Starting /dee2/code/volunteer_pipeline.sh SRR6945015 current disk space = 1552306552832 free memory = 1332540320 SRR6945015 SRAfilesize 73411072d7c9e9c8f1f01d3f6a65b61d SRR6945015.sra SRR6945015.sra file validated SRR6945015 is paired end SRR6945015 is conventional basespace SRR6945015 read1 length is 101 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR6945015_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 101 %GC 50 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 31.23825 33.0 33.0 33.0 33.0 33.0 2 32.011 33.0 33.0 33.0 27.0 33.0 3 32.207 33.0 33.0 33.0 33.0 33.0 4 32.3715 33.0 33.0 33.0 33.0 33.0 5 32.352 33.0 33.0 33.0 33.0 33.0 6 35.85475 37.0 37.0 37.0 33.0 37.0 7 36.063 37.0 37.0 37.0 37.0 37.0 8 36.01225 37.0 37.0 37.0 37.0 37.0 9 36.09025 37.0 37.0 37.0 37.0 37.0 10-11 36.016875 37.0 37.0 37.0 37.0 37.0 12-13 36.00025 37.0 37.0 37.0 37.0 37.0 14-15 35.780375 37.0 37.0 37.0 37.0 37.0 16-17 35.817499999999995 37.0 37.0 37.0 37.0 37.0 18-19 35.684625 37.0 37.0 37.0 35.0 37.0 20-21 35.605374999999995 37.0 37.0 37.0 35.0 37.0 22-23 35.604625 37.0 37.0 37.0 35.0 37.0 24-25 35.166124999999994 37.0 37.0 37.0 33.0 37.0 26-27 35.20325 37.0 37.0 37.0 35.0 37.0 28-29 35.430625 37.0 37.0 37.0 33.0 37.0 30-31 35.170874999999995 37.0 37.0 37.0 33.0 37.0 32-33 35.457 37.0 37.0 37.0 35.0 37.0 34-35 34.877625 37.0 37.0 37.0 30.0 37.0 36-37 35.099875 37.0 37.0 37.0 30.0 37.0 38-39 35.197375 37.0 37.0 37.0 33.0 37.0 40-41 35.177125000000004 37.0 37.0 37.0 33.0 37.0 42-43 35.494625 37.0 37.0 37.0 35.0 37.0 44-45 35.349625 37.0 37.0 37.0 33.0 37.0 46-47 35.502125 37.0 37.0 37.0 35.0 37.0 48-49 35.256249999999994 37.0 37.0 37.0 33.0 37.0 50-51 35.576125000000005 37.0 37.0 37.0 37.0 37.0 52-53 35.425250000000005 37.0 37.0 37.0 35.0 37.0 54-55 35.50025 37.0 37.0 37.0 35.0 37.0 56-57 35.609375 37.0 37.0 37.0 37.0 37.0 58-59 35.592625 37.0 37.0 37.0 37.0 37.0 60-61 35.4015 37.0 37.0 37.0 35.0 37.0 62-63 35.47775 37.0 37.0 37.0 35.0 37.0 64-65 35.44325 37.0 37.0 37.0 35.0 37.0 66-67 35.3855 37.0 37.0 37.0 35.0 37.0 68-69 35.445125 37.0 37.0 37.0 33.0 37.0 70-71 35.446375 37.0 37.0 37.0 33.0 37.0 72-73 35.5295 37.0 37.0 37.0 35.0 37.0 74-75 35.49025 37.0 37.0 37.0 35.0 37.0 76-77 35.5345 37.0 37.0 37.0 35.0 37.0 78-79 35.530249999999995 37.0 37.0 37.0 35.0 37.0 80-81 35.4315 37.0 37.0 37.0 35.0 37.0 82-83 35.371875 37.0 37.0 37.0 33.0 37.0 84-85 35.206125 37.0 37.0 37.0 35.0 37.0 86-87 35.173375 37.0 37.0 37.0 33.0 37.0 88-89 35.165 37.0 37.0 37.0 33.0 37.0 90-91 35.156000000000006 37.0 37.0 37.0 33.0 37.0 92-93 35.144375 37.0 37.0 37.0 33.0 37.0 94-95 34.755 37.0 37.0 37.0 33.0 37.0 96-97 34.951375 37.0 37.0 37.0 33.0 37.0 98-99 34.400125 37.0 37.0 37.0 33.0 37.0 100-101 33.788125 37.0 37.0 37.0 30.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 21.0 3 11.0 4 7.0 5 5.0 6 8.0 7 2.0 8 2.0 9 5.0 10 0.0 11 2.0 12 0.0 13 0.0 14 3.0 15 2.0 16 5.0 17 2.0 18 0.0 19 4.0 20 2.0 21 3.0 22 13.0 23 19.0 24 14.0 25 13.0 26 18.0 27 23.0 28 31.0 29 40.0 30 35.0 31 58.0 32 74.0 33 94.0 34 152.0 35 300.0 36 3032.