Starting /dee2/code/volunteer_pipeline.sh ERR6133568 current disk space = 1544404742144 free memory = 1419896984 ERR6133568 SRAfilesize 64078f99e7018d09c83c627ac7c80050 ERR6133568.sra ERR6133568.sra file validated ERR6133568 is single end ERR6133568 is conventional basespace ERR6133568 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133568_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 35.36125 37.0 33.0 37.0 33.0 37.0 2 36.41325 37.0 37.0 37.0 37.0 37.0 3 35.99425 37.0 37.0 37.0 33.0 37.0 4 35.41275 37.0 37.0 37.0 33.0 37.0 5 35.2675 37.0 37.0 37.0 33.0 37.0 6 35.729 37.0 37.0 37.0 33.0 37.0 7 37.47875 40.0 37.0 40.0 33.0 40.0 8 37.6 40.0 37.0 40.0 33.0 40.0 9 37.63525 40.0 37.0 40.0 33.0 40.0 10-11 37.613625 38.5 37.0 40.0 33.0 40.0 12-13 37.528 38.5 37.0 40.0 33.0 40.0 14-15 37.458 37.0 37.0 40.0 33.0 40.0 16-17 37.403125 37.0 37.0 40.0 33.0 40.0 18-19 37.301 37.0 37.0 40.0 33.0 40.0 20-21 37.203875 37.0 37.0 40.0 33.0 40.0 22-23 37.205625 37.0 37.0 40.0 33.0 40.0 24-25 37.272999999999996 37.0 37.0 40.0 33.0 40.0 26-27 37.227999999999994 37.0 37.0 40.0 33.0 40.0 28-29 37.187875 37.0 37.0 40.0 33.0 40.0 30-31 37.056124999999994 37.0 37.0 40.0 33.0 40.0 32-33 36.945875 37.0 37.0 40.0 33.0 40.0 34-35 36.7635 37.0 37.0 40.0 33.0 40.0 36-37 36.729875 37.0 37.0 40.0 33.0 40.0 38-39 36.45075 37.0 37.0 40.0 33.0 40.0 40-41 36.236875 37.0 37.0 40.0 33.0 40.0 42-43 36.118875 37.0 37.0 40.0 33.0 40.0 44-45 35.809875000000005 37.0 35.0 40.0 33.0 40.0 46-47 35.504625 37.0 33.0 37.0 33.0 40.0 48-49 35.397625000000005 37.0 33.0 37.0 30.0 40.0 50-51 35.308375 37.0 33.0 37.0 30.0 40.0 52-53 34.9855 37.0 33.0 37.0 27.0 40.0 54-55 34.994875 37.0 33.0 37.0 30.0 40.0 56-57 34.7535 37.0 33.0 37.0 27.0 38.5 58-59 33.51925 37.0 33.0 37.0 27.0 37.0 60-61 34.030875 37.0 33.0 37.0 27.0 37.0 62-63 34.199875 37.0 33.0 37.0 27.0 37.0 64-65 34.137375 37.0 33.0 37.0 27.0 37.0 66-67 34.164625 37.0 33.0 37.0 27.0 37.0 68-69 33.361000000000004 35.0 33.0 37.0 27.0 37.0 70-71 33.50998080055124 35.0 33.0 37.0 27.0 37.0 72-73 33.855955401879285 37.0 33.0 37.0 27.0 37.0 74-75 33.52572619202234 37.0 33.0 37.0 27.0 37.0 76-77 33.768958652123786 37.0 33.0 37.0 27.0 37.0 78-79 33.88602041504598 37.0 33.0 37.0 27.0 37.0 80-81 33.71858915133638 37.0 33.0 37.0 27.0 37.0 82-83 33.61286360774804 37.0 33.0 37.0 27.0 37.0 84-85 33.55899147104765 37.0 33.0 37.0 27.0 37.0 86-87 33.48074948665298 37.0 33.0 37.0 27.0 37.0 88-89 33.614989733059545 37.0 33.0 37.0 27.0 37.0 90-91 33.36575975359343 37.0 33.0 37.0 27.0 37.0 92-93 33.22920944558521 37.0 33.0 37.0 27.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 16.0 21 11.0 22 26.0 23 21.0 24 23.0 25 31.0 26 38.0 27 41.0 28 64.0 29 74.0 30 99.0 31 94.0 32 129.0 33 177.0 34 285.0 35 426.0 36 843.0 37 941.0 38 652.0 39 9.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 85.15 2.725 3.8249999999999997 8.3 2 66.425 19.475 9.025 5.075 3 33.575 37.7 17.175 11.55 4 33.15 26.275 20.225 20.349999999999998 5 24.125 30.775000000000002 26.200000000000003 18.9 6 19.55 37.85 25.124999999999996 17.474999999999998 7 32.95 30.575000000000003 21.025 15.45 8 30.349999999999998 29.325000000000003 23.974999999999998 16.35 9 24.425 28.849999999999998 28.499999999999996 18.224999999999998 10-11 24.7875 27.275 28.4 19.537499999999998 12-13 25.9875 26.25 27.85 19.9125 14-15 22.287499999999998 30.025000000000002 28.8625 18.825 16-17 23.6125 31.374999999999996 24.9125 