Starting /dee2/code/volunteer_pipeline.sh ERR6133362 current disk space = 1548199227392 free memory = 1600101068 ERR6133362 SRAfilesize d16f0146b21fecebfa7f54c11d0a4d3d ERR6133362.sra ERR6133362.sra file validated ERR6133362 is single end ERR6133362 is conventional basespace ERR6133362 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133362_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 45 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.356 37.0 37.0 37.0 33.0 37.0 2 36.7155 37.0 37.0 37.0 37.0 37.0 3 36.69975 37.0 37.0 37.0 37.0 37.0 4 36.45675 37.0 37.0 37.0 37.0 37.0 5 36.492 37.0 37.0 37.0 37.0 37.0 6 36.56625 37.0 37.0 37.0 37.0 37.0 7 38.80275 40.0 37.0 40.0 37.0 40.0 8 38.86625 40.0 37.0 40.0 37.0 40.0 9 38.892 40.0 37.0 40.0 37.0 40.0 10-11 38.890875 40.0 37.0 40.0 37.0 40.0 12-13 38.87675 40.0 37.0 40.0 37.0 40.0 14-15 38.865875 40.0 37.0 40.0 37.0 40.0 16-17 38.820625 40.0 37.0 40.0 37.0 40.0 18-19 38.78275 40.0 37.0 40.0 37.0 40.0 20-21 38.733375 40.0 37.0 40.0 37.0 40.0 22-23 38.665125 40.0 37.0 40.0 37.0 40.0 24-25 38.554125 40.0 37.0 40.0 37.0 40.0 26-27 38.587374999999994 40.0 37.0 40.0 37.0 40.0 28-29 38.667 40.0 37.0 40.0 37.0 40.0 30-31 38.569625 40.0 37.0 40.0 37.0 40.0 32-33 38.407125 40.0 37.0 40.0 37.0 40.0 34-35 38.37175 40.0 37.0 40.0 37.0 40.0 36-37 38.24125 40.0 37.0 40.0 37.0 40.0 38-39 38.249375 40.0 37.0 40.0 37.0 40.0 40-41 38.119625 40.0 37.0 40.0 37.0 40.0 42-43 37.930375 37.0 37.0 40.0 37.0 40.0 44-45 37.772000000000006 37.0 37.0 40.0 37.0 40.0 46-47 37.689 37.0 37.0 40.0 37.0 40.0 48-49 37.5215 37.0 37.0 40.0 37.0 40.0 50-51 37.36625 37.0 37.0 40.0 35.0 40.0 52-53 37.173 37.0 37.0 40.0 33.0 40.0 54-55 37.0295 37.0 37.0 37.0 33.0 40.0 56-57 36.84287500000001 37.0 37.0 37.0 33.0 40.0 58-59 36.667249999999996 37.0 37.0 37.0 33.0 40.0 60-61 36.622875 37.0 37.0 37.0 33.0 40.0 62-63 36.379000000000005 37.0 37.0 37.0 33.0 37.0 64-65 36.239125 37.0 37.0 37.0 33.0 37.0 66-67 36.128375000000005 37.0 37.0 37.0 33.0 37.0 68-69 35.248999999999995 35.0 35.0 37.0 33.0 37.0 70-71 35.46412550200803 37.0 35.0 37.0 33.0 37.0 72-73 35.88016903273412 37.0 37.0 37.0 33.0 37.0 74-75 35.73657186555479 37.0 37.0 37.0 33.0 37.0 76-77 35.77886627553851 37.0 37.0 37.0 33.0 37.0 78-79 35.822426348239674 37.0 37.0 37.0 33.0 37.0 80-81 35.767591544942306 37.0 37.0 37.0 33.0 37.0 82-83 35.67568069986842 37.0 37.0 37.0 33.0 37.0 84-85 35.735209032659974 37.0 37.0 37.0 33.0 37.0 86-87 35.62011173184358 37.0 35.0 37.0 33.0 37.0 88-89 35.62423516892791 37.0 37.0 37.0 33.0 37.0 90-91 35.59404096834264 37.0 35.0 37.0 33.0 37.0 92-93 35.48230912476723 37.0 33.0 37.0 33.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 1.0 21 4.0 22 2.0 23 2.0 24 4.0 25 5.0 26 4.0 27 8.0 28 11.0 29 13.0 30 19.0 31 34.0 32 50.0 33 60.0 34 79.0 35 180.0 36 730.0 37 1207.0 38 1528.0 39 59.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 64.5 9.925 10.100000000000001 15.475 2 48.175000000000004 26.700000000000003 15.8 9.325 3 30.225 37.05 18.5 14.224999999999998 4 30.325000000000003 27.55 20.775 21.349999999999998 5 25.124999999999996 26.525 28.000000000000004 20.349999999999998 6 21.15 34.1 26.85 17.9 7 34.675 26.375 20.825 18.125 8 28.725 27.250000000000004 25.8 18.224999999999998 9 23.799999999999997 27.85 27.775 20.575 10-11 23.8375 28.325 28.962500000000002 18.875 12-13 23.7 28.050000000000004 27.9125 20.3375 14-15 21.425 29.799999999999997 30.2 18.575 16-17 24.15 30.3875 