Starting /dee2/code/volunteer_pipeline.sh SRR6257527 current disk space = 1544307519488 free memory = 1436858716 SRR6257527 SRAfilesize d243611608c140ca7536a3cb061e2f75 SRR6257527.sra SRR6257527.sra file validated SRR6257527 is paired end SRR6257527 is conventional basespace SRR6257527 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR6257527_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 45 >>END_MODULE >>Per base sequence quality fail #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 23.26275 25.0 18.0 30.0 18.0 32.0 2 24.693 27.0 18.0 29.0 18.0 31.0 3 29.5555 30.0 27.0 33.0 25.0 33.0 4 30.693 32.0 32.0 33.0 27.0 33.0 5 31.88975 33.0 32.0 33.0 30.0 33.0 6 35.96975 37.0 36.0 38.0 33.0 38.0 7 37.1235 38.0 37.0 38.0 36.0 38.0 8 37.32675 38.0 38.0 38.0 36.0 38.0 9 37.2105 38.0 38.0 38.0 36.0 38.0 10-14 37.1374 38.0 38.0 38.0 35.8 38.0 15-19 37.4696 38.0 38.0 38.0 37.2 38.0 20-24 36.83605 38.0 37.8 38.0 34.4 38.0 25-29 36.5914 38.0 37.4 38.0 34.0 38.0 30-34 36.479499999999994 38.0 36.8 38.0 32.6 38.0 35-39 37.07775 38.0 37.8 38.0 35.4 38.0 40-44 37.42100000000001 38.0 38.0 38.0 37.0 38.0 45-49 35.3144 37.6 34.2 38.0 28.2 38.0 50-54 35.25675 38.0 34.8 38.0 25.0 38.0 55-59 37.0249 38.0 37.8 38.0 35.6 38.0 60-64 37.2145 38.0 38.0 38.0 36.0 38.0 65-69 37.18945 38.0 38.0 38.0 36.0 38.0 70-74 36.38075 38.0 37.4 38.0 33.0 38.0 75-79 35.110200000000006 37.8 34.6 38.0 29.0 38.0 80-84 36.647299999999994 38.0 38.0 38.0 34.4 38.0 85-89 36.583099999999995 38.0 38.0 38.0 34.2 38.0 90-94 36.66245 38.0 38.0 38.0 34.2 38.0 95-99 36.592349999999996 38.0 38.0 38.0 34.4 38.0 100-104 36.36825 38.0 37.8 38.0 33.6 38.0 105-109 36.2254 38.0 37.2 38.0 33.6 38.0 110-114 35.2911 38.0 36.0 38.0 28.8 38.0 115-119 34.45745 37.8 34.2 38.0 25.0 38.0 120-124 35.52265 38.0 36.0 38.0 30.6 38.0 125-129 35.053250000000006 38.0 35.0 38.0 28.4 38.0 130-134 31.1173 35.4 24.6 38.0 18.2 38.0 135-139 31.117900000000002 35.4 26.0 38.0 16.8 38.0 140-144 30.546699999999998 35.6 25.6 38.0 15.2 38.0 145-149 30.2069 35.6 27.2 38.0 8.8 38.0 150-151 22.785125 31.0 2.0 36.5 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 13 1.0 14 0.0 15 0.0 16 3.0 17 2.0 18 1.0 19 3.0 20 6.0 21 6.0 22 5.0 23 5.0 24 8.0 25 14.0 26 20.0 27 29.0 28 36.0 29 50.0 30 89.0 31 120.0 32 130.0 33 263.0 34 424.0 35 831.0 36 1351.0 37 603.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 37.89446456285566 11.536471805483703 7.087428867046043 43.48163476461459 2 22.836418209104554 10.505252626313156 33.16658329164582 33.49174587293647 3 20.45 16.825000000000003 27.1 35.625 4 23.625 24.474999999999998 24.025 27.875 5 23.879849812265334 30.9386733416771 23.9549436795995 21.226533166458072 6 21.3 31.8 26.375 20.525 7 15.325 25.1 41.85 17.724999999999998 8 17.474999999999998 24.825 33.225 24.474999999999998 9 17.825 23.525 36.175000000000004 22.475 10-14 20.035 30.09 26.26 23.615 15-19 20.89 28.525 27.29 23.294999999999998 20-24 19.900000000000002 28.425 27.939999999999998 23.735 25-29 22.129425885177035 27.81056211242248 26.690338067613524 23.36967393478696 30-34 21.86 27.93 27.095000000000002 23.115 35-39 21.195 29.015 27.265 22.525000000000002 40-44 20.345 28.044999999999998 27.905 23.705000000000002 45-49 19.89 27.91 27.555000000000003 24.645 50-54 20.001000050002503 27.641382069103454 27.971398569928496 24.386219310965547 55-59 20.465 27.189999999999998 27.474999999999998 24.87 60-64 20.025000000000002 27.894999999999996 27.985 24.095 65-69 20.552055205520553 28.337833783378336 26.4976497649765 24.61246124612461 70-74 21.945 27.950000000000003 25.395 24.709999999999997 75-79 21.29 27.650000000000002 26.97 24.09 80-84 21.826091304565228 28.23141157057853 26.18630931546577 23.756187809390468 85-89 21.634326865373072 27.735547109421884 27.1754350870174 23.454690938187635 90-94 21.12316847527129 28.259238885832875 26.8440266039906 23.773566034905237 95-99 21.402140214021404 28.83288328832883 25.52755275527553 24.237423742374236 100-104 20.69 28.999999999999996 25.845000000000002 24.465 105-109 20.65 28.12 26.545 24.685000000000002 110-114 20.855 