Starting /dee2/code/volunteer_pipeline.sh ERR6133491 current disk space = 1544562327552 free memory = 1600204480 ERR6133491 SRAfilesize 5a541682c05dd0339ab94005354fb85e ERR6133491.sra ERR6133491.sra file validated ERR6133491 is single end ERR6133491 is conventional basespace ERR6133491 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133491_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 44 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 35.20475 37.0 33.0 37.0 33.0 37.0 2 36.43075 37.0 37.0 37.0 33.0 37.0 3 36.166 37.0 37.0 37.0 33.0 37.0 4 35.9085 37.0 37.0 37.0 33.0 37.0 5 35.69325 37.0 37.0 37.0 33.0 37.0 6 35.90075 37.0 37.0 37.0 33.0 37.0 7 37.881 40.0 37.0 40.0 33.0 40.0 8 37.7915 40.0 37.0 40.0 33.0 40.0 9 37.8815 40.0 37.0 40.0 33.0 40.0 10-11 37.753625 40.0 37.0 40.0 33.0 40.0 12-13 37.672 40.0 37.0 40.0 33.0 40.0 14-15 37.655875 40.0 37.0 40.0 33.0 40.0 16-17 37.482124999999996 40.0 37.0 40.0 33.0 40.0 18-19 37.407125 40.0 37.0 40.0 33.0 40.0 20-21 37.227125 37.0 37.0 40.0 33.0 40.0 22-23 37.2235 37.0 37.0 40.0 33.0 40.0 24-25 37.34525 38.5 37.0 40.0 33.0 40.0 26-27 37.296375 37.0 37.0 40.0 33.0 40.0 28-29 37.31575 37.0 37.0 40.0 33.0 40.0 30-31 37.2645 37.0 37.0 40.0 33.0 40.0 32-33 37.100375 37.0 37.0 40.0 33.0 40.0 34-35 36.939875 37.0 37.0 40.0 33.0 40.0 36-37 36.77475 37.0 37.0 40.0 33.0 40.0 38-39 36.45625 37.0 37.0 40.0 33.0 40.0 40-41 36.257374999999996 37.0 37.0 40.0 33.0 40.0 42-43 35.973124999999996 37.0 37.0 40.0 33.0 40.0 44-45 35.364000000000004 37.0 33.0 40.0 27.0 40.0 46-47 34.876 37.0 33.0 37.0 27.0 40.0 48-49 34.91275 37.0 33.0 37.0 30.0 40.0 50-51 34.732875 37.0 33.0 37.0 27.0 40.0 52-53 34.41575 37.0 33.0 37.0 27.0 40.0 54-55 34.500375000000005 37.0 33.0 37.0 27.0 40.0 56-57 33.916125 37.0 33.0 37.0 27.0 40.0 58-59 31.594375 33.0 30.0 37.0 22.0 37.0 60-61 33.261875 35.0 33.0 37.0 27.0 37.0 62-63 33.41137500000001 37.0 33.0 37.0 27.0 37.0 64-65 33.456125 37.0 33.0 37.0 27.0 37.0 66-67 33.016 37.0 33.0 37.0 27.0 37.0 68-69 32.432 35.0 33.0 37.0 24.5 37.0 70-71 32.60814267834793 33.0 33.0 37.0 27.0 37.0 72-73 32.947284533025815 35.0 33.0 37.0 27.0 37.0 74-75 32.70756217093147 37.0 33.0 37.0 22.0 37.0 76-77 33.042551055706454 37.0 33.0 37.0 27.0 37.0 78-79 33.01451956214886 35.0 33.0 37.0 27.0 37.0 80-81 33.12697897903503 37.0 33.0 37.0 27.0 37.0 82-83 32.91979172997766 33.0 33.0 37.0 27.0 37.0 84-85 32.48420291365238 33.0 33.0 37.0 24.5 37.0 86-87 32.5138960370561 33.0 33.0 37.0 27.0 37.0 88-89 32.75797735460628 33.0 33.0 37.0 27.0 37.0 90-91 32.25450334534226 33.0 33.0 37.0 22.0 37.0 92-93 32.33286155429748 33.0 33.0 37.0 24.5 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 14.0 21 21.0 22 29.0 23 22.0 24 37.0 25 46.0 26 54.0 27 53.0 28 58.0 29 71.0 30 117.0 31 140.0 32 160.0 33 208.0 34 272.0 35 487.0 36 779.0 37 888.0 38 536.0 39 8.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 78.475 5.025 8.225 8.275 2 59.150000000000006 24.25 10.825 5.775 3 27.800000000000004 38.574999999999996 17.349999999999998 16.275000000000002 4 28.975 25.7 20.9 24.425 5 24.95 24.825 34.575 15.65 6 16.975 39.4 24.65 18.975 7 35.8 29.9 18.9 15.4 8 28.4 29.725 24.375 17.5 9 21.475 28.199999999999996 29.5 20.825 10-11 20.5875 26.700000000000003 32.2 20.5125 12-13 21.725 29.025000000000002 25.937500000000004 23.3125 14-15 20.1 33.1125 28.037499999999998 18.75 16-17 23.5375 32.275 22.775000000000002 21.4125 18-19 21.762500000000003 28.5875 30.2625 19.3875 20-21 25.874999999999996 25.95 29.2875 18.8875 22-23 29.7375 21.637500000000003 29.275000000000002 19.35 24-25 24.85 29.4875 27.6375 18.025 26-27 