Starting /dee2/code/volunteer_pipeline.sh ERR6133467 current disk space = 1545124421632 free memory = 1600421072 ERR6133467 SRAfilesize 67c2c13290c2f7537d52e488e291925c ERR6133467.sra ERR6133467.sra file validated ERR6133467 is single end ERR6133467 is conventional basespace ERR6133467 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133467_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 34.8 37.0 33.0 37.0 33.0 37.0 2 36.18425 37.0 37.0 37.0 33.0 37.0 3 35.23875 37.0 33.0 37.0 33.0 37.0 4 34.883 37.0 33.0 37.0 33.0 37.0 5 34.825 37.0 33.0 37.0 27.0 37.0 6 35.22775 37.0 37.0 37.0 33.0 37.0 7 36.7855 37.0 37.0 40.0 33.0 40.0 8 36.90725 37.0 37.0 40.0 33.0 40.0 9 36.98325 37.0 37.0 40.0 33.0 40.0 10-11 36.94525 37.0 37.0 40.0 33.0 40.0 12-13 36.883250000000004 37.0 37.0 40.0 33.0 40.0 14-15 36.767875000000004 37.0 37.0 40.0 33.0 40.0 16-17 36.683125000000004 37.0 37.0 40.0 33.0 40.0 18-19 36.35825 37.0 37.0 40.0 33.0 40.0 20-21 36.238375000000005 37.0 37.0 40.0 33.0 40.0 22-23 35.875125 37.0 33.0 40.0 33.0 40.0 24-25 36.03575 37.0 35.0 40.0 33.0 40.0 26-27 36.185500000000005 37.0 37.0 40.0 33.0 40.0 28-29 36.16525 37.0 37.0 40.0 33.0 40.0 30-31 36.324625 37.0 37.0 40.0 33.0 40.0 32-33 36.2365 37.0 37.0 40.0 33.0 40.0 34-35 36.195625 37.0 37.0 40.0 33.0 40.0 36-37 36.16125 37.0 37.0 40.0 33.0 40.0 38-39 35.99225 37.0 33.0 40.0 33.0 40.0 40-41 35.802625 37.0 33.0 40.0 33.0 40.0 42-43 35.776125 37.0 33.0 40.0 33.0 40.0 44-45 35.52525 37.0 33.0 38.5 30.0 40.0 46-47 35.551874999999995 37.0 33.0 37.0 33.0 40.0 48-49 35.432500000000005 37.0 33.0 37.0 33.0 40.0 50-51 35.351875 37.0 33.0 37.0 33.0 40.0 52-53 35.139375 37.0 33.0 37.0 33.0 40.0 54-55 35.076499999999996 37.0 33.0 37.0 33.0 40.0 56-57 34.913125 37.0 33.0 37.0 33.0 38.5 58-59 34.324 37.0 33.0 37.0 27.0 37.0 60-61 34.39275 37.0 33.0 37.0 27.0 37.0 62-63 34.29325 37.0 33.0 37.0 27.0 37.0 64-65 34.304249999999996 37.0 33.0 37.0 27.0 37.0 66-67 34.081999999999994 37.0 33.0 37.0 27.0 37.0 68-69 33.215625 35.0 33.0 37.0 27.0 37.0 70-71 33.389187014045646 33.0 33.0 37.0 27.0 37.0 72-73 33.776978768728284 37.0 33.0 37.0 27.0 37.0 74-75 33.88168161641231 37.0 33.0 37.0 27.0 37.0 76-77 33.878464945517266 37.0 33.0 37.0 27.0 37.0 78-79 33.82420977974982 37.0 33.0 37.0 27.0 37.0 80-81 33.81172923272988 37.0 33.0 37.0 27.0 37.0 82-83 33.57751672465492 37.0 33.0 37.0 27.0 37.0 84-85 33.466949650931 35.0 33.0 37.0 27.0 37.0 86-87 33.32043834169527 35.0 33.0 37.0 27.0 37.0 88-89 33.47398996567203 37.0 33.0 37.0 27.0 37.0 90-91 33.0678637443887 33.0 33.0 37.0 27.0 37.0 92-93 33.16807499339847 33.0 33.0 37.0 27.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 14.0 21 11.0 22 20.0 23 22.0 24 28.0 25 42.0 26 53.0 27 47.0 28 61.0 29 70.0 30 96.0 31 133.0 32 158.0 33 220.0 34 311.0 35 517.0 36 863.0 37 900.0 38 421.0 39 13.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 86.02499999999999 3.075 3.175 7.725 2 69.19999999999999 18.875 7.9 4.025 3 36.075 36.25 15.325 12.35 4 31.275 29.2 19.475 20.05 5 27.250000000000004 27.6 27.1 18.05 6 18.85 38.975 25.1 17.075000000000003 7 37.775 27.825 19.725 14.674999999999999 8 28.499999999999996 30.625000000000004 22.225 18.65 9 24.325 31.85 27.575 16.25 10-11 23.4625 28.3625 29.3875 18.787499999999998 12-13 24.75 28.775000000000002 27.6 18.875 14-15 20.349999999999998 33.975 27.487499999999997 18.1875 16-17 24.2625 30.349999999999998 