28.21 26.525 24.41 115-119 20.979999999999997 28.349999999999998 26.085 24.585 120-124 19.875 29.104999999999997 25.5 25.52 125-129 20.849999999999998 29.255 25.319999999999997 24.575 130-134 22.184436887377476 28.535707141428286 25.08501700340068 24.194838967793558 135-139 22.210552638159538 28.512128032008 25.26631657914479 24.01100275068767 140-144 23.5094037615046 28.311324529811927 25.33013205282113 22.849139655862345 145-149 21.166058302915143 29.301465073253663 25.151257562878143 24.381219060953047 150-151 20.75708197543244 28.891952870393585 25.720732013035846 24.63023314113813 >>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 0.0 17 0.0 18 0.0 19 0.5 20 2.5 21 3.5 22 6.0 23 7.5 24 7.5 25 7.0 26 10.5 27 19.5 28 26.5 29 29.0 30 39.5 31 42.5 32 34.0 33 40.5 34 60.5 35 76.5 36 105.5 37 168.0 38 194.0 39 179.5 40 181.5 41 192.0 42 197.0 43 206.5 44 195.5 45 170.0 46 150.0 47 128.0 48 117.5 49 96.5 50 81.5 51 83.5 52 83.5 53 99.0 54 116.0 55 138.5 56 131.5 57 97.5 58 91.5 59 80.0 60 65.5 61 53.0 62 39.0 63 34.0 64 33.5 65 31.5 66 18.5 67 7.0 68 4.0 69 3.0 70 3.0 71 2.5 72 1.5 73 1.0 74 1.5 75 2.0 76 1.0 77 0.0 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 3.35 2 0.05 3 0.0 4 0.0 5 0.125 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 0.02 30-34 0.0 35-39 0.0 40-44 0.0 45-49 0.0 50-54 0.005 55-59 0.0 60-64 0.0 65-69 0.01 70-74 0.0 75-79 0.0 80-84 0.005 85-89 0.02 90-94 0.015 95-99 0.01 100-104 0.0 105-109 0.0 110-114 0.0 115-119 0.0 120-124 0.0 125-129 0.0 130-134 0.02 135-139 0.025 140-144 0.04 145-149 0.005 150-151 0.27499999999999997 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 83.975 #Duplication Level Percentage of deduplicated Percentage of total 1 90.80083358142305 76.25 2 5.507591545102709 9.25 3 1.6969336111938078 4.275 4 0.8335814230425722 2.8000000000000003 5 0.5954153021732659 2.5 6 0.029770765108663295 0.15 7 0.17862459065197975 1.05 8 0.08931229532598987 0.6 9 0.029770765108663295 0.22499999999999998 >10 0.23816612086930636 2.9000000000000004 >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 CTTTCTTTTCTTCAAAAATTCTTATATGTTAGCGGAAAAACCTTATCCAT 24 0.6 No Hit GCTTTCTTTTCTTCAAAAATTCTTATATGTTAGCGGAAAAACCTTATCCA 21 0.525 No Hit GCGGGAACTTCAAGAGCAGCTAGATCTAGAGGGAAGTTGTGAGCATTACG 16 0.4 No Hit CTCGCGAATACCATCAATATCTACTGGAGGGGCTGCGATGAAGGCGATAA 12 0.3 No Hit GGGAACTTCAAGAGCAGCTAGATCTAGAGGGAAGTTGTGAGCATTACGTT 12 0.3 No Hit CTTTTCTTCAAAAATTCTTATATGTTAGCGGAAAAACCTTATCCATTAAT 11 0.27499999999999997 No Hit GGCCAAAATAACCATGAGCAGCCACAATATTATAAGTCTCTTCCTCTTGA 10 0.25 No Hit GGATGCATAAGGATGTTGTGCTCTGCCTGGAATACAATCATAAAGTTGAA 10 0.25 No Hit CCCGAAGTTACGGGGCTATTTTGCCGAGTTCCTTAGAGAGAGTTGTCTCG 9 0.22499999999999998 No Hit GGTGGTTCGCTGGAGTAGGCTGCGAGGCCCAAGCGGCCAAGGAGTGCAGC 8 0.2 No Hit CTTTGGAGTAGGCTGTGAGACCTAAGCGGGTCAGGAATGCAGCGGCCCGT 8 0.2 No Hit GTTCGCTGGAGTAGGCTGCGAGGCCCAAGCGGCCAAGGAGTGCAGCGGCC 8 0.2 No Hit CCCAAGTATTAATAACGCGACCTTGACTATCAACTACAGATTGGTTGAAA 7 0.17500000000000002 No Hit AGCGGAAAAACCTTATCCATTAATAGCGGGAACTTCAAGAGCAGCTAGAT 7 0.17500000000000002 No Hit GCTCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCTAAA 7 0.17500000000000002 No Hit CCCTCTTCAAATAGATCTAATGGATAAGCTACATAACAGATCCATTGACT 7 0.17500000000000002 No Hit CTCATAAGGACCACCATTGTATAACCATTCATCAACGGATGCAGCTTCCC 7 0.17500000000000002 No Hit GCGGAAAAACCTTATCCATTAATAGCGGGAACTTCAAGAGCAGCTAGATC 7 0.17500000000000002 No Hit GGGGCTGCGATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAAGGT 6 0.15 No Hit CTTGGTTTCATACTCCGGGGTGTAGTAAGTCAATCTATAATCTTTAACAC 5 0.125 No Hit GGCATGATGACTTGGCCTCATCCTCTCCTTCCTCCGGCTTAACACCGGCG 5 0.125 No Hit TCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCTAAAGG 5 0.125 No Hit CCATATAACAAGCTACACCAAGTAAGAAGTGTAGAACAATTAGCTCATAA 5 0.125 No Hit CCACCATTGTATAACCATTCATCAACGGATGCAGCTTCCCAAATTGGGTA 5 0.125 No Hit TTCTTTTCTTCAAAAATTCTTATATGTTAGCGGAAAAACCTTATCCATTA 5 0.125 No Hit GTGGTTCGCTGGAGTAGGCTGCGAGGCCCAAGCGGCCAAGGAGTGCAGCG 5 0.125 No Hit GGAATTCGTAGATCCTCCAGACGTAGAGCACGTAGGGCTTTGAAACCAAA 5 0.125 No Hit CTCTTGACCAAATTTGTAACCCTCATTAGCAGATTCATTTTCAGTAGTTT 