 0.08750000000000001 36-37 0.0 38-39 0.0 40-41 0.05 42-43 0.125 44-45 0.05 46-47 0.0 48-49 0.0125 50-51 0.0 52-53 0.0625 54-55 0.0 56-57 0.0 58-59 0.0 60-61 0.0 62-63 0.0 64-65 0.0 66-67 0.0 68-69 0.0 70-71 0.0 72-73 0.0 74-75 0.0 76-77 0.0 78-79 0.0 80-81 0.0 82-83 0.0 84-85 0.0 86-87 0.0 88-89 0.0 90-91 0.0 92-93 0.0 >>END_MODULE >>Sequence Length Distribution warn #Length Count 70 4.0 71 2.0 72 6.0 73 4.0 74 5.0 75 3.0 76 5.0 77 4.0 78 5.0 79 4.0 80 3.0 81 7.0 82 7.0 83 6.0 84 10.0 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 3925.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 77.825 #Duplication Level Percentage of deduplicated Percentage of total 1 91.712174751044 71.375 2 4.946996466431095 7.7 3 1.188564086090588 2.775 4 0.578220366206232 1.7999999999999998 5 0.289110183103116 1.125 6 0.256986829424992 1.2 7 0.256986829424992 1.4000000000000001 8 0.064246707356248 0.4 9 0.09637006103437198 0.675 >10 0.578220366206232 8.625 >50 0.0 0.0 >100 0.032123353678124 2.9250000000000003 >500 0.0 0.0 >1k 0.0 0.0 >5k 0.0 0.0 >10k+ 0.0 0.0 >>END_MODULE >>Overrepresented sequences fail #Sequence Count Percentage Possible Source GGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGC 117 2.9250000000000003 No Hit GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 42 1.05 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 37 0.9249999999999999 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 31 0.775 No Hit GGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGG 29 0.7250000000000001 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 26 0.65 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 26 0.65 No Hit GGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTT 23 0.575 No Hit GTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAA 15 0.375 No Hit GGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGGG 15 0.375 No Hit GGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAA 13 0.325 No Hit GGCCTGTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCG 12 0.3 No Hit GGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAA 12 0.3 No Hit GGAAGAGCCCGAGCTGCTGCAGCAGGTTTTGAAAAGGGAATCGATCGTGA 11 0.27499999999999997 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 11 0.27499999999999997 No Hit GGAGTATCCTTGATATATAAATATATAGATAAATAGATTTAAATGGAAAA 11 0.27499999999999997 No Hit GTATTTAGCCTTGCAAGGTGGTCCTTGCTGATTCACACGGGATTCCACGT 11 0.27499999999999997 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 10 0.25 No Hit GGTTTTGAAAAGGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAA 10 0.25 No Hit GGGAAAAGAGGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTT 9 0.22499999999999998 No Hit GGAGTCCCATATATATATGTATAAGATGCCAGCCCGGTTTCGTCAACCAT 9 0.22499999999999998 No Hit GGAAAAGAAAGCAAAAGCGATTCCCGTAGTAGCGGCGAGCGAAATGGGAG 9 0.22499999999999998 No Hit GGATTTGAAGAAAAAAAAGACTTCGATTCATTTTCTATTTATTTCGTTAG 8 0.2 No Hit GGGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTG 8 0.2 No Hit GGGAGTATTATGAAAGGAGATTAATCATAGATTATCAAAAACCCTAGAAA 7 0.17500000000000002 No Hit GGAATAAGAATAAATCGCAACTCCTTTCCACTACACATAAAAATTGATTT 7 0.17500000000000002 No Hit GGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGC 7 0.17500000000000002 No Hit GGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTT 7 0.17500000000000002 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 7 0.17500000000000002 No Hit GGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAACCCTCTTAACT 7 0.17500000000000002 No Hit GGGGAAGTACACCAGCGACGGCGAGGCCGCCGCCGCCAAGGAAGGCATGT 7 0.17500000000000002 No Hit GGAAAAGAGGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTTG 7 0.17500000000000002 No Hit GGTGGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGC 6 0.15 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 6 0.15 No Hit GGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCTAAATGGATTC 6 0.15 No Hit GGTGGGGCAATGGGCATTCCGTTGAGTTTGTATGGTGGGTGCTGTTTTGC 6 0.15 No Hit GGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTG 6 0.15 No Hit GGGCCGGGTATCTCTCTGCATGTACGTATGCCTGTAATGTACGTAGCTAC 6 0.15 No Hit GGGATTACGACGAGAAAGAAGAAGAAGAAGAAACGCATGGTGCCCTGCTT 6 0.15 No Hit GTACAAGCTCGTAACGAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAAT 6 0.15 No Hit GGGATGGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACGA 5 0.125 No Hit CAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCT 5 0.125 No Hit GGGGTTGTGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTG 5 0.125 No Hit GGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGCA 5 0.125 No Hit GAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGC 5 0.125 No Hit GAAGGAACAAACGAGGATAAGATAAAATTTCTTTAAATTTATTTTGCCCA 5 0.125 No Hit GGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGT 5 0.125 No Hit GGGGTGTTGTAGGTCACCGAGGCTGTTCTGAGATTGCGACCAAGCACGTA 5 0.125 No Hit GGGCCATTTGTGGCATGCAGGAAGAGCCCGAGCTGCTGCAGCAGGTTTTG 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 0.025 0.0 0.0 0.0 0.0 38-39 0.05 0.0 0.0 0.0 0.0 40-41 0.05 0.0 0.0 0.0 0.0 42-43 0.05 0.0 0.0 0.0 0.0 44-45 0.05 0.0 0.0 0.0 0.0 46-47 0.05 0.0 0.0 0.0 0.0 48-49 0.05 0.0 0.0 0.0 0.0 50-51 0.05 0.0 0.0 0.0 0.0 52-53 0.05 0.0 0.0 0.0 0.0 54-55 0.05 0.0 0.0 0.0 0.0 56-57 0.05 0.0 0.0 0.0 0.0 58-59 0.05 0.0 0.0 0.0 0.0 60-61 0.05 0.0 0.0 0.0 0.0 62-63 0.05 0.0 0.0 0.0 0.0 64-65 0.05 0.0 0.0 0.0 0.0 66-67 0.05 0.0 0.0 0.0 0.0 68-69 0.05 0.0 0.0 0.0 0.0 70-71 0.05 0.0 0.0 0.0 0.0 72-73 0.05 0.0 0.0 0.0 0.0 74-75 0.05 0.0 0.0 0.0 0.0 76-77 0.05 0.0 0.0 0.0 0.0 78-79 0.05 0.0 0.0 0.0 0.0 80-81 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 CGTTCAA 15 8.7132835E-4 87.0 3 CAACCTA 15 8.7132835E-4 87.0 7 AACCTAA 15 8.7132835E-4 87.0 8 GTTCAAC 15 8.7132835E-4 87.0 4 GATTCTG 15 8.7132835E-4 87.0 6 GGGATGA 15 8.7132835E-4 87.0 1 ACCTAAA 15 8.7132835E-4 87.0 9 ATTCTGT 15 8.7132835E-4 87.0 7 GGGAGAG 30 1.9132603E-6 72.5 1 TCAACCT 20 0.0027298967 65.25 6 GATGATT 20 0.0027298967 65.25 3 TCTGTAT 20 0.0027298967 65.25 9 GGAGAGC 30 1.7769479E-4 58.0 2 GAGAGCA 30 1.7769479E-4 58.0 3 ATGATTC 25 0.006606883 52.2 4 TTCAACC 25 0.006606883 52.2 5 TGATTCT 25 0.006606883 52.2 5 GCAATAC 25 0.006606883 52.2 7 CAATACA 25 0.006606883 52.2 8 GCGTTCA 25 0.006606883 52.2 2 >>END_MODULE Rejected 231009 READS because READLEN < 1 Read 231009 spots for ERR6133543.sra Written 231009 spots for ERR6133543.sra Rejected 231009 READS because READLEN < 1 Read 231009 spots for ERR6133543.sra Written 231009 spots for ERR6133543.sra Rejected 231009 READS because READLEN < 1 Read 231009 spots for ERR6133543.sra Written 231009 spots for ERR6133543.sra Rejected 231009 READS because READLEN < 1 Read 231009 spots for ERR6133543.sra Written 231009 spots for ERR6133543.sra Rejected 231009 READS because READLEN < 1 Read 231009 spots for ERR6133543.sra Written 231009 spots for ERR6133543.sra