25.05 25.0125 33.1125 16.825000000000003 28-29 24.9125 30.0875 26.687499999999996 18.3125 30-31 26.424999999999997 26.637499999999996 28.375 18.5625 32-33 24.8625 26.8125 29.362500000000004 18.9625 34-35 21.1375 33.5125 25.2 20.150000000000002 36-37 26.597474052769787 27.135175690884083 23.983993997749156 22.283356258596974 38-39 29.739869934967484 22.873936968484244 29.952476238119058 17.433716858429214 40-41 25.912499999999998 25.374999999999996 26.387500000000003 22.325 42-43 27.131782945736433 29.469867466866717 25.10627656914228 18.292073018254566 44-45 21.94298574643661 28.382095523880967 32.04551137784446 17.62940735183796 46-47 25.85646411602901 25.881470367591895 28.257064266066518 20.005001250312578 48-49 22.875 26.987499999999997 30.2 19.9375 50-51 20.868259727261353 28.024521456274236 28.875265857625422 22.231952958838985 52-53 25.791119449656037 26.441525953721072 24.30268918073796 23.464665415884927 54-55 25.7125 24.125 33.800000000000004 16.3625 56-57 29.512500000000003 26.8375 26.387500000000003 17.2625 58-59 23.65 25.575 31.587500000000002 19.1875 60-61 27.3125 27.6875 28.3875 16.6125 62-63 18.8125 32.7125 31.525 16.950000000000003 64-65 19.3125 32.8625 30.8 17.025000000000002 66-67 23.425 32.1125 26.1625 18.3 68-69 20.349999999999998 27.0875 27.9375 24.625 70-71 22.689180737961227 30.49405878674171 27.392120075046904 19.424640400250155 72-73 25.402010050251256 25.125628140703515 28.693467336683415 20.77889447236181 74-75 24.25580221997982 27.800201816347126 30.33551967709385 17.608476286579215 76-77 22.070361933687675 26.044039483675018 24.879777271576817 27.00582131106049 78-79 26.21371529978451 26.251742933198123 29.775636962859682 17.758904804157687 80-81 21.423116089613035 34.99236252545825 27.838594704684315 15.745926680244398 82-83 21.292386436340372 26.87140115163148 29.63531669865643 22.20089571337172 84-85 21.726840549916485 22.30502376975459 35.44905563407427 20.519080046254658 86-87 20.92125579001544 27.599073597529593 29.18167781780752 22.297992794647453 88-89 17.91044776119403 32.83582089552239 29.38754503345342 19.86618630983016 90-91 27.09727225939269 26.865671641791046 28.56407617086979 17.472979927946476 92-93 21.10138960370561 33.06742151312403 27.766340710241895 18.06484817292846 >>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 1.5 17 31.5 18 36.0 19 7.5 20 3.0 21 5.0 22 7.0 23 9.5 24 11.0 25 8.0 26 8.5 27 11.5 28 23.5 29 35.5 30 33.0 31 37.5 32 43.5 33 56.5 34 71.5 35 75.5 36 109.5 37 201.5 38 278.0 39 224.5 40 164.0 41 188.0 42 229.5 43 254.0 44 210.0 45 157.5 46 149.5 47 142.5 48 139.5 49 170.5 50 220.0 51 209.5 52 144.5 53 119.5 54 153.5 55 117.5 56 41.0 57 28.5 58 29.5 59 27.5 60 20.5 61 15.0 62 11.0 63 11.5 64 12.5 65 9.5 66 6.0 67 3.5 68 3.5 69 3.0 70 3.5 71 5.0 72 6.0 73 6.5 74 4.5 75 2.0 76 1.0 77 0.5 78 0.5 79 1.0 80 0.5 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 0.0 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 0.0 36-37 0.0375 38-39 0.05 40-41 0.0 42-43 0.025 44-45 0.025 46-47 0.025 48-49 0.0 50-51 0.08750000000000001 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 5.0 71 8.0 72 14.0 73 7.0 74 4.0 75 10.0 76 2.0 77 4.0 78 3.0 79 11.0 80 8.0 81 13.0 82 7.0 83 7.0 84 11.0 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 3886.0 >>END_MODULE >>Sequence Duplication Levels warn #Total Deduplicated Percentage 60.475 #Duplication Level Percentage of deduplicated Percentage of total 1 89.2104175279041 53.949999999999996 2 5.126085159156676 6.2 3 1.7362546506821002 3.15 4 0.7441091360066143 1.7999999999999998 5 0.6200909466721786 1.875 6 0.49607275733774286 