Starting /dee2/code/volunteer_pipeline.sh ERR6133525 current disk space = 1544442867712 free memory = 1435679636 ERR6133525 SRAfilesize a05787606a7bd66b07b744db3820f5dd ERR6133525.sra ERR6133525.sra file validated ERR6133525 is single end ERR6133525 is conventional basespace ERR6133525 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133525_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 36.56025 37.0 37.0 37.0 37.0 37.0 2 36.778 37.0 37.0 37.0 37.0 37.0 3 36.569 37.0 37.0 37.0 37.0 37.0 4 36.01725 37.0 37.0 37.0 33.0 37.0 5 36.173 37.0 37.0 37.0 33.0 37.0 6 36.27625 37.0 37.0 37.0 33.0 37.0 7 38.40275 40.0 37.0 40.0 37.0 40.0 8 38.4955 40.0 37.0 40.0 37.0 40.0 9 38.51825 40.0 37.0 40.0 37.0 40.0 10-11 38.47924999999999 40.0 37.0 40.0 37.0 40.0 12-13 38.373000000000005 40.0 37.0 40.0 37.0 40.0 14-15 38.343875 40.0 37.0 40.0 37.0 40.0 16-17 38.288625 40.0 37.0 40.0 37.0 40.0 18-19 38.22525 40.0 37.0 40.0 37.0 40.0 20-21 38.182625 40.0 37.0 40.0 37.0 40.0 22-23 38.379374999999996 40.0 37.0 40.0 37.0 40.0 24-25 38.23825 40.0 37.0 40.0 37.0 40.0 26-27 38.215125 40.0 37.0 40.0 37.0 40.0 28-29 38.201875 40.0 37.0 40.0 37.0 40.0 30-31 38.24225 40.0 37.0 40.0 37.0 40.0 32-33 38.289125 40.0 37.0 40.0 37.0 40.0 34-35 38.15 40.0 37.0 40.0 37.0 40.0 36-37 38.0875 40.0 37.0 40.0 37.0 40.0 38-39 37.952625 38.5 37.0 40.0 37.0 40.0 40-41 37.71725 37.0 37.0 40.0 35.0 40.0 42-43 37.69 37.0 37.0 40.0 37.0 40.0 44-45 37.401250000000005 37.0 37.0 40.0 35.0 40.0 46-47 37.31575 37.0 37.0 40.0 33.0 40.0 48-49 37.174875 37.0 37.0 40.0 33.0 40.0 50-51 37.028625 37.0 37.0 38.5 33.0 40.0 52-53 36.712875 37.0 37.0 37.0 33.0 40.0 54-55 36.678375 37.0 37.0 37.0 33.0 40.0 56-57 36.490125000000006 37.0 37.0 37.0 33.0 40.0 58-59 35.98675 37.0 37.0 37.0 33.0 38.5 60-61 36.171375 37.0 37.0 37.0 33.0 37.0 62-63 36.087500000000006 37.0 37.0 37.0 33.0 37.0 64-65 35.914249999999996 37.0 37.0 37.0 33.0 37.0 66-67 35.886375 37.0 37.0 37.0 33.0 37.0 68-69 34.955375000000004 35.0 35.0 37.0 33.0 37.0 70-71 35.18279658092848 37.0 33.0 37.0 33.0 37.0 72-73 35.62681280345644 37.0 33.0 37.0 33.0 37.0 74-75 35.600208769745805 37.0 35.0 37.0 33.0 37.0 76-77 35.572883400621066 37.0 33.0 37.0 33.0 37.0 78-79 35.47704399711935 37.0 33.0 37.0 33.0 37.0 80-81 35.292144669010725 37.0 33.0 37.0 33.0 37.0 82-83 35.262658942009594 37.0 33.0 37.0 33.0 37.0 84-85 35.03817143404659 37.0 33.0 37.0 33.0 37.0 86-87 35.09344692005243 37.0 33.0 37.0 33.0 37.0 88-89 35.057273918741814 37.0 33.0 37.0 33.0 37.0 90-91 34.9735255570118 37.0 33.0 37.0 33.0 37.0 92-93 34.95845347313237 37.0 33.0 37.0 33.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 2.0 21 0.0 22 1.0 23 11.0 24 4.0 25 7.0 26 12.0 27 8.0 28 14.0 29 18.0 30 24.0 31 34.0 32 54.0 33 58.0 34 94.0 35 294.0 36 975.0 37 1445.0 38 919.0 39 26.