Starting /dee2/code/volunteer_pipeline.sh ERR6133429 current disk space = 1546765942784 free memory = 1600641964 ERR6133429 SRAfilesize 693468e3c9a3953bcaa986ebcc9a4cb6 ERR6133429.sra ERR6133429.sra file validated ERR6133429 is single end ERR6133429 is conventional basespace ERR6133429 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133429_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 46 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 34.97175 37.0 33.0 37.0 33.0 37.0 2 36.308 37.0 37.0 37.0 33.0 37.0 3 35.6945 37.0 37.0 37.0 33.0 37.0 4 35.56225 37.0 37.0 37.0 33.0 37.0 5 35.447 37.0 37.0 37.0 33.0 37.0 6 35.6845 37.0 37.0 37.0 33.0 37.0 7 37.35625 37.0 37.0 40.0 33.0 40.0 8 37.4435 37.0 37.0 40.0 33.0 40.0 9 37.50525 37.0 37.0 40.0 33.0 40.0 10-11 37.5025 37.0 37.0 40.0 33.0 40.0 12-13 37.329750000000004 37.0 37.0 40.0 33.0 40.0 14-15 37.307125 37.0 37.0 40.0 33.0 40.0 16-17 37.1975 37.0 37.0 40.0 33.0 40.0 18-19 37.438375 37.0 37.0 40.0 33.0 40.0 20-21 37.488 37.0 37.0 40.0 33.0 40.0 22-23 37.436 37.0 37.0 40.0 33.0 40.0 24-25 37.354749999999996 37.0 37.0 40.0 33.0 40.0 26-27 37.116375000000005 37.0 37.0 40.0 33.0 40.0 28-29 37.236875 37.0 37.0 40.0 33.0 40.0 30-31 37.296375 37.0 37.0 40.0 33.0 40.0 32-33 37.13075 37.0 37.0 40.0 33.0 40.0 34-35 36.92325 37.0 37.0 40.0 33.0 40.0 36-37 36.918875 37.0 37.0 40.0 33.0 40.0 38-39 36.807 37.0 37.0 40.0 33.0 40.0 40-41 36.630375 37.0 37.0 40.0 33.0 40.0 42-43 36.521875 37.0 37.0 40.0 33.0 40.0 44-45 36.23225 37.0 37.0 40.0 33.0 40.0 46-47 36.267125 37.0 37.0 38.5 33.0 40.0 48-49 36.1185 37.0 37.0 37.0 33.0 40.0 50-51 35.918125 37.0 35.0 37.0 33.0 40.0 52-53 35.741625 37.0 35.0 37.0 33.0 40.0 54-55 35.6 37.0 33.0 37.0 33.0 40.0 56-57 35.497125 37.0 33.0 37.0 33.0 38.5 58-59 35.0865 37.0 33.0 37.0 33.0 37.0 60-61 34.981624999999994 37.0 33.0 37.0 33.0 37.0 62-63 34.826499999999996 37.0 33.0 37.0 33.0 37.0 64-65 34.19125 37.0 33.0 37.0 30.0 37.0 66-67 34.161 37.0 33.0 37.0 27.0 37.0 68-69 33.11725 35.0 33.0 35.0 27.0 37.0 70-71 33.419222597597596 33.0 33.0 37.0 27.0 37.0 72-73 34.15433121718959 37.0 33.0 37.0 27.0 37.0 74-75 34.49028851545879 37.0 33.0 37.0 33.0 37.0 76-77 34.56052714116729 37.0 33.0 37.0 33.0 37.0 78-79 34.349965608314804 37.0 33.0 37.0 33.0 37.0 80-81 34.241456627795316 37.0 33.0 37.0 33.0 37.0 82-83 33.82685666276696 37.0 33.0 37.0 27.0 37.0 84-85 33.86162289696637 37.0 33.0 37.0 27.0 37.0 86-87 33.87873796249366 37.0 33.0 37.0 27.0 37.0 88-89 33.78484541307654 37.0 33.0 37.0 27.0 37.0 90-91 33.6112519006589 35.0 33.0 37.0 27.0 37.0 92-93 33.374936644703496 33.0 33.0 37.0 27.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 10.0 21 4.0 22 14.0 23 13.0 24 21.0 25 24.0 26 28.0 27 29.0 28 43.0 29 45.0 30 67.0 31 85.0 32 141.0 33 171.0 34 247.0 35 550.0 36 894.0 37 1130.0 38 479.0 39 5.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 85.2 3.775 3.6249999999999996 7.3999999999999995 2 66.90863579474343 19.299123904881103 8.360450563204006 5.4317897371714645 3 37.6 37.2 13.875000000000002 11.325000000000001 4 33.35 27.925 18.275 20.45 5 26.424999999999997 31.075000000000003 23.775 18.725 6 19.05 39.0 25.124999999999996 16.825000000000003 7 32.300000000000004 30.0 20.175 17.525 8 29.275000000000002 27.700000000000003 25.424999999999997 17.599999999999998 9 24.2 25.825 29.825000000000003 20.150000000000002 10-11 25.9875 26.775 26.4625 20.775 12-13 28.5875 24.925 25.924999999999997 20.5625 14-15 23.7 28.025 29.599999999999998 18.675 16-17 25.650000000000002 29.812499999999996 25.837500000000002 18.7 18-19 23.400000000000002 27.962500000000002 24.6875 23.95 20-21 24.2 28.1375 26.474999999999998 21.1875 22-23 26.887499999999996 