1.7999999999999998 7 0.37205456800330716 1.575 8 0.24803637866887143 1.2 9 0.1653575857792476 0.8999999999999999 >10 1.0748243075651096 13.5 >50 0.0826787928896238 3.375 >100 0.12401818933443572 10.674999999999999 >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 TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 151 3.775 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 145 3.6249999999999996 No Hit GGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGC 131 3.2750000000000004 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 70 1.7500000000000002 No Hit GGAGTATCCTTGATATATAAATATATAGATAAATAGATTTAAATGGAAAA 65 1.625 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 48 1.2 No Hit GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 46 1.15 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 44 1.0999999999999999 No Hit CAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCT 27 0.675 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 25 0.625 No Hit GGGGATGGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACG 23 0.575 No Hit GTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCT 23 0.575 No Hit GTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAG 22 0.5499999999999999 No Hit GGGATGGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACGA 21 0.525 No Hit TCAAAAGAGGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGGA 21 0.525 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 20 0.5 No Hit GGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGC 20 0.5 No Hit GGGAGTATTATGAAAGGAGATTAATCATAGATTATCAAAAACCCTAGAAA 18 0.44999999999999996 No Hit GGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAAGGCGATCAAATTC 16 0.4 No Hit GGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAA 16 0.4 No Hit GGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGG 16 0.4 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 16 0.4 No Hit GAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTG 16 0.4 No Hit GTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAA 15 0.375 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTTTTTA 14 0.35000000000000003 No Hit GGGGTACTCTTTCTACACCTATATTAGTATTAGTACCGAAATGCTTTAAA 13 0.325 No Hit GAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGC 13 0.325 No Hit GGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGGG 12 0.3 No Hit GGCCTGTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCG 12 0.3 No Hit GTACAAGCTCGTAACGAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAAT 12 0.3 No Hit GGGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTG 11 0.27499999999999997 No Hit GGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGC 9 0.22499999999999998 No Hit GGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAAA 9 0.22499999999999998 No Hit GGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAA 9 0.22499999999999998 No Hit CAACATAGGTCATCGAAAAGATCTCGGACGACTCACCAAAGCACGAAAGC 9 0.22499999999999998 No Hit GGGCATTCGTATTTCATAGTCAGAGGTGAAATTCTTGGATTTATGAAAGA 8 0.2 No Hit GGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTT 8 0.2 No Hit GGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTT 8 0.2 No Hit GTATTTAGCCTTGCAAGGTGGTCCTTGCTGATTCACACGGGATTCCACGT 8 0.2 No Hit GGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCTAAA 8 0.2 No Hit AACGAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGC 8 0.2 No Hit GCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATC 7 0.17500000000000002 No Hit GGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGT 7 0.17500000000000002 No Hit GGTGGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGC 7 0.17500000000000002 No Hit GAAGCCTGTGTACAAGCTCGTAACGAAGGGCGCGATCTTGCTCGTGAAGG 7 0.17500000000000002 No Hit AACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCG 7 0.17500000000000002 No Hit GATACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGC 7 0.17500000000000002 No Hit AGTCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAA 7 0.17500000000000002 No Hit GGGAGTATCCTTGATATATAAATATATAGATAAATAGATTTAAATGGAAA 7 0.17500000000000002 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTTA 7 0.17500000000000002 No Hit GGTATTAGTACTATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATC 6 0.15 No Hit GTACTATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTT 6 0.15 No Hit CACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTTCGGGGAGT 6 0.15 No Hit GGGAGGGGCTTGGCTACAATTCCGAATACGCTATTACATGTTTGCGCTAG 6 0.15 No Hit CTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGT 6 0.15 No Hit GGGCCGGGTATCTCTCTGCATGTACGTATGCCTGTAATGTACGTAGCTAC 6 0.15 No Hit GGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGCA 6 0.15 No Hit GGGGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCT 6 0.15 No Hit GGGGCATTCGTATTTCATAGTCAGAGGTGAAATTCTTGGATTTATGAAAG 6 0.15 No Hit GGTTTTGAAAAGGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAA 6 0.15 No Hit GGAAAAAGTGCTAACAAATTCTTGTCTTATCTGCATTAGACAAAATGAAG 6 0.15 No Hit CAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTG 6 0.15 No Hit GCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGGTATG 5 0.125 No Hit GGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCTAAATGGATTC 5 0.125 No Hit GGAAGAGTCCTCTTAATATTTATCTAATCTTATATAGGTTTCAGTATATT 5 0.125 No Hit GGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTG 5 0.125 No Hit GGAGAAGAACACTTCCTCCGTGCATATGCGTGTACGTGGGTTGATCGGTG 5 0.125 No Hit GGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGGAAGGGCGTA 5 0.125 No Hit GATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAAT 5 0.125 No Hit GGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTA 5 0.125 No Hit GTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAAGGCGATCAAATTCGAG 5 0.125 No Hit GGAAGAGCCCGAGCTGCTGCAGCAGGTTTTGAAAAGGGAATCGATCGTGA 5 0.125 No Hit GTATTAGTACTATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATCT 5 0.125 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTTTTAA 5 0.125 No Hit CACGAACGTAATGCTCACAACTTCCCTCTAGATCTAGCTGCTCTTGAAGT 5 0.125 No Hit GGATTTGTTAAATCAAATCCTTGGTTTAATAACGAACGGTGTTAACTTAC 5 0.125 No Hit GAACGTAATGCTCACAACTTCCCTCTAGATCTAGCTGCTCTTGAAGTTCC 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 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GGAGAGC 15 9.013085E-4 86.262505 2 GCAATAC 15 9.013085E-4 86.262505 7 GGGAGAG 15 9.013085E-4 86.262505 1 CAATACA 15 9.013085E-4 86.262505 8 GAGCAAT 15 9.013085E-4 86.262505 5 AGAGCAA 15 9.013085E-4 86.262505 4 GAGAGCA 15 9.013085E-4 86.262505 3 AATACAA 15 9.013085E-4 86.262505 9 AGCAATA 15 9.013085E-4 86.262505 6 GGCACCC 55 0.0 78.420456 7 CTAGGCA 55 0.0 78.420456 4 AGGCACC 55 0.0 78.420456 6 GCACCCA 55 0.0 78.420456 8 TACCTAG 55 0.0 78.420456 1 ACCTAGG 55 0.0 78.420456 2 CCTAGGC 55 0.0 78.420456 3 TAGGCAC 55 0.0 78.420456 5 CACCCAG 65 0.0 66.35577 9 TCCCAAA 50 1.8189894E-11 44.23718 84-85 CCAAATA 50 1.8189894E-11 44.23718 86-87 >>END_MODULE Rejected 337336 READS because READLEN < 1 Read 337336 spots for ERR6133491.sra Written 337336 spots for ERR6133491.sra Rejected 337336 READS because READLEN < 1 Read 337336 spots for ERR6133491.sra Written 337336 spots for ERR6133491.sra Rejected 337336 READS because READLEN < 1 Read 337336 spots for ERR6133491.sra Written 337336 spots