Starting /dee2/code/volunteer_pipeline.sh ERR3450078 current disk space = 1542922395648 free memory = 1599121660 ERR3450078 SRAfilesize d0448c78ec91faf79a5ebc688a9ac4e0 ERR3450078.sra ERR3450078.sra file validated ERR3450078 is paired end ERR3450078 is conventional basespace ERR3450078 read1 length is 101 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR3450078_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 51 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.19325 37.0 37.0 37.0 37.0 37.0 2 36.3005 37.0 37.0 37.0 37.0 37.0 3 36.403 37.0 37.0 37.0 37.0 37.0 4 36.448 37.0 37.0 37.0 37.0 37.0 5 36.447 37.0 37.0 37.0 37.0 37.0 6 36.5195 37.0 37.0 37.0 37.0 37.0 7 36.4245 37.0 37.0 37.0 37.0 37.0 8 36.424 37.0 37.0 37.0 37.0 37.0 9 36.5035 37.0 37.0 37.0 37.0 37.0 10-11 36.5095 37.0 37.0 37.0 37.0 37.0 12-13 36.464 37.0 37.0 37.0 37.0 37.0 14-15 36.492999999999995 37.0 37.0 37.0 37.0 37.0 16-17 36.43675 37.0 37.0 37.0 37.0 37.0 18-19 36.43625 37.0 37.0 37.0 37.0 37.0 20-21 36.47025 37.0 37.0 37.0 37.0 37.0 22-23 36.431749999999994 37.0 37.0 37.0 37.0 37.0 24-25 36.40575 37.0 37.0 37.0 37.0 37.0 26-27 36.426 37.0 37.0 37.0 37.0 37.0 28-29 36.429 37.0 37.0 37.0 37.0 37.0 30-31 36.37775 37.0 37.0 37.0 37.0 37.0 32-33 36.3765 37.0 37.0 37.0 37.0 37.0 34-35 36.336749999999995 37.0 37.0 37.0 37.0 37.0 36-37 36.335750000000004 37.0 37.0 37.0 37.0 37.0 38-39 36.291250000000005 37.0 37.0 37.0 37.0 37.0 40-41 36.28175 37.0 37.0 37.0 37.0 37.0 42-43 36.157 37.0 37.0 37.0 37.0 37.0 44-45 36.229749999999996 37.0 37.0 37.0 37.0 37.0 46-47 36.1605 37.0 37.0 37.0 37.0 37.0 48-49 36.2905 37.0 37.0 37.0 37.0 37.0 50-51 36.2615 37.0 37.0 37.0 37.0 37.0 52-53 36.126999999999995 37.0 37.0 37.0 37.0 37.0 54-55 36.14175 37.0 37.0 37.0 37.0 37.0 56-57 36.155 37.0 37.0 37.0 37.0 37.0 58-59 36.19425 37.0 37.0 37.0 37.0 37.0 60-61 36.1235 37.0 37.0 37.0 37.0 37.0 62-63 36.173249999999996 37.0 37.0 37.0 37.0 37.0 64-65 36.122249999999994 37.0 37.0 37.0 37.0 37.0 66-67 36.091750000000005 37.0 37.0 37.0 37.0 37.0 68-69 36.063 37.0 37.0 37.0 37.0 37.0 70-71 35.9725 37.0 37.0 37.0 37.0 37.0 72-73 36.03575 37.0 37.0 37.0 37.0 37.0 74-75 36.0225 37.0 37.0 37.0 37.0 37.0 76-77 36.0945 37.0 37.0 37.0 37.0 37.0 78-79 35.960750000000004 37.0 37.0 37.0 37.0 37.0 80-81 36.031499999999994 37.0 37.0 37.0 37.0 37.0 82-83 35.96925 37.0 37.0 37.0 37.0 37.0 84-85 35.99725 37.0 37.0 37.0 37.0 37.0 86-87 35.8965 37.0 37.0 37.0 37.0 37.0 88-89 35.95125 37.0 37.0 37.0 37.0 37.0 90-91 35.8955 37.0 37.0 37.0 37.0 37.0 92-93 35.85325 37.0 37.0 37.0 37.0 37.0 94-95 35.876000000000005 37.0 37.0 37.0 37.0 37.0 96-97 35.8375 37.0 37.0 37.0 37.0 37.0 98-99 35.914 37.0 37.0 37.0 37.0 37.0 100-101 35.802 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 19 1.0 20 1.0 21 0.0 22 0.0 23 2.0 24 4.0 25 6.0 26 15.0 27 11.0 28 18.0 29 33.0 30 43.0 31 56.0 32 59.0 33 87.0 34 132.0 35 228.0 36 1825.0 37 1479.