Starting /dee2/code/volunteer_pipeline.sh ERR6133509 current disk space = 1544411209728 free memory = 1452642276 ERR6133509 SRAfilesize 7b85d6be7b24ae82952ee8ceb5ae2a71 ERR6133509.sra ERR6133509.sra file validated ERR6133509 is single end ERR6133509 is conventional basespace ERR6133509 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133509_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 36.62225 37.0 37.0 37.0 37.0 37.0 2 36.83925 37.0 37.0 37.0 37.0 37.0 3 36.5265 37.0 37.0 37.0 37.0 37.0 4 35.84825 37.0 37.0 37.0 33.0 37.0 5 35.94125 37.0 37.0 37.0 33.0 37.0 6 36.29075 37.0 37.0 37.0 33.0 37.0 7 38.30575 40.0 37.0 40.0 37.0 40.0 8 38.24025 40.0 37.0 40.0 37.0 40.0 9 38.268 40.0 37.0 40.0 37.0 40.0 10-11 38.283249999999995 40.0 37.0 40.0 37.0 40.0 12-13 38.20575 40.0 37.0 40.0 37.0 40.0 14-15 38.160624999999996 40.0 37.0 40.0 37.0 40.0 16-17 38.09175 40.0 37.0 40.0 37.0 40.0 18-19 37.999875 40.0 37.0 40.0 35.0 40.0 20-21 38.0165 40.0 37.0 40.0 35.0 40.0 22-23 38.099374999999995 40.0 37.0 40.0 37.0 40.0 24-25 37.983375 40.0 37.0 40.0 37.0 40.0 26-27 38.013374999999996 40.0 37.0 40.0 37.0 40.0 28-29 37.958625 40.0 37.0 40.0 37.0 40.0 30-31 38.008250000000004 40.0 37.0 40.0 37.0 40.0 32-33 38.031000000000006 40.0 37.0 40.0 37.0 40.0 34-35 37.937749999999994 40.0 37.0 40.0 37.0 40.0 36-37 37.880875 37.0 37.0 40.0 37.0 40.0 38-39 37.7325 37.0 37.0 40.0 37.0 40.0 40-41 37.608374999999995 37.0 37.0 40.0 35.0 40.0 42-43 37.55025 37.0 37.0 40.0 37.0 40.0 44-45 37.354749999999996 37.0 37.0 40.0 35.0 40.0 46-47 37.18075 37.0 37.0 40.0 33.0 40.0 48-49 37.0325 37.0 37.0 38.5 33.0 40.0 50-51 36.790625 37.0 37.0 37.0 33.0 40.0 52-53 36.433875 37.0 37.0 37.0 33.0 40.0 54-55 36.460875 37.0 37.0 37.0 33.0 40.0 56-57 36.31325 37.0 37.0 37.0 33.0 38.5 58-59 35.948 37.0 37.0 37.0 33.0 37.0 60-61 36.048375 37.0 37.0 37.0 33.0 37.0 62-63 35.97525 37.0 37.0 37.0 33.0 37.0 64-65 35.872749999999996 37.0 37.0 37.0 33.0 37.0 66-67 35.82925 37.0 37.0 37.0 33.0 37.0 68-69 34.949875 35.0 35.0 37.0 33.0 37.0 70-71 35.13114912280702 37.0 33.0 37.0 33.0 37.0 72-73 35.66312366031235 37.0 35.0 37.0 33.0 37.0 74-75 35.623147682156244 37.0 35.0 37.0 33.0 37.0 76-77 35.543987141383504 37.0 33.0 37.0 33.0 37.0 78-79 35.52089998933504 37.0 33.0 37.0 33.0 37.0 80-81 35.460855191595726 37.0 33.0 37.0 33.0 37.0 82-83 35.33004631471265 37.0 33.0 37.0 33.0 37.0 84-85 35.18236030274467 37.0 33.0 37.0 33.0 37.0 86-87 35.00792028615227 37.0 33.0 37.0 33.0 37.0 88-89 35.016223811957076 37.0 33.0 37.0 33.0 37.0 90-91 35.047393970362805 37.0 33.0 37.0 33.0 37.0 92-93 34.99578436382218 37.0 33.0 37.0 33.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 4.0 21 3.0 22 2.0 23 6.0 24 5.0 25 4.0 26 7.0 27 13.0 28 20.0 29 22.0 30 23.0 31 26.0 32 70.0 33 58.0 34 104.0 35 302.0 36 1117.0 37 1431.0 38 768.0 39 15.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 88.9 2.4 2.55 6.15 2 74.15 15.425 6.275 4.15 3 37.775 38.525 12.8 10.9 4 33.5 28.075 18.8 19.625 5 23.95 30.9 27.500000000000004 17.65 6 20.25 37.574999999999996 25.15 17.025000000000002 7 37.0 30.599999999999998 18.3 14.099999999999998 8 30.425 34.55 21.425 13.600000000000001 9 26.325 28.875 27.725 17.075000000000003 10-11 26.237500000000004 27.400000000000002 28.3375 18.025 12-13 27.487499999999997 27.05 27.700000000000003 17.7625 14-15 22.400000000000002 31.175000000000004 28.8625 17.5625 16-17 21.837500000000002 33.0125 26.25 18.9 18-19 22.75 29.049999999999997 27.85 20.349999999999998 20-21 24.087043521760883 27.363681840920464 28.77688844422211 19.772386193096548 22-23 27.375 23.9 28.199999999999996 20.525 24-25 25.8625 26.487500000000004 27.950000000000003 19.7 26-27 23.974999999999998 