Starting /dee2/code/volunteer_pipeline.sh SRR12682214 current disk space = 1547297075200 free memory = 1600344676 SRR12682214 SRAfilesize e60ff960f52e1f3a1f5b8df987d52008 SRR12682214.sra SRR12682214.sra file validated SRR12682214 is single end SRR12682214 is conventional basespace SRR12682214 read1 length is 54-150 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12682214_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 54-150 %GC 52 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 31.5675 32.0 32.0 32.0 32.0 32.0 2 31.5645 32.0 32.0 32.0 32.0 32.0 3 31.559 32.0 32.0 32.0 32.0 32.0 4 31.609 32.0 32.0 32.0 32.0 32.0 5 31.579 32.0 32.0 32.0 32.0 32.0 6 34.78725 36.0 36.0 36.0 36.0 36.0 7 35.25875 36.0 36.0 36.0 36.0 36.0 8 35.1805 36.0 36.0 36.0 36.0 36.0 9 35.0935 36.0 36.0 36.0 36.0 36.0 10-14 35.11364999999999 36.0 36.0 36.0 36.0 36.0 15-19 35.02675000000001 36.0 36.0 36.0 36.0 36.0 20-24 34.95865 36.0 36.0 36.0 35.2 36.0 25-29 34.8107 36.0 36.0 36.0 33.6 36.0 30-34 34.742650000000005 36.0 36.0 36.0 32.0 36.0 35-39 34.74849999999999 36.0 36.0 36.0 32.0 36.0 40-44 34.6999 36.0 36.0 36.0 32.0 36.0 45-49 34.51865 36.0 36.0 36.0 32.0 36.0 50-54 34.4863 36.0 36.0 36.0 32.0 36.0 55-59 34.32085401759747 36.0 36.0 36.0 32.0 36.0 60-64 34.13605942200204 36.0 36.0 36.0 32.0 36.0 65-69 34.07081515221503 36.0 36.0 36.0 32.0 36.0 70-74 34.078069076994595 36.0 36.0 36.0 31.0 36.0 75-79 34.01998662072667 36.0 36.0 36.0 31.0 36.0 80-84 33.9113353898438 36.0 36.0 36.0 30.0 36.0 85-89 33.764457570949695 36.0 36.0 36.0 27.0 36.0 90-94 33.84150087223514 36.0 36.0 36.0 29.0 36.0 95-99 33.79654206699204 36.0 36.0 36.0 28.0 36.0 100-104 33.647105169566856 36.0 36.0 36.0 27.0 36.0 105-109 33.31049654281942 36.0 33.6 36.0 27.0 36.0 110-114 33.225153743302016 36.0 32.8 36.0 27.0 36.0 115-119 32.766467214744004 36.0 32.0 36.0 27.0 36.0 120-124 32.23248700833148 34.4 32.0 36.0 24.6 36.0 125-129 32.17518701419685 34.4 32.0 36.0 24.6 36.0 130-134 31.759349337801854 33.6 32.0 36.0 22.2 36.0 135-139 31.555040502693053 32.8 32.0 36.0 21.0 36.0 140-144 31.84894892421972 35.2 32.0 36.0 22.2 36.0 145-149 31.58682996331073 32.0 32.0 36.0 21.0 36.0 150 26.104536489151872 27.0 14.0 32.0 14.0 36.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 18 2.0 19 0.0 20 2.0 21 4.0 22 6.0 23 16.0 24 14.0 25 20.0 26 54.0 27 71.0 28 88.0 29 116.0 30 130.0 31 170.0 32 229.0 33 380.0 34 883.0 35 1815.