Starting /dee2/code/volunteer_pipeline.sh SRR28716046 current disk space = 1543054479360 free memory = 1595976076 SRR28716046 SRAfilesize 15329a1afc0c47cf9f4007540f74d010 SRR28716046.sra SRR28716046.sra file validated SRR28716046 is single end SRR28716046 is conventional basespace SRR28716046 read1 length is 120 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR28716046_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 120 %GC 53 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.37825 38.0 38.0 38.0 32.0 38.0 2 36.68775 38.0 38.0 38.0 32.0 38.0 3 36.97825 38.0 38.0 38.0 32.0 38.0 4 36.48275 38.0 38.0 38.0 32.0 38.0 5 36.88775 38.0 38.0 38.0 32.0 38.0 6 38.883 40.0 38.0 40.0 38.0 40.0 7 38.9425 40.0 38.0 40.0 38.0 40.0 8 38.956 40.0 38.0 40.0 38.0 40.0 9 38.895 40.0 38.0 40.0 38.0 40.0 10-11 38.83125 40.0 38.0 40.0 38.0 40.0 12-13 38.8365 40.0 38.0 40.0 38.0 40.0 14-15 38.63875 40.0 38.0 40.0 38.0 40.0 16-17 38.77275 40.0 38.0 40.0 38.0 40.0 18-19 38.78 40.0 38.0 40.0 38.0 40.0 20-21 38.7685 40.0 38.0 40.0 38.0 40.0 22-23 38.785875000000004 40.0 38.0 40.0 38.0 40.0 24-25 38.54275 40.0 38.0 40.0 38.0 40.0 26-27 38.634 40.0 38.0 40.0 38.0 40.0 28-29 38.6405 40.0 38.0 40.0 38.0 40.0 30-31 38.647875 40.0 38.0 40.0 38.0 40.0 32-33 38.58825 40.0 38.0 40.0 38.0 40.0 34-35 38.66575 40.0 38.0 40.0 38.0 40.0 36-37 38.656375 40.0 38.0 40.0 38.0 40.0 38-39 38.597125 40.0 38.0 40.0 38.0 40.0 40-41 38.5965 40.0 38.0 40.0 38.0 40.0 42-43 38.558375 40.0 38.0 40.0 38.0 40.0 44-45 38.45325 40.0 38.0 40.0 38.0 40.0 46-47 38.41 40.0 38.0 40.0 38.0 40.0 48-49 38.109125000000006 40.0 38.0 40.0 38.0 40.0 50-51 38.250375 40.0 38.0 40.0 38.0 40.0 52-53 38.2445 40.0 38.0 40.0 38.0 40.0 54-55 38.223124999999996 40.0 38.0 40.0 38.0 40.0 56-57 38.2535 40.0 38.0 40.0 38.0 40.0 58-59 38.255750000000006 40.0 38.0 40.0 38.0 40.0 60-61 37.561625 39.0 38.0 40.0 35.0 40.0 62-63 38.16025 40.0 38.0 40.0 38.0 40.0 64-65 38.1335 40.0 38.0 40.0 38.0 40.0 66-67 38.076625 40.0 38.0 40.0 38.0 40.0 68-69 38.172 40.0 38.0 40.0 38.0 40.0 70-71 38.140375 40.0 38.0 40.0 38.0 40.0 72-73 37.8845 40.0 38.0 40.0 38.0 40.0 74-75 37.939875 40.0 38.0 40.0 38.0 40.0 76-77 37.089625 39.0 38.0 40.0 32.5 40.0 78-79 37.436499999999995 38.0 38.0 40.0 32.0 40.0 80-81 37.85625 38.0 38.0 40.0 38.0 40.0 82-83 37.831875 39.0 38.0 40.0 35.0 40.0 84-85 37.78375 39.0 38.0 40.0 35.0 40.0 86-87 37.67175 38.0 38.0 40.0 32.0 40.0 88-89 37.609375 38.0 38.0 40.0 32.0 40.0 90-91 37.708 38.0 38.0 40.0 32.0 40.0 92-93 37.58225 38.0 38.0 40.0 32.0 40.0 94-95 37.505125 38.0 38.0 40.0 32.0 40.0 96-97 37.4435 38.0 38.0 40.0 32.0 40.0 98-99 37.327875 38.0 38.0 40.0 32.0 40.0 100-101 37.32875 38.0 38.0 40.0 32.0 40.0 102-103 35.723749999999995 38.0 35.0 38.0 29.5 38.0 104-105 37.455875000000006 38.0 38.0 40.0 32.0 40.0 106-107 37.94725 40.0 38.0 40.0 38.0 40.0 108-109 37.892375 40.0 38.0 40.0 38.0 40.0 110-111 37.953375 40.0 38.0 40.0 38.0 40.0 112-113 37.87125 40.0 38.0 40.0 38.0 40.0 114-115 37.481375 38.0 38.0 40.0 32.0 40.0 116-117 37.6835 39.0 38.0 40.0 38.0 40.0 118-119 37.412125 38.0 38.0 40.0 38.0 40.0 120 33.882 38.0 32.0 38.0 27.0 40.0 >>END_MODULE >>Per tile sequence quality pass #Tile Base Mean 1101 1 0.0 1101 2 0.0 1101 3 0.0 1101 4 0.0 1101 5 0.0 1101 6 0.0 1101 7 0.0 1101 8 0.0 1101 9 0.0 1101 10-11 0.0 1101 12-13 0.0 1101 14-15 0.0 1101 16-17 0.0 1101 18-19 0.0 1101 20-21 0.0 1101 22-23 0.0 1101 24-25 0.0 1101 26-27 0.0 1101 28-29 0.0 1101 30-31 0.0 1101 32-33 0.0 1101 34-35 0.0 1101 36-37 0.0 1101 38-39 0.0 1101 40-41 0.0 1101 42-43 0.0 1101 44-45 0.0 1101 46-47 0.0 1101 48-49 0.0 1101 50-51 0.0 1101 52-53 0.0 1101 54-55 0.0 1101 56-57 0.0 1101 58-59 0.0 1101 60-61 0.0 1101 62-63 0.0 1101 64-65 0.0 1101 66-67 0.0 1101 68-69 0.0 1101 70-71 0.0 1101 72-73 0.0 1101 74-75 0.0 1101 76-77 0.0 1101 78-79 0.0 1101 80-81 0.0 1101 82-83 0.0 1101 84-85 0.0 1101 86-87 0.0 1101 88-89 0.0 1101 90-91 0.0 1101 92-93 0.0 1101 94-95 0.0 1101 96-97 0.0 1101 98-99 0.0 1101 100-101 0.0 1101 102-103 0.0 1101 104-105 0.0 1101 106-107 0.0 1101 108-109 0.0 1101 110-111 0.0 1101 112-113 0.0 1101 114-115 0.0 1101 116-117 0.0 1101 118-119 0.0 1101 120 0.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 16 1.0 17 0.0 18 2.0 19 0.0 20 0.0 21 1.0 22 2.0 23 3.0 24 5.0 25 8.0 26 7.0 27 22.0 28 17.0 29 34.0 30 40.0 31 50.0 32 57.0 33 88.0 34 96.0 35 141.0 36 187.0 37 312.0 38 776.0 39 2151.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 32.95136236312707 8.683473389355742 4.45632798573975 53.90883626177744 2 19.75 11.0 38.85 30.4 3 18.4 12.5 24.8 44.3 4 27.0 20.200000000000003 21.6 31.2 5 26.525 25.75 23.974999999999998 23.75 6 22.35 27.85 25.074999999999996 24.725 7 18.975 19.0 38.1 23.925 8 19.625 18.099999999999998 32.4 29.875 9 20.65 17.549999999999997 33.4 28.4 10-11 23.849999999999998 25.912499999999998 21.637500000000003 28.599999999999998 12-13 22.787499999999998 19.3625 26.787499999999998 31.0625 14-15 23.1875 21.1875 26.687499999999996 28.9375 16-17 25.424999999999997 20.7125 23.962500000000002 29.9 18-19 22.8875 22.625 24.95 29.5375 20-21 24.2 21.5625 26.187500000000004 28.050000000000004 22-23 24.275 21.7 25.35 28.675 24-25 25.25 21.6875 25.05 28.012500000000003 26-27 23.9875 20.8875 25.900000000000002 29.225 28-29 23.4375 20.925 25.412499999999998 30.225 30-31 24.349999999999998 19.725 26.0125 29.912499999999998 32-33 25.6125 20.45 24.7375 29.2 34-35 24.087500000000002 20.837500000000002 25.424999999999997 29.65 36-37 24.0625 21.775 25.4375 28.725 38-39 22.7125 20.825 26.05 30.412499999999998 40-41 24.887500000000003 21.0375 24.224999999999998 29.849999999999998 42-43 25.3 21.4375 24.8125 28.449999999999996 44-45 25.4375 20.7875 25.8 27.975 46-47 23.5875 20.674999999999997 27.237499999999997 28.499999999999996 48-49 23.400000000000002 19.9625 25.1875 31.45 50-51 23.025000000000002 21.05 25.75 30.175 52-53 23.9 21.25 25.174999999999997 29.675 54-55 24.525 21.4125 24.775 29.2875 56-57 22.975 21.4 26.0125 29.612500000000004 58-59 24.025 21.587500000000002 25.8 28.5875 60-61 24.525 20.575 26.075 28.825 62-63 24.8125 20.1375 25.974999999999998 29.075 64-65 23.549999999999997 20.65 26.2125 29.5875 66-67 24.3875 22.6125 24.587500000000002 28.4125 68-69 23.674999999999997 22.1 25.3125 28.9125 70-71 25.05 21.1375 25.074999999999996 