20.1 18-19 22.85 26.487500000000004 28.6875 21.975 20-21 25.324999999999996 24.825 29.312500000000004 20.5375 22-23 27.250000000000004 22.375 28.725 21.65 24-25 25.575 25.224999999999998 28.775000000000002 20.424999999999997 26-27 24.3875 24.0375 32.05 19.525000000000002 28-29 25.887500000000003 25.162499999999998 29.099999999999998 19.85 30-31 25.387500000000003 26.775 27.825 20.0125 32-33 24.275 26.200000000000003 29.175 20.349999999999998 34-35 24.1875 27.150000000000002 27.987499999999997 20.674999999999997 36-37 25.3 25.5375 27.474999999999998 21.6875 38-39 25.704269437836487 25.241016652059596 29.38525103292851 19.66946287717541 40-41 24.990600325855368 25.968166436896855 28.274219827045993 20.76701341020178 42-43 25.76894223555889 26.906726681670417 27.069267316829208 20.255063765941486 44-45 23.5625 24.925 30.4875 21.025 46-47 24.775 25.2375 28.849999999999998 21.1375 48-49 24.4125 25.3125 29.725 20.549999999999997 50-51 23.6875 26.450000000000003 28.7 21.1625 52-53 25.253791201905003 26.19375861636797 27.13372603083093 21.4187241508961 54-55 22.9625 27.575 29.625 19.8375 56-57 26.875 25.624999999999996 28.3625 19.1375 58-59 24.75 24.4375 29.2 21.6125 60-61 25.5125 25.025 29.425 20.0375 62-63 21.837500000000002 27.175 32.15 18.8375 64-65 22.2625 28.549999999999997 29.45 19.7375 66-67 23.45 26.5875 30.0875 19.875 68-69 21.825 27.212500000000002 28.3375 22.625 70-71 24.064572644224754 26.46727568514579 28.09410586910274 21.374045801526716 72-73 24.50364413169138 25.182206584568988 28.56245287760744 21.751696406132194 74-75 24.25081843364392 27.839335180055404 28.3807605137245 19.529085872576175 76-77 23.50416561474375 25.48598838677102 28.528149457207775 22.481696541277454 78-79 23.62184767456596 25.01584083132683 30.566468128247372 20.795843365859838 80-81 23.020117137764196 28.80061115355233 29.44996180290298 18.729309905780493 82-83 21.993872861884096 26.525402093438856 29.793209088588206 21.687515956088845 84-85 24.10565457109886 23.682523400435954 31.286062315681495 20.92575971278369 86-87 21.842915811088297 26.283367556468175 31.90451745379877 19.969199178644764 88-89 21.586242299794662 27.28439425051335 31.968685831622178 19.160677618069816 90-91 25.59034907597536 25.51334702258727 28.93993839835729 19.956365503080082 92-93 22.189425051334702 29.992299794661193 28.824435318275153 18.993839835728956 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 0.0 1 0.0 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10 0.0 11 0.0 12 0.0 13 0.0 14 0.0 15 0.0 16 1.0 17 6.0 18 6.0 19 2.5 20 2.5 21 1.5 22 0.5 23 2.5 24 3.0 25 2.5 26 5.5 27 9.0 28 14.0 29 18.5 30 23.5 31 33.5 32 53.5 33 73.5 34 85.5 35 91.0 36 108.0 37 152.5 38 209.5 39 213.5 40 199.5 41 207.5 42 203.5 43 203.0 44 204.5 45 214.0 46 215.0 47 185.0 48 144.0 49 137.5 50 154.5 51 150.5 52 127.5 53 123.5 54 125.0 55 94.5 56 66.5 57 61.5 58 57.5 59 44.5 60 30.5 61 26.0 62 32.0 63 34.5 64 28.0 65 25.0 66 21.0 67 18.0 68 15.5 69 13.0 70 9.5 71 4.0 72 5.5 73 6.0 74 3.5 75 1.0 76 0.5 77 0.5 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 0.1625 40-41 0.2625 42-43 0.025 44-45 0.0 46-47 0.0 48-49 0.0 50-51 0.0 52-53 0.2625 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 9.0 71 7.0 72 10.0 73 0.0 74 6.0 75 4.0 76 6.0 77 8.0 78 9.0 79 13.0 80 2.0 81 5.0 82 8.0 83 10.0 84 7.0 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 3896.