Starting /dee2/code/volunteer_pipeline.sh SRR12670145 current disk space = 3056989958144 free memory = 1472616720 SRR12670145 SRAfilesize c4c43abb6857a04d1739b3eb81ce16f5 SRR12670145.sra SRR12670145.sra file validated SRR12670145 is paired end SRR12670145 is conventional basespace SRR12670145 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12670145_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 45 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.641 37.0 37.0 37.0 37.0 37.0 2 36.471 37.0 37.0 37.0 37.0 37.0 3 36.691 37.0 37.0 37.0 37.0 37.0 4 36.5985 37.0 37.0 37.0 37.0 37.0 5 36.632 37.0 37.0 37.0 37.0 37.0 6 36.7005 37.0 37.0 37.0 37.0 37.0 7 36.6735 37.0 37.0 37.0 37.0 37.0 8 36.6085 37.0 37.0 37.0 37.0 37.0 9 36.624 37.0 37.0 37.0 37.0 37.0 10-14 36.6143 37.0 37.0 37.0 37.0 37.0 15-19 36.5935 37.0 37.0 37.0 37.0 37.0 20-24 36.5732 37.0 37.0 37.0 37.0 37.0 25-29 36.5607 37.0 37.0 37.0 37.0 37.0 30-34 36.548 37.0 37.0 37.0 37.0 37.0 35-39 36.559 37.0 37.0 37.0 37.0 37.0 40-44 36.4719 37.0 37.0 37.0 37.0 37.0 45-49 36.428700000000006 37.0 37.0 37.0 37.0 37.0 50-54 36.4564 37.0 37.0 37.0 37.0 37.0 55-59 36.4312 37.0 37.0 37.0 37.0 37.0 60-64 36.376799999999996 37.0 37.0 37.0 37.0 37.0 65-69 36.3701 37.0 37.0 37.0 37.0 37.0 70-74 36.3497 37.0 37.0 37.0 37.0 37.0 75-79 36.3835 37.0 37.0 37.0 37.0 37.0 80-84 36.3449 37.0 37.0 37.0 37.0 37.0 85-89 36.2888 37.0 37.0 37.0 37.0 37.0 90-94 36.2609 37.0 37.0 37.0 37.0 37.0 95-99 36.2866 37.0 37.0 37.0 37.0 37.0 100-104 36.2685 37.0 37.0 37.0 37.0 37.0 105-109 36.2879 37.0 37.0 37.0 37.0 37.0 110-114 36.1396 37.0 37.0 37.0 37.0 37.0 115-119 36.1941 37.0 37.0 37.0 37.0 37.0 120-124 36.042500000000004 37.0 37.0 37.0 37.0 37.0 125-129 35.9756 37.0 37.0 37.0 37.0 37.0 130-134 35.8669 37.0 37.0 37.0 37.0 37.0 135-139 35.6689 37.0 37.0 37.0 37.0 37.0 140-144 35.5389 37.0 37.0 37.0 37.0 37.0 145-149 35.3716 37.0 37.0 37.0 37.0 37.0 150-151 35.09225 37.0 37.0 37.0 31.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 21 1.0 22 0.0 23 1.0 24 1.0 25 4.0 26 6.0 27 3.0 28 14.0 29 21.0 30 21.0 31 34.0 32 35.0 33 58.0 34 128.0 35 345.0 36 2936.0 37 392.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 41.449999999999996 10.475 6.075 42.0 2 19.539078156312627 12.274549098196392 37.70040080160321 30.485971943887773 3 17.424999999999997 15.725 28.525 38.324999999999996 4 23.674999999999997 24.3 24.15 27.875 5 25.025 29.925 25.124999999999996 19.925 6 20.974999999999998 33.75 23.799999999999997 21.475 7 14.75 27.250000000000004 40.475 17.525 8 18.099999999999998 24.075 33.225 24.6 9 17.65 23.799999999999997 35.05 23.5 10-14 20.51 29.645 26.935 22.91 15-19 21.085 27.060000000000002 27.74 24.115000000000002 20-24 20.775 27.584999999999997 28.255000000000003 23.385 25-29 20.119999999999997 28.22 27.544999999999998 24.115000000000002 30-34 