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 39.17338185599168 8.188198596308812 5.0688848453340265 47.56953470236548 2 22.625 9.45 36.425000000000004 31.5 3 20.875 11.05 21.775 46.300000000000004 4 27.150000000000002 17.1 20.525 35.225 5 29.549999999999997 23.200000000000003 23.625 23.625 6 24.224999999999998 29.599999999999998 22.825 23.35 7 19.85 25.05 36.975 18.125 8 19.875 23.974999999999998 31.35 24.8 9 19.825 22.5 34.35 23.325000000000003 10-11 22.325 30.662499999999998 24.85 22.162499999999998 12-13 22.5 24.6 27.987499999999997 24.9125 14-15 22.725 25.35 26.924999999999997 25.0 16-17 23.400000000000002 25.074999999999996 25.2375 26.2875 18-19 23.150000000000002 25.775 25.525 25.55 20-21 23.400000000000002 27.0 25.162499999999998 24.4375 22-23 24.2625 25.424999999999997 24.6125 25.7 24-25 23.4375 25.8625 25.2625 25.4375 26-27 23.2625 25.6 25.55 25.587500000000002 28-29 23.65 25.55 24.0375 26.7625 30-31 23.493373343335833 24.76869217304326 24.593648412103025 27.144286071517882 32-33 22.912499999999998 25.4375 25.5125 26.137500000000003 34-35 24.2875 24.2625 24.7 26.75 36-37 24.4875 24.212500000000002 24.837500000000002 26.4625 38-39 23.9375 25.887500000000003 24.6875 25.4875 40-41 23.7375 25.6125 24.474999999999998 26.174999999999997 42-43 24.0 25.650000000000002 24.675 25.674999999999997 44-45 24.087500000000002 24.625 24.6625 26.625 46-47 23.8125 26.200000000000003 24.175 25.8125 48-49 23.974999999999998 24.9875 24.099999999999998 26.937499999999996 50-51 23.6875 25.5125 25.2 25.6 52-53 23.5375 25.7125 24.25 26.5 54-55 23.2625 24.8125 25.6 26.325 56-57 23.8625 24.8 25.2 26.137500000000003 58-59 24.75 24.5375 24.712500000000002 26.0 60-61 23.2125 25.575 25.025 26.187500000000004 62-63 23.9 24.825 25.15 26.125 64-65 23.5875 24.4375 24.4125 27.5625 66-67 24.2625 25.162499999999998 24.0 26.575 68-69 23.799999999999997 25.45 25.137500000000003 25.6125 70-71 25.0 25.15 24.212500000000002 25.637500000000003 72-73 24.425 24.6125 24.2625 26.700000000000003 74-75 23.7 25.4375 24.275 26.5875 76-77 24.725 24.337500000000002 24.8125 26.125 78-79 23.625 25.275 24.65 26.450000000000003 80-81 24.55 24.575 24.75 26.125 82-83 24.474999999999998 25.45 24.125 25.95 84-85 24.175 24.025 24.925 26.875 86-87 24.5125 25.2375 24.775 25.474999999999998 88-89 24.962500000000002 25.0 23.7625 26.275 90-91 23.925 25.2 24.1875 26.687499999999996 92-93 24.5 24.7875 24.8625 25.85 94-95 24.85621405351338 24.281070267566893 24.3935983995999 26.469117279319832 96-97 24.099999999999998 24.5625 24.325 27.0125 98-99 25.4875 24.3125 24.4875 25.7125 100-101 24.75 24.125 24.55 26.575 >>END_MODULE >>Per sequence GC content fail #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 0.5 19 0.5 20 0.0 21 0.0 22 0.0 23 0.0 24 0.0 25 1.0 26 1.0 27 0.0 28 1.0 29 1.5 30 2.0 31 7.0 32 12.0 33 16.0 34 21.0 35 27.5 36 40.5 37 56.5 38 68.5 39 88.0 40 103.5 41 116.5 42 147.0 43 173.0 44 183.5 45 174.5 46 178.0 47 193.0 48 180.0 49 173.0 50 171.5 51 162.0 52 162.0 53 155.5 54 139.0 55 134.5 56 120.5 57 90.0 58 77.0 59 73.0 60 69.5 61 75.5 62 73.5 63 70.0 64 72.0 65 60.5 66 50.5 67 48.0 68 48.0 69 38.5 70 29.5 71 30.5 72 24.0 73 16.0 74 10.0 75 8.5 76 8.5 77 6.5 78 4.5 79 2.5 80 1.5 81 0.5 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 3.8249999999999997 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 