Starting /dee2/code/volunteer_pipeline.sh SRR6793148 current disk space = 3089663922176 free memory = 1446629608 SRR6793148 SRAfilesize 7d45987957f3f533149d4e2051541441 SRR6793148.sra SRR6793148.sra file validated SRR6793148 is single end SRR6793148 is conventional basespace SRR6793148 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR6793148_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 47 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 31.54975 32.0 32.0 32.0 32.0 32.0 2 31.68975 32.0 32.0 32.0 32.0 32.0 3 31.7135 32.0 32.0 32.0 32.0 32.0 4 31.7495 32.0 32.0 32.0 32.0 32.0 5 31.66575 32.0 32.0 32.0 32.0 32.0 6 35.17625 36.0 36.0 36.0 36.0 36.0 7 35.38775 36.0 36.0 36.0 36.0 36.0 8 35.4 36.0 36.0 36.0 36.0 36.0 9 35.472 36.0 36.0 36.0 36.0 36.0 10-14 35.34855 36.0 36.0 36.0 36.0 36.0 15-19 35.3693 36.0 36.0 36.0 36.0 36.0 20-24 35.3312 36.0 36.0 36.0 36.0 36.0 25-29 35.30815 36.0 36.0 36.0 36.0 36.0 30-34 35.22695 36.0 36.0 36.0 36.0 36.0 35-39 35.17245 36.0 36.0 36.0 36.0 36.0 40-44 35.1072 36.0 36.0 36.0 36.0 36.0 45-49 35.0593 36.0 36.0 36.0 36.0 36.0 50-54 35.05875 36.0 36.0 36.0 36.0 36.0 55-59 34.99130000000001 36.0 36.0 36.0 36.0 36.0 60-64 34.90805 36.0 36.0 36.0 34.4 36.0 65-69 34.81665 36.0 36.0 36.0 33.6 36.0 70-74 34.62305 36.0 36.0 36.0 32.0 36.0 75-79 34.670500000000004 36.0 36.0 36.0 32.0 36.0 80-84 34.476600000000005 36.0 36.0 36.0 32.0 36.0 85-89 34.5886 36.0 36.0 36.0 32.0 36.0 90-94 34.424600000000005 36.0 36.0 36.0 32.0 36.0 95-99 34.35090000000001 36.0 36.0 36.0 32.0 36.0 100-104 34.4019 36.0 36.0 36.0 32.0 36.0 105-109 34.2264 36.0 36.0 36.0 32.0 36.0 110-114 34.18145 36.0 36.0 36.0 32.0 36.0 115-119 34.09225 36.0 36.0 36.0 31.0 36.0 120-124 34.06 36.0 36.0 36.0 32.0 36.0 125-129 33.82195 36.0 36.0 36.0 27.0 36.0 130-134 33.78575 36.0 34.4 36.0 27.0 36.0 135-139 33.19930000000001 36.0 32.0 36.0 27.0 36.0 140-144 33.275 36.0 32.0 36.0 27.0 36.0 145-149 32.51235 36.0 32.0 36.0 27.0 36.0 150-151 30.47 34.0 29.5 36.0 20.5 36.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 19 1.0 20 3.0 21 4.0 22 5.0 23 11.0 24 14.0 25 17.0 26 19.0 27 39.0 28 52.0 29 59.0 30 79.0 31 121.0 32 184.0 33 280.0 34 675.0 35 2437.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 24.5 12.275 13.05 50.175000000000004 2 22.3 18.575 33.525 25.6 3 20.225 23.525 24.125 32.125 4 26.55 27.150000000000002 18.925 27.375 5 25.75 30.175 21.775 22.3 6 22.230595327807084 33.860838985179605 21.602612408942477 22.305953278070838 7 18.275 17.549999999999997 41.725 22.45 8 20.5 20.3 31.2 28.000000000000004 9 22.375 21.25 31.324999999999996 25.05 10-14 22.785 27.0 26.240000000000002 23.974999999999998 15-19 23.51 26.52 27.575 22.395 20-24 23.455000000000002 26.875 26.72 22.95 25-29 23.855 26.295 25.7 24.15 30-34 22.71 26.02 26.25 25.019999999999996 35-39 23.97 26.545 26.045 23.44 40-44 23.330000000000002 25.645 27.145000000000003 23.880000000000003 45-49 22.755 26.33 26.855 24.060000000000002 50-54 23.365 27.05 26.26 23.325000000000003 55-59 22.384999999999998 27.084999999999997 