for ERR6133491.sra Rejected 337336 READS because READLEN < 1 Read 337336 spots for ERR6133491.sra Written 337336 spots for ERR6133491.sra Rejected 337336 READS because READLEN < 1 Read 337336 spots for ERR6133491.sra Written 337336 spots for ERR6133491.sra Rejected 337336 READS because READLEN < 1 Read 337336 spots for ERR6133491.sra Written 337336 spots for ERR6133491.sra Rejected 337336 READS because READLEN < 1 Read 337336 spots for ERR6133491.sra Written 337336 spots for ERR6133491.sra Rejected 337336 READS because READLEN < 1 Read 337336 spots for ERR6133491.sra Written 337336 spots for ERR6133491.sra Rejected 337336 READS because READLEN < 1 Read 337336 spots for ERR6133491.sra Written 337336 spots for ERR6133491.sra Rejected 337336 READS because READLEN < 1 Read 337336 spots for ERR6133491.sra Written 337336 spots for ERR6133491.sra Rejected 337336 READS because READLEN < 1 Read 337336 spots for ERR6133491.sra Written 337336 spots for ERR6133491.sra Rejected 337336 READS because READLEN < 1 Read 337336 spots for ERR6133491.sra Written 337336 spots for ERR6133491.sra Rejected 337336 READS because READLEN < 1 Read 337336 spots for ERR6133491.sra Written 337336 spots for ERR6133491.sra Rejected 337336 READS because READLEN < 1 Read 337336 spots for ERR6133491.sra Written 337336 spots for ERR6133491.sra Rejected 337336 READS because READLEN < 1 Read 337336 spots for ERR6133491.sra Written 337336 spots for ERR6133491.sra Rejected 337336 READS because READLEN < 1 Read 337336 spots for ERR6133491.sra Written 337336 spots for ERR6133491.sra Rejected 337336 READS because READLEN < 1 Read 337336 spots for ERR6133491.sra Written 337336 spots for ERR6133491.sra Rejected 337352 READS because READLEN < 1 Read 337352 spots for ERR6133491.sra Written 337352 spots for ERR6133491.sra Rejected 337336 READS because READLEN < 1 Read 337336 spots for ERR6133491.sra Written 337336 spots for ERR6133491.sra Rejected 337336 READS because READLEN < 1 Read 337336 spots for ERR6133491.sra Written 337336 spots for ERR6133491.sra SRR ids: ['ERR6133491.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_b_9uivsa ERR6133491.sra spots: 6746736 blocks: [[1, 337336], [337337, 674672], [674673, 1012008], [1012009, 1349344], [1349345, 1686680], [1686681, 2024016], [2024017, 2361352], [2361353, 2698688], [2698689, 3036024], [3036025, 3373360], [3373361, 3710696], [3710697, 4048032], [4048033, 4385368], [4385369, 4722704], [4722705, 5060040], [5060041, 5397376], [5397377, 5734712], [5734713, 6072048], [6072049, 6409384], [6409385, 6746736]] ERR6133491 file size 1493583 ERR6133491 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 ERR6133491 ERR6133491_1.fastq Input file: ERR6133491_1.fastq trimmed: ERR6133491-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 07:12:32 2024 >> started Sat Dec 7 07:12:35 2024 >> done (3.286s) 6746736 reads processed; of these: 258 ( 0.00%) short reads filtered out after trimming by size control 34 ( 0.00%) empty reads filtered out after trimming by size control 6746444 (100.00%) reads available; of these: 94439 ( 1.40%) trimmed reads available after processing 6652005 (98.60%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 31 0.00% 19 59 0.00% 20 46 0.00% 21 63 0.00% 22 70 0.00% 23 20 0.00% 24 21 0.00% 25 18 0.00% 26 17 0.00% 27 32 0.00% 28 62 0.00% 29 67 0.00% 30 48 0.00% 31 74 0.00% 32 39 0.00% 33 43 0.00% 34 57 0.00% 35 634 0.01% 36 667 0.01% 37 50 0.00% 38 77 0.00% 39 297 0.00% 40 151 0.00% 41 156 0.00% 42 16 0.00% 43 21 0.00% 44 19 0.00% 45 17 0.00% 46 15 0.00% 47 16 0.00% 48 11 0.00% 49 16 0.00% 50 13 0.00% 51 