0.025 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 0.025 96-97 0.0 98-99 0.0 100-101 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 101 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 98.225 #Duplication Level Percentage of deduplicated Percentage of total 1 98.57470094171545 96.825 2 1.1453296004072282 2.25 3 0.17816238228556885 0.525 4 0.10180707559175363 0.4 5 0.0 0.0 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 pass >>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 0.037500000000000006 0.0 0.0 0.0 0.0 50-51 0.05 0.0 0.0 0.0 0.0 52-53 0.05 0.0 0.0 0.0 0.0 54-55 0.05 0.0 0.0 0.0 0.0 56-57 0.05 0.0 0.0 0.0 0.0 58-59 0.05 0.0 0.0 0.0 0.0 60-61 0.05 0.0 0.0 0.0 0.0 62-63 0.075 0.0 0.0 0.0 0.0 64-65 0.0875 0.0 0.0 0.0 0.0 66-67 0.1375 0.0 0.0 0.0 0.0 68-69 0.175 0.0 0.0 0.0 0.0 70-71 0.175 0.0 0.0 0.0 0.0 72-73 0.2 0.0 0.0 0.0 0.0 74-75 0.21250000000000002 0.0 0.0 0.0 0.0 76-77 0.2625 0.0 0.0 0.0 0.0 78-79 0.36250000000000004 0.0 0.0 0.0 0.0 80-81 0.44999999999999996 0.0 0.0 0.0 0.0 82-83 0.5125 0.0 0.0 0.0 0.0 84-85 0.625 0.0 0.0 0.0 0.0 86-87 0.7375 0.0 0.0 0.0 0.0 88-89 0.925 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE SRR6945015 read2 length is 101 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR6945015_2.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 101 %GC 51 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 31.53975 33.0 33.0 33.0 33.0 33.0 2 31.4745 33.0 33.0 33.0 33.0 33.0 3 31.47 33.0 33.0 33.0 33.0 33.0 4 31.4465 33.0 33.0 33.0 33.0 33.0 5 31.67075 33.0 33.0 33.0 33.0 33.0 6 34.93325 37.0 37.0 37.0 33.0 37.0 7 35.048 37.0 37.0 37.0 33.0 37.0 8 35.016 37.0 37.0 37.0 33.0 37.0 9 35.09 37.0 37.0 37.0 33.0 37.0 10-11 35.170125 37.0 37.0 37.0 33.0 37.0 12-13 35.223 37.0 37.0 37.0 35.0 37.0 14-15 35.183125000000004 37.0 37.0 37.0 33.0 37.0 16-17 35.192 37.0 37.0 37.0 33.0 37.0 18-19 35.300125 37.0 37.0 37.0 35.0 37.0 20-21 35.3485 37.0 37.0 37.0 35.0 37.0 22-23 35.28175 37.0 37.0 37.0 33.0 37.0 24-25 35.261625 37.0 37.0 37.0 33.0 37.0 26-27 35.25325 37.0 37.0 37.0 33.0 37.0 28-29 34.913624999999996 37.0 37.0 37.0 33.0 37.0 30-31 35.087 37.0 37.0 37.0 33.0 37.0 32-33 34.933125000000004 37.0 37.0 37.0 33.0 37.0 34-35 34.901125 37.0 37.0 37.0 33.0 37.0 36-37 34.84975 37.0 37.0 37.0 30.0 37.0 38-39 35.037375 37.0 37.0 37.0 33.0 37.0 40-41 34.945750000000004 37.0 37.0 37.0 33.0 37.0 42-43 35.130875 37.0 37.0 37.0 33.0 37.0 44-45 35.121750000000006 37.0 37.0 37.0 33.0 37.0 46-47 35.175125 37.0 37.0 37.0 33.0 37.0 48-49 34.9415 37.0 37.0 37.0 33.0 37.0 50-51 34.935500000000005 37.0 37.0 37.0 33.0 37.0 52-53 34.884625 37.0 37.0 37.0 33.0 37.0 54-55 34.928875 37.0 37.0 37.0 33.0 37.0 56-57 35.0295 37.0 37.0 37.0 33.0 37.0 58-59 34.695375 37.0 37.0 37.0 30.0 37.0 60-61 34.736875 37.0 37.0 37.0 33.0 37.0 62-63 34.878875 37.0 37.0 37.0 33.0 37.0 64-65 34.778 37.0 37.0 37.0 33.0 37.0 66-67 34.62975 37.0 37.0 37.0 30.0 37.0 68-69 34.69625 37.0 37.0 37.0 30.0 37.0 70-71 34.532250000000005 37.0 37.0 37.0 30.0 37.0 72-73 34.253125 37.0 37.0 37.0 27.0 37.0 74-75 34.500375 37.0 37.0 37.0 30.0 37.0 76-77 34.355375 37.0 37.0 37.0 27.0 37.0 78-79 34.22875 37.0 37.0 37.0 27.0 