Starting /dee2/code/volunteer_pipeline.sh SRR6793142 current disk space = 3089439358976 free memory = 1482720820 SRR6793142 SRAfilesize eb58cf322d3bb91915c189cee5cb4e3a SRR6793142.sra SRR6793142.sra file validated SRR6793142 is single end SRR6793142 is conventional basespace SRR6793142 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR6793142_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 48 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 31.4805 32.0 32.0 32.0 32.0 32.0 2 31.5955 32.0 32.0 32.0 32.0 32.0 3 31.64375 32.0 32.0 32.0 32.0 32.0 4 31.7375 32.0 32.0 32.0 32.0 32.0 5 31.7135 32.0 32.0 32.0 32.0 32.0 6 35.11475 36.0 36.0 36.0 36.0 36.0 7 35.40675 36.0 36.0 36.0 36.0 36.0 8 35.23325 36.0 36.0 36.0 36.0 36.0 9 35.421 36.0 36.0 36.0 36.0 36.0 10-14 35.3039 36.0 36.0 36.0 36.0 36.0 15-19 35.32225 36.0 36.0 36.0 36.0 36.0 20-24 35.2445 36.0 36.0 36.0 36.0 36.0 25-29 35.24175 36.0 36.0 36.0 36.0 36.0 30-34 35.20225 36.0 36.0 36.0 36.0 36.0 35-39 35.1189 36.0 36.0 36.0 36.0 36.0 40-44 35.14184999999999 36.0 36.0 36.0 36.0 36.0 45-49 34.998749999999994 36.0 36.0 36.0 36.0 36.0 50-54 35.075900000000004 36.0 36.0 36.0 36.0 36.0 55-59 34.99425 36.0 36.0 36.0 36.0 36.0 60-64 34.8719 36.0 36.0 36.0 34.4 36.0 65-69 34.8521 36.0 36.0 36.0 32.8 36.0 70-74 34.677499999999995 36.0 36.0 36.0 32.0 36.0 75-79 34.6468 36.0 36.0 36.0 32.0 36.0 80-84 34.4759 36.0 36.0 36.0 32.0 36.0 85-89 34.546400000000006 36.0 36.0 36.0 32.0 36.0 90-94 34.4115 36.0 36.0 36.0 32.0 36.0 95-99 34.34824999999999 36.0 36.0 36.0 32.0 36.0 100-104 34.3505 36.0 36.0 36.0 32.0 36.0 105-109 34.20975 36.0 36.0 36.0 32.0 36.0 110-114 34.17915 36.0 36.0 36.0 32.0 36.0 115-119 34.048449999999995 36.0 36.0 36.0 32.0 36.0 120-124 34.056349999999995 36.0 36.0 36.0 31.0 36.0 125-129 33.802949999999996 36.0 34.4 36.0 28.0 36.0 130-134 33.76375 36.0 34.4 36.0 27.0 36.0 135-139 33.2024 36.0 32.0 36.0 27.0 36.0 140-144 33.285700000000006 36.0 32.0 36.0 27.0 36.0 145-149 32.56835 36.0 32.0 36.0 27.0 36.0 150-151 30.367375000000003 34.0 29.5 36.0 20.5 36.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 17 1.0 18 0.0 19 0.0 20 2.0 21 1.0 22 2.0 23 10.0 24 8.0 25 10.0 26 28.0 27 33.0 28 47.0 29 87.0 30 82.0 31 122.0 32 179.0 33 285.0 34 777.0 35 2326.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 21.2 13.625000000000002 11.425 53.75 2 20.95 20.95 37.075 21.025 3 21.925 24.55 23.400000000000002 30.125 4 28.15 29.875 16.775000000000002 25.2 5 29.099999999999998 29.925 20.1 20.875 6 20.38712921065862 34.66566113624937 23.02664655605832 21.920563097033686 7 19.75 16.5 40.625 23.125 8 21.725 18.025 29.125 31.125000000000004 9 22.625 20.375 31.45 25.55 10-14 23.535 26.840000000000003 25.135 24.490000000000002 15-19 24.665 25.3 26.415 23.62 20-24 24.81 25.75 25.69 23.75 25-29 23.755000000000003 26.275 24.72 25.25 30-34 23.195 24.490000000000002 26.435 25.88 35-39 23.66 25.619999999999997 25.650000000000002 25.069999999999997 40-44 23.72 25.39 26.405 24.485 45-49 23.87 26.015 25.965 24.15 50-54 24.044999999999998 26.064999999999998 26.479999999999997 23.41 