27.389999999999997 23.14 60-64 22.145 25.03 28.21 24.615000000000002 65-69 22.905 26.755000000000003 26.805 23.535 70-74 22.939999999999998 27.015 26.064999999999998 23.98 75-79 23.350837709427356 27.561890472618156 25.541385346336583 23.545886471617905 80-84 22.759103641456583 26.010404161664667 26.370548219287716 24.859943977591037 85-89 23.97339068674036 27.61466513279648 25.764017406092133 22.64792677437103 90-94 23.796898449224614 27.1935967983992 26.343171585792895 22.666333166583293 95-99 23.322491868901675 27.715786840130097 25.8443832874656 23.117338003502628 100-104 23.169999999999998 27.755000000000003 25.919999999999998 23.155 105-109 23.75994794534261 27.263626808148555 25.782071174733467 23.194354071775365 110-114 24.016614953458113 27.14943449104194 24.772295065559003 24.061655489940946 115-119 24.34826119589692 27.555666750062546 24.673505128846635 23.422566925193898 120-124 25.076269067266814 28.122030507626906 23.74593648412103 23.055763940985248 125-129 24.94492289204887 28.10935309433206 22.947125976366912 23.998598037252155 130-134 24.943730305606962 28.655029260241083 22.587905767018455 23.813334667133496 135-139 25.17650593360373 28.77171899253918 21.29587902458565 24.755896049271445 140-144 25.342808527674908 28.385546992293065 21.28415574016615 24.987488739865878 145-149 24.16224867460238 28.74362308692608 21.246373912173652 25.84775432629789 150-151 22.885385385385383 29.404404404404406 21.77177177177177 25.93843843843844 >>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 0.0 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 0.5 22 0.5 23 0.0 24 0.5 25 0.5 26 1.0 27 3.0 28 4.0 29 3.5 30 5.5 31 9.5 32 21.5 33 33.5 34 40.0 35 53.0 36 86.0 37 102.5 38 94.5 39 111.5 40 133.5 41 146.0 42 167.5 43 163.0 44 194.0 45 235.5 46 231.0 47 218.5 48 207.5 49 207.5 50 190.5 51 155.5 52 143.5 53 142.0 54 123.0 55 126.5 56 132.5 57 126.5 58 98.5 59 63.0 60 52.0 61 38.5 62 23.5 63 17.0 64 12.0 65 9.0 66 8.0 67 8.0 68 9.0 69 11.5 70 8.5 71 3.0 72 4.5 73 7.5 74 5.0 75 2.5 76 2.0 77 1.5 78 0.5 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 0.475 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 0.025 80-84 0.04 85-89 0.034999999999999996 90-94 0.05 95-99 0.075 100-104 0.0 105-109 0.105 110-114 0.09 115-119 0.075 120-124 0.025 125-129 0.13999999999999999 130-134 0.034999999999999996 135-139 0.145 140-144 0.09 145-149 0.03 150-151 0.1 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 80.5 #Duplication Level Percentage of deduplicated Percentage of total 1 90.0 72.45 2 5.217391304347826 8.4 3 1.9875776397515528 4.8 4 0.8385093167701863 2.7 5 0.7763975155279503 3.125 6 0.4968944099378882 2.4 7 0.15527950310559005 0.8750000000000001 8 0.12422360248447205 0.8 9 0.15527950310559005 1.125 >10 0.2484472049689441 3.325 >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 28 0.7000000000000001 No Hit CTTCCGTCAATTCCTTTAAGTTTCAGCCTTGCGACCATACTCCCCCCAGA 23 0.575 No Hit CCCAACTTTCGTTCTTGATTAATGAAAACATCCTTGGCAAATGCTTTCGC 23 0.575 No Hit CGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCT 