Starting /dee2/code/volunteer_pipeline.sh SRR12671342 current disk space = 3048415571968 free memory = 1443134804 SRR12671342 SRAfilesize fb473ab25c9f0b8f3b35d236291907b7 SRR12671342.sra SRR12671342.sra file validated SRR12671342 is paired end SRR12671342 is conventional basespace SRR12671342 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12671342_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 44 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.599 37.0 37.0 37.0 37.0 37.0 2 36.28675 37.0 37.0 37.0 37.0 37.0 3 36.625 37.0 37.0 37.0 37.0 37.0 4 36.6515 37.0 37.0 37.0 37.0 37.0 5 36.5995 37.0 37.0 37.0 37.0 37.0 6 36.5975 37.0 37.0 37.0 37.0 37.0 7 36.637 37.0 37.0 37.0 37.0 37.0 8 36.6375 37.0 37.0 37.0 37.0 37.0 9 36.62 37.0 37.0 37.0 37.0 37.0 10-14 36.636199999999995 37.0 37.0 37.0 37.0 37.0 15-19 36.592800000000004 37.0 37.0 37.0 37.0 37.0 20-24 36.6063 37.0 37.0 37.0 37.0 37.0 25-29 36.5218 37.0 37.0 37.0 37.0 37.0 30-34 36.5431 37.0 37.0 37.0 37.0 37.0 35-39 36.567400000000006 37.0 37.0 37.0 37.0 37.0 40-44 36.5535 37.0 37.0 37.0 37.0 37.0 45-49 36.495000000000005 37.0 37.0 37.0 37.0 37.0 50-54 36.5192 37.0 37.0 37.0 37.0 37.0 55-59 36.4617 37.0 37.0 37.0 37.0 37.0 60-64 36.468 37.0 37.0 37.0 37.0 37.0 65-69 36.467200000000005 37.0 37.0 37.0 37.0 37.0 70-74 36.4425 37.0 37.0 37.0 37.0 37.0 75-79 36.393499999999996 37.0 37.0 37.0 37.0 37.0 80-84 36.3856 37.0 37.0 37.0 37.0 37.0 85-89 36.3103 37.0 37.0 37.0 37.0 37.0 90-94 36.33910000000001 37.0 37.0 37.0 37.0 37.0 95-99 36.265100000000004 37.0 37.0 37.0 37.0 37.0 100-104 36.2595 37.0 37.0 37.0 37.0 37.0 105-109 36.2916 37.0 37.0 37.0 37.0 37.0 110-114 36.208299999999994 37.0 37.0 37.0 37.0 37.0 115-119 36.224199999999996 37.0 37.0 37.0 37.0 37.0 120-124 36.203399999999995 37.0 37.0 37.0 37.0 37.0 125-129 36.1749 37.0 37.0 37.0 37.0 37.0 130-134 36.1 37.0 37.0 37.0 37.0 37.0 135-139 36.0915 37.0 37.0 37.0 37.0 37.0 140-144 35.996500000000005 37.0 37.0 37.0 37.0 37.0 145-149 35.99100000000001 37.0 37.0 37.0 37.0 37.0 150-151 35.931 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 22 1.0 23 1.0 24 4.0 25 2.0 26 3.0 27 5.0 28 14.0 29 13.0 30 16.0 31 44.0 32 33.0 33 50.0 34 71.0 35 247.0 36 3021.0 37 475.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 44.875 10.475 5.45 39.2 2 20.382005529027396 13.244533802462929 37.49685850716261 28.87660216134707 3 19.875 18.025 28.15 33.95 4 24.325 25.324999999999996 23.200000000000003 27.150000000000002 5 24.275 31.7 23.724999999999998 20.3 6 18.35 34.525 24.975 22.15 7 14.45 25.6 43.375 16.575 8 16.150000000000002 24.05 35.35 24.45 9 17.925 22.75 34.5 24.825 10-14 20.064999999999998 30.145 26.965 22.825 15-19 19.37 28.645 28.68 23.305 20-24 20.525 28.444999999999997 27.089999999999996 23.94 25-29 20.02 28.685 27.0 24.295 30-34 19.259999999999998 28.955 27.884999999999998 23.9 35-39 20.135 28.935 27.155 23.775 40-44 20.369999999999997 27.884999999999998 28.33 23.415 45-49 19.869999999999997 28.68 27.29 24.16 50-54 20.25 29.049999999999997 27.445000000000004 23.255 55-59 19.8 28.33 27.88 23.990000000000002 60-64 19.865 28.33 27.200000000000003 24.605 65-69 20.03 27.900000000000002 