55-59 24.48 25.435000000000002 26.38 23.705000000000002 60-64 24.169999999999998 25.1 26.095000000000002 24.635 65-69 24.12 25.629999999999995 26.235000000000003 24.015 70-74 23.47 26.169999999999998 26.115 24.245 75-79 24.0886132919938 26.128919337900687 25.538830824623695 24.243636545481824 80-84 24.147073536768385 25.41770885442721 25.842921460730366 24.592296148074038 85-89 24.165874643589618 25.856635485968688 26.216797558901504 23.760692311540193 90-94 24.22832557906849 26.744709590274653 25.293911651408273 23.733053179248586 95-99 23.76138524672205 25.367831047943152 27.029326393754378 23.84145731158042 100-104 24.506225311265563 26.431321566078303 25.496274813740687 23.566178308915443 105-109 24.256682350585645 26.03864250675743 26.198818700570627 23.505856442086294 110-114 25.639485408219453 26.1150322871302 24.35801171347049 23.887470591179856 115-119 24.61207328060867 26.71438582440685 24.672139353288618 24.001401541695866 120-124 26.192857857357204 26.79803941182355 23.4370311093328 23.572071621486444 125-129 25.348161506863036 27.066426209798617 22.54283137962128 25.04258090371706 130-134 24.912456228114056 27.293646823411706 23.351675837918958 24.44222111055528 135-139 25.768806971852147 28.152859861765002 21.761995392166682 24.31633777421617 140-144 25.5043299794764 27.346448415678033 21.965260049056415 25.183961555789157 145-149 25.41143514581562 27.132209494272423 21.829823420539242 25.626531939372715 150-151 24.846664163224432 28.02603579922393 20.95381149079985 26.173488546751784 >>END_MODULE >>Per sequence GC content pass #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 0.5 14 0.5 15 0.0 16 0.0 17 0.0 18 0.5 19 0.5 20 0.5 21 1.0 22 1.0 23 1.0 24 0.5 25 1.0 26 2.5 27 2.5 28 1.5 29 2.0 30 4.0 31 7.5 32 9.5 33 11.0 34 17.0 35 42.0 36 71.5 37 84.5 38 86.5 39 94.0 40 107.5 41 116.5 42 126.5 43 131.0 44 168.5 45 202.0 46 202.0 47 215.5 48 230.0 49 225.5 50 186.0 51 170.5 52 175.0 53 175.0 54 182.5 55 164.0 56 140.5 57 138.5 58 114.5 59 76.5 60 68.5 61 55.0 62 42.0 63 35.5 64 19.5 65 11.0 66 10.0 67 10.5 68 13.0 69 13.0 70 9.0 71 6.5 72 4.0 73 3.0 74 2.5 75 1.0 76 1.0 77 1.0 78 1.0 79 0.0 80 0.0 81 0.5 82 0.5 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 0.5499999999999999 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 0.05 85-89 0.045 90-94 0.055 95-99 0.09 100-104 0.005 105-109 0.11 110-114 0.11499999999999999 115-119 0.11 120-124 0.03 125-129 0.19 130-134 0.05 135-139 0.16999999999999998 140-144 0.11499999999999999 145-149 0.045 150-151 0.13749999999999998 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 75.47500000000001 #Duplication Level Percentage of deduplicated Percentage of total 1 86.48559125538257 65.275 2 6.724080821464061 10.15 3 3.2461079827757535 7.35 4 1.3580655846306724 4.1000000000000005 5 0.4968532626697582 1.875 6 0.4306061609804571 1.95 7 0.23186485591255385 1.225 8 0.33123550844650546 2.0 9 0.09937065253395165 0.675 >10 0.5962239152037099 5.4 >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 CCCGACTGTCCCTGTTAATCATTACTCCGATCCCGAAGGCCAACACAATA 24 0.6 No Hit