37.0 80-81 34.379875 37.0 37.0 37.0 27.0 37.0 82-83 34.3805 37.0 37.0 37.0 27.0 37.0 84-85 34.519875 37.0 37.0 37.0 33.0 37.0 86-87 34.50175 37.0 37.0 37.0 33.0 37.0 88-89 34.45075 37.0 37.0 37.0 30.0 37.0 90-91 34.230125 37.0 37.0 37.0 27.0 37.0 92-93 34.1005 37.0 37.0 37.0 30.0 37.0 94-95 34.104 37.0 37.0 37.0 27.0 37.0 96-97 33.994625 37.0 37.0 37.0 27.0 37.0 98-99 33.847750000000005 37.0 37.0 37.0 27.0 37.0 100-101 32.3795 37.0 35.0 37.0 14.5 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 68.0 3 6.0 4 9.0 5 4.0 6 7.0 7 4.0 8 2.0 9 1.0 10 2.0 11 4.0 12 3.0 13 5.0 14 1.0 15 4.0 16 2.0 17 7.0 18 6.0 19 2.0 20 7.0 21 5.0 22 13.0 23 15.0 24 21.0 25 22.0 26 32.0 27 36.0 28 38.0 29 47.0 30 39.0 31 55.0 32 93.0 33 101.0 34 144.0 35 319.0 36 2876.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 29.59312610563558 19.282284559009348 9.123073035127621 42.00151630022744 2 30.874178878221326 22.612430520464883 27.31177362304194 19.201616978271854 3 21.12177867609904 26.099039919151085 28.322385042950987 24.456796361798887 4 25.416877210712478 28.448711470439612 21.829206670035372 24.30520464881253 5 29.537995455693007 30.39636455440545 19.919212320121183 20.14642766978036 6 24.243951612903224 34.65221774193548 19.657258064516128 21.446572580645164 7 24.50214267708596 20.0907486765818 32.24098815225611 23.16612049407613 8 24.091826437941474 21.796165489404643 25.630676084762865 28.481331987891018 9 24.124023191328458 23.418200151247795 27.955633980337787 24.50214267708596 10-11 25.98941265439879 27.577514494580285 22.11998991681371 24.31308293420721 12-13 27.111167128812703 22.87622888832871 23.89715149987396 26.115452482984626 14-15 26.01462062011596 25.25838164860096 24.388706831358707 24.338290899924374 16-17 27.52709856314595 24.250063019914293 22.309049659692462 25.913788757247293 18-19 26.200378071833647 25.330812854442343 23.364839319470697 25.103969754253306 20-21 28.069069826065036 24.602974539954626 23.20393244265188 24.124023191328458 22-23 27.577514494580285 24.363498865641542 22.87622888832871 25.182757751449458 24-25 25.875976808671542 23.682883791278044 24.489538694227374 25.95160070582304 26-27 27.539702546004534 24.527350642803125 23.418200151247795 24.514746659944542 28-29 27.111167128812703 24.716410385681876 23.392992185530627 24.77943029997479 30-31 26.068322198411696 24.643892600529433 24.24051430732384 25.04727089373503 32-33 26.342324174439124 24.77943029997479 23.77111167128813 25.10713385429796 34-35 27.01033526594404 24.855054197126293 22.964456768338795 25.170153768590875 36-37 25.89465725806452 24.810987903225808 23.475302419354836 25.819052419354836 38-39 26.29190824300479 24.74161835139904 24.338290899924374 24.62818250567179 40-41 26.978326612903224 24.29435483870968 23.714717741935484 25.012600806451612 42-43 26.238185255198488 24.171392564587272 24.373030875866412 25.217391304347824 44-45 26.193775985888873 24.78266347486456 24.064508000503967 24.959052538742597 46-47 26.90854119425548 24.20005039052658 24.099269337364575 24.792139077853363 48-49 26.750629722921914 24.357682619647356 23.50125944584383 25.3904282115869 50-51 26.600302419354836 25.025201612903224 23.954133064516128 24.420362903225808 