Starting /dee2/code/volunteer_pipeline.sh ERR3450075 current disk space = 1542976233472 free memory = 1596608432 ERR3450075 SRAfilesize b62434a2b53e53bc861c69b0f5ebb102 ERR3450075.sra ERR3450075.sra file validated ERR3450075 is paired end ERR3450075 is conventional basespace ERR3450075 read1 length is 101 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR3450075_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 52 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.25125 37.0 37.0 37.0 37.0 37.0 2 36.333 37.0 37.0 37.0 37.0 37.0 3 36.462 37.0 37.0 37.0 37.0 37.0 4 36.5505 37.0 37.0 37.0 37.0 37.0 5 36.559 37.0 37.0 37.0 37.0 37.0 6 36.498 37.0 37.0 37.0 37.0 37.0 7 36.4965 37.0 37.0 37.0 37.0 37.0 8 36.4585 37.0 37.0 37.0 37.0 37.0 9 36.5775 37.0 37.0 37.0 37.0 37.0 10-11 36.50425 37.0 37.0 37.0 37.0 37.0 12-13 36.494 37.0 37.0 37.0 37.0 37.0 14-15 36.546 37.0 37.0 37.0 37.0 37.0 16-17 36.475750000000005 37.0 37.0 37.0 37.0 37.0 18-19 36.46 37.0 37.0 37.0 37.0 37.0 20-21 36.444 37.0 37.0 37.0 37.0 37.0 22-23 36.435 37.0 37.0 37.0 37.0 37.0 24-25 36.460750000000004 37.0 37.0 37.0 37.0 37.0 26-27 36.424 37.0 37.0 37.0 37.0 37.0 28-29 36.363 37.0 37.0 37.0 37.0 37.0 30-31 36.389250000000004 37.0 37.0 37.0 37.0 37.0 32-33 36.333 37.0 37.0 37.0 37.0 37.0 34-35 36.307249999999996 37.0 37.0 37.0 37.0 37.0 36-37 36.268249999999995 37.0 37.0 37.0 37.0 37.0 38-39 36.26525 37.0 37.0 37.0 37.0 37.0 40-41 36.3455 37.0 37.0 37.0 37.0 37.0 42-43 36.20375 37.0 37.0 37.0 37.0 37.0 44-45 36.15325 37.0 37.0 37.0 37.0 37.0 46-47 36.199 37.0 37.0 37.0 37.0 37.0 48-49 36.20525 37.0 37.0 37.0 37.0 37.0 50-51 36.13575 37.0 37.0 37.0 37.0 37.0 52-53 36.194 37.0 37.0 37.0 37.0 37.0 54-55 36.192750000000004 37.0 37.0 37.0 37.0 37.0 56-57 36.092749999999995 37.0 37.0 37.0 37.0 37.0 58-59 36.02875 37.0 37.0 37.0 37.0 37.0 60-61 36.217749999999995 37.0 37.0 37.0 37.0 37.0 62-63 35.99725 37.0 37.0 37.0 37.0 37.0 64-65 36.04975 37.0 37.0 37.0 37.0 37.0 66-67 36.033500000000004 37.0 37.0 37.0 37.0 37.0 68-69 35.96975 37.0 37.0 37.0 37.0 37.0 70-71 35.90925 37.0 37.0 37.0 37.0 37.0 72-73 36.09375 37.0 37.0 37.0 37.0 37.0 74-75 36.07875 37.0 37.0 37.0 37.0 37.0 76-77 36.076 37.0 37.0 37.0 37.0 37.0 78-79 36.07599999999999 37.0 37.0 37.0 37.0 37.0 80-81 36.03125 37.0 37.0 37.0 37.0 37.0 82-83 36.06675 37.0 37.0 37.0 37.0 37.0 84-85 35.94125 37.0 37.0 37.0 37.0 37.0 86-87 36.022000000000006 37.0 37.0 37.0 37.0 37.0 88-89 36.02625 37.0 37.0 37.0 37.0 37.0 90-91 36.07575 37.0 37.0 37.0 37.0 37.0 92-93 35.93575 37.0 37.0 37.0 37.0 37.0 94-95 35.99375 37.0 37.0 37.0 37.0 37.0 96-97 35.9275 37.0 37.0 37.0 37.0 37.0 98-99 35.93875 37.0 37.0 37.0 37.0 37.0 100-101 35.91775 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 19 1.0 20 0.0 21 1.0 22 1.0 23 0.0 24 4.0 25 5.0 26 10.0 27 12.0 28 25.0 29 28.0 30 49.0 31 52.0 32 74.0 33 90.0 34 119.0 35 204.0 36 1818.0 37 1507.