Starting /dee2/code/volunteer_pipeline.sh ERR6133548 current disk space = 1544522379264 free memory = 1598239468 ERR6133548 SRAfilesize 30f819bf56ae7d063dd1634ab13f2aff ERR6133548.sra ERR6133548.sra file validated ERR6133548 is single end ERR6133548 is conventional basespace ERR6133548 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133548_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 34.02225 37.0 33.0 37.0 33.0 37.0 2 36.0545 37.0 37.0 37.0 33.0 37.0 3 35.08325 37.0 33.0 37.0 33.0 37.0 4 35.3205 37.0 37.0 37.0 33.0 37.0 5 35.25575 37.0 37.0 37.0 33.0 37.0 6 35.4605 37.0 37.0 37.0 33.0 37.0 7 37.284 37.0 37.0 40.0 33.0 40.0 8 37.2905 37.0 37.0 40.0 33.0 40.0 9 37.3805 37.0 37.0 40.0 33.0 40.0 10-11 37.436875 37.0 37.0 40.0 33.0 40.0 12-13 37.305 37.0 37.0 40.0 33.0 40.0 14-15 37.314375 37.0 37.0 40.0 33.0 40.0 16-17 37.207499999999996 37.0 37.0 40.0 33.0 40.0 18-19 37.1845 37.0 37.0 40.0 33.0 40.0 20-21 37.007875 37.0 37.0 40.0 33.0 40.0 22-23 36.97525 37.0 37.0 40.0 33.0 40.0 24-25 37.07925 37.0 37.0 40.0 33.0 40.0 26-27 37.0985 37.0 37.0 40.0 33.0 40.0 28-29 37.024125 37.0 37.0 40.0 33.0 40.0 30-31 36.89875 37.0 37.0 40.0 33.0 40.0 32-33 36.765875 37.0 37.0 40.0 33.0 40.0 34-35 36.619749999999996 37.0 37.0 40.0 33.0 40.0 36-37 36.377625 37.0 37.0 40.0 33.0 40.0 38-39 36.356625 37.0 37.0 40.0 33.0 40.0 40-41 35.954 37.0 37.0 40.0 33.0 40.0 42-43 35.979124999999996 37.0 37.0 40.0 33.0 40.0 44-45 35.583749999999995 37.0 33.0 37.0 33.0 40.0 46-47 35.386375 37.0 33.0 37.0 33.0 40.0 48-49 35.388625000000005 37.0 33.0 37.0 33.0 40.0 50-51 35.32725 37.0 33.0 37.0 33.0 40.0 52-53 35.065749999999994 37.0 33.0 37.0 30.0 40.0 54-55 35.05375 37.0 33.0 37.0 33.0 37.0 56-57 34.95675 37.0 33.0 37.0 33.0 37.0 58-59 34.28475 37.0 33.0 37.0 27.0 37.0 60-61 34.57125 37.0 33.0 37.0 27.0 37.0 62-63 34.5445 37.0 33.0 37.0 27.0 37.0 64-65 34.588499999999996 37.0 33.0 37.0 30.0 37.0 66-67 34.707499999999996 37.0 33.0 37.0 33.0 37.0 68-69 33.7065 35.0 33.0 37.0 30.0 37.0 70-71 33.79739488991744 35.0 33.0 37.0 27.0 37.0 72-73 34.04480655767035 37.0 33.0 37.0 27.0 37.0 74-75 33.945210843770795 37.0 33.0 37.0 27.0 37.0 76-77 34.041750878685725 37.0 33.0 37.0 27.0 37.0 78-79 34.2931043256575 37.0 33.0 37.0 27.0 37.0 80-81 34.14991549634642 37.0 33.0 37.0 27.0 37.0 82-83 33.99859348614113 37.0 33.0 37.0 27.0 37.0 84-85 33.984291017086576 37.0 33.0 37.0 27.0 37.0 86-87 33.869193466054114 37.0 33.0 37.0 27.0 37.0 88-89 33.96937212863706 37.0 33.0 37.0 27.0 37.0 90-91 33.731495661051554 37.0 33.0 37.0 27.0 37.0 92-93 33.75204185809086 37.0 33.0 37.0 27.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 12.0 21 14.0 22 13.0 23 32.0 24 22.0 25 47.0 26 24.0 27 32.0 28 60.0 29 73.0 30 86.0 31 94.0 32 137.0 33 150.0 34 241.0 35 414.0 36 1089.0 37 909.0 38 539.0 39 12.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 87.325 2.85 3.45 6.375 2 74.35000000000001 14.625 6.35 4.675 3 42.1 34.449999999999996 12.475 10.975 4 29.675 34.699999999999996 16.85 18.775 5 32.550000000000004 26.25 25.6 15.6 6 17.075000000000003 45.35 22.425 15.15 7 43.75 24.75 16.75 14.75 8 26.700000000000003 28.449999999999996 19.45 25.4 9 22.8 37.025000000000006 23.474999999999998 16.7 10-11 21.7 31.4 29.4375 17.4625 12-13 23.549999999999997 30.425 23.8375 22.1875 14-15 18.987499999999997 39.625 24.9 16.4875 16-17 26.7625 28.449999999999996 