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 80.875 #Duplication Level Percentage of deduplicated Percentage of total 1 93.57032457496136 75.675 2 3.6476043276661514 5.8999999999999995 3 0.9273570324574961 2.25 4 0.401854714064915 1.3 5 0.401854714064915 1.625 6 0.1545595054095827 0.75 7 0.1545595054095827 0.8750000000000001 8 0.12364760432766615 0.8 9 0.061823802163833076 0.44999999999999996 >10 0.5255023183925811 8.9 >50 0.030911901081916538 1.4749999999999999 >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 GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 59 1.4749999999999999 No Hit GGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGC 42 1.05 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 37 0.9249999999999999 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 36 0.8999999999999999 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 31 0.775 No Hit GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 29 0.7250000000000001 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 29 0.7250000000000001 No Hit GTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAA 27 0.675 No Hit GGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGG 23 0.575 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 14 0.35000000000000003 No Hit GGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTT 12 0.3 No Hit GGGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTG 12 0.3 No Hit GGCCTGTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCG 11 0.27499999999999997 No Hit CAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCT 11 0.27499999999999997 No Hit GGAGTATCCTTGATATATAAATATATAGATAAATAGATTTAAATGGAAAA 11 0.27499999999999997 No Hit GGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAA 11 0.27499999999999997 No Hit CAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATAT 10 0.25 No Hit GGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGGG 10 0.25 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 9 0.22499999999999998 No Hit GGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAACCCTCTTAACT 9 0.22499999999999998 No Hit GGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCG 8 0.2 No Hit GGGAGTATTATGAAAGGAGATTAATCATAGATTATCAAAAACCCTAGAAA 8 0.2 No Hit GGGGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCT 8 0.2 No Hit GTATTTAGCCTTGCAAGGTGGTCCTTGCTGATTCACACGGGATTCCACGT 8 0.2 No Hit GGTGGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGC 7 0.17500000000000002 No Hit GAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGC 7 0.17500000000000002 No Hit GATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAAT 7 0.17500000000000002 No Hit GGGACGCATGCAACGACCATCTACATATAGCTACTCGATCTACCGCTACC 7 0.17500000000000002 No Hit GGAAAAGAAAGCAAAAGCGATTCCCGTAGTAGCGGCGAGCGAAATGGGAG 7 0.17500000000000002 No Hit GGGAAAAGAGGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTT 6 0.15 No Hit GTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCT 6 0.15 No Hit GGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTT 6 0.15 No Hit GGAAAAGAGGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTTG 6 0.15 No Hit GGTTTTGAAAAGGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAA 6 0.15 No Hit GGCTTTAGAAGCCTGTGTACAAGCTCGTAACGAAGGGCGCGATCTTGCTC 5 0.125 No Hit GGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTA 5 0.125 No Hit AGTATGGCATCGGTTACATACTTCAGTGCCGTAGCGCCTGGTATGAGCCT 5 0.125 No Hit GGAAGAGCCCGAGCTGCTGCAGCAGGTTTTGAAAAGGGAATCGATCGTGA 5 0.125 No Hit GGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGC 5 0.125 No Hit GGGGGTCGCAGTGACCAGGCCCGGGCGACTGTTTACCAAAAACACAGGTC 5 0.125 No Hit GGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCG 5 0.125 No Hit GTACTATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTT 5 0.125 No Hit GGAGATCGAGTTGTTACTTGAGAGTTTGTAACCCTTTATCATGCCATGTC 5 0.125 No Hit GGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAA 5 0.125 No Hit GTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAG 5 0.125 No Hit GAGAGCAAATGGGAAAAGAGGGGTTACTTTTTTTCATTTTTCCCTTAAAA 5 0.125 No Hit GGGTCGAGACCGACTTCAGGACCGGCGAGAACCCATGGTGGAAATAAGCA 5 0.125 No Hit >>END_MODULE >>Adapter Content pass #Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence SOLID Small RNA Adapter 1 0.0 0.0 0.0 0.0 0.0 2 0.0 0.0 0.0 0.0 0.0 3 0.0 0.0 0.0 0.0 0.0 4 0.0 0.0 0.0 0.0 0.0 5 0.0 0.0 0.0 0.0 0.0 6 0.0 0.0 0.0 0.0 0.0 7 0.0 0.0 0.0 0.0 0.0 8 0.0 0.0 0.0 0.0 0.0 9 0.0 0.0 0.0 0.0 0.0 10-11 0.0 0.0 0.0 0.0 0.0 12-13 0.0 0.0 0.0 0.0 0.0 14-15 0.0 0.0 0.0 0.0 0.0 16-17 0.0 0.0 0.0 0.0 0.0 18-19 0.0 0.0 0.0 0.0 0.0 20-21 0.0 0.0 0.0 0.0 0.0 22-23 0.0 0.0 0.0 0.0 0.0 24-25 0.0 0.0 0.0 0.0 0.0 26-27 0.0 0.0 0.0 0.0 0.0 28-29 0.0 0.0 0.0 0.0 0.0 30-31 0.0 0.0 0.0 0.0 0.0 32-33 0.0 0.0 0.0 0.0 0.0 34-35 0.0 0.0 0.0 0.0 0.0 36-37 0.0 0.0 0.0 0.0 0.0 38-39 0.0 0.0 0.0 0.0 0.0 40-41 0.0 0.0 0.0 0.0 0.0 42-43 0.0 0.0 0.0 0.0 0.0 44-45 0.0 0.0 0.0 0.0 0.0 46-47 0.0 0.0 0.0 0.0 0.0 48-49 0.0 0.0 0.0 0.0 0.0 50-51 0.0 0.0 0.0 0.0 0.0 52-53 0.0 0.0 0.0 0.0 0.0 54-55 0.0 0.0 0.0 0.0 0.0 56-57 0.0 0.0 0.0 0.0 0.0 58-59 0.0 0.0 0.0 0.0 0.0 60-61 0.0 0.0 0.0 0.0 0.0 62-63 0.0 0.0 0.0 0.0 0.0 64-65 0.0 0.0 0.0 0.0 0.0 66-67 0.0 0.0 0.0 0.0 0.0 68-69 0.0 0.0 0.0 0.0 0.0 70-71 0.0 0.0 0.0 0.0 0.0 72-73 0.025 0.0 0.0 0.0 0.0 74-75 0.025 0.0 0.0 0.0 0.0 76-77 0.025 0.0 0.0 0.0 0.0 78-79 0.025 0.0 0.0 0.0 0.0 80-81 0.037500000000000006 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TTCAATT 15 8.9305255E-4 86.4625 4 CAATTTC 15 8.9305255E-4 86.4625 6 GGATTCA 15 8.9305255E-4 86.4625 1 TTTCAAC 15 8.9305255E-4 86.4625 9 TCAATTT 15 8.9305255E-4 86.4625 5 ATTCAAT 15 8.9305255E-4 86.4625 3 AATTTCA 20 0.002797807 64.84688 7 GATTCAA 20 0.002797807 64.84688 2 ATTTCAA 20 0.002797807 64.84688 8 GTCGCGT 35 3.9246414E-4 49.407143 2 TCGCGTT 35 3.9246414E-4 49.407143 3 GGTCGCG 35 3.9246414E-4 49.407143 1 ATGGAAG 20 7.5768435E-4 43.778484 52-53 TGGAAGT 20 7.5768435E-4 43.778484 52-53 CGTTATT 40 7.582973E-4 43.23125 6 GGAAGTA 20 8.0674305E-4 43.23125 54-55 GCGTTAT 40 7.582973E-4 43.23125 5 GTTATTA 40 7.582973E-4 43.23125 7 CGCGTTA 40 7.582973E-4 43.23125 4 TTATTAA 45 0.0013541994 38.427776 8 >>END_MODULE Rejected 280955 READS because READLEN < 1 Read 280955 spots for ERR6133568.sra Written 280955 spots for ERR6133568.sra Rejected 280955 READS because READLEN < 1 Read 280955 spots for ERR6133568.sra Written 280955 spots for ERR6133568.sra Rejected 280955 READS because READLEN < 1 Read 280955 spots for ERR6133568.sra Written 280955 spots for ERR6133568.sra Rejected 280955 READS because READLEN < 1 Read 280955 spots for ERR6133568.sra Written 280955 spots for ERR6133568.sra Rejected 280955 READS because READLEN < 1 Read 280955 spots for ERR6133568.sra Written 280955 spots for ERR6133568.sra Rejected 280955 READS because READLEN < 1 Read 280955 spots for ERR6133568.sra Written 280955 spots for ERR6133568.sra Rejected 280955 READS because READLEN < 1 Read 