28.025 24.044999999999998 70-74 19.869999999999997 28.215 27.255000000000003 24.66 75-79 20.355 28.449999999999996 27.52 23.674999999999997 80-84 19.765 28.110000000000003 27.555000000000003 24.57 85-89 20.435 29.15 27.18 23.235 90-94 20.369999999999997 28.1 27.63 23.9 95-99 20.150000000000002 28.68 27.715 23.455000000000002 100-104 20.025000000000002 28.405 27.74 23.830000000000002 105-109 21.11 28.425 26.924999999999997 23.54 110-114 20.36 28.375 27.255000000000003 24.01 115-119 20.44 28.439999999999998 27.52 23.599999999999998 120-124 20.71 28.175 27.85 23.265 125-129 20.535 28.725 27.07 23.669999999999998 130-134 21.365000000000002 28.025 27.55 23.06 135-139 20.9 27.744999999999997 27.26 24.095 140-144 20.59 28.294999999999998 27.79 23.325000000000003 145-149 20.555 28.025 27.82 23.599999999999998 150-151 21.2375 28.012500000000003 26.85 23.9 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 2.0 1 1.0 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 1.5 18 1.5 19 1.0 20 1.0 21 0.5 22 3.0 23 4.5 24 2.5 25 2.5 26 6.5 27 10.5 28 14.5 29 15.0 30 18.5 31 30.5 32 37.0 33 41.5 34 42.0 35 63.0 36 94.0 37 101.0 38 132.0 39 165.5 40 165.0 41 207.5 42 248.5 43 221.0 44 234.5 45 256.5 46 262.0 47 261.0 48 232.0 49 218.0 50 201.0 51 161.0 52 123.5 53 91.5 54 69.0 55 56.0 56 47.0 57 38.5 58 24.5 59 24.5 60 23.5 61 16.0 62 9.0 63 5.5 64 2.5 65 3.0 66 3.0 67 1.0 68 1.5 69 1.0 70 0.0 71 0.0 72 0.0 73 0.0 74 0.0 75 0.0 76 0.0 77 0.0 78 0.0 79 0.0 80 0.0 81 0.0 82 0.0 83 0.0 84 0.0 85 0.0 86 0.0 87 0.0 88 0.0 89 0.0 90 0.0 91 0.0 92 0.0 93 0.0 94 0.0 95 0.0 96 0.0 97 0.0 98 0.0 99 0.0 100 0.0 >>END_MODULE >>Per base N content pass #Base N-Count 1 0.0 2 0.525 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10-14 0.0 15-19 0.0 20-24 0.0 25-29 0.0 30-34 0.0 35-39 0.0 40-44 0.0 45-49 0.0 50-54 0.0 55-59 0.0 60-64 0.0 65-69 0.0 70-74 0.0 75-79 0.0 80-84 0.0 85-89 0.0 90-94 0.0 95-99 0.0 100-104 0.0 105-109 0.0 110-114 0.0 115-119 0.0 120-124 0.0 125-129 0.0 130-134 0.0 135-139 0.0 140-144 0.0 145-149 0.0 150-151 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 84.05 #Duplication Level Percentage of deduplicated Percentage of total 1 85.24687685901249 71.65 2 11.659726353361094 19.6 3 2.3200475907198097 5.8500000000000005 4 0.5056513979773943 1.7000000000000002 5 0.1784651992861392 0.75 6 0.0892325996430696 0.44999999999999996 7 0.0 0.0 8 0.0 0.0 9 0.0 0.0 >10 0.0 0.0 >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 CTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATT 6 0.15 No Hit CTCACGGACACTTTTGTTTGTTCACTCCACACCCACAAGTACAGAAGAAC 6 0.15 No Hit GTGGTATTCTTCTGCTCGGTAGAATTTTTTGGCAGGTAAAATCTCCGTGA 6 0.15 No Hit TGGCAATGATGAAGATGAAAAGATGATTGGTTTTTGAATAGGAGCAGTGA 5 0.125 No Hit GCCCGATTCAGCATCCGAATCCAGAAGCTAAAAACAAAAACAAAGTAGAA 5 0.125 No Hit CTTGCAACAATAATGCCAATCGTGGTCCGAATCCCAAGTTTCGATTCATT 5 0.125 No Hit TGCTGATCAAGTTGACAATCGCATTGGGGCAGCACTTTGCTACTCCCTCG 5 0.125 No Hit GCTCATCAAAAAGCTCCCATGAAACAAAGGAGACAACTCTCACAGCCTTG 5 0.125 No Hit GAAAAATCCAGAAACACTACTTGCACCTAACACTGTAGCACCTTCACCAA 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 0.025 0.0 36-37 0.0 0.0 0.0 0.025 0.0 