20.39 27.52 28.189999999999998 23.9 35-39 20.655 27.97 26.924999999999997 24.45 40-44 20.575 27.900000000000002 28.335 23.189999999999998 45-49 20.77 27.58 27.455000000000002 24.195 50-54 21.07 28.1 28.189999999999998 22.64 55-59 20.14 27.889999999999997 27.52 24.45 60-64 20.73 28.345 27.98 22.945 65-69 20.59 27.63 28.53 23.25 70-74 21.135 28.470000000000002 27.33 23.064999999999998 75-79 21.099999999999998 27.85 27.845 23.205000000000002 80-84 20.86 27.91 27.935 23.294999999999998 85-89 20.724999999999998 27.675 27.675 23.925 90-94 21.205 28.849999999999998 27.36 22.585 95-99 21.584999999999997 28.325 26.985 23.105 100-104 21.055 28.799999999999997 26.695 23.45 105-109 21.375 28.544999999999998 26.305 23.775 110-114 21.044999999999998 28.95 26.179999999999996 23.825 115-119 21.77 28.79 25.705 23.735 120-124 21.645 28.685 25.515 24.154999999999998 125-129 21.165 27.55 26.025 25.259999999999998 130-134 21.349999999999998 27.63 26.229999999999997 24.79 135-139 21.42 27.905 25.745 24.93 140-144 21.58 27.189999999999998 25.71 25.52 145-149 22.02 27.395000000000003 26.14 24.445 150-151 21.775 25.8125 26.700000000000003 25.7125 >>END_MODULE >>Per sequence GC content pass #GC Content Count 0 0.0 1 0.0 2 0.5 3 0.5 4 0.0 5 0.0 6 0.0 7 0.5 8 0.5 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 0.5 18 1.0 19 0.5 20 0.5 21 1.0 22 1.0 23 1.5 24 2.5 25 2.0 26 1.5 27 4.0 28 7.0 29 10.5 30 18.0 31 22.0 32 27.5 33 40.5 34 46.5 35 56.0 36 79.5 37 100.5 38 114.5 39 138.5 40 167.0 41 189.0 42 238.5 43 271.5 44 261.5 45 265.0 46 267.5 47 248.5 48 248.5 49 233.0 50 173.0 51 144.0 52 131.5 53 98.5 54 88.5 55 80.5 56 54.0 57 41.0 58 30.0 59 26.5 60 26.0 61 12.0 62 5.0 63 9.0 64 6.5 65 1.5 66 1.5 67 1.5 68 0.5 69 0.0 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 0.2 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 82.425 #Duplication Level Percentage of deduplicated Percentage of total 1 83.5001516530179 68.825 2 12.951167728237792 21.349999999999998 3 2.6084319077949654 6.45 4 0.6066120715802245 2.0 5 0.33363663936912347 1.375 6 0.0 0.0 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 TCTGCGTTAAGGAGATCATCCTCGCCGTCTGATACGACTTGTATGATTAA 5 0.125 No Hit GCCCTCTCTTTTTCTTCACCTTTTGAGCCCAACCAACAAGGCCTGCTTGC 5 0.125 No Hit CCACTGTAACGGACTTTCTTAATGATCTCTCGCCCTGCCCATAGCACTTC 5 0.125 No Hit GTTCCAACCATTTCAATCCACATCCATATCCATACCATATTGGACAGTGT 5 0.125 No Hit GTCGTCGGACGGGGAAGTCGGAGGAGGTTGTTGTTGTTGGGGTTTTCGAG 5 0.125 No Hit GCTTGCTTAATGACCGCATGTGCAGGTAGTGCAAGTGCAGCCAGTACCGC 5 0.125 No Hit GAGGGAGCGGCGGCTTGAGCAGATGAGAGGCAAGGGAGGGGGCTGTGTGC 5 0.125 No Hit TGTTGGGCTTGGTTGTATGTATCCTTTTCCTACAAATGCAGATGCTGGCC 5 0.125 No Hit GCTGGTGCATATCTAGGAACTGGTAAAGGAGGTAAATCCTGCCATTTCCT 5 0.125 No Hit AAGCACCTCTTCAAATCGCTCTGCTTCATTTGCTGATGCAGCTTCGGCAA 5 0.125 No Hit CACTGCACTAGCACCTAATGTGTCATACAAAGGAACACAGTAGAGGCCAT 