Starting /dee2/code/volunteer_pipeline.sh SRR8846532 current disk space = 1515318882304 free memory = 1570799968 SRR8846532 SRAfilesize bbc3ca24ebe010a6c57eb28c82db9dfb SRR8846532.sra SRR8846532.sra file validated SRR8846532 is single end SRR8846532 is conventional basespace SRR8846532 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR8846532_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 151 %GC 40 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 34.03875 35.0 35.0 35.0 32.0 35.0 2 34.491 35.0 35.0 35.0 35.0 35.0 3 34.56125 35.0 35.0 35.0 35.0 35.0 4 34.58025 35.0 35.0 35.0 35.0 35.0 5 34.621 35.0 35.0 35.0 35.0 35.0 6 39.29175 40.0 40.0 40.0 39.0 40.0 7 39.22175 40.0 40.0 40.0 39.0 40.0 8 39.27725 40.0 40.0 40.0 39.0 40.0 9 39.30825 40.0 40.0 40.0 39.0 40.0 10-14 39.3206 40.0 40.0 40.0 39.0 40.0 15-19 39.19495 40.0 39.8 40.0 38.8 40.0 20-24 38.887350000000005 40.0 39.0 40.0 37.8 40.0 25-29 38.709050000000005 40.0 39.4 40.0 37.4 40.0 30-34 38.485299999999995 40.0 39.8 40.0 36.6 40.0 35-39 38.1609 40.0 39.0 40.0 36.0 40.0 40-44 37.93115 40.0 39.0 40.0 35.6 40.0 45-49 37.69785 40.0 39.0 40.0 35.2 40.0 50-54 37.52105 40.0 39.0 40.0 34.6 40.0 55-59 37.32315 40.0 39.0 40.0 34.0 40.0 60-64 37.14765 40.0 39.0 40.0 34.0 40.0 65-69 37.08815 40.0 39.0 40.0 34.0 40.0 70-74 36.80095 40.0 39.0 40.0 31.8 40.0 75-79 36.8893 40.0 39.0 40.0 32.8 40.0 80-84 36.8706 40.0 39.0 40.0 33.4 40.0 85-89 36.92885 40.0 39.0 40.0 33.4 40.0 90-94 36.902150000000006 40.0 39.0 40.0 34.0 40.0 95-99 36.635650000000005 40.0 39.0 40.0 31.0 40.0 100-104 34.268249999999995 36.6 35.0 38.4 27.6 38.6 105-109 36.485800000000005 39.8 38.8 40.0 30.8 40.0 110-114 36.6229 40.0 39.0 40.0 32.2 40.0 115-119 36.29655 40.0 39.0 40.0 29.2 40.0 120-124 36.16244999999999 40.0 39.0 40.0 29.4 40.0 125-129 35.8553 40.0 38.6 40.0 27.2 40.0 130-134 35.38905 40.0 38.2 40.0 18.0 40.0 135-139 34.84015000000001 39.6 37.8 40.0 13.2 40.0 140-144 34.153800000000004 39.0 36.8 40.0 4.0 40.0 145-149 33.1385 39.0 36.0 40.0 2.0 40.0 150-151 26.10725 33.5 19.0 38.0 2.0 39.5 >>END_MODULE >>Per sequence quality scores pass #Quality Count 5 2.0 6 7.0 7 4.0 8 10.0 9 25.0 10 23.0 11 34.0 12 24.0 13 28.0 14 13.0 15 6.0 16 12.0 17 4.0 18 4.0 19 2.0 20 7.0 21 7.0 22 11.0 23 10.0 24 15.0 25 14.0 26 15.0 27 21.0 28 29.0 29 35.0 30 40.0 31 45.0 32 55.0 33 59.0 34 78.0 35 123.0 36 137.0 37 220.0 38 508.0 39 2373.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 37.1356783919598 36.4321608040201 1.3567839195979898 25.075376884422113 2 18.099999999999998 37.724999999999994 26.75 17.424999999999997 3 16.075 35.05 30.525000000000002 18.35 4 17.075000000000003 35.199999999999996 28.475 19.25 5 16.1 38.725 26.474999999999998 18.7 6 15.675 41.175 26.700000000000003 16.45 7 13.0 44.675 25.75 16.575 8 13.450000000000001 44.65 25.924999999999997 15.975 9 13.075000000000001 42.1 28.775000000000002 16.05 10-14 15.115 32.98 32.385000000000005 19.52 