Starting /dee2/code/volunteer_pipeline.sh SRR6793151 current disk space = 3089321181184 free memory = 1495872876 SRR6793151 SRAfilesize ff26ea85da9dccfefe429ec1db49a778 SRR6793151.sra SRR6793151.sra file validated SRR6793151 is single end SRR6793151 is conventional basespace SRR6793151 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR6793151_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 46 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 31.61625 32.0 32.0 32.0 32.0 32.0 2 31.63825 32.0 32.0 32.0 32.0 32.0 3 31.6425 32.0 32.0 32.0 32.0 32.0 4 31.74875 32.0 32.0 32.0 32.0 32.0 5 31.72575 32.0 32.0 32.0 32.0 32.0 6 35.18075 36.0 36.0 36.0 36.0 36.0 7 35.31375 36.0 36.0 36.0 36.0 36.0 8 35.30525 36.0 36.0 36.0 36.0 36.0 9 35.35125 36.0 36.0 36.0 36.0 36.0 10-14 35.305899999999994 36.0 36.0 36.0 36.0 36.0 15-19 35.340599999999995 36.0 36.0 36.0 36.0 36.0 20-24 35.334849999999996 36.0 36.0 36.0 36.0 36.0 25-29 35.230199999999996 36.0 36.0 36.0 36.0 36.0 30-34 35.178000000000004 36.0 36.0 36.0 36.0 36.0 35-39 35.11135 36.0 36.0 36.0 36.0 36.0 40-44 35.106849999999994 36.0 36.0 36.0 36.0 36.0 45-49 35.00415 36.0 36.0 36.0 36.0 36.0 50-54 35.0543 36.0 36.0 36.0 36.0 36.0 55-59 34.93005000000001 36.0 36.0 36.0 36.0 36.0 60-64 34.8497 36.0 36.0 36.0 34.4 36.0 65-69 34.7672 36.0 36.0 36.0 32.8 36.0 70-74 34.6262 36.0 36.0 36.0 32.0 36.0 75-79 34.636 36.0 36.0 36.0 32.0 36.0 80-84 34.45405 36.0 36.0 36.0 32.0 36.0 85-89 34.5022 36.0 36.0 36.0 32.0 36.0 90-94 34.346000000000004 36.0 36.0 36.0 32.0 36.0 95-99 34.33305 36.0 36.0 36.0 32.0 36.0 100-104 34.30075000000001 36.0 36.0 36.0 32.0 36.0 105-109 34.2082 36.0 36.0 36.0 32.0 36.0 110-114 34.18335 36.0 36.0 36.0 32.0 36.0 115-119 34.09739999999999 36.0 36.0 36.0 32.0 36.0 120-124 34.0088 36.0 36.0 36.0 31.0 36.0 125-129 33.7221 36.0 36.0 36.0 27.0 36.0 130-134 33.73845 36.0 34.4 36.0 28.0 36.0 135-139 33.0135 36.0 32.0 36.0 27.0 36.0 140-144 33.06445 36.0 32.0 36.0 27.0 36.0 145-149 32.28915 36.0 32.0 36.0 25.8 36.0 150-151 29.943625 34.0 29.5 36.0 17.5 36.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 18 1.0 19 3.0 20 4.0 21 4.0 22 4.0 23 8.0 24 20.0 25 14.0 26 23.0 27 51.0 28 48.0 29 73.0 30 95.0 31 118.0 32 156.0 33 269.0 34 699.0 35 2410.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 24.85 13.5 15.325 46.325 2 20.974999999999998 20.7 33.35 24.975 3 21.625 23.875 24.85 29.65 4 25.575 29.45 19.325 25.650000000000002 5 25.4 30.725 22.225 21.65 6 21.239606953892668 33.10657596371882 24.011085915847822 21.642731166540692 7 18.325 16.55 43.9 21.224999999999998 8 21.65 18.875 30.45 29.025000000000002 9 21.325 21.15 32.0 25.525 10-14 22.005 27.765 27.250000000000004 22.98 15-19 24.14 27.075 27.250000000000004 21.535 20-24 22.939999999999998 27.345000000000002 27.115000000000002 22.6 25-29 23.275000000000002 26.845000000000002 25.540000000000003 24.34 30-34 23.66 26.215 25.715 24.41 35-39 23.085 26.735 25.785000000000004 24.395 40-44 22.785 26.305 26.765 24.145 45-49 22.655 26.935 26.945000000000004 23.465 50-54 22.93 27.500000000000004 26.834999999999997 22.735 55-59 22.264999999999997 27.425 27.73 22.58 