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 0.0 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 0.0125 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 0.05 0.0 0.0 0.0 0.0 56-57 0.075 0.0 0.0 0.0 0.0 58-59 0.0875 0.0 0.0 0.0 0.0 60-61 0.125 0.0 0.0 0.0 0.0 62-63 0.175 0.0 0.0 0.0 0.0 64-65 0.3125 0.0 0.0 0.0 0.0 66-67 0.425 0.0 0.0 0.0 0.0 68-69 0.5249999999999999 0.0 0.0 0.0 0.0 70-71 0.65 0.0 0.0 0.0 0.0 72-73 0.9125 0.0 0.0 0.0 0.0 74-75 1.025 0.0 0.0 0.0 0.0 76-77 1.2 0.0 0.0 0.0 0.0 78-79 1.35 0.0 0.0 0.0 0.0 80-81 1.725 0.0 0.0 0.0 0.0 82-83 2.1375 0.0 0.0 0.0 0.0 84-85 2.5 0.0 0.0 0.0 0.0 86-87 2.9625 0.0 0.0 0.0 0.0 88-89 3.6624999999999996 0.0 0.0 0.0 0.0 90-91 4.45 0.0 0.0 0.0 0.0 92-93 5.225 0.0 0.0 0.0 0.0 94-95 5.9125 0.0 0.0 0.0 0.0 96-97 6.8125 0.0 0.0 0.0 0.0 98-99 7.7625 0.0 0.0 0.0 0.0 100-101 8.6625 0.0 0.0 0.0 0.0 102-103 9.7 0.0 0.0 0.0 0.0 104-105 10.575 0.0 0.0 0.0 0.0 106-107 11.7875 0.0 0.0 0.0 0.0 108-109 13.1 0.0 0.0 0.0 0.0 110-111 13.912500000000001 0.0 0.0 0.0 0.0 112-113 14.912500000000001 0.0 0.0 0.0 0.0 114-115 16.2 0.0 0.0 0.0 0.0 116-117 17.25 0.0 0.0 0.0 0.0 118-119 17.975 0.0 0.0 0.0 0.0 120-121 18.85 0.0 0.0 0.0 0.0 122-123 19.8375 0.0 0.0 0.0 0.0 124-125 21.1125 0.0 0.0 0.0 0.0 126-127 22.0625 0.0 0.0 0.0 0.0 128-129 23.0125 0.0 0.0 0.0 0.0 130-131 24.1125 0.0 0.0 0.0 0.0 132-133 25.125 0.0 0.0 0.0 0.0 134-135 26.175 0.0 0.0 0.0 0.0 136-137 27.325000000000003 0.0 0.0 0.0 0.0 138-139 28.4125 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position CTCTCTC 45 6.5511256E-4 19.333332 85-89 >>END_MODULE SRR12670145 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12670145_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 45 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.284 37.0 37.0 37.0 37.0 37.0 2 36.318 37.0 37.0 37.0 37.0 37.0 3 36.2845 37.0 37.0 37.0 37.0 37.0 4 36.399 37.0 37.0 37.0 37.0 37.0 5 36.426 37.0 37.0 37.0 37.0 37.0 6 36.409 37.0 37.0 37.0 37.0 37.0 7 36.361 37.0 37.0 37.0 37.0 37.0 8 36.5115 37.0 37.0 37.0 37.0 37.0 9 36.4975 37.0 37.0 37.0 37.0 37.0 10-14 36.4662 37.0 37.0 37.0 37.0 37.0 15-19 36.4538 37.0 37.0 37.0 37.0 37.0 20-24 36.3621 37.0 37.0 37.0 37.0 37.0 25-29 36.3746 37.0 37.0 37.0 37.0 37.0 30-34 36.3254 37.0 37.0 37.0 37.0 37.0 35-39 36.3478 37.0 37.0 37.0 37.0 37.0 40-44 36.2937 37.0 37.0 37.0 37.0 37.0 45-49 36.307900000000004 37.0 37.0 37.0 37.0 37.0 50-54 36.2399 37.0 37.0 37.0 37.0 37.0 55-59 36.254 37.0 37.0 37.0 37.0 37.0 60-64 36.1882 37.0 37.0 37.0 37.0 37.0 65-69 36.231700000000004 37.0 37.0 37.0 37.0 37.0 70-74 36.1652 37.0 37.0 37.0 37.0 37.0 75-79 36.1622 37.0 37.0 37.0 37.0 37.0 80-84 36.0965 37.0 37.0 37.0 37.0 37.0 85-89 36.111000000000004 37.0 37.0 37.0 37.0 37.0 90-94 36.0814 37.0 37.0 37.0 37.0 37.0 95-99 36.0023 37.0 37.0 37.0 37.0 37.0 100-104 35.911500000000004 