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 31.7 8.774999999999999 9.025 50.5 2 23.05 12.55 30.725 33.675 3 21.875 13.775 21.025 43.325 4 27.35 21.8 18.525 32.324999999999996 5 27.650000000000002 26.6 22.2 23.549999999999997 6 22.045855379188712 31.065759637188208 24.666162761400855 22.22222222222222 7 18.9 21.975 37.75 21.375 8 20.125 19.275000000000002 31.624999999999996 28.975 9 20.125 19.225 33.900000000000006 26.75 10-14 22.85 24.935 24.7 27.515 15-19 23.064999999999998 23.375 26.5 27.060000000000002 20-24 23.65 24.025 25.040000000000003 27.284999999999997 25-29 23.535 23.419999999999998 24.58 28.465 30-34 23.135 23.14 24.9 28.825 35-39 23.835 23.39 24.675 28.1 40-44 24.785 23.669999999999998 24.01 27.534999999999997 45-49 24.075 23.715 24.865000000000002 27.345000000000002 50-54 22.965 24.39 24.945 27.700000000000003 55-59 23.130034522439587 23.095011757642467 25.18136788912793 28.593585830790012 60-64 22.99449173760641 22.213319979969956 26.179268903355034 28.6129193790686 65-69 22.55137844611529 23.66416040100251 25.50375939849624 28.280701754385966 70-74 23.635541260428184 22.600261332797267 26.037792742989247 27.726404663785303 75-79 24.67584884718228 23.09671560466172 24.827203471066042 27.400232077089953 80-84 23.643175374645605 23.00526528959093 24.60004050222762 28.751518833535844 85-89 23.606590724165986 22.853946297803095 24.577908868999188 28.961554109031734 90-94 24.64437939711395 22.805936424793302 24.53140245468084 28.018281723411903 95-99 23.047628984297564 23.110230058949348 25.45777035839115 28.38437059836194 100-104 24.056301983365323 23.021966304116013 24.5361484325016 28.385583280017062 105-109 23.79281995067142 23.40367223896958 25.530282269114824 27.273225541244177 110-114 25.028376844494893 23.1838819523269 24.040862656072644 27.746878547105563 115-119 24.322561517936556 22.875778238956418 25.31870738215239 27.48295286095464 120-124 23.866259122949284 23.367225999625727 24.652236292183893 28.1142785852411 125-129 23.510785671878093 23.801042285111155 22.98964311630055 29.698528926710203 130-134 24.583830863243662 22.771651331038843 24.26072908618389 28.38378871953361 135-139 25.490640096618357 23.641304347826086 23.91304347826087 26.955012077294686 140-144 24.284087211194272 22.80344939798243 24.048161405792385 28.864301985030917 145-149 25.52831029870709 22.987070887204634 23.23673651359786 28.247882300490414 150 26.232741617357004 0.0 33.13609467455622 40.63116370808679 >>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 0.0 20 0.0 21 0.0 22 0.0 23 0.0 24 0.0 25 0.5 26 1.5 27 1.0 28 1.0 29 2.0 30 1.0 31 0.0 32 1.5 33 6.5 34 10.5 35 15.0 36 34.0 37 48.0 38 44.0 39 59.0 40 72.0 41 73.5 42 86.5 43 103.5 44 113.5 45 124.5 46 155.5 47 183.5 48 205.5 49 222.5 50 211.0 51 192.0 52 198.5 53 211.5 54 191.0 55 171.0 56 166.5 57 156.0 58 129.5 59 99.0 60 84.5 61 83.5 62 79.0 63 67.5 64 66.0 65 53.5 66 46.5 67 43.5 68 36.0 69 30.0 70 29.0 71 28.5 72 20.5 73 15.0 74 10.0 75 9.5 76 