24.2875 26.6 22.225 24-25 28.1 22.7625 27.3375 21.8 26-27 26.200000000000003 25.912499999999998 29.862499999999997 18.025 28-29 26.687499999999996 27.6125 25.525 20.175 30-31 28.6375 26.0 24.875 20.4875 32-33 23.0625 30.325000000000003 25.85 20.7625 34-35 25.85 24.025 27.975 22.15 36-37 24.85 23.3375 29.6375 22.175 38-39 25.087500000000002 26.387500000000003 29.799999999999997 18.725 40-41 27.900000000000002 26.5125 24.0625 21.525 42-43 25.5375 28.5625 24.5625 21.337500000000002 44-45 23.5875 25.162499999999998 27.875 23.375 46-47 24.6125 23.525 26.700000000000003 25.162499999999998 48-49 25.05 24.175 30.925000000000004 19.85 50-51 27.3125 26.224999999999998 27.3125 19.15 52-53 25.874999999999996 28.6125 25.5125 20.0 54-55 23.0375 30.312499999999996 26.674999999999997 19.975 56-57 27.1625 24.1375 27.4125 21.2875 58-59 23.25 23.25 29.45 24.05 60-61 25.650000000000002 22.900000000000002 28.8625 22.5875 62-63 22.900000000000002 27.462500000000002 31.525 18.1125 64-65 24.8125 26.087500000000002 28.825 20.275000000000002 66-67 25.887500000000003 27.700000000000003 26.6125 19.8 68-69 23.9875 27.4125 26.1 22.5 70-71 27.56378189094547 23.58679339669835 26.28814407203602 22.56128064032016 72-73 26.678356713426854 23.371743486973948 27.15430861723447 22.79559118236473 74-75 22.912743251726305 28.210922787193976 28.085373509102325 20.7909604519774 76-77 21.62162162162162 27.0144563167819 29.063482086737903 22.30043997485858 78-79 24.650811627029068 23.316974959104066 30.28815905373097 21.7440543601359 80-81 24.684820978315685 28.10136157337368 29.601613716591025 17.612203731719617 82-83 24.510917581724094 23.917707938912027 29.206108797172785 22.36526568219109 84-85 25.53514882837239 21.823939202026597 29.28435718809373 23.35655478150728 86-87 23.428788646730865 25.405473897617842 31.702990369994932 19.46274708565636 88-89 22.820577800304108 30.11910795742524 29.181449569183982 17.87886467308667 90-91 27.597567156614293 25.595539787126203 27.318803852002027 19.488089204257474 92-93 24.252407501267108 29.320831221490117 27.736948808920424 18.68981246832235 >>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 8.0 18 9.5 19 3.5 20 4.0 21 6.0 22 7.5 23 9.0 24 10.5 25 7.5 26 7.5 27 12.5 28 21.5 29 28.0 30 26.5 31 25.5 32 36.0 33 52.0 34 61.0 35 73.0 36 78.0 37 98.0 38 131.0 39 138.0 40 131.0 41 151.5 42 184.5 43 191.0 44 176.5 45 156.0 46 233.5 47 248.0 48 186.0 49 197.0 50 185.5 51 172.5 52 165.5 53 189.0 54 166.0 55 94.0 56 70.5 57 64.5 58 66.5 59 55.5 60 52.5 61 55.5 62 45.0 63 37.5 64 36.0 65 32.5 66 31.0 67 25.5 68 16.5 69 13.5 70 6.0 71 2.0 72 1.5 73 2.0 74 2.0 75 1.0 76 0.5 77 0.0 78 0.5 79 0.5 80 0.0 81 0.0 82 0.0 83 0.5 84 0.5 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 0.125 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 0.0506393214330928 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 4.0 71 3.0 72 2.0 73 5.0 74 7.0 75 1.0 76 1.0 77 2.0 78 3.0 79 4.0 80 4.0 81 1.0 82 3.0 83 7.0 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 3946.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 74.575 #Duplication Level Percentage of deduplicated Percentage of total 1 91.51860543077439 68.25 2 5.19611129735166 7.75 3 1.24036205162588 2.775 4 0.4358028830036876 1.3 5 0.3352329869259135 1.25 6 0.2011397921555481 0.8999999999999999 7 0.16761649346295676 0.8750000000000001 8 0.10056989607777406 0.6 9 0.03352329869259135 0.22499999999999998 >10 0.7039892725444183 11.475 >50 0.0670465973851827 4.6 >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 97 2.4250000000000003 No Hit GGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGG 87 2.175 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 50 