GCCAGTAGTCATATGCTTGTCTCAAAGATTAAGCCATGCATGTGTAAGTA 16 0.4 No Hit CTGCCAGTAGTCATATGCTTGTCTCAAAGATTAAGCCATGCATGTGTAAG 15 0.375 No Hit CAGGTCCAGACATAGTAAGGATTGACAGACTGAGAGCTCTTTCTTGATTC 13 0.325 No Hit CAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGAATTCCT 13 0.325 No Hit CCCGTGTCAGGATTGGGTAATTTGCGCGCCTGCTGCCTTCCTTGGATGTG 12 0.3 No Hit GTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCAT 11 0.27499999999999997 No Hit CCGCAGGCTCCACTCCTGGTGGTGCCCTTCCGTCAATTCCTTTAAGTTTC 11 0.27499999999999997 No Hit CAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGG 11 0.27499999999999997 No Hit CTCCGTCACCCGTCACCACCATGGTAGGCCTCTATCCTACCATCGAAAGT 10 0.25 No Hit CGAACAACTGCGAAAGCATTTGCCAAGGATGTTTTCATTAATCAAGAACG 10 0.25 No Hit CAACAACTTAAATATACGCTATTGGAGCTGGAATTACCGCGGCTGCTGGC 10 0.25 No Hit CCAGAACCCAAAAACTTTGATTTCTCATAAGGTGCTGGCGGAGTCCTAAA 10 0.25 No Hit CCTGCCAGTAGTCATATGCTTGTCTCAAAGATTAAGCCATGCATGTGTAA 10 0.25 No Hit CTAATTCTCCGTCACCCGTCACCACCATGGTAGGCCTCTATCCTACCATC 10 0.25 No Hit ACCAGGTCCAGACATAGTAAGGATTGACAGACTGAGAGCTCTTTCTTGAT 10 0.25 No Hit CTCAGGTGTGCACCGGTCGCCTCGTCCCTTCTACCGGCGATGCGCTCCTG 10 0.25 No Hit CCAGGTCCAGACATAGTAAGGATTGACAGACTGAGAGCTCTTTCTTGATT 10 0.25 No Hit CCGGAATCGAACCCTAATTCTCCGTCACCCGTCACCACCATGGTAGGCCT 9 0.22499999999999998 No Hit CTCCGATCCCGAAGGCCAACACAATAGGATCGAAATCCTATGATGTTATC 9 0.22499999999999998 No Hit CTGAGGTCTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAAC 9 0.22499999999999998 No Hit CTTACCAGGTCCAGACATAGTAAGGATTGACAGACTGAGAGCTCTTTCTT 8 0.2 No Hit CTTTTATCTAATAAATGCGTCCCTTCCAGAAGTCGGGGTTTGTTGCACGT 8 0.2 No Hit CAACTTTCGTTCTTGATTAATGAAAACATCCTTGGCAAATGCTTTCGCAG 8 0.2 No Hit CCGAAGGCCAACACAATAGGATCGAAATCCTATGATGTTATCCCATGCTA 8 0.2 No Hit CGTCAATTCCTTTAAGTTTCAGCCTTGCGACCATACTCCCCCCAGAACCC 8 0.2 No Hit CTTCCGTCAATTCCTTTAAGTTTCAGCCTTGCGACCATACTCCCCCCAGA 8 0.2 No Hit GTAATTCTAGAGCTAATACGTGCAACAAACCCCGACTTCTGGAAGGGACG 8 0.2 No Hit GTCATATGCTTGTCTCAAAGATTAAGCCATGCATGTGTAAGTATGAACTA 8 0.2 No Hit CTTAGATGTTCTGGGCCGCACGCGCGCTACACTGATGTATTCAACGAGTC 8 0.2 No Hit CTCAAACTTCCTTGGCCTGGAAGGCCATAGTCCCTCTAAGAAGCTGGCCG 8 0.2 No Hit GTCCTAGTCTCAACCATAAACGATGCCGACCAGGGATTGGCGGATGTTGC 7 0.17500000000000002 No Hit TAAGGATTGACAGACTGAGAGCTCTTTCTTGATTCTATGGGTGGTGGTGC 7 0.17500000000000002 No Hit CTTGCTTTGAGCACTCTAATTTCTTCAAAGTAACAGCACCGGAGGCACGA 7 0.17500000000000002 No Hit CAAACCCCGACTTCTGGAAGGGACGCATTTATTAGATAAAAGGTCGACGC 7 0.17500000000000002 No Hit CGATCAGATACCGTCCTAGTCTCAACCATAAACGATGCCGACCAGGGATT 7 0.17500000000000002 No Hit CCAACTTTCGTTCTTGATTAATGAAAACATCCTTGGCAAATGCTTTCGCA 7 0.17500000000000002 No Hit CCCAACTTTCGTTCTTGATTAATGAAAACATCCTTGGCAAATGCTTTCGC 7 0.17500000000000002 No Hit CTCGAAGACGATCAGATACCGTCCTAGTCTCAACCATAAACGATGCCGAC 6 0.15 No Hit CTTGTCTCAAAGATTAAGCCATGCATGTGTAAGTATGAACTAATTCAGAC 6 0.15 No Hit GTCAATTCCTTTAAGTTTCAGCCTTGCGACCATACTCCCCCCAGAACCCA 6 0.15 No Hit AGAAATTTGAATGATGCGTCGCCAGCACGAAGGCCGTGCGATCCGTCGAG 6 0.15 No Hit CTTTGGGTTGGGTCGGCCGGTCCGCCTCAGGTGTGCACCGGTCGCCTCGT 6 0.15 No Hit CAAAGATTAAGCCATGCATGTGTAAGTATGAACTAATTCAGACTGTGAAA 6 0.15 No Hit CTGGAAGGGACGCATTTATTAGATAAAAGGTCGACGCGGGCTCTGCCCGT 