28.7375 72-73 24.4 21.8625 24.4125 29.325000000000003 74-75 24.85 21.8125 24.9875 28.349999999999998 76-77 25.387500000000003 21.325 24.575 28.712500000000002 78-79 24.15 20.8125 24.837500000000002 30.2 80-81 23.2875 21.712500000000002 25.2 29.799999999999997 82-83 24.637500000000003 21.7875 24.625 28.95 84-85 23.7375 20.8 24.099999999999998 31.362499999999997 86-87 23.7875 21.775 24.962500000000002 29.475 88-89 24.85 20.875 25.0625 29.212500000000002 90-91 24.15 21.775 23.962500000000002 30.112499999999997 92-93 25.0375 20.8875 25.4 28.675 94-95 23.625 21.575 24.712500000000002 30.0875 96-97 22.5125 22.5875 25.35 29.549999999999997 98-99 24.4375 21.325 24.962500000000002 29.275000000000002 100-101 23.6625 22.162499999999998 24.762500000000003 29.4125 102-103 23.75 22.425 25.324999999999996 28.499999999999996 104-105 24.375 22.2625 24.55 28.812500000000004 106-107 24.4 22.0625 25.25 28.287499999999998 108-109 24.337500000000002 21.5 24.587500000000002 29.575000000000003 110-111 23.4625 22.3875 26.0625 28.0875 112-113 24.4375 23.474999999999998 24.5 27.5875 114-115 25.624999999999996 22.175 23.5 28.7 116-117 25.0375 23.125 23.3125 28.525 118-119 24.375 22.725 24.125 28.775000000000002 120 26.025 23.1 22.650000000000002 28.225 >>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 0.0 22 0.0 23 0.0 24 0.0 25 0.5 26 0.5 27 1.5 28 1.5 29 1.0 30 2.5 31 1.5 32 3.5 33 7.0 34 5.5 35 5.0 36 13.5 37 24.0 38 25.0 39 27.5 40 34.5 41 46.0 42 50.5 43 63.0 44 79.5 45 87.0 46 105.5 47 126.5 48 137.0 49 161.0 50 180.0 51 173.0 52 167.5 53 203.5 54 250.0 55 277.0 56 295.0 57 244.5 58 203.0 59 186.0 60 145.0 61 111.0 62 80.0 63 79.5 64 79.0 65 64.0 66 53.0 67 40.5 68 34.5 69 23.5 70 19.0 71 22.0 72 20.0 73 12.5 74 5.5 75 8.0 76 8.0 77 3.0 78 1.5 79 0.5 80 0.0 81 0.0 82 0.0 83 0.0 84 0.0 85 0.0 86 0.0 87 0.0 88 0.0 89 0.0 90 0.0 91 0.0 92 0.0 93 0.0 94 0.0 95 0.0 96 0.0 97 0.0 98 0.0 99 0.0 100 0.0 >>END_MODULE >>Per base N content pass #Base N-Count 1 1.825 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10-11 0.0 12-13 0.0 14-15 0.0 16-17 0.0 18-19 0.0 20-21 0.0 22-23 0.0 24-25 0.0 26-27 0.0 28-29 0.0 30-31 0.0 32-33 0.0 34-35 0.0 36-37 0.0 38-39 0.0 40-41 0.0 42-43 0.0 44-45 0.0 46-47 0.0 48-49 0.0 50-51 0.0 52-53 0.0 54-55 0.0 56-57 0.0 58-59 0.0 60-61 0.0 62-63 0.0 64-65 0.0 66-67 0.0 68-69 0.0 70-71 0.0 72-73 0.0 74-75 0.0 76-77 0.0 78-79 0.0 80-81 0.0 82-83 0.0 84-85 0.0 86-87 0.0 88-89 0.0 90-91 0.0 92-93 0.0 94-95 0.0 96-97 0.0 98-99 0.0 100-101 0.0 102-103 0.0 104-105 0.0 106-107 0.0 108-109 0.0 110-111 0.0 112-113 0.0 114-115 0.0 116-117 0.0 118-119 0.0 120 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 120 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 72.225 #Duplication Level Percentage of deduplicated Percentage of total 1 80.5815160955348 58.199999999999996 2 10.695742471443406 15.45 3 4.084458290065767 8.85 4 2.3883696780893042 6.9 5 0.9691934925579786 3.5000000000000004 6 0.4845967462789893 2.1 7 0.24229837313949465 1.225 8 0.3115264797507788 1.7999999999999998 9 0.06922810661128419 0.44999999999999996 >10 0.17307026652821045 1.525 >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 