24.462500000000002 21.0 18-19 23.125 25.974999999999998 30.325000000000003 20.575 20-21 25.775 26.0375 27.9125 20.275000000000002 22-23 28.849999999999998 23.25 27.224999999999998 20.674999999999997 24-25 24.025 26.1625 28.725 21.087500000000002 26-27 26.387500000000003 23.8375 29.7 20.075000000000003 28-29 25.3 26.7125 27.8375 20.150000000000002 30-31 25.825 26.0 28.012500000000003 20.1625 32-33 25.0 25.2125 28.8375 20.95 34-35 23.05 29.549999999999997 26.8375 20.5625 36-37 25.087500000000002 26.825 25.2125 22.875 38-39 26.887499999999996 25.025 27.1375 20.95 40-41 25.2125 25.825 28.3125 20.65 42-43 25.45 29.825000000000003 26.650000000000002 18.075 44-45 22.1375 27.875 29.9875 20.0 46-47 25.8 25.637500000000003 27.0 21.5625 48-49 25.2625 25.087500000000002 28.537499999999998 21.1125 50-51 22.4375 27.0625 29.512500000000003 20.9875 52-53 25.5625 26.674999999999997 26.987499999999997 20.775 54-55 25.337500000000002 26.887499999999996 28.375 19.400000000000002 56-57 25.7 28.0625 27.462500000000002 18.775 58-59 23.7625 27.9375 28.825 19.475 60-61 26.3625 28.225 25.900000000000002 19.5125 62-63 22.7625 27.750000000000004 29.75 19.7375 64-65 23.075000000000003 30.075000000000003 28.0875 18.7625 66-67 24.0125 29.7375 26.474999999999998 19.775000000000002 68-69 21.7875 27.6 27.0875 23.525 70-71 24.574148296593187 27.730460921843687 27.104208416833668 20.59118236472946 72-73 26.06335983844503 26.89637763473432 27.969203584500818 19.07105894231983 74-75 24.57681048746341 27.618683976072294 28.891434389716174 18.913071146748123 76-77 21.601537475976937 27.059577194106343 27.738629083920564 23.600256245996157 78-79 26.064516129032256 26.464516129032255 28.064516129032256 19.406451612903226 80-81 23.099909055476157 31.31090035078602 26.919579056775365 18.669611536962453 82-83 22.422172599500854 28.333114409562587 27.715749376067254 21.528963614869305 84-85 21.36604774535809 25.477453580901855 30.689655172413794 22.46684350132626 86-87 20.63048683160415 27.919659483905296 27.30779462623038 24.142059058260177 88-89 20.68369247140197 29.05027932960894 29.981378026070765 20.28465017291833 90-91 23.077946262303804 27.893056664006384 28.10587922319766 20.92311785049215 92-93 22.133546155892525 28.983772279861665 27.68023410481511 21.202447459430697 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 0.0 1 0.0 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10 0.0 11 0.0 12 0.0 13 0.0 14 0.0 15 0.0 16 0.0 17 1.5 18 2.0 19 1.5 20 1.5 21 2.0 22 2.0 23 4.5 24 6.0 25 3.5 26 8.0 27 15.0 28 21.5 29 26.0 30 33.0 31 41.5 32 46.0 33 56.5 34 75.5 35 88.0 36 102.5 37 158.5 38 192.0 39 170.0 40 200.0 41 232.0 42 270.0 43 321.0 44 254.0 45 199.5 46 186.5 47 160.0 48 141.5 49 124.5 50 154.5 51 171.0 52 146.5 53 141.5 54 161.5 55 133.0 56 89.5 57 85.5 58 68.5 59 41.5 60 24.5 61 20.5 62 17.5 63 15.5 64 14.0 65 8.0 66 10.0 67 10.5 68 12.5 69 14.5 70 7.0 71 2.0 72 1.0 73 0.0 74 0.5 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 0.0 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 0.0 38-39 0.0 40-41 0.0 42-43 0.0 44-45 0.0 46-47 0.0 48-49 0.0 50-51 0.0 52-53 0.0 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 16.0 71 14.0 72 17.0 73 19.0 74 11.0 75 13.0 76 15.0 77 12.0 78 16.0 79 13.0 80 11.0 81 27.0 82 19.0 83 16.0 84 22.0 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 3759.