280955 spots for ERR6133568.sra Written 280955 spots for ERR6133568.sra Rejected 280955 READS because READLEN < 1 Read 280955 spots for ERR6133568.sra Written 280955 spots for ERR6133568.sra Rejected 280955 READS because READLEN < 1 Read 280955 spots for ERR6133568.sra Written 280955 spots for ERR6133568.sra Rejected 280955 READS because READLEN < 1 Read 280955 spots for ERR6133568.sra Written 280955 spots for ERR6133568.sra Rejected 280974 READS because READLEN < 1 Read 280974 spots for ERR6133568.sra Written 280974 spots for ERR6133568.sra Rejected 280955 READS because READLEN < 1 Read 280955 spots for ERR6133568.sra Written 280955 spots for ERR6133568.sra Rejected 280955 READS because READLEN < 1 Read 280955 spots for ERR6133568.sra Written 280955 spots for ERR6133568.sra Rejected 280955 READS because READLEN < 1 Read 280955 spots for ERR6133568.sra Written 280955 spots for ERR6133568.sra Rejected 280955 READS because READLEN < 1 Read 280955 spots for ERR6133568.sra Written 280955 spots for ERR6133568.sra Rejected 280955 READS because READLEN < 1 Read 280955 spots for ERR6133568.sra Written 280955 spots for ERR6133568.sra Rejected 280955 READS because READLEN < 1 Read 280955 spots for ERR6133568.sra Written 280955 spots for ERR6133568.sra Rejected 280955 READS because READLEN < 1 Read 280955 spots for ERR6133568.sra Written 280955 spots for ERR6133568.sra Rejected 280955 READS because READLEN < 1 Read 280955 spots for ERR6133568.sra Written 280955 spots for ERR6133568.sra Rejected 280955 READS because READLEN < 1 Read 280955 spots for ERR6133568.sra Written 280955 spots for ERR6133568.sra SRR ids: ['ERR6133568.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_g4yu3ozm ERR6133568.sra spots: 5619119 blocks: [[1, 280955], [280956, 561910], [561911, 842865], [842866, 1123820], [1123821, 1404775], [1404776, 1685730], [1685731, 1966685], [1966686, 2247640], [2247641, 2528595], [2528596, 2809550], [2809551, 3090505], [3090506, 3371460], [3371461, 3652415], [3652416, 3933370], [3933371, 4214325], [4214326, 4495280], [4495281, 4776235], [4776236, 5057190], [5057191, 5338145], [5338146, 5619119]] ERR6133568 file size 1243535 ERR6133568 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 ERR6133568 ERR6133568_1.fastq Input file: ERR6133568_1.fastq trimmed: ERR6133568-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -- maximum error ratio allowed (-r): 0.100 -- maximum indel error ratio allowed (-d): 0.030 -- end quality threshold (-q): 10 -- minimum read length allowed after trimming (-l): 18 -- file format (-f): Sanger/Illumina 1.8+ FASTQ -- minimum overlap length for adapter detection (-k): inf -- number of concurrent threads (-t): 20 Sat Dec 7 08:50:17 2024 >> started Sat Dec 7 08:50:20 2024 >> done (2.867s) 5619119 reads processed; of these: 289 ( 0.01%) short reads filtered out after trimming by size control 41 ( 0.00%) empty reads filtered out after trimming by size control 5618789 (99.99%) reads available; of these: 117932 ( 2.10%) trimmed reads available after processing 5500857 (97.90%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 58 0.00% 19 124 0.00% 20 31 0.00% 21 58 0.00% 22 56 0.00% 23 23 0.00% 24 19 0.00% 25 14 0.00% 26 15 0.00% 27 20 0.00% 28 46 0.00% 29 30 0.00% 30 25 0.00% 31 38 0.00% 32 45 0.00% 33 27 0.00% 34 26 0.00% 35 178 0.00% 36 588 0.01% 37 33 0.00% 38 49 0.00% 39 157 0.00% 40 138 0.00% 41 56 0.00% 42 16 0.00% 43 17 0.00% 