52-53 26.717076244486453 24.612476370510397 24.13358538122243 24.53686200378072 54-55 25.724729014368542 25.23317368288379 24.300478951348627 24.74161835139904 56-57 26.493571968742124 24.77943029997479 24.59037055709604 24.13662717418704 58-59 26.569195865893626 24.073607259894125 24.111419208469876 25.245777665742374 60-61 26.184475806451612 24.672379032258064 25.189012096774192 23.954133064516128 62-63 26.21897442358574 25.727604888496913 24.039309562807105 24.014111125110244 64-65 27.07231040564374 23.796926177878557 24.842529604434365 24.288233812043337 66-67 26.155978329343583 24.80786191256142 24.543278316744363 24.492881441350637 68-69 26.567615210274493 25.232938806346006 24.024175270712668 24.175270712666837 70-71 27.77777777777778 23.29302091206853 24.225245653817083 24.70395565633661 72-73 26.748141615219858 24.19050018898828 24.669270505228678 24.392087690563187 74-75 26.927923387096776 24.936995967741936 24.21875 23.916330645161292 76-77 26.549899193548388 23.525705645161292 24.949596774193548 24.974798387096776 78-79 25.547996976568406 25.132275132275133 24.086671705719326 25.233056185437135 80-81 26.184475806451612 25.47883064516129 24.508568548387096 23.828125 82-83 27.451474665994454 23.556843962692213 23.89715149987396 25.094529871439374 84-85 26.524697580645164 24.911794354838708 24.155745967741936 24.407762096774192 86-87 26.14066044870179 24.19964708847996 24.981094025712125 24.678598437106125 88-89 27.46283698664651 23.356009070294785 24.452003023431594 24.72915091962711 90-91 27.000125992188483 24.770064256016127 24.732266599470833 23.497543152324557 92-93 26.606198034769463 24.90551776266062 24.16225749559083 24.326026706979086 94-95 26.713709677419356 23.865927419354836 24.495967741935484 24.92439516129032 96-97 26.362948006057547 24.709742554265524 24.444724886421 24.482584553255933 98-99 26.936154136758596 24.39239390504974 24.581286991562777 24.090164966628887 100-101 27.3116654069035 24.36381960191484 23.960695389266817 24.36381960191484 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 28.0 1 15.5 2 1.5 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 0.5 20 0.5 21 0.0 22 0.5 23 0.5 24 0.0 25 0.0 26 0.0 27 1.5 28 3.0 29 1.5 30 1.5 31 5.0 32 9.5 33 15.0 34 18.5 35 20.5 36 26.0 37 42.5 38 62.5 39 75.0 40 97.0 41 112.0 42 129.0 43 167.0 44 173.5 45 152.0 46 168.5 47 191.0 48 183.0 49 181.5 50 175.0 51 157.5 52 139.5 53 130.5 54 133.5 55 128.0 56 107.0 57 96.5 58 87.5 59 86.5 60 87.5 61 78.0 62 83.0 63 81.0 64 75.5 65 70.0 66 67.5 67 67.0 68 54.0 69 39.5 70 36.5 71 34.0 72 27.0 73 23.5 74 20.0 75 12.0 76 8.5 77 9.5 78 7.0 79 5.0 80 2.0 81 0.0 82 0.5 83 0.5 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 1.075 2 1.05 3 1.05 4 1.05 5 0.975 6 0.8 7 0.8250000000000001 8 0.8999999999999999 9 0.8250000000000001 10-11 0.8250000000000001 12-13 0.8250000000000001 14-15 0.8250000000000001 16-17 0.8250000000000001 18-19 0.8125 20-21 0.8250000000000001 22-23 0.8250000000000001 24-25 0.8250000000000001 26-27 0.8250000000000001 28-29 0.8250000000000001 30-31 0.8375 32-33 0.8250000000000001 34-35 0.8250000000000001 36-37 0.8 38-39 0.8250000000000001 40-41 0.8 42-43 0.8125 44-45 0.7875 46-47 0.775 48-49 