Rejected 231009 READS because READLEN < 1 Read 231009 spots for ERR6133543.sra Written 231009 spots for ERR6133543.sra Rejected 231009 READS because READLEN < 1 Read 231009 spots for ERR6133543.sra Written 231009 spots for ERR6133543.sra Rejected 231009 READS because READLEN < 1 Read 231009 spots for ERR6133543.sra Written 231009 spots for ERR6133543.sra Rejected 231009 READS because READLEN < 1 Read 231009 spots for ERR6133543.sra Written 231009 spots for ERR6133543.sra Rejected 231009 READS because READLEN < 1 Read 231009 spots for ERR6133543.sra Written 231009 spots for ERR6133543.sra Rejected 231009 READS because READLEN < 1 Read 231009 spots for ERR6133543.sra Written 231009 spots for ERR6133543.sra Rejected 231009 READS because READLEN < 1 Read 231009 spots for ERR6133543.sra Written 231009 spots for ERR6133543.sra Rejected 231009 READS because READLEN < 1 Read 231009 spots for ERR6133543.sra Written 231009 spots for ERR6133543.sra Rejected 231009 READS because READLEN < 1 Read 231009 spots for ERR6133543.sra Written 231009 spots for ERR6133543.sra Rejected 231009 READS because READLEN < 1 Read 231009 spots for ERR6133543.sra Written 231009 spots for ERR6133543.sra Rejected 231011 READS because READLEN < 1 Read 231011 spots for ERR6133543.sra Written 231011 spots for ERR6133543.sra Rejected 231009 READS because READLEN < 1 Read 231009 spots for ERR6133543.sra Written 231009 spots for ERR6133543.sra Rejected 231009 READS because READLEN < 1 Read 231009 spots for ERR6133543.sra Written 231009 spots for ERR6133543.sra Rejected 231009 READS because READLEN < 1 Read 231009 spots for ERR6133543.sra Written 231009 spots for ERR6133543.sra Rejected 231009 READS because READLEN < 1 Read 231009 spots for ERR6133543.sra Written 231009 spots for ERR6133543.sra SRR ids: ['ERR6133543.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_7epxpmch ERR6133543.sra spots: 4620182 blocks: [[1, 231009], [231010, 462018], [462019, 693027], [693028, 924036], [924037, 1155045], [1155046, 1386054], [1386055, 1617063], [1617064, 1848072], [1848073, 2079081], [2079082, 2310090], [2310091, 2541099], [2541100, 2772108], [2772109, 3003117], [3003118, 3234126], [3234127, 3465135], [3465136, 3696144], [3696145, 3927153], [3927154, 4158162], [4158163, 4389171], [4389172, 4620182]] ERR6133543 file size 1023659 ERR6133543 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 ERR6133543 ERR6133543_1.fastq Input file: ERR6133543_1.fastq trimmed: ERR6133543-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 08:20:59 2024 >> started Sat Dec 7 08:21:01 2024 >> done (2.271s) 4620182 reads processed; of these: 113 ( 0.00%) short reads filtered out after trimming by size control 16 ( 0.00%) empty reads filtered out after trimming by size control 4620053 (100.00%) reads available; of these: 84077 ( 1.82%) trimmed reads available after processing 4535976 (98.18%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 13 0.00% 19 30 0.00% 20 5 0.00% 21 8 0.00% 22 11 0.00% 23 6 0.00% 24 4 0.00% 25 4 0.00% 26 8 0.00% 27 6 0.00% 28 6 0.00% 29 18 0.00% 30 13 0.00% 31 4 0.00% 32 15 0.00% 33 17 0.00% 34 12 0.00% 35 57 0.00% 36 695 0.02% 37 12 0.00% 38 15 0.00% 39 39 0.00% 40 55 0.00% 41 17 0.00% 42 3 0.00% 43 3 0.00% 44 18 0.00% 45 12 0.00% 46 6 0.00% 47 6 0.00% 48 5 0.00% 49 5 0.00% 50 8 0.00% 51 22 0.00% 52 11 0.00% 53 5 0.00% 54 2 0.00% 55 5 0.00% 56 5 0.00% 57 9 0.00% 