38-39 0.0 0.0 0.0 0.025 0.0 40-41 0.0 0.0 0.0 0.025 0.0 42-43 0.0 0.0 0.0 0.025 0.0 44-45 0.0 0.0 0.0 0.025 0.0 46-47 0.0 0.0 0.0 0.025 0.0 48-49 0.0 0.0 0.0 0.025 0.0 50-51 0.0 0.0 0.0 0.025 0.0 52-53 0.0 0.0 0.0 0.025 0.0 54-55 0.0 0.0 0.0 0.025 0.0 56-57 0.0 0.0 0.0 0.025 0.0 58-59 0.0 0.0 0.0 0.025 0.0 60-61 0.0 0.0 0.0 0.025 0.0 62-63 0.0 0.0 0.0 0.025 0.0 64-65 0.0 0.0 0.0 0.025 0.0 66-67 0.0 0.0 0.0 0.025 0.0 68-69 0.0125 0.0 0.0 0.025 0.0 70-71 0.025 0.0 0.0 0.025 0.0 72-73 0.025 0.0 0.0 0.025 0.0 74-75 0.025 0.0 0.0 0.025 0.0 76-77 0.025 0.0 0.0 0.025 0.0 78-79 0.025 0.0 0.0 0.025 0.0 80-81 0.037500000000000006 0.0 0.0 0.025 0.0 82-83 0.0625 0.0 0.0 0.025 0.0 84-85 0.075 0.0 0.0 0.025 0.0 86-87 0.075 0.0 0.0 0.025 0.0 88-89 0.1125 0.0 0.0 0.025 0.0 90-91 0.1375 0.0 0.0 0.025 0.0 92-93 0.2125 0.0 0.0 0.025 0.0 94-95 0.32499999999999996 0.0 0.0 0.025 0.0 96-97 0.375 0.0 0.0 0.025 0.0 98-99 0.4125 0.0 0.0 0.025 0.0 100-101 0.44999999999999996 0.0 0.0 0.025 0.0 102-103 0.5874999999999999 0.0 0.0 0.025 0.0 104-105 0.65 0.0 0.0 0.025 0.0 106-107 0.7625 0.0 0.0 0.025 0.0 108-109 0.8125 0.0 0.0 0.025 0.0 110-111 0.9125000000000001 0.0 0.0 0.025 0.0 112-113 1.0625 0.0 0.0 0.025 0.0 114-115 1.1875 0.0 0.0 0.025 0.0 116-117 1.3 0.0 0.0 0.025 0.0 118-119 1.5 0.0 0.0 0.025 0.0 120-121 1.65 0.0 0.0 0.025 0.0 122-123 1.8250000000000002 0.0 0.0 0.025 0.0 124-125 2.05 0.0 0.0 0.025 0.0 126-127 2.125 0.0 0.0 0.025 0.0 128-129 2.25 0.0 0.0 0.025 0.0 130-131 2.4125 0.0 0.0 0.025 0.0 132-133 2.7125 0.0 0.0 0.025 0.0 134-135 3.0125 0.0 0.0 0.025 0.0 136-137 3.25 0.0 0.0 0.025 0.0 138-139 3.625 0.0 0.0 0.025 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE SRR12671342 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12671342_2.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 151 %GC 44 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.2505 37.0 37.0 37.0 37.0 37.0 2 35.924 37.0 37.0 37.0 37.0 37.0 3 36.236 37.0 37.0 37.0 37.0 37.0 4 36.227 37.0 37.0 37.0 37.0 37.0 5 36.217 37.0 37.0 37.0 37.0 37.0 6 36.3075 37.0 37.0 37.0 37.0 37.0 7 36.1615 37.0 37.0 37.0 37.0 37.0 8 36.316 37.0 37.0 37.0 37.0 37.0 9 36.251 37.0 37.0 37.0 37.0 37.0 10-14 36.2625 37.0 37.0 37.0 37.0 37.0 15-19 36.238099999999996 37.0 37.0 37.0 37.0 37.0 20-24 36.15219999999999 37.0 37.0 37.0 37.0 37.0 25-29 36.26049999999999 37.0 37.0 37.0 37.0 37.0 30-34 36.112100000000005 37.0 37.0 37.0 37.0 37.0 35-39 36.1216 37.0 37.0 37.0 37.0 37.0 40-44 36.1319 37.0 37.0 37.0 37.0 37.0 45-49 36.079899999999995 37.0 37.0 37.0 37.0 37.0 50-54 36.0455 37.0 37.0 37.0 37.0 37.0 55-59 36.048700000000004 37.0 37.0 37.0 37.0 37.0 60-64 36.0102 37.0 37.0 37.0 37.0 37.0 65-69 36.018699999999995 37.0 37.0 37.0 37.0 37.0 70-74 35.9408 37.0 37.0 37.0 37.0 37.0 75-79 35.9388 37.0 37.0 37.0 37.0 37.0 80-84 35.9027 37.0 37.0 37.0 37.0 37.0 85-89 36.0169 37.0 37.0 37.0 37.0 37.0 90-94 35.9213 37.0 37.0 37.0 37.0 37.0 95-99 35.8655 37.0 37.0 37.0 37.0 37.0 100-104 35.8283 37.0 37.0 37.0 37.0 37.0 105-109 35.7671 37.0 37.0 37.0 37.0 37.0 110-114 35.728300000000004 37.0 37.0 37.0 37.0 37.0 115-119 35.8363 37.0 37.0 37.0 37.0 37.0 120-124 35.7541 37.0 37.0 37.0 37.0 37.0 125-129 35.7664 37.0 37.0 37.0 37.0 37.0 130-134 35.6748 37.0 37.0 37.0 37.0 37.0 135-139 35.60730000000001 37.0 37.0 37.0 37.0 37.0 140-144 35.6315 37.0 37.0 37.0 37.0 37.0 145-149 35.558800000000005 37.0 37.0 37.0 37.0 37.0 150-151 35.29175 37.0 37.0 37.0 31.