17 0.42500000000000004 No Hit CGCGCCTGCTGCCTTCCTTGGATGTGGTAGCCGTTTCTCAGGCTCCCTCT 11 0.27499999999999997 No Hit CAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGG 11 0.27499999999999997 No Hit CGCCTGCTGCCTTCCTTGGATGTGGTAGCCGTTTCTCAGGCTCCCTCTCC 10 0.25 No Hit CCAGAACCCAAAAACTTTGATTTCTCATAAGGTGCTGGCGGAGTCCTAAA 10 0.25 No Hit CCCCGACTGTCCCTGTTAATCATTACTCCGATCCCGAAGGCCAACACAAT 9 0.22499999999999998 No Hit CTGCCAGTAGTCATATGCTTGTCTCAAAGATTAAGCCATGCATGTGTAAG 9 0.22499999999999998 No Hit CCCCAACTTTCGTTCTTGATTAATGAAAACATCCTTGGCAAATGCTTTCG 9 0.22499999999999998 No Hit GTTAATCATTACTCCGATCCCGAAGGCCAACACAATAGGATCGAAATCCT 9 0.22499999999999998 No Hit CTCCGATCCCGAAGGCCAACACAATAGGATCGAAATCCTATGATGTTATC 9 0.22499999999999998 No Hit CCCGTGTCAGGATTGGGTAATTTGCGCGCCTGCTGCCTTCCTTGGATGTG 8 0.2 No Hit CGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCA 8 0.2 No Hit CCTTCCGTCAATTCCTTTAAGTTTCAGCCTTGCGACCATACTCCCCCCAG 8 0.2 No Hit GTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACT 8 0.2 No Hit CTTACCAGGTCCAGACATAGTAAGGATTGACAGACTGAGAGCTCTTTCTT 7 0.17500000000000002 No Hit GCCGTTCTTAGTTGGTGGAGCGATTTGTCTGGTTAATTCCGTTAACGAAC 7 0.17500000000000002 No Hit GTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCT 7 0.17500000000000002 No Hit TGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTT 7 0.17500000000000002 No Hit GGAAGTTTGAGGCAATAACAGGTCTGTGATGCCCTTAGATGTTCTGGGCC 7 0.17500000000000002 No Hit CAAATTTCTGCCCTATCAACTTTCGATGGTAGGATAGAGGCCTACCATGG 6 0.15 No Hit CCTGCCAGTAGTCATATGCTTGTCTCAAAGATTAAGCCATGCATGTGTAA 6 0.15 No Hit TGACCCTCCGCGGCCAGCTTCTTAGAGGGACTATGGCCTTCCAGGCCAAG 6 0.15 No Hit GTTTGAGGCAATAACAGGTCTGTGATGCCCTTAGATGTTCTGGGCCGCAC 6 0.15 No Hit CTCGTCCCTTCTACCGGCGATGCGCTCCTGGCCTTAACTGGCCGGGTCGT 6 0.15 No Hit GTCGAGTTATCATGAATCATCAGAGCAACGGGCAGAGCCCGCGTCGACCT 6 0.15 No Hit CAACTTTCGTTCTTGATTAATGAAAACATCCTTGGCAAATGCTTTCGCAG 6 0.15 No Hit GCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGC 6 0.15 No Hit GCGCTCCTGGCCTTAACTGGCCGGGTCGTGCCTCCGGTGCTGTTACTTTG 6 0.15 No Hit GCGCCTGCTGCCTTCCTTGGATGTGGTAGCCGTTTCTCAGGCTCCCTCTC 6 0.15 No Hit GTGAAATTCTTGGATTTATGAAAGACGAACAACTGCGAAAGCATTTGCCA 6 0.15 No Hit GTTTTCATTAATCAAGAACGAAAGTTGGGGGCTCGAAGACGATCAGATAC 6 0.15 No Hit CGATCAGATACCGTCCTAGTCTCAACCATAAACGATGCCGACCAGGGATT 6 0.15 No Hit CCAACTTTCGTTCTTGATTAATGAAAACATCCTTGGCAAATGCTTTCGCA 6 0.15 No Hit CGCGGCTGCTGGCACCAGACTTGCCCTCCAATGGATCCTCGTTAAGGGAT 6 0.15 No Hit GCCAGTAGTCATATGCTTGTCTCAAAGATTAAGCCATGCATGTGTAAGTA 6 0.15 No Hit CTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAAC 5 0.125 No Hit TCCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAA 5 0.125 No Hit GTCGGCATCGTTTATGGTTGAGACTAGGACGGTATCTGATCGTCTTCGAG 5 0.125 No Hit CTGCTAACTAGCTATGCGGAGGTGACCCTCCGCGGCCAGCTTCTTAGAGG 5 0.125 No Hit CAAACCCCGACTTCTGGAAGGGACGCATTTATTAGATAAAAGGTCGACGC 5 0.125 No Hit CTGTGATGCCCTTAGATGTTCTGGGCCGCACGCGCGCTACACTGATGTAT 5 0.125 No Hit GCCTGCTGCCTTCCTTGGATGTGGTAGCCGTTTCTCAGGCTCCCTCTCCG 5 0.125 No Hit CCGTCAATTCCTTTAAGTTTCAGCCTTGCGACCATACTCCCCCCAGAACC 5 0.125 No Hit