15-19 13.495 29.580000000000002 37.805 19.12 20-24 13.055 30.69 38.495000000000005 17.76 25-29 14.89074453722686 32.926646332316615 34.00170008500425 18.180909045452275 30-34 16.22243336500475 34.72020803120468 29.94949242386358 19.107866179926987 35-39 16.20567198519482 35.26234181963687 28.339918971640078 20.192067223528234 40-44 17.728864432216106 35.1575787893947 27.298649324662332 19.814907453726864 45-49 17.85267790168525 34.820223033455015 26.408961344201632 20.9181377206581 50-54 17.627339137396177 34.749324527169016 25.833083158210744 21.790253177224056 55-59 16.963570856685347 35.41333066453162 25.9757806244996 21.647317854283425 60-64 16.95093282648927 34.81718601510529 25.48892112239284 22.742960036012605 65-69 18.199549887471868 34.3935983995999 24.59114778694674 22.815703925981495 70-74 17.725066306360407 35.66031126457489 23.860281239053197 22.75434119001151 75-79 18.354177088544272 34.272136068034015 24.262131065532767 23.111555777888945 80-84 17.14857428714357 35.81790895447724 23.631815907953975 23.401700850425215 85-89 17.72 35.435 22.1 24.745 90-94 17.83 35.6 22.28 24.29 95-99 18.145 34.8 21.775 25.28 100-104 18.709999999999997 35.4 21.224999999999998 24.665 105-109 18.63 35.17 20.815 25.385 110-114 18.005 35.165 21.310000000000002 25.52 115-119 18.395 34.22 21.099999999999998 26.284999999999997 120-124 18.55 34.495 21.055 25.900000000000002 125-129 18.54 33.77 21.46 26.229999999999997 130-134 18.895 33.095 21.46 26.55 135-139 18.69 33.405 21.495 26.41 140-144 18.01 33.489999999999995 21.834999999999997 26.665 145-149 17.755000000000003 33.2 22.18 26.865 150-151 14.649999999999999 34.7625 21.45 29.1375 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 0.0 1 0.0 2 0.0 3 1.5 4 2.0 5 4.0 6 5.0 7 3.5 8 4.5 9 4.0 10 4.0 11 7.0 12 7.0 13 4.0 14 10.5 15 14.0 16 12.0 17 10.0 18 7.5 19 9.0 20 8.5 21 9.5 22 8.0 23 6.0 24 8.5 25 14.0 26 22.0 27 33.0 28 40.0 29 45.5 30 48.5 31 71.5 32 99.0 33 122.0 34 156.5 35 183.5 36 216.5 37 258.0 38 292.0 39 300.0 40 284.5 41 285.0 42 284.5 43 259.5 44 211.5 45 164.5 46 137.0 47 101.5 48 70.5 49 51.5 50 35.0 51 23.5 52 15.5 53 6.5 54 4.0 55 5.5 56 3.0 57 1.5 58 1.5 59 1.0 60 1.0 61 0.0 62 0.0 63 0.0 64 0.0 65 0.0 66 0.0 67 0.0 68 0.0 69 0.0 70 0.0 71 0.0 72 0.0 73 0.0 74 0.0 75 0.0 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 0.5 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10-14 0.0 15-19 0.0 20-24 0.0 25-29 0.005 30-34 0.015 35-39 0.034999999999999996 40-44 0.05 45-49 0.015 50-54 0.06999999999999999 55-59 0.08 60-64 0.034999999999999996 65-69 0.025 70-74 0.08499999999999999 75-79 0.05 80-84 0.05 85-89 0.0 90-94 0.0 95-99 0.0 100-104 0.0 105-109 0.0 110-114 0.0 115-119 0.0 120-124 0.0 125-129 0.0 130-134 0.0 135-139 0.0 140-144 0.0 145-149 0.0 150-151 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 84.55 #Duplication Level Percentage of deduplicated Percentage of total 1 91.98698994677706 77.775 2 5.351862803075103 