25.637500000000003 32.625 17.7625 28-29 26.05 27.6625 27.375 18.912499999999998 30-31 25.853231653956744 27.078384798099762 27.91598949868734 19.15239404925616 32-33 23.3625 28.175 28.9375 19.525000000000002 34-35 24.8 26.6 28.0875 20.5125 36-37 24.525 26.150000000000002 28.8375 20.4875 38-39 25.825 25.687500000000004 29.925 18.5625 40-41 28.26603325415677 25.090636329541194 26.090761345168147 20.55256907113389 42-43 24.50306288286036 27.815976997124643 27.453431678959873 20.22752844105513 44-45 23.2625 27.750000000000004 29.799999999999997 19.1875 46-47 23.5 25.0625 29.4125 22.025 48-49 24.15 24.7375 32.0625 19.05 50-51 25.62820352544068 26.515814476809602 29.16614576822103 18.68983622952869 52-53 24.61152882205514 27.75689223057644 27.43107769423559 20.20050125313283 54-55 24.6125 28.975 29.375 17.0375 56-57 25.337500000000002 25.724999999999998 29.875 19.0625 58-59 25.45 24.4375 29.1625 20.95 60-61 23.9875 26.5 30.2625 19.25 62-63 21.975 28.4 31.387500000000003 18.2375 64-65 23.9875 27.275 30.7625 17.974999999999998 66-67 24.3875 27.1375 29.5875 18.8875 68-69 22.7625 28.1625 27.712500000000002 21.3625 70-71 23.57947434292866 27.571964956195245 28.31038798498123 20.538172715894866 72-73 24.5605223505776 25.10045203415369 29.105976896032143 21.233048719236564 74-75 23.555331738637793 27.45813924209996 29.409542993831046 19.576986025431196 76-77 23.218797372410307 26.629610914603337 27.829711975745326 22.321879737241034 78-79 22.848101265822784 25.696202531645568 32.050632911392405 19.40506329113924 80-81 22.560588757771857 28.75269635833016 30.42761070930085 18.259104174597134 82-83 23.009412363266343 25.680488425337067 31.238870516408042 20.07122869498855 84-85 24.492661135928525 23.81620931716656 31.01467772814295 20.676451818761965 86-87 22.84108329075115 25.919775166070515 32.588145120081755 18.65099642309658 88-89 20.54164537557486 29.07511497189576 31.47675012774655 18.90648952478283 90-91 26.277465508431273 25.06387327542156 29.68829841594277 18.970362800204395 92-93 21.972406745017885 30.21205927439959 28.93459376596832 18.880940214614206 >>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 0.5 17 3.5 18 3.5 19 0.5 20 1.0 21 2.0 22 4.5 23 6.0 24 6.5 25 7.0 26 6.0 27 11.0 28 18.0 29 20.0 30 29.5 31 40.5 32 45.5 33 54.5 34 67.5 35 82.0 36 112.0 37 143.0 38 198.0 39 212.0 40 193.5 41 203.0 42 222.5 43 248.0 44 221.0 45 201.5 46 243.0 47 237.5 48 209.0 49 206.0 50 187.5 51 164.5 52 138.5 53 140.5 54 107.5 55 57.5 56 50.0 57 49.0 58 35.5 59 22.0 60 20.0 61 16.5 62 13.0 63 9.0 64 10.5 65 10.5 66 5.5 67 6.0 68 7.5 69 10.0 70 9.0 71 5.0 72 2.5 73 1.5 74 2.0 75 1.0 76 0.5 77 0.0 78 0.0 79 0.5 80 0.5 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 0.05 22-23 0.0 24-25 0.0 26-27 0.0 28-29 0.0 30-31 0.0125 32-33 0.0 34-35 0.0 36-37 0.0 38-39 0.0 40-41 0.0125 42-43 0.0125 44-45 0.0 46-47 0.0 48-49 0.0 50-51 0.0125 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 0.0 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 10.0 71 4.0 72 8.0 73 4.0 74 5.0 75 9.0 76 4.0 77 4.0 78 4.0 79 6.0 80 3.0 81 6.0 82 4.0 83 8.0 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 3914.