CTGCGAATGGCTCATTAAATCAGTTATAGTTTGTTTGATGGTATTTGCTA 5 0.125 No Hit TGTTAATCATTACTCCGATCCCGAAGGCCAACACAATAGGATCGAAATCC 5 0.125 No Hit CCCCCGACTGTCCCTGTTAATCATTACTCCGATCCCGAAGGCCAACACAA 5 0.125 No Hit CGAGTCTATAGCCTTGGCCGACAGGCCCGGGTAATCTTTGAAATTTCATC 5 0.125 No Hit CTCAAACTTCCTTGGCCTGGAAGGCCATAGTCCCTCTAAGAAGCTGGCCG 5 0.125 No Hit GCTCAAAGCAAGCCTACGCTCTGGATACATTAGCATGGGATAACATCATA 5 0.125 No Hit CTCAAAGCAAGCCTACGCTCTGGATACATTAGCATGGGATAACATCATAG 5 0.125 No Hit CGGATATCTCGGCTCTCGCATCGATGAAGAACGTAGCGAAATGCGATACT 5 0.125 No Hit CAGGTCCAGACATAGTAAGGATTGACAGACTGAGAGCTCTTTCTTGATTC 5 0.125 No Hit CCGACATCGAAGGATCAAAAAGCAACGTCGCTATGAACGCTTGGCTGCCA 5 0.125 No Hit CGTCAATTCCTTTAAGTTTCAGCCTTGCGACCATACTCCCCCCAGAACCC 5 0.125 No Hit CTGTTAATCATTACTCCGATCCCGAAGGCCAACACAATAGGATCGAAATC 5 0.125 No Hit CTTGCTTTGAGCACTCTAATTTCTTCAAAGTAACAGCACCGGAGGCACGA 5 0.125 No Hit CTGCTGCCTTCCTTGGATGTGGTAGCCGTTTCTCAGGCTCCCTCTCCGGA 5 0.125 No Hit TGCTGCCTTCCTTGGATGTGGTAGCCGTTTCTCAGGCTCCCTCTCCGGAA 5 0.125 No Hit CTCAGGTGTGCACCGGTCGCCTCGTCCCTTCTACCGGCGATGCGCTCCTG 5 0.125 No Hit GTCGGGGGCATTCGTATTTCATAGTCAGAGGTGAAATTCTTGGATTTATG 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 0.0125 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 0.05 0.0 0.0 0.0 0.0 42-43 0.05 0.0 0.0 0.0 0.0 44-45 0.05 0.0 0.0 0.0 0.0 46-47 0.0625 0.0 0.0 0.0 0.0 48-49 0.075 0.0 0.0 0.0 0.0 50-51 0.0875 0.0 0.0 0.0 0.0 52-53 0.1 0.0 0.0 0.0 0.0 54-55 0.1 0.0 0.0 0.0 0.0 56-57 0.1 0.0 0.0 0.0 0.0 58-59 0.1 0.0 0.0 0.0 0.0 60-61 0.1 0.0 0.0 0.0 0.0 62-63 0.1 0.0 0.0 0.0 0.0 64-65 0.125 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 0.1375 0.0 0.0 0.0 0.0 72-73 0.15 0.0 0.0 0.0 0.0 74-75 0.16249999999999998 0.0 0.0 0.0 0.0 76-77 0.2 0.0 0.0 0.0 0.0 78-79 0.21250000000000002 0.0 0.0 0.0 0.0 80-81 0.3125 0.0 0.0 0.0 0.0 82-83 0.4125 0.0 0.0 0.0 0.0 84-85 0.475 0.0 0.0 0.0 0.0 86-87 0.6125 0.0 0.0 0.0 0.0 88-89 0.8374999999999999 0.0 0.0 0.0 0.0 90-91 1.025 0.0 0.0 0.0 0.0 92-93 1.325 0.0 0.0 0.0 0.0 94-95 1.7875 0.0 0.0 0.0 0.0 96-97 2.1500000000000004 0.0 0.0 0.0 0.0 98-99 2.65 0.0 0.0 0.0 0.0 100-101 3.175 0.0 0.0 0.0 0.0 102-103 3.7 0.0 0.0 0.0 0.0 104-105 4.7125 0.0 0.0 0.0 0.0 106-107 5.8125 0.0 0.0 0.0 0.0 108-109 7.2875 0.0 0.0 0.0 0.0 110-111 8.2 0.0 0.0 0.0 0.0 112-113 9.350000000000001 0.0 0.0 0.0 0.0 114-115 10.7875 0.0 0.0 0.0 0.0 116-117 12.399999999999999 0.0 0.0 0.0 0.0 118-119 13.8625 0.0 0.0 0.0 0.0 120-121 15.4625 0.0 0.0 0.0 0.0 122-123 17.35 0.0 0.0 0.0 0.0 124-125 19.475 0.0 0.0 0.0 0.0 126-127 21.674999999999997 0.0 0.0 0.0 0.0 128-129 23.575 0.0 0.0 0.0 0.0 130-131 25.4625 0.0 0.0 0.0 0.0 132-133 27.6875 0.0 0.0 0.0 0.0 134-135 29.7375 0.0 0.0 0.0 0.0 136-137 32.05 0.0 0.0 0.0 0.0 138-139 34.45 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GTCATAT 10 0.006830828 145.0 8 AGTAGTC 10 0.006830828 145.0 4 CAGTAGT 10 0.006830828 145.0 3 CTCCACT 10 0.006830828 145.0 7 TAGTCAT 10 0.006830828 145.0 6 CCACTCC 10 0.006830828 145.0 9 CGCAGGC 10 0.006830828 145.0 1 AGTCATA 10 0.006830828 145.0 7 CAAAAAC 35 0.0033124194 62.14286 9 CCAAAAA 