37.0 37.0 37.0 37.0 37.0 105-109 35.85940000000001 37.0 37.0 37.0 37.0 37.0 110-114 35.7864 37.0 37.0 37.0 37.0 37.0 115-119 35.7485 37.0 37.0 37.0 37.0 37.0 120-124 35.5264 37.0 37.0 37.0 37.0 37.0 125-129 35.3732 37.0 37.0 37.0 37.0 37.0 130-134 35.1418 37.0 37.0 37.0 29.8 37.0 135-139 34.8143 37.0 37.0 37.0 25.0 37.0 140-144 34.5874 37.0 37.0 37.0 25.0 37.0 145-149 34.1606 37.0 37.0 37.0 25.0 37.0 150-151 33.8305 37.0 37.0 37.0 25.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 13 1.0 14 1.0 15 1.0 16 2.0 17 1.0 18 0.0 19 2.0 20 1.0 21 1.0 22 4.0 23 6.0 24 6.0 25 3.0 26 6.0 27 9.0 28 11.0 29 20.0 30 29.0 31 30.0 32 72.0 33 110.0 34 265.0 35 584.0 36 2489.0 37 346.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 38.15 22.8 9.85 29.2 2 25.174999999999997 25.7 31.7 17.424999999999997 3 20.1 26.3 34.4 19.2 4 24.45 33.85 23.599999999999998 18.099999999999998 5 24.55 36.025 22.25 17.175 6 19.725 38.75 22.875 18.65 7 19.875 21.525 39.15 19.45 8 21.275 25.025 28.725 24.975 9 21.625 24.625 30.725 23.025000000000002 10-14 22.285 29.080000000000002 27.339999999999996 21.295 15-19 22.15 27.779999999999998 28.09 21.98 20-24 22.935 29.15 27.084999999999997 20.830000000000002 25-29 22.715 28.16 28.07 21.055 30-34 22.384999999999998 28.449999999999996 27.865000000000002 21.3 35-39 22.645 28.65 27.505000000000003 21.2 40-44 22.634999999999998 28.725 27.125 21.515 45-49 22.735 28.105000000000004 28.050000000000004 21.11 50-54 22.925 28.71 27.315 21.05 55-59 22.985 28.04 28.455000000000002 20.52 60-64 23.145 28.33 27.495000000000005 21.029999999999998 65-69 22.75 27.54 27.955000000000002 21.755 70-74 23.36 27.950000000000003 26.865 21.825 75-79 23.57 27.755000000000003 27.52 21.154999999999998 80-84 23.325000000000003 27.88 27.065 21.73 85-89 24.555 28.285 26.135 21.025 90-94 23.72 28.84 26.334999999999997 21.105 95-99 24.834999999999997 28.34 26.474999999999998 20.349999999999998 100-104 25.445 27.68 26.615 20.26 105-109 25.545 28.24 26.43 19.785 110-114 26.8 28.015 25.71 19.475 115-119 26.68 28.749999999999996 25.465 19.105 120-124 27.22 27.775 26.095000000000002 18.91 125-129 28.449999999999996 27.08 25.205 19.265 130-134 28.915000000000003 27.894999999999996 24.665 18.525 135-139 30.28 25.94 25.230000000000004 18.55 140-144 30.79 26.265 24.715 18.23 145-149 32.495000000000005 25.595000000000002 24.3 17.61 150-151 33.875 25.7125 23.075000000000003 17.3375 >>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 0.5 9 0.5 10 0.0 11 0.0 12 0.5 13 0.5 14 0.0 15 0.0 16 0.5 17 1.0 18 1.0 19 1.0 20 1.5 21 3.0 22 2.0 23 1.0 24 2.0 25 2.0 26 3.0 27 6.5 28 12.0 29 13.5 30 16.5 31 24.0 32 26.0 33 36.0 34 55.0 35 62.0 36 75.0 37 104.0 38 135.0 39 164.0 40 190.0 41 218.5 42 254.5 43 272.0 44 267.5 45 275.5 46 265.5 47 251.5 48 229.0 49 188.0 50 158.0 51 124.0 52 105.0 53 96.0 54 78.0 55 