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 72.85000000000001 #Duplication Level Percentage of deduplicated Percentage of total 1 90.80301990391216 66.14999999999999 2 3.809196980096088 5.55 3 1.956074124914207 4.275 4 1.269732326698696 3.6999999999999997 5 0.34317089910775567 1.25 6 0.34317089910775567 1.5 7 0.24021962937542896 1.225 8 0.10295126973232671 0.6 9 0.20590253946465342 1.35 >10 0.8236101578586137 9.2 >50 0.10295126973232671 5.2 >100 0.0 0.0 >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 88 2.1999999999999997 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 63 1.575 No Hit CAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCT 57 1.425 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 48 1.2 No Hit GGAAAAGAAAGCAAAAGCGATTCCCGTAGTAGCGGCGAGCGAAATGGGAG 31 0.775 No Hit TCAAAAGAGGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGGA 21 0.525 No Hit CAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATAT 18 0.44999999999999996 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 17 0.42500000000000004 No Hit GTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGGT 16 0.4 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 15 0.375 No Hit GGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTCCT 15 0.375 No Hit GGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTT 14 0.35000000000000003 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 14 0.35000000000000003 No Hit GGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGG 13 0.325 No Hit AGTCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAA 13 0.325 No Hit GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 13 0.325 No Hit CAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTG 13 0.325 No Hit GGGGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCT 12 0.3 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 11 0.27499999999999997 No Hit GCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGGTATG 11 0.27499999999999997 No Hit GGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAA 11 0.27499999999999997 No Hit GGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGC 11 0.27499999999999997 No Hit GTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAA 11 0.27499999999999997 No Hit GGGCGTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAGCATAGAT 10 0.25 No Hit GGAAGGGCGTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAGCAT 10 0.25 No Hit GATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGC 10 0.25 No Hit GAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGC 10 0.25 No Hit GAGGAAGGGCGTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAGC 9 0.22499999999999998 No Hit GCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATC 9 0.22499999999999998 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 9 0.22499999999999998 No Hit GTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAG 9 0.22499999999999998 No Hit GGTTGAGTGCCGCACCCTAGATGGCTAAAGTCCAGTAGCCGAAAGCATCA 9 0.22499999999999998 No Hit GGGTGAGAGCCCCGTCCGGCCCGGACCCTGTCGCCCCACGAGGCGCCGTC 9 0.22499999999999998 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 8 0.2 No Hit GTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAGCATAGATCCGG 8 0.2 No Hit CGAGGAAGGGCGTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAG 8 0.2 No Hit GGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCTAAATGGATTC 7 0.17500000000000002 No Hit GGAGGGTGAGAGCCCCGTCCGGCCCGGACCCTGTCGCCCCACGAGGCGCC 7 0.17500000000000002 No Hit GGTTGTGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAG 7 