45 0.008957279 48.333332 8 >>END_MODULE Rejected 2014559 READS because READLEN < 1 Read 2014559 spots for SRR6793148.sra Written 2014559 spots for SRR6793148.sra Rejected 2014559 READS because READLEN < 1 Read 2014559 spots for SRR6793148.sra Written 2014559 spots for SRR6793148.sra Rejected 2014559 READS because READLEN < 1 Read 2014559 spots for SRR6793148.sra Written 2014559 spots for SRR6793148.sra Rejected 2014559 READS because READLEN < 1 Read 2014559 spots for SRR6793148.sra Written 2014559 spots for SRR6793148.sra Rejected 2014559 READS because READLEN < 1 Read 2014559 spots for SRR6793148.sra Written 2014559 spots for SRR6793148.sra Rejected 2014559 READS because READLEN < 1 Read 2014559 spots for SRR6793148.sra Written 2014559 spots for SRR6793148.sra Rejected 2014559 READS because READLEN < 1 Read 2014559 spots for SRR6793148.sra Written 2014559 spots for SRR6793148.sra Rejected 2014559 READS because READLEN < 1 Read 2014559 spots for SRR6793148.sra Written 2014559 spots for SRR6793148.sra Rejected 2014559 READS because READLEN < 1 Read 2014559 spots for SRR6793148.sra Written 2014559 spots for SRR6793148.sra Rejected 2014559 READS because READLEN < 1 Read 2014559 spots for SRR6793148.sra Written 2014559 spots for SRR6793148.sra Rejected 2014559 READS because READLEN < 1 Read 2014559 spots for SRR6793148.sra Written 2014559 spots for SRR6793148.sra Rejected 2014559 READS because READLEN < 1 Read 2014559 spots for SRR6793148.sra Written 2014559 spots for SRR6793148.sra Rejected 2014559 READS because READLEN < 1 Read 2014559 spots for SRR6793148.sra Written 2014559 spots for SRR6793148.sra Rejected 2014559 READS because READLEN < 1 Read 2014559 spots for SRR6793148.sra Written 2014559 spots for SRR6793148.sra Rejected 2014559 READS because READLEN < 1 Read 2014559 spots for SRR6793148.sra Written 2014559 spots for SRR6793148.sra Rejected 2014559 READS because READLEN < 1 Read 2014559 spots for SRR6793148.sra Written 2014559 spots for SRR6793148.sra Rejected 2014559 READS because READLEN < 1 Read 2014559 spots for SRR6793148.sra Written 2014559 spots for SRR6793148.sra Rejected 2014559 READS because READLEN < 1 Read 2014559 spots for SRR6793148.sra Written 2014559 spots for SRR6793148.sra Rejected 2014559 READS because READLEN < 1 Read 2014559 spots for SRR6793148.sra Written 2014559 spots for SRR6793148.sra Rejected 2014571 READS because READLEN < 1 Read 2014571 spots for SRR6793148.sra Written 2014571 spots for SRR6793148.sra SRR ids: ['SRR6793148.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_v025jo2i SRR6793148.sra spots: 40291192 blocks: [[1, 2014559], [2014560, 4029118], [4029119, 6043677], [6043678, 8058236], [8058237, 10072795], [10072796, 12087354], [12087355, 14101913], [14101914, 16116472], [16116473, 18131031], [18131032, 20145590], [20145591, 22160149], [22160150, 24174708], [24174709, 26189267], [26189268, 28203826], [28203827, 30218385], [30218386, 32232944], [32232945, 34247503], [34247504, 36262062], [36262063, 38276621], [38276622, 40291192]] SRR6793148 