Starting /dee2/code/volunteer_pipeline.sh ERR6133559 current disk space = 1544510722048 free memory = 1435648116 ERR6133559 SRAfilesize bd9f4d43d16a133338658117ba34a07d ERR6133559.sra ERR6133559.sra file validated ERR6133559 is single end ERR6133559 is conventional basespace ERR6133559 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133559_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 35.486 37.0 33.0 37.0 33.0 37.0 2 36.57575 37.0 37.0 37.0 37.0 37.0 3 36.13 37.0 37.0 37.0 33.0 37.0 4 35.66925 37.0 37.0 37.0 33.0 37.0 5 35.37625 37.0 37.0 37.0 33.0 37.0 6 35.84225 37.0 37.0 37.0 33.0 37.0 7 37.68275 40.0 37.0 40.0 33.0 40.0 8 37.7295 40.0 37.0 40.0 33.0 40.0 9 37.776 40.0 37.0 40.0 33.0 40.0 10-11 37.7415 40.0 37.0 40.0 33.0 40.0 12-13 37.6455 38.5 37.0 40.0 33.0 40.0 14-15 37.612375 40.0 37.0 40.0 33.0 40.0 16-17 37.513999999999996 38.5 37.0 40.0 33.0 40.0 18-19 37.472 37.0 37.0 40.0 33.0 40.0 20-21 37.385000000000005 37.0 37.0 40.0 33.0 40.0 22-23 37.341875 37.0 37.0 40.0 33.0 40.0 24-25 37.448375 37.0 37.0 40.0 33.0 40.0 26-27 37.418 37.0 37.0 40.0 33.0 40.0 28-29 37.405625 37.0 37.0 40.0 33.0 40.0 30-31 37.216125 37.0 37.0 40.0 33.0 40.0 32-33 37.062124999999995 37.0 37.0 40.0 33.0 40.0 34-35 36.929125 37.0 37.0 40.0 33.0 40.0 36-37 36.807125 37.0 37.0 40.0 33.0 40.0 38-39 36.590125 37.0 37.0 40.0 33.0 40.0 40-41 36.500875 37.0 37.0 40.0 33.0 40.0 42-43 36.354375000000005 37.0 37.0 40.0 33.0 40.0 44-45 36.120000000000005 37.0 37.0 40.0 33.0 40.0 46-47 35.7945 37.0 33.0 37.0 33.0 40.0 48-49 35.6285 37.0 33.0 37.0 33.0 40.0 50-51 35.49125 37.0 33.0 37.0 33.0 40.0 52-53 35.107 37.0 33.0 37.0 30.0 40.0 54-55 35.1305 37.0 33.0 37.0 33.0 40.0 56-57 34.905 37.0 33.0 37.0 33.0 38.5 58-59 33.81525 37.0 33.0 37.0 27.0 37.0 60-61 34.406375 37.0 33.0 37.0 27.0 37.0 62-63 34.413875000000004 37.0 33.0 37.0 27.0 37.0 64-65 34.3005 37.0 33.0 37.0 27.0 37.0 66-67 34.444 37.0 33.0 37.0 27.0 37.0 68-69 33.736875 35.0 33.0 37.0 30.0 37.0 70-71 33.76900613573754 35.0 33.0 37.0 27.0 37.0 72-73 34.15456617638992 37.0 33.0 37.0 27.0 37.0 74-75 33.843631667231634 37.0 33.0 37.0 27.0 37.0 76-77 33.99710023137951 37.0 33.0 37.0 27.0 37.0 78-79 34.07520066020206 37.0 33.0 37.0 27.0 37.0 80-81 34.01813732959542 37.0 33.0 37.0 27.0 37.0 82-83 33.978345611493 37.0 33.0 37.0 27.0 37.0 84-85 33.89075834097015 37.0 33.0 37.0 27.0 37.0 86-87 33.651312403499745 37.0 33.0 37.0 27.0 37.0 88-89 33.73327328872877 37.0 33.0 37.0 27.0 37.0 90-91 33.52380339680906 37.0 33.0 37.0 27.0 37.0 92-93 33.40195573854864 37.0 33.0 37.0 27.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 11.0 21 6.0 22 22.0 23 22.0 24 21.0 25 29.0 26 38.0 27 34.0 28 49.0 29 51.0 30 81.0 31 100.0 32 128.0 33 164.0 34 276.0 35 428.0 36 894.0 37 981.0 38 649.0 39 16.