60-64 21.905 25.985000000000003 29.065 23.044999999999998 65-69 22.939999999999998 27.62 27.195000000000004 22.245 70-74 22.765 26.895000000000003 26.729999999999997 23.61 75-79 23.82857428614292 26.75901385207781 26.46396959543932 22.948442266339953 80-84 23.83572607673453 25.89165124305938 27.002150967935574 23.27047171227052 85-89 23.999599839935975 26.68567426970788 26.850740296118445 22.463985594237695 90-94 23.45672836418209 27.368684342171086 26.728364182091045 22.446223111555778 95-99 22.795515964367933 27.409668701831645 27.099389450505456 22.695425883294966 100-104 23.337333733373335 28.472847284728473 26.017601760176017 22.172217221722175 105-109 23.48465889183643 27.889283747935334 26.072375994794534 22.553681365433707 110-114 24.644573488185824 27.6431718061674 25.0100120144173 22.702242691229475 115-119 24.740978026928275 28.039441413484155 24.27548926372691 22.94409129586065 120-124 24.849969993998798 28.515703140628123 23.71974394878976 22.914582916583317 125-129 24.542950162784873 28.379664412722267 22.58953168044077 24.48785374405209 130-134 24.394757903161267 29.39675870348139 22.739095638255304 23.46938775510204 135-139 24.04207362885049 29.156023040320562 22.163786626596544 24.638116704232406 140-144 24.324053675145205 28.960544762667734 21.59022631684358 25.125175245343478 145-149 23.630633785203344 29.218148166675007 21.37962082937322 25.771597218748436 150-151 22.25838758137206 29.719579369053577 21.357035553329993 26.664997496244368 >>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 0.5 12 1.0 13 0.5 14 0.0 15 0.0 16 0.0 17 0.0 18 0.0 19 0.0 20 0.0 21 0.5 22 1.5 23 1.5 24 1.0 25 2.5 26 3.0 27 3.5 28 7.5 29 11.5 30 14.0 31 18.0 32 23.0 33 32.5 34 37.5 35 55.0 36 95.5 37 98.0 38 93.5 39 114.0 40 131.5 41 141.0 42 153.0 43 176.5 44 215.5 45 244.5 46 258.5 47 255.5 48 224.5 49 204.0 50 180.5 51 154.5 52 152.5 53 155.0 54 123.5 55 100.5 56 103.5 57 104.5 58 92.5 59 56.5 60 40.5 61 30.0 62 20.0 63 16.5 64 5.0 65 3.5 66 3.0 67 5.0 68 6.5 69 8.0 70 7.5 71 2.5 72 1.0 73 1.5 74 1.5 75 1.0 76 0.5 77 0.5 78 1.0 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 0.5 >>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 0.0 60-64 0.0 65-69 0.0 70-74 0.0 75-79 0.015 80-84 0.045 85-89 0.04 90-94 0.05 95-99 0.09 100-104 0.01 105-109 0.105 110-114 0.12 115-119 0.105 120-124 0.02 125-129 0.17500000000000002 130-134 0.04 135-139 0.17500000000000002 140-144 0.13999999999999999 145-149 0.045 150-151 0.15 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 79.85 #Duplication Level Percentage of deduplicated Percentage of total 1 90.54477144646211 72.3 2 4.19536631183469 6.7 3 2.0663744520976834 4.95 4 1.0644959298685035 3.4000000000000004 5 0.7827175954915466 3.125 6 0.37570444583594237 1.7999999999999998 7 0.21916092673763304 1.225 8 0.21916092673763304 1.4000000000000001 9 0.12523481527864747 0.8999999999999999 >10 0.4070131496556042 4.2 >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 CTTCCGTCAATTCCTTTAAGTTTCAGCCTTGCGACCATACTCCCCCCAGA 19 0.475 No Hit CCCGACTGTCCCTGTTAATCATTACTCCGATCCCGAAGGCCAACACAATA 18 0.44999999999999996 No Hit CGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCT 16 0.4 No Hit CCCAACTTTCGTTCTTGATTAATGAAAACATCCTTGGCAAATGCTTTCGC 15 0.375 No Hit CTCCGATCCCGAAGGCCAACACAATAGGATCGAAATCCTATGATGTTATC 15 0.375 No Hit CGCGCCTGCTGCCTTCCTTGGATGTGGTAGCCGTTTCTCAGGCTCCCTCT 12 0.3 No Hit CCAACTTTCGTTCTTGATTAATGAAAACATCCTTGGCAAATGCTTTCGCA 12 0.3 No Hit GTCGGCATCGTTTATGGTTGAGACTAGGACGGTATCTGATCGTCTTCGAG 11 0.27499999999999997 No Hit AGAAATTTGAATGATGCGTCGCCAGCACGAAGGCCGTGCGATCCGTCGAG 10 0.25 No Hit CTGCCAGTAGTCATATGCTTGTCTCAAAGATTAAGCCATGCATGTGTAAG 10 0.25 No Hit CAACTTTCGTTCTTGATTAATGAAAACATCCTTGGCAAATGCTTTCGCAG 10 0.25 No Hit CCGACTGTCCCTGTTAATCATTACTCCGATCCCGAAGGCCAACACAATAG 10 0.25 No Hit CAGAAATTTGAATGATGCGTCGCCAGCACGAAGGCCGTGCGATCCGTCGA 10 0.25 No Hit CTCGTCCCTTCTACCGGCGATGCGCTCCTGGCCTTAACTGGCCGGGTCGT 9 0.22499999999999998 No Hit CGCCTGCTGCCTTCCTTGGATGTGGTAGCCGTTTCTCAGGCTCCCTCTCC 9 0.22499999999999998 No Hit CAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGG 9 0.22499999999999998 No Hit ACCAGGTCCAGACATAGTAAGGATTGACAGACTGAGAGCTCTTTCTTGAT 9 0.22499999999999998 No Hit CTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAAC 8 0.2 No Hit CGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCA 8 0.2 No Hit CTCAAACTTCCTTGGCCTGGAAGGCCATAGTCCCTCTAAGAAGCTGGCCG 8 0.2 No Hit CGTCAATTCCTTTAAGTTTCAGCCTTGCGACCATACTCCCCCCAGAACCC 8 0.2 No Hit CCAGAACCCAAAAACTTTGATTTCTCATAAGGTGCTGGCGGAGTCCTAAA 8 0.2 No Hit CTGCTGCCTTCCTTGGATGTGGTAGCCGTTTCTCAGGCTCCCTCTCCGGA 8 0.2 No Hit CGCGGCTGCTGGCACCAGACTTGCCCTCCAATGGATCCTCGTTAAGGGAT 8 0.2 No Hit GCCGTTCTTAGTTGGTGGAGCGATTTGTCTGGTTAATTCCGTTAACGAAC 7 0.17500000000000002 No Hit CGACCTTTTATCTAATAAATGCGTCCCTTCCAGAAGTCGGGGTTTGTTGC 7 0.17500000000000002 No Hit CGGCCTTCGTGCTGGCGACGCATCATTCAAATTTCTGCCCTATCAACTTT 7 0.17500000000000002 No Hit CCCAGAACCCAAAAACTTTGATTTCTCATAAGGTGCTGGCGGAGTCCTAA 7 0.17500000000000002 No Hit CCCGTGTCAGGATTGGGTAATTTGCGCGCCTGCTGCCTTCCTTGGATGTG 7 0.17500000000000002 No Hit CAGGTCCAGACATAGTAAGGATTGACAGACTGAGAGCTCTTTCTTGATTC 7 0.17500000000000002 No Hit CGACTGTCCCTGTTAATCATTACTCCGATCCCGAAGGCCAACACAATAGG 7 0.17500000000000002 No Hit CTTACCAGGTCCAGACATAGTAAGGATTGACAGACTGAGAGCTCTTTCTT 6 0.15 No Hit GTCGACCTTTTATCTAATAAATGCGTCCCTTCCAGAAGTCGGGGTTTGTT 6 0.15 No Hit CACGGCCTTCGTGCTGGCGACGCATCATTCAAATTTCTGCCCTATCAACT 6 0.15 No Hit CTTAGATGTTCTGGGCCGCACGCGCGCTACACTGATGTATTCAACGAGTC 6 0.15 No Hit GGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGC 6 0.15 No Hit ATCACGATGAAATTTCAAAGATTACCCGGGCCTGTCGGCCAAGGCTATAG 6 0.15 No Hit GTCGAGTTATCATGAATCATCAGAGCAACGGGCAGAGCCCGCGTCGACCT 6 0.15 No Hit GGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGAATT 6 0.15 No Hit CCGTCCTAGTCTCAACCATAAACGATGCCGACCAGGGATTGGCGGATGTT 6 0.15 No Hit GTGCCCTTCCGTCAATTCCTTTAAGTTTCAGCCTTGCGACCATACTCCCC 6 0.15 No Hit CGATCAGATACCGTCCTAGTCTCAACCATAAACGATGCCGACCAGGGATT 6 0.15 No Hit CCGATCCCGAAGGCCAACACAATAGGATCGAAATCCTATGATGTTATCCC 6 0.15 No Hit CAAATTTCTGCCCTATCAACTTTCGATGGTAGGATAGAGGCCTACCATGG 5 0.125 No Hit AAACGATGCCGACCAGGGATTGGCGGATGTTGCTTTTAGGACTCCGCCAG 5 0.125 No Hit TAAGGATTGACAGACTGAGAGCTCTTTCTTGATTCTATGGGTGGTGGTGC 5 0.125 No Hit CTGCCTTCCTTGGATGTGGTAGCCGTTTCTCAGGCTCCCTCTCCGGAATC 