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 76.825 #Duplication Level Percentage of deduplicated Percentage of total 1 91.89716889033518 70.6 2 4.490725675235926 6.9 3 1.464367068011715 3.375 4 0.6182883176049463 1.9 5 0.26033192320208265 1.0 6 0.22779043280182232 1.05 7 0.195248942401562 1.05 8 0.06508298080052066 0.4 9 0.06508298080052066 0.44999999999999996 >10 0.683371298405467 11.5 >50 0.03254149040026033 1.775 >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 71 1.775 No Hit GGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGG 49 1.225 No Hit GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 42 1.05 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 41 1.0250000000000001 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 35 0.8750000000000001 No Hit GGGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTG 35 0.8750000000000001 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 26 0.65 No Hit GGGATGGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACGA 25 0.625 No Hit GTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAA 24 0.6 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 21 0.525 No Hit GGCCTGTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCG 20 0.5 No Hit GGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGGG 19 0.475 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 14 0.35000000000000003 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 14 0.35000000000000003 No Hit GGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAA 13 0.325 No Hit GGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTT 13 0.325 No Hit GGAAAAGAGGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTTG 13 0.325 No Hit CAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCT 12 0.3 No Hit GAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGC 12 0.3 No Hit GGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAA 12 0.3 No Hit GGGCAAGGAGAAGTACAAGTGCGGATCCAACGTCTTCTGGAAATGGTGAA 10 0.25 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 10 0.25 No Hit GGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTT 9 0.22499999999999998 No Hit GAGGAAGGGCGTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAGC 9 0.22499999999999998 No Hit GGTGGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGC 8 0.2 No Hit GGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGC 8 0.2 No Hit GGGAAAAGAGGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTT 7 0.17500000000000002 No Hit GGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCG 7 0.17500000000000002 No Hit GGGGATGGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACG 7 0.17500000000000002 No Hit GGAGTCCCATATATATATGTATAAGATGCCAGCCCGGTTTCGTCAACCAT 7 0.17500000000000002 No Hit GGAAGAGCCCGAGCTGCTGCAGCAGGTTTTGAAAAGGGAATCGATCGTGA 7 0.17500000000000002 No Hit GGTGGGGCAATGGGCATTCCGTTGAGTTTGTATGGTGGGTGCTGTTTTGC 7 0.17500000000000002 No Hit GGAAGAGACTTATAATATTGTGGCTGCTCATGGTTATTTTGGCCGATTAA 6 0.15 No Hit CAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATAT 6 0.15 No Hit GGAGTATCCTTGATATATAAATATATAGATAAATAGATTTAAATGGAAAA 6 0.15 No Hit GGGCGAAAAGTGAGTTGTTTAGGTCCTGGAGGGTTGACTGGGAGAACTGC 6 0.15 No Hit GGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAACCCTCTTAACT 6 0.15 No Hit GGGCACTGTAGCCAGTGTGTCAGTCGTTGTTAAATTACAGGTTGAGATCA 6 0.15 No Hit GGGCCATTTGTGGCATGCAGGAAGAGCCCGAGCTGCTGCAGCAGGTTTTG 6 0.15 No Hit GGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAAGGCGATCAAATTC 5 0.125 No Hit GGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACGAGCCGT 5 0.125 No Hit GGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAAA 5 0.125 No Hit GGGGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCT 5 0.125 No Hit GGAACAAACGAGGATAAGATAAAATTTCTTTAAATTTATTTTGCCCAAGT 5 0.125 No Hit GTAACGAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCA 5 0.125 No Hit GGAGATGACCCTACAGATCGATCCATTGATGTGGATGCGATGCCATGGAG 5 0.125 No Hit GGTTTTGAAAAGGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAA 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 0.025 0.0 0.0 0.0 0.0 32-33 0.025 0.0 0.0 0.0 0.0 34-35 0.025 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 0.075 0.0 0.0 0.0 0.0 42-43 0.1 0.0 0.0 0.0 0.0 44-45 0.1 0.0 0.0 0.0 