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 87.0 2.4 3.175 7.425 2 70.025 18.05 7.1 4.825 3 34.300000000000004 38.925 15.0 11.774999999999999 4 34.2 27.075 19.400000000000002 19.325 5 24.099999999999998 30.375000000000004 26.125 19.400000000000002 6 18.475 39.15 25.775 16.6 7 35.85 29.775000000000002 19.675 14.7 8 30.15 30.4 24.275 15.174999999999999 9 26.0 26.5 28.499999999999996 19.0 10-11 24.45 28.025 28.0875 19.4375 12-13 27.3 26.7125 26.487500000000004 19.5 14-15 22.25 29.2875 29.075 19.3875 16-17 24.3625 31.7125 24.775 19.15 18-19 23.4625 27.450000000000003 26.987499999999997 22.1 20-21 25.0125 25.5375 28.3375 21.1125 22-23 27.5875 23.849999999999998 26.650000000000002 21.912499999999998 24-25 25.362499999999997 25.650000000000002 28.225 20.7625 26-27 24.9375 25.3 31.574999999999996 18.1875 28-29 25.7125 26.637499999999996 27.8125 19.8375 30-31 26.25 25.8625 27.975 19.9125 32-33 24.325 27.6875 27.200000000000003 20.7875 34-35 25.35 26.8625 27.4125 20.375 36-37 24.4875 25.6 27.987499999999997 21.925 38-39 25.331332833208304 24.568642160540136 31.48287071767942 18.617154288572145 40-41 27.063531765882942 25.200100050025014 26.563281640820406 21.173086543271637 42-43 24.915614451806476 28.253531691461433 27.97849731216402 18.85235654456807 44-45 24.1375 26.687499999999996 28.487499999999997 20.6875 46-47 24.45 25.95 27.3875 22.2125 48-49 24.925 25.087500000000002 30.675 19.3125 50-51 24.25 25.624999999999996 30.65 19.475 52-53 25.025062656641605 27.25563909774436 26.79197994987469 20.927318295739347 54-55 24.975 27.3 27.950000000000003 19.775000000000002 56-57 26.437500000000004 25.825 28.3625 19.375 58-59 24.75 24.85 29.725 20.674999999999997 60-61 24.4375 25.8 29.7125 20.05 62-63 22.4875 28.812500000000004 30.6375 18.0625 64-65 23.849999999999998 26.987499999999997 30.012499999999996 19.15 66-67 24.00300037504688 28.153519189898734 28.2410301287661 19.602450306288286 68-69 22.55 27.250000000000004 28.925 21.275 70-71 26.04779181784061 24.82171900412861 29.050419116727138 20.08007006130364 72-73 26.001255492780917 24.770872567482737 28.67545511613308 20.552416823603263 74-75 24.870923057549426 25.928724342022413 30.12215086261176 19.078201737816396 76-77 22.891414141414142 27.108585858585858 29.065656565656568 20.934343434343432 78-79 23.924050632911392 24.734177215189874 31.518987341772153 19.82278481012658 80-81 23.30072417735993 27.92529538813365 29.678566891119303 19.095413543387117 82-83 23.098519652884125 26.09749872383869 29.772843287391527 21.031138335885654 84-85 23.34575356546319 24.232301169214956 31.774380059103173 20.647565206218683 86-87 21.603190941842513 26.402470406587753 32.39835306227483 19.595985589294905 88-89 22.272259392691716 29.46474523932064 28.872876994338654 19.390118373648995 90-91 26.569737519300052 25.488934637159034 29.336078229541947 18.60524961399897 92-93 22.14359238291302 29.45187853834277 30.378281008749358 18.026248069994853 >>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 1.0 16 1.5 17 13.5 18 15.5 19 3.0 20 0.5 21 1.5 22 2.0 23 4.5 24 6.0 25 3.5 26 8.0 27 13.5 28 14.5 29 15.0 30 20.5 31 33.5 32 52.0 33 73.5 34 85.5 35 93.5 36 113.0 37 141.0 38 167.0 39 178.0 40 200.5 41 207.5 42 209.5 43 226.5 44 203.5 45 183.0 46 197.0 47 192.0 48 176.5 49 176.5 50 172.5 51 158.0 52 137.0 53 137.5 54 121.5 55 76.0 56 59.0 57 62.0 58 56.5 59 45.0 60 35.0 61 31.5 62 27.5 63 26.0 64 28.5 65 28.0 66 20.5 67 18.5 68 17.0 69 12.0 70 10.0 71 6.0 72 6.0 73 4.5 74 3.0 75 3.0 76 2.0 77 0.5 78 0.5 79 0.5 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 0.025 40-41 0.05 42-43 0.0125 44-45 0.0 46-47 0.0 48-49 0.0 50-51 0.0 52-53 0.25 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 0.0125 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 7.0 71 7.0 72 7.0 73 6.0 74 5.0 75 6.0 76 4.0 77 6.0 78 4.0 79 8.0 80 9.0 81 8.0 82 10.0 83 16.0 84 11.0 85 0.0 86 0.0 87 0.0 88 0.0 89 0.0 90 0.0 91 0.0 92 0.0 93 3886.