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 80.85 4.575 7.775 6.800000000000001 2 64.5 19.925 9.65 5.925 3 33.475 35.475 16.225 14.825 4 29.625 29.375 19.0 22.0 5 28.749999999999996 25.8 29.099999999999998 16.35 6 18.099999999999998 39.375 25.25 17.275 7 37.5 27.0 20.125 15.375 8 29.599999999999998 29.349999999999998 22.325 18.725 9 24.85 31.374999999999996 25.8 17.974999999999998 10-11 23.175 29.762499999999996 28.012500000000003 19.05 12-13 24.5625 28.025 26.5625 20.849999999999998 14-15 21.55 35.075 25.9625 17.4125 16-17 25.05 30.562499999999996 24.45 19.9375 18-19 23.925 27.175 29.0875 19.8125 20-21 25.9407425928241 25.17814726840855 29.753719214901864 19.127390923865484 22-23 29.475 22.125 28.9875 19.412499999999998 24-25 23.4375 27.0125 28.6375 20.9125 26-27 26.2875 24.5375 30.012499999999996 19.162499999999998 28-29 23.962500000000002 28.025 28.775000000000002 19.2375 30-31 29.0875 25.025 26.887499999999996 19.0 32-33 24.962500000000002 26.7125 28.0875 20.2375 34-35 22.3875 32.2875 25.124999999999996 20.200000000000003 36-37 25.6 25.674999999999997 26.237500000000004 22.4875 38-39 30.025000000000002 23.400000000000002 28.7375 17.837500000000002 40-41 23.80595148787197 24.85621405351338 30.532633158289574 20.80520130032508 42-43 26.19404851212803 30.820205051262818 25.893973493373345 17.09177294323581 44-45 23.3 27.2625 31.1875 18.25 46-47 25.95 24.5625 27.625 21.8625 48-49 24.45 24.2 29.612500000000004 21.7375 50-51 21.065133141642704 27.903487935992 28.216027003375423 22.815351918989872 52-53 24.430252942649634 25.45704983721513 25.59479088404708 24.517906336088156 54-55 24.553069133641706 24.915614451806476 31.378922365295665 19.15239404925616 56-57 26.3 27.187499999999996 27.212500000000002 19.3 58-59 23.0625 25.874999999999996 31.912499999999998 19.15 60-61 26.950000000000003 26.875 28.249999999999996 17.925 62-63 20.925 29.299999999999997 31.5 18.275 64-65 21.625 32.237500000000004 28.549999999999997 17.5875 66-67 23.4875 31.662499999999998 27.2625 17.5875 68-69 21.425 26.650000000000002 28.9 23.025000000000002 70-71 21.9536631183469 29.079524107701943 27.91484032561052 21.05197244834064 72-73 26.544766708701133 25.535939470365697 29.936948297604037 17.98234552332913 74-75 25.06977924384674 28.72367419436691 28.051256026389243 18.155290535397107 76-77 20.93467464663186 24.411053100725837 27.67095377562715 26.983318477015157 78-79 26.375735858715128 26.798054773483493 28.871256718710008 17.954952649091375 80-81 21.449723187846015 34.23458220677224 27.732715334105833 16.58297927127591 82-83 23.45614945511157 26.141670991177996 28.165542293720808 22.23663725998962 84-85 21.56965336821452 24.931327665140614 33.34205362982342 20.156965336821454 86-87 20.0 28.75491480996068 28.401048492791613 22.84403669724771 88-89 19.29226736566186 29.580602883355176 29.921363040629096 21.205766710353867 90-91 25.897771952817823 28.872870249017033 28.36173001310616 16.86762778505898 92-93 21.022280471821755 30.432503276539975 29.1218872870249 19.42332896461337 >>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 1.0 16 2.0 17 14.0 18 18.0 19 5.5 20 0.5 21 2.0 22 4.0 23 4.0 24 5.0 25 6.5 26 10.0 27 16.0 28 27.0 29 34.0 30 27.5 31 27.5 32 35.5 33 52.5 34 67.0 35 75.0 36 104.5 37 146.0 38 195.5 39 206.5 40 208.0 41 220.0 42 222.5 43 233.0 44 218.0 45 186.5 46 189.0 47 187.0 48 169.0 49 169.0 50 205.0 51 195.0 52 139.5 53 131.5 54 188.0 