25.324999999999996 20.0625 18-19 24.2875 26.325 29.475 19.9125 20-21 26.113056528264135 26.388194097048522 29.164582291145575 18.33416708354177 22-23 27.474999999999998 23.225 28.1875 21.1125 24-25 23.6375 24.7375 30.25 21.375 26-27 25.05 25.275 30.337500000000002 19.3375 28-29 23.200000000000003 29.3875 28.9 18.512500000000003 30-31 26.8 26.075 27.6125 19.5125 32-33 25.362499999999997 25.4 27.462500000000002 21.775 34-35 22.8125 31.412499999999998 26.0125 19.7625 36-37 24.887500000000003 25.6125 26.0125 23.4875 38-39 29.341167645955746 24.00300037504688 29.678709838729837 16.977122140267532 40-41 25.890736342042754 24.678084760595073 29.016127015876986 20.415051881485187 42-43 24.696457629240207 29.81599699586932 26.89948679434222 18.588058580548253 44-45 24.16552069008626 26.665833229153645 30.54131766470809 18.627328416052006 46-47 25.137500000000003 25.074999999999996 26.987499999999997 22.8 48-49 24.7375 25.0125 29.512500000000003 20.7375 50-51 22.5625 28.1375 29.225 20.075000000000003 52-53 23.213615317231888 26.83018395695157 26.429733450131398 23.526467275685146 54-55 23.1375 25.9875 31.2875 19.5875 56-57 26.3125 28.4375 26.174999999999997 19.075 58-59 23.8375 25.4375 30.025000000000002 20.7 60-61 27.3625 26.2125 29.025000000000002 17.4 62-63 20.525 27.787499999999998 31.612499999999997 20.075000000000003 64-65 20.962500000000002 32.087500000000006 28.15 18.8 66-67 24.0375 29.7375 27.9375 18.2875 68-69 20.5125 27.3375 28.825 23.325000000000003 70-71 22.098409916113685 27.469638162013272 27.757606109928634 22.67434581194441 72-73 26.628859483301824 25.267800882167613 29.388783868935096 18.714555765595463 74-75 24.82233502538071 28.185279187817258 27.86802030456853 19.1243654822335 76-77 22.568690095846645 25.54632587859425 27.47603833865815 24.40894568690096 78-79 23.223236087906436 26.911708006682943 29.597738079938313 20.267317825472304 80-81 20.416882444329364 33.22112894873123 28.120145002589332 18.241843604350077 82-83 22.552858261550508 27.78647872618115 27.029496215087445 22.631166797180892 84-85 21.433276248188644 25.372151231721773 32.36727703859834 20.82729548149124 86-87 20.279904937945602 29.548455241616058 28.822286770530763 21.34935304990758 88-89 19.60654871930288 28.294164246105098 31.18563506733562 20.913651967256403 90-91 25.442302614206497 27.71322946923686 28.518616318986005 18.325851597570637 92-93 20.992870345920252 29.706891998943757 29.152363348296806 20.147874306839185 >>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 0.5 15 0.5 16 0.5 17 6.5 18 7.0 19 1.0 20 1.0 21 1.0 22 4.5 23 8.0 24 7.0 25 9.0 26 14.5 27 20.0 28 28.5 29 34.5 30 45.5 31 52.0 32 58.5 33 77.5 34 93.5 35 105.5 36 129.0 37 162.0 38 194.5 39 187.5 40 185.0 41 197.0 42 204.0 43 227.0 44 203.5 45 188.0 46 178.5 47 156.5 48 157.5 49 160.0 50 143.5 51 123.0 52 118.5 53 125.0 54 181.0 55 155.0 56 70.5 57 60.0 58 47.5 59 31.5 60 26.5 61 29.5 62 29.5 63 22.5 64 17.0 65 17.5 66 18.5 67 14.0 68 10.0 69 9.0 70 7.0 71 4.0 72 5.5 73 5.5 74 2.5 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 0.05 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 0.0 38-39 0.0125 40-41 0.0125 42-43 0.13749999999999998 44-45 0.0125 46-47 0.0 48-49 0.0 50-51 0.0 52-53 0.11249999999999999 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 13.0 71 14.0 72 11.0 73 16.0 74 12.0 75 14.0 76 15.0 77 10.0 78 9.0 79 18.0 80 12.0 81 20.0 82 10.0 83 22.0 84 17.0 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 3787.