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 82.15 #Duplication Level Percentage of deduplicated Percentage of total 1 93.85270846013391 77.10000000000001 2 3.8040170419963477 6.25 3 0.699939135727328 1.725 4 0.426049908703591 1.4000000000000001 5 0.2738892270237371 1.125 6 0.09129640900791236 0.44999999999999996 7 0.06086427267194157 0.35000000000000003 8 0.12172854534388314 0.8 9 0.15216068167985392 1.125 >10 0.48691418137553255 8.225 >50 0.030432136335970784 1.4500000000000002 >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 GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 58 1.4500000000000002 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 47 1.175 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 34 0.8500000000000001 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 29 0.7250000000000001 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 28 0.7000000000000001 No Hit GGAGTATCCTTGATATATAAATATATAGATAAATAGATTTAAATGGAAAA 27 0.675 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 23 0.575 No Hit GGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGGG 19 0.475 No Hit GGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAA 16 0.4 No Hit GGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAA 15 0.375 No Hit GGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGG 15 0.375 No Hit GGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGC 15 0.375 No Hit GGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTT 13 0.325 No Hit GGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTT 13 0.325 No Hit CAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCT 12 0.3 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 12 0.3 No Hit GGAAAAGAGGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTTG 11 0.27499999999999997 No Hit GTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAA 9 0.22499999999999998 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 9 0.22499999999999998 No Hit GGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGC 9 0.22499999999999998 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 9 0.22499999999999998 No Hit GGTTTTGAAAAGGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAA 9 0.22499999999999998 No Hit GGGATGGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACGA 8 0.2 No Hit GGGAGTATTATGAAAGGAGATTAATCATAGATTATCAAAAACCCTAGAAA 8 0.2 No Hit GGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAACCCTCTTAACT 8 0.2 No Hit GGGCACTGTAGCCAGTGTGTCAGTCGTTGTTAAATTACAGGTTGAGATCA 8 0.2 No Hit GAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGC 7 0.17500000000000002 No Hit GGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTG 7 0.17500000000000002 No Hit GGGAAAAGAGGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTT 6 0.15 No Hit GGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAAA 6 0.15 No