1.25 No Hit GGGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTG 43 1.075 No Hit GGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTT 40 1.0 No Hit GGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGGG 35 0.8750000000000001 No Hit GGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAA 31 0.775 No Hit GGGAGTATTATGAAAGGAGATTAATCATAGATTATCAAAAACCCTAGAAA 27 0.675 No Hit GGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAA 25 0.625 No Hit GGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGC 24 0.6 No Hit GGTGGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGC 21 0.525 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 21 0.525 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 20 0.5 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 17 0.42500000000000004 No Hit GGAGTATCCTTGATATATAAATATATAGATAAATAGATTTAAATGGAAAA 16 0.4 No Hit GGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCG 14 0.35000000000000003 No Hit GGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGC 13 0.325 No Hit GTACAAGCTCGTAACGAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAAT 11 0.27499999999999997 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 11 0.27499999999999997 No Hit CAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAACGAAGGG 10 0.25 No Hit GGAGTCCCATATATATATGTATAAGATGCCAGCCCGGTTTCGTCAACCAT 10 0.25 No Hit GGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAACCCTCTTAACT 10 0.25 No Hit GAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGC 10 0.25 No Hit GGGCCATTTGTGGCATGCAGGAAGAGCCCGAGCTGCTGCAGCAGGTTTTG 9 0.22499999999999998 No Hit GTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAA 8 0.2 No Hit GGAAGAGCCCGAGCTGCTGCAGCAGGTTTTGAAAAGGGAATCGATCGTGA 8 0.2 No Hit GTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAG 8 0.2 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 7 0.17500000000000002 No Hit GGGAGGGGCTTGGCTACAATTCCGAATACGCTATTACATGTTTGCGCTAG 7 0.17500000000000002 No Hit GAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAAT 7 0.17500000000000002 No Hit GGATTTGAAGAAAAAAAAGACTTCGATTCATTTTCTATTTATTTCGTTAG 7 0.17500000000000002 No Hit TTAGACTTAGAACACTAACAGGTAAAATGTGAGATTTTTATTAAGTAAAA 7 0.17500000000000002 No Hit GAAGGAACAAACGAGGATAAGATAAAATTTCTTTAAATTTATTTTGCCCA 6 0.15 No Hit GATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGGGG 6 0.15 No Hit GTAACGAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCA 6 0.15 No Hit GCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGA 6 0.15 No Hit GAAGCCTGTGTACAAGCTCGTAACGAAGGGCGCGATCTTGCTCGTGAAGG 6 0.15 No Hit CAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCT 6 0.15 No Hit GGTGGGGCAATGGGCATTCCGTTGAGTTTGTATGGTGGGTGCTGTTTTGC 5 0.125 No Hit GAAAAAAAAGACTTCGATTCATTTTCTATTTATTTCGTTAGTTTTTCTTA 5 0.125 No Hit CAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATAT 5 0.125 No Hit GGGATGGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACGA 5 0.125 No Hit GGGTCACACCGATTTTATGTACCTTTTTCACACGTTTGTTTCATGTTGTA 5 0.125 No Hit GGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAAA 5 0.125 No Hit GAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTA 5 0.125 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 5 0.125 No Hit GAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTG 5 0.125 No Hit GGGCTTGGCTACAATTCCGAATACGCTATTACATGTTTGCGCTAGTTTTT 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 0.0 0.0 0.0 0.0 0.0 74-75 0.0 0.0 0.0 0.0 0.0 76-77 0.0 0.0 0.0 0.0 0.0 78-79 0.0 0.0 0.0 0.0 0.0 80-81 0.0 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position CAATTTG 25 0.0023757957 34.705 18-19 ATTACAA 25 0.0023757957 34.705 14-15 TACAATT 25 0.0023757957 34.705 16-17 CTGTATT 25 0.0023757957 