0.17500000000000002 No Hit GCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCT 7 0.17500000000000002 No Hit GGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAAA 7 0.17500000000000002 No Hit GGGTTGTGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGA 7 0.17500000000000002 No Hit CTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATATCATC 7 0.17500000000000002 No Hit GGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGGG 6 0.15 No Hit GGATACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATG 6 0.15 No Hit GGCCTGTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCG 6 0.15 No Hit GTCAAAAGAGGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGG 6 0.15 No Hit GGAGCAGCCTAAACCGTGAAAACGGGGTTGTGGGAGAGCAATACAAGCGT 6 0.15 No Hit GTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTC 6 0.15 No Hit GGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGCA 6 0.15 No Hit GGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGC 6 0.15 No Hit TCTCATGGAGAGTTCGATCCTGGCTCAGGATGAACGCTGGCGGCATGCTT 6 0.15 No Hit GGGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTA 6 0.15 No Hit TAGTTTCCACCGCCTGTCCAGGGTTGAGCCCTGGGATTTGACGGCGGACT 5 0.125 No Hit ATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGG 5 0.125 No Hit GTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAA 5 0.125 No Hit GGAGTACGGTAGGGGCAGAGGGAATTTCCGGTGGAGCGGTGAAATGCATT 5 0.125 No Hit GGACCCTGTCGCCCCACGAGGCGCCGTCAACGAGTCGGGTTGTTTGGGAA 5 0.125 No Hit GAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTG 5 0.125 No Hit CGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGGTATGG 5 0.125 No Hit AGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTG 5 0.125 No Hit CAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAACGTAATGCTCACA 5 0.125 No Hit GTGAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTA 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 0.0125 0.0 0.0 0.0 0.0 16-17 0.025 0.0 0.0 0.0 0.0 18-19 0.025 0.0 0.0 0.0 0.0 20-21 0.025 0.0 0.0 0.0 0.0 22-23 0.025 0.0 0.0 0.0 0.0 24-25 0.025 0.0 0.0 0.0 0.0 26-27 0.025 0.0 0.0 0.0 0.0 28-29 0.025 0.0 0.0 0.0 0.0 30-31 0.075 0.0 0.0 0.0 0.0 32-33 0.075 0.0 0.0 0.0 0.0 34-35 0.075 0.0 0.0 0.0 0.0 36-37 0.075 0.0 0.0 0.0 0.0 38-39 0.075 0.0 0.0 0.0 0.0 40-41 0.075 0.0 0.0 0.0 0.0 42-43 0.075 0.0 0.0 0.0 0.0 44-45 0.075 0.0 0.0 0.0 0.0 46-47 0.075 0.0 0.0 0.0 0.0 48-49 0.075 0.0 0.0 0.0 0.0 50-51 0.075 0.0 0.0 0.0 0.0 52-53 0.075 0.0 0.0 0.0 0.0 54-55 0.075 0.0 0.0 0.0 0.0 56-57 0.075 0.0 0.0 0.0 0.0 58-59 0.075 0.0 0.0 0.0 0.0 60-61 0.075 0.0 0.0 0.0 0.0 62-63 0.075 0.0 0.0 0.0 0.0 64-65 0.075 0.0 0.0 0.0 0.0 66-67 0.075 0.0 0.0 0.0 0.0 68-69 0.075 0.0 0.0 0.0 0.0 70-71 0.075 0.0 0.0 0.0 0.0 72-73 0.075 0.0 0.0 0.0 0.0 74-75 0.075 0.0 0.0 0.0 0.0 76-77 0.075 0.0 0.0 0.0 0.0 78-79 0.075 0.0 0.0 0.0 0.0 80-81 0.075 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Rejected 146517 READS because READLEN < 1 Read 146517 spots for ERR6133362.sra Written 146517 spots for ERR6133362.sra Rejected 146517 READS because READLEN < 1 Read 146517 spots for ERR6133362.sra Written 146517 spots for ERR6133362.sra Rejected 146517 READS because READLEN < 1 Read 146517 spots for ERR6133362.sra Written 146517 spots for ERR6133362.sra Rejected 146517 READS because READLEN < 1 Read 146517 spots for ERR6133362.sra Written 146517 spots for ERR6133362.sra Rejected 146517 READS because READLEN < 1 Read 146517 spots for ERR6133362.sra Written 146517 