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 37.653547254951114 10.654299323138632 10.127851591877663 41.56430183003259 2 21.625 14.7 30.675 33.0 3 21.175 17.150000000000002 24.45 37.225 4 27.150000000000002 22.6 18.7 31.55 5 25.874999999999996 27.85 21.575 24.7 6 22.775000000000002 30.975 24.224999999999998 22.025 7 18.8 22.425 39.4 19.375 8 21.125 21.7 31.05 26.125 9 23.200000000000003 20.3 31.5 25.0 10-11 24.0 28.7375 23.0875 24.175 12-13 24.55 22.412499999999998 25.8625 27.175 14-15 23.0625 25.2875 26.2125 25.4375 16-17 23.3 24.725 25.362499999999997 26.6125 18-19 23.724999999999998 24.575 25.224999999999998 26.474999999999998 20-21 24.6875 25.362499999999997 24.575 25.374999999999996 22-23 23.575 24.212500000000002 25.575 26.637499999999996 24-25 23.9125 24.325 25.0625 26.700000000000003 26-27 24.8125 24.825 24.05 26.3125 28-29 24.962500000000002 23.9125 23.825 27.3 30-31 23.8875 23.025000000000002 24.1125 28.975 32-33 24.099999999999998 24.025 24.2375 27.6375 34-35 24.85 23.5875 25.35 26.2125 36-37 23.8875 23.4625 24.45 28.199999999999996 38-39 24.212500000000002 25.1 24.1375 26.55 40-41 24.175 24.45 23.400000000000002 27.975 42-43 25.374999999999996 23.9875 24.55 26.087500000000002 44-45 23.9125 24.099999999999998 24.625 27.3625 46-47 24.65 24.462500000000002 24.9 25.9875 48-49 23.474999999999998 24.6625 24.0 27.8625 50-51 22.787499999999998 23.925 25.2375 28.050000000000004 52-53 24.9125 24.3875 23.400000000000002 27.3 54-55 24.2625 24.45 23.45 27.8375 56-57 23.925 23.8125 23.962500000000002 28.299999999999997 58-59 23.674999999999997 24.462500000000002 24.337500000000002 27.525 60-61 25.137500000000003 23.0375 24.2875 27.537499999999998 62-63 24.7 23.5375 24.712500000000002 27.05 64-65 25.15 24.55 24.2625 26.0375 66-67 24.9125 23.6375 23.8125 27.6375 68-69 24.762500000000003 23.5125 25.025 26.700000000000003 70-71 24.9375 23.525 25.25 26.2875 72-73 25.112499999999997 24.1125 23.5875 27.187499999999996 74-75 24.5625 24.1625 24.0375 27.237499999999997 76-77 25.025 24.0 23.7375 27.237499999999997 78-79 24.15 24.6875 23.549999999999997 27.6125 80-81 23.849999999999998 24.675 23.375 28.1 82-83 25.637500000000003 24.0125 22.8 27.55 84-85 24.212500000000002 23.8625 23.7 28.225 86-87 25.1875 23.599999999999998 23.599999999999998 27.6125 88-89 24.4 23.35 24.6125 27.6375 90-91 25.0625 23.4125 23.962500000000002 27.5625 92-93 25.0125 24.4125 24.275 26.3 94-95 24.575 24.5 23.400000000000002 27.525 96-97 24.2625 23.724999999999998 24.0125 28.000000000000004 98-99 24.837500000000002 23.925 23.35 27.8875 100-101 25.412499999999998 24.6125 23.6875 26.2875 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 3.0 1 3.5 2 3.0 3 1.0 4 0.5 5 2.0 6 1.5 7 0.5 8 1.5 9 1.0 10 0.5 11 0.5 12 0.0 13 0.5 14 1.5 15 1.0 16 0.0 17 0.0 18 0.5 19 1.0 20 0.5 21 1.0 22 1.0 23 1.5 24 2.0 25 0.5 26 0.0 27 0.5 28 1.5 29 2.0 30 1.5 31 3.5 32 5.0 33 6.0 34 8.0 35 12.0 36 18.5 37 34.0 38 42.5 39 56.5 40 79.0 41 103.0 42 130.0 43 147.5 44 163.5 45 166.0 46 170.5 47 194.5 48 207.5 49 189.0 50 181.5 51 168.5 52 156.0 53 146.0 54 141.5 55 141.0 56 120.0 57 114.5 58 110.5 59 100.5 60 85.0 61 76.0 62 71.0 63 55.5 64 48.0 65 52.5 66 59.0 67 57.5 68 48.5 69 43.5 70 38.5 71 32.5 72 33.5 73 33.0 74 27.0 75 21.0 76 16.5 77 11.5 78 13.5 79 15.0 80 6.5 81 1.5 82 0.5 83 0.0 84 0.5 85 0.5 86 0.0 87 0.5 88 0.5 89 0.0 90 0.0 91 0.0 92 0.0 93 0.0 94 0.0 95 0.5 96 0.5 97 0.0 98 0.0 99 0.0 100 0.0 >>END_MODULE >>Per base N content pass #Base N-Count 1 