5 0.125 No Hit CTCCACGCGGCATTGCTCCGTCAGGCTTTCGCCCATTGCGGAAAATTCCC 5 0.125 No Hit CCGGGAACGGATTCACCGCCGTATGGCTGACCGGCGATTACTAGCGATTC 5 0.125 No Hit CCCCACTGCTGCCTCCCGTAGGAGTCTGGGCCGTGTCTCAGTCCCAGTGT 5 0.125 No Hit CTTTCTTTTCCTCTGGCTACTAAGATGTTTCAGTTCGCCAGGTTGTCTCT 5 0.125 No Hit GGCAGTTGTCGCTGCTCTGTGAAGCCAGCCTCACGCTGTGCCTGCCAACA 5 0.125 No Hit GCCAAGAAGAAGTGTAAAGAACGAGAGTTGTTGAAACTAGCATATTGGAA 5 0.125 No Hit GTTGTGCTCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTC 5 0.125 No Hit GTCGGTTTCGGGTACAGGTACCCTTTTGTTGAAGGTCGTTCGAGCTTTTC 5 0.125 No Hit CTGGCATCGAGCTATTTTGCCGCAGGACCTCCCCTACAGTATCGTCACCG 5 0.125 No Hit CCCTCATTAGCAGATTCATTTTCAGTAGTTTCCCTGATCAAACTAGAGGT 5 0.125 No Hit GTTGAAACTAGCATATTGGAAGATTAATCGGCCAAAATAACCATGAGCAG 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 0.0 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 0.0125 0.0 0.0 0.0 0.0 60-61 0.025 0.0 0.0 0.0 0.0 62-63 0.025 0.0 0.0 0.0 0.0 64-65 0.075 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 0.15 0.0 0.0 0.0 0.0 72-73 0.16249999999999998 0.0 0.0 0.0 0.0 74-75 0.32499999999999996 0.0 0.0 0.0 0.0 76-77 0.4 0.0 0.0 0.0 0.0 78-79 0.5125 0.0 0.0 0.0 0.0 80-81 0.6375 0.0 0.0 0.0 0.0 82-83 0.825 0.0 0.0 0.0 0.0 84-85 1.075 0.0 0.0 0.0 0.0 86-87 1.325 0.0 0.0 0.0 0.0 88-89 1.575 0.0 0.0 0.0 0.0 90-91 1.825 0.0 0.0 0.0 0.0 92-93 2.0375 0.0 0.0 0.0 0.0 94-95 2.35 0.0 0.0 0.0 0.0 96-97 2.7 0.0 0.0 0.0 0.0 98-99 2.9625 0.0 0.0 0.0 0.0 100-101 3.1875 0.0 0.0 0.0 0.0 102-103 3.7125000000000004 0.0 0.0 0.0 0.0 104-105 4.0875 0.0 0.0 0.0 0.0 106-107 4.637499999999999 0.0 0.0 0.0 0.0 108-109 5.15 0.0 0.0 0.0 0.0 110-111 5.6375 0.0 0.0 0.0 0.0 112-113 6.1875 0.0 0.0 0.0 0.0 114-115 6.737500000000001 0.0 0.0 0.0 0.0 116-117 7.2125 0.0 0.0 0.0 0.0 118-119 7.7625 0.0 0.0 0.0 0.0 120-121 8.462499999999999 0.0 0.0 0.0 0.0 122-123 8.9625 0.0 0.0 0.0 0.0 124-125 9.525 0.0 0.0 0.0 0.0 126-127 10.05 0.0 0.0 0.0 0.0 128-129 10.5875 0.0 0.0 0.0 0.0 130-131 11.1875 0.0 0.0 0.0 0.0 132-133 12.05 0.0 0.0 0.0 0.0 134-135 12.6875 0.0 0.0 0.0 0.0 136-137 13.2625 0.0 0.0 0.0 0.0 138-139 13.9875 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position ATTCGGC 10 0.0068343505 144.975 5 GATTCGG 10 0.0068343505 144.975 4 TTCGGCA 10 0.0068343505 144.975 6 GTCTGAA 60 0.0044970433 14.4974985 135-139 >>END_MODULE SRR6257527 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR6257527_2.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 151 %GC 45 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 32.0915 33.0 32.0 33.0 28.0 34.0 2 32.532 33.0 33.0 34.0 32.0 34.0 3 29.3675 33.0 27.0 33.0 18.0 34.0 4 31.14675 33.0 32.0 33.0 27.0 34.0 5 32.255 33.0 32.0 34.0 31.0 34.0 6 36.75475 38.0 38.0 38.0 35.0 38.0 7 37.074 38.0 38.0 38.0 36.0 38.0 8 31.70475 38.0 28.0 38.0 16.0 38.0 9 35.6135 38.0 36.0 38.0 30.0 38.0 10-14 35.8955 38.0 37.0 38.0 30.8 38.0 15-19 36.15355000000001 38.0 36.4 38.0 31.2 38.0 20-24 37.106849999999994 38.0 38.0 38.0 36.6 38.0 25-29 37.16555000000001 38.0 38.0 38.0 36.6 38.0 30-34 37.0369 38.0 38.0 38.0 36.2 38.0 35-39 37.106550000000006 38.0 38.0 38.0 36.2 38.0 40-44 37.13065 38.0 38.0 38.0 36.2 38.0 45-49 36.9575 38.0 38.0 38.0 36.0 38.0 50-54 36.7956 38.0 38.0 38.0 35.4 38.0 55-59 36.686099999999996 38.0 38.0 38.0 34.8 38.0 60-64 36.7976 38.0 38.0 38.0 35.2 38.0 65-69 36.745400000000004 38.0 38.0 38.0 34.8 38.0 70-74 36.682100000000005 38.0 38.0 38.0 34.8 38.0 75-79 36.71645 38.0 38.0 38.0 34.8 38.0 80-84 35.350199999999994 38.0 35.4 38.0 28.8 38.0 85-89 36.366699999999994 38.0 37.8 38.0 33.2 38.0 90-94 35.06445 37.8 35.0 38.0 28.8 38.0 95-99 33.9089 37.4 32.4 38.0 24.8 38.0 100-104 35.7925 38.0 36.4 38.0 31.8 38.0 105-109 35.7033 38.0 36.4 38.0 31.4 38.0 110-114 32.8137 36.6 29.2 38.0 22.4 38.0 115-119 35.0949 38.0 35.6 38.0 28.0 38.0 120-124 35.2402 38.0 35.6 38.0 29.6 38.0 125-129 34.903499999999994 38.0 35.2 38.0 28.0 38.0 130-134 34.3147 38.0 33.6 38.0 25.8 38.0 135-139 33.502750000000006 38.0 33.0 38.0 22.2 38.0 140-144 30.5844 35.6 26.0 38.0 13.4 38.0 145-149 30.91805 37.6 30.8 38.0 6.2 38.0 150-151 25.262375 33.0 15.5 37.0 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 4.0 3 0.0 4 2.0 5 1.0 6 1.0 7 0.0 8 0.0 9 0.0 10 2.0 11 3.0 12 1.0 13 3.0 14 2.0 15 0.0 16 1.0 17 4.0 18 3.0 19 6.0 20 8.0 21 6.0 22 8.0 23 10.0 24 17.0 25 16.0 26 28.0 27 30.0 28 45.0 29 45.0 30 69.0 31 115.0 32 123.0 33 216.0 34 293.0 35 575.0 36 1199.0 37 1164.