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 13 3.0 14 1.0 15 3.0 16 0.0 17 0.0 18 0.0 19 1.0 20 0.0 21 2.0 22 4.0 23 3.0 24 4.0 25 9.0 26 4.0 27 7.0 28 12.0 29 17.0 30 25.0 31 41.0 32 66.0 33 88.0 34 209.0 35 571.0 36 2738.0 37 192.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 39.050000000000004 24.4 8.774999999999999 27.775 2 25.525 26.525 33.074999999999996 14.875 3 21.025 27.950000000000003 32.2 18.825 4 24.525 34.4 22.225 18.85 5 25.275 38.824999999999996 21.275 14.625 6 18.6 40.725 22.275 18.4 7 18.95 21.425 41.6 18.025 8 19.8 22.650000000000002 31.075000000000003 26.474999999999998 9 21.2 23.7 30.875000000000004 24.224999999999998 10-14 22.595000000000002 29.375 27.150000000000002 20.880000000000003 15-19 22.91 27.97 27.845 21.275 20-24 23.07 28.65 27.73 20.549999999999997 25-29 22.52 28.1 28.705000000000002 20.674999999999997 30-34 22.35 27.384999999999998 28.349999999999998 21.915000000000003 35-39 22.405 27.915 27.99 21.69 40-44 22.525000000000002 28.51 27.839999999999996 21.125 45-49 22.615 28.105000000000004 28.015 21.265 50-54 22.355 28.605000000000004 28.1 20.94 55-59 22.545 28.26 27.815 21.38 60-64 22.845 27.58 27.889999999999997 21.685 65-69 23.155 27.744999999999997 27.639999999999997 21.46 70-74 22.765 28.215 27.3 21.72 75-79 22.45 28.57 27.55 21.43 80-84 22.78 28.34 27.200000000000003 21.68 85-89 23.075000000000003 27.345000000000002 27.595 21.985 90-94 23.025000000000002 28.105000000000004 27.29 21.58 95-99 23.330000000000002 28.215 27.47 20.985 100-104 23.285 27.025 28.365000000000002 21.325 105-109 23.485 27.51 28.199999999999996 20.805 110-114 23.7 28.03 27.91 20.36 115-119 23.65 28.52 27.505000000000003 20.325 120-124 23.165 28.494999999999997 27.779999999999998 20.560000000000002 125-129 24.36 27.845 27.275 20.52 130-134 23.195 28.15 27.37 21.285 135-139 24.25 27.07 28.075 20.605 140-144 24.25 27.455000000000002 27.529999999999998 20.765 145-149 25.415 27.63 27.075 19.88 150-151 24.65 28.462500000000002 26.974999999999998 19.9125 >>END_MODULE >>Per sequence GC content pass #GC Content Count 0 0.0 1 0.0 2 0.0 3 0.5 4 0.5 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 0.5 17 0.5 18 0.0 19 1.0 20 1.0 21 0.5 22 1.5 23 4.5 24 5.0 25 3.5 26 5.0 27 9.5 28 10.5 29 8.5 30 13.5 31 17.5 32 27.0 33 40.5 34 45.0 35 64.5 36 90.5 37 105.0 38 137.5 39 186.0 40 208.0 41 232.5 42 259.5 43 261.5 44 270.5 45 260.5 46 251.0 47 258.5 48 226.0 49 187.0 50 167.5 51 133.5 52 104.5 53 79.5 54 64.0 55 59.0 56 53.5 57 40.5 58 25.5 59 24.5 60 19.5 61 11.5 62 6.0 63 3.5 64 3.0 65 2.5 66 1.5 67 1.0 68 0.0 69 0.0 70 0.5 71 0.5 72 0.0 73 0.0 74 0.0 75 0.0 76 0.0 77 0.0 78 0.0 79 0.0 80 0.5 81 0.5 82 0.0 83 0.0 84 0.0 85 0.5 86 0.5 87 0.0 88 0.5 89 1.0 90 0.5 91 0.0 92 0.0 93 0.0 94 0.0 95 0.0 96 0.0 97 0.0 98 0.0 99 0.0 100 0.0 >>END_MODULE >>Per base N content pass #Base N-Count 1 0.0 