0.75 50-51 0.8 52-53 0.8125 54-55 0.8250000000000001 56-57 0.8250000000000001 58-59 0.8250000000000001 60-61 0.8 62-63 0.7875 64-65 0.775 66-67 0.7875 68-69 0.7250000000000001 70-71 0.775 72-73 0.7875 74-75 0.8 76-77 0.8 78-79 0.775 80-81 0.8 82-83 0.8250000000000001 84-85 0.8 86-87 0.8250000000000001 88-89 0.775 90-91 0.7875 92-93 0.775 94-95 0.8 96-97 0.95 98-99 0.7374999999999999 100-101 0.775 >>END_MODULE >>Sequence Length Distribution pass #Length Count 101 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 98.575 #Duplication Level Percentage of deduplicated Percentage of total 1 99.23915800152169 97.82499999999999 2 0.7354805985290388 1.4500000000000002 3 0.0 0.0 4 0.0 0.0 5 0.0 0.0 6 0.0 0.0 7 0.0 0.0 8 0.0 0.0 9 0.0 0.0 >10 0.025361399949277198 0.7250000000000001 >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 NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN 29 0.7250000000000001 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 0.037500000000000006 0.0 0.0 0.0 0.0 50-51 0.05 0.0 0.0 0.0 0.0 52-53 0.05 0.0 0.0 0.0 0.0 54-55 0.05 0.0 0.0 0.0 0.0 56-57 0.05 0.0 0.0 0.0 0.0 58-59 0.05 0.0 0.0 0.0 0.0 60-61 0.05 0.0 0.0 0.0 0.0 62-63 0.075 0.0 0.0 0.0 0.0 64-65 0.0875 0.0 0.0 0.0 0.0 66-67 0.1375 0.0 0.0 0.0 0.0 68-69 0.175 0.0 0.0 0.0 0.0 70-71 0.175 0.0 0.0 0.0 0.0 72-73 0.2 0.0 0.0 0.0 0.0 74-75 0.21250000000000002 0.0 0.0 0.0 0.0 76-77 0.2625 0.0 0.0 0.0 0.0 78-79 0.36250000000000004 0.0 0.0 0.0 0.0 80-81 0.44999999999999996 0.0 0.0 0.0 0.0 82-83 0.5125 0.0 0.0 0.0 0.0 84-85 0.625 0.0 0.0 0.0 0.0 86-87 0.7375 0.0 0.0 0.0 0.0 88-89 0.9 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Read 3115897 spots for SRR6945015.sra Written 3115897 spots for SRR6945015.sra Read 3115897 spots for SRR6945015.sra Written 3115897 spots for SRR6945015.sra Read 3115897 spots for SRR6945015.sra Written 3115897 spots for SRR6945015.sra Read 3115897 spots for SRR6945015.sra Written 3115897 spots for SRR6945015.sra Read 3115897 spots for SRR6945015.sra Written 3115897 spots for SRR6945015.sra Read 3115897 spots for SRR6945015.sra Written 3115897 spots for SRR6945015.sra Read 3115897 spots for SRR6945015.sra Written 3115897 spots for SRR6945015.sra Read 3115897 spots for SRR6945015.sra Written 3115897 spots for SRR6945015.sra Read 3115897 spots for SRR6945015.sra Written 3115897 spots for SRR6945015.sra Read 3115897 spots for SRR6945015.sra Written 3115897 spots for SRR6945015.sra Read 3115897 spots for SRR6945015.sra Written 3115897 spots for SRR6945015.sra Read 3115908 spots for SRR6945015.sra Written 3115908 spots for SRR6945015.sra Read 3115897 spots for SRR6945015.sra Written 3115897 spots for SRR6945015.sra Read 3115897 spots for SRR6945015.sra Written 3115897 spots for SRR6945015.sra Read 3115897 spots for SRR6945015.sra Written 3115897 spots for SRR6945015.sra Read 3115897 spots for SRR6945015.sra Written 3115897 spots for SRR6945015.sra Read 3115897 spots for SRR6945015.sra Written 3115897 spots for SRR6945015.sra Read 3115897 spots for SRR6945015.sra Written 3115897 spots for SRR6945015.sra Read 3115897 spots for SRR6945015.sra Written 3115897 spots for SRR6945015.sra Read 3115897 spots for SRR6945015.sra Written 3115897 spots for SRR6945015.sra SRR ids: ['SRR6945015.