41 0.00% 52 8 0.00% 53 11 0.00% 54 11 0.00% 55 11 0.00% 56 18 0.00% 57 28 0.00% 58 20 0.00% 59 14 0.00% 60 22 0.00% 61 18 0.00% 62 3 0.00% 63 6 0.00% 64 3 0.00% 65 9 0.00% 66 10 0.00% 67 18 0.00% 68 39 0.00% 69 114 0.00% 70 13301 0.20% 71 11861 0.18% 72 14664 0.22% 73 11280 0.17% 74 12342 0.18% 75 12964 0.19% 76 10909 0.16% 77 10954 0.16% 78 13656 0.20% 79 15514 0.23% 80 14790 0.22% 81 18543 0.27% 82 19025 0.28% 83 18466 0.27% 84 16097 0.24% 85 273 0.00% 86 465 0.01% 87 810 0.01% 88 1492 0.02% 89 2637 0.04% 90 5538 0.08% 91 16533 0.25% 92 61012 0.90% 93 6439971 95.46% 6746444 reads passed initial QC criterion=sequence-density sequence-density=0.50 sequence-density-rank=1 fanout-score=1.00 fanout-score-rank=31 prefix-density=0.01 prefix-fanout=1.0 sequence=GGGAGTATTATGAAAGGAGATTAATCATAGATTATCAAAAACCCTAGAAAAAATTCTTCCTGGGTCGATGCCCGAGCGGTTAATGGGGACGGACTGTAAATTCGTTGACAAAATGTCTACGCTGGTTCAAATCCAGCTCGGCCCAAAAATCTGGGGCTTCGTGAATATGAACTAAATCTTTTTATTTTTC criterion=fanout-score sequence-density=0.01 sequence-density-rank=39 fanout-score=59.25 fanout-score-rank=1 prefix-density=0.37 prefix-fanout=1.0 sequence=GGCATTTTGGATTTCAGGGCTTTTAGCCCCGATTAGTGAAGGACCCGAAAAGCTTTCTAGTTATGAATCGGGTATAGAACCCATGGGAGGGGCTTGGCTACAATTCCGAATACGCTATTACATGTTTGCGCTAGTTTTTGTTGTTTTTGATGTGGAAACCGTCTTTCTCTACCCTTGGGCAATGAGTTTCGACGTATTGGGTGTATCCGTTTTTATCGAAGCTTTCATTTTCGTGCTTATCCTAGTTGTTGGTTTAGTTTATGCATGGCGAAAAGGAGCCTTGGAATGGTCTTAACTGAATATTTA Started job on | Dec 07 07:12:50 Started mapping on | Dec 07 07:12:51 Finished on | Dec 07 07:12:58 Mapping speed, Million of reads per hour | 3469.60 Number of input reads | 6746444 Average input read length | 92 UNIQUE READS: Uniquely mapped reads number | 2970019 Uniquely mapped reads % | 44.02% Average mapped length | 91.76 Number of splices: Total | 90379 Number of splices: Annotated (sjdb) | 65895 Number of splices: GT/AG | 81868 Number of splices: GC/AG | 2399 Number of splices: AT/AC | 245 Number of splices: Non-canonical | 5867 Mismatch rate per base, % | 0.50% Deletion rate per base | 0.06% Deletion average length | 1.80 Insertion rate per base | 0.03% Insertion average length | 1.82 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 3541169 % of reads mapped to multiple loci | 52.49% Number of reads mapped to too many loci | 124844 % of reads mapped to too many loci | 1.85% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.51% % of reads unmapped: other | 0.13% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 235256 235256 235256 N_multimapping 3541169 3541169 3541169 N_noFeature 354239 388986 2844175 N_ambiguous 108455 17145 900 UnstrandedReadsAssigned:2507325 PositiveStrandReadsAssigned:2563888 NegativeStrandReadsAssigned:124944 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=93 echo kmer=89 ERR6133491 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: ERR6133491-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 6,746,444 reads, 5,033,819 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,021 rounds 52973 ERR6133491.ke.tsv 35125 ERR6133491.se.tsv 88098 total ==> ERR6133491.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 837 0 0 PNS24247 1044 945 0 0 PNS24249 1928 1829 4.00219 0.576988 PNS24246 1044 945 0 0 PNS24248 1044 945 0 0 PNS24244 1471 1372 60.9978 11.7231 PNS24243 293 194 0 0 KQK14069 1603 1504 40 7.01286 KQK14071 474 375 0 0 ==> ERR6133491.se.tsv <== BRADI_1g14170v3 40 BRADI_1g53295v3 28 BRADI_1g59795v3 17 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 22 BRADI_1g74790v3 20 BRADI_1g09890v3 0 BRADI_1g77505v3 66 BRADI_1g48960v3 0 ERR6133491 completed mapping pipeline successfully