9.049999999999999 3 0.9757539917208753 2.475 4 0.6209343583678296 2.1 5 0.384387936132466 1.625 6 0.17740981667652278 0.8999999999999999 7 0.11827321111768185 0.7000000000000001 8 0.029568302779420463 0.2 9 0.029568302779420463 0.22499999999999998 >10 0.3252513305736251 4.95 >50 0.0 0.0 >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 warn #Sequence Count Percentage Possible Source GCGAACAAAACTTTGCTCATTCTTTTTTCATTCATTCATAGGGATAGCGA 39 0.975 No Hit CTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 21 0.525 No Hit GTAAAATTAACTTCAACTATTTGTATTATATCAAAATACTTCGGAGTTGA 19 0.475 No Hit ATTTTGTTTCTTTTTATTTAGACCTTCTTCATATTTAGTTTTATCTATTA 18 0.44999999999999996 No Hit CTAAATATTCAGTTAAGACCATTCCAAGGCTCCTTTTCGCCATGCATAAA 17 0.42500000000000004 No Hit CAAACATGTGGTAGATAAATATCAAGAGATGTGTAGCACATGACGTGTCT 17 0.42500000000000004 No Hit ATTTAGACCTTCTTCATATTTAGTTTTATCTATTAATCGATAGTATCTAC 16 0.4 No Hit GTATAACAAACACTTTTATTCCACGTATACCCAATGTATATGCATGTACA 16 0.4 No Hit CTTTATTCTGTCCCCTTATCTTTCATTCAGAAAAAGGAATGAATGGCTCG 13 0.325 No Hit GAAGAACAAAGATGCCCGGATTCATCTCACAAATAACCGAGGGATATTAC 11 0.27499999999999997 No Hit GTTTCTTTTTATTTAGACCTTCTTCATATTTAGTTTTATCTATTAATCGA 11 0.27499999999999997 No Hit ACAAAATATACTTATCTTAATATGTATAACCGGAGTTTATATTACATGCC 9 0.22499999999999998 No Hit GCAGCAAATTTTCTCTTCCCGCTGATTTTCAATACCAAACGATAACAGAG 8 0.2 No Hit GTATAATATTACATGTATATGTGTGTATATGTGTAGTCAGGGTTCAAATG 7 0.17500000000000002 No Hit GTCCCAAAATTGACGATATTTTCCACGTAAAATGACAACAGTTCCAATTA 7 0.17500000000000002 No Hit CTTTTACAAAATATACTTATCTTAATATGTATAACCGGAGTTTATATTAC 7 0.17500000000000002 No Hit AGCACACAATTGGATGATTTATTATACAGACTGTATGTAGGAGTAAGTAC 7 0.17500000000000002 No Hit GGCAGGGTAGCTTGGATGATTAATAAAGTTGAGCACACATACATAGAGAT 6 0.15 No Hit AAGAGTAAAACGCTGGCATATATATCGAGTTCAGTACACCTCGCAGGGGA 6 0.15 No Hit GAACAAAGCAAGATACGATCCAAATTAATTGCCACCACACAACAGACGTG 6 0.15 No Hit ACGGAAAGATAAAATTTATTATGAAAGTTCTCAAGACCAGAGCACGCGAA 6 0.15 No Hit AGGCACAACAAAGATCATCATCGTCACAAGATACTACAGCACTGAACCAT 6 0.15 No Hit AGGCAGGGTAGCTTGGATGATTAATAAAGTTGAGCACACATACATAGAGA 6 0.15 No Hit GGCACATGACGTGTCTCCTTCAAAAAGGAGAGCCAAATTTAACGGAAAAC 5 0.125 No Hit GATGAAAATGGTATTATAATTATATAGTTGATGTCTTTTGGTCACAAGAT 5 0.125 No Hit ATGCGAATTACGTACATTTCATCAGCAAATACAAGTACTGTTACATGCTT 5 0.125 No Hit ATAACAAACACTTTTATTCCACGTATACCCAATGTATATGCATGTACAGT 5 0.125 No Hit AGAGTAAAACGCTGGCATATATATCGAGTTCAGTACACCTCGCAGGGGAA 5 0.125 No Hit GGCTCAACCATCAAATCCATTAATTTCAGTACGTACATAAATACTAGCAG 5 0.125 No Hit AAGAAAACATAACTACTTATGGAGTATTATTAGATAATTATTGCCGGCCT 5 0.125 No Hit CAGACAGTAGAATTACACACGGGCTCACTTATTCATCATAATAGTTCATA 5 0.125 No Hit ATTCTGTCCCCTTATCTTTCATTCAGAAAAAGGAATGAATGGCTCGGCTA 5 0.125 No Hit GGAATCAATGCTATGCGAATTACGTACATTTCATCAGCAAATACAAGTAC 5 0.125 No Hit GAAGAAAATATTCTTGGACATTATTAAGAGACCATGCATATTAATGGAAT 5 0.125 No Hit AAACAACTAAATAACCTTTTTATTCGCTCCTCTAGTCCCAGAAGGATCCA 5 0.125 No Hit GAAACAACTAAATAACCTTTTTATTCGCTCCTCTAGTCCCAGAAGGATCC 5 0.125 No Hit >>END_MODULE >>Adapter Content fail #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 0.025 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 0.037500000000000006 0.0 0.0 0.0 0.0 22-23 0.0625 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 0.175 0.0 0.0 0.0 0.0 36-37 0.275 0.0 0.0 0.0 0.0 38-39 0.35 0.0 0.0 0.0 0.0 40-41 0.4125 0.0 0.0 0.0 0.0 42-43 0.475 0.0 0.0 0.0 0.0 44-45 0.55 0.0 0.0 0.0 0.0 46-47 0.5874999999999999 0.0 0.0 0.0 0.0 48-49 0.7 0.0 0.0 0.0 0.0 50-51 0.8875 0.0 0.0 0.0 0.0 52-53 1.0625 0.0 0.0 0.0 0.0 54-55 1.225 0.0 0.0 0.0 0.0 56-57 1.4 0.0 0.0 0.0 0.0 58-59 1.65 0.0 0.0 0.0 0.0 60-61 1.8625 0.0 0.0 0.0 0.0 62-63 2.2125000000000004 0.0 0.0 0.0 0.0 64-65 2.625 0.0 0.0 0.0 0.0 66-67 2.9625000000000004 0.0 0.0 0.0 0.0 68-69 3.3625 0.0 0.0 0.0 0.0 70-71 3.7125 0.0 0.0 0.0 0.0 72-73 4.1375 0.0 0.0 0.0 0.0 74-75 4.675 0.0 0.0 0.0 0.0 76-77 5.2125 0.0 0.0 0.0 0.0 78-79 5.8375 0.0 0.0 0.0 0.0 80-81 6.4 0.0 0.0 0.0 0.0 82-83 7.225 0.0 0.0 0.0 0.0 84-85 7.9375 0.0 0.0 0.0 0.0 86-87 8.8 0.0 0.0 0.0 0.0 88-89 9.8 0.0 0.0 0.0 0.0 90-91 11.0625 0.0 0.0 0.0 0.0 92-93 12.3125 0.0 0.0 0.0 0.0 94-95 13.6125 0.0 0.0 0.0 0.0 96-97 14.5875 0.0 0.0 0.0 0.0 98-99 15.7625 0.0 0.0 0.0 0.0 100-101 17.275 0.0 0.0 0.0 0.0 102-103 18.6 0.0 0.0 0.0 0.0 104-105 20.0625 0.0 0.0 0.0 0.0 106-107 21.7875 0.0 0.0 0.0 0.0 108-109 23.05 0.0 0.0 0.0 0.0 110-111 24.2 0.0 0.0 0.0 0.0 112-113 25.7125 0.0 0.0 0.0 0.0 114-115 27.325000000000003 0.0 0.0 0.0 0.0 116-117 29.1 0.0 0.0 0.0 0.0 118-119 30.4125 0.0 0.0 0.0 0.0 120-121 31.7875 0.0 0.0 0.0 0.0 122-123 33.0625 0.0 0.0 0.0 0.0 124-125 34.400000000000006 0.0 0.0 0.0 0.0 126-127 36.2125 0.0 0.0 0.0 0.0 128-129 37.5 0.0 0.0 0.0 0.0 130-131 38.6875 0.0 0.0 0.0 0.0 132-133 39.825 0.0 0.0 0.0 0.0 134-135 40.8875 0.0 0.0 0.0 0.0 136-137 42.225 0.0 0.0 0.0 0.0 138-139 43.2875 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content fail #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position CTTTTTT 70 1.9790605E-9 72.50001 1 AAAAAAA 210 0.00580008 13.809524 145 >>END_MODULE Rejected 1252146 READS because READLEN < 1 Read 1252146 spots for SRR8846532.sra Written 1252146 spots for SRR8846532.sra Rejected 1252146 READS because READLEN < 1 Read 1252146 spots for SRR8846532.sra Written 1252146 spots for SRR8846532.sra Rejected 1252146 READS because READLEN < 1 Read 1252146 spots for SRR8846532.sra Written 1252146 spots for SRR8846532.sra Rejected 1252146 READS because READLEN < 1 Read 1252146 spots for SRR8846532.sra Written 1252146 spots for SRR8846532.sra Rejected 1252146 READS because READLEN < 1 Read 1252146 spots for SRR8846532.sra Written 1252146 spots for SRR8846532.sra Rejected 1252146 READS because READLEN < 1 Read 1252146 spots for SRR8846532.sra Written 1252146 spots for SRR8846532.sra Rejected 1252146 READS because READLEN < 1 Read 1252146 spots for SRR8846532.sra Written 1252146 spots for SRR8846532.sra Rejected 1252146 READS