6 0.15 No Hit GTCCGCCTCAGGTGTGCACCGGTCGCCTCGTCCCTTCTACCGGCGATGCG 6 0.15 No Hit CGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCT 6 0.15 No Hit GACGGATCGCACGGCCTTCGTGCTGGCGACGCATCATTCAAATTTCTGCC 6 0.15 No Hit CTGAGAGCTCTTTCTTGATTCTATGGGTGGTGGTGCATGGCCGTTCTTAG 6 0.15 No Hit CTCGTCCCTTCTACCGGCGATGCGCTCCTGGCCTTAACTGGCCGGGTCGT 6 0.15 No Hit CTCAACCATAAACGATGCCGACCAGGGATTGGCGGATGTTGCTTTTAGGA 6 0.15 No Hit CTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAAC 5 0.125 No Hit CAGTAGTCATATGCTTGTCTCAAAGATTAAGCCATGCATGTGTAAGTATG 5 0.125 No Hit CTGGCCGCGGAGGGTCACCTCCGCATAGCTAGTTAGCAGGCTGAGGTCTC 5 0.125 No Hit GTCGGCATCGTTTATGGTTGAGACTAGGACGGTATCTGATCGTCTTCGAG 5 0.125 No Hit CTGCTGCCTTCCTTGGATGTGGTAGCCGTTTCTCAGGCTCCCTCTCCGGA 5 0.125 No Hit CTGTGATGCCCTTAGATGTTCTGGGCCGCACGCGCGCTACACTGATGTAT 5 0.125 No Hit GTTAATCATTACTCCGATCCCGAAGGCCAACACAATAGGATCGAAATCCT 5 0.125 No Hit CTGACTATGAAATACGAATGCCCCCGACTGTCCCTGTTAATCATTACTCC 5 0.125 No Hit CCTAATTCTCCGTCACCCGTCACCACCATGGTAGGCCTCTATCCTACCAT 5 0.125 No Hit CGCGCCTGCTGCCTTCCTTGGATGTGGTAGCCGTTTCTCAGGCTCCCTCT 5 0.125 No Hit CTTGGATGTGGTAGCCGTTTCTCAGGCTCCCTCTCCGGAATCGAACCCTA 5 0.125 No Hit CAACAAACCCCGACTTCTGGAAGGGACGCATTTATTAGATAAAAGGTCGA 5 0.125 No Hit CGAGTCTATAGCCTTGGCCGACAGGCCCGGGTAATCTTTGAAATTTCATC 5 0.125 No Hit CCAGTAGTCATATGCTTGTCTCAAAGATTAAGCCATGCATGTGTAAGTAT 5 0.125 No Hit CAGCCTGCTAACTAGCTATGCGGAGGTGACCCTCCGCGGCCAGCTTCTTA 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 0.0125 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 0.025 0.0 0.0 0.0 0.0 22-23 0.025 0.0 0.0 0.0 0.0 24-25 0.025 0.0 0.0 0.0 0.0 26-27 0.025 0.0 0.0 0.0 0.0 28-29 0.025 0.0 0.0 0.0 0.0 30-31 0.025 0.0 0.0 0.0 0.0 32-33 0.025 0.0 0.0 0.0 0.0 34-35 0.025 0.0 0.0 0.0 0.0 36-37 0.025 0.0 0.0 0.0 0.0 38-39 0.025 0.0 0.0 0.0 0.0 40-41 0.025 0.0 0.0 0.0 0.0 42-43 0.037500000000000006 0.0 0.0 0.0 0.0 44-45 0.05 0.0 0.0 0.0 0.0 46-47 0.05 0.0 0.0 0.0 0.0 48-49 0.05 0.0 0.0 0.0 0.0 50-51 0.05 0.0 0.0 0.0 0.0 52-53 0.075 0.0 0.0 0.0 0.0 54-55 0.075 0.0 0.0 0.0 0.0 56-57 0.075 0.0 0.0 0.0 0.0 58-59 0.075 0.0 0.0 0.0 0.0 60-61 0.075 0.0 0.0 0.0 0.0 62-63 0.075 0.0 0.0 0.0 0.0 64-65 0.075 0.0 0.0 0.0 0.0 66-67 0.15000000000000002 0.0 0.0 0.0 0.0 68-69 0.2 0.0 0.0 0.0 0.0 70-71 0.2 0.0 0.0 0.0 0.0 72-73 0.275 0.0 0.0 0.0 0.0 74-75 0.3 0.0 0.0 0.0 0.0 76-77 0.325 0.0 0.0 0.0 0.0 78-79 0.4125 0.0 0.0 0.0 0.0 80-81 0.45 0.0 0.0 0.0 0.0 82-83 0.5 0.0 0.0 0.0 0.0 84-85 0.5874999999999999 0.0 0.0 0.0 0.0 86-87 0.625 0.0 0.0 0.0 0.0 88-89 0.7 0.0 0.0 0.0 0.0 90-91 0.8125 0.0 0.0 0.0 0.0 92-93 0.925 0.0 0.0 0.0 0.0 94-95 1.175 0.0 0.0 0.0 0.0 96-97 1.4 0.0 0.0 0.0 0.0 98-99 1.6625 0.0 0.0 0.0 0.0 100-101 1.9500000000000002 0.0 0.0 0.0 0.0 102-103 2.35 0.0 0.0 0.0 0.0 104-105 2.825 0.0 0.0 0.0 0.0 106-107 3.4125 0.0 0.0 0.0 0.0 108-109 4.125 0.0 0.0 0.0 0.0 110-111 4.8375 0.0 0.0 0.0 0.0 112-113 5.800000000000001 0.0 0.0 0.0 0.0 114-115 6.95 0.0 0.0 0.0 0.0 116-117 7.9625 0.0 0.0 0.0 0.0 118-119 9.0875 0.0 0.0 0.0 0.0 120-121 10.287500000000001 0.0 0.0 0.0 0.0 122-123 11.675 0.0 0.0 0.0 0.0 124-125 12.825 0.0 