34.705 10-11 GTATTAC 30 0.0058029913 28.920834 12-13 TGGAGGA 30 0.0058029913 28.920834 26-27 ATTTGGT 30 0.0058029913 28.920834 20-21 TTGGTGG 30 0.0058029913 28.920834 22-23 >>END_MODULE Rejected 432420 READS because READLEN < 1 Read 432420 spots for ERR6133429.sra Written 432420 spots for ERR6133429.sra Rejected 432420 READS because READLEN < 1 Read 432420 spots for ERR6133429.sra Written 432420 spots for ERR6133429.sra Rejected 432420 READS because READLEN < 1 Read 432420 spots for ERR6133429.sra Written 432420 spots for ERR6133429.sra Rejected 432420 READS because READLEN < 1 Read 432420 spots for ERR6133429.sra Written 432420 spots for ERR6133429.sra Rejected 432420 READS because READLEN < 1 Read 432420 spots for ERR6133429.sra Written 432420 spots for ERR6133429.sra Rejected 432420 READS because READLEN < 1 Read 432420 spots for ERR6133429.sra Written 432420 spots for ERR6133429.sra Rejected 432420 READS because READLEN < 1 Read 432420 spots for ERR6133429.sra Written 432420 spots for ERR6133429.sra Rejected 432420 READS because READLEN < 1 Read 432420 spots for ERR6133429.sra Written 432420 spots for ERR6133429.sra Rejected 432420 READS because READLEN < 1 Read 432420 spots for ERR6133429.sra Written 432420 spots for ERR6133429.sra Rejected 432420 READS because READLEN < 1 Read 432420 spots for ERR6133429.sra Written 432420 spots for ERR6133429.sra Rejected 432420 READS because READLEN < 1 Read 432420 spots for ERR6133429.sra Written 432420 spots for ERR6133429.sra Rejected 432420 READS because READLEN < 1 Read 432420 spots for ERR6133429.sra Written 432420 spots for ERR6133429.sra Rejected 432420 READS because READLEN < 1 Read 432420 spots for ERR6133429.sra Written 432420 spots for ERR6133429.sra Rejected 432420 READS because READLEN < 1 Read 432420 spots for ERR6133429.sra Written 432420 spots for ERR6133429.sra Rejected 432420 READS because READLEN < 1 Read 432420 spots for ERR6133429.sra Written 432420 spots for ERR6133429.sra Rejected 432420 READS because READLEN < 1 Read 432420 spots for ERR6133429.sra Written 432420 spots for ERR6133429.sra Rejected 432420 READS because READLEN < 1 Read 432420 spots for ERR6133429.sra Written 432420 spots for ERR6133429.sra Rejected 432420 READS because READLEN < 1 Read 432420 spots for ERR6133429.sra Written 432420 spots for ERR6133429.sra Rejected 432420 READS because READLEN < 1 Read 432420 spots for ERR6133429.sra Written 432420 spots for ERR6133429.sra Rejected 432420 READS because READLEN < 1 Read 432420 spots for ERR6133429.sra Written 432420 spots for ERR6133429.sra SRR ids: ['ERR6133429.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_qt1wgqhe ERR6133429.sra spots: 8648400 blocks: [[1, 432420], [432421, 864840], [864841, 1297260], [1297261, 1729680], [1729681, 2162100], [2162101, 2594520], [2594521, 3026940], [3026941, 3459360], [3459361, 3891780], [3891781, 4324200], [4324201, 4756620], [4756621, 5189040], [5189041, 5621460], [5621461, 6053880], [6053881, 6486300], [6486301, 6918720], [6918721, 7351140], [7351141, 7783560], [7783561, 8215980], [8215981, 8648400]] ERR6133429 file size 1920063 ERR6133429 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 ERR6133429 ERR6133429_1.fastq Input file: ERR6133429_1.fastq trimmed: ERR6133429-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 05:08:18 2024 >> started Sat Dec 7 05:08:22 2024 >> done (4.229s) 8648400 reads processed; of these: 2992 ( 0.03%) short reads filtered out after trimming by size control 17 ( 0.00%) empty reads filtered out after trimming by size control 8645391 (99.97%) reads available; of these: 121248 ( 1.40%) trimmed reads available after processing 8524143 (98.60%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 55 0.00% 19 42 0.00% 20 36 0.00% 21 31 0.00% 22 23 0.00% 23 24 0.00% 24 19 0.00% 25 9 0.00% 26 16 0.00% 27 14 0.00% 28 18 0.00% 29 29 0.00% 30 4 0.00% 31 14 0.00% 32 27 0.00% 33 14 0.00% 34 14 0.00% 35 10 0.00% 36 7 0.00% 37 15 0.00% 38 29 0.00% 39 31 0.00% 40 38 0.00% 41 26 0.00% 42 34 0.00% 43 45 0.00% 44 27 0.00% 45 34 0.00% 46 38 0.00% 47 35 0.00% 48 37 0.00% 49 43 0.00% 50 32 0.00% 51 45 0.00% 52 37 0.00% 53 48 0.00% 54 35 0.00% 55 35 0.00% 56 35 0.00% 57 24 0.00% 58 23 0.00% 59 36 0.00% 60 26 0.00% 61 40 0.00% 62 7 0.00% 63 5 0.00% 64 2 0.00% 65 8 0.00% 66 19 0.00% 67 14 0.00% 68 25 0.00% 69 109 0.00% 70 7774 0.09% 71 6514 0.08% 72 7225 0.08% 73 6346 0.07% 74 6868 0.08% 75 6956 0.08% 76 5806 0.07% 77 6125 0.07% 78 7421 0.09% 79 8668 0.10% 80 7192 0.08% 81 6925 0.08% 82 7716 0.09% 83 9642 0.11% 84 6942 0.08% 85 239 0.00% 86 484 0.01% 87 766 0.01% 88 1492 0.02% 89 3027 0.04% 90 7344 0.08% 91 21151 0.24% 92 83518 0.97% 93 8417807 97.37% 8645391 reads passed initial QC criterion=sequence-density sequence-density=0.40 sequence-density-rank=1 fanout-score=2.36 fanout-score-rank=25 prefix-density=0.43 prefix-fanout=2.2 sequence=GTCCGCATCATCGGCTTCGACAACACCCGGCAGGTGCAGTGCATCAGCTTCATCGCCTTCAAGCC criterion=fanout-score sequence-density=0.01 sequence-density-rank=25 fanout-score=38.33 fanout-score-rank=1 prefix-density=0.15 prefix-fanout=3.5 sequence=GGAAGAGGAGGATGCAGTCAGGGCTCACAAACAACCTGCCACTGCCGCCATTGGCCTTCTAAAACAGGAGAGGAGGGGTTAGATAGTTTCGATCTGCAAGGGGGTGGGGCAATGGGCATTCCGTTGAGTTTGTATGGTGGGTGCTGTTTTGCAGAAGCTGTATGCTTATGAGCAGCTATGGTACTTATCGAGGACAGTAGCGTACTTGAGGTGTTGTATT Started job on | Dec 07 05:08:34 Started mapping on | Dec 07 05:08:34 Finished on | Dec 07 05:08:43 Mapping speed, Million of reads per hour | 3458.16 Number of input reads | 8645391 Average input read length | 92 UNIQUE READS: Uniquely mapped reads number | 5750242 Uniquely mapped reads % | 66.51% Average mapped length | 92.47 Number of splices: Total | 395730 Number of splices: Annotated (sjdb) | 329374 Number of splices: GT/AG | 384280 Number of splices: GC/AG | 6700 Number of splices: AT/AC | 279 Number of splices: Non-canonical | 4471 Mismatch rate per base, % | 0.39% Deletion rate per base | 0.04% Deletion average length | 1.82 Insertion rate per base | 0.01% Insertion average length | 1.95 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 2761499 % of reads mapped to multiple loci | 31.94% Number of reads mapped to too many loci | 19873 % of reads mapped to too many loci | 0.23% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.30% % of reads unmapped: other | 0.02% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 133650 133650 133650 N_multimapping 2761499 2761499 2761499 N_noFeature 316787 367792 5514110 N_ambiguous 208573 23629 666 UnstrandedReadsAssigned:5224882 PositiveStrandReadsAssigned:5358821 NegativeStrandReadsAssigned:235466 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=93 echo kmer=89 ERR6133429 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: ERR6133429-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 8,645,391 reads, 7,578,194 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,100 rounds 52973 ERR6133429.ke.tsv 35125 ERR6133429.se.tsv 88098 total ==> ERR6133429.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 125 15.4209 PNS24243 293 194 0 0 KQK14069 1603 1504 83 9.34082 KQK14071 474 375 0 0 ==> ERR6133429.se.tsv <== BRADI_1g14170v3 83 BRADI_1g53295v3 62 BRADI_1g59795v3 58 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 87 BRADI_1g74790v3 39 BRADI_1g09890v3 0 BRADI_1g77505v3 144 BRADI_1g48960v3 0 ERR6133429 completed mapping pipeline successfully