21.5625 23.225 18-19 26.987499999999997 24.4 29.812499999999996 18.8 20-21 27.953494186773348 23.32791598949869 30.703837979747465 18.0147518439805 22-23 29.625 20.575 29.599999999999998 20.200000000000003 24-25 23.9375 23.35 29.025000000000002 23.6875 26-27 27.925 22.4625 28.275 21.337500000000002 28-29 22.475 29.912499999999998 29.599999999999998 18.0125 30-31 33.9625 23.6125 24.3 18.125 32-33 27.4125 23.5375 24.8 24.25 34-35 21.48305614605477 35.863448793297486 23.446292359634864 19.20720270101288 36-37 28.050000000000004 22.975 23.3 25.674999999999997 38-39 35.5125 21.6125 25.837500000000002 17.0375 40-41 23.93397524071527 23.22120795298237 34.05026885081906 18.794547955483306 42-43 28.231760730822174 30.18395695157052 24.05205856588662 17.532223751720686 44-45 26.172314617981744 23.658872077028885 32.03701388020508 18.131799424784294 46-47 28.225 20.9 25.674999999999997 25.2 48-49 26.778347293411674 23.215401925240656 26.828353544193025 23.177897237154642 50-51 21.0375 29.1375 25.275 24.55 52-53 22.32232232232232 24.74974974974975 23.173173173173172 29.754754754754753 54-55 21.9625 23.962500000000002 31.087500000000002 22.9875 56-57 29.65 28.487499999999997 24.712500000000002 17.150000000000002 58-59 21.85 27.975 30.625000000000004 19.55 60-61 33.7875 22.925 25.7 17.5875 62-63 19.412499999999998 25.4375 34.2625 20.8875 64-65 20.275000000000002 37.2 25.900000000000002 16.625 66-67 26.5625 31.55 25.1 16.7875 68-69 19.650000000000002 24.8125 29.7 25.837500000000002 70-71 21.433037389020885 29.923721395523323 24.871826935100664 23.77141428035513 72-73 28.66817155756208 21.344369199899674 31.264108352144472 18.72335089039378 74-75 26.65575421808109 29.438428607403676 26.693528078569628 17.212289095945604 76-77 21.10704829151431 22.15357458075905 24.158365905938723 32.58101122178792 78-79 25.723310170562225 28.060644346178144 27.858496525584332 18.3575489576753 80-81 20.866042035958472 37.69308685743226 26.08255254494809 15.35831856166118 82-83 24.65021622996693 24.06512337827525 26.062070719918594 25.222589671839224 84-85 20.035709730901672 25.188113760999876 34.67669940058666 20.099477107511795 86-87 20.010209290454313 30.538540071465032 26.735579377233282 22.71567126084737 88-89 17.508933129147525 25.612557427258803 32.93772332822869 23.940786115364983 90-91 28.062787136294027 27.884124553343543 26.42930066360388 17.62378764675855 92-93 19.29555895865237 26.199591628381828 31.240428790199083 23.264420622766718 >>END_MODULE >>Per sequence GC content fail #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 1.0 17 5.5 18 6.0 19 2.5 20 1.5 21 3.0 22 4.0 23 6.5 24 7.5 25 6.0 26 7.5 27 9.0 28 18.0 29 28.0 30 30.0 31 34.5 32 44.0 33 57.5 34 68.5 35 76.5 36 86.5 37 119.0 38 176.5 39 172.0 40 161.0 41 171.0 42 184.5 43 210.5 44 180.5 45 158.5 46 172.5 47 156.5 48 135.5 49 133.5 50 150.0 51 147.5 52 117.5 53 139.5 54 338.5 55 312.0 56 84.5 57 53.0 58 51.5 59 46.5 60 35.5 61 27.5 62 25.5 63 21.5 64 21.0 65 25.0 66 20.0 67 12.5 68 13.0 69 12.5 70 9.0 71 7.0 72 4.5 73 1.5 74 1.0 75 0.5 76 0.0 77 0.0 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 0.0 20-21 0.0125 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 0.0375 36-37 0.0 38-39 0.0 40-41 0.0375 42-43 0.11249999999999999 44-45 0.0375 46-47 0.0 48-49 0.0125 50-51 0.0 52-53 0.1 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 3.0 71 4.0 72 