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 73.85000000000001 #Duplication Level Percentage of deduplicated Percentage of total 1 91.6723087339201 67.7 2 4.129993229519296 6.1 3 1.4556533513879486 3.225 4 0.7447528774542992 2.1999999999999997 5 0.6093432633716994 2.25 6 0.2031144211238998 0.8999999999999999 7 0.2031144211238998 1.05 8 0.13540961408259986 0.8 9 0.2708192281651997 1.7999999999999998 >10 0.47393364928909953 6.775 >50 0.06770480704129993 2.9499999999999997 >100 0.033852403520649964 4.25 >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 170 4.25 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 59 1.4749999999999999 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 59 1.4749999999999999 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 45 1.125 No Hit GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 29 0.7250000000000001 No Hit GGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTT 27 0.675 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 26 0.65 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 21 0.525 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 17 0.42500000000000004 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 16 0.4 No Hit GGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAA 15 0.375 No Hit GGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGC 15 0.375 No Hit GGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTT 13 0.325 No Hit GGAGTATCCTTGATATATAAATATATAGATAAATAGATTTAAATGGAAAA 13 0.325 No Hit GGCCTGTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCG 12 0.3 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 11 0.27499999999999997 No Hit CAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCT 11 0.27499999999999997 No Hit GGGAAAAGAGGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTT 9 0.22499999999999998 No Hit GGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAAGGCGATCAAATTC 9 0.22499999999999998 No Hit CAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATAT 9 0.22499999999999998 No Hit GTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAA 9 0.22499999999999998 No Hit GGGGATGGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACG 9 0.22499999999999998 No Hit GGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAACCCTCTTAACT 9 0.22499999999999998 No Hit GGGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTG 9 0.22499999999999998 No Hit GTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAG 9 0.22499999999999998 No Hit GGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTG 8 0.2 No Hit GGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGC 8 0.2 No Hit GGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGG 8 0.2 No Hit GGGCTTGGCTACAATTCCGAATACGCTATTACATGTTTGCGCTAGTTTTT 8 0.2 No Hit GGTGGGGCAATGGGCATTCCGTTGAGTTTGTATGGTGGGTGCTGTTTTGC 7 0.17500000000000002 No Hit GGAAGGGCGTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAGCAT 7 0.17500000000000002 No Hit GGAACAAACGAGGATAAGATAAAATTGCTTTAAATTTATTTTGCCCAAGT 7 0.17500000000000002 No Hit GGAAAAGAGGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTTG 7 0.17500000000000002 No Hit GGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTTGAAATCGGAG 7 0.17500000000000002 No Hit GGGGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCT 7 0.17500000000000002 No