CCTAGATGTCCAGTCAACTGCTGCGCCTCAACGCATTTCGGGGAGAACCA 15 0.375 No Hit CTCAGAGCCAATCCTTTTCCCGAAGTTACGGATCCGTTTTGCCGACTTCC 13 0.325 No Hit CCGACATCGAAGGATCAAAAAGCAACGTCGCTATGAACGCTTGGCTGCCA 12 0.3 No Hit GTCGGGGCAGGCGGCGGGCGCAGGCGCCGCTTGCTAGCTTGGATTCTGAC 11 0.27499999999999997 No Hit CTCCTATAGTGTGACGGGCGGTGTGTACAAGGCCCGGGAACGGATTCACC 10 0.25 No Hit CTTTTGTTCCACACGAGATTTCTGTTCTCGTTGAGCTCATCTTAGGACAC 9 0.22499999999999998 No Hit GTCCTTTTCATCTTTCCCTCGCGGTACTTGTTCGCTATCGGTCTCTCGCC 9 0.22499999999999998 No Hit CCCGAAGTTACGGATCCGTTTTGCCGACTTCCCTTGCCTACATTGTTCCA 8 0.2 No Hit CCCGACTGTCCCTATTAATCATTACTCCGATCCCGAAGGCCAACACAATA 8 0.2 No Hit GCTGTGGTTTCGCTGGATAGTAGACAGGGACAGTGGGAATCTCGTTAATC 8 0.2 No Hit CTTAAACCTATAACCATCTTTCGGCTAACCTAGCCTCCTCCGTCCCTCCG 8 0.2 No Hit GCTTGTATTGCTCTCCCACAACCCCGTTTTCACGGTTTAGGCTGCTCCCA 8 0.2 No Hit CTCCACGCGGCATTGCTCCGTCAGGCTTTCGCCCATTGCGGAAAATTCCC 8 0.2 No Hit CCGGGAACGGATTCACCGCCGTATGGCTGACCGGCGATTACTAGCGATTC 8 0.2 No Hit GTTCTAGGTTAGCGCGCAGTTGGGCACCGTAACCCGGCTTCCGGTTCATC 8 0.2 No Hit CTTTCTTTTCCTCTGGCTACTAAGATGTTTCAGTTCGCCAGGTTGTCTCT 8 0.2 No Hit CCGCTGATTCCGCCAAGCCCGTTCCCTTGGCTGTGGTTTCGCTGGATAGT 7 0.17500000000000002 No Hit GGCATGATGACTTGGCCTCATCCTCTCCTTCCTCCGGCTTAACACCGGCG 7 0.17500000000000002 No Hit CTCCTACTCATCGGGGCATGGCGCTCGCCCAGATGGCCGGGTGTGGGTCG 7 0.17500000000000002 No Hit CATCGTTTACGGCTAGGACTACTGGGGTCTCTAATCCCATTTGCTCCCCT 7 0.17500000000000002 No Hit CAGGGTTCCAAACTCATAGTGGCAACTAAACACGAGGGTTGCGCTCGTTG 7 0.17500000000000002 No Hit GTCCAGTCAACTGCTGCGCCTCAACGCATTTCGGGGAGAACCAGCTAGCT 7 0.17500000000000002 No Hit CCCTTTTGTTCCACACGAGATTTCTGTTCTCGTTGAGCTCATCTTAGGAC 7 0.17500000000000002 No Hit ATCGCTTCGAGCCTCCACCAGAGTTTCCTCTGGCTTCGCCCCGCTCAGGC 6 0.15 No Hit CCCCGCTCAGGCATAGTTCACCATCTTTCGGGTCCCGACAGGCGTGCTCC 6 0.15 No Hit CTTGTCCGTACCAGTTCTGAGTCGACTGTTCAGCGCTCGGGGAAAGCCCC 6 0.15 No Hit GCTCATCTTAGGACACCTGCGTTATCTTTTAACAGATGTGCCGCCCCAGC 6 0.15 No Hit GTCAGTATCGCTTCGAGCCTCCACCAGAGTTTCCTCTGGCTTCGCCCCGC 6 0.15 No Hit CACGGTTTCACGTTCTATTTCACTACCCACTGGGGGTTCTTTTCACCTTT 6 0.15 No Hit CCTCGCGGTACTTGTTCGCTATCGGTCTCTCGCCTGTATTTAGCCTTGGA 6 0.15 No Hit CCCTACCGTACTCCAGCTTGGTAGTTTCCACCGCCTGTCCAGGGTTGAGC 6 0.15 No Hit CACGCTTTCACGGTTCGTATTCGTACTGGAAATCAGAATCAAACGAGCTT 6 0.15 No Hit GCCCAATCATTCCGGATAACGCTTGCATCCTCTGTCTTACCGCGGCTGCT 6 0.15 No Hit AGCACGTGTGTCGCCCAGGGCATAAGGGGCATGATGACTTGGCCTCATCC 6 0.15 No Hit CGCTTGTATTGCTCTCCCACAACCCCGTTTTCACGGTTTAGGCTGCTCCC 6 0.15 No Hit TTTTGTTCCACACGAGATTTCTGTTCTCGTTGAGCTCATCTTAGGACACC 6 0.15 No Hit CTCTGCCCCTACCGTACTCCAGCTTGGTAGTTTCCACCGCCTGTCCAGGG 6 0.15 No Hit CACCTCTCAAGTCATTTCACAAAGTCGGACTAGAGTCAAGCTCAACAGGG 5 0.125 No Hit CTCTGACTATGAAATACGAATGCCCCCGACTGTCCCTATTAATCATTACT 5 0.125 No Hit GTTCTATTTCACTACCCACTGGGGGTTCTTTTCACCTTTCCCTCACGGTA 5 0.125 No Hit GTCTTTCGCCCCTATACCCAAGTCAGACGAACGATTTGCACGTCAGTATC 5 0.125 No Hit CTCAAGCCGACATTCTCGCTTCCGCTTCGTCGACCCCCGCTTTCGCGGTT 5 0.125 No Hit GTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACT 5 0.125 No Hit CCCGGCTTCCGGTTCATCCCGCATCGCCAGTTCTGCTTACCAAAAATGGC 5 0.125 No Hit GTGGTATTTCACTTGCGCCCGTAAAGGCTCCCACTTATCCTACACCTCTC 5 0.125 No Hit CCCTTGCCTACATTGTTCCATTGGCCAGAGGCTGTTCACCTTGGAGACCT 