62.5 56 46.0 57 33.0 58 32.0 59 31.5 60 25.0 61 13.5 62 9.0 63 7.0 64 2.5 65 0.5 66 0.0 67 1.0 68 2.0 69 2.0 70 1.0 71 0.0 72 0.5 73 0.5 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 0.5 86 0.5 87 0.0 88 0.0 89 0.5 90 1.0 91 0.5 92 0.0 93 0.0 94 0.0 95 0.5 96 1.0 97 1.0 98 0.5 99 0.0 100 1.0 >>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 82.125 #Duplication Level Percentage of deduplicated Percentage of total 1 83.71385083713851 68.75 2 12.420091324200913 20.4 3 2.8614916286149166 7.049999999999999 4 0.6392694063926941 2.1 5 0.273972602739726 1.125 6 0.06088280060882801 0.3 7 0.0 0.0 8 0.0 0.0 9 0.0 0.0 >10 0.030441400304414005 0.27499999999999997 >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 AGAGAACACATTCATACTCCAAGTCTTTTAGTTCATCCATTTAAGCTTAA 11 0.27499999999999997 No Hit CTTGATTGAAGTAGAGAAAGCAAAGGAAGCTAAGGATGGAAAGCCATCGA 6 0.15 No Hit CATTCATACTCCAAGTCTTTTAGTTCATCCATTTAAGCTTAATCAATCAA 6 0.15 No Hit CTTCATTGATGGTTATTGGAAGCCACAGAGGCGGATTCTCAATGTTGTGA 5 0.125 No Hit GGCGTAAACACTCGAAATTAGCACACGAATGCAAATCCGTCCTCGAGATT 5 0.125 No Hit GAAGAAAAACCCTAAACCTATCTCTTTCACACCCAGCCGCCGCCACCCAC 5 0.125 No Hit CTTAACTACTGTCATGAGAAGCTCCGAAACTTATAGGAGCCCAAACCTCC 5 0.125 No Hit CTTCTATATGTTTTTGCTGGATATGGAACAATTGATTTTGTGCATTCACA 5 0.125 No Hit GAGTTACTTGCTGCTACAGCAAAACTAACAGAAGCACAAGCTGAGCTTAG 5 0.125 No Hit GTGTATTGCACGCCAAAAATACCTGCATTTAAAGGTTCAGCTCCAATAAA 5 0.125 No Hit GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 5 0.125 No Hit CACACAATGGAGCGCTTTTCTCTGCTCGCTCTCCTCCTTCTTACACTCAT 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 0.0 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 0.0125 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 0.05 0.0 0.0 0.0 0.0 56-57 0.075 0.0 0.0 0.0 0.0 58-59 0.0875 0.0 0.0 0.0 0.0 60-61 0.125 0.0 0.0 0.0 0.0 62-63 0.175 0.0 0.0 0.0 0.0 64-65 0.3125 0.0 0.0 0.0 0.0 66-67 0.425 0.0 0.0 0.0 0.0 68-69 0.5249999999999999 0.0 0.0 0.0 0.0 70-71 0.65 0.0 0.0 0.0 0.0 72-73 0.9125 0.0 0.0 0.0 0.0 74-75 1.025 0.0 0.0 0.0 0.0 76-77 1.2 0.0 0.0 0.0 0.0 78-79 1.3624999999999998 0.0 0.0 0.0 0.0 80-81 1.75 0.0 0.0 0.0 0.0 82-83 2.1624999999999996 0.0 0.0 0.0 0.0 84-85 2.5625 0.0 0.0 0.0 0.0 86-87 3.0250000000000004 0.0 0.0 0.0 0.0 88-89 3.725 0.0 0.0 0.0 0.0 90-91 4.525 0.0 0.0 0.0 0.0 92-93 5.300000000000001 0.0 0.0 0.0 0.0 94-95 5.9875 0.0 0.0 0.0 0.0 96-97 6.8875 0.0 0.0 0.0 0.0 98-99 7.9 0.0 0.0 0.0 0.0 100-101 8.7875 0.0 0.0 0.0 0.0 102-103 9.825 0.0 0.0 0.0 0.0 104-105 10.7 0.0 0.0 0.0 0.0 106-107 11.925 0.0 0.0 0.0 0.0 108-109 13.2375 0.0 0.0 0.0 0.0 110-111 14.037500000000001 0.0 0.0 0.0 0.0 112-113 15.05 0.0 0.0 0.0 0.0 114-115 16.375 0.0 0.0 0.0 0.0 116-117 17.45 0.0 0.0 0.0 0.0 118-119 18.1875 0.0 0.0 0.0 0.0 120-121 19.025 0.0 0.0 0.0 0.0 122-123 20.0125 0.0 0.0 0.0 0.0 124-125 21.2875 0.0 0.0 0.0 0.0 126-127 22.2125 0.0 