55 154.5 56 53.5 57 43.5 58 36.5 59 24.0 60 13.5 61 10.5 62 11.5 63 11.0 64 10.0 65 8.0 66 6.0 67 7.0 68 8.0 69 4.5 70 2.5 71 3.0 72 2.0 73 1.5 74 1.0 75 0.0 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 0.0 36-37 0.0 38-39 0.0 40-41 0.025 42-43 0.025 44-45 0.0 46-47 0.0 48-49 0.0 50-51 0.0125 52-53 0.17500000000000002 54-55 0.0125 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 15.0 71 12.0 72 16.0 73 12.0 74 8.0 75 5.0 76 11.0 77 8.0 78 12.0 79 10.0 80 15.0 81 12.0 82 20.0 83 14.0 84 15.0 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 3815.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 73.02499999999999 #Duplication Level Percentage of deduplicated Percentage of total 1 92.2629236562821 67.375 2 4.3478260869565215 6.35 3 1.1982197877439233 2.625 4 0.6162273194111606 1.7999999999999998 5 0.20540910647038688 0.75 6 0.3081136597055803 1.35 7 0.17117425539198905 0.8750000000000001 8 0.13693940431359122 0.8 9 0.06846970215679561 0.44999999999999996 >10 0.5819924683327627 8.275 >50 0.034234851078397806 1.425 >100 0.06846970215679561 7.925 >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 207 5.175 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 110 2.75 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 57 1.425 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 50 1.25 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 48 1.2 No Hit GGAGTATCCTTGATATATAAATATATAGATAAATAGATTTAAATGGAAAA 27 0.675 No Hit GGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGG 21 0.525 No Hit GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 21 0.525 No Hit GTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAA 20 0.5 No Hit GGCCTGTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCG 20 0.5 No Hit GGGAGTATTATGAAAGGAGATTAATCATAGATTATCAAAAACCCTAGAAA 19 0.475 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 15 0.375 No Hit GGGGATGGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACG 15 0.375 No Hit GGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAAGGCGATCAAATTC 12 0.3 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 12 0.3 No Hit GGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAA 11 0.27499999999999997 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 10 0.25 No Hit GATACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGC 10 0.25 No Hit GAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGC 10 0.25 No Hit TCAAAAGAGGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGGA 10 0.25 No Hit CAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCT 9 0.22499999999999998 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 9 0.22499999999999998 No Hit GGTGGGGCAATGGGCATTCCGTTGAGTTTGTATGGTGGGTGCTGTTTTGC 8 0.2 No Hit GGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGGG 8 0.2 No Hit GGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTT 8 0.2 No Hit CGAGGAAGGGCGTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAG 8 0.2 No Hit GGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTT 7 0.17500000000000002 No Hit GGGAGTATCCTTGATATATAAATATATAGATAAATAGATTTAAATGGAAA 7 