9.5 77 8.5 78 9.0 79 5.0 80 1.5 81 1.0 82 0.5 83 0.5 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 0.775 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 0.015007503751875937 60-64 0.020026033843997197 65-69 0.005012280086211217 70-74 0.02512184092850324 75-79 0.0 80-84 0.0050625221485344 85-89 0.005085176709890668 90-94 0.015403573629081948 95-99 0.026076979242724525 100-104 0.026651031394914985 105-109 0.016440157825515125 110-114 0.005675046819136258 115-119 0.011857473172466947 120-124 0.0062375249500997995 125-129 0.013191741969527075 130-134 0.007023458350891979 135-139 0.007547739452034115 140-144 0.008134710811030668 145-149 0.0 150 0.0 >>END_MODULE >>Sequence Length Distribution warn #Length Count 54-55 2.0 56-57 0.0 58-59 2.0 60-61 1.0 62-63 2.0 64-65 2.0 66-67 1.0 68-69 4.0 70-71 6.0 72-73 4.0 74-75 8.0 76-77 7.0 78-79 4.0 80-81 7.0 82-83 6.0 84-85 6.0 86-87 9.0 88-89 13.0 90-91 20.0 92-93 21.0 94-95 26.0 96-97 25.0 98-99 39.0 100-101 27.0 102-103 49.0 104-105 38.0 106-107 44.0 108-109 44.0 110-111 58.0 112-113 57.0 114-115 70.0 116-117 60.0 118-119 54.0 120-121 79.0 122-123 74.0 124-125 67.0 126-127 65.0 128-129 76.0 130-131 72.0 132-133 84.0 134-135 79.0 136-137 78.0 138-139 70.0 140-141 82.0 142-143 77.0 144-145 69.0 146-147 102.0 148-149 689.0 150-151 1521.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 77.4 #Duplication Level Percentage of deduplicated Percentage of total 1 86.46640826873386 66.925 2 7.525839793281654 11.65 3 2.5193798449612403 5.8500000000000005 4 1.3888888888888888 4.3 5 0.710594315245478 2.75 6 0.6136950904392765 2.85 7 0.2583979328165375 1.4000000000000001 8 0.16149870801033592 1.0 9 0.09689922480620156 0.675 >10 0.2583979328165375 2.6 >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 CTCAGAGCCAATCCTTTTCCCGAAGTTACGGATCCGTTTTGCCGACTTCC 16 0.4 No Hit CCTAATTCTCCGTCACCCGTCACCACCATGGTAGGCCCCTATCCTACCAT 14 0.35000000000000003 No Hit CCCGACTGTCCCTATTAATCATTACTCCGATCCCGAAGGCCAACACAATA 14 0.35000000000000003 No Hit CCGACATCGAAGGATCAAAAAGCAACGTCGCTATGAACGCTTGGCTGCCA 14 0.35000000000000003 No Hit CCCGGAACCCAAAGACTTTGATTTCTCATAAGGTGCCGGCGGAGTCCTAT 12 0.3 No Hit CCGGAACCCAAAGACTTTGATTTCTCATAAGGTGCCGGCGGAGTCCTATA 12 0.3 No Hit CAGCCTTTTATCTAATAAATGCGCCCCTCCCAGAAGTCGGGGTTTGTTGC 12 0.3 No Hit GTCCTTTTCATCTTTCCCTCGCGGTACTTGTTCGCTATCGGTCTCTCGCC 10 0.25 No Hit CCCCGGAACCCAAAGACTTTGATTTCTCATAAGGTGCCGGCGGAGTCCTA 9 0.22499999999999998 No Hit CTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATT 9 0.22499999999999998 No Hit CCGAAGGCCAACACAATAGGACCGGAATCCTATGATGTTATCCCATGCTA 9 0.22499999999999998 No Hit CCCGTGTCAGGATTGGGTAATTTGCGCGCCTGCTGCCTTCCTTGGATGTG 8 0.2 No Hit GCCCGGTATTGTTATTTATTGTCACTACCTCCCCGTGTCAGGATTGGGTA 