0.0 0.0 0.0 126-127 14.2 0.0 0.0 0.0 0.0 128-129 15.675 0.0 0.0 0.0 0.0 130-131 17.5125 0.0 0.0 0.0 0.0 132-133 19.1625 0.0 0.0 0.0 0.0 134-135 20.9625 0.0 0.0 0.0 0.0 136-137 22.275 0.0 0.0 0.0 0.0 138-139 23.9125 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position CGTCTGA 80 0.0018040554 36.25 145 >>END_MODULE Rejected 1908362 READS because READLEN < 1 Read 1908362 spots for SRR6793142.sra Written 1908362 spots for SRR6793142.sra Rejected 1908362 READS because READLEN < 1 Read 1908362 spots for SRR6793142.sra Written 1908362 spots for SRR6793142.sra Rejected 1908362 READS because READLEN < 1 Read 1908362 spots for SRR6793142.sra Written 1908362 spots for SRR6793142.sra Rejected 1908362 READS because READLEN < 1 Read 1908362 spots for SRR6793142.sra Written 1908362 spots for SRR6793142.sra Rejected 1908362 READS because READLEN < 1 Read 1908362 spots for SRR6793142.sra Written 1908362 spots for SRR6793142.sra Rejected 1908362 READS because READLEN < 1 Read 1908362 spots for SRR6793142.sra Written 1908362 spots for SRR6793142.sra Rejected 1908362 READS because READLEN < 1 Read 1908362 spots for SRR6793142.sra Written 1908362 spots for SRR6793142.sra Rejected 1908362 READS because READLEN < 1 Read 1908362 spots for SRR6793142.sra Written 1908362 spots for SRR6793142.sra Rejected 1908362 READS because READLEN < 1 Read 1908362 spots for SRR6793142.sra Written 1908362 spots for SRR6793142.sra Rejected 1908362 READS because READLEN < 1 Read 1908362 spots for SRR6793142.sra Written 1908362 spots for SRR6793142.sra Rejected 1908362 READS because READLEN < 1 Read 1908362 spots for SRR6793142.sra Written 1908362 spots for SRR6793142.sra Rejected 1908362 READS because READLEN < 1 Read 1908362 spots for SRR6793142.sra Written 1908362 spots for SRR6793142.sra Rejected 1908362 READS because READLEN < 1 Read 1908362 spots for SRR6793142.sra Written 1908362 spots for SRR6793142.sra Rejected 1908364 READS because READLEN < 1 Read 1908364 spots for SRR6793142.sra Written 1908364 spots for SRR6793142.sra Rejected 1908362 READS because READLEN < 1 Read 1908362 spots for SRR6793142.sra Written 1908362 spots for SRR6793142.sra Rejected 1908362 READS because READLEN < 1 Read 1908362 spots for SRR6793142.sra Written 1908362 spots for SRR6793142.sra Rejected 1908362 READS because READLEN < 1 Read 1908362 spots for SRR6793142.sra Written 1908362 spots for SRR6793142.sra Rejected 1908362 READS because READLEN < 1 Read 1908362 spots for SRR6793142.sra Written 1908362 spots for SRR6793142.sra Rejected 1908362 READS because READLEN < 1 Read 1908362 spots for SRR6793142.sra Written 1908362 spots for SRR6793142.sra Rejected 1908362 READS because READLEN < 1 Read 1908362 spots for SRR6793142.sra Written 1908362 spots for SRR6793142.sra SRR ids: ['SRR6793142.