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 41.66457758836801 9.501128102281275 9.125094008523439 39.70920030082728 2 21.75 13.075000000000001 29.575000000000003 35.6 3 20.849999999999998 16.3 24.125 38.725 4 29.599999999999998 20.9 17.775 31.724999999999998 5 27.6 25.424999999999997 21.95 25.025 6 24.099999999999998 29.849999999999998 23.9 22.15 7 20.974999999999998 22.5 35.9 20.625 8 22.575 20.724999999999998 29.975 26.724999999999998 9 22.900000000000002 22.225 29.95 24.925 10-11 23.8375 28.6625 21.825 25.674999999999997 12-13 23.4875 23.0625 25.8 27.650000000000002 14-15 24.175 24.325 24.725 26.775 16-17 24.0375 23.8375 24.6125 27.5125 18-19 24.275 24.2375 25.0 26.487500000000004 20-21 24.6625 25.2625 25.174999999999997 24.9 22-23 25.650000000000002 23.3625 24.3625 26.625 24-25 24.45 23.599999999999998 25.224999999999998 26.724999999999998 26-27 24.8125 23.4625 24.3125 27.4125 28-29 26.137500000000003 24.025 23.75 26.087500000000002 30-31 24.4375 23.8875 23.275000000000002 28.4 32-33 23.825 24.5 23.7 27.975 34-35 24.95 24.0 24.0 27.05 36-37 24.6875 23.925 24.325 27.0625 38-39 23.674999999999997 24.2875 25.1 26.937499999999996 40-41 25.45 24.1375 23.3875 27.025 42-43 24.837500000000002 24.95 24.9 25.3125 44-45 25.224999999999998 22.55 24.125 28.1 46-47 25.2625 23.5 24.275 26.9625 48-49 24.1125 23.8125 24.474999999999998 27.6 50-51 24.65 23.7625 24.3875 27.200000000000003 52-53 25.05 24.325 23.275000000000002 27.35 54-55 25.074999999999996 23.375 24.2 27.35 56-57 24.712500000000002 23.9875 23.5625 27.737499999999997 58-59 24.349999999999998 23.7125 24.4375 27.500000000000004 60-61 25.937500000000004 23.849999999999998 24.0125 26.200000000000003 62-63 24.325 23.849999999999998 24.6625 27.1625 64-65 25.3125 23.6875 25.15 25.85 66-67 25.575 23.75 23.0875 27.5875 68-69 26.487500000000004 24.3625 22.825 26.325 70-71 25.4625 23.175 23.7125 27.650000000000002 72-73 26.400000000000002 23.474999999999998 23.2375 26.887499999999996 74-75 25.825 23.549999999999997 23.6875 26.937499999999996 76-77 26.325 24.725 22.6 26.35 78-79 25.85 24.212500000000002 22.875 27.0625 80-81 25.05 24.375 23.4875 27.0875 82-83 26.424999999999997 24.55 22.3 26.724999999999998 84-85 25.75 23.6875 23.275000000000002 27.287499999999998 86-87 25.575 24.3125 22.95 27.1625 88-89 26.575 23.575 23.2625 26.5875 90-91 25.4 24.325 23.1125 27.1625 92-93 26.525 23.8875 23.225 26.3625 94-95 26.187500000000004 24.224999999999998 22.8875 26.700000000000003 96-97 25.45 25.124999999999996 22.5625 26.8625 98-99 24.9375 24.675 23.65 26.737499999999997 100-101 26.437500000000004 23.9875 22.4625 27.1125 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 7.0 1 3.5 2 1.5 3 2.0 4 0.5 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10 0.0 11 0.5 12 1.0 13 0.5 14 0.0 15 0.5 16 0.5 17 0.0 18 0.0 19 0.5 20 1.0 21 0.5 22 1.5 23 2.5 24 1.5 25 2.0 26 2.5 27 1.5 28 0.5 29 0.0 