8 0.2 No Hit GTCAATTCCTTTAAGTTTCAGCCTTGCGACCATACTCCCCCCGGAACCCA 8 0.2 No Hit CCTCGCGGTACTTGTTCGCTATCGGTCTCTCGCCTGTATTTAGCCTTGGA 8 0.2 No Hit CCCATCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCT 8 0.2 No Hit CTGACTATGAAATACGAATGCCCCCGACTGTCCCTATTAATCATTACTCC 7 0.17500000000000002 No Hit CTAGAATTACTACGGTTATCCGAGTAGCACGTACCATCAAACAAACTATA 7 0.17500000000000002 No Hit CGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACT 7 0.17500000000000002 No Hit CCCGAAGTTACGGATCCGTTTTGCCGACTTCCCTTGCCTACATTGTTCCA 7 0.17500000000000002 No Hit CTCTGACTATGAAATACGAATGCCCCCGACTGTCCCTATTAATCATTACT 7 0.17500000000000002 No Hit CGCATAGCTAGTTAGCAGGCTGAGGTCTCGTTCGTTAACGGAATTAACCA 7 0.17500000000000002 No Hit GCCACGCTTTCACGGTTCGTATTCGTACTGGAAATCAGAATCAAACGAGC 7 0.17500000000000002 No Hit CCCCGACTGTCCCTATTAATCATTACTCCGATCCCGAAGGCCAACACAAT 7 0.17500000000000002 No Hit CCCGCGTCAGCCTTTTATCTAATAAATGCGCCCCTCCCAGAAGTCGGGGT 6 0.15 No Hit CTTGTTACGACTTCTCCTTCCTCTAAATGATAAGGTTCAATGGACTTCTC 6 0.15 No Hit CCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAAT 6 0.15 No Hit CTGTTATTGCCTCAAACTTCCGTCGCCTAAACGGCGATAGTCCCTCTAAG 6 0.15 No Hit CCACGCTTTCACGGTTCGTATTCGTACTGGAAATCAGAATCAAACGAGCT 6 0.15 No Hit CCCAACTTTCGTTCTTGATTAATGAAAACATCCTTGGCAAATGCTTTCGC 6 0.15 No Hit GCTGGAATTACCGCGGCTGCTGGCACCAGACTTGCCCTCCAATGGATCCT 6 0.15 No Hit CGGTATTGTTATTTATTGTCACTACCTCCCCGTGTCAGGATTGGGTAATT 6 0.15 No Hit GGCATCGTTTATGGTTGAGACTAGGACGGTATCTGATCGTCTTCGAGCCC 6 0.15 No Hit CTTTAAGTTTCAGCCTTGCGACCATACTCCCCCCGGAACCCAAAGACTTT 6 0.15 No Hit GCAGAAATTTGAATGATGCGTCGCCGGCACGAGGGCCGTGCGATCCGTCG 6 0.15 No Hit CCCTGGTCGGCATCGTTTATGGTTGAGACTAGGACGGTATCTGATCGTCT 6 0.15 No Hit CGGAAACCTTGTTACGACTTCTCCTTCCTCTAAATGATAAGGTTCAATGG 6 0.15 No Hit GCTCATCTTAGGACACCTGCGTTATCTTTTAACAGATGTGCCGCCCCAGC 6 0.15 No Hit CAACAACTTAAATATACGCTATTGGAGCTGGAATTACCGCGGCTGCTGGC 6 0.15 No Hit CGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCAT 6 0.15 No Hit GTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCAT 6 0.15 No Hit CGCGGCACGGTCATCAGTAGGGTAAAACTAACCTGTCTCACGACGGTCTA 6 0.15 No Hit ATCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCTATA 6 0.15 No Hit GTTCGATTAGTCTTTCGCCCCTATACCCAAGTCAGACGAACGATTTGCAC 5 0.125 No Hit GTCGCCGGCACGAGGGCCGTGCGATCCGTCGAGTTATCATGAATCATCGG 5 0.125 No Hit CTCCCACTTATCCTACACCTCTCAAGTCATTTCACAAAGTCGGACTAGAG 5 0.125 No Hit CTTGGCAAATGCTTTCGCAGTTGTTCGTCTTTCATAAATCCAAGAATTTC 5 0.125 No Hit GTCGGCATCGTTTATGGTTGAGACTAGGACGGTATCTGATCGTCTTCGAG 5 0.125 No Hit CTCGCGGTACTTGTTCGCTATCGGTCTCTCGCCTGTATTTAGCCTTGGAC 5 0.125 No Hit GGCTTGCTTTGAGCACTCTAATTTCTTCAAAGTAACGATGCCGGAGGCAC 5 0.125 No Hit CCCTTTTGTTCCACACGAGATTTCTGTTCTCGTTGAGCTCATCTTAGGAC 5 0.125 No Hit