0.27499999999999997 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 >>END_MODULE >>Sequence Length Distribution pass #Length Count 101 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 81.175 #Duplication Level Percentage of deduplicated Percentage of total 1 82.93809670465045 67.325 2 13.427779488758853 21.8 3 2.402217431475208 5.8500000000000005 4 0.6775485063135201 2.1999999999999997 5 0.21558361564521095 0.8750000000000001 6 0.1847859562673237 0.8999999999999999 7 0.09239297813366185 0.525 8 0.030797659377887282 0.2 9 0.0 0.0 >10 0.030797659377887282 0.325 >50 0.0 0.0 >100 0.0 0.0 >500 0.0 0.0 >1k 0.0 0.0 >5k 0.0 0.0 >10k+ 0.0 0.0 >>END_MODULE >>Overrepresented sequences warn #Sequence Count Percentage Possible Source CCCGACTGTCCCTATTAATCATTACTCCGATCCCGAAGGCCAACACAATA 13 0.325 No Hit AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 8 0.2 No Hit GTCACTACCTCCCCGTGTCAGGATTGGGTAATTTGCGCGCCTGCTGCCTT 7 0.17500000000000002 No Hit CCCCATCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGC 7 0.17500000000000002 No Hit GTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACT 7 0.17500000000000002 No Hit CTGACTATGAAATACGAATGCCCCCGACTGTCCCTATTAATCATTACTCC 6 0.15 No Hit CTTGTTACGACTTCTCCTTCCTCTAAATGATAAGGTTCAATGGACTTCTC 6 0.15 No Hit CCCGTCACCACCATGGTAGGCCCCTATCCTACCATCGAAAGTTGATAGGG 6 0.15 No Hit CCGGAATCGAACCCTAATTCTCCGTCACCCGTCACCACCATGGTAGGCCC 6 0.15 No Hit GCCCCTCCCAGAAGTCGGGGTTTGTTGCACGTATTAGCTCTAGAATTACT 6 0.15 No Hit ATCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCTATA 6 0.15 No Hit CTAGAAGAGAAGGGGTGGGGAGAGGCAGTGGTGAACACTAGAGGCTAGAA 5 0.125 No Hit CCTAATTCTCCGTCACCCGTCACCACCATGGTAGGCCCCTATCCTACCAT 5 0.125 No Hit CCGGTATTGTTATTTATTGTCACTACCTCCCCGTGTCAGGATTGGGTAAT 5 0.125 No Hit CCGGAACCCAAAGACTTTGATTTCTCATAAGGTGCCGGCGGAGTCCTATA 5 0.125 No Hit CTCCAATGGATCCTCGTTAAGGGATTTAGATTGTACTCATTCCAATTACC 5 0.125 No Hit GGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTC 5 0.125 No Hit CTATGATGTTATCCCATGCTAATGTATCCAGAGCGATGGCTTGCTTTGAG 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 0.025 0.0 0.0 0.0 0.0 34-35 0.025 0.0 0.0 0.0 0.0 36-37 0.025 0.0 0.0 0.0 0.0 38-39 0.05 0.0 0.0 0.0 0.0 40-41 0.05 0.0 0.0 0.0 0.0 42-43 0.075 0.0 0.0 0.0 0.0 44-45 0.075 0.0 0.0 0.0 0.0 46-47 0.1 0.0 0.0 0.0 0.0 48-49 0.175 0.0 0.0 0.0 0.0 50-51 0.275 0.0 0.0 0.0 0.0 52-53 0.3 0.0 0.0 0.0 0.0 54-55 0.4125 0.0 0.0 0.0 0.0 56-57 0.48750000000000004 0.0 0.0 0.0 0.0 58-59 0.5874999999999999 0.0 0.0 0.0 0.0 60-61 0.65 0.0 0.0 0.0 0.0 62-63 0.8375 0.0 0.0 0.0 0.0 64-65 1.1 0.0 0.0 0.0 0.0 66-67 1.3875000000000002 0.0 0.0 0.0 0.0 68-69 1.525 0.0 0.0 0.0 0.0 70-71 1.7375 0.0 0.0 0.0 0.025 72-73 2.0375 0.0 0.0 0.0 0.025 74-75 2.3375 0.0 0.0 0.0 0.025 76-77 2.55 0.0 0.0 0.0 0.025 78-79 2.8875 0.0 0.0 0.0 0.025 80-81 3.225 0.0 0.0 0.0 0.025 82-83 3.625 0.0 0.0 0.0 0.025 84-85 4.0375 0.0 0.0 0.0 0.025 86-87 4.525 0.0 0.0 0.0 0.025 88-89 4.9625 0.0 0.0 0.0 0.025 >>END_MODULE >>Kmer Content pass >>END_MODULE ERR3450078 read2 length is 101 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR3450078_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 52 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 35.891 37.0 37.0 37.0 37.0 37.0 2 35.799 