because READLEN < 1 Read 1252146 spots for SRR8846532.sra Written 1252146 spots for SRR8846532.sra Rejected 1252146 READS because READLEN < 1 Read 1252146 spots for SRR8846532.sra Written 1252146 spots for SRR8846532.sra Rejected 1252146 READS because READLEN < 1 Read 1252146 spots for SRR8846532.sra Written 1252146 spots for SRR8846532.sra Rejected 1252146 READS because READLEN < 1 Read 1252146 spots for SRR8846532.sra Written 1252146 spots for SRR8846532.sra Rejected 1252146 READS because READLEN < 1 Read 1252146 spots for SRR8846532.sra Written 1252146 spots for SRR8846532.sra Rejected 1252146 READS because READLEN < 1 Read 1252146 spots for SRR8846532.sra Written 1252146 spots for SRR8846532.sra Rejected 1252148 READS because READLEN < 1 Read 1252148 spots for SRR8846532.sra Written 1252148 spots for SRR8846532.sra Rejected 1252146 READS because READLEN < 1 Read 1252146 spots for SRR8846532.sra Written 1252146 spots for SRR8846532.sra Rejected 1252146 READS because READLEN < 1 Read 1252146 spots for SRR8846532.sra Written 1252146 spots for SRR8846532.sra Rejected 1252146 READS because READLEN < 1 Read 1252146 spots for SRR8846532.sra Written 1252146 spots for SRR8846532.sra Rejected 1252146 READS because READLEN < 1 Read 1252146 spots for SRR8846532.sra Written 1252146 spots for SRR8846532.sra Rejected 1252146 READS because READLEN < 1 Read 1252146 spots for SRR8846532.sra Written 1252146 spots for SRR8846532.sra Rejected 1252146 READS because READLEN < 1 Read 1252146 spots for SRR8846532.sra Written 1252146 spots for SRR8846532.sra SRR ids: ['SRR8846532.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_i2r8912_ SRR8846532.sra spots: 25042922 blocks: [[1, 1252146], [1252147, 2504292], [2504293, 3756438], [3756439, 5008584], [5008585, 6260730], [6260731, 7512876], [7512877, 8765022], [8765023, 10017168], [10017169, 11269314], [11269315, 12521460], [12521461, 13773606], [13773607, 15025752], [15025753, 16277898], [16277899, 17530044], [17530045, 18782190], [18782191, 20034336], [20034337, 21286482], [21286483, 22538628], [22538629, 23790774], [23790775, 25042922]] SRR8846532 file size 8464524 SRR8846532 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 SRR8846532 SRR8846532_1.fastq Input file: SRR8846532_1.fastq trimmed: SRR8846532-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 Thu Dec 12 02:57:36 2024 >> started Thu Dec 12 02:57:50 2024 >> done (14.129s) 25042922 reads processed; of these: 13511 ( 0.05%) short reads filtered out after trimming by size control 3617 ( 0.01%) empty reads filtered out after trimming by size control 25025794 (99.93%) reads available; of these: 15958775 (63.77%) trimmed reads available after processing 9067019 (36.23%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 3477 0.01% 19 14158 0.06% 20 3357 0.01% 21 4088 0.02% 22 5623 0.02% 23 7562 0.03% 24 10251 0.04% 25 12560 0.05% 26 14521 0.06% 27 14871 0.06% 28 18753 0.07% 29 19678 