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10-14 0.0 15-19 0.0 20-24 0.0 25-29 0.0 30-34 0.0 35-39 0.0 40-44 0.0 45-49 0.0 50-54 0.0 55-59 0.0 60-64 0.0 65-69 0.0 70-74 0.0 75-79 0.0 80-84 0.0 85-89 0.0 90-94 0.0 95-99 0.0 100-104 0.0 105-109 0.0 110-114 0.0 115-119 0.0 120-124 0.0 125-129 0.0 130-134 0.0 135-139 0.0 140-144 0.0 145-149 0.0 150-151 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 84.425 #Duplication Level Percentage of deduplicated Percentage of total 1 85.75658868818478 72.39999999999999 2 11.341427302339355 19.15 3 2.013621557595499 5.1 4 0.5922416345869115 2.0 5 0.207284572105419 0.8750000000000001 6 0.059224163458691144 0.3 7 0.029612081729345572 0.17500000000000002 8 0.0 0.0 9 0.0 0.0 >10 0.0 0.0 >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 AGAACACATTCATACTCCAAGTCTTTTAGTTCATCCATTTAAGCTTAATC 7 0.17500000000000002 No Hit AGAGAACACATTCATACTCCAAGTCTTTTAGTTCATCCATTTAAGCTTAA 6 0.15 No Hit AGCTAGACTAACCATCATGGCACCTAGAGCATTAGACTATGAATCGTTGA 6 0.15 No Hit GGCTGGAGTCATCTATGTCATGACCCATGATTCCATTGGACTTGGAGAAG 5 0.125 No Hit CACATTCATACTCCAAGTCTTTTAGTTCATCCATTTAAGCTTAATCAATC 5 0.125 No Hit CAGAAACCACACCACAGAGTAACCATACTGTTCTTTTTTCCCTTCTGTTT 5 0.125 No Hit ACCACATATAGAGGGTGTAATAGCTAAGTAGCCTGTAAGAGATGGCTTCC 5 0.125 No Hit CTTGTTTACCACATGATGAAGCCCCCATTGGAGCAGTGTGAGATTGTTGA 5 0.125 No Hit ACCAGGTCCAGACATAGTAAGGATTGACAGACTGAGAGCTCTTTCTTGAT 5 0.125 No Hit CTCAGTTCTTCACCTCTATGATGTTGTGAATGCTCCCGGGGTCACTGCTG 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 0.0125 0.0 0.0 0.0 0.0 70-71 0.025 0.0 0.0 0.0 0.0 72-73 0.025 0.0 0.0 0.0 0.0 74-75 0.025 0.0 0.0 0.0 0.0 76-77 0.025 0.0 0.0 0.0 0.0 78-79 0.025 0.0 0.0 0.0 0.0 80-81 0.037500000000000006 0.0 0.0 0.0 0.0 82-83 0.0625 0.0 0.0 0.0 0.0 84-85 0.075 0.0 0.0 0.0 0.0 86-87 0.075 0.0 0.0 0.0 0.0 88-89 0.1125 0.0 0.0 0.0 0.0 90-91 0.1375 0.0 0.0 0.0 0.0 92-93 0.2125 0.0 0.0 0.0 0.0 94-95 0.32499999999999996 0.0 0.0 0.0 0.0 96-97 0.375 0.0 0.0 0.0 0.0 98-99 0.4125 0.0 0.0 0.0 0.0 100-101 0.44999999999999996 0.0 0.0 0.0 0.0 102-103 0.5874999999999999 0.0 0.0 0.0 0.0 104-105 0.625 0.0 0.0 0.0 0.0 106-107 0.7375 0.0 0.0 0.0 0.0 108-109 0.7875000000000001 0.0 0.0 0.0 0.0 110-111 0.9125000000000001 0.0 0.0 0.0 0.0 112-113 1.0499999999999998 0.0 0.0 0.0 0.0 114-115 1.1625 0.0 0.0 0.0 0.0 116-117 1.275 0.0 0.0 0.0 0.0 118-119 1.475 0.0 0.0 0.0 0.0 120-121 1.625 0.0 0.0 0.0 0.0 122-123 1.7999999999999998 0.0 0.0 0.0 0.0 124-125 2.025 0.0 0.0 0.0 0.0 126-127 2.1 0.0 0.0 0.0 0.0 128-129 2.225 0.0 0.0 0.0 0.0 130-131 2.375 0.0 0.0 0.0 0.0 132-133 2.6625 0.0 0.0 0.0 0.0 134-135 2.9625 0.0 0.0 0.0 0.0 136-137 3.2 0.0 0.0 0.0 0.0 138-139 3.575 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position AGTACTT 10 0.006830828 145.0 5 CAAATAG 10 0.006830828 145.0 145 >>END_MODULE Read 1406024 spots for SRR12671342.sra Written 1406024 spots for SRR12671342.sra Read 1406024 spots for SRR12671342.sra Written 1406024 spots for SRR12671342.sra Read 1406024 spots for SRR12671342.sra Written 1406024 spots for SRR12671342.sra Read 1406024 spots for SRR12671342.sra Written 1406024 spots for SRR12671342.sra Read 1406024 spots for SRR12671342.sra