37.0 37.0 37.0 37.0 37.0 3 35.907 37.0 37.0 37.0 37.0 37.0 4 35.9905 37.0 37.0 37.0 37.0 37.0 5 36.083 37.0 37.0 37.0 37.0 37.0 6 35.9555 37.0 37.0 37.0 37.0 37.0 7 36.1545 37.0 37.0 37.0 37.0 37.0 8 36.136 37.0 37.0 37.0 37.0 37.0 9 36.13 37.0 37.0 37.0 37.0 37.0 10-11 36.033500000000004 37.0 37.0 37.0 37.0 37.0 12-13 36.0985 37.0 37.0 37.0 37.0 37.0 14-15 36.03874999999999 37.0 37.0 37.0 37.0 37.0 16-17 36.02075000000001 37.0 37.0 37.0 37.0 37.0 18-19 35.960499999999996 37.0 37.0 37.0 37.0 37.0 20-21 35.9995 37.0 37.0 37.0 37.0 37.0 22-23 35.8565 37.0 37.0 37.0 37.0 37.0 24-25 35.975750000000005 37.0 37.0 37.0 37.0 37.0 26-27 35.899 37.0 37.0 37.0 37.0 37.0 28-29 35.87975 37.0 37.0 37.0 37.0 37.0 30-31 35.8775 37.0 37.0 37.0 37.0 37.0 32-33 35.926500000000004 37.0 37.0 37.0 37.0 37.0 34-35 35.888000000000005 37.0 37.0 37.0 37.0 37.0 36-37 35.951 37.0 37.0 37.0 37.0 37.0 38-39 35.90375 37.0 37.0 37.0 37.0 37.0 40-41 35.972750000000005 37.0 37.0 37.0 37.0 37.0 42-43 35.8475 37.0 37.0 37.0 37.0 37.0 44-45 35.87175 37.0 37.0 37.0 37.0 37.0 46-47 35.65925 37.0 37.0 37.0 37.0 37.0 48-49 35.81575 37.0 37.0 37.0 37.0 37.0 50-51 35.8095 37.0 37.0 37.0 37.0 37.0 52-53 35.828 37.0 37.0 37.0 37.0 37.0 54-55 35.84675 37.0 37.0 37.0 37.0 37.0 56-57 35.88525 37.0 37.0 37.0 37.0 37.0 58-59 35.82125 37.0 37.0 37.0 37.0 37.0 60-61 35.7265 37.0 37.0 37.0 37.0 37.0 62-63 35.818250000000006 37.0 37.0 37.0 37.0 37.0 64-65 35.770250000000004 37.0 37.0 37.0 37.0 37.0 66-67 35.834500000000006 37.0 37.0 37.0 37.0 37.0 68-69 35.771 37.0 37.0 37.0 37.0 37.0 70-71 35.73375 37.0 37.0 37.0 37.0 37.0 72-73 35.76875 37.0 37.0 37.0 37.0 37.0 74-75 35.694500000000005 37.0 37.0 37.0 37.0 37.0 76-77 35.77525 37.0 37.0 37.0 37.0 37.0 78-79 35.620000000000005 37.0 37.0 37.0 37.0 37.0 80-81 35.72025 37.0 37.0 37.0 37.0 37.0 82-83 35.71775 37.0 37.0 37.0 37.0 37.0 84-85 35.666 37.0 37.0 37.0 37.0 37.0 86-87 35.74725 37.0 37.0 37.0 37.0 37.0 88-89 35.54625 37.0 37.0 37.0 37.0 37.0 90-91 35.575500000000005 37.0 37.0 37.0 37.0 37.0 92-93 35.655 37.0 37.0 37.0 37.0 37.0 94-95 35.5925 37.0 37.0 37.0 37.0 37.0 96-97 35.556 37.0 37.0 37.0 37.0 37.0 98-99 35.44525 37.0 37.0 37.0 37.0 37.0 100-101 35.407 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 13 1.0 14 4.0 15 5.0 16 8.0 17 4.0 18 4.0 19 6.0 20 3.0 21 10.0 22 10.0 23 14.0 24 11.0 25 16.0 26 12.0 27 21.0 28 20.0 29 38.0 30 29.0 31 34.0 32 56.0 33 80.0 34 131.0 35 318.0 36 2238.0 37 927.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 42.4 17.375 10.5 29.725 2 26.8 23.625 25.35 24.224999999999998 3 25.8 23.325000000000003 28.000000000000004 22.875 4 29.5 27.55 17.8 25.15 5 30.4 30.125 17.7 21.775 6 22.75 34.9 21.15 21.2 7 25.900000000000002 19.15 31.724999999999998 23.225 8 25.25 21.3 22.95 30.5 9 27.05 21.725 25.424999999999997 25.8 10-11 28.65 26.974999999999998 19.287499999999998 25.087500000000002 12-13 27.700000000000003 22.900000000000002 22.875 26.525 14-15 26.700000000000003 25.3 22.9875 25.0125 16-17 27.125 25.362499999999997 22.75 24.762500000000003 18-19 27.737499999999997 25.124999999999996 22.925 24.212500000000002 20-21 27.287499999999998 25.387500000000003 22.55 24.775 22-23 28.375 24.75 21.9375 24.9375 