5 0.125 No Hit CTGTGATGCCCTTAGATGTTCTGGGCCGCACGCGCGCTACACTGATGTAT 5 0.125 No Hit CCGTCAATTCCTTTAAGTTTCAGCCTTGCGACCATACTCCCCCCAGAACC 5 0.125 No Hit GTTACTTTGAAGAAATTAGAGTGCTCAAAGCAAGCCTACGCTCTGGATAC 5 0.125 No Hit GCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTC 5 0.125 No Hit TGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTT 5 0.125 No Hit AGACGATCAGATACCGTCCTAGTCTCAACCATAAACGATGCCGACCAGGG 5 0.125 No Hit CCTTCCGTCAATTCCTTTAAGTTTCAGCCTTGCGACCATACTCCCCCCAG 5 0.125 No Hit CTCAAAGCAAGCCTACGCTCTGGATACATTAGCATGGGATAACATCATAG 5 0.125 No Hit CTCTAAGAAGCTGGCCGCGGAGGGTCACCTCCGCATAGCTAGTTAGCAGG 5 0.125 No Hit GTCAATTCCTTTAAGTTTCAGCCTTGCGACCATACTCCCCCCAGAACCCA 5 0.125 No Hit GCGCCTGCTGCCTTCCTTGGATGTGGTAGCCGTTTCTCAGGCTCCCTCTC 5 0.125 No Hit CTTGCTTTGAGCACTCTAATTTCTTCAAAGTAACAGCACCGGAGGCACGA 5 0.125 No Hit ACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAG 5 0.125 No Hit GTTAATCATTACTCCGATCCCGAAGGCCAACACAATAGGATCGAAATCCT 5 0.125 No Hit TGCTGCCTTCCTTGGATGTGGTAGCCGTTTCTCAGGCTCCCTCTCCGGAA 5 0.125 No Hit CAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGAATTCCT 5 0.125 No Hit GGAAGTTTGAGGCAATAACAGGTCTGTGATGCCCTTAGATGTTCTGGGCC 5 0.125 No Hit ATGAAATTTCAAAGATTACCCGGGCCTGTCGGCCAAGGCTATAGACTCGT 5 0.125 No Hit CCTAGTCTCAACCATAAACGATGCCGACCAGGGATTGGCGGATGTTGCTT 5 0.125 No Hit TCCAGACATAGTAAGGATTGACAGACTGAGAGCTCTTTCTTGATTCTATG 5 0.125 No Hit GCCAGTAGTCATATGCTTGTCTCAAAGATTAAGCCATGCATGTGTAAGTA 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 0.0125 0.0 0.0 0.0 0.0 44-45 0.025 0.0 0.0 0.0 0.0 46-47 0.025 0.0 0.0 0.0 0.0 48-49 0.025 0.0 0.0 0.0 0.0 50-51 0.025 0.0 0.0 0.0 0.0 52-53 0.025 0.0 0.0 0.0 0.0 54-55 0.025 0.0 0.0 0.0 0.0 56-57 0.025 0.0 0.0 0.0 0.0 58-59 0.025 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 0.025 0.0 0.0 0.0 0.0 66-67 0.05 0.0 0.0 0.0 0.0 68-69 0.07500000000000001 0.0 0.0 0.0 0.0 70-71 0.125 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 0.15 0.0 0.0 0.0 0.0 80-81 0.25 0.0 0.0 0.0 0.0 82-83 0.3125 0.0 0.0 0.0 0.0 84-85 0.4125 0.0 0.0 0.0 0.0 86-87 0.575 0.0 0.0 0.0 0.0 88-89 0.8500000000000001 0.0 0.0 0.0 0.0 90-91 1.025 0.0 0.0 0.0 0.0 92-93 1.4125 0.0 0.0 0.0 0.0 94-95 1.85 0.0 0.0 0.0 0.0 96-97 2.4375 0.0 0.0 0.0 0.0 98-99 2.9875 0.0 0.0 0.0 0.0 100-101 3.5999999999999996 0.0 0.0 0.0 0.0 102-103 4.7 0.0 0.0 0.0 0.0 104-105 5.7625 0.0 0.0 0.0 0.0 106-107 6.8125 0.0 0.0 0.0 0.0 108-109 8.125 0.0 0.0 0.0 0.0 110-111 9.837499999999999 0.0 0.0 0.0 0.0 112-113 11.375 0.0 0.0 0.0 0.0 114-115 13.162500000000001 0.0 0.0 0.0 0.0 116-117 14.95 0.0 0.0 0.0 0.0 118-119 16.5375 0.0 0.0 0.0 0.0 120-121 18.675 0.0 0.0 0.0 0.0 122-123 20.7375 0.0 0.0 0.0 0.0 124-125 22.5875 0.0 0.0 0.0 0.0 126-127 24.8125 0.0 0.0 0.0 0.0 128-129 27.1625 0.0 0.0 0.0 0.0 130-131 29.375 0.0 0.0 0.0 0.0 132-133 31.5375 0.0 0.0 0.0 0.0 134-135 33.825 0.0 0.0 0.0 0.0 136-137 36.025 0.0 0.0 0.0 0.0 138-139 38.462500000000006 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position ATCAGAT 10 0.006830828 145.0 3 TACCGTC 10 0.006830828 145.0 9 TCAGATA 10 0.006830828 145.0 4 CAGATAC 10 0.006830828 145.0 5 ATACCGT 10 0.006830828 145.0 8 CAGATCA 40 0.0076550315 