CTTTTGTTCCACACGAGATTTCTGTTCTCGTTGAGCTCATCTTAGGACAC 5 0.125 No Hit CAACTACGAGCTTTTTAACTGCAACAACTTAAATATACGCTATTGGAGCT 5 0.125 No Hit CTTTTATCTAATAAATGCGCCCCTCCCAGAAGTCGGGGTTTGTTGCACGT 5 0.125 No Hit CCGGAATCGAACCCTAATTCTCCGTCACCCGTCACCACCATGGTAGGCCC 5 0.125 No Hit GCCCGTTCCCTTGGCTGTGGTTTCGCTGGATAGTAGACAGGGACAGTGGG 5 0.125 No Hit GTCGGGGCAGGCGGCGGGCGCAGGCGCCGCTTGCTAGCTTGGATTCTGAC 5 0.125 No Hit CCCATGCTAATGTATCCAGAGCGATGGCTTGCTTTGAGCACTCTAATTTC 5 0.125 No Hit CACTTATCCTACACCTCTCAAGTCATTTCACAAAGTCGGACTAGAGTCAA 5 0.125 No Hit CGTCAATTCCTTTAAGTTTCAGCCTTGCGACCATACTCCCCCCGGAACCC 5 0.125 No Hit CTGGCTTCGCCCCGCTCAGGCATAGTTCACCATCTTTCGGGTCCCGACAG 5 0.125 No Hit CTCCGTCACCCGTCACCACCATGGTAGGCCCCTATCCTACCATCGAAAGT 5 0.125 No Hit GCCGACATCGAAGGATCAAAAAGCAACGTCGCTATGAACGCTTGGCTGCC 5 0.125 No Hit GTGCGACGTGGGGCTGGATCTCAGTGGATCGTGGCAGCAAGGCCACTCTG 5 0.125 No Hit GCCGCAGGCTCCACGCCTGGTGGTGCCCTTCCGTCAATTCCTTTAAGTTT 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 82-83 0.0 0.0 0.0 0.0 0.0 84-85 0.0 0.0 0.0 0.0 0.0 86-87 0.0 0.0 0.0 0.0 0.0 88-89 0.0 0.0 0.0 0.0 0.0 90-91 0.0 0.0 0.0 0.0 0.0 92-93 0.0 0.0 0.0 0.0 0.0 94-95 0.0 0.0 0.0 0.0 0.0 96-97 0.0 0.0 0.0 0.0 0.0 98-99 0.0 0.0 0.0 0.0 0.0 100-101 0.0 0.0 0.0 0.0 0.0 102-103 0.0 0.0 0.0 0.0 0.0 104-105 0.0 0.0 0.0 0.0 0.0 106-107 0.0 0.0 0.0 0.0 0.0 108-109 0.0 0.0 0.0 0.0 0.0 110-111 0.0 0.0 0.0 0.0 0.0 112-113 0.0 0.0 0.0 0.0 0.0 114-115 0.0125 0.0 0.0 0.0 0.0 116-117 0.05 0.0 0.0 0.0 0.0 118-119 0.05 0.0 0.0 0.0 0.0 120-121 0.05 0.0 0.0 0.0 0.0 122-123 0.05 0.0 0.0 0.0 0.0 124-125 0.0625 0.0 0.0 0.0 0.0 126-127 0.075 0.0 0.0 0.0 0.0 128-129 0.075 0.0 0.0 0.0 0.0 130-131 0.075 0.0 0.0 0.0 0.0 132-133 0.075 0.0 0.0 0.0 0.0 134-135 0.075 0.0 0.0 0.0 0.0 136-137 0.075 0.0 0.0 0.0 0.0 138 0.075 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position AAGTCAT 10 0.008784307 133.3 6 CCGGCAG 10 0.008784307 133.3 1 >>END_MODULE Rejected 1332598 READS because READLEN < 1 Read 1332598 spots for SRR12682214.sra Written 1332598 spots for SRR12682214.sra Rejected 1332598 READS because READLEN < 1 Read 1332598 spots for SRR12682214.sra Written 1332598 spots for SRR12682214.sra Rejected 1332598 READS because READLEN < 1 Read 1332598 spots for SRR12682214.sra Written 1332598 spots for SRR12682214.sra Rejected 1332598 READS because READLEN < 1 Read 1332598 spots for SRR12682214.sra Written 1332598 spots for SRR12682214.sra Rejected 1332598 READS because READLEN < 1 Read 1332598 spots for SRR12682214.sra Written 1332598 spots for SRR12682214.sra Rejected 1332598 READS because READLEN < 1 Read 1332598 spots for SRR12682214.sra Written 1332598 spots for SRR12682214.sra Rejected 1332598 READS because READLEN < 1 Read 