file size 13631662 SRR6793148 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 SRR6793148 SRR6793148_1.fastq Input file: SRR6793148_1.fastq trimmed: SRR6793148-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 14:33:24 2025 >> started Thu Feb 13 14:33:46 2025 >> done (22.133s) 40291192 reads processed; of these: 2329 ( 0.01%) short reads filtered out after trimming by size control 12256 ( 0.03%) empty reads filtered out after trimming by size control 40276607 (99.96%) reads available; of these: 6332486 (15.72%) trimmed reads available after processing 33944121 (84.28%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 113 0.00% 19 127 0.00% 20 123 0.00% 21 149 0.00% 22 153 0.00% 23 185 0.00% 24 251 0.00% 25 293 0.00% 26 363 0.00% 27 351 0.00% 28 469 0.00% 29 461 0.00% 30 528 0.00% 31 531 0.00% 32 570 0.00% 33 610 0.00% 34 639 0.00% 35 785 0.00% 36 793 0.00% 37 797 0.00% 38 933 0.00% 39 809 0.00% 40 919 0.00% 41 982 0.00% 42 946 0.00% 43 1010 0.00% 44 1026 0.00% 45 1007 0.00% 46 1109 0.00% 47 1101 0.00% 48 1213 0.00% 49 1170 0.00% 50 1234 0.00% 51 1238 0.00% 52 1303 0.00% 53 1418 0.00% 54 1378 0.00% 55 1623 0.00% 56 1561 0.00% 57 1654 0.00% 58 1739 0.00% 59 2466 0.01% 60 2365 0.01% 61 2313 0.01% 62 2347 0.01% 63 2337 0.01% 64 2283 0.01% 65 2350 0.01% 66 2500 0.01% 67 2590 0.01% 68 2949 0.01% 69 3186 0.01% 70 3483 0.01% 71 4562 0.01% 72 4768 0.01% 73 5938 0.01% 74 6114 0.02% 75 7381 0.02% 76 8164 0.02% 77 8611 0.02% 78 10068 0.02% 79 11079 0.03% 80 13611 0.03% 81 15233 0.04% 82 18231 0.05% 83 20904 0.05% 84 24595 0.06% 85 25892 0.06% 86 28560 0.07% 87 31127 0.08% 88 35184 0.09% 89 40424 0.10% 90 45681 0.11% 91 53593 0.13% 92 62979 0.16% 93 70686 0.18% 94 77416 0.19% 95 86350 0.21% 96 94033 0.23% 97 101522 0.25% 98 112793 0.28% 99 129436 0.32% 100 127922 0.32% 101 145819 0.36% 102 161576 0.40% 103 178011 0.44% 104 185969 0.46% 105 191189 0.47% 106 202888 0.50% 107 221536 0.55% 108 233847 0.58% 109 251672 0.62% 110 255151 0.63% 111 304080 0.75% 112 308749 0.77% 113 302406 0.75% 114 322991 0.80% 115 334059 0.83% 116 356177 0.88% 117 332539 0.83% 118 332731 0.83% 119 357259 0.89% 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 55 0.00% 131 189 0.00% 132 101 0.00% 133 115 0.00% 134 173 0.00% 135 208 0.00% 136 106 0.00% 137 27 0.00% 138 52 0.00% 139 14 0.00% 140 0 0.00% 141 21 0.00% 142 20 0.00% 143 487 0.00% 144 290 0.00% 145 26 0.00% 146 49 0.00% 147 216 0.00% 148 893 0.00% 149 613 0.00% 150 2492 0.01% 151 33944121 84.28% 40276607 reads passed initial QC criterion=sequence-density sequence-density=18.75 sequence-density-rank=1 fanout-score=41.48 fanout-score-rank=1 prefix-density=21.62 prefix-fanout=36.0 sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACGCCAATATCTCGTATGCCGTCTTCTGCTTG criterion=fanout-score sequence-density=18.75 sequence-density-rank=1 fanout-score=41.48 fanout-score-rank=1 prefix-density=21.62 prefix-fanout=36.0 sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACGCCAATATCTCGTATGCCGTCTTCTGCTTG 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 