spots for ERR6133362.sra Rejected 146517 READS because READLEN < 1 Read 146517 spots for ERR6133362.sra Written 146517 spots for ERR6133362.sra Rejected 146517 READS because READLEN < 1 Read 146517 spots for ERR6133362.sra Written 146517 spots for ERR6133362.sra Rejected 146517 READS because READLEN < 1 Read 146517 spots for ERR6133362.sra Written 146517 spots for ERR6133362.sra Rejected 146517 READS because READLEN < 1 Read 146517 spots for ERR6133362.sra Written 146517 spots for ERR6133362.sra Rejected 146517 READS because READLEN < 1 Read 146517 spots for ERR6133362.sra Written 146517 spots for ERR6133362.sra Rejected 146517 READS because READLEN < 1 Read 146517 spots for ERR6133362.sra Written 146517 spots for ERR6133362.sra Rejected 146517 READS because READLEN < 1 Read 146517 spots for ERR6133362.sra Written 146517 spots for ERR6133362.sra Rejected 146517 READS because READLEN < 1 Read 146517 spots for ERR6133362.sra Written 146517 spots for ERR6133362.sra Rejected 146517 READS because READLEN < 1 Read 146517 spots for ERR6133362.sra Written 146517 spots for ERR6133362.sra Rejected 146517 READS because READLEN < 1 Read 146517 spots for ERR6133362.sra Written 146517 spots for ERR6133362.sra Rejected 146517 READS because READLEN < 1 Read 146517 spots for ERR6133362.sra Written 146517 spots for ERR6133362.sra Rejected 146520 READS because READLEN < 1 Read 146520 spots for ERR6133362.sra Written 146520 spots for ERR6133362.sra Rejected 146517 READS because READLEN < 1 Read 146517 spots for ERR6133362.sra Written 146517 spots for ERR6133362.sra Rejected 146517 READS because READLEN < 1 Read 146517 spots for ERR6133362.sra Written 146517 spots for ERR6133362.sra Rejected 146517 READS because READLEN < 1 Read 146517 spots for ERR6133362.sra Written 146517 spots for ERR6133362.sra SRR ids: ['ERR6133362.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_j2xfhz4i ERR6133362.sra spots: 2930343 blocks: [[1, 146517], [146518, 293034], [293035, 439551], [439552, 586068], [586069, 732585], [732586, 879102], [879103, 1025619], [1025620, 1172136], [1172137, 1318653], [1318654, 1465170], [1465171, 1611687], [1611688, 1758204], [1758205, 1904721], [1904722, 2051238], [2051239, 2197755], [2197756, 2344272], [2344273, 2490789], [2490790, 2637306], [2637307, 2783823], [2783824, 2930343]] ERR6133362 file size 645216 ERR6133362 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 ERR6133362 ERR6133362_1.fastq Input file: ERR6133362_1.fastq trimmed: ERR6133362-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 01:27:05 2024 >> started Sat Dec 7 01:27:08 2024 >> done (2.112s) 2930343 reads processed; of these: 265 ( 0.01%) short reads filtered out after trimming by size control 3 ( 0.00%) empty reads filtered out after trimming by size control 2930075 (99.99%) reads available; of these: 16036 ( 0.55%) trimmed reads available after processing 2914039 (99.45%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 20 0.00% 19 48 0.00% 20 32 0.00% 21 25 0.00% 22 28 0.00% 23 18 0.00% 24 22 0.00% 25 15 0.00% 26 15 0.00% 27 23 0.00% 28 133 0.00% 29 338 0.01% 30 19 0.00% 31 21 0.00% 32 50 0.00% 33 29 0.00% 34 17 0.00% 35 38 0.00% 36 11 0.00% 37 21 0.00% 38 30 0.00% 39 77 0.00% 40 100 0.00% 41 25 0.00% 42 11 0.00% 43 27 0.00% 44 25 0.00% 45 17 0.00% 46 14 0.00% 47 8 0.00% 48 9 0.00% 49 6 0.00% 50 20 0.00% 51 114 0.00% 52 13 0.00% 53 14 0.00% 54 13 0.00% 55 13 0.00% 56 12 0.00% 57 37 0.00% 58 13 