5 0.125 No Hit CCTTAAACCTATAACCATCTTTCGGCTAACCTAGCCTCCTCCGTCCCTCC 5 0.125 No Hit GTCAATTCCTTTAAGTTTCAGCCTTGCGACCATACTCCCCCCGGAACCCA 5 0.125 No Hit CCTAGAGTAACTTTTATCCGTTGAGCGACGGCCCTTCCACTCGGCACCGT 5 0.125 No Hit GTTCGAGCTTTTCCTGGGAGTATGGCATCGGTTACATACTTCAGTGCCGT 5 0.125 No Hit CTCACGGTACTACTTCGCTATCGGTCACCCAGGAGTATTTAGCCTTGCAA 5 0.125 No Hit CTCCAGCTATCCTGAGGGAAACTTCGGAGGGAACCAGCTACTAGATGGTT 5 0.125 No Hit CGTCAATTCCTTTAAGTTTCAGCCTTGCGACCATACTCCCCCCGGAACCC 5 0.125 No Hit CTTAGAGAGAGTTGTCTCGCGCCCCTAGGTATTCTCTACCTACCCACCTG 5 0.125 No Hit CTCCTTTTGCTCCTCAGCCTACGGGGTATTAGCAACCGTTTCCAGTTGTT 5 0.125 No Hit CCTCTCCGCACTTGGCTACCCAGCGTTTACCGTAGGCACGATAACTGGTA 5 0.125 No Hit GTTCAGGGTTCCAAACTCATAGTGGCAACTAAACACGAGGGTTGCGCTCG 5 0.125 No Hit CTAGCTTTCGTCTCTCAGTGTCAGTGTCGGCCCAGCAGAGTGCTTTCGCC 5 0.125 No Hit CCCCTTCTTACCCTGAAAAAGCAGGGTCACCTTGTGTCCTTAAACCTATA 5 0.125 No Hit ATTCAGAGCACTGGGCAGAAATCACATTGCGTCAGCATCCGCGAGGACCA 5 0.125 No Hit CCCAACTTTCGTTCTTGATTAATGAAAACATCCTTGGCAAATGCTTTCGC 5 0.125 No Hit GTTCAGTCATAATCCGGCACACGGTAGCTTCGCGCCACTGGCTTTTCAAC 5 0.125 No Hit CTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGG 5 0.125 No Hit CCTGTGTCGGTTTCGGGTACAGGTACCCTTTTGTTGAAGGTCGTTCGAGC 5 0.125 No Hit GTTCCCTATTGGTGGGTGAACAATCCAACACTTGGTGAATTCTGCTTCAC 5 0.125 No Hit >>END_MODULE >>Adapter Content warn #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 0.0125 0.0 0.0 0.0 0.0 52-53 0.025 0.0 0.0 0.0 0.0 54-55 0.025 0.0 0.0 0.0 0.0 56-57 0.025 0.0 0.0 0.0 0.0 58-59 0.037500000000000006 0.0 0.0 0.0 0.0 60-61 0.1 0.0 0.0 0.0 0.0 62-63 0.1375 0.0 0.0 0.0 0.0 64-65 0.16249999999999998 0.0 0.0 0.0 0.0 66-67 0.175 0.0 0.0 0.0 0.0 68-69 0.21250000000000002 0.0 0.0 0.0 0.0 70-71 0.2375 0.0 0.0 0.0 0.0 72-73 0.25 0.0 0.0 0.0 0.0 74-75 0.325 0.0 0.0 0.0 0.0 76-77 0.44999999999999996 0.0 0.0 0.0 0.0 78-79 0.5625 0.0 0.0 0.0 0.0 80-81 0.6875 0.0 0.0 0.0 0.0 82-83 0.825 0.0 0.0 0.0 0.0 84-85 0.9375 0.0 0.0 0.0 0.0 86-87 1.0 0.0 0.0 0.0 0.0 88-89 1.1625 0.0 0.0 0.0 0.0 90-91 1.3624999999999998 0.0 0.0 0.0 0.0 92-93 1.525 0.0 0.0 0.0 0.0 94-95 1.8375 0.0 0.0 0.0 0.0 96-97 2.2625 0.0 0.0 0.0 0.0 98-99 2.6624999999999996 0.0 0.0 0.0 0.0 100-101 3.05 0.0 0.0 0.0 0.0 102-103 3.6125 0.0 0.0 0.0 0.0 104-105 4.3 0.0 0.0 0.0 0.0 106-107 5.225 0.0 0.0 0.0 0.0 108 5.875 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Read 1259933 spots for SRR28716046.sra Written 1259933 spots for SRR28716046.sra Read 1259933 spots for SRR28716046.sra Written 1259933 spots for SRR28716046.sra Read 1259933 spots for SRR28716046.sra Written 1259933 spots for SRR28716046.sra Read 1259933 spots for SRR28716046.sra Written 1259933 spots for SRR28716046.sra Read 1259933 spots for SRR28716046.sra Written 1259933 spots for SRR28716046.sra Read 1259933 spots for SRR28716046.sra Written 1259933 spots for SRR28716046.sra Read 1259933 spots for SRR28716046.sra Written 1259933 spots for SRR28716046.sra Read 1259948 spots for SRR28716046.sra Written 1259948 spots for SRR28716046.sra Read 1259933 spots for SRR28716046.sra Written 1259933 spots for SRR28716046.sra Read 1259933 spots for SRR28716046.sra Written 1259933 