Hit GAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTG 6 0.15 No Hit GGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCG 5 0.125 No Hit GGAAGAGCCCGAGCTGCTGCAGCAGGTTTTGAAAAGGGAATCGATCGTGA 5 0.125 No Hit GGGGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCT 5 0.125 No Hit GATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAAT 5 0.125 No Hit GTATTTAGCCTTGCAAGGTGGTCCTTGCTGATTCACACGGGATTCCACGT 5 0.125 No Hit GGGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTG 5 0.125 No Hit GGGGAAGTACACCAGCGACGGCGAGGCCGCCGCCGCCAAGGAAGGCATGT 5 0.125 No Hit GGGCTTGGCTACAATTCCGAATACGCTATTACATGTTTGCGCTAGTTTTT 5 0.125 No Hit CAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTG 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 0.037500000000000006 0.0 0.0 0.0 0.0 20-21 0.075 0.0 0.0 0.0 0.0 22-23 0.075 0.0 0.0 0.0 0.0 24-25 0.075 0.0 0.0 0.0 0.0 26-27 0.075 0.0 0.0 0.0 0.0 28-29 0.075 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 0.1 0.0 0.0 0.0 0.0 38-39 0.125 0.0 0.0 0.0 0.0 40-41 0.125 0.0 0.0 0.0 0.0 42-43 0.125 0.0 0.0 0.0 0.0 44-45 0.125 0.0 0.0 0.0 0.0 46-47 0.125 0.0 0.0 0.0 0.0 48-49 0.125 0.0 0.0 0.0 0.0 50-51 0.125 0.0 0.0 0.0 0.0 52-53 0.125 0.0 0.0 0.0 0.0 54-55 0.125 0.0 0.0 0.0 0.0 56-57 0.125 0.0 0.0 0.0 0.0 58-59 0.125 0.0 0.0 0.0 0.0 60-61 0.125 0.0 0.0 0.0 0.0 62-63 0.125 0.0 0.0 0.0 0.0 64-65 0.125 0.0 0.0 0.0 0.0 66-67 0.125 0.0 0.0 0.0 0.0 68-69 0.125 0.0 0.0 0.0 0.0 70-71 0.125 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 0.0125 0.0 >>END_MODULE >>Kmer Content fail #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GGGGAAA 35 4.917576E-6 61.848217 1 ATGCACC 30 1.8192135E-4 57.725002 7 AATGCAC 30 1.8192135E-4 57.725002 6 AAATGCA 30 1.8192135E-4 57.725002 5 TGCACCT 40 1.0857459E-5 54.117188 8 GCACCTG 40 1.0857459E-5 54.117188 9 GGGAAAT 35 3.8967488E-4 49.478573 2 GGAAATG 40 7.5291813E-4 43.29375 3 GAAATGC 50 0.0022566824 34.635002 4 CACCTGG 35 3.236378E-4 30.924109 10-11 CCTGGTG 35 3.236378E-4 30.924109 12-13 TCGTGAA 30 0.0048499764 29.987013 82-83 GCTCGTG 30 0.0048499764 29.987013 80-81 GTGAAGG 30 0.0048499764 29.987013 84-85 CGTGAAG 30 0.0048499764 29.987013 84-85 CTCGTGA 30 0.0048499764 29.987013 82-83 TTGCTCG 30 0.0048499764 29.987013 78-79 GAAGGTA 30 0.0048499764 29.987013 86-87 AGCCTGT 30 0.0058605517 28.862501 44-45 AGCTCGT 30 0.0058605517 28.862501 56-57 >>END_MODULE Rejected 146705 READS because READLEN < 1 Read 146705 spots for ERR6133559.sra Written 146705 spots for ERR6133559.sra Rejected 146705 READS because READLEN < 1 Read 146705 spots for ERR6133559.sra Written 146705 spots for ERR6133559.sra Rejected 146705 READS because READLEN < 1 Read 146705 spots for ERR6133559.sra Written 146705 spots for ERR6133559.sra Rejected 146705 READS because READLEN < 1 Read 146705 spots for ERR6133559.sra Written 146705 spots for ERR6133559.sra Rejected 146705 READS because READLEN < 1 Read 146705 spots for ERR6133559.sra Written 146705 spots for ERR6133559.sra Rejected 146705 READS because READLEN < 1 Read 146705 spots for ERR6133559.sra Written 146705 spots for ERR6133559.sra Rejected 146705 READS because READLEN < 1 Read 146705 spots for ERR6133559.sra Written 146705 