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_2j83eh53 SRR6793142.sra spots: 38167242 blocks: [[1, 1908362], [1908363, 3816724], [3816725, 5725086], [5725087, 7633448], [7633449, 9541810], [9541811, 11450172], [11450173, 13358534], [13358535, 15266896], [15266897, 17175258], [17175259, 19083620], [19083621, 20991982], [20991983, 22900344], [22900345, 24808706], [24808707, 26717068], [26717069, 28625430], [28625431, 30533792], [30533793, 32442154], [32442155, 34350516], [34350517, 36258878], [36258879, 38167242]] SRR6793142 file size 12911925 SRR6793142 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 SRR6793142 SRR6793142_1.fastq Input file: SRR6793142_1.fastq trimmed: SRR6793142-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 14:47:28 2025 >> started Thu Feb 13 14:47:53 2025 >> done (24.163s) 38167242 reads processed; of these: 4869 ( 0.01%) short reads filtered out after trimming by size control 299 ( 0.00%) empty reads filtered out after trimming by size control 38162074 (99.99%) reads available; of these: 4077551 (10.68%) trimmed reads available after processing 34084523 (89.32%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 313 0.00% 19 283 0.00% 20 270 0.00% 21 302 0.00% 22 344 0.00% 23 329 0.00% 24 334 0.00% 25 389 0.00% 26 498 0.00% 27 512 0.00% 28 544 0.00% 29 573 0.00% 30 655 0.00% 31 561 0.00% 32 778 0.00% 33 705 0.00% 34 746 0.00% 35 830 0.00% 36 951 0.00% 37 809 0.00% 38 971 0.00% 39 851 0.00% 40 1008 0.00% 41 1152 0.00% 42 1103 0.00% 43 1105 0.00% 44 1170 0.00% 45 1242 0.00% 46 1194 0.00% 47 1274 0.00% 48 1309 0.00% 49 1374 0.00% 50 1339 0.00% 51 1425 0.00% 52 1408 0.00% 53 1555 0.00% 54 1533 0.00% 55 1633 0.00% 56 1544 0.00% 57 1767 0.00% 58 1692 0.00% 59 2060 0.01% 60 2261 0.01% 61 2235 0.01% 62 2220 0.01% 63 2276 0.01% 64 2270 0.01% 65 2144 0.01% 66 2388 0.01% 67 2576 0.01% 68 2547 0.01% 69 2666 0.01% 70 3044 0.01% 71 3693 0.01% 72 3734 0.01% 73 4028 0.01% 74 4295 0.01% 75 4894 0.01% 76 5249 0.01% 77 5336 0.01% 78 6234 0.02% 79 6639 0.02% 80 7649 0.02% 81 9174 0.02% 82 10182 0.03% 83 11487 0.03% 84 12596 0.03% 85 14496 0.04% 86 16806 0.04% 87 17423 0.05% 88 19039 0.05% 89 22325 0.06% 90 25721 0.07% 91 29069 0.08% 92 35739 0.09% 93 39910 0.10% 94 42216 0.11% 95 47414 0.12% 96 50850 0.13% 97 58451 0.15% 98 64246 0.17% 99 73293 0.19% 100 73584 0.19% 101 84906 0.22% 102 96194 0.25% 103 101119 0.26% 104 114625 0.30% 105 116685 0.31% 106 123856 0.32% 107 137154 0.36% 108 146518 0.38% 109 159368 0.42% 110 164737 0.43% 111 199073 0.52% 112 203008 0.53% 113 207707 0.54% 114 218930 0.57% 115 227844 0.60% 116 250084 0.66% 117 235868 0.62% 118 238369 0.62% 119 252742 0.66% 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 67 0.00% 131 172 0.00% 132 73 0.00% 133 127 0.00% 134 169 0.00% 135 170 0.00% 136 101 0.00% 137 31 0.00% 138 50 0.00% 139 3 0.00% 140 0 0.00% 141 24 0.00% 142 18 0.00% 143 425 0.00% 144 279 0.00% 145 33 0.00% 146 35 0.00% 147 187 0.00% 148 900 0.00% 149 584 0.00% 150 2482 0.01% 151 34084523 89.32% 38162074 reads passed initial QC criterion=sequence-density sequence-density=15.53 sequence-density-rank=1 fanout-score=39.14 fanout-score-rank=1 prefix-density=18.14 prefix-fanout=33.5 sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACGTCCGCACATCTCGTATGCCGTCTTCTGCTTG criterion=fanout-score sequence-density=15.53 sequence-density-rank=1 fanout-score=39.14 