1332598 spots for SRR12682214.sra Written 1332598 spots for SRR12682214.sra Rejected 1332598 READS because READLEN < 1 Read 1332598 spots for SRR12682214.sra Written 1332598 spots for SRR12682214.sra Rejected 1332603 READS because READLEN < 1 Read 1332603 spots for SRR12682214.sra Written 1332603 spots for SRR12682214.sra Rejected 1332598 READS because READLEN < 1 Read 1332598 spots for SRR12682214.sra Written 1332598 spots for SRR12682214.sra Rejected 1332598 READS because READLEN < 1 Read 1332598 spots for SRR12682214.sra Written 1332598 spots for SRR12682214.sra Rejected 1332598 READS because READLEN < 1 Read 1332598 spots for SRR12682214.sra Written 1332598 spots for SRR12682214.sra Rejected 1332598 READS because READLEN < 1 Read 1332598 spots for SRR12682214.sra Written 1332598 spots for SRR12682214.sra Rejected 1332598 READS because READLEN < 1 Read 1332598 spots for SRR12682214.sra Written 1332598 spots for SRR12682214.sra Rejected 1332598 READS because READLEN < 1 Read 1332598 spots for SRR12682214.sra Written 1332598 spots for SRR12682214.sra Rejected 1332598 READS because READLEN < 1 Read 1332598 spots for SRR12682214.sra Written 1332598 spots for SRR12682214.sra Rejected 1332598 READS because READLEN < 1 Read 1332598 spots for SRR12682214.sra Written 1332598 spots for SRR12682214.sra Rejected 1332598 READS because READLEN < 1 Read 1332598 spots for SRR12682214.sra Written 1332598 spots for SRR12682214.sra Rejected 1332598 READS because READLEN < 1 Read 1332598 spots for SRR12682214.sra Written 1332598 spots for SRR12682214.sra Rejected 1332598 READS because READLEN < 1 Read 1332598 spots for SRR12682214.sra Written 1332598 spots for SRR12682214.sra SRR ids: ['SRR12682214.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_h1hf5q78 SRR12682214.sra spots: 26651965 blocks: [[1, 1332598], [1332599, 2665196], [2665197, 3997794], [3997795, 5330392], [5330393, 6662990], [6662991, 7995588], [7995589, 9328186], [9328187, 10660784], [10660785, 11993382], [11993383, 13325980], [13325981, 14658578], [14658579, 15991176], [15991177, 17323774], [17323775, 18656372], [18656373, 19988970], [19988971, 21321568], [21321569, 22654166], [22654167, 23986764], [23986765, 25319362], [25319363, 26651965]] SRR12682214 file size 8299329 SRR12682214 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 SRR12682214 SRR12682214_1.fastq Input file: SRR12682214_1.fastq trimmed: SRR12682214-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 02:48:55 2024 >> started Sat Dec 7 02:49:13 2024 >> done (18.155s) 26651965 reads processed; of these: 1 ( 0.00%) short reads filtered out after trimming by size control 4160 ( 0.02%) empty reads filtered out after trimming