Written 1406024 spots for SRR12671342.sra Read 1406024 spots for SRR12671342.sra Written 1406024 spots for SRR12671342.sra Read 1406024 spots for SRR12671342.sra Written 1406024 spots for SRR12671342.sra Read 1406024 spots for SRR12671342.sra Written 1406024 spots for SRR12671342.sra Read 1406024 spots for SRR12671342.sra Written 1406024 spots for SRR12671342.sra Read 1406024 spots for SRR12671342.sra Written 1406024 spots for SRR12671342.sra Read 1406030 spots for SRR12671342.sra Written 1406030 spots for SRR12671342.sra Read 1406024 spots for SRR12671342.sra Written 1406024 spots for SRR12671342.sra Read 1406024 spots for SRR12671342.sra Written 1406024 spots for SRR12671342.sra Read 1406024 spots for SRR12671342.sra Written 1406024 spots for SRR12671342.sra Read 1406024 spots for SRR12671342.sra Written 1406024 spots for SRR12671342.sra Read 1406024 spots for SRR12671342.sra Written 1406024 spots for SRR12671342.sra Read 1406024 spots for SRR12671342.sra Written 1406024 spots for SRR12671342.sra Read 1406024 spots for SRR12671342.sra Written 1406024 spots for SRR12671342.sra Read 1406024 spots for SRR12671342.sra Written 1406024 spots for SRR12671342.sra Read 1406024 spots for SRR12671342.sra Written 1406024 spots for SRR12671342.sra SRR ids: ['SRR12671342.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_27n37ynp SRR12671342.sra spots: 28120486 blocks: [[1, 1406024], [1406025, 2812048], [2812049, 4218072], [4218073, 5624096], [5624097, 7030120], [7030121, 8436144], [8436145, 9842168], [9842169, 11248192], [11248193, 12654216], [12654217, 14060240], [14060241, 15466264], [15466265, 16872288], [16872289, 18278312], [18278313, 19684336], [19684337, 21090360], [21090361, 22496384], [22496385, 23902408], [23902409, 25308432], [25308433, 26714456], [26714457, 28120486]] SRR12671342 file size 9534871 SRR12671342 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 SRR12671342 SRR12671342_1.fastq SRR12671342_2.fastq Input file: SRR12671342_1.fastq Paired file: SRR12671342_2.fastq trimmed: SRR12671342-trimmed-pair1.fastq, SRR12671342-trimmed-pair2.fastq Parameters used: -- 3' end adapter sequence (-x): AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -- paired 3' end adapter sequence (-y): AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA -- maximum error ratio allowed (-r): 0.100 -- maximum indel error ratio allowed (-d): 0.030 -- end quality threshold (-q): 10 -- minimum read length allowed after trimming (-l): 18 -- file format (-f): Sanger/Illumina 1.8+ FASTQ -- number of concurrent threads (-t): 20 Tue Feb 11 17:03:40 2025 >> started Tue Feb 11 17:04:11 2025 >> done (30.359s) 28120486 read pairs processed; of these: 95 ( 0.00%) short read pairs filtered out after trimming by size control 2613 ( 0.01%) empty read pairs filtered out after trimming by size control 28117778 (99.99%) read pairs available; of these: 1404699 ( 5.00%) trimmed read pairs available after processing 26713079 (95.00%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 3 0.00% 19 16 0.00% 20 5 0.00% 21 9 0.00% 22 14 0.00% 23 13 0.00% 24 23 0.00% 25 24 0.00% 26 20 0.00% 27 34 0.00% 28 25 0.00% 29 21 0.00% 