fanout-score-rank=1 prefix-density=18.14 prefix-fanout=33.5 sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACGTCCGCACATCTCGTATGCCGTCTTCTGCTTG 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 AGATCGGAAGAGCACACGTCTGAACTCCAGTCACGTCCGCACATCTCGTATGCCGTCTTCTGCTTG -o SRR6793142 - Input file: STDIN trimmed: SRR6793142-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): AGATCGGAAGAGCACACGTCTGAACTCCAGTCACGTCCGCACATCTCGTATGCCGTCTTCTGCT -- 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 14:49:47 2025 >> started Thu Feb 13 14:50:31 2025 >> done (44.595s) 33391815 reads processed; of these: 310 ( 0.00%) short reads filtered out after trimming by size control 97 ( 0.00%) empty reads filtered out after trimming by size control 33391408 (100.00%) reads available; of these: 8764673 (26.25%) trimmed reads available after processing 24626735 (73.75%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 281 0.00% 19 252 0.00% 20 248 0.00% 21 273 0.00% 22 301 0.00% 23 304 0.00% 24 289 0.00% 25 346 0.00% 26 442 0.00% 27 447 0.00% 28 472 0.00% 29 517 0.00% 30 566 0.00% 31 506 0.00% 32 684 0.00% 33 636 0.00% 34 649 0.00% 35 726 0.00% 36 855 0.00% 37 712 0.00% 38 882 0.00% 39 746 0.00% 40 868 0.00% 41 1013 0.00% 42 963 0.00% 43 970 0.00% 44 1021 0.00% 45 1098 0.00% 46 1053 0.00% 47 1130 0.00% 48 1130 0.00% 49 1207 0.00% 50 1182 0.00% 51 1263 0.00% 52 1266 0.00% 53 1348 0.00% 54 1354 0.00% 55 1438 0.00% 56 1377 0.00% 57 1591 0.00% 58 1491 0.00% 59 1822 0.01% 60 1978 0.01% 61 1974 0.01% 62 1960 0.01% 63 2032 0.01% 64 2030 0.01% 65 1883 0.01% 66 2104 0.01% 67 2273 0.01% 68 2265 0.01% 69 2339 0.01% 70 2667 0.01% 71 3229 0.01% 72 3227 0.01% 73 3522 0.01% 74 3859 0.01% 75 4338 0.01% 76 4582 0.01% 77 4719 0.01% 78 5446 0.02% 79 5876 0.02% 80 6812 0.02% 81 8074 0.02% 82 8895 0.03% 83 9999 0.03% 84 11085 0.03% 85 12729 0.04% 86 14718 0.04% 87 15322 0.05% 88 16828 0.05% 89 19912 0.06% 90 22992 0.07% 91 25897 0.08% 92 31401 0.09% 93 34832 0.10% 94 37183 0.11% 95 41545 0.12% 96 44396 0.13% 97 51498 0.15% 98 56304 0.17% 99 64801 0.19% 100 64675 0.19% 101 74432 0.22% 102 84242 0.25% 103 88829 0.27% 104 101103 0.30% 105 102871 0.31% 106 108659 0.33% 107 120632 0.36% 108 128403 0.38% 109 140039 0.42% 110 143910 0.43% 111 174328 0.52% 112 178387 0.53% 113 182425 0.55% 114 192335 0.58% 115 198963 0.60% 116 218457 0.65% 117 204592 0.61% 118 207745 0.62% 119 225739 0.68% 120 246724 0.74% 121 252736 0.76% 122 255832 0.77% 123 265685 0.80% 124 254557 0.76% 125 266619 0.80% 126 286363 0.86% 127 276422 0.83% 128 306899 0.92% 129 282399 0.85% 130 298071 0.89% 131 284578 0.85% 132 297434 0.89% 133 320451 0.96% 134 311148 0.93% 135 312012 0.93% 136 290951 0.87% 137 294157 0.88% 138 285340 0.85% 139 282049 0.84% 140 282147 0.84% 141 285031 0.85% 142 289961 0.87% 143 304427 0.91% 144 300841 0.90% 145 293830 0.88% 146 306226 0.92% 147 357552 1.07% 148 626330 1.88% 149 419 0.00% 150 1670 0.01% 151 21098536 63.19% criterion=sequence-density sequence-density=0.46 sequence-density-rank=1 fanout-score=1.99 fanout-score-rank=23 prefix-density=0.45 prefix-fanout=2.0 