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_ejyqtwja SRR6945015.sra spots: 62317951 blocks: [[1, 3115897], [3115898, 6231794], [6231795, 9347691], [9347692, 12463588], [12463589, 15579485], [15579486, 18695382], [18695383, 21811279], [21811280, 24927176], [24927177, 28043073], [28043074, 31158970], [31158971, 34274867], [34274868, 37390764], [37390765, 40506661], [40506662, 43622558], [43622559, 46738455], [46738456, 49854352], [49854353, 52970249], [52970250, 56086146], [56086147, 59202043], [59202044, 62317951]] SRR6945015 file size 15010071 SRR6945015 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 SRR6945015 SRR6945015_1.fastq SRR6945015_2.fastq Input file: SRR6945015_1.fastq Paired file: SRR6945015_2.fastq trimmed: SRR6945015-trimmed-pair1.fastq, SRR6945015-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 Fri Dec 6 09:54:17 2024 >> started Fri Dec 6 09:55:25 2024 >> done (68.211s) 62317951 read pairs processed; of these: 592903 ( 0.95%) short read pairs filtered out after trimming by size control 1237488 ( 1.99%) empty read pairs filtered out after trimming by size control 60487560 (97.06%) read pairs available; of these: 11690346 (19.33%) trimmed read pairs available after processing 48797214 (80.67%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 225 0.00% 19 428 0.00% 20 642 0.00% 21 764 0.00% 22 986 0.00% 23 1037 0.00% 24 1160 0.00% 25 1256 0.00% 26 1334 0.00% 27 1460 0.00% 28 1535 0.00% 29 1617 0.00% 30 1745 0.00% 31 1834 0.00% 32 1854 0.00% 33 2033 0.00% 34 2086 0.00% 35 2201 0.00% 36 2302 0.00% 37 2343 0.00% 38 2593 0.00% 39 2756 0.00% 40 2867 0.00% 41 3096 0.01% 42 3176 0.01% 43 3337 0.01% 44 3510 0.01% 45 3695 0.01% 46 3959 0.01% 47 4336 0.01% 48 4726 0.01% 49 5117 0.01% 50 5670 0.01% 51 6333 0.01% 52 6852 0.01% 53 7451 0.01% 54 8158 0.01% 55 9075 0.02% 56 10228 0.02% 57 11943 0.02% 58 14718 0.02% 59 29793 0.05% 60 35606 0.06% 61 32907 0.05% 62 33361 0.06% 63 33439 0.06% 64 33108 0.05% 65 34395 0.06% 66 33963 0.06% 67 34010 0.06% 68 35657 0.06% 69 38948 0.06% 70 38402 0.06% 71 40836 0.07% 72 40787 0.07% 73 42102 0.07% 74 44009 0.07% 75 45803 0.08% 76 49694 0.08% 77 51744 0.09% 78 53830 0.09% 79 57109 0.09% 80 60449 0.10% 81 64381 0.11% 82 69782 0.12% 83 75157 0.12% 84 82141 0.14% 85 89483 0.15% 86 99315 0.16% 87 104817 0.17% 88 111081 0.18% 89 121370 0.20% 90 134148 0.22% 91 148982 0.25% 92 168102 0.28% 93 189235 0.31% 94 222081 0.37% 95 265646 0.44% 96 330041 0.55% 97 446837 0.74% 98 662338 1.09% 99 1180308 1.95% 100 6072711 10.04% 101 48797214 80.67% 60487560 reads passed initial QC criterion=sequence-density sequence-density=0.11 sequence-density-rank=1 fanout-score=1.99 fanout-score-rank=39 prefix-density=0.10 prefix-fanout=2.0 sequence=ATTGGTTGAGACGGCATGTGGCTTATTCTTCTCGCAAGC criterion=fanout-score sequence-density=0.03 sequence-density-rank=29 fanout-score=199.94 fanout-score-rank=1 prefix-density=0.37 prefix-fanout=17.4 sequence=GGCGGCGGCGAACCGCCCCCGTCGCCGCGATCCGAACACTTCACCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGCATTCCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCTATATACTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCAAACTTCCGTCGCCTAAACGGCGATAGTCCCTCTAAGAAGCTAGCTGCGGAGGGATGGCTCCGCATAGCTAGTTAGCAGGCTGAGGTCTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCATGCACCACCACCCATAGAATCAAGAAAGAGCTCTCAGTCTGTCAATCCTTGCT