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 38.675 18.725 14.424999999999999 28.175 2 28.925 20.95 32.5 17.625 3 20.325 25.55 35.225 18.9 4 24.725 32.1 24.825 18.35 5 26.075 33.925 23.375 16.625 6 22.15 35.425000000000004 24.75 17.675 7 19.3 22.35 39.0 19.35 8 22.775000000000002 25.6 27.900000000000002 23.724999999999998 9 24.2 22.075 31.75 21.975 10-14 24.47 27.439999999999998 28.249999999999996 19.84 15-19 25.045 26.105 28.205000000000002 20.645 20-24 24.025 26.165 29.310000000000002 20.5 25-29 24.72 26.33 28.455000000000002 20.495 30-34 25.245 26.25 28.050000000000004 20.455000000000002 35-39 25.480000000000004 26.86 27.825 19.835 40-44 24.09 27.505000000000003 28.1 20.305 45-49 24.05 27.794999999999998 27.584999999999997 20.57 50-54 24.67 26.495 28.34 20.495 55-59 23.765 28.12 27.034999999999997 21.08 60-64 23.905 26.745 28.585 20.765 65-69 24.065 26.700000000000003 28.749999999999996 20.485 70-74 24.884999999999998 26.75 28.199999999999996 20.165 75-79 25.34 25.355 28.28 21.025 80-84 24.95 25.319999999999997 29.294999999999998 20.435 85-89 24.865000000000002 27.16 27.639999999999997 20.335 90-94 24.709999999999997 26.455000000000002 27.365000000000002 21.47 95-99 25.0 26.745 27.725 20.53 100-104 24.709999999999997 28.4 27.205000000000002 19.685 105-109 25.990000000000002 26.169999999999998 27.87 19.97 110-114 25.669999999999998 26.745 27.395000000000003 20.19 115-119 25.115 27.139999999999997 27.534999999999997 20.21 120-124 25.705 26.640000000000004 26.985 20.669999999999998 125-129 26.255 27.62 25.865 20.26 130-134 25.905 27.994999999999997 26.405 19.695 135-139 26.314999999999998 26.715 26.895000000000003 20.075000000000003 140-144 26.95134756737837 26.866343317165857 26.926346317315865 19.255962798139905 145-149 26.525 27.02 26.87 19.585 150-151 27.02228900576008 26.82193839218633 27.07237665915352 19.083395942900076 >>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 0.5 13 1.0 14 0.5 15 0.0 16 0.0 17 0.0 18 0.0 19 1.0 20 2.0 21 4.0 22 5.5 23 6.5 24 9.0 25 11.0 26 12.5 27 21.0 28 29.5 29 32.0 30 35.0 31 45.0 32 48.5 33 55.5 34 82.5 35 109.5 36 123.0 37 133.0 38 149.0 39 174.5 40 193.0 41 189.0 42 184.5 43 182.0 44 194.0 45 181.5 46 137.5 47 118.0 48 110.0 49 93.5 50 86.5 51 88.0 52 77.5 53 84.5 54 119.5 55 144.0 56 122.0 57 90.0 58 81.5 59 76.5 60 74.5 61 64.5 62 52.0 63 49.5 64 36.0 65 21.5 66 15.5 67 9.0 68 7.5 69 7.5 70 7.5 71 5.0 72 1.5 73 0.0 74 1.5 75 2.0 76 0.5 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 0.0 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10-14 0.0 15-19 0.0 20-24 0.0 25-29 0.0 30-34 0.0 35-39 0.0 40-44 0.0 45-49 0.0 50-54 0.0 55-59 0.0 60-64 0.0 65-69 0.0 70-74 0.0 75-79 0.0 80-84 0.0 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 0.005 145-149 0.0 150-151 0.17500000000000002 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 87.225 #Duplication Level Percentage of deduplicated Percentage of total 1 92.03210088850675 80.27499999999999 2 4.901117798796217 8.55 3 1.6623674405273718 4.35 4 0.7738607050730868 2.7 5 0.3725995987388937 1.625 6 0.028661507595299514 0.15 7 0.028661507595299514 0.17500000000000002 8 0.028661507595299514 0.2 9 0.05732301519059903 0.44999999999999996 >10 0.11464603038119806 1.525 >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 TATCTATATTATTTCTAGTTAATATGTGTGCTTGGGAGTCCTTGCAATTT 24 0.6 No Hit CCTTGTTATTGTGAGAATTCTTAATTCAAGAGTTGTAAGGAGGGACTTAT 15 0.375 No Hit GTTCGATCCTGGCTCAGGATGAACGCTGGCGGCATGCTTAACACATGCAA 12 0.3 No Hit CTATATTATTTCTAGTTAATATGTGTGCTTGGGAGTCCTTGCAATTTGAA 10 0.25 No Hit CAGTGACCAGGCCCGGGCGACTGTTTACCAAAAACACAGGTCTCCGCAAA 9 0.22499999999999998 No Hit ATTATCTATATTATTTCTAGTTAATATGTGTGCTTGGGAGTCCTTGCAAT 9 0.22499999999999998 No Hit GTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAG 8 0.2 No Hit GGAAACTACTGAAAATGAATCTGCTAATGAGGGTTACAAATTTGGTCAAG 7 0.17500000000000002 No Hit GGGAAACTACTGAAAATGAATCTGCTAATGAGGGTTACAAATTTGGTCAA 6 0.15 No Hit CTATTCAGTGCTATGCATGGTTCCTTGGTAACCTCTAGTTTGATCAGGGA 5 0.125 No Hit CAAGATCTTACCATGACTGCAATTTTAGAGAGACGCGAAAGTACAAGCCT 5 0.125 No Hit CGTTAGCGTGAGCTTGTAACCCGAGTGGGGGCATTAAGGGTGGCGTGGAC 5 0.125 No Hit GCTTGCGGTGGATACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGC 5 0.125 No Hit CGAAAGTACAAGCCTGTGGGGTCGCTTCTGCAACTGGATAACTAGCACTG 5 0.125 No Hit CCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTTCG 5 0.125 No Hit GGTACTTTCAACTTTATGATTGTATTCCAGGCAGAGCACAACATCCTTAT 5 0.125 No Hit TCTTAATTCAAGAGTTGTAAGGAGGGACTTATGTCACCACAAACAGAAAC 5 0.125 No Hit GTTAGCGTGAGCTTGTAACCCGAGTGGGGGCATTAAGGGTGGCGTGGACT 5 0.125 No Hit GAAAATGCCTCGAGCCGAGGTCCGAGTACCAAGCGCTGCAGCGCTGAAGT 5 0.125 No Hit AGGGAAACTACTGAAAATGAATCTGCTAATGAGGGTTACAAATTTGGTCA 5 0.125 No Hit CCTTACCAGGGCTTGACATGCCGCGAATCCTCTTGAAAGAGAGGGGTGCC 5 0.125 No Hit GTTTAGTGGTAAAAGTGTGATTCGTTCTATTAATAACTGAATTTAAAATG 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 0.0 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 0.0125 0.0 0.0 0.0 0.0 60-61 0.025 0.0 0.0 0.0 0.0 62-63 0.025 0.0 0.0 0.0 0.0 64-65 0.075 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 0.15 0.0 0.0 0.0 0.0 72-73 0.1875 0.0 0.0 0.0 0.0 74-75 0.375 0.0 0.0 0.0 0.0 76-77 0.45 0.0 0.0 0.0 0.0 78-79 0.5375 0.0 0.0 0.0 0.0 80-81 0.6625 0.0 0.0 0.0 0.0 82-83 0.8500000000000001 0.0 0.0 0.0 0.0 84-85 1.0625 0.0 0.0 0.0 0.0 86-87 1.25 0.0 0.0 0.0 0.0 88-89 1.475 0.0 0.0 0.0 0.0 90-91 1.6749999999999998 0.0 0.0 0.0 0.0 92-93 1.85 0.0 0.0 0.0 0.0 94-95 2.125 0.0 0.0 0.0 0.0 96-97 2.475 0.0 0.0 0.0 0.0 98-99 2.7375 0.0 0.0 0.0 0.0 100-101 2.9125 0.0 0.0 0.0 0.0 102-103 3.2875 0.0 0.0 0.0 0.0 104-105 3.5250000000000004 0.0 0.0 0.0 0.0 106-107 4.025 0.0 0.0 0.0 0.0 108-109 4.4125 0.0 0.0 0.0 0.0 110-111 4.8625 0.0 0.0 0.0 0.0 112-113 5.425 0.0 0.0 0.0 0.0 114-115 6.0375 0.0 0.0 0.0 0.0 116-117 6.5125 0.0 0.0 0.0 0.0 118-119 7.0875 0.0 0.0 0.0 0.0 120-121 7.8375 0.0 0.0 0.0 0.0 122-123 8.4875 0.0 0.0 0.0 0.0 124-125 9.125 0.0 0.0 0.0 0.0 126-127 9.8375 0.0 0.0 0.0 0.0 128-129 10.55 0.0 0.0 0.0 0.0 130-131 11.2875 0.0 0.0 0.0 0.0 132-133 12.275 0.0 0.0 0.0 0.0 134-135 13.075 0.0 0.0 0.0 0.0 136-137 13.6875 0.0 0.0 0.0 0.0 138-139 14.5125 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position AACCACT 10 0.006830828 145.0 4 AAGAGCG 65 0.0076375785 13.384615 125-129 >>END_MODULE Read 763988 spots for SRR6257527.sra Written 763988 spots for SRR6257527.sra Read 763988 spots for SRR6257527.sra Written 763988 spots for SRR6257527.sra Read 763988 spots for SRR6257527.sra Written 763988 spots for SRR6257527.sra Read 763988 spots for SRR6257527.sra Written 763988 spots for SRR6257527.sra Read 763988 spots for SRR6257527.sra Written 763988 spots for SRR6257527.sra Read 763988 spots for SRR6257527.sra Written 763988 spots for SRR6257527.sra Read 763988 spots for SRR6257527.sra Written 763988 spots for SRR6257527.sra Read 763988 spots for SRR6257527.sra Written 763988 spots for SRR6257527.sra Read 763988 spots for SRR6257527.sra Written 763988 spots for SRR6257527.sra Read 763988 spots for SRR6257527.sra Written 763988 spots for SRR6257527.sra Read 763988 spots for SRR6257527.sra Written 763988 spots for SRR6257527.sra Read 763988 spots for SRR6257527.sra Written 763988 spots for SRR6257527.sra Read 763988 spots for SRR6257527.sra Written 763988 spots for SRR6257527.sra Read 763988 spots for SRR6257527.sra Written 763988 spots for SRR6257527.sra Read 763988 spots for SRR6257527.sra Written 763988 spots for SRR6257527.sra Read 763990 spots for SRR6257527.sra Written 763990 spots for SRR6257527.sra Read 763988 spots for SRR6257527.sra Written 763988 spots for SRR6257527.sra Read 763988 spots for SRR6257527.sra Written 763988 spots for SRR6257527.sra Read 763988 spots for SRR6257527.sra Written 763988 spots for SRR6257527.sra Read 763988 spots for SRR6257527.sra Written 763988 spots for SRR6257527.sra SRR ids: ['SRR6257527.