12.0 73 7.0 74 6.0 75 2.0 76 1.0 77 6.0 78 3.0 79 4.0 80 6.0 81 11.0 82 8.0 83 4.0 84 5.0 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 3918.0 >>END_MODULE >>Sequence Duplication Levels warn #Total Deduplicated Percentage 65.525 #Duplication Level Percentage of deduplicated Percentage of total 1 90.99580312857688 59.62499999999999 2 4.883632201449829 6.4 3 1.3735215566577643 2.7 4 0.45784051888592137 1.2 5 0.4196871423120946 1.375 6 0.15261350629530715 0.6 7 0.2670736360167875 1.225 8 0.38153376573826786 2.0 9 0.15261350629530715 0.8999999999999999 >10 0.8012209080503624 9.875 >50 0.07630675314765357 3.05 >100 0.03815337657382679 11.05 >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 442 11.05 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 66 1.6500000000000001 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 56 1.4000000000000001 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 49 1.225 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 43 1.075 No Hit GGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGG 33 0.8250000000000001 No Hit GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 28 0.7000000000000001 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 23 0.575 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 22 0.5499999999999999 No Hit GGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTT 19 0.475 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 16 0.4 No Hit GTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAA 15 0.375 No Hit GGAAGAGCCCGAGCTGCTGCAGCAGGTTTTGAAAAGGGAATCGATCGTGA 15 0.375 No Hit GGCCTGTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCG 14 0.35000000000000003 No Hit CAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCT 14 0.35000000000000003 No Hit GGAAAAGAAAGCAAAAGCGATTCCCGTAGTAGCGGCGAGCGAAATGGGAG 14 0.35000000000000003 No Hit GGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCG 13 0.325 No Hit GGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAA 12 0.3 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 12 0.3 No Hit GGAGTCCCATATATATATGTATAAGATGCCAGCCCGGTTTCGTCAACCAT 12 0.3 No Hit GGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGGG 11 0.27499999999999997 No Hit CAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATAT 10 0.25 No Hit GGAGCAGCCTAAACCGTGAAAACGGGGTTGTGGGAGAGCAATACAAGCGT 10 0.25 No Hit GGGTTGTGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGA 10 0.25 No Hit GTACTATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTT 9 0.22499999999999998 No Hit GGGAGTATTATGAAAGGAGATTAATCATAGATTATCAAAAACCCTAGAAA 9 0.22499999999999998 No Hit GGAAAAGAGGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTTG 9 0.22499999999999998 No Hit GGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAA 9 0.22499999999999998 No Hit GGGATGGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACGA 8 0.2 No Hit GGTGGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGC 8 0.2 No Hit GGATTTGAAGAAAAAAAAGACTTCGATTCATTTTCTATTTATTTCGTTAG 8 0.2 No Hit GGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAACCCTCTTAACT 8 0.2 No Hit GGAGTATCCTTGATATATAAATATATAGATAAATAGATTTAAATGGAAAA 8 0.2 No Hit GGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGCA 8 0.2 No Hit GGGCCATTTGTGGCATGCAGGAAGAGCCCGAGCTGCTGCAGCAGGTTTTG 8 0.2 No Hit GGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGC 8 0.2 No Hit GGTTTTGAAAAGGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAA 8 0.2 No Hit GGGTGAGAGCCCCGTCCGGCCCGGACCCTGTCGCCCCACGAGGCGCCGTC 8 0.2 No Hit GGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCTAAATGGATTC 7 0.17500000000000002 No Hit GCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATC 7 0.17500000000000002 No Hit GGAAGGGCGTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAGCAT 7 0.17500000000000002 No Hit GGGGATGGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACG 7 0.17500000000000002 No Hit GTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAA 7 0.17500000000000002 No Hit GGGCAAGGAGAAGTACAAGTGCGGATCCAACGTCTTCTGGAAATGGTGAA 7 0.17500000000000002 No Hit GGGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTG 7 0.17500000000000002 No Hit GGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAA 6 0.15 No Hit GAGGAAGGGCGTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAGC 6 0.15 No Hit GGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAAA 6 0.15 No Hit GGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCTAAA 6 0.15 No Hit GGGCTGCGAGGAATCCGGCAAGGCATAAACAACCAAGGACAGCTCCGTAT 5 0.125 No Hit GGAGTGGGGGTGCCATACGCAAAAAGGAAGCGACTCATAGAATGGCAGAG 5 0.125 No Hit GGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCG 5 0.125 No Hit GCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCT 5 0.125 No Hit GGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAACCCTCTTAACTA 5 0.125 No Hit GGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTT 5 0.125 No Hit GGGAAACAACGACGTCATCATCGACATGATATATTGCTGCTATTTTCCAC 5 0.125 No Hit GGAATAAGAATAAATCGCAACTCCTTTCCACTACACATAAAAATTGATTT 5 0.125 No Hit GTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCT 5 0.125 No Hit GAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGC 5 0.125 No Hit CAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTG 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 0.025 0.0 0.0 0.0 0.0 74-75 0.025 0.0 0.0 0.0 0.0 76-77 0.025 0.0 0.0 0.0 0.0 78-79 0.025 0.0 0.0 0.0 0.0 80-81 0.025 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GTTCAAC 20 0.002796204 64.85625 4 CAATACA 60 5.456968E-12 64.85625 8 GGAGAGC 65 1.2732926E-11 59.86731 2 GCAATAC 65 1.2732926E-11 59.86731 7 GGGAGAG 65 1.2732926E-11 59.86731 1 GAGCAAT 65 1.2732926E-11 59.86731 5 AGAGCAA 65 1.2732926E-11 59.86731 4 AATACAA 65 1.2732926E-11 59.86731 9 AGCAATA 65 1.2732926E-11 59.86731 6 GAGAGCA 70 2.7284841E-11 55.591072 3 ATCACTA 50 1.8189894E-11 44.346153 84-85 CACTAGC 50 1.8189894E-11 44.346153 86-87 ACTAGCT 45 3.3469405E-10 44.346153 86-87 GCATCAC 50 1.8189894E-11 44.346153 82-83 AAGCATC 50 1.8189894E-11 44.346153 80-81 CCGAAAG 50 1.8189894E-11 44.346153 76-77 CAGTAGC 50 2.0008883E-11 43.78481 70-71 TCCAGTA 55 1.8189894E-12 43.78481 68-69 AGCCGAA 50 2.0008883E-11 43.78481 74-75 GTAGCCG 50 2.0008883E-11 43.78481 72-73 >>END_MODULE Rejected 269870 READS because READLEN < 1 Read 269870 spots for ERR6133548.sra Written 269870 spots for ERR6133548.sra Rejected 269870 READS because READLEN < 1 Read 269870 spots for ERR6133548.sra Written 269870 spots for ERR6133548.sra Rejected 269870 READS because READLEN < 1 Read 269870 spots for ERR6133548.sra Written 269870 spots for ERR6133548.sra Rejected 269870 READS because READLEN < 1 Read 269870 spots for ERR6133548.sra Written 269870 spots for ERR6133548.sra Rejected 269870 READS because