0.17500000000000002 No Hit GGGACGCATGCAACGACCATCTACATATAGCTACTCGATCTACCGCTACC 7 0.17500000000000002 No Hit GGATTCTTCTTTTTTGTGGGCCATTTGTGGCATGCAGGAAGAGCCCGAGC 7 0.17500000000000002 No Hit CAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTG 7 0.17500000000000002 No Hit GAAGGAACAAACGAGGATAAGATAAAATTTCTTTAAATTTATTTTGCCCA 6 0.15 No Hit GGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAA 6 0.15 No Hit GTACTATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTT 6 0.15 No Hit GGGATGGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACGA 6 0.15 No Hit ACACGTCTGAACTCCAGTCACACCGGCATCTCGTATGCCGTCTTCTGCTT 6 0.15 Illumina PCR Primer Index 3 (96% over 27bp) GGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTCCT 6 0.15 No Hit CTGAGCCGTGCTCTCTTCTGTGTACATCTTCATGTCATTTTAGCGATTCT 6 0.15 No Hit GGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGC 6 0.15 No Hit TTCACAAGTCTGGTTCAGGGTGTCCTCCGGTGGAGTTGTCGCGTGTCTGA 6 0.15 No Hit GGAAGGCGATCAAATTCGAGTTCGCGCCGGTAGATACTATCGATTAATAG 5 0.125 No Hit GAAGTATGGAAGGCGATCAAATTCGAGTTCGCGCCGGTAGATACTATCGA 5 0.125 No Hit GACACCATGCTTCCTGGAGAGATGTAGGTGCTTCAACATGAAGACTTTCC 5 0.125 No Hit GTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCT 5 0.125 No Hit GATATCTATCTGAACTGAGAACTGAGTCAGTATATACCAGTCTGTATCAC 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 0.037500000000000006 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 0.075 0.0 0.0 0.0 0.0 52-53 0.1 0.0 0.0 0.0 0.0 54-55 0.1 0.0 0.0 0.0 0.0 56-57 0.1 0.0 0.0 0.0 0.0 58-59 0.1 0.0 0.0 0.0 0.0 60-61 0.1 0.0 0.0 0.0 0.0 62-63 0.1 0.0 0.0 0.0 0.0 64-65 0.1 0.0 0.0 0.0 0.0 66-67 0.1 0.0 0.0 0.0 0.0 68-69 0.1 0.0 0.0 0.0 0.0 70-71 0.1 0.0 0.0 0.0 0.0 72-73 0.125 0.0 0.0 0.0 0.0 74-75 0.125 0.0 0.0 0.0 0.0 76-77 0.125 0.0 0.0 0.0 0.0 78-79 0.125 0.0 0.0 0.0 0.0 80-81 0.125 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GGGATGA 20 2.4532965E-5 86.4875 1 GGATGAT 15 8.920271E-4 86.487495 2 ATGATTC 15 8.920271E-4 86.487495 4 TTCTGTA 15 8.920271E-4 86.487495 8 TGATTCT 15 8.920271E-4 86.487495 5 ATTCTGT 15 8.920271E-4 86.487495 7 GGAGAGC 20 0.0027946017 64.86562 2 GATGATT 20 0.0027946017 64.86562 3 GCAATAC 20 0.0027946017 64.86562 7 GGGAGAG 20 0.0027946017 64.86562 1 CAATACA 20 0.0027946017 64.86562 8 GAGCAAT 20 0.0027946017 64.86562 5 TCTGTAT 20 0.0027946017 64.86562 9 AGAGCAA 20 0.0027946017 64.86562 4 AATACAA 20 0.0027946017 64.86562 9 AGCAATA 20 0.0027946017 64.86562 6 GATTCTG 25 0.006763133 51.8925 6 GAGAGCA 25 0.006763133 51.8925 3 >>END_MODULE Rejected 32119 READS because READLEN < 1 Read 32119 spots for ERR6133525.sra Written 32119 spots for ERR6133525.sra Rejected 32119 READS because READLEN < 1 Read 32119 spots for ERR6133525.sra Written 32119 spots for ERR6133525.sra Rejected 32119 READS because READLEN < 1 Read 32119 spots for ERR6133525.sra Written 32119 spots for ERR6133525.sra Rejected 32119 READS because READLEN < 1 Read 32119 spots for ERR6133525.sra Written 32119 spots for ERR6133525.sra Rejected 32119 READS because READLEN < 1 Read 32119 spots for ERR6133525.sra Written 32119 spots for ERR6133525.sra Rejected 32119 READS because