spots for SRR28716046.sra Read 1259933 spots for SRR28716046.sra Written 1259933 spots for SRR28716046.sra Read 1259933 spots for SRR28716046.sra Written 1259933 spots for SRR28716046.sra Read 1259933 spots for SRR28716046.sra Written 1259933 spots for SRR28716046.sra Read 1259933 spots for SRR28716046.sra Written 1259933 spots for SRR28716046.sra Read 1259933 spots for SRR28716046.sra Written 1259933 spots for SRR28716046.sra Read 1259933 spots for SRR28716046.sra Written 1259933 spots for SRR28716046.sra Read 1259933 spots for SRR28716046.sra Written 1259933 spots for SRR28716046.sra Read 1259933 spots for SRR28716046.sra Written 1259933 spots for SRR28716046.sra Read 1259933 spots for SRR28716046.sra Written 1259933 spots for SRR28716046.sra Read 1259933 spots for SRR28716046.sra Written 1259933 spots for SRR28716046.sra SRR ids: ['SRR28716046.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_x_0tp6e5 SRR28716046.sra spots: 25198675 blocks: [[1, 1259933], [1259934, 2519866], [2519867, 3779799], [3779800, 5039732], [5039733, 6299665], [6299666, 7559598], [7559599, 8819531], [8819532, 10079464], [10079465, 11339397], [11339398, 12599330], [12599331, 13859263], [13859264, 15119196], [15119197, 16379129], [16379130, 17639062], [17639063, 18898995], [18898996, 20158928], [20158929, 21418861], [21418862, 22678794], [22678795, 23938727], [23938728, 25198675]] SRR28716046 file size 8244613 SRR28716046 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 SRR28716046 SRR28716046_1.fastq Input file: SRR28716046_1.fastq trimmed: SRR28716046-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 Sat Dec 7 13:00:11 2024 >> started Sat Dec 7 13:00:24 2024 >> done (13.629s) 25198675 reads processed; of these: 1808 ( 0.01%) short reads filtered out after trimming by size control 4501 ( 0.02%) empty reads filtered out after trimming by size control 25192366 (99.97%) reads available; of these: 2870587 (11.39%) trimmed reads available after processing 22321779 (88.61%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 206 0.00% 19 265 0.00% 20 262 0.00% 21 293 0.00% 22 377 0.00% 23 549 0.00% 24 608 0.00% 25 779 0.00% 26 1124 0.00% 27 799 0.00% 28 600 0.00% 29 697 0.00% 30 668 0.00% 31 826 0.00% 32 856 0.00% 33 882 0.00% 34 948 0.00% 35 979 0.00% 36 1083 0.00% 37 1216 0.00% 38 1199 0.00% 39 1190 0.00% 40 1110 0.00% 41 1322 0.01% 42 1236 0.00% 43 1319 0.01% 44 1329 0.01% 45 1349 0.01% 46 1387 0.01% 47 1442 0.01% 48 1637 0.01% 49 1676 0.01% 50 1769 0.01% 51 1868 0.01% 52 2011 0.01% 53 2129 0.01% 54 2138 0.01% 55 2377 0.01% 56 2436 0.01% 57 2495 0.01% 58 2597 0.01% 59 2839 0.01% 60 3167 0.01% 61 3553 0.01% 62 3810 0.02% 63 4013 0.02% 64 4304 0.02% 65 4564 0.02% 66 4888 0.02% 67 5241 0.02% 68 5805 0.02% 69 6002 0.02% 70 6394 0.03% 71 7162 0.03% 72 8098 0.03% 73 8833 0.04% 74 9438 0.04% 75 10111 0.04% 76 11204 0.04% 77 11535 0.05% 78 12594 0.05% 79 15252 0.06% 80 16045 0.06% 81 17288 0.07% 82 18967 0.08% 83 20032 0.08% 84 22009 0.09% 85 25803 0.10% 86 27330 0.11% 87 28851 0.11% 88 31294 0.12% 89 3031 0.01% 90 3232 0.01% 91 3392 0.01% 92 3575 0.01% 93 3888 0.02% 94 3950 0.02% 95 4066 0.02% 96 4480 