by size control 26647804 (99.98%) reads available; of these: 13392 ( 0.05%) trimmed reads available after processing 26634412 (99.95%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 19 1 0.00% 20 0 0.00% 21 0 0.00% 22 19 0.00% 23 18 0.00% 24 28 0.00% 25 37 0.00% 26 55 0.00% 27 94 0.00% 28 101 0.00% 29 126 0.00% 30 179 0.00% 31 157 0.00% 32 207 0.00% 33 211 0.00% 34 294 0.00% 35 335 0.00% 36 367 0.00% 37 454 0.00% 38 609 0.00% 39 677 0.00% 40 811 0.00% 41 925 0.00% 42 1008 0.00% 43 1003 0.00% 44 992 0.00% 45 1076 0.00% 46 1247 0.00% 47 1501 0.01% 48 1827 0.01% 49 2244 0.01% 50 2420 0.01% 51 2584 0.01% 52 2990 0.01% 53 2934 0.01% 54 2970 0.01% 55 3332 0.01% 56 3561 0.01% 57 4103 0.02% 58 4942 0.02% 59 5250 0.02% 60 5767 0.02% 61 6274 0.02% 62 7014 0.03% 63 6975 0.03% 64 7594 0.03% 65 8179 0.03% 66 8765 0.03% 67 9660 0.04% 68 10272 0.04% 69 11069 0.04% 70 11728 0.04% 71 13732 0.05% 72 14792 0.06% 73 16628 0.06% 74 17659 0.07% 75 18485 0.07% 76 20214 0.08% 77 21119 0.08% 78 22853 0.09% 79 25063 0.09% 80 27096 0.10% 81 29570 0.11% 82 32348 0.12% 83 33739 0.13% 84 37164 0.14% 85 41975 0.16% 86 46576 0.17% 87 49337 0.19% 88 52187 0.20% 89 54104 0.20% 90 58171 0.22% 91 60894 0.23% 92 68529 0.26% 93 74111 0.28% 94 77917 0.29% 95 85830 0.32% 96 92575 0.35% 97 96950 0.36% 98 108714 0.41% 99 109325 0.41% 100 111105 0.42% 101 113779 0.43% 102 122829 0.46% 103 130968 0.49% 104 136903 0.51% 105 138019 0.52% 106 144903 0.54% 107 155445 0.58% 108 148087 0.56% 109 162564 0.61% 110 163739 0.61% 111 172545 0.65% 112 187707 0.70% 113 184777 0.69% 114 198628 0.75% 115 211909 0.80% 116 216536 0.81% 117 208840 0.78% 118 208933 0.78% 119 218737 0.82% 120 232423 0.87% 121 222518 0.84% 122 245197 0.92% 123 253884 0.95% 124 240012 0.90% 125 241567 0.91% 126 248751 0.93% 127 245890 0.92% 128 249972 0.94% 129 266380 1.00% 130 252504 0.95% 131 251260 0.94% 132 255466 0.96% 133 260596 0.98% 134 249535 0.94% 135 254541 0.96% 136 260643 0.98% 137 261018 0.98% 138 251761 0.94% 139 256011 0.96% 140 252031 0.95% 141 244381 0.92% 142 242257 0.91% 143 241941 0.91% 144 249067 0.93% 145 239158 0.90% 146 290522 1.09% 147 468989 1.76% 148 1025675 3.85% 149 3565177 13.38% 150 9939081 37.30% 26647804 reads passed initial QC criterion=sequence-density sequence-density=1.15 sequence-density-rank=1 fanout-score=2.85 fanout-score-rank=30 prefix-density=1.16 prefix-fanout=2.8 sequence=CCCAGCTCACGTTCCCTATTGGTGGGTGAACAATCCAACACTTGGTGAATTCTGCTTCACAATGATAGGAAGAGCCGACATCGAAGGATCAAAAAGCAACGTCGCTATGAACGCTTGGCTGCCACAAGCCAGTTATCCCTGTGGTAACTTTTCTGACACCTCTAGCTTCAAACTCCGAAGATCTAAAGGATCGATAGGCCACGCTTTCACGGTTCGTATTCGTACTGGAAATCAGAATCAAACGAGCTTTTACCCTTTTGTTCCACACGAGATTTCTGTTCTCGTTGAGCTCATCTTAGGACACCTGCGTTATCTTTTAACAGATGTGCCGCCCCAGCCAAACTCCCCACCTGACAATGTCTTCCGCCCGGATCGGCCCGGTCAGACCGGGCCTTGGAGCCAAAAGGAGGGGACTTGCCCCGCTTCCGACCCACGGAATAAGTAAAATAACGTTAAAAGTAGTGGTATTTCACTTGCGCCCGTAAAGGCTCCCACTTATCCTACACCTCTC