READLEN < 1 Read 32119 spots for ERR6133525.sra Written 32119 spots for ERR6133525.sra Rejected 32119 READS because READLEN < 1 Read 32119 spots for ERR6133525.sra Written 32119 spots for ERR6133525.sra Rejected 32119 READS because READLEN < 1 Read 32119 spots for ERR6133525.sra Written 32119 spots for ERR6133525.sra Rejected 32119 READS because READLEN < 1 Read 32119 spots for ERR6133525.sra Written 32119 spots for ERR6133525.sra Rejected 32119 READS because READLEN < 1 Read 32119 spots for ERR6133525.sra Written 32119 spots for ERR6133525.sra Rejected 32119 READS because READLEN < 1 Read 32119 spots for ERR6133525.sra Written 32119 spots for ERR6133525.sra Rejected 32119 READS because READLEN < 1 Read 32119 spots for ERR6133525.sra Written 32119 spots for ERR6133525.sra Rejected 32119 READS because READLEN < 1 Read 32119 spots for ERR6133525.sra Written 32119 spots for ERR6133525.sra Rejected 32119 READS because READLEN < 1 Read 32119 spots for ERR6133525.sra Written 32119 spots for ERR6133525.sra Rejected 32119 READS because READLEN < 1 Read 32119 spots for ERR6133525.sra Written 32119 spots for ERR6133525.sra Rejected 32119 READS because READLEN < 1 Read 32119 spots for ERR6133525.sra Written 32119 spots for ERR6133525.sra Rejected 32119 READS because READLEN < 1 Read 32119 spots for ERR6133525.sra Written 32119 spots for ERR6133525.sra Rejected 32119 READS because READLEN < 1 Read 32119 spots for ERR6133525.sra Written 32119 spots for ERR6133525.sra Rejected 32119 READS because READLEN < 1 Read 32119 spots for ERR6133525.sra Written 32119 spots for ERR6133525.sra Rejected 32122 READS because READLEN < 1 Read 32122 spots for ERR6133525.sra Written 32122 spots for ERR6133525.sra SRR ids: ['ERR6133525.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_i0q3egrp ERR6133525.sra spots: 642383 blocks: [[1, 32119], [32120, 64238], [64239, 96357], [96358, 128476], [128477, 160595], [160596, 192714], [192715, 224833], [224834, 256952], [256953, 289071], [289072, 321190], [321191, 353309], [353310, 385428], [385429, 417547], [417548, 449666], [449667, 481785], [481786, 513904], [513905, 546023], [546024, 578142], [578143, 610261], [610262, 642383]] ERR6133525 file size 140620 ERR6133525 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 ERR6133525 ERR6133525_1.fastq Input file: ERR6133525_1.fastq trimmed: ERR6133525-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 07:55:14 2024 >> started Sat Dec 7 07:55:15 2024 >> done (0.512s) 642383 reads processed; of these: 217 ( 0.03%) short reads filtered out after trimming by size control 16 ( 0.00%) empty reads filtered out after trimming by size control 642150 (99.96%) reads available; of these: 3533 ( 0.55%) trimmed reads available after processing 638617 (99.45%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 42 0.01% 19 44 0.01% 20 15 0.00% 21 16 0.00% 22 13 0.00% 23 8 0.00% 24 5 0.00% 25 8 0.00% 26 9 0.00% 27 10 0.00% 28 21 0.00% 29 21 0.00% 30 13 0.00% 31 14 0.00% 32 19 0.00% 33 12 0.00% 34 11 0.00% 35 110 0.02% 36 87 0.01% 37 8 0.00% 38 23 0.00% 39 45 0.01% 40 57 0.01% 41 24 0.00% 