18.125 4 GTCACCA 60 0.004491891 14.500001 130-134 AGAGCAC 150 0.0022674922 8.700001 140-144 TCGGAAG 175 0.009100538 7.457143 135-139 >>END_MODULE Rejected 2262982 READS because READLEN < 1 Read 2262982 spots for SRR6793151.sra Written 2262982 spots for SRR6793151.sra Rejected 2262982 READS because READLEN < 1 Read 2262982 spots for SRR6793151.sra Written 2262982 spots for SRR6793151.sra Rejected 2262982 READS because READLEN < 1 Read 2262982 spots for SRR6793151.sra Written 2262982 spots for SRR6793151.sra Rejected 2262982 READS because READLEN < 1 Read 2262982 spots for SRR6793151.sra Written 2262982 spots for SRR6793151.sra Rejected 2262982 READS because READLEN < 1 Read 2262982 spots for SRR6793151.sra Written 2262982 spots for SRR6793151.sra Rejected 2262982 READS because READLEN < 1 Read 2262982 spots for SRR6793151.sra Written 2262982 spots for SRR6793151.sra Rejected 2262989 READS because READLEN < 1 Read 2262989 spots for SRR6793151.sra Written 2262989 spots for SRR6793151.sra Rejected 2262982 READS because READLEN < 1 Read 2262982 spots for SRR6793151.sra Written 2262982 spots for SRR6793151.sra Rejected 2262982 READS because READLEN < 1 Read 2262982 spots for SRR6793151.sra Written 2262982 spots for SRR6793151.sra Rejected 2262982 READS because READLEN < 1 Read 2262982 spots for SRR6793151.sra Written 2262982 spots for SRR6793151.sra Rejected 2262982 READS because READLEN < 1 Read 2262982 spots for SRR6793151.sra Written 2262982 spots for SRR6793151.sra Rejected 2262982 READS because READLEN < 1 Read 2262982 spots for SRR6793151.sra Written 2262982 spots for SRR6793151.sra Rejected 2262982 READS because READLEN < 1 Read 2262982 spots for SRR6793151.sra Written 2262982 spots for SRR6793151.sra Rejected 2262982 READS because READLEN < 1 Read 2262982 spots for SRR6793151.sra Written 2262982 spots for SRR6793151.sra Rejected 2262982 READS because READLEN < 1 Read 2262982 spots for SRR6793151.sra Written 2262982 spots for SRR6793151.sra Rejected 2262982 READS because READLEN < 1 Read 2262982 spots for SRR6793151.sra Written 2262982 spots for SRR6793151.sra Rejected 2262982 READS because READLEN < 1 Read 2262982 spots for SRR6793151.sra Written 2262982 spots for SRR6793151.sra Rejected 2262982 READS because READLEN < 1 Read 2262982 spots for SRR6793151.sra Written 2262982 spots for SRR6793151.sra Rejected 2262982 READS because READLEN < 1 Read 2262982 spots for SRR6793151.sra Written 2262982 spots for SRR6793151.sra Rejected 2262982 READS because READLEN < 1 Read 2262982 spots for SRR6793151.sra Written 2262982 spots for SRR6793151.sra SRR ids: ['SRR6793151.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_zerq2iyp SRR6793151.sra spots: 45259647 blocks: [[1, 2262982], [2262983, 4525964], [4525965, 6788946], [6788947, 9051928], [9051929, 11314910], [11314911, 13577892], [13577893, 15840874], [15840875, 18103856], [18103857, 20366838], [20366839, 22629820], [22629821, 24892802], [24892803, 27155784], [27155785, 29418766], [29418767, 31681748], [31681749, 33944730], [33944731, 36207712], [36207713, 38470694], [38470695, 40733676], [40733677, 42996658], [42996659, 