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_uj6zyf9k SRR6257527.sra spots: 15279762 blocks: [[1, 763988], [763989, 1527976], [1527977, 2291964], [2291965, 3055952], [3055953, 3819940], [3819941, 4583928], [4583929, 5347916], [5347917, 6111904], [6111905, 6875892], [6875893, 7639880], [7639881, 8403868], [8403869, 9167856], [9167857, 9931844], [9931845, 10695832], [10695833, 11459820], [11459821, 12223808], [12223809, 12987796], [12987797, 13751784], [13751785, 14515772], [14515773, 15279762]] SRR6257527 file size 5156109 SRR6257527 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 SRR6257527 SRR6257527_1.fastq SRR6257527_2.fastq Input file: SRR6257527_1.fastq Paired file: SRR6257527_2.fastq trimmed: SRR6257527-trimmed-pair1.fastq, SRR6257527-trimmed-pair2.fastq Parameters used: -- 3' end adapter sequence (-x): AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -- paired 3' end adapter sequence (-y): AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA -- 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 -- number of concurrent threads (-t): 20 Sat Dec 7 09:05:54 2024 >> started Sat Dec 7 09:07:46 2024 >> done (112.854s) 15279762 read pairs processed; of these: 9403 ( 0.06%) short read pairs filtered out after trimming by size control 12269 ( 0.08%) empty read pairs filtered out after trimming by size control 15258090 (99.86%) read pairs available; of these: 8814748 (57.77%) trimmed read pairs available after processing 6443342 (42.23%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 7 0.00% 19 4 0.00% 20 4 0.00% 21 2 0.00% 22 2 0.00% 23 2 0.00% 24 8 0.00% 25 9 0.00% 26 10 0.00% 27 26 0.00% 28 19 0.00% 29 25 0.00% 30 30 0.00% 31 39 0.00% 32 56 0.00% 33 45 0.00% 34 45 0.00% 35 52 0.00% 36 80 0.00% 37 95 0.00% 38 93 0.00% 39 138 0.00% 40 164 0.00% 41 186 0.00% 42 212 0.00% 43 189 0.00% 44 203 0.00% 45 193 0.00% 46 257 0.00% 47 323 0.00% 48 384 0.00% 49 432 0.00% 50 477 0.00% 51 524 0.00% 52 618 0.00% 53 586 0.00% 54 659 0.00% 55 779 0.01% 56 752 0.00% 57 863 0.01% 58 1035 0.01% 59 1195 0.01% 60 1474 0.01% 61 1651 0.01% 62 1775 0.01% 63 2133 0.01% 64 2389 0.02% 65 2593 0.02% 66 2787 0.02% 67 3157 0.02% 68 3650 0.02% 69 4460 0.03% 70 4614 0.03% 71 4632 0.03% 72 6128 0.04% 73 6571 0.04% 74 6378 0.04% 75 7035 0.05% 76 8006 0.05% 77 7897 0.05% 78 7668 0.05% 79 8132 0.05% 80 9012 0.06% 81 9690 0.06% 82 10791 0.07% 83 12012 0.08% 84 13178 0.09% 85 15539 0.10% 86 15682 0.10% 87 16295 0.11% 88 18040 0.12% 89 18033 0.12% 90 19060 0.12% 91 19478 0.13% 92 22343 0.15% 93 23505 0.15% 94 24884 0.16% 95 26642 0.17% 96 27547 0.18% 97 29112 0.19% 98 29211 0.19% 99 30482 0.20% 100 30913 0.20% 101 33708 0.22% 102 35965 0.24% 103 37034 0.24% 104 39798 0.26% 105 39546 0.26% 106 43641 0.29% 107 47953 0.31% 108 41854 0.27% 109 43803 0.29% 110 43125 0.28% 111 45620 0.30% 112 47682 0.31% 113 45754 0.30% 114 48119 0.32% 115 48316 0.32% 116 49809 0.33% 117 48767 0.32% 118 47553 0.31% 119 48762 0.32% 120 50616 0.33% 121 51762 0.34% 122 53626 0.35% 123 56016 0.37% 124 58291 0.38% 125 60117 0.39% 126 60597 0.40% 127 61332 0.40% 128 61681 0.40% 129 65263 0.43% 130 64811 0.42% 131 68369 0.45% 132 67807 0.44% 133 67458 0.44% 134 71950 0.47% 135 73356 0.48% 136 80119 0.53% 137 81050 0.53% 138 86287 0.57% 139 93513 0.61% 140 97006 0.64% 141 107722 0.71% 142 112930 0.74% 143 128873 0.84% 144 147927 0.97% 145 178664 1.17% 146 219482 1.44% 147 287749 1.89% 148 430635 2.82% 149 821715 5.39% 150 3585814 23.50% 151 6443342 42.23% 15258090 reads passed initial QC criterion=sequence-density sequence-density=2.96 sequence-density-rank=1 fanout-score=1.92 fanout-score-rank=34 prefix-density=2.85 prefix-fanout=1.9 sequence=CCAGCCTCACGC criterion=fanout-score sequence-density=0.01 sequence-density-rank=34 fanout-score=88.41 fanout-score-rank=1 prefix-density=0.17 prefix-fanout=5.1 