READLEN < 1 Read 269870 spots for ERR6133548.sra Written 269870 spots for ERR6133548.sra Rejected 269870 READS because READLEN < 1 Read 269870 spots for ERR6133548.sra Written 269870 spots for ERR6133548.sra Rejected 269870 READS because READLEN < 1 Read 269870 spots for ERR6133548.sra Written 269870 spots for ERR6133548.sra Rejected 269870 READS because READLEN < 1 Read 269870 spots for ERR6133548.sra Written 269870 spots for ERR6133548.sra Rejected 269870 READS because READLEN < 1 Read 269870 spots for ERR6133548.sra Written 269870 spots for ERR6133548.sra Rejected 269875 READS because READLEN < 1 Read 269875 spots for ERR6133548.sra Written 269875 spots for ERR6133548.sra Rejected 269870 READS because READLEN < 1 Read 269870 spots for ERR6133548.sra Written 269870 spots for ERR6133548.sra Rejected 269870 READS because READLEN < 1 Read 269870 spots for ERR6133548.sra Written 269870 spots for ERR6133548.sra Rejected 269870 READS because READLEN < 1 Read 269870 spots for ERR6133548.sra Written 269870 spots for ERR6133548.sra Rejected 269870 READS because READLEN < 1 Read 269870 spots for ERR6133548.sra Written 269870 spots for ERR6133548.sra Rejected 269870 READS because READLEN < 1 Read 269870 spots for ERR6133548.sra Written 269870 spots for ERR6133548.sra Rejected 269870 READS because READLEN < 1 Read 269870 spots for ERR6133548.sra Written 269870 spots for ERR6133548.sra Rejected 269870 READS because READLEN < 1 Read 269870 spots for ERR6133548.sra Written 269870 spots for ERR6133548.sra Rejected 269870 READS because READLEN < 1 Read 269870 spots for ERR6133548.sra Written 269870 spots for ERR6133548.sra Rejected 269870 READS because READLEN < 1 Read 269870 spots for ERR6133548.sra Written 269870 spots for ERR6133548.sra Rejected 269870 READS because READLEN < 1 Read 269870 spots for ERR6133548.sra Written 269870 spots for ERR6133548.sra SRR ids: ['ERR6133548.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_aokcm5qd ERR6133548.sra spots: 5397405 blocks: [[1, 269870], [269871, 539740], [539741, 809610], [809611, 1079480], [1079481, 1349350], [1349351, 1619220], [1619221, 1889090], [1889091, 2158960], [2158961, 2428830], [2428831, 2698700], [2698701, 2968570], [2968571, 3238440], [3238441, 3508310], [3508311, 3778180], [3778181, 4048050], [4048051, 4317920], [4317921, 4587790], [4587791, 4857660], [4857661, 5127530], [5127531, 5397405]] ERR6133548 file size 1196464 ERR6133548 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 ERR6133548 ERR6133548_1.fastq Input file: ERR6133548_1.fastq trimmed: ERR6133548-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 08:24:02 2024 >> started Sat Dec 7 08:24:04 2024 >> done (2.781s) 5397405 reads processed; of these: 115 ( 0.00%) short reads filtered out after trimming by size control 10 ( 0.00%) empty reads filtered out after trimming by size control 5397280 (100.00%) reads available; of these: 89459 ( 1.66%) trimmed reads available after processing 5307821 (98.34%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 8 0.00% 19 35 0.00% 20 11 0.00% 21 5 0.00% 22 6 0.00% 23 6 0.00% 24 9 0.00% 25 4 0.00% 26 6 0.00% 27 7 0.00% 28 5 0.00% 29 8 0.00% 30 1 0.00% 31 5 0.00% 32 13 0.00% 33 11 0.00% 34 8 0.00% 35 59 0.00% 36 439 0.01% 37 18 0.00% 38 19 0.00% 39 29 0.00% 40 53 0.00% 41 15 0.00% 42 7 0.00% 43 7 0.00% 44 7 0.00% 45 7 0.00% 46 4 0.00% 47 7 