45259647]] SRR6793151 file size 15315308 SRR6793151 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 SRR6793151 SRR6793151_1.fastq Input file: SRR6793151_1.fastq trimmed: SRR6793151-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 Feb 13 15:01:53 2025 >> started Thu Feb 13 15:02:19 2025 >> done (26.280s) 45259647 reads processed; of these: 1910 ( 0.00%) short reads filtered out after trimming by size control 27210 ( 0.06%) empty reads filtered out after trimming by size control 45230527 (99.94%) reads available; of these: 8658291 (19.14%) trimmed reads available after processing 36572236 (80.86%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 89 0.00% 19 112 0.00% 20 108 0.00% 21 127 0.00% 22 194 0.00% 23 210 0.00% 24 201 0.00% 25 328 0.00% 26 353 0.00% 27 377 0.00% 28 492 0.00% 29 482 0.00% 30 520 0.00% 31 578 0.00% 32 612 0.00% 33 701 0.00% 34 709 0.00% 35 765 0.00% 36 763 0.00% 37 774 0.00% 38 927 0.00% 39 832 0.00% 40 871 0.00% 41 894 0.00% 42 919 0.00% 43 881 0.00% 44 935 0.00% 45 1005 0.00% 46 1039 0.00% 47 976 0.00% 48 1117 0.00% 49 1167 0.00% 50 1247 0.00% 51 1289 0.00% 52 1263 0.00% 53 1414 0.00% 54 1373 0.00% 55 1585 0.00% 56 1509 0.00% 57 1763 0.00% 58 1970 0.00% 59 2434 0.01% 60 2405 0.01% 61 2638 0.01% 62 2619 0.01% 63 2645 0.01% 64 2695 0.01% 65 2776 0.01% 66 3203 0.01% 67 3757 0.01% 68 4274 0.01% 69 5085 0.01% 70 5897 0.01% 71 7627 0.02% 72 8219 0.02% 73 9786 0.02% 74 10244 0.02% 75 12302 0.03% 76 13242 0.03% 77 14266 0.03% 78 17268 0.04% 79 18983 0.04% 80 23772 0.05% 81 27135 0.06% 82 32990 0.07% 83 37252 0.08% 84 41697 0.09% 85 43728 0.10% 86 47643 0.11% 87 54407 0.12% 88 59151 0.13% 89 66140 0.15% 90 75924 0.17% 91 87441 0.19% 92 103051 0.23% 93 116066 0.26% 94 122530 0.27% 95 130730 0.29% 96 147329 0.33% 97 154123 0.34% 98 170264 0.38% 99 189998 0.42% 100 186815 0.41% 101 213081 0.47% 102 231140 0.51% 103 258188 0.57% 104 263330 0.58% 105 264383 0.58% 106 284050 0.63% 107 299822 0.66% 108 316030 0.70% 109 330035 0.73% 110 342265 0.76% 111 397893 0.88% 112 403311 0.89% 113 398538 0.88% 114 409218 0.90% 115 423086 0.94% 116 450610 1.00% 117 415443 0.92% 118 415330 0.92% 119 431793 0.95% 120 0 0.00% 121 0 0.00% 122 0 0.00% 123 0 0.00% 124 0 0.00% 125 0 0.00% 126 0 0.00% 127 0 0.00% 128 0 0.00% 129 0 0.00% 130 57 0.00% 131 227 0.00% 132 93 0.00% 133 145 0.00% 134 185 0.00% 135 176 0.00% 136 91 0.00% 137 22 0.00% 138 53 0.00% 139 11 0.00% 140 0 0.00% 141 13 0.00% 142 11 0.00% 143 594 0.00% 144 302 0.00% 145 29 0.00% 146 36 0.00% 147 217 0.00% 148 1077 0.00% 149 613 0.00% 150 2771 0.01% 151 36572236 80.86% 45230527 reads passed initial QC criterion=sequence-density sequence-density=19.06 sequence-density-rank=1 fanout-score=45.01 fanout-score-rank=1 prefix-density=21.87 prefix-fanout=39.2 sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGATCATCTCGTATGCCGTCTTCTGCTTG criterion=fanout-score sequence-density=19.06 sequence-density-rank=1 fanout-score=45.01 fanout-score-rank=1 prefix-density=21.87 prefix-fanout=39.2 sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGATCATCTCGTATGCCGTCTTCTGCTTG 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 AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGATCATCTCGTATGCCGTCTTCTGCTTG -o SRR6793151 - Input file: STDIN trimmed: SRR6793151-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGATCATCTCGTATGCCGTCTTCTGCTTG -- 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 Feb 13 15:04:19 2025 >> started Thu Feb 13 15:05:06 2025 >> done (46.508s) 40707474 reads processed; of these: 108 ( 0.00%) short reads filtered out after trimming by size control 890 ( 0.00%) empty reads filtered out after trimming by size control 40706476 (100.00%) reads available; of these: 12882551 (31.65%) trimmed reads available after processing 27823925 (68.35%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 84 0.00% 19 98 0.00% 20 99 0.00% 21 115 0.00% 22 171 0.00% 23 192 0.00% 24 186 0.00% 25 307 0.00% 26 324 0.00% 27 348 0.00% 28 433 0.00% 29 437 0.00% 30 480 0.00% 31 516 0.00% 32 556 0.00% 33 646 0.00% 34 654 0.00% 35 690 0.00% 36 703 0.00% 37 687 0.00% 38 843 0.00% 39 767 0.00% 40 797 0.00% 41 786 0.00% 42 824 0.00% 43 789 0.00% 44 862 0.00% 45 938 0.00% 46 938 0.00% 47 875 0.00% 48 992 0.00% 49 1060 0.00% 50 1135 0.00% 51 1126 0.00% 52 1150 0.00% 53 1294 0.00% 54 1237 0.00% 55 1435 0.00% 56 1369 0.00% 57 1624 0.00% 58 1802 0.00% 59 2214 0.01% 60 2181 0.01% 61 2385 0.01% 62 2334 0.01% 63 2399 0.01% 64 2458 0.01% 65 2550 0.01% 66 2988 0.01% 67 3436 0.01% 68 3862 0.01% 69 4572 0.01% 70 5411 0.01% 71 6960 0.02% 72 7397 0.02% 73 8751 0.02% 74 9349 0.02% 75 11224 0.03% 76 12052 0.03% 77 13088 0.03% 78 15766 0.04% 79 17261 0.04% 80 21560 0.05% 81 24650 0.06% 82 29930 0.07% 83 33566 0.08% 84 37873 0.09% 85 39481 0.10% 86 43045 0.11% 87 49406 0.12% 88 54034 0.13% 89 60621 0.15% 90 71517 0.18% 91 79512 0.20% 92 92745 0.23% 93 101780 0.25% 94 110228 0.27% 95 117867 0.29% 96 132787 0.33% 97 139380 0.34% 98 153846 0.38% 99 172329 0.42% 100 168911 0.41% 101 192639 0.47% 102 208412 0.51% 103 232248 0.57% 104 238010 0.58% 105 238919 0.59% 106 256092 0.63% 107 271830 0.67% 108 284952 0.70% 109 298618 0.73% 110 306939 0.75% 111 358745 0.88% 112 364243 0.89% 113 359387 0.88% 114 368965 0.91% 115 380611 0.94% 116 404600 0.99% 117 368921 0.91% 118 371864 0.91% 119 398138 0.98% 120 426788 1.05% 121 453191 1.11% 122 430377 1.06% 123 427889 1.05% 124 424515 1.04% 125 445285 1.09% 126 449370 1.10% 127 439379 1.08% 128 456818 1.12% 129 432182 1.06% 130 435524 1.07% 131 420757 1.03% 132 429073 1.05% 133 452703 1.11% 134 482852 1.19% 135 459904 1.13% 136 437149 1.07% 137 427943 1.05% 138 404934 0.99% 139 388287 0.95% 140 389302 0.96% 141 394393 0.97% 142 394464 0.97% 143 420037 1.03% 144 406163 1.00% 145 386060 0.95% 146 422818 1.04% 147 454268 1.12% 148 767214 1.88% 149 396 0.00% 150 1765 0.00% 151 20136468 49.47% criterion=sequence-density sequence-density=0.21 sequence-density-rank=1 fanout-score=9.56 fanout-score-rank=9 prefix-density=0.80 prefix-fanout=2.5 sequence=CTGCTGGCACCTCCATGACTACGGAGGAGACATAGTTCTTCTCAGTCTCGACGATGCCAGCAGTGTAGCTGCTTCCCTTCTTGACACACTGGGTCTTGTCAGCGCAGTCGCAGGTGTCGCAGGTGCTAGACATGATGATTGATTGATTAAGCTTAAATGGATGAACTAAAAGACTTGGAGTATGAATGTGTTCT criterion=fanout-score