58 11 0.00% 59 7 0.00% 60 11 0.00% 61 6 0.00% 62 8 0.00% 63 3 0.00% 64 2 0.00% 65 7 0.00% 66 12 0.00% 67 17 0.00% 68 33 0.00% 69 89 0.00% 70 6513 0.14% 71 5756 0.12% 72 5823 0.13% 73 5253 0.11% 74 5988 0.13% 75 5696 0.12% 76 5063 0.11% 77 5388 0.12% 78 6053 0.13% 79 6964 0.15% 80 6443 0.14% 81 7253 0.16% 82 7910 0.17% 83 7975 0.17% 84 6578 0.14% 85 178 0.00% 86 366 0.01% 87 562 0.01% 88 1075 0.02% 89 2162 0.05% 90 4755 0.10% 91 14042 0.30% 92 58065 1.26% 93 4442791 96.16% 4620053 reads passed initial QC criterion=sequence-density sequence-density=0.27 sequence-density-rank=1 fanout-score=16.06 fanout-score-rank=7 prefix-density=0.76 prefix-fanout=5.7 sequence=GAAGAAGAAGAAACGCATGGTGCCCTGCTTCCGTCTGTCGGCTGCTTGCTTGGCAACGGCAGAGCAGAGCTTGGTGCAGTAAAACTACTGGTTATACTCTCTGTATGTAAAGTTAAAATTTTCACACACAGCTATGTGCTAAAGGA criterion=fanout-score sequence-density=0.01 sequence-density-rank=30 fanout-score=87.33 fanout-score-rank=1 prefix-density=0.16 prefix-fanout=6.5 sequence=AAAAGAAGGGGTGTTCCATCTCCGGACGACGATCCTGCCTGCGGAGGAAGACATGCCGGCGATCATGTCGAGCTTCAAGAAGTTCAACGACTCATTCATGGAGCAATACCAAGACTACTCCAGGCTGTGATGTGAAGAGGGAAACAACGACGTCATCATCGACATGATATATTGCTGCTATTTTCCACCAGCGATTAAAAGTTAAAAAATTTAGCTGTAAGCTGTAACTATCTTGAAGAAACTAAACTGGTTGCTGTGCTT Started job on | Dec 07 08:21:14 Started mapping on | Dec 07 08:21:14 Finished on | Dec 07 08:21:20 Mapping speed, Million of reads per hour | 2772.03 Number of input reads | 4620053 Average input read length | 92 UNIQUE READS: Uniquely mapped reads number | 3253542 Uniquely mapped reads % | 70.42% Average mapped length | 92.29 Number of splices: Total | 160445 Number of splices: Annotated (sjdb) | 133140 Number of splices: GT/AG | 154165 Number of splices: GC/AG | 3859 Number of splices: AT/AC | 89 Number of splices: Non-canonical | 2332 Mismatch rate per base, % | 0.41% Deletion rate per base | 0.03% Deletion average length | 1.66 Insertion rate per base | 0.01% Insertion average length | 1.83 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 1281481 % of reads mapped to multiple loci | 27.74% Number of reads mapped to too many loci | 22550 % of reads mapped to too many loci | 0.49% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.32% % of reads unmapped: other | 0.03% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 85030 85030 85030 N_multimapping 1281481 1281481 1281481 N_noFeature 209463 242001 3109705 N_ambiguous 125155 13891 428 UnstrandedReadsAssigned:2918924 PositiveStrandReadsAssigned:2997650 NegativeStrandReadsAssigned:143409 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=93 echo kmer=89 ERR6133543 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: ERR6133543-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 4,620,053 reads, 3,809,652 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,063 rounds 52973 ERR6133543.ke.tsv 35125 ERR6133543.se.tsv 88098 total ==> ERR6133543.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 837 0 0 PNS24247 1044 945 0 0 PNS24249 1928 1829 0 0 PNS24246 1044 945 0 0 PNS24248 1044 945 0 0 PNS24244 1471 1372 118 29.722 PNS24243 293 194 0 0 KQK14069 1603 1504 163 37.4533 KQK14071 474 375 0 0 ==> ERR6133543.se.tsv <== BRADI_1g14170v3 162 BRADI_1g53295v3 14 BRADI_1g59795v3 16 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 37 BRADI_1g74790v3 26 BRADI_1g09890v3 0 BRADI_1g77505v3 121 BRADI_1g48960v3 0 ERR6133543 completed mapping pipeline successfully