Hit GGGAAATAGCTAATGTAGAATTTATCTGATATAGAACACTCATATCGATA 6 0.15 No Hit GGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGGG 6 0.15 No Hit GTATGGAAGGCGATCAAATTCGAGTTCGCGCCGGTAGATACTATCGATTA 6 0.15 No Hit GGAGTCCCATATATATATGTATAAGATGCCAGCCCGGTTTCGTCAACCAT 6 0.15 No Hit GGAAGAGCCCGAGCTGCTGCAGCAGGTTTTGAAAAGGGAATCGATCGTGA 6 0.15 No Hit GAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGC 6 0.15 No Hit GGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAA 5 0.125 No Hit GCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATC 5 0.125 No Hit GGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCG 5 0.125 No Hit GGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGGAAGGGCGTA 5 0.125 No Hit GGGATGGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACGA 5 0.125 No Hit GGAAGGCGATCAAATTCGAGTTCGCGCCGGTAGATACTATCGATTAATAG 5 0.125 No Hit GGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAACCCTCTTAACTA 5 0.125 No Hit GGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAAA 5 0.125 No Hit GGACTGGGTATCCATGCCAGGTGTTATACCAGTAGCTTCAGGTGGTATTC 5 0.125 No Hit GTATTTAGCCTTGCAAGGTGGTCCTTGCTGATTCACACGGGATTCCACGT 5 0.125 No Hit GGGGTTGTGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTG 5 0.125 No Hit GTACAAGCTCGTAACGAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAAT 5 0.125 No Hit GGGGAAGTACACCAGCGACGGCGAGGCCGCCGCCGCCAAGGAAGGCATGT 5 0.125 No Hit GGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGCA 5 0.125 No Hit GAAGGAACAAACGAGGATAAGATAAAATTGCTTTAAATTTATTTTGCCCA 5 0.125 No Hit GGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAA 5 0.125 No Hit GGTTTTGAAAAGGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAA 5 0.125 No Hit GGAAAAGAAAGCAAAAGCGATTCCCGTAGTAGCGGCGAGCGAAATGGGAG 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 0.0125 0.0 0.0 0.0 0.0 42-43 0.025 0.0 0.0 0.0 0.0 44-45 0.025 0.0 0.0 0.0 0.0 46-47 0.025 0.0 0.0 0.0 0.0 48-49 0.025 0.0 0.0 0.0 0.0 50-51 0.025 0.0 0.0 0.0 0.0 52-53 0.025 0.0 0.0 0.0 0.0 54-55 0.025 0.0 0.0 0.0 0.0 56-57 0.025 0.0 0.0 0.0 0.0 58-59 0.025 0.0 0.0 0.0 0.0 60-61 0.025 0.0 0.0 0.0 0.0 62-63 0.025 0.0 0.0 0.0 0.0 64-65 0.025 0.0 0.0 0.0 0.0 66-67 0.025 0.0 0.0 0.0 0.0 68-69 0.025 0.0 0.0 0.0 0.0 70-71 0.025 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 GGAGAGC 20 0.0028431658 64.58437 2 GCAATAC 20 0.0028431658 64.58437 7 GAGCAAT 20 0.0028431658 64.58437 5 AGAGCAA 20 0.0028431658 64.58437 4 GAGAGCA 20 0.0028431658 64.58437 3 AATACAA 20 0.0028431658 64.58437 9 GGGAGAG 25 0.006880399 51.6675 1 CAATACA 25 0.006880399 51.6675 8 AGCAATA 25 0.006880399 51.6675 6 TTCCCTC 25 0.0016727957 37.23784 84-85 ACTTCCC 25 0.0016727957 37.23784 82-83 AACTTCC 25 0.0016727957 37.23784 82-83 CTTCCCT 25 0.0016727957 37.23784 84-85 TCCCTCT 25 0.0016727957 37.23784 86-87 CACAACT 25 0.0017884045 36.741333 78-79 TCACAAC 25 0.0017884045 36.741333 78-79 TGCTCAC 25 0.0021736815 35.328205 74-75 ATGCTCA 25 0.0021736815 35.328205 74-75 AATGCTC 25 0.0021736815 35.328205 72-73 CTCACAA 25 0.0021736815 35.328205 76-77 >>END_MODULE Rejected 96013 READS because READLEN < 1 Read 96013 spots for ERR6133467.sra Written 96013 spots for ERR6133467.sra Rejected 96011 READS because READLEN < 1 Read 96011 spots for ERR6133467.sra Written 96011 spots for ERR6133467.sra Rejected 96011 READS because READLEN < 1 Read 96011 spots for ERR6133467.sra Written 96011 spots for ERR6133467.sra Rejected 