0.0 0.0 0.0 128-129 23.1875 0.0 0.0 0.0 0.0 130-131 24.2875 0.0 0.0 0.0 0.0 132-133 25.299999999999997 0.0 0.0 0.0 0.0 134-135 26.35 0.0 0.0 0.0 0.0 136-137 27.525 0.0 0.0 0.0 0.0 138-139 28.6 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GAGGGAG 10 0.006830828 145.0 4 GGGGGGG 280 3.765308E-10 12.946429 145 >>END_MODULE Read 552479 spots for SRR12670145.sra Written 552479 spots for SRR12670145.sra Read 552479 spots for SRR12670145.sra Written 552479 spots for SRR12670145.sra Read 552479 spots for SRR12670145.sra Written 552479 spots for SRR12670145.sra Read 552479 spots for SRR12670145.sra Written 552479 spots for SRR12670145.sra Read 552479 spots for SRR12670145.sra Written 552479 spots for SRR12670145.sra Read 552479 spots for SRR12670145.sra Written 552479 spots for SRR12670145.sra Read 552480 spots for SRR12670145.sra Written 552480 spots for SRR12670145.sra Read 552479 spots for SRR12670145.sra Written 552479 spots for SRR12670145.sra Read 552479 spots for SRR12670145.sra Written 552479 spots for SRR12670145.sra Read 552479 spots for SRR12670145.sra Written 552479 spots for SRR12670145.sra Read 552479 spots for SRR12670145.sra Written 552479 spots for SRR12670145.sra Read 552479 spots for SRR12670145.sra Written 552479 spots for SRR12670145.sra Read 552479 spots for SRR12670145.sra Written 552479 spots for SRR12670145.sra Read 552479 spots for SRR12670145.sra Written 552479 spots for SRR12670145.sra Read 552479 spots for SRR12670145.sra Written 552479 spots for SRR12670145.sra Read 552479 spots for SRR12670145.sra Written 552479 spots for SRR12670145.sra Read 552479 spots for SRR12670145.sra Written 552479 spots for SRR12670145.sra Read 552479 spots for SRR12670145.sra Written 552479 spots for SRR12670145.sra Read 552479 spots for SRR12670145.sra Written 552479 spots for SRR12670145.sra Read 552479 spots for SRR12670145.sra Written 552479 spots for SRR12670145.sra SRR ids: ['SRR12670145.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_p9w4eso1 SRR12670145.sra spots: 11049581 blocks: [[1, 552479], [552480, 1104958], [1104959, 1657437], [1657438, 2209916], [2209917, 2762395], [2762396, 3314874], [3314875, 3867353], [3867354, 4419832], [4419833, 4972311], [4972312, 5524790], [5524791, 6077269], [6077270, 6629748], [6629749, 7182227], [7182228, 7734706], [7734707, 8287185], [8287186, 8839664], [8839665, 9392143], [9392144, 9944622], [9944623, 10497101], [10497102, 11049581]] SRR12670145 file size 3733430 SRR12670145 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 SRR12670145 SRR12670145_1.fastq SRR12670145_2.fastq Input file: SRR12670145_1.fastq Paired file: SRR12670145_2.fastq trimmed: SRR12670145-trimmed-pair1.fastq, SRR12670145-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 02:27:47 2025 >> started Tue Feb 11 02:34:03 2025 >> done (376.106s) 11049581 read