sequence=AAAAAAAAGGGGGGGTAAGGACCCGCTAAGCTCCTACTTTTTCATGTTTCCAATCCGATCCCTCCGATTACTATAGAGATGAACCCAATCCAGAATATGAACCATAAAAGAAAACACCTACTAAACCAATCACAAGAATACCAGTTACCGTACCTATCAGCCAAAGAGGAATTCTTCCAGTAGTATCGGCCATTTCCCCTACTTTCCTCCACATTTTATCAAGTGGTCATGCTAGAGACAAAAACAGTCATGGATAGTTATGTTATAAGGATGGTATCCTTCCAAATGGGATAAGAGAGTTCTTACTACTCTCTTCTTTTCTCTCAATTAAAGAAGTAATTGGAAAACAAAACAGCAAGTACAAAAATGAGTAATAAACCCCAGTATAGACTGGTACGATTCAATTCAACATTTTGTTCATTCGGGTTTGATTGTGTCATAGTTCTATAGTTGGAATTTAGTTTATCGTTGGATGAACTGCATTGCTGATATTGATCCCAAGAAAAAAACA criterion=sequence-density sequence-density=1.65 sequence-density-rank=1 fanout-score=1.71 fanout-score-rank=33 prefix-density=2.81 prefix-fanout=1.0 sequence=TTGCGTAGTGGGCCGTTGGAGCTTAAGCGAAAGCTAGGCTTCGCGGCCCATAATGTTGGCAGGCACAGCGTGAGGCTG criterion=fanout-score sequence-density=0.01 sequence-density-rank=31 fanout-score=89.45 fanout-score-rank=1 prefix-density=1.18 prefix-fanout=1.1 sequence=AGAAGGGGTGCCCCCTCACAAAAGGGGGTCGCAGTGACCAGGCCCGGGCGACTGTTTACCAAAAACACAGGTCTCCGCAAAGTCGTAAGACCATGTATGGGGGCTGACGCCTGCCCAGTGCCGGAAGGTCAAGGAAGTTGGTGAACTGATGACAGGGAAGCCGGCGACCGAAGCCCCGGTGAACGGCGGCCGTAAC Potential 3prime adapter identified. Now checking if in reference sequence /dee2/code/volunteer_pipeline.sh: line 905: -f: command not found /dee2/code/volunteer_pipeline.sh: line 906: -f: command not found 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 CCAGCCTCACGC -y TTGCGTAGTGGGCCGTTGGAGCTTAAGCGAAAGCTAGGCTTCGCGGCCCATAATGTTGGCAGGCACAGCGTGAGGCTG -o SRR6257527 SRR6257527_1.fastq SRR6257527_2.fastq Input file: SRR6257527_1.fastq Paired file: SRR6257527_2.fastq trimmed: SRR6257527-trimmed-pair1.fastq, SRR6257527-trimmed-pair2.fastq Parameters used: -- 3' end adapter sequence (-x): CCAGCCTCACGC -- paired 3' end adapter sequence (-y): TTGCGTAGTGGGCCGTTGGAGCTTAAGCGAAAGCTAGGCTTCGCGGCCCATAATGTTGGCAGGC -- 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 -- number of concurrent threads (-t): 20 Sat Dec 7 09:16:04 2024 >> started Sat Dec 7 09:16:43 2024 >> done (39.109s) 5086030 read pairs processed; of these: 981 ( 0.02%) short read pairs filtered out after trimming by size control 3259 ( 0.06%) empty read pairs filtered out after trimming by size control 5081790 (99.92%) read pairs available; of these: 2008 ( 0.04%) trimmed read pairs available after processing 5079782 (99.96%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 1 0.00% 19 2 0.00% 20 0 0.00% 21 1 0.00% 22 0 0.00% 23 0 0.00% 24 1 0.00% 25 1 0.00% 26 3 0.00% 27 10 0.00% 28 5 0.00% 29 9 0.00% 30 15 0.00% 31 10 0.00% 32 16 0.00% 33 14 0.00% 34 11 0.00% 35 15 0.00% 36 33 0.00% 37 37 0.00% 38 23 0.00% 39 49 0.00% 40 58 0.00% 41 72 0.00% 42 77 0.00% 43 50 0.00% 44 73 0.00% 45 68 0.00% 46 96 0.00% 47 111 0.00% 48 138 0.00% 49 138 0.00% 50 158 0.00% 51 183 0.00% 52 216 0.00% 53 204 0.00% 54 205 0.00% 55 263 0.01% 56 245 0.00% 57 300 0.01% 58 329 0.01% 59 448 0.01% 60 496 0.01% 61 521 0.01% 62 588 0.01% 63 721 0.01% 64 783 0.02% 65 909 0.02% 66 924 0.02% 67 1031 0.02% 68 1199 0.02% 69 1507 0.03% 70 1555 0.03% 71 1539 0.03% 72 2069 0.04% 73 2152 0.04% 74 2072 0.04% 75 2364 0.05% 76 2697 0.05% 77 2665 0.05% 78 2582 0.05% 79 2788 0.05% 80 2893 0.06% 81 3285 0.06% 82 3571 0.07% 83 3906 0.08% 84 4367 0.09% 85 5031 0.10% 86 5253 0.10% 87 5406 0.11% 88 6103 0.12% 89 6091 0.12% 90 6355 0.13% 91 6616 0.13% 92 7514 0.15% 93 7791 0.15% 94 8342 0.16% 95 8965 0.18% 96 9240 0.18% 97 9454 0.19% 98 9701 0.19% 99 10197 0.20% 100 10362 0.20% 101 11173 0.22% 102 12171 0.24% 103 12382 0.24% 104 13271 0.26% 105 13353 0.26% 106 14624 0.29% 107 15981 0.31% 108 14006 0.28% 109 14537 0.29% 110 14308 0.28% 111 15380 0.30% 112 15839 0.31% 113 15336 0.30% 114 16035 0.32% 115 15964 0.31% 116 16749 0.33% 117 16321 0.32% 118 15829 0.31% 119 16250 0.32% 120 16842 0.33% 121 17131 0.34% 122 17951 0.35% 123 18823 0.37% 124 19462 0.38% 125 20123 0.40% 126 20308 0.40% 127 20627 0.41% 128 20725 0.41% 129 21698 0.43% 130 21573 0.42% 131 22762 0.45% 132 22565 0.44% 133 22460 0.44% 134 23985 0.47% 135 24510 0.48% 136 26633 0.52% 137 27064 0.53% 138 28593 0.56% 139 31100 0.61% 140 32573 0.64% 141 35799 0.70% 142 37819 0.74% 143 42945 0.85% 144 48931 0.96% 145 59290 1.17% 146 73057 1.44% 147 95838 1.89% 148 143370 2.82% 149 273696 5.39% 150 1193681 