0.08% 30 23398 0.09% 31 29822 0.12% 32 31182 0.12% 33 33874 0.14% 34 36923 0.15% 35 38891 0.16% 36 46032 0.18% 37 43973 0.18% 38 47918 0.19% 39 50537 0.20% 40 52356 0.21% 41 56281 0.22% 42 56247 0.22% 43 58056 0.23% 44 60385 0.24% 45 59181 0.24% 46 59967 0.24% 47 60121 0.24% 48 60334 0.24% 49 60298 0.24% 50 60278 0.24% 51 57750 0.23% 52 58746 0.23% 53 58352 0.23% 54 58022 0.23% 55 57953 0.23% 56 59204 0.24% 57 60485 0.24% 58 61511 0.25% 59 61233 0.24% 60 63079 0.25% 61 64392 0.26% 62 65712 0.26% 63 66442 0.27% 64 67757 0.27% 65 70047 0.28% 66 68831 0.28% 67 70727 0.28% 68 73227 0.29% 69 76580 0.31% 70 79981 0.32% 71 83861 0.34% 72 86552 0.35% 73 92110 0.37% 74 95804 0.38% 75 100273 0.40% 76 102067 0.41% 77 104860 0.42% 78 105564 0.42% 79 110980 0.44% 80 112502 0.45% 81 113679 0.45% 82 114650 0.46% 83 118492 0.47% 84 123646 0.49% 85 127674 0.51% 86 131132 0.52% 87 135432 0.54% 88 138718 0.55% 89 140455 0.56% 90 141245 0.56% 91 142782 0.57% 92 145082 0.58% 93 148017 0.59% 94 151838 0.61% 95 156281 0.62% 96 161377 0.64% 97 165187 0.66% 98 168443 0.67% 99 174283 0.70% 100 177629 0.71% 101 185329 0.74% 102 178303 0.71% 103 178390 0.71% 104 182896 0.73% 105 185328 0.74% 106 186613 0.75% 107 191060 0.76% 108 189445 0.76% 109 191825 0.77% 110 191406 0.76% 111 194948 0.78% 112 190746 0.76% 113 192604 0.77% 114 187833 0.75% 115 189460 0.76% 116 189277 0.76% 117 187510 0.75% 118 181372 0.72% 119 174278 0.70% 120 6270 0.03% 121 6553 0.03% 122 6913 0.03% 123 7035 0.03% 124 7257 0.03% 125 7522 0.03% 126 7873 0.03% 127 8474 0.03% 128 8718 0.03% 129 9503 0.04% 130 9694 0.04% 131 10324 0.04% 132 10954 0.04% 133 11265 0.05% 134 12101 0.05% 135 12991 0.05% 136 14777 0.06% 137 15654 0.06% 138 19220 0.08% 139 18868 0.08% 140 21647 0.09% 141 25467 0.10% 142 27861 0.11% 143 33673 0.13% 144 42483 0.17% 145 55416 0.22% 146 70167 0.28% 147 95942 0.38% 148 167952 0.67% 149 328814 1.31% 150 5003165 19.99% 151 9067019 36.23% 25025794 reads passed initial QC criterion=sequence-density sequence-density=11.06 sequence-density-rank=1 fanout-score=35.52 fanout-score-rank=6 prefix-density=12.26 prefix-fanout=32.0 sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACGATCACATCTCGTATGCCGTCTTCTGCTTGAAAA criterion=fanout-score sequence-density=0.01 sequence-density-rank=15 fanout-score=229.89 fanout-score-rank=1 prefix-density=0.33 prefix-fanout=5.9 sequence=GAAACACACAAACACGTACCGGTAAATTATCATAATCAGAATTTGTCGACGAATTTGATATTCTTTTACAAAATATACTTATCTTAATATGTATAACCGGAGTTTATATTACATGCCCCTCTCCCAACGATAGTTGTAGTACTCTTATAATAGTAGTACTCATGAATACAGTTAATCCGGGTTGTTGGGAGAGATCACATGCATAAATACAACATGAAACAAACGTGTGAAAAAGGTACATAAAATCGGTGTGACCCGTTCTTGTATTATAAGAAATCAACTTGCTTAGGCCTTGCCGGACTCCTCACAACCCGGTGGCTTGAAGGCGATGAAGCTGATGCACTGCACTTGCCTGGTGTTGTCGAAGCCGATGATGCGGACATAGGC 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: 1 (100.00%) aligned 0 times 0 (0.00%) aligned exactly 1 time 0 (0.00%) aligned >1 times 0.00% overall alignment rate Adapter