0.00% 59 14 0.00% 60 20 0.00% 61 24 0.00% 62 4 0.00% 63 8 0.00% 64 11 0.00% 65 8 0.00% 66 20 0.00% 67 31 0.00% 68 47 0.00% 69 64 0.00% 70 10984 0.37% 71 10186 0.35% 72 10293 0.35% 73 9840 0.34% 74 9421 0.32% 75 9310 0.32% 76 9073 0.31% 77 10186 0.35% 78 10277 0.35% 79 10849 0.37% 80 10884 0.37% 81 14286 0.49% 82 15017 0.51% 83 12691 0.43% 84 14620 0.50% 85 113 0.00% 86 151 0.01% 87 245 0.01% 88 361 0.01% 89 581 0.02% 90 1152 0.04% 91 2384 0.08% 92 7791 0.27% 93 2747608 93.77% 2930075 reads passed initial QC criterion=sequence-density sequence-density=2.75 sequence-density-rank=1 fanout-score=2.04 fanout-score-rank=24 prefix-density=2.80 prefix-fanout=2.0 sequence=CAAGGCTAAATAC criterion=fanout-score sequence-density=0.01 sequence-density-rank=29 fanout-score=49.36 fanout-score-rank=1 prefix-density=0.09 prefix-fanout=4.0 sequence=CTTTTTTCCTTAGAAAAATAACTCAATCAAAATCCAATTATTTACTCTACAAGAACGAAATGCTTGTTATGCCTAATATACTTAGTTTAACCTGTATCTGTTTTAATTGTGTTCTTTATCCGACTAGTTTTTTCTTTGCTAAACTACCCGAAGCTTATGCTATTTTCAACCCAATCGTGGATGTTATGCCTGTCATACCTCTATTCTTTTTTCTATTAGCCTTTGTTTGGCAAGCTGCTGTAAGTTTTCGATGAAATCTTTACTACTCCGTCTGCCAAATTGAATGGTCTATTCATTCCAAAACC 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: 0 (0.00%) aligned 0 times 0 (0.00%) aligned exactly 1 time 1 (100.00%) aligned >1 times 100.00% overall alignment rate Potential adapter found in reference sequence. Continuing without clipping. Started job on | Dec 07 01:27:20 Started mapping on | Dec 07 01:27:21 Finished on | Dec 07 01:27:27 Mapping speed, Million of reads per hour | 1758.04 Number of input reads | 2930075 Average input read length | 92 UNIQUE READS: Uniquely mapped reads number | 1407607 Uniquely mapped reads % | 48.04% Average mapped length | 91.22 Number of splices: Total | 49479 Number of splices: Annotated (sjdb) | 39018 Number of splices: GT/AG | 46370 Number of splices: GC/AG | 968 Number of splices: AT/AC | 104 Number of splices: Non-canonical | 2037 Mismatch rate per base, % | 0.40% Deletion rate per base | 0.04% Deletion average length | 1.71 Insertion rate per base | 0.02% Insertion average length | 1.88 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 1347479 % of reads mapped to multiple loci | 45.99% Number of reads mapped to too many loci | 105289 % of reads mapped to too many loci | 3.59% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 2.21% % of reads unmapped: other | 0.16% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 174989 174989 174989 N_multimapping 1347479 1347479 1347479 N_noFeature 121035 134805 1350641 N_ambiguous 51155 7974 230 UnstrandedReadsAssigned:1235417 PositiveStrandReadsAssigned:1264828 NegativeStrandReadsAssigned:56736 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=93 echo kmer=89 ERR6133362 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: ERR6133362-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 2,930,075 reads, 1,996,982 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 918 rounds 52973 ERR6133362.ke.tsv 35125 ERR6133362.se.tsv 88098 total ==> ERR6133362.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 55 26.8363 PNS24243 293 194 0 0 KQK14069 1603 1504 33 14.6886 KQK14071 474 375 0 0 ==> ERR6133362.se.tsv <== BRADI_1g14170v3 33 BRADI_1g53295v3 3 BRADI_1g59795v3 24 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 10 BRADI_1g74790v3 14 BRADI_1g09890v3 0 BRADI_1g77505v3 24 BRADI_1g48960v3 0 ERR6133362 completed mapping pipeline successfully