criterion=sequence-density sequence-density=0.13 sequence-density-rank=1 fanout-score=5.16 fanout-score-rank=27 prefix-density=0.19 prefix-fanout=3.4 sequence=CGGCCATGGCGG criterion=fanout-score sequence-density=0.06 sequence-density-rank=25 fanout-score=222.97 fanout-score-rank=1 prefix-density=0.75 prefix-fanout=18.9 sequence=CGCCGCCGCCGTC SRR6945015 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 06 09:56:09 Started mapping on | Dec 06 09:56:09 Finished on | Dec 06 09:58:51 Mapping speed, Million of reads per hour | 1344.17 Number of input reads | 60487560 Average input read length | 199 UNIQUE READS: Uniquely mapped reads number | 55515581 Uniquely mapped reads % | 91.78% Average mapped length | 199.42 Number of splices: Total | 35056838 Number of splices: Annotated (sjdb) | 33614444 Number of splices: GT/AG | 34612803 Number of splices: GC/AG | 384189 Number of splices: AT/AC | 20331 Number of splices: Non-canonical | 39515 Mismatch rate per base, % | 0.21% Deletion rate per base | 0.01% Deletion average length | 2.13 Insertion rate per base | 0.01% Insertion average length | 2.11 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 611118 % of reads mapped to multiple loci | 1.01% Number of reads mapped to too many loci | 514971 % of reads mapped to too many loci | 0.85% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 0.91% % of reads unmapped: other | 5.45% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 4412224 4412224 4412224 N_multimapping 611118 611118 611118 N_noFeature 1307626 54093609 1734969 N_ambiguous 1160962 5612 172513 UnstrandedReadsAssigned:53046993 PositiveStrandReadsAssigned:1416360 NegativeStrandReadsAssigned:53608099 Dataset is classified negative stranded MeadianReadLen=101 20thPercentileLength=101 echo kmer=97 SRR6945015 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: 52,972 [index] number of k-mers: 66,720,672 [index] number of equivalence classes: 111,837 [quant] running in paired-end mode [quant] will process pair 1: SRR6945015-trimmed-pair1.fastq SRR6945015-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 60,487,560 reads, 53,907,575 reads pseudoaligned [quant] estimated average fragment length: 210.674 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,498 rounds 52973 SRR6945015.ke.tsv 35125 SRR6945015.se.tsv 88098 total ==> SRR6945015.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 726.404 54.7136 2.00425 PNS24247 1044 834.326 94.5076 3.01415 PNS24249 1928 1718.33 218.474 3.38321 PNS24246 1044 834.326 94.5076 3.01415 PNS24248 1044 834.326 94.5076 3.01415 PNS24244 1471 1261.33 236.289 4.98484 PNS24243 293 105.616 0 0 KQK14069 1603 1393.33 43.945 0.839249 KQK14071 474 267.182 4.6359 0.461701 ==> SRR6945015.se.tsv <== BRADI_1g14170v3 59 BRADI_1g53295v3 189 BRADI_1g59795v3 544 BRADI_1g07683v3 0 BRADI_1g00485v3 64 BRADI_1g20270v3 3292 BRADI_1g74790v3 1180 BRADI_1g09890v3 0 BRADI_1g77505v3 210 BRADI_1g48960v3 0 SRR6945015 completed mapping pipeline successfully