0.02% 97 4486 0.02% 98 4908 0.02% 99 5366 0.02% 100 6048 0.02% 101 7006 0.03% 102 2578 0.01% 103 3980 0.02% 104 5175 0.02% 105 6740 0.03% 106 8578 0.03% 107 10851 0.04% 108 13261 0.05% 109 15731 0.06% 110 18942 0.08% 111 23724 0.09% 112 29479 0.12% 113 37614 0.15% 114 49923 0.20% 115 68484 0.27% 116 100280 0.40% 117 151358 0.60% 118 332074 1.32% 119 1527928 6.07% 120 22321779 88.61% 25192366 reads passed initial QC criterion=sequence-density sequence-density=4.77 sequence-density-rank=1 fanout-score=54.47 fanout-score-rank=1 prefix-density=6.17 prefix-fanout=42.1 sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGT criterion=fanout-score sequence-density=4.77 sequence-density-rank=1 fanout-score=54.47 fanout-score-rank=1 prefix-density=6.17 prefix-fanout=42.1 sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGT 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 AGATCGGAAGAGCACACGTCTGAACTCCAGT -o SRR28716046 - Input file: STDIN trimmed: SRR28716046-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): AGATCGGAAGAGCACACGTCTGAACTCCAGT -- 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 Sat Dec 7 13:01:44 2024 >> started Sat Dec 7 13:02:07 2024 >> done (23.076s) 15115420 reads processed; of these: 12 ( 0.00%) short reads filtered out after trimming by size control 12 ( 0.00%) empty reads filtered out after trimming by size control 15115396 (100.00%) reads available; of these: 1778976 (11.77%) trimmed reads available after processing 13336420 (88.23%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 125 0.00% 19 170 0.00% 20 152 0.00% 21 186 0.00% 22 238 0.00% 23 341 0.00% 24 356 0.00% 25 455 0.00% 26 655 0.00% 27 491 0.00% 28 376 0.00% 29 430 0.00% 30 377 0.00% 31 488 0.00% 32 520 0.00% 33 519 0.00% 34 567 0.00% 35 594 0.00% 36 661 0.00% 37 709 0.00% 38 695 0.00% 39 714 0.00% 40 682 0.00% 41 791 0.01% 42 731 0.00% 43 760 0.01% 44 804 0.01% 45 807 0.01% 46 831 0.01% 47 884 0.01% 48 994 0.01% 49 1059 0.01% 50 1071 0.01% 51 1120 0.01% 52 1189 0.01% 53 1287 0.01% 54 1279 0.01% 55 1416 0.01% 56 1471 0.01% 57 1482 0.01% 58 1557 0.01% 59 1713 0.01% 60 1883 0.01% 61 2096 0.01% 62 2262 0.01% 63 2422 0.02% 64 2576 0.02% 65 2756 0.02% 66 2868 0.02% 67 3152 0.02% 68 3505 0.02% 69 3655 0.02% 70 3858 0.03% 71 4353 0.03% 72 4925 0.03% 73 5319 0.04% 74 5643 0.04% 75 6071 0.04% 76 6678 0.04% 77 6954 0.05% 78 7501 0.05% 79 9211 0.06% 80 9667 0.06% 81 10557 0.07% 82 11377 0.08% 83 11920 0.08% 84 13160 0.09% 85 15412 0.10% 86 16299 0.11% 87 17201 0.11% 88 19210 0.13% 89 20040 0.13% 90 21840 0.14% 91 23259 0.15% 92 26375 0.17% 93 28824 0.19% 94 30612 0.20% 95 33617 0.22% 96 35606 0.24% 97 39701 0.26% 98 42776 0.28% 99 45457 0.30% 100 48361 0.32% 101 51711 0.34% 102 52716 0.35% 103 56250 0.37% 104 59668 0.39% 105 60807 0.40% 106 65714 0.43% 107 72153 0.48% 108 74639 0.49% 109 84508 0.56% 110 86981 0.58% 111 92461 0.61% 112 102166 0.68% 113 101858 0.67% 114 120533 0.80% 115 146689 0.97% 116 189486 1.25% 117 294376 1.95% 118 177726 1.18% 119 808480 5.35% 120 11775768 77.91% criterion=sequence-density sequence-density=2.63 sequence-density-rank=1 fanout-score=2.02 fanout-score-rank=28 