criterion=fanout-score sequence-density=0.05 sequence-density-rank=26 fanout-score=50.96 fanout-score-rank=1 prefix-density=2.45 prefix-fanout=1.1 sequence=CCCCCGGAATAAGTA Started job on | Dec 07 02:49:34 Started mapping on | Dec 07 02:49:34 Finished on | Dec 07 02:51:13 Mapping speed, Million of reads per hour | 969.01 Number of input reads | 26647804 Average input read length | 136 UNIQUE READS: Uniquely mapped reads number | 9831264 Uniquely mapped reads % | 36.89% Average mapped length | 136.93 Number of splices: Total | 3917893 Number of splices: Annotated (sjdb) | 3697240 Number of splices: GT/AG | 3864634 Number of splices: GC/AG | 47192 Number of splices: AT/AC | 2797 Number of splices: Non-canonical | 3270 Mismatch rate per base, % | 0.24% Deletion rate per base | 0.01% Deletion average length | 1.60 Insertion rate per base | 0.00% Insertion average length | 1.12 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 1110354 % of reads mapped to multiple loci | 4.17% Number of reads mapped to too many loci | 13575068 % of reads mapped to too many loci | 50.94% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.34% % of reads unmapped: other | 6.66% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 15706186 15706186 15706186 N_multimapping 1110354 1110354 1110354 N_noFeature 562394 9581584 640868 N_ambiguous 208228 967 38277 UnstrandedReadsAssigned:9060642 PositiveStrandReadsAssigned:248713 NegativeStrandReadsAssigned:9152119 Dataset is classified negative stranded MeadianReadLen=149 20thPercentileLength=121 echo kmer=117 SRR12682214 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: SRR12682214-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 26,647,804 reads, 9,392,170 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,138 rounds 52973 SRR12682214.ke.tsv 35125 SRR12682214.se.tsv 88098 total ==> SRR12682214.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 837 2.5322 0.480686 PNS24247 1044 945 21.5199 3.61825 PNS24249 1928 1829 82.5069 7.16746 PNS24246 1044 945 21.5199 3.61825 PNS24248 1044 945 21.5199 3.61825 PNS24244 1471 1372 89.401 10.3533 PNS24243 293 194 1 0.819006 KQK14069 1603 1504 7151.86 755.544 KQK14071 474 375 225.646 95.6058 ==> SRR12682214.se.tsv <== BRADI_1g14170v3 7786 BRADI_1g53295v3 63 BRADI_1g59795v3 178 BRADI_1g07683v3 0 BRADI_1g00485v3 3 BRADI_1g20270v3 764 BRADI_1g74790v3 256 BRADI_1g09890v3 1 BRADI_1g77505v3 120 BRADI_1g48960v3 0 SRR12682214 completed mapping pipeline successfully