pairs processed; of these: 62 ( 0.00%) short read pairs filtered out after trimming by size control 3700 ( 0.03%) empty read pairs filtered out after trimming by size control 11045819 (99.97%) read pairs available; of these: 3628658 (32.85%) trimmed read pairs available after processing 7417161 (67.15%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 2 0.00% 19 5 0.00% 20 6 0.00% 21 12 0.00% 22 9 0.00% 23 18 0.00% 24 17 0.00% 25 20 0.00% 26 47 0.00% 27 35 0.00% 28 36 0.00% 29 36 0.00% 30 57 0.00% 31 51 0.00% 32 57 0.00% 33 71 0.00% 34 71 0.00% 35 90 0.00% 36 124 0.00% 37 160 0.00% 38 182 0.00% 39 126 0.00% 40 226 0.00% 41 236 0.00% 42 225 0.00% 43 244 0.00% 44 235 0.00% 45 279 0.00% 46 349 0.00% 47 365 0.00% 48 486 0.00% 49 601 0.01% 50 795 0.01% 51 817 0.01% 52 916 0.01% 53 915 0.01% 54 957 0.01% 55 1101 0.01% 56 1242 0.01% 57 1419 0.01% 58 1682 0.02% 59 1971 0.02% 60 2307 0.02% 61 2589 0.02% 62 3012 0.03% 63 3319 0.03% 64 3712 0.03% 65 3914 0.04% 66 4182 0.04% 67 4712 0.04% 68 5387 0.05% 69 6130 0.06% 70 6929 0.06% 71 7774 0.07% 72 9104 0.08% 73 9974 0.09% 74 10998 0.10% 75 11627 0.11% 76 12949 0.12% 77 13463 0.12% 78 14498 0.13% 79 16083 0.15% 80 17655 0.16% 81 19465 0.18% 82 21396 0.19% 83 23194 0.21% 84 25188 0.23% 85 27124 0.25% 86 28190 0.26% 87 29102 0.26% 88 30932 0.28% 89 31362 0.28% 90 33593 0.30% 91 35649 0.32% 92 36964 0.33% 93 39811 0.36% 94 41077 0.37% 95 43583 0.39% 96 44801 0.41% 97 45206 0.41% 98 45617 0.41% 99 47019 0.43% 100 47454 0.43% 101 47559 0.43% 102 50210 0.45% 103 50888 0.46% 104 52360 0.47% 105 52658 0.48% 106 54579 0.49% 107 54290 0.49% 108 53618 0.49% 109 54249 0.49% 110 53369 0.48% 111 54269 0.49% 112 55165 0.50% 113 54975 0.50% 114 56021 0.51% 115 56453 0.51% 116 57522 0.52% 117 58093 0.53% 118 57475 0.52% 119 56717 0.51% 120 57034 0.52% 121 56289 0.51% 122 56546 0.51% 123 57440 0.52% 124 57171 0.52% 125 56994 0.52% 126 58177 0.53% 127 57642 0.52% 128 57012 0.52% 129 56312 0.51% 130 56571 0.51% 131 55737 0.50% 132 54979 0.50% 133 55309 0.50% 134 54782 0.50% 135 55734 0.50% 136 55098 0.50% 137 55271 0.50% 138 55095 0.50% 139 55571 0.50% 140 54472 0.49% 141 54330 0.49% 142 54443 0.49% 143 53004 0.48% 144 54348 0.49% 145 53598 0.49% 146 53693 0.49% 147 53316 0.48% 148 53193 0.48% 149 52441 0.47% 150 53248 0.48% 151 7417161 67.15% 11045819 reads passed initial QC criterion=sequence-density sequence-density=0.33 sequence-density-rank=1 fanout-score=2.00 fanout-score-rank=23 prefix-density=0.33 prefix-fanout=2.0 sequence=CGGTAGACCCAACCTTTCTCCAACTCGAATTCCAAGCAAGGAACCCACTT criterion=fanout-score sequence-density=0.10 sequence-density-rank=22 fanout-score=17.24 fanout-score-rank=1 prefix-density=0.27 prefix-fanout=6.4 sequence=TGCTGCCATTGCT criterion=sequence-density sequence-density=0.48 sequence-density-rank=1 fanout-score=2.03 fanout-score-rank=29 