prefix-density=2.66 prefix-fanout=2.0 sequence=TTTCCTCTGGCT criterion=fanout-score sequence-density=0.01 sequence-density-rank=33 fanout-score=161.29 fanout-score-rank=1 prefix-density=1.10 prefix-fanout=1.0 sequence=CTCGCTTTCTTTTCTTCAAAAATTCTTATATGTTAGCGGAAAAACCTTATCCATTAATAGCGGGAACTTCAAGAGCAGCTAGATCTAGAGGGAAGTTGTGAGCATTACGTTCGTGCATTACTTCCATACCAAGATTAGCACGGTTGATGATATCAGCCCAAGTATTAATAACGCGACCTTGACTATCAACTACAGATTGGTTGAAATTGAATCCATTTAGGTTGAACGCCATAGTACTAATACCTAAAGCAGTGAACCAGATTCCTACTACAGGCCAAGCAGCCAAGAAGAAGTGTAAAGAACGAGAGTTGTTGAAACTAGCATATTGGAAGATTAATCGGCCAAAATAACCATGAGCAGCCACAATATTATAAGTCTCTTCCTCTTGACCAAATTTGTAACCCTCATTAGCAGATTCATTTTCAGTAGTTTCCCTGATCAAACTAGAGGTTACCAAGGAACCATGCATAGCACTGAATAGGGAACCGCCGAAAACACCAGCTACACCTAA Started job on | Dec 07 13:02:31 Started mapping on | Dec 07 13:02:31 Finished on | Dec 07 13:03:29 Mapping speed, Million of reads per hour | 1563.66 Number of input reads | 25192342 Average input read length | 118 UNIQUE READS: Uniquely mapped reads number | 7096458 Uniquely mapped reads % | 28.17% Average mapped length | 117.47 Number of splices: Total | 2238933 Number of splices: Annotated (sjdb) | 2105719 Number of splices: GT/AG | 2198640 Number of splices: GC/AG | 29163 Number of splices: AT/AC | 910 Number of splices: Non-canonical | 10220 Mismatch rate per base, % | 0.37% Deletion rate per base | 0.02% Deletion average length | 2.48 Insertion rate per base | 0.01% Insertion average length | 2.24 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 8434964 % of reads mapped to multiple loci | 33.48% Number of reads mapped to too many loci | 8763217 % of reads mapped to too many loci | 34.79% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 0.55% % of reads unmapped: other | 3.01% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 9660920 9660920 9660920 N_multimapping 8434964 8434964 8434964 N_noFeature 1441709 6943353 1484919 N_ambiguous 132623 519 22874 UnstrandedReadsAssigned:5522126 PositiveStrandReadsAssigned:152586 NegativeStrandReadsAssigned:5588665 Dataset is classified negative stranded MeadianReadLen=120 20thPercentileLength=119 echo kmer=115 SRR28716046 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: 52,972 [index] number of k-mers: 66,720,672 [index] number of equivalence classes: 111,837 [quant] running in single-end mode [quant] will process file 1: SRR28716046-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 25,192,342 reads, 6,696,736 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,068 rounds 52973 SRR28716046.ke.tsv 35125 SRR28716046.se.tsv 88098 total ==> SRR28716046.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 837 47.9613 10.2484 PNS24247 1044 945 0 0 PNS24249 1928 1829 14.217 1.39022 PNS24246 1044 945 0 0 PNS24248 1044 945 0 0 PNS24244 1471 1372 23.8217 3.10534 PNS24243 293 194 0 0 KQK14069 1603 1504 1163.69 138.382 KQK14071 474 375 212.547 101.371 ==> SRR28716046.se.tsv <== BRADI_1g14170v3 1594 BRADI_1g53295v3 57 BRADI_1g59795v3 17 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 93 BRADI_1g74790v3 42 BRADI_1g09890v3 0 BRADI_1g77505v3 119 BRADI_1g48960v3 0 SRR28716046 completed mapping pipeline successfully