23.49% 151 2145054 42.21% criterion=sequence-density sequence-density=2.98 sequence-density-rank=1 fanout-score=1.94 fanout-score-rank=31 prefix-density=2.93 prefix-fanout=1.9 sequence=CCAGCCTCACGC criterion=fanout-score sequence-density=0.01 sequence-density-rank=34 fanout-score=118.58 fanout-score-rank=1 prefix-density=0.18 prefix-fanout=5.9 sequence=AAAAAAAAGGGGGGGTAAGGACCCGCTAAGCTCCTACTTTTTCATGTTTCCAATCCGATCCCTCCGATTACTATAGAGATGAACCCAATCCAGAATATGAACCATAAAAGAAAACACCTACTAAACCAATCACAAGAATACCAGTTACCGTACCTATCAGCCAAAGAGGAATTCTTCCAGTAGTATCGGCCATTTCCCCTACTTTCCTCCACATTTTATCAAGTGGTCATGCTAGAGACAAAAACAGTCATGGATAGTTATGTTATAAGGATGGTATCCTTCCAAATGGGATAAGAGAGTTCTTACTACTCTCTTCTTTTCTCTCAATTAAAGAAGTAATTGGAAAACAAAACAGCAAGTACAAAAATGAGTAATAAACCCCAGTATAGACTGGTACGATTCAATTCAACATTTTGTTCATTCGGGTTTGATTGTGTCATAGTTCTATAGTTGGAATTTAGTTTATCGTTGGATGAACTGCATTGCTGATATTGATCCCAAGAAAAAAACA criterion=sequence-density sequence-density=1.65 sequence-density-rank=1 fanout-score=1.73 fanout-score-rank=30 prefix-density=2.82 prefix-fanout=1.0 sequence=TTGCGTAGTGGGCCGTTGGAGCTTAAGCGAAAGCTAGGCTTCGCGGCCCATAATGTTGGCAGGCACAGCGTGAGGCTG criterion=fanout-score sequence-density=0.02 sequence-density-rank=29 fanout-score=79.04 fanout-score-rank=1 prefix-density=1.19 prefix-fanout=1.1 sequence=AGAAGGGGTGCCCCCTCACAAAAGGGGGTCGCAGTGACCAGGCCCGGGCGACTGTTTACCAAAAACACAGGTCTCCGCAAAGTCGTAAGACCATGTATGGGGGCTGACGCCTGCCCAGTGCCGGAAGGTCAAGGAAGTTGGTGAACTGATGACAGGGAAGCCGGCGACCGAAGCCCCGGTGAACGGCGGCCGTAAC SRR6257527 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 07 09:21:40 Started mapping on | Dec 07 09:21:41 Finished on | Dec 07 09:34:09 Mapping speed, Million of reads per hour | 73.41 Number of input reads | 15253850 Average input read length | 287 UNIQUE READS: Uniquely mapped reads number | 8415914 Uniquely mapped reads % | 55.17% Average mapped length | 289.75 Number of splices: Total | 1918460 Number of splices: Annotated (sjdb) | 1746977 Number of splices: GT/AG | 1838752 Number of splices: GC/AG | 23395 Number of splices: AT/AC | 5662 Number of splices: Non-canonical | 50651 Mismatch rate per base, % | 0.20% Deletion rate per base | 0.01% Deletion average length | 1.67 Insertion rate per base | 0.01% Insertion average length | 2.27 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 5793456 % of reads mapped to multiple loci | 37.98% Number of reads mapped to too many loci | 80826 % of reads mapped to too many loci | 0.53% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 3.99% % of reads unmapped: other | 2.33% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 1050307 1050307 1050307 N_multimapping 5793456 5793456 5793456 N_noFeature 3356214 8086726 3501743 N_ambiguous 407586 5470 232918 UnstrandedReadsAssigned:4652114 PositiveStrandReadsAssigned:323718 NegativeStrandReadsAssigned:4681253 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=144 echo kmer=139 SRR6257527 Starting Kallisto paired end mapping to ensembl reference transcriptome [quant] fragment length distribution will be estimated from the data [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 paired-end mode [quant] will process pair 1: SRR6257527-trimmed-pair1.fastq SRR6257527-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 15,253,850 reads, 7,436,485 reads pseudoaligned [quant] estimated average fragment length: 210.972 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 965 rounds 52973 SRR6257527.ke.tsv 35125 SRR6257527.se.tsv 88098 total ==> SRR6257527.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 726.523 0 0 PNS24247 1044 834.028 3.76054 0.504977 PNS24249 1928 1718.03 0 0 PNS24246 1044 834.028 3.76054 0.504977 PNS24248 1044 834.028 3.76054 0.504977 PNS24244 1471 1261.03 9.71839 0.863123 PNS24243 293 112.101 0 0 KQK14069 1603 1393.03 596.355 47.9455 KQK14071 474 270.174 7.85896 3.2578 ==> SRR6257527.se.tsv <== BRADI_1g14170v3 790 BRADI_1g53295v3 4 BRADI_1g59795v3 33 BRADI_1g07683v3 0 BRADI_1g00485v3 2 BRADI_1g20270v3 212 BRADI_1g74790v3 22 BRADI_1g09890v3 1 BRADI_1g77505v3 31 BRADI_1g48960v3 0 SRR6257527 completed mapping pipeline successfully