0.00% 48 5 0.00% 49 13 0.00% 50 4 0.00% 51 13 0.00% 52 7 0.00% 53 4 0.00% 54 1 0.00% 55 1 0.00% 56 5 0.00% 57 4 0.00% 58 8 0.00% 59 2 0.00% 60 4 0.00% 61 6 0.00% 62 3 0.00% 63 5 0.00% 64 3 0.00% 65 8 0.00% 66 17 0.00% 67 20 0.00% 68 27 0.00% 69 91 0.00% 70 6869 0.13% 71 5752 0.11% 72 5984 0.11% 73 5591 0.10% 74 5991 0.11% 75 5824 0.11% 76 5462 0.10% 77 5718 0.11% 78 6549 0.12% 79 7552 0.14% 80 7367 0.14% 81 9100 0.17% 82 9857 0.18% 83 8875 0.16% 84 8252 0.15% 85 195 0.00% 86 345 0.01% 87 568 0.01% 88 1077 0.02% 89 2167 0.04% 90 4920 0.09% 91 15228 0.28% 92 62206 1.15% 93 5204761 96.43% 5397280 reads passed initial QC criterion=sequence-density sequence-density=0.52 sequence-density-rank=1 fanout-score=1.99 fanout-score-rank=27 prefix-density=0.52 prefix-fanout=2.0 sequence=CAAGGCTAAATAC criterion=fanout-score sequence-density=0.01 sequence-density-rank=34 fanout-score=59.94 fanout-score-rank=1 prefix-density=0.09 prefix-fanout=5.9 sequence=AAAAGAAGGGGTGTTCCATCTCCGGACGACGATCCTGCCTGCGGAGGAAGACATGCCGGCGATCATGTCGAGCTTCAAGAAGTTCAACGACTCATTCATGGAGCAATACCAAGACTACTCCAGGCTGTGATGTGAAGAGGGAAACAACGACGTCATCATCGACATGATATATTGCTGCTATTTTCCACCAGCGATTAAAAGTTAAAAAATTTAGCTGTAAGCTGTAACTATCTTGAAGAAACTAAACTGGTTGCTGTGCTTGATATGTATAGGGAAAACATAATTTATGAGACAATCATACTGTGCAACTCTTGGCTCCATCGATTAATTAATACTCCTTGTTATTGCTTGCATGGT Started job on | Dec 07 08:24:16 Started mapping on | Dec 07 08:24:16 Finished on | Dec 07 08:24:24 Mapping speed, Million of reads per hour | 2428.78 Number of input reads | 5397280 Average input read length | 92 UNIQUE READS: Uniquely mapped reads number | 2897114 Uniquely mapped reads % | 53.68% Average mapped length | 92.24 Number of splices: Total | 127063 Number of splices: Annotated (sjdb) | 103759 Number of splices: GT/AG | 121174 Number of splices: GC/AG | 3020 Number of splices: AT/AC | 137 Number of splices: Non-canonical | 2732 Mismatch rate per base, % | 0.42% Deletion rate per base | 0.04% Deletion average length | 1.75 Insertion rate per base | 0.03% Insertion average length | 2.17 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 2387980 % of reads mapped to multiple loci | 44.24% Number of reads mapped to too many loci | 46286 % of reads mapped to too many loci | 0.86% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.17% % of reads unmapped: other | 0.05% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 112186 112186 112186 N_multimapping 2387980 2387980 2387980 N_noFeature 246166 279012 2765670 N_ambiguous 112621 13971 450 UnstrandedReadsAssigned:2538327 PositiveStrandReadsAssigned:2604131 NegativeStrandReadsAssigned:130994 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=93 echo kmer=89 ERR6133548 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: ERR6133548-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 5,397,280 reads, 3,753,015 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 996 rounds 52973 ERR6133548.ke.tsv 35125 ERR6133548.se.tsv 88098 total ==> ERR6133548.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 94 23.9914 PNS24243 293 194 0 0 KQK14069 1603 1504 388.079 90.3553 KQK14071 474 375 0 0 ==> ERR6133548.se.tsv <== BRADI_1g14170v3 395 BRADI_1g53295v3 18 BRADI_1g59795v3 24 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 24 BRADI_1g74790v3 27 BRADI_1g09890v3 0 BRADI_1g77505v3 48 BRADI_1g48960v3 0 ERR6133548 completed mapping pipeline successfully