seq not found in reference. Now shuffling file before clipping skewer v0.2.2 [April 4, 2016] COMMAND LINE: skewer -f sanger -l 18 -t 20 -x AGATCGGAAGAGCACACGTCTGAACTCCAGTCACGATCACATCTCGTATGCCGTCTTCTGCTTGAAAA -o SRR8846532 - Input file: STDIN trimmed: SRR8846532-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): AGATCGGAAGAGCACACGTCTGAACTCCAGTCACGATCACATCTCGTATGCCGTCTTCTGCTTG -- maximum error ratio allowed (-r): 0.100 -- maximum indel error ratio allowed (-d): 0.030 -- minimum read length allowed after trimming (-l): 18 -- file format (-f): Sanger/Illumina 1.8+ FASTQ -- minimum overlap length for adapter detection (-k): 3 -- number of concurrent threads (-t): 20 Thu Dec 12 02:58:57 2024 >> started Thu Dec 12 02:59:20 2024 >> done (22.884s) 20854828 reads processed; of these: 184 ( 0.00%) short reads filtered out after trimming by size control 7 ( 0.00%) empty reads filtered out after trimming by size control 20854637 (100.00%) reads available; of these: 4190822 (20.10%) trimmed reads available after processing 16663815 (79.90%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 2901 0.01% 19 11949 0.06% 20 2815 0.01% 21 3410 0.02% 22 4676 0.02% 23 6325 0.03% 24 8534 0.04% 25 10525 0.05% 26 12077 0.06% 27 12426 0.06% 28 15650 0.08% 29 16453 0.08% 30 19567 0.09% 31 24912 0.12% 32 26064 0.12% 33 28245 0.14% 34 30913 0.15% 35 32551 0.16% 36 38478 0.18% 37 36761 0.18% 38 40042 0.19% 39 42204 0.20% 40 43701 0.21% 41 46946 0.23% 42 46896 0.22% 43 48523 0.23% 44 50403 0.24% 45 49457 0.24% 46 50057 0.24% 47 50101 0.24% 48 50640 0.24% 49 50379 0.24% 50 50397 0.24% 51 48471 0.23% 52 49053 0.24% 53 48964 0.23% 54 48599 0.23% 55 48482 0.23% 56 49500 0.24% 57 50979 0.24% 58 51480 0.25% 59 51237 0.25% 60 52634 0.25% 61 53784 0.26% 62 55312 0.27% 63 55846 0.27% 64 57303 0.27% 65 58806 0.28% 66 57576 0.28% 67 59248 0.28% 68 61507 0.29% 69 64243 0.31% 70 67132 0.32% 71 70088 0.34% 72 72492 0.35% 73 77440 0.37% 74 80338 0.39% 75 84040 0.40% 76 85867 0.41% 77 88003 0.42% 78 88838 0.43% 79 92968 0.45% 80 94480 0.45% 81 96090 0.46% 82 96507 0.46% 83 99617 0.48% 84 103243 0.50% 85 107216 0.51% 86 110282 0.53% 87 113618 0.54% 88 117067 0.56% 89 117717 0.56% 90 118669 0.57% 91 119739 0.57% 92 121694 0.58% 93 124605 0.60% 94 127152 0.61% 95 131282 0.63% 96 135122 0.65% 97 138377 0.66% 98 140806 0.68% 99 146278 0.70% 100 149309 0.72% 101 155230 0.74% 102 149667 0.72% 103 149715 0.72% 104 154252 0.74% 105 155401 0.75% 106 156832 0.75% 107 159382 0.76% 108 158395 0.76% 109 160290 0.77% 110 159774 0.77% 111 163404 0.78% 112 160769 0.77% 113 161841 0.78% 114 157177 0.75% 115 157458 0.76% 116 156909 0.75% 117 153394 0.74% 118 149497 0.72% 119 147056 0.71% 120 151321 0.73% 121 152808 0.73% 122 150550 0.72% 123 155612 0.75% 124 161265 0.77% 125 156291 0.75% 126 155668 0.75% 127 151620 0.73% 128 148813 0.71% 129 147721 0.71% 130 142475 0.68% 131 141045 0.68% 132 140426 0.67% 133 135159 0.65% 134 130345 