42 7 0.00% 43 7 0.00% 44 14 0.00% 45 10 0.00% 46 7 0.00% 47 3 0.00% 48 2 0.00% 49 7 0.00% 50 6 0.00% 51 17 0.00% 52 11 0.00% 53 6 0.00% 54 3 0.00% 55 2 0.00% 56 9 0.00% 57 5 0.00% 58 3 0.00% 59 2 0.00% 60 7 0.00% 61 7 0.00% 62 1 0.00% 63 1 0.00% 64 1 0.00% 65 0 0.00% 66 2 0.00% 67 3 0.00% 68 1 0.00% 69 9 0.00% 70 2226 0.35% 71 1965 0.31% 72 2083 0.32% 73 1931 0.30% 74 1975 0.31% 75 1849 0.29% 76 1579 0.25% 77 1706 0.27% 78 1957 0.30% 79 2150 0.33% 80 1841 0.29% 81 2073 0.32% 82 2379 0.37% 83 2379 0.37% 84 1907 0.30% 85 6 0.00% 86 16 0.00% 87 30 0.00% 88 64 0.01% 89 99 0.02% 90 172 0.03% 91 446 0.07% 92 1769 0.28% 93 608760 94.80% 642150 reads passed initial QC criterion=sequence-density sequence-density=6.83 sequence-density-rank=1 fanout-score=1.44 fanout-score-rank=22 prefix-density=0.26 prefix-fanout=1.4 sequence=GGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGCACCCTAGATGGCTAAAGTCCAGTAGCCGAAAGCATCACTAGCTTACGCTCTGACCCGAGTAGCATGGGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAAT criterion=fanout-score sequence-density=0.12 sequence-density-rank=15 fanout-score=33.97 fanout-score-rank=1 prefix-density=4.09 prefix-fanout=1.0 sequence=GGAGATTCCCAGATAG Potential 3prime adapter identified. Now checking if in reference sequence Warning: gzbuffer added in zlib v1.2.3.5. Unable to change buffer size from default of 8192. 1 reads; of these: 1 (100.00%) were unpaired; of these: 1 (100.00%) aligned 0 times 0 (0.00%) aligned exactly 1 time 0 (0.00%) aligned >1 times 0.00% overall alignment rate Adapter seq not found in reference. Now shuffling file before clipping skewer v0.2.2 [April 4, 2016] COMMAND LINE: skewer -f sanger -l 18 -t 20 -x GGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGCACCCTAGATGGCTAAAGTCCAGTAGCCGAAAGCATCACTAGCTTACGCTCTGACCCGAGTAGCATGGGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAAT -o ERR6133525 - Input file: STDIN trimmed: ERR6133525-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): GGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGCACCCTAGATGGCTA -- maximum error ratio allowed (-r): 0.100 -- maximum indel error ratio allowed (-d): 0.030 -- minimum read length allowed after trimming (-l): 18 -- file format (-f): Sanger/Illumina 1.8+ FASTQ -- minimum overlap length for adapter detection (-k): 3 -- number of concurrent threads (-t): 20 Sat Dec 7 07:55:19 2024 >> started Sat Dec 7 07:55:20 2024 >> done (0.681s) 458679 reads processed; of these: 1236 ( 0.27%) short reads filtered out after trimming by size control 30499 ( 6.65%) empty reads filtered out after trimming by size control 426944 (93.08%) reads available; of these: 6074 ( 1.42%) trimmed reads available after processing 420870 (98.58%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 30 0.01% 19 33 0.01% 20 10 0.00% 21 10 0.00% 22 15 0.00% 23 6 0.00% 24 5 0.00% 25 9 0.00% 26 7 0.00% 27 10 0.00% 28 16 0.00% 29 13 0.00% 30 11 0.00% 31 151 0.04% 32 18 0.00% 33 9 0.00% 34 10 0.00% 35 76 0.02% 36 64 0.01% 37 24 0.01% 38 16 0.00% 39 33 0.01% 40 40 0.01% 41 19 0.00% 42 7 0.00% 43 2 0.00% 44 14 0.00% 45 12 0.00% 46 7 0.00% 47 3 0.00% 48 2 