24-25 27.3875 24.637500000000003 22.4875 25.4875 26-27 27.962500000000002 24.6625 22.4625 24.9125 28-29 28.8625 24.1875 23.05 23.9 30-31 28.025 23.9875 22.3375 25.650000000000002 32-33 26.6625 25.474999999999998 23.275000000000002 24.587500000000002 34-35 27.537499999999998 24.8 23.2375 24.425 36-37 26.150000000000002 24.8125 23.5875 25.45 38-39 26.337500000000002 25.162499999999998 23.3 25.2 40-41 27.625 24.65 22.925 24.8 42-43 26.724999999999998 25.05 23.1625 25.0625 44-45 27.5625 24.675 22.925 24.837500000000002 46-47 28.449999999999996 23.549999999999997 23.2625 24.7375 48-49 26.924999999999997 24.637500000000003 22.6375 25.8 50-51 26.1125 25.9875 22.2625 25.637500000000003 52-53 27.1 24.925 22.8125 25.162499999999998 54-55 27.224999999999998 24.9375 23.1125 24.725 56-57 27.237499999999997 25.412499999999998 23.0125 24.337500000000002 58-59 27.212500000000002 24.975 22.4625 25.35 60-61 27.675 24.975 22.825 24.525 62-63 27.4125 24.525 23.5 24.5625 64-65 27.8625 24.125 23.4125 24.6 66-67 27.1625 24.85 23.75 24.2375 68-69 27.1375 25.337500000000002 23.3 24.224999999999998 70-71 27.8375 25.912499999999998 21.8875 24.3625 72-73 28.1625 25.674999999999997 22.0125 24.15 74-75 27.175 25.55 22.4875 24.7875 76-77 29.2875 24.325 21.912499999999998 24.474999999999998 78-79 26.424999999999997 25.75 23.0625 24.762500000000003 80-81 28.15 25.162499999999998 22.4875 24.2 82-83 27.962500000000002 24.462500000000002 23.075000000000003 24.5 84-85 28.3625 24.4 23.5375 23.7 86-87 28.762500000000003 24.837500000000002 22.8375 23.5625 88-89 27.575 25.775 22.275 24.375 90-91 28.3125 24.925 22.6 24.1625 92-93 28.5875 25.5125 22.5125 23.3875 94-95 29.575000000000003 24.5375 22.0125 23.875 96-97 28.175 26.0125 22.225 23.5875 98-99 28.6125 25.5375 22.175 23.674999999999997 100-101 28.487499999999997 25.7125 22.537499999999998 23.2625 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 3.0 1 1.5 2 0.0 3 0.5 4 0.5 5 0.0 6 0.5 7 1.5 8 1.0 9 1.0 10 1.5 11 0.5 12 1.0 13 1.5 14 1.0 15 0.5 16 0.5 17 1.5 18 2.0 19 1.0 20 1.0 21 2.5 22 3.0 23 2.0 24 1.0 25 1.0 26 2.0 27 3.5 28 2.5 29 1.0 30 2.0 31 4.5 32 5.5 33 7.0 34 8.0 35 9.5 36 18.0 37 29.0 38 47.0 39 72.5 40 93.5 41 105.5 42 120.5 43 142.5 44 149.5 45 146.0 46 148.5 47 165.0 48 176.0 49 185.0 50 189.5 51 174.5 52 150.0 53 126.0 54 125.5 55 128.0 56 124.0 57 119.5 58 113.5 59 99.5 60 82.5 61 75.0 62 64.5 63 61.5 64 69.0 65 71.0 66 69.5 67 58.5 68 61.0 69 63.0 70 48.5 71 45.5 72 37.0 73 29.0 74 26.5 75 22.0 76 18.5 77 11.0 78 8.5 79 9.0 80 7.5 81 7.5 82 3.5 83 4.0 84 7.0 85 3.0 86 0.5 87 1.0 88 1.5 89 1.0 90 0.0 91 0.0 92 0.0 93 0.5 94 0.5 95 0.0 96 1.5 97 1.5 98 0.5 99 1.0 100 2.0 >>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 10-11 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 >>END_MODULE >>Sequence Length Distribution pass #Length Count 101 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 82.375 #Duplication Level Percentage of deduplicated Percentage of total 1 83.88467374810318 69.1 2 12.534142640364188 20.65 3 2.6100151745068287 6.45 4 0.6069802731411229 2.0 5 0.21244309559939303 0.8750000000000001 6 0.06069802731411229 0.3 7 0.06069802731411229 0.35000000000000003 8 0.0 0.0 9 0.0 0.0 >10 0.030349013657056147 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 CCTGCCAGTAGTCATATGCTTGTCTCAAAGATTAAGCCATGCATGTGCAA 11 0.27499999999999997 No Hit CTTGGATTTATGAAAGACGAACAACTGCGAAAGCATTTGCCAAGGATGTT 7 0.17500000000000002 No Hit GTTAAAAAGCTCGTAGTTGGACTTTGGGCCGGGTCGGCCGGTCCGCCTCA 7 0.17500000000000002 No Hit CGGGGGCATTCGTATTTCATAGTCAGAGGTGAAATTCTTGGATTTATGAA 6 0.15 No Hit GTTCTGGGCCGCACGCGCGCTACACTGATGTATTCAACGAGTATATAGCC 6 0.15 No Hit CCAGCTCCAATAGCGTATATTTAAGTTGTTGCAGTTAAAAAGCTCGTAGT 5 0.125 No Hit GTGCCTCCGGCATCGTTACTTTGAAGAAATTAGAGTGCTCAAAGCAAGCC 5 0.125 No Hit GTAATTCTAGAGCTAATACGTGCAACAAACCCCGACTTCTGGGAGGGGCG 5 0.125 No Hit GCCAGGTTCTACATCATCCAGCGCTGCGTCGTCATGCTCCTCCGGTGGCA 5 0.125 No Hit CCGACAGGCCCGGGTAATCTTGGGAAATTTCATCGTGATGGGGATAGATC 5 0.125 No Hit ATCGCGGATGCCCCCACCAACGTGCAGCTCCCTGGGATGTACAACAAGGA 5 0.125 No Hit GTGACAATAAATAACAATACCGGGCACATTAGTGTCTGGTAATTGGAATG 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 0.025 0.0 0.0 0.0 0.0 34-35 0.025 0.0 0.0 0.0 0.0 36-37 0.025 0.0 0.0 0.0 0.0 38-39 0.05 0.0 0.0 0.0 0.0 40-41 0.05 0.0 0.0 0.0 0.0 42-43 0.075 0.0 0.0 0.0 0.0 44-45 0.075 0.0 0.0 0.0 0.0 46-47 0.1 0.0 0.0 0.0 0.0 48-49 0.175 0.0 0.0 0.0 0.0 50-51 0.25 0.0 0.0 0.0 0.0 52-53 0.275 0.0 0.0 0.0 0.0 54-55 0.38749999999999996 0.0 0.0 0.0 0.0 56-57 0.48750000000000004 0.0 0.0 0.0 0.0 58-59 0.5874999999999999 0.0 0.0 0.0 0.0 60-61 0.65 0.0 0.0 0.0 0.0 62-63 0.8375 0.0 0.0 0.0 0.0 64-65 1.0875 0.0 0.0 0.0 0.0 66-67 1.3624999999999998 0.0 0.0 0.0 0.0 68-69 1.5125 0.0 0.0 0.0 0.0 70-71 1.7375 0.0 0.0 0.0 0.0 72-73 2.0125 0.0 0.0 0.0 0.0 74-75 2.3125 0.0 0.0 0.0 0.0 76-77 2.55 0.0 0.0 0.0 0.0 78-79 2.9375 0.0 0.0 0.0 0.0 80-81 3.225 0.0 0.0 0.0 0.0 82-83 3.625 0.0 0.0 0.0 0.0 84-85 4.0375 0.0 0.0 0.0 0.0 86-87 4.5375 0.0 0.0 0.0 0.0 88-89 4.975 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Read 842412 spots for ERR3450078.sra Written 842412 spots for ERR3450078.sra Read 842412 spots for ERR3450078.sra Written 842412 spots for ERR3450078.sra Read 842412 spots for ERR3450078.sra Written 842412 spots for ERR3450078.sra Read 842412 spots for ERR3450078.sra Written 842412 spots for ERR3450078.sra Read 842412 spots for ERR3450078.sra Written 842412 spots for ERR3450078.sra Read 842412 spots for ERR3450078.sra Written 842412 spots for ERR3450078.sra Read 842412 spots for ERR3450078.sra Written 842412 spots for ERR3450078.sra Read 842412 spots for ERR3450078.sra Written 842412 spots for ERR3450078.sra Read 842412 spots for ERR3450078.sra Written 842412 spots for ERR3450078.sra Read 842412 spots for ERR3450078.sra Written 842412 spots for ERR3450078.sra Read 842412 spots for ERR3450078.sra Written 842412 spots for ERR3450078.sra Read 842412 spots for ERR3450078.sra Written 842412 spots for ERR3450078.sra Read 842420 spots for ERR3450078.sra Written 842420 spots for ERR3450078.sra Read 842412 spots for ERR3450078.sra Written 842412 spots for ERR3450078.sra Read 842412 spots for ERR3450078.sra Written 842412 spots for ERR3450078.sra Read 842412 spots for ERR3450078.sra Written 842412 spots for ERR3450078.sra Read 842412 spots for ERR3450078.sra Written 842412 spots for ERR3450078.sra Read 842412 spots for ERR3450078.sra Written 842412 spots for ERR3450078.sra Read 842412 spots for ERR3450078.sra Written 842412 spots for ERR3450078.sra Read 842412 spots for ERR3450078.sra Written 842412 spots for ERR3450078.sra SRR ids: ['ERR3450078.