prefix-density=0.48 prefix-fanout=2.0 sequence=TGTAAGAGATGGCTTCCTC criterion=fanout-score sequence-density=0.19 sequence-density-rank=15 fanout-score=26.12 fanout-score-rank=1 prefix-density=0.44 prefix-fanout=11.4 sequence=AAGAAAAGAAAA SRR12670145 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 11 03:36:18 Started mapping on | Feb 11 03:36:33 Finished on | Feb 11 05:55:42 Mapping speed, Million of reads per hour | 4.76 Number of input reads | 11045819 Average input read length | 275 UNIQUE READS: Uniquely mapped reads number | 8024021 Uniquely mapped reads % | 72.64% Average mapped length | 282.49 Number of splices: Total | 8280685 Number of splices: Annotated (sjdb) | 8084330 Number of splices: GT/AG | 8108179 Number of splices: GC/AG | 129063 Number of splices: AT/AC | 5714 Number of splices: Non-canonical | 37729 Mismatch rate per base, % | 0.41% Deletion rate per base | 0.03% Deletion average length | 2.93 Insertion rate per base | 0.02% Insertion average length | 2.45 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 217190 % of reads mapped to multiple loci | 1.97% Number of reads mapped to too many loci | 184475 % of reads mapped to too many loci | 1.67% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 23.45% % of reads unmapped: other | 0.27% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 2804608 2804608 2804608 N_multimapping 217190 217190 217190 N_noFeature 337893 7889837 387050 N_ambiguous 210981 1645 124890 UnstrandedReadsAssigned:7475147 PositiveStrandReadsAssigned:132539 NegativeStrandReadsAssigned:7512081 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=125 echo kmer=121 SRR12670145 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: SRR12670145-trimmed-pair1.fastq SRR12670145-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 11,045,819 reads, 9,766,997 reads pseudoaligned [quant] estimated average fragment length: 192.039 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,060 rounds 52401 SRR12670145.ke.tsv 34699 SRR12670145.se.tsv 87100 total ==> SRR12670145.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1826.96 301 16.0598 Potri.005G024800.1.v4.1 1035 843.961 99 11.4345 Potri.004G059700.1.v4.1 961 770.048 6 0.759514 Potri.007G009000.2.v4.1 1416 1224.96 0 0 Potri.003G141000.2.v4.1 2943 2751.96 581.924 20.6123 Potri.016G087400.1.v4.1 270 119.073 486 397.856 Potri.015G069301.1.v4.1 564 379.658 0 0 Potri.010G195200.1.v4.1 1773 1581.96 36 2.21824 Potri.012G127500.1.v4.1 977 786.018 112 13.8895 ==> SRR12670145.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 90 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 94 Potri.001G212900.v4.1 1 Potri.001G182400.v4.1 0 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 0 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 0 SRR12670145 completed mapping pipeline successfully