30 22 0.00% 31 24 0.00% 32 38 0.00% 33 30 0.00% 34 34 0.00% 35 36 0.00% 36 36 0.00% 37 33 0.00% 38 39 0.00% 39 51 0.00% 40 58 0.00% 41 62 0.00% 42 46 0.00% 43 49 0.00% 44 61 0.00% 45 65 0.00% 46 68 0.00% 47 77 0.00% 48 91 0.00% 49 94 0.00% 50 100 0.00% 51 109 0.00% 52 139 0.00% 53 156 0.00% 54 163 0.00% 55 170 0.00% 56 190 0.00% 57 204 0.00% 58 236 0.00% 59 271 0.00% 60 342 0.00% 61 411 0.00% 62 388 0.00% 63 456 0.00% 64 510 0.00% 65 551 0.00% 66 632 0.00% 67 769 0.00% 68 781 0.00% 69 902 0.00% 70 1031 0.00% 71 1119 0.00% 72 1346 0.00% 73 1439 0.01% 74 1629 0.01% 75 1876 0.01% 76 2041 0.01% 77 2212 0.01% 78 2377 0.01% 79 2611 0.01% 80 2827 0.01% 81 3180 0.01% 82 3476 0.01% 83 3938 0.01% 84 4337 0.02% 85 4613 0.02% 86 4960 0.02% 87 5319 0.02% 88 5435 0.02% 89 5831 0.02% 90 6269 0.02% 91 6667 0.02% 92 7085 0.03% 93 7738 0.03% 94 8279 0.03% 95 8787 0.03% 96 9246 0.03% 97 9698 0.03% 98 9820 0.03% 99 10342 0.04% 100 10763 0.04% 101 11040 0.04% 102 11582 0.04% 103 12322 0.04% 104 12538 0.04% 105 12926 0.05% 106 13760 0.05% 107 14216 0.05% 108 14998 0.05% 109 15034 0.05% 110 15489 0.06% 111 15638 0.06% 112 16100 0.06% 113 16733 0.06% 114 17143 0.06% 115 17865 0.06% 116 18632 0.07% 117 19210 0.07% 118 19907 0.07% 119 20445 0.07% 120 21096 0.08% 121 21394 0.08% 122 21679 0.08% 123 22181 0.08% 124 23253 0.08% 125 23649 0.08% 126 25026 0.09% 127 25043 0.09% 128 25757 0.09% 129 25944 0.09% 130 27384 0.10% 131 27300 0.10% 132 28003 0.10% 133 29024 0.10% 134 28910 0.10% 135 29910 0.11% 136 30428 0.11% 137 31340 0.11% 138 32186 0.11% 139 33292 0.12% 140 33798 0.12% 141 34400 0.12% 142 34818 0.12% 143 35250 0.13% 144 36711 0.13% 145 36984 0.13% 146 37710 0.13% 147 39225 0.14% 148 40401 0.14% 149 40339 0.14% 150 41694 0.15% 151 26713079 95.00% 28117778 reads passed initial QC criterion=sequence-density sequence-density=0.54 sequence-density-rank=1 fanout-score=1.96 fanout-score-rank=30 prefix-density=0.54 prefix-fanout=1.9 sequence=CGGTAGACCCAACCTTTCTCCAACTCGAATTCCAAGCAAGGAACCCACTTCGAGCGAAGAAGGTAATCAATTTCCTTGGCCAATTCCTCCTCTGTGAGATCTGGAAGGTAAGAAAGAGTCTCGAACTTCTTCAATCCAGTTGGTGGCCACACCTGCATGCATTGAACTCGTCCACCATTGCTTGCAATGGAAGTAATGTCATTAGCCTTTCTGGTACTGACTGGGAAAGCTGCGGCAGACTTGAGACCATTGAATGGTGCCACCAT criterion=fanout-score sequence-density=0.03 sequence-density-rank=31 fanout-score=52.19 fanout-score-rank=1 prefix-density=0.19 prefix-fanout=6.9 sequence=CAAGCTCCTTCCTTGATTAGGCAAGCATGTTCACCAGTGTTCCTCACTTGGGGGTGAAAGCAGAAAAAACGGTGGCATGACCAGGATCTGCAAGGTGAGCAAAGAGGTTGTCGATAGGACCAGTGCCAGTGTAAATGTGTTGGAACCAAGCACCCATGACAGCCAACATAGCCAA criterion=sequence-density sequence-density=0.84 sequence-density-rank=1 fanout-score=1.96 fanout-score-rank=31 prefix-density=0.84 prefix-fanout=2.0 sequence=AACCGCACCCCGGCACA criterion=fanout-score sequence-density=0.01 sequence-density-rank=32 fanout-score=90.67 fanout-score-rank=1 prefix-density=0.10 prefix-fanout=10.5 sequence=AAACCCAAAGCTCAAAAAAAATCTTAACTGCACCCGCTCATCCAGCAATGGCAGCAGCAACAATGGCCCTCTCCTCCCCTTCGCTAGCCGGAAAGGCGGTGAAGCTCAACCCCTCCTCCTCTGAGATCATGGGCAATGGCCGTGTCTCCATGAGGAAAACCACCAAGCCTGTTCCCTCCGGGAGCCCATGGTACGGACCAGACCGTGTTAAATACTTGGGCCCGTTCTCTGGTGAGCCCCCATCCTACTTGACTGGTGAGTTCCCTGGTGACTACGGCTGGGACACTGCTGGCCTCTCTGCTGACCCAGAGACCTTTGCCAAGAACCGTGAGCTTGAAGTCATCCATTCCAGGTGGGCCATGCTTGGAGCTCTTGGATGCGTCTTCCCCGAGCTCTTGTCCCGCAACGGTGTCAAGTTCGGCGAGGCTGTATGGTTCAAGGCTGGAGCCCAGATCTTCAGCGAGGGTGGACTTGACTACTTGGGCAACCCAAGCTTGATCCACGCACAAAG