96011 READS because READLEN < 1 Read 96011 spots for ERR6133467.sra Written 96011 spots for ERR6133467.sra Rejected 96011 READS because READLEN < 1 Read 96011 spots for ERR6133467.sra Written 96011 spots for ERR6133467.sra Rejected 96011 READS because READLEN < 1 Read 96011 spots for ERR6133467.sra Written 96011 spots for ERR6133467.sra Rejected 96011 READS because READLEN < 1 Read 96011 spots for ERR6133467.sra Written 96011 spots for ERR6133467.sra Rejected 96011 READS because READLEN < 1 Read 96011 spots for ERR6133467.sra Written 96011 spots for ERR6133467.sra Rejected 96011 READS because READLEN < 1 Read 96011 spots for ERR6133467.sra Written 96011 spots for ERR6133467.sra Rejected 96011 READS because READLEN < 1 Read 96011 spots for ERR6133467.sra Written 96011 spots for ERR6133467.sra Rejected 96011 READS because READLEN < 1 Read 96011 spots for ERR6133467.sra Written 96011 spots for ERR6133467.sra Rejected 96011 READS because READLEN < 1 Read 96011 spots for ERR6133467.sra Written 96011 spots for ERR6133467.sra Rejected 96011 READS because READLEN < 1 Read 96011 spots for ERR6133467.sra Written 96011 spots for ERR6133467.sra Rejected 96011 READS because READLEN < 1 Read 96011 spots for ERR6133467.sra Written 96011 spots for ERR6133467.sra Rejected 96011 READS because READLEN < 1 Read 96011 spots for ERR6133467.sra Written 96011 spots for ERR6133467.sra Rejected 96011 READS because READLEN < 1 Read 96011 spots for ERR6133467.sra Written 96011 spots for ERR6133467.sra Rejected 96011 READS because READLEN < 1 Read 96011 spots for ERR6133467.sra Written 96011 spots for ERR6133467.sra Rejected 96011 READS because READLEN < 1 Read 96011 spots for ERR6133467.sra Written 96011 spots for ERR6133467.sra Rejected 96011 READS because READLEN < 1 Read 96011 spots for ERR6133467.sra Written 96011 spots for ERR6133467.sra Rejected 96011 READS because READLEN < 1 Read 96011 spots for ERR6133467.sra Written 96011 spots for ERR6133467.sra SRR ids: ['ERR6133467.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_dftfghxz ERR6133467.sra spots: 1920222 blocks: [[1, 96011], [96012, 192022], [192023, 288033], [288034, 384044], [384045, 480055], [480056, 576066], [576067, 672077], [672078, 768088], [768089, 864099], [864100, 960110], [960111, 1056121], [1056122, 1152132], [1152133, 1248143], [1248144, 1344154], [1344155, 1440165], [1440166, 1536176], [1536177, 1632187], [1632188, 1728198], [1728199, 1824209], [1824210, 1920222]] ERR6133467 file size 422332 ERR6133467 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 ERR6133467 ERR6133467_1.fastq Input file: ERR6133467_1.fastq trimmed: ERR6133467-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 06:40:13 2024 >> started Sat Dec 7 06:40:15 2024 >> done (1.273s) 1920222 reads processed; of these: 70 ( 0.00%) short reads filtered out after trimming by size control 7 ( 0.00%) empty reads filtered out after trimming by size control 1920145 (100.00%) reads available; of these: 26950 ( 1.40%) trimmed reads available after processing 1893195 (98.60%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 14 0.00% 19 16 0.00% 20 9 0.00% 21 14 0.00% 22 10 0.00% 23 1 0.00% 24 8 0.00% 25 3 0.00% 26 2 0.00% 27 5 0.00% 28 13 0.00% 29 43 0.00% 30 10 0.00% 31 13 0.00% 32 14 0.00% 33 7 0.00% 34 9 0.00% 35 96 0.00% 36 223 0.01% 37 9 0.00% 38 9 0.00% 39 47 0.00% 40 46 0.00% 41 19 0.00% 42 9 0.00% 43 