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_c94v17gc ERR3450078.sra spots: 16848248 blocks: [[1, 842412], [842413, 1684824], [1684825, 2527236], [2527237, 3369648], [3369649, 4212060], [4212061, 5054472], [5054473, 5896884], [5896885, 6739296], [6739297, 7581708], [7581709, 8424120], [8424121, 9266532], [9266533, 10108944], [10108945, 10951356], [10951357, 11793768], [11793769, 12636180], [12636181, 13478592], [13478593, 14321004], [14321005, 15163416], [15163417, 16005828], [16005829, 16848248]] ERR3450078 file size 4042281 ERR3450078 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 ERR3450078 ERR3450078_1.fastq ERR3450078_2.fastq Input file: ERR3450078_1.fastq Paired file: ERR3450078_2.fastq trimmed: ERR3450078-trimmed-pair1.fastq, ERR3450078-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 Sat Dec 7 14:47:31 2024 >> started Sat Dec 7 14:47:45 2024 >> done (14.432s) 16848248 read pairs processed; of these: 75 ( 0.00%) short read pairs filtered out after trimming by size control 15057 ( 0.09%) empty read pairs filtered out after trimming by size control 16833116 (99.91%) read pairs available; of these: 1683349 (10.00%) trimmed read pairs available after processing 15149767 (90.00%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 13 0.00% 19 30 0.00% 20 71 0.00% 21 213 0.00% 22 312 0.00% 23 176 0.00% 24 136 0.00% 25 207 0.00% 26 327 0.00% 27 422 0.00% 28 677 0.00% 29 871 0.01% 30 1032 0.01% 31 1161 0.01% 32 1247 0.01% 33 1248 0.01% 34 1254 0.01% 35 1249 0.01% 36 1443 0.01% 37 1629 0.01% 38 1990 0.01% 39 2196 0.01% 40 2710 0.02% 41 3109 0.02% 42 3466 0.02% 43 3708 0.02% 44 3549 0.02% 45 3480 0.02% 46 3822 0.02% 47 4126 0.02% 48 4631 0.03% 49 5158 0.03% 50 5759 0.03% 51 6244 0.04% 52 7029 0.04% 53 7380 0.04% 54 7884 0.05% 55 8297 0.05% 56 8719 0.05% 57 8950 0.05% 58 10044 0.06% 59 10957 0.07% 60 11902 0.07% 61 12901 0.08% 62 14087 0.08% 63 15484 0.09% 64 15925 0.09% 65 16366 0.10% 66 17394 0.10% 67 18560 0.11% 68 18941 0.11% 69 20104 0.12% 70 21067 0.13% 71 23086 0.14% 72 24756 0.15% 73 26596 0.16% 74 27240 0.16% 75 28554 0.17% 76 29834 0.18% 77 30607 0.18% 78 32086 0.19% 79 33702 0.20% 80 35101 0.21% 81 36424 0.22% 82 38794 0.23% 83 39811 0.24% 84 41895 0.25% 85 43722 0.26% 86 44639 0.27% 87 46748 0.28% 88 48238 0.29% 89 49812 0.30% 90 51270 0.30% 91 54293 0.32% 92 56842 0.34% 93 58001 0.34% 94 60614 0.36% 95 61733 0.37% 96 63454 0.38% 97 65346 0.39% 98 66358 0.39% 99 67388 0.40% 100 76748 0.46% 101 15149767 90.00% 16833116 reads passed initial QC criterion=sequence-density sequence-density=0.26 sequence-density-rank=1 fanout-score=2.56 fanout-score-rank=31 prefix-density=0.22 prefix-fanout=2.6 sequence=GTCAAATTAAGCCGCAGGCTCCACGCCTGGTGGTGCCCTTCCGTCAATTCCTTTAAGTTTCAGCCTTGCGACCATACTCCCCCCGGAACCCAAAGACTTTGATTTCTCATAAGGTGCCGGCGGAGTCCTATAAGCAACATCCGCCGATCCCTGGTCGGCATCGTTTATGGTTGAGACTAGGACGGTATCTGATCGTCTTCGAGCCCCCAACTTTCGTTCTTGATTAATGAAAACATCCTTGGCAAATGCTTTCGCAGTTGTTCGTCTTTCATAAATCCAAGAATTTCACCTCTGACTATGAAATACGAATGCCCCCGACTGTCCCTATTAATCATTACTCCGATCCCGAAGGCCAACACAATAGGACCGGAATCCTATGATGTTATCCCATGCTAATGTATCCAGAGCGATGGCTTGCTTTGAGCACTCTAATTTCTTCAAAGTAACGATGCCGGAGGCACGACCCGGCCAATTAAGGCTAGGAGCGCATCGCCGGCTGAAGGGTCGAGTA