SRR12671342 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 11 17:04:52 Started mapping on | Feb 11 17:04:52 Finished on | Feb 11 17:07:52 Mapping speed, Million of reads per hour | 562.36 Number of input reads | 28117778 Average input read length | 299 UNIQUE READS: Uniquely mapped reads number | 26349279 Uniquely mapped reads % | 93.71% Average mapped length | 297.97 Number of splices: Total | 26583728 Number of splices: Annotated (sjdb) | 26031685 Number of splices: GT/AG | 26068767 Number of splices: GC/AG | 424679 Number of splices: AT/AC | 15359 Number of splices: Non-canonical | 74923 Mismatch rate per base, % | 0.38% Deletion rate per base | 0.03% Deletion average length | 3.16 Insertion rate per base | 0.03% Insertion average length | 2.23 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 643291 % of reads mapped to multiple loci | 2.29% Number of reads mapped to too many loci | 82112 % of reads mapped to too many loci | 0.29% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 3.63% % of reads unmapped: other | 0.08% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 1125208 1125208 1125208 N_multimapping 643291 643291 643291 N_noFeature 960247 25937505 1103667 N_ambiguous 431816 1839 162769 UnstrandedReadsAssigned:24957216 PositiveStrandReadsAssigned:409935 NegativeStrandReadsAssigned:25082843 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=151 echo kmer=147 SRR12671342 Starting Kallisto paired end mapping to ensembl reference transcriptome [quant] fragment length distribution will be estimated from the data [index] k-mer length: 31 [index] number of targets: 52,400 [index] number of k-mers: 62,057,036 [index] number of equivalence classes: 130,681 [quant] running in paired-end mode [quant] will process pair 1: SRR12671342-trimmed-pair1.fastq SRR12671342-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 28,117,778 reads, 24,967,441 reads pseudoaligned [quant] estimated average fragment length: 298.27 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,094 rounds 52401 SRR12671342.ke.tsv 34699 SRR12671342.se.tsv 87100 total ==> SRR12671342.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1720.73 1438 30.0654 Potri.005G024800.1.v4.1 1035 737.73 347 16.922 Potri.004G059700.1.v4.1 961 663.965 8 0.433476 Potri.007G009000.2.v4.1 1416 1118.73 0 0 Potri.003G141000.2.v4.1 2943 2645.73 1531.48 20.825 Potri.016G087400.1.v4.1 270 72.4843 1028.35 510.409 Potri.015G069301.1.v4.1 564 286.569 0 0 Potri.010G195200.1.v4.1 1773 1475.73 110 2.68168 Potri.012G127500.1.v4.1 977 679.862 141 7.46137 ==> SRR12671342.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 417 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 326 Potri.001G212900.v4.1 5 Potri.001G182400.v4.1 1 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 3 Potri.001G416900.v4.1 1 Potri.001G452600.v4.1 20 SRR12671342 completed mapping pipeline successfully