0.0 46-47 0.1 0.0 0.0 0.0 0.0 48-49 0.1 0.0 0.0 0.0 0.0 50-51 0.1 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 pass >>END_MODULE Rejected 138104 READS because READLEN < 1 Read 138104 spots for ERR6133509.sra Written 138104 spots for ERR6133509.sra Rejected 138104 READS because READLEN < 1 Read 138104 spots for ERR6133509.sra Written 138104 spots for ERR6133509.sra Rejected 138104 READS because READLEN < 1 Read 138104 spots for ERR6133509.sra Written 138104 spots for ERR6133509.sra Rejected 138104 READS because READLEN < 1 Read 138104 spots for ERR6133509.sra Written 138104 spots for ERR6133509.sra Rejected 138104 READS because READLEN < 1 Read 138104 spots for ERR6133509.sra Written 138104 spots for ERR6133509.sra Rejected 138104 READS because READLEN < 1 Read 138104 spots for ERR6133509.sra Written 138104 spots for ERR6133509.sra Rejected 138104 READS because READLEN < 1 Read 138104 spots for ERR6133509.sra Written 138104 spots for ERR6133509.sra Rejected 138104 READS because READLEN < 1 Read 138104 spots for ERR6133509.sra Written 138104 spots for ERR6133509.sra Rejected 138104 READS because READLEN < 1 Read 138104 spots for ERR6133509.sra Written 138104 spots for ERR6133509.sra Rejected 138104 READS because READLEN < 1 Read 138104 spots for ERR6133509.sra Written 138104 spots for ERR6133509.sra Rejected 138104 READS because READLEN < 1 Read 138104 spots for ERR6133509.sra Written 138104 spots for ERR6133509.sra Rejected 138104 READS because READLEN < 1 Read 138104 spots for ERR6133509.sra Written 138104 spots for ERR6133509.sra Rejected 138120 READS because READLEN < 1 Read 138120 spots for ERR6133509.sra Written 138120 spots for ERR6133509.sra Rejected 138104 READS because READLEN < 1 Read 138104 spots for ERR6133509.sra Written 138104 spots for ERR6133509.sra Rejected 138104 READS because READLEN < 1 Read 138104 spots for ERR6133509.sra Written 138104 spots for ERR6133509.sra Rejected 138104 READS because READLEN < 1 Read 138104 spots for ERR6133509.sra Written 138104 spots for ERR6133509.sra Rejected 138104 READS because READLEN < 1 Read 138104 spots for ERR6133509.sra Written 138104 spots for ERR6133509.sra Rejected 138104 READS because READLEN < 1 Read 138104 spots for ERR6133509.sra Written 138104 spots for ERR6133509.sra Rejected 138104 READS because READLEN < 1 Read 138104 spots for ERR6133509.sra Written 138104 spots for ERR6133509.sra Rejected 138104 READS because READLEN < 1 Read 138104 spots for ERR6133509.sra Written 138104 spots for ERR6133509.sra SRR ids: ['ERR6133509.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_r8y0kcf5 ERR6133509.sra spots: 2762096 blocks: [[1, 138104], [138105, 276208], [276209, 414312], [414313, 552416], [552417, 690520], [690521, 828624], [828625, 966728], [966729, 1104832], [1104833, 1242936], [1242937, 1381040], [1381041, 1519144], [1519145, 1657248], [1657249, 1795352], [1795353, 1933456], [1933457, 2071560], [2071561, 2209664], [2209665, 2347768], [2347769, 2485872], [2485873, 2623976], [2623977, 2762096]] ERR6133509 file size 610825 ERR6133509 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 ERR6133509 ERR6133509_1.fastq Input file: ERR6133509_1.fastq trimmed: ERR6133509-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 07:37:26 2024 >> started Sat Dec 7 07:37:28 2024 >> done (2.028s) 2762096 reads processed; of these: 261 ( 0.01%) short reads filtered out after trimming by size control 7 ( 0.00%) empty reads filtered out after trimming by size control 2761828 (99.99%) reads available; of these: 12698 ( 0.46%) trimmed reads available after processing 2749130 (99.54%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 31 0.00% 19 68 