sequence-density=0.01 sequence-density-rank=37 fanout-score=100.35 fanout-score-rank=1 prefix-density=0.87 prefix-fanout=1.3 sequence=CGCATCGCCGGCCCCCATCCACTTCCCTCCCGACAATTTCAAGCACTCTTTGACTCTCTTTTCAAAGTCCTTTTCATCTTTCCCTCGCGGTACTTGTTTGCTATCGGTCTCTCGCCCGTATTTAGCCTTGGACGGAATTTACCGCCCGATTGGGGCTGCATTCCCAAACAACCCGACTCGCAGACAGCGCCTCGTGGTGCGGCAGGGTCCAGCCACGACGGGGCTCTCACCCTCTCCGGCGCCCCTTTCCAGGGGACTTGGGCCTGGTCCGCCGCTGAGGACGCTTCTCCAGACTACAATTCGGACGCCGCAGGCGCCAGATTCTCAAGCTGGGCATTTCCCGGTTCGCTCGCCGTTACTAGGGGAATCCTTGTAAGTTTCTTTTCCT Started job on | Feb 13 15:05:44 Started mapping on | Feb 13 15:05:44 Finished on | Feb 13 15:07:49 Mapping speed, Million of reads per hour | 1302.61 Number of input reads | 45229529 Average input read length | 137 UNIQUE READS: Uniquely mapped reads number | 24146299 Uniquely mapped reads % | 53.39% Average mapped length | 137.04 Number of splices: Total | 9033351 Number of splices: Annotated (sjdb) | 8788488 Number of splices: GT/AG | 8845465 Number of splices: GC/AG | 133134 Number of splices: AT/AC | 11398 Number of splices: Non-canonical | 43354 Mismatch rate per base, % | 0.48% Deletion rate per base | 0.03% Deletion average length | 2.80 Insertion rate per base | 0.03% Insertion average length | 2.72 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 2178912 % of reads mapped to multiple loci | 4.82% Number of reads mapped to too many loci | 17866041 % of reads mapped to too many loci | 39.50% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 2.03% % of reads unmapped: other | 0.26% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 18904318 18904318 18904318 N_multimapping 2178912 2178912 2178912 N_noFeature 1899771 12843488 12974354 N_ambiguous 339793 56164 55916 UnstrandedReadsAssigned:21906735 PositiveStrandReadsAssigned:11246647 NegativeStrandReadsAssigned:11116029 Dataset is classified unstranded MeadianReadLen=148 20thPercentileLength=120 echo kmer=115 SRR6793151 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: 52,400 [index] number of k-mers: 62,057,036 [index] number of equivalence classes: 130,681 [quant] running in single-end mode [quant] will process file 1: SRR6793151-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 45,229,529 reads, 36,602,511 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,089 rounds 52401 SRR6793151.ke.tsv 34699 SRR6793151.se.tsv 87100 total ==> SRR6793151.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1919 2989.28 58.0602 Potri.005G024800.1.v4.1 1035 936 447 17.8 Potri.004G059700.1.v4.1 961 862 10 0.432394 Potri.007G009000.2.v4.1 1416 1317 0 0 Potri.003G141000.2.v4.1 2943 2844 1966.28 25.7693 Potri.016G087400.1.v4.1 270 171 1397.88 304.692 Potri.015G069301.1.v4.1 564 465 0 0 Potri.010G195200.1.v4.1 1773 1674 2590 57.6676 Potri.012G127500.1.v4.1 977 878 983 41.7298 ==> SRR6793151.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 236 Potri.001G233950.v4.1 1 Potri.001G122700.v4.1 469 Potri.001G212900.v4.1 1 Potri.001G182400.v4.1 0 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 26 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 4 SRR6793151 completed mapping pipeline successfully