44 19 0.00% 45 10 0.00% 46 10 0.00% 47 7 0.00% 48 9 0.00% 49 14 0.00% 50 11 0.00% 51 59 0.00% 52 21 0.00% 53 5 0.00% 54 7 0.00% 55 5 0.00% 56 9 0.00% 57 20 0.00% 58 10 0.00% 59 15 0.00% 60 19 0.00% 61 12 0.00% 62 3 0.00% 63 6 0.00% 64 6 0.00% 65 4 0.00% 66 13 0.00% 67 17 0.00% 68 39 0.00% 69 118 0.00% 70 10871 0.19% 71 10954 0.19% 72 11264 0.20% 73 10612 0.19% 74 11178 0.20% 75 10941 0.19% 76 10089 0.18% 77 10523 0.19% 78 11421 0.20% 79 12393 0.22% 80 11865 0.21% 81 12861 0.23% 82 15085 0.27% 83 14837 0.26% 84 13616 0.24% 85 240 0.00% 86 441 0.01% 87 680 0.01% 88 1295 0.02% 89 2438 0.04% 90 5283 0.09% 91 15904 0.28% 92 87051 1.55% 93 5324592 94.76% 5618789 reads passed initial QC criterion=sequence-density sequence-density=0.26 sequence-density-rank=1 fanout-score=10.42 fanout-score-rank=18 prefix-density=0.49 prefix-fanout=5.5 sequence=ATGCATGCATGC criterion=fanout-score sequence-density=0.01 sequence-density-rank=41 fanout-score=106.90 fanout-score-rank=1 prefix-density=0.10 prefix-fanout=6.3 sequence=AAAAGAAGGGGTGTTCCATCTCCGGACGACGATCCTGCCTGCGGAGGAAGACATGCCGGCGATCATGTCGAGCTTCAAGAAGTTCAACGACTCATTCATGGAGCAATACCAAGACTACTCCAGGCTGTGATGTGAAGAGGGAAACAACGACGTCATCATCGACATGATATATTGCTGCTATTTTCCACCAGCGATTAAAAGTTAAAAAATTTAGCTGTAAGCTGTAACTATCTTGAAGAAACTAAACTGGTTGCTGTGCTTGATATGTATAGGGAAAACATAATTTATGAGACAATCATACTGTGCAACTCTTGGCTCCATCGATTAATTAATACTCCTTGTTATTGCTTGC Started job on | Dec 07 08:50:37 Started mapping on | Dec 07 08:50:37 Finished on | Dec 07 08:50:44 Mapping speed, Million of reads per hour | 2889.66 Number of input reads | 5618789 Average input read length | 92 UNIQUE READS: Uniquely mapped reads number | 3948756 Uniquely mapped reads % | 70.28% Average mapped length | 92.00 Number of splices: Total | 179634 Number of splices: Annotated (sjdb) | 146595 Number of splices: GT/AG | 172110 Number of splices: GC/AG | 3455 Number of splices: AT/AC | 104 Number of splices: Non-canonical | 3965 Mismatch rate per base, % | 0.40% Deletion rate per base | 0.04% Deletion average length | 1.86 Insertion rate per base | 0.02% Insertion average length | 1.92 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 1536979 % of reads mapped to multiple loci | 27.35% Number of reads mapped to too many loci | 54287 % of reads mapped to too many loci | 0.97% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.34% % of reads unmapped: other | 0.06% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 133054 133054 133054 N_multimapping 1536979 1536979 1536979 N_noFeature 278286 318682 3774470 N_ambiguous 149773 15844 553 UnstrandedReadsAssigned:3520697 PositiveStrandReadsAssigned:3614230 NegativeStrandReadsAssigned:173733 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=93 echo kmer=89 ERR6133568 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: ERR6133568-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 5,618,789 reads, 4,662,967 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,118 rounds 52973 ERR6133568.ke.tsv 35125 ERR6133568.se.tsv 88098 total ==> ERR6133568.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 129 26.554 PNS24243 293 194 0 0 KQK14069 1603 1504 21 3.94336 KQK14071 474 375 0 0 ==> ERR6133568.se.tsv <== BRADI_1g14170v3 21 BRADI_1g53295v3 91 BRADI_1g59795v3 42 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 49 BRADI_1g74790v3 25 BRADI_1g09890v3 0 BRADI_1g77505v3 105 BRADI_1g48960v3 0 ERR6133568 completed mapping pipeline successfully