criterion=fanout-score sequence-density=0.05 sequence-density-rank=29 fanout-score=211.77 fanout-score-rank=1 prefix-density=0.53 prefix-fanout=21.1 sequence=CGCCGCCGCCGA criterion=sequence-density sequence-density=0.21 sequence-density-rank=1 fanout-score=1.97 fanout-score-rank=32 prefix-density=0.21 prefix-fanout=2.0 sequence=CAAGTGTTGGATT criterion=fanout-score sequence-density=0.07 sequence-density-rank=24 fanout-score=207.29 fanout-score-rank=1 prefix-density=1.29 prefix-fanout=11.0 sequence=CGCCGCCGCCGG ERR3450078 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 07 14:48:26 Started mapping on | Dec 07 14:48:26 Finished on | Dec 07 14:49:47 Mapping speed, Million of reads per hour | 748.14 Number of input reads | 16833116 Average input read length | 198 UNIQUE READS: Uniquely mapped reads number | 12191873 Uniquely mapped reads % | 72.43% Average mapped length | 197.86 Number of splices: Total | 7861633 Number of splices: Annotated (sjdb) | 7460575 Number of splices: GT/AG | 7760349 Number of splices: GC/AG | 87428 Number of splices: AT/AC | 5228 Number of splices: Non-canonical | 8628 Mismatch rate per base, % | 0.23% Deletion rate per base | 0.01% Deletion average length | 2.10 Insertion rate per base | 0.01% Insertion average length | 1.93 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 716133 % of reads mapped to multiple loci | 4.25% Number of reads mapped to too many loci | 686379 % of reads mapped to too many loci | 4.08% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 2.93% % of reads unmapped: other | 16.31% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 3925110 3925110 3925110 N_multimapping 716133 716133 716133 N_noFeature 387600 11752606 651642 N_ambiguous 210158 1878 36360 UnstrandedReadsAssigned:11594115 PositiveStrandReadsAssigned:437389 NegativeStrandReadsAssigned:11503871 Dataset is classified negative stranded MeadianReadLen=101 20thPercentileLength=101 echo kmer=97 ERR3450078 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: ERR3450078-trimmed-pair1.fastq ERR3450078-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 16,833,116 reads, 12,048,998 reads pseudoaligned [quant] estimated average fragment length: 184.318 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,225 rounds 52973 ERR3450078.ke.tsv 35125 ERR3450078.se.tsv 88098 total ==> ERR3450078.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 752.806 47.3412 7.89129 PNS24247 1044 860.682 6.87151 1.00185 PNS24249 1928 1744.68 131.299 9.44358 PNS24246 1044 860.682 6.87151 1.00185 PNS24248 1044 860.682 6.87151 1.00185 PNS24244 1471 1287.68 30.7452 2.99613 PNS24243 293 130.577 0 0 KQK14069 1603 1419.68 1171.65 103.561 KQK14071 474 294.518 36.9312 15.7352 ==> ERR3450078.se.tsv <== BRADI_1g14170v3 1250 BRADI_1g53295v3 12 BRADI_1g59795v3 112 BRADI_1g07683v3 0 BRADI_1g00485v3 47 BRADI_1g20270v3 2220 BRADI_1g74790v3 104 BRADI_1g09890v3 4 BRADI_1g77505v3 163 BRADI_1g48960v3 1 ERR3450078 completed mapping pipeline successfully