sequence=GTATTTAGCCTTG criterion=fanout-score sequence-density=0.07 sequence-density-rank=26 fanout-score=32.11 fanout-score-rank=1 prefix-density=1.55 prefix-fanout=1.4 sequence=GCTGCTGGCACAGAGTTAGCCGATGCTTATTCCCCAGATACCGTCATTGCTTCTTCTCCGGGAAAAGAAGTTCACGACCCGTAGGCCTTCTACCTCCACGCGGCATTGCTCCGTCAAGCTTTCGCCCATTGCGGAAAATTCCCCACTGCTGCCTCCCGTAGGAGTCTGGGCCGTGTCTCAGTCCCAGTGTGGCTGATCATCCTCTCGGACCAGCTACTGATCATCGCCTTGGTAAGCTATTGCCTCACCAACTAGCTAATCAGACGCGAGCCCCTCCTCGGGCGGATTCCTCCTTTTGCTCCTCAGCCTACGGGGTATTAGCAGCCGTTTCCAGCTGTTGTTCCCCTCCCAAGGGCAGGTTCTTACGCGTTACTCACCCGTCCGCCACTGGAAACACCACTTCCCGTCCGACTTGCATGTGTTAAGCATGCCGCCAGCGTTCATCCTGAGCCAGGATCG Started job on | Feb 13 14:51:17 Started mapping on | Feb 13 14:51:21 Finished on | Feb 13 14:54:06 Mapping speed, Million of reads per hour | 832.62 Number of input reads | 38161667 Average input read length | 142 UNIQUE READS: Uniquely mapped reads number | 15463895 Uniquely mapped reads % | 40.52% Average mapped length | 141.70 Number of splices: Total | 5512709 Number of splices: Annotated (sjdb) | 5384598 Number of splices: GT/AG | 5399977 Number of splices: GC/AG | 84641 Number of splices: AT/AC | 7389 Number of splices: Non-canonical | 20702 Mismatch rate per base, % | 0.63% Deletion rate per base | 0.03% Deletion average length | 2.32 Insertion rate per base | 0.03% Insertion average length | 2.69 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 2759202 % of reads mapped to multiple loci | 7.23% Number of reads mapped to too many loci | 19274343 % of reads mapped to too many loci | 50.51% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.25% % of reads unmapped: other | 0.49% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 19938570 19938570 19938570 N_multimapping 2759202 2759202 2759202 N_noFeature 2361739 8708181 8781135 N_ambiguous 411332 37942 37325 UnstrandedReadsAssigned:12690824 PositiveStrandReadsAssigned:6717772 NegativeStrandReadsAssigned:6645435 Dataset is classified unstranded MeadianReadLen=151 20thPercentileLength=131 echo kmer=127 SRR6793142 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: SRR6793142-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 38,161,667 reads, 28,859,047 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,176 rounds 52401 SRR6793142.ke.tsv 34699 SRR6793142.se.tsv 87100 total ==> SRR6793142.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1919 3743 78.1425 Potri.005G024800.1.v4.1 1035 936 266 11.3854 Potri.004G059700.1.v4.1 961 862 10 0.464767 Potri.007G009000.2.v4.1 1416 1317 0 0 Potri.003G141000.2.v4.1 2943 2844 819.274 11.5409 Potri.016G087400.1.v4.1 270 171 357.733 83.8117 Potri.015G069301.1.v4.1 564 465 0 0 Potri.010G195200.1.v4.1 1773 1674 51 1.22055 Potri.012G127500.1.v4.1 977 878 158 7.20949 ==> SRR6793142.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 358 Potri.001G233950.v4.1 1 Potri.001G122700.v4.1 166 Potri.001G212900.v4.1 1 Potri.001G182400.v4.1 0 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 4 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 0 SRR6793142 completed mapping pipeline successfully