0.00% 20 36 0.00% 21 42 0.00% 22 37 0.00% 23 14 0.00% 24 15 0.00% 25 13 0.00% 26 14 0.00% 27 16 0.00% 28 69 0.00% 29 107 0.00% 30 13 0.00% 31 25 0.00% 32 16 0.00% 33 18 0.00% 34 22 0.00% 35 145 0.01% 36 399 0.01% 37 22 0.00% 38 29 0.00% 39 87 0.00% 40 75 0.00% 41 39 0.00% 42 6 0.00% 43 11 0.00% 44 21 0.00% 45 15 0.00% 46 25 0.00% 47 10 0.00% 48 9 0.00% 49 10 0.00% 50 9 0.00% 51 49 0.00% 52 15 0.00% 53 7 0.00% 54 3 0.00% 55 7 0.00% 56 8 0.00% 57 19 0.00% 58 7 0.00% 59 7 0.00% 60 9 0.00% 61 8 0.00% 62 0 0.00% 63 1 0.00% 64 0 0.00% 65 0 0.00% 66 3 0.00% 67 7 0.00% 68 5 0.00% 69 25 0.00% 70 4697 0.17% 71 4204 0.15% 72 4117 0.15% 73 3757 0.14% 74 4254 0.15% 75 4109 0.15% 76 3480 0.13% 77 3640 0.13% 78 4214 0.15% 79 4595 0.17% 80 4186 0.15% 81 4494 0.16% 82 5357 0.19% 83 5243 0.19% 84 4435 0.16% 85 28 0.00% 86 69 0.00% 87 100 0.00% 88 189 0.01% 89 365 0.01% 90 740 0.03% 91 1868 0.07% 92 7337 0.27% 93 2684702 97.21% 2761828 reads passed initial QC criterion=sequence-density sequence-density=0.27 sequence-density-rank=1 fanout-score=2.09 fanout-score-rank=33 prefix-density=0.28 prefix-fanout=2.1 sequence=CAAGGCTAAATAC criterion=fanout-score sequence-density=0.02 sequence-density-rank=29 fanout-score=60.89 fanout-score-rank=1 prefix-density=0.14 prefix-fanout=6.6 sequence=AAAAGAAGGGGTGTTCCATCTCCGGACGACGATCCTGCCTGCAGAGGAAGACATGCCGGCGATCATGTCGAGCTTCAAGAAGTTCAACGACTCATTCATGGAGCAATACCAAGACTACTCCAGGCTGTGATGTGAAGAGGGAAACAACGAGGTCATCATCGACATGATATATTGCTGCTATTTTCCACCAGCGATTAAAAGTTAAAAAATTTAGCTGTAAGCTGTAACTATCTTGAAGAAACTAAACTGGTTGCTGTGCTTGATATGTATAGGGAAAACATAATTTATGAGACAATCATACTGTGCAACTCTTGGCTCCATCGATTAATTAATACTCCTTGTTATTGCTTGCATGGTGG Started job on | Dec 07 07:37:48 Started mapping on | Dec 07 07:37:48 Finished on | Dec 07 07:37:58 Mapping speed, Million of reads per hour | 994.26 Number of input reads | 2761828 Average input read length | 92 UNIQUE READS: Uniquely mapped reads number | 1861799 Uniquely mapped reads % | 67.41% Average mapped length | 92.24 Number of splices: Total | 97632 Number of splices: Annotated (sjdb) | 80604 Number of splices: GT/AG | 93869 Number of splices: GC/AG | 2137 Number of splices: AT/AC | 73 Number of splices: Non-canonical | 1553 Mismatch rate per base, % | 0.43% Deletion rate per base | 0.05% Deletion average length | 1.89 Insertion rate per base | 0.03% Insertion average length | 1.91 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 814658 % of reads mapped to multiple loci | 29.50% Number of reads mapped to too many loci | 15009 % of reads mapped to too many loci | 0.54% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 2.52% % of reads unmapped: other | 0.03% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 85371 85371 85371 N_multimapping 814658 814658 814658 N_noFeature 152110 169522 1778566 N_ambiguous 76296 10603 343 UnstrandedReadsAssigned:1633393 PositiveStrandReadsAssigned:1681674 NegativeStrandReadsAssigned:82890 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=93 echo kmer=89 ERR6133509 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: ERR6133509-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 2,761,828 reads, 2,311,310 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 988 rounds 52973 ERR6133509.ke.tsv 35125 ERR6133509.se.tsv 88098 total ==> ERR6133509.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 65 27.2863 PNS24243 293 194 0 0 KQK14069 1603 1504 62 23.7427 KQK14071 474 375 0 0 ==> ERR6133509.se.tsv <== BRADI_1g14170v3 62 BRADI_1g53295v3 27 BRADI_1g59795v3 33 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 11 BRADI_1g74790v3 11 BRADI_1g09890v3 0 BRADI_1g77505v3 40 BRADI_1g48960v3 0 ERR6133509 completed mapping pipeline successfully