AGATCGGAAGAGCACACGTCTGAACTCCAGTCACGCCAATATCTCGTATGCCGTCTTCTGCTTG -o SRR6793148 - Input file: STDIN trimmed: SRR6793148-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): AGATCGGAAGAGCACACGTCTGAACTCCAGTCACGCCAATATCTCGTATGCCGTCTTCTGCTTG -- 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 14:35:25 2025 >> started Thu Feb 13 14:36:07 2025 >> done (41.746s) 36036964 reads processed; of these: 82 ( 0.00%) short reads filtered out after trimming by size control 337 ( 0.00%) empty reads filtered out after trimming by size control 36036545 (100.00%) reads available; of these: 11146818 (30.93%) trimmed reads available after processing 24889727 (69.07%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 112 0.00% 19 118 0.00% 20 108 0.00% 21 139 0.00% 22 146 0.00% 23 176 0.00% 24 232 0.00% 25 275 0.00% 26 336 0.00% 27 333 0.00% 28 423 0.00% 29 417 0.00% 30 479 0.00% 31 481 0.00% 32 534 0.00% 33 558 0.00% 34 585 0.00% 35 705 0.00% 36 722 0.00% 37 716 0.00% 38 841 0.00% 39 748 0.00% 40 832 0.00% 41 892 0.00% 42 862 0.00% 43 894 0.00% 44 926 0.00% 45 894 0.00% 46 992 0.00% 47 1001 0.00% 48 1083 0.00% 49 1053 0.00% 50 1134 0.00% 51 1133 0.00% 52 1167 0.00% 53 1268 0.00% 54 1253 0.00% 55 1469 0.00% 56 1403 0.00% 57 1503 0.00% 58 1575 0.00% 59 2241 0.01% 60 2103 0.01% 61 2041 0.01% 62 2117 0.01% 63 2129 0.01% 64 2064 0.01% 65 2152 0.01% 66 2236 0.01% 67 2334 0.01% 68 2651 0.01% 69 2874 0.01% 70 3195 0.01% 71 4076 0.01% 72 4294 0.01% 73 5266 0.01% 74 5511 0.02% 75 6749 0.02% 76 7410 0.02% 77 7858 0.02% 78 9092 0.03% 79 10085 0.03% 80 12333 0.03% 81 13700 0.04% 82 16411 0.05% 83 18743 0.05% 84 22207 0.06% 85 23229 0.06% 86 25760 0.07% 87 28115 0.08% 88 31876 0.09% 89 36686 0.10% 90 42466 0.12% 91 48610 0.13% 92 56532 0.16% 93 62055 0.17% 94 69244 0.19% 95 77364 0.21% 96 84357 0.23% 97 91446 0.25% 98 101375 0.28% 99 116445 0.32% 100 114915 0.32% 101 130965 0.36% 102 144936 0.40% 103 159442 0.44% 104 167231 0.46% 105 171707 0.48% 106 181726 0.50% 107 199500 0.55% 108 209458 0.58% 109 226133 0.63% 110 228197 0.63% 111 272738 0.76% 112 276995 0.77% 113 271265 0.75% 114 289246 0.80% 115 298947 0.83% 116 318208 0.88% 117 294349 0.82% 118 296954 0.82% 119 325674 0.90% 120 353583 0.98% 121 377951 1.05% 122 358861 1.00% 123 362849 1.01% 124 351788 0.98% 125 363663 1.01% 126 386417 1.07% 127 366883 1.02% 128 398026 1.10% 129 368066 1.02% 130 385717 1.07% 131 364506 1.01% 132 384923 1.07% 133 389601 1.08% 134 421605 1.17% 135 408215 1.13% 136 390719 1.08% 137 383370 1.06% 138 355820 0.99% 139 353461 0.98% 140 341376 0.95% 141 343352 0.95% 142 350717 0.97% 143 362737 1.01% 144 353709 0.98% 145 344298 0.96% 146 362874 1.01% 147 401608 1.11% 148 684687 1.90% 149 394 0.00% 150 1614 0.00% 151 19286619 53.52% criterion=sequence-density sequence-density=0.24 sequence-density-rank=1 fanout-score=10.04 fanout-score-rank=9 prefix-density=0.98 prefix-fanout=2.4 sequence=CTGCTGGCACCTCCATGACTACGGAGGAGACATAGTTCTTCTCAGTCTCGACGATGCCAGCAGTGTAGCTGCTTCCCTTCTTGACACACTGGGTCTTGTCAGCGCAGTCGCAGGTGTCGCAGGTGCTAGACATGATGATTGATTGATTAAGCTTAAATGGATGAACTAAAAGACTTGGAGTATGAATGTGTTCT