0.00% 49 10 0.00% 50 4 0.00% 51 15 0.00% 52 10 0.00% 53 7 0.00% 54 3 0.00% 55 2 0.00% 56 7 0.00% 57 4 0.00% 58 3 0.00% 59 2 0.00% 60 4 0.00% 61 5 0.00% 62 1 0.00% 63 1 0.00% 64 0 0.00% 65 0 0.00% 66 3 0.00% 67 31 0.01% 68 17 0.00% 69 48 0.01% 70 1591 0.37% 71 1388 0.33% 72 1502 0.35% 73 1333 0.31% 74 1376 0.32% 75 1336 0.31% 76 1142 0.27% 77 1552 0.36% 78 1468 0.34% 79 1805 0.42% 80 1301 0.30% 81 1591 0.37% 82 1522 0.36% 83 1706 0.40% 84 1306 0.31% 85 9 0.00% 86 57 0.01% 87 101 0.02% 88 276 0.06% 89 952 0.22% 90 3694 0.87% 91 317 0.07% 92 1153 0.27% 93 397607 93.13% criterion=sequence-density sequence-density=2.05 sequence-density-rank=1 fanout-score=1.99 fanout-score-rank=22 prefix-density=0.11 prefix-fanout=2.0 sequence=GGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGCACCCTAGATGGCTAAAGTCCAGTAGCCGAAAGCATCACTAGCTTACGCTCTGACCCGAGTAGCATGGGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAAT criterion=fanout-score sequence-density=0.13 sequence-density-rank=15 fanout-score=34.01 fanout-score-rank=1 prefix-density=4.31 prefix-fanout=1.0 sequence=GGAGATTCCCAGATAG Started job on | Dec 07 07:55:35 Started mapping on | Dec 07 07:55:35 Finished on | Dec 07 07:55:39 Mapping speed, Million of reads per hour | 549.37 Number of input reads | 610415 Average input read length | 92 UNIQUE READS: Uniquely mapped reads number | 398475 Uniquely mapped reads % | 65.28% Average mapped length | 91.72 Number of splices: Total | 22915 Number of splices: Annotated (sjdb) | 19228 Number of splices: GT/AG | 22258 Number of splices: GC/AG | 366 Number of splices: AT/AC | 12 Number of splices: Non-canonical | 279 Mismatch rate per base, % | 0.22% Deletion rate per base | 0.02% Deletion average length | 1.52 Insertion rate per base | 0.01% Insertion average length | 1.55 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 192700 % of reads mapped to multiple loci | 31.57% Number of reads mapped to too many loci | 3365 % of reads mapped to too many loci | 0.55% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 2.57% % of reads unmapped: other | 0.03% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 19240 19240 19240 N_multimapping 192700 192700 192700 N_noFeature 28650 32681 381368 N_ambiguous 15019 1905 79 UnstrandedReadsAssigned:354806 PositiveStrandReadsAssigned:363889 NegativeStrandReadsAssigned:17028 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=93 echo kmer=89 ERR6133525 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: ERR6133525-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 610,415 reads, 484,537 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 819 rounds 52973 ERR6133525.ke.tsv 35125 ERR6133525.se.tsv 88098 total ==> ERR6133525.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 5 10.0026 PNS24243 293 194 0 0 KQK14069 1603 1504 32 58.3983 KQK14071 474 375 0 0 ==> ERR6133525.se.tsv <== BRADI_1g14170v3 32 BRADI_1g53295v3 4 BRADI_1g59795v3 3 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 4 BRADI_1g74790v3 1 BRADI_1g09890v3 0 BRADI_1g77505v3 9 BRADI_1g48960v3 0 ERR6133525 completed mapping pipeline successfully