spots for ERR6133559.sra Rejected 146705 READS because READLEN < 1 Read 146705 spots for ERR6133559.sra Written 146705 spots for ERR6133559.sra Rejected 146705 READS because READLEN < 1 Read 146705 spots for ERR6133559.sra Written 146705 spots for ERR6133559.sra Rejected 146705 READS because READLEN < 1 Read 146705 spots for ERR6133559.sra Written 146705 spots for ERR6133559.sra Rejected 146705 READS because READLEN < 1 Read 146705 spots for ERR6133559.sra Written 146705 spots for ERR6133559.sra Rejected 146705 READS because READLEN < 1 Read 146705 spots for ERR6133559.sra Written 146705 spots for ERR6133559.sra Rejected 146705 READS because READLEN < 1 Read 146705 spots for ERR6133559.sra Written 146705 spots for ERR6133559.sra Rejected 146705 READS because READLEN < 1 Read 146705 spots for ERR6133559.sra Written 146705 spots for ERR6133559.sra Rejected 146705 READS because READLEN < 1 Read 146705 spots for ERR6133559.sra Written 146705 spots for ERR6133559.sra Rejected 146705 READS because READLEN < 1 Read 146705 spots for ERR6133559.sra Written 146705 spots for ERR6133559.sra Rejected 146705 READS because READLEN < 1 Read 146705 spots for ERR6133559.sra Written 146705 spots for ERR6133559.sra Rejected 146720 READS because READLEN < 1 Read 146720 spots for ERR6133559.sra Written 146720 spots for ERR6133559.sra Rejected 146705 READS because READLEN < 1 Read 146705 spots for ERR6133559.sra Written 146705 spots for ERR6133559.sra Rejected 146705 READS because READLEN < 1 Read 146705 spots for ERR6133559.sra Written 146705 spots for ERR6133559.sra SRR ids: ['ERR6133559.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_zsntwghk ERR6133559.sra spots: 2934115 blocks: [[1, 146705], [146706, 293410], [293411, 440115], [440116, 586820], [586821, 733525], [733526, 880230], [880231, 1026935], [1026936, 1173640], [1173641, 1320345], [1320346, 1467050], [1467051, 1613755], [1613756, 1760460], [1760461, 1907165], [1907166, 2053870], [2053871, 2200575], [2200576, 2347280], [2347281, 2493985], [2493986, 2640690], [2640691, 2787395], [2787396, 2934115]] ERR6133559 file size 648136 ERR6133559 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 ERR6133559 ERR6133559_1.fastq Input file: ERR6133559_1.fastq trimmed: ERR6133559-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 08:38:58 2024 >> started Sat Dec 7 08:39:00 2024 >> done (1.697s) 2934115 reads processed; of these: 159 ( 0.01%) short reads filtered out after trimming by size control 20 ( 0.00%) empty reads filtered out after trimming by size control 2933936 (99.99%) reads available; of these: 53231 ( 1.81%) trimmed reads available after processing 2880705 (98.19%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 42 0.00% 19 59 0.00% 20 32 0.00% 21 33 0.00% 22 46 0.00% 23 10 0.00% 24 11 0.00% 25 4 0.00% 26 4 0.00% 27 12 0.00% 28 41 0.00% 29 26 0.00% 30 9 0.00% 31 31 0.00% 32 17 0.00% 33 14 0.00% 34 20 0.00% 35 174 0.01% 36 275 0.01% 37 27 0.00% 38 41 0.00% 39 131 0.00% 40 90 0.00% 41 30 0.00% 42 12 0.00% 43 7 0.00% 44 12 0.00% 45 12 0.00% 46 10 0.00% 47 3 0.00% 48 5 0.00% 49 6 0.00% 50 10 0.00% 51 27 0.00% 52 3 0.00% 53 4 0.00% 54 1 0.00% 55 6 0.00% 56 6 0.00% 57 