criterion=fanout-score sequence-density=0.03 sequence-density-rank=32 fanout-score=40.38 fanout-score-rank=1 prefix-density=0.88 prefix-fanout=1.5 sequence=CGCATCGCCGGCCCCCATCCACTTCCCTCCCGACAATTTCAAGCACTCTTTGACTCTCTTTTCAAAGTCCTTTTCATCTTTCCCTCGCGGTACTTGTTTGCTATCGGTCTCTCGCCCGTATTTAGCCTTGGACGGAATTTACCGCCCGATTGGGGCTGCATTCCCAAACAACCCGACTCGCAGACAGCGCCTCGTGGTGCGGCAGGGTCCAGCCACGACGGGGCTCTCACCCTCTCCGGCGCCCCTTTCCAGGGGACTTGGGCCTGGTCCGCCGCTGAGGACGCTTCTCCAGACTACAATTCGGACGCCGCAGGCGCCAGATTCTCAAGCTGGGCATTTCCCGGTTCGCTCGCCGTTACTAGGGGAATCCTTGTAAGTTTCTTTTCCT Started job on | Feb 13 14:36:45 Started mapping on | Feb 13 14:36:45 Finished on | Feb 13 14:38:41 Mapping speed, Million of reads per hour | 1249.95 Number of input reads | 40276188 Average input read length | 139 UNIQUE READS: Uniquely mapped reads number | 20230079 Uniquely mapped reads % | 50.23% Average mapped length | 138.79 Number of splices: Total | 7393353 Number of splices: Annotated (sjdb) | 7179334 Number of splices: GT/AG | 7241255 Number of splices: GC/AG | 106894 Number of splices: AT/AC | 8301 Number of splices: Non-canonical | 36903 Mismatch rate per base, % | 0.52% Deletion rate per base | 0.03% Deletion average length | 2.78 Insertion rate per base | 0.03% Insertion average length | 2.84 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 2193020 % of reads mapped to multiple loci | 5.44% Number of reads mapped to too many loci | 17054294 % of reads mapped to too many loci | 42.34% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.67% % of reads unmapped: other | 0.31% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 17853089 17853089 17853089 N_multimapping 2193020 2193020 2193020 N_noFeature 1963907 10913239 11056509 N_ambiguous 317045 46878 46440 UnstrandedReadsAssigned:17949127 PositiveStrandReadsAssigned:9269962 NegativeStrandReadsAssigned:9127130 Dataset is classified unstranded MeadianReadLen=151 20thPercentileLength=124 echo kmer=119 SRR6793148 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: SRR6793148-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 40,276,188 reads, 31,725,344 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,078 rounds 52401 SRR6793148.ke.tsv 34699 SRR6793148.se.tsv 87100 total ==> SRR6793148.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1919 2822 57.9121 Potri.005G024800.1.v4.1 1035 936 393 16.535 Potri.004G059700.1.v4.1 961 862 4 0.182743 Potri.007G009000.2.v4.1 1416 1317 0 0 Potri.003G141000.2.v4.1 2943 2844 1419.71 19.6588 Potri.016G087400.1.v4.1 270 171 1249 287.643 Potri.015G069301.1.v4.1 564 465 0 0 Potri.010G195200.1.v4.1 1773 1674 3513.8 82.6624 Potri.012G127500.1.v4.1 977 878 593 26.5979 ==> SRR6793148.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 149 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 389 Potri.001G212900.v4.1 0 Potri.001G182400.v4.1 3 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 55 Potri.001G416900.v4.1 4 Potri.001G452600.v4.1 4 SRR6793148 completed mapping pipeline successfully