0.63% 135 129803 0.62% 136 129267 0.62% 137 129657 0.62% 138 131240 0.63% 139 129598 0.62% 140 131916 0.63% 141 131744 0.63% 142 136224 0.65% 143 138447 0.66% 144 141833 0.68% 145 150354 0.72% 146 173335 0.83% 147 251569 1.21% 148 379930 1.82% 149 197258 0.95% 150 2768542 13.28% 151 5112280 24.51% criterion=sequence-density sequence-density=0.72 sequence-density-rank=1 fanout-score=3.22 fanout-score-rank=38 prefix-density=0.85 prefix-fanout=2.7 sequence=TTCAAATGTACA criterion=fanout-score sequence-density=0.01 sequence-density-rank=36 fanout-score=294.07 fanout-score-rank=1 prefix-density=0.23 prefix-fanout=8.7 sequence=AACTCAAAACTCGAAAGATCAAAGACGCAGGTATTGGTGAAGAGTGATCAGAGATGCAATGCACACTAAGAGCACAATATAATAAATATTACAAGCGTGCACGCAGCACGCGTACAAATTTACATGTTACACCCACCCTCAGCATTTTAAACCTCTCTCACGCACTACATTCCATGGACGATGGGTACCATCATGGCGATGCACGGATCGA Started job on | Dec 12 02:59:49 Started mapping on | Dec 12 02:59:49 Finished on | Dec 12 03:00:23 Mapping speed, Million of reads per hour | 2649.77 Number of input reads | 25025603 Average input read length | 122 UNIQUE READS: Uniquely mapped reads number | 22564905 Uniquely mapped reads % | 90.17% Average mapped length | 124.69 Number of splices: Total | 152604 Number of splices: Annotated (sjdb) | 25437 Number of splices: GT/AG | 76534 Number of splices: GC/AG | 7722 Number of splices: AT/AC | 191 Number of splices: Non-canonical | 68157 Mismatch rate per base, % | 0.27% Deletion rate per base | 0.00% Deletion average length | 1.31 Insertion rate per base | 0.00% Insertion average length | 1.10 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 1551501 % of reads mapped to multiple loci | 6.20% Number of reads mapped to too many loci | 322086 % of reads mapped to too many loci | 1.29% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 2.28% % of reads unmapped: other | 0.06% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 909197 909197 909197 N_multimapping 1551501 1551501 1551501 N_noFeature 1080866 21640401 1396917 N_ambiguous 680133 1778 78259 UnstrandedReadsAssigned:20803906 PositiveStrandReadsAssigned:922726 NegativeStrandReadsAssigned:21089729 Dataset is classified negative stranded MeadianReadLen=134 20thPercentileLength=92 echo kmer=87 SRR8846532 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: SRR8846532-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 25,025,603 reads, 21,704,141 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,198 rounds 52973 SRR8846532.ke.tsv 35125 SRR8846532.se.tsv 88098 total ==> SRR8846532.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 582 25.4151 PNS24243 293 194 0 0 KQK14069 1603 1504 6951 276.899 KQK14071 474 375 0 0 ==> SRR8846532.se.tsv <== BRADI_1g14170v3 6911 BRADI_1g53295v3 78 BRADI_1g59795v3 121 BRADI_1g07683v3 0 BRADI_1g00485v3 8 BRADI_1g20270v3 1003 BRADI_1g74790v3 154 BRADI_1g09890v3 13 BRADI_1g77505v3 363 BRADI_1g48960v3 0 SRR8846532 completed mapping pipeline successfully