7 0.00% 58 6 0.00% 59 8 0.00% 60 11 0.00% 61 8 0.00% 62 1 0.00% 63 4 0.00% 64 8 0.00% 65 5 0.00% 66 7 0.00% 67 12 0.00% 68 22 0.00% 69 75 0.00% 70 6192 0.21% 71 6207 0.21% 72 6757 0.23% 73 6085 0.21% 74 6194 0.21% 75 6083 0.21% 76 5503 0.19% 77 5679 0.19% 78 6217 0.21% 79 6953 0.24% 80 6186 0.21% 81 6590 0.22% 82 7717 0.26% 83 8132 0.28% 84 6876 0.23% 85 111 0.00% 86 229 0.01% 87 323 0.01% 88 602 0.02% 89 1063 0.04% 90 2380 0.08% 91 6731 0.23% 92 39253 1.34% 93 2784396 94.90% 2933936 reads passed initial QC criterion=sequence-density sequence-density=0.28 sequence-density-rank=1 fanout-score=8.63 fanout-score-rank=17 prefix-density=0.46 prefix-fanout=5.2 sequence=ATGCATGCATGC criterion=fanout-score sequence-density=0.02 sequence-density-rank=22 fanout-score=203.63 fanout-score-rank=1 prefix-density=0.56 prefix-fanout=6.8 sequence=GAAGAAGAAAAGTTTTCTCAACATGGGGAGGAAGTCCCTCCGAAATTTGATTTGTTATTGTATTGTAAGGGGCTTTTTTAGTATTTATCTAAAGGAAGGAACAAACGAGGATAAGATAAAATTTCTTTAAATTTATTTTGCCCAAGTGGGATATATGGCATACTATTCTTTCCATTTTCATCTTTTTTTCTATTCCACTCCATCTAGATATAAGAAAGAACCCAATGCAATGAAATTCCACTAATATACAATACAAAAAAGAAGAATAGATACAGGGTCTCAAACCTTGCTATAGAGTTTTTGC Started job on | Dec 07 08:39:17 Started mapping on | Dec 07 08:39:17 Finished on | Dec 07 08:39:22 Mapping speed, Million of reads per hour | 2112.43 Number of input reads | 2933936 Average input read length | 92 UNIQUE READS: Uniquely mapped reads number | 2063940 Uniquely mapped reads % | 70.35% Average mapped length | 92.01 Number of splices: Total | 91060 Number of splices: Annotated (sjdb) | 76122 Number of splices: GT/AG | 87473 Number of splices: GC/AG | 2205 Number of splices: AT/AC | 51 Number of splices: Non-canonical | 1331 Mismatch rate per base, % | 0.39% Deletion rate per base | 0.04% Deletion average length | 1.80 Insertion rate per base | 0.02% Insertion average length | 1.92 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 807083 % of reads mapped to multiple loci | 27.51% Number of reads mapped to too many loci | 24245 % of reads mapped to too many loci | 0.83% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.27% % of reads unmapped: other | 0.05% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 62913 62913 62913 N_multimapping 807083 807083 807083 N_noFeature 134586 154631 1968025 N_ambiguous 85033 9048 312 UnstrandedReadsAssigned:1844321 PositiveStrandReadsAssigned:1900261 NegativeStrandReadsAssigned:95603 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=93 echo kmer=89 ERR6133559 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: ERR6133559-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 2,933,936 reads, 2,471,988 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,016 rounds 52973 ERR6133559.ke.tsv 35125 ERR6133559.se.tsv 88098 total ==> ERR6133559.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 78 30.8489 PNS24243 293 194 0 0 KQK14069 1603 1504 14 5.05102 KQK14071 474 375 0 0 ==> ERR6133559.se.tsv <== BRADI_1g14170v3 14 BRADI_1g53295v3 41 BRADI_1g59795v3 26 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 30 BRADI_1g74790v3 43 BRADI_1g09890v3 0 BRADI_1g77505v3 79 BRADI_1g48960v3 0 ERR6133559 completed mapping pipeline successfully