1 0.00% 44 8 0.00% 45 4 0.00% 46 5 0.00% 47 3 0.00% 48 4 0.00% 49 7 0.00% 50 8 0.00% 51 10 0.00% 52 5 0.00% 53 4 0.00% 54 4 0.00% 55 4 0.00% 56 3 0.00% 57 2 0.00% 58 10 0.00% 59 2 0.00% 60 7 0.00% 61 7 0.00% 62 1 0.00% 63 2 0.00% 64 2 0.00% 65 3 0.00% 66 8 0.00% 67 9 0.00% 68 18 0.00% 69 71 0.00% 70 6677 0.35% 71 5859 0.31% 72 6266 0.33% 73 5641 0.29% 74 6199 0.32% 75 6040 0.31% 76 5274 0.27% 77 5476 0.29% 78 6634 0.35% 79 7251 0.38% 80 6624 0.34% 81 7895 0.41% 82 8970 0.47% 83 8259 0.43% 84 7398 0.39% 85 52 0.00% 86 109 0.01% 87 165 0.01% 88 348 0.02% 89 687 0.04% 90 1482 0.08% 91 4610 0.24% 92 17589 0.92% 93 1793779 93.42% 1920145 reads passed initial QC criterion=sequence-density sequence-density=0.95 sequence-density-rank=1 fanout-score=2.00 fanout-score-rank=31 prefix-density=0.95 prefix-fanout=2.0 sequence=CAAGGCTAAATAC criterion=fanout-score sequence-density=0.02 sequence-density-rank=28 fanout-score=45.92 fanout-score-rank=1 prefix-density=0.11 prefix-fanout=6.5 sequence=AAAAGAAGGGGTGTTCCATCTCCGGACGACGATCCTGCCTGCGGAGGAAGACATGCCGGCGATCATGTCGAGCTTCAAGAAGTTCAACGACTCATTCATGGAGCAATACCAAGACTACTCCAGGCTGTGATGTGAAGAGGGAAACAACGACGTCATCATCGACATGATATATTGCTGCTATTTTCCACCAGCGATTAAAAGTTAAAAAATTTAGCTGTAAGCTGTAACTATCTTGAAGAAACTAAACTGGTTGCTGTGCTTGATATGTATAGGGAAAACATAATTTATGAGACAATCATACTGTGCAACTCTTGGCTCCATCGATTAATTAATACTCCTTGTTATTGCTTGCATGGTGG Started job on | Dec 07 06:40:26 Started mapping on | Dec 07 06:40:26 Finished on | Dec 07 06:40:30 Mapping speed, Million of reads per hour | 1728.13 Number of input reads | 1920145 Average input read length | 92 UNIQUE READS: Uniquely mapped reads number | 1153256 Uniquely mapped reads % | 60.06% Average mapped length | 91.58 Number of splices: Total | 55991 Number of splices: Annotated (sjdb) | 47694 Number of splices: GT/AG | 53781 Number of splices: GC/AG | 1122 Number of splices: AT/AC | 65 Number of splices: Non-canonical | 1023 Mismatch rate per base, % | 0.44% Deletion rate per base | 0.04% Deletion average length | 1.85 Insertion rate per base | 0.02% Insertion average length | 1.88 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 717354 % of reads mapped to multiple loci | 37.36% Number of reads mapped to too many loci | 22717 % of reads mapped to too many loci | 1.18% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.31% % of reads unmapped: other | 0.09% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 49535 49535 49535 N_multimapping 717354 717354 717354 N_noFeature 106908 118455 1105685 N_ambiguous 42617 6514 282 UnstrandedReadsAssigned:1003731 PositiveStrandReadsAssigned:1028287 NegativeStrandReadsAssigned:47289 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=93 echo kmer=89 ERR6133467 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: ERR6133467-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 1,920,145 reads, 1,457,390 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 894 rounds 52973 ERR6133467.ke.tsv 35125 ERR6133467.se.tsv 88098 total ==> ERR6133467.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 25 16.5924 PNS24243 293 194 0 0 KQK14069 1603 1504 17 10.2926 KQK14071 474 375 0 0 ==> ERR6133467.se.tsv <== BRADI_1g14170v3 17 BRADI_1g53295v3 2 BRADI_1g59795v3 9 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 9 BRADI_1g74790v3 10 BRADI_1g09890v3 0 BRADI_1g77505v3 25 BRADI_1g48960v3 0 ERR6133467 completed mapping pipeline successfully