30 0.0 31 1.5 32 4.5 33 5.5 34 11.0 35 14.0 36 19.0 37 26.5 38 29.5 39 56.5 40 77.0 41 83.0 42 107.0 43 130.5 44 138.0 45 149.5 46 175.0 47 185.0 48 187.0 49 192.0 50 189.0 51 172.5 52 169.5 53 160.5 54 140.0 55 152.5 56 141.5 57 114.5 58 112.0 59 103.5 60 88.5 61 73.5 62 67.0 63 65.0 64 59.0 65 66.5 66 73.0 67 67.5 68 55.5 69 45.5 70 45.5 71 40.0 72 34.5 73 34.5 74 27.5 75 17.5 76 11.5 77 8.5 78 12.0 79 10.5 80 5.0 81 3.5 82 2.0 83 3.0 84 2.5 85 1.5 86 1.0 87 1.0 88 1.0 89 0.5 90 0.5 91 0.0 92 0.0 93 0.0 94 0.0 95 0.0 96 0.0 97 0.0 98 0.0 99 0.0 100 0.0 >>END_MODULE >>Per base N content pass #Base N-Count 1 0.27499999999999997 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 82.175 #Duplication Level Percentage of deduplicated Percentage of total 1 84.02798904776392 69.05 2 12.655917249771829 20.8 3 2.433830240340736 6.0 4 0.4867660480681472 1.6 5 0.18253726802555523 0.75 6 0.09126863401277761 0.44999999999999996 7 0.0 0.0 8 0.0608457560085184 0.4 9 0.0 0.0 >10 0.0608457560085184 0.95 >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 GATCGGAAGAGCACACGTCTGAACTCCAGTCACAGCGATAGATCTCGTAT 28 0.7000000000000001 TruSeq Adapter, Index 1 (97% over 36bp) GCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGCATTCC 10 0.25 No Hit CTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATT 8 0.2 No Hit CCCGACTGTCCCTATTAATCATTACTCCGATCCCGAAGGCCAACACAATA 8 0.2 No Hit GTCGGCATCGTTTATGGTTGAGACTAGGACGGTATCTGATCGTCTTCGAG 6 0.15 No Hit GCAGAAATTTGAATGATGCGTCGCCGGCACGAGGGCCGTGCGATCCGTCG 6 0.15 No Hit CCCATCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCT 6 0.15 No Hit GGCAAATGCTTTCGCAGTTGTTCGTCTTTCATAAATCCAAGAATTTCACC 5 0.125 No Hit GTCGCCGGCACGAGGGCCGTGCGATCCGTCGAGTTATCATGAATCATCGG 5 0.125 No Hit GCTGGAATTACCGCGGCTGCTGGCACCAGACTTGCCCTCCAATGGATCCT 5 0.125 No Hit CTCCAATGGATCCTCGTTAAGGGATTTAGATTGTACTCATTCCAATTACC 5 0.125 No Hit CTTGGTGATATCGTAGTTCTTGATACCAGAATAGAATATCTGAAACCTTT 5 0.125 No Hit GGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCG 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 0.025 0.0 0.0 0.0 0.0 22-23 0.025 0.0 0.0 0.0 0.0 24-25 0.025 0.0 0.0 0.0 0.0 26-27 0.025 0.0 0.0 0.0 0.0 28-29 0.05 0.0 0.0 0.0 0.0 30-31 0.05 0.0 0.0 0.0 0.0 32-33 0.075 0.0 0.0 0.0 0.0 34-35 0.1125 0.0 0.0 0.0 0.0 36-37 0.15 0.0 0.0 0.0 0.0 38-39 0.15 0.0 0.0 0.0 0.0 40-41 0.15 0.0 0.0 0.0 0.0 42-43 0.23750000000000002 0.0 0.0 0.0 0.0 44-45 0.2875 0.0 0.0 0.0 0.0 46-47 0.4375 0.0 0.0 0.0 0.0 48-49 0.5625 0.0 0.0 0.0 0.0 50-51 0.6 0.0 0.0 0.0 0.0 52-53 0.825 0.0 0.0 0.0 0.0 54-55 0.9375 0.0 0.0 0.0 0.0 56-57 1.1124999999999998 0.0 0.0 0.0 0.0 58-59 1.3625 0.0 0.0 0.0 0.0 60-61 1.5875 0.0 0.0 0.0 0.0 62-63 1.9375 0.0 0.0 0.0 0.0 64-65 2.2125 0.0 0.0 0.0 0.0 66-67 2.4000000000000004 0.0 0.0 0.0 0.0 68-69 2.725 0.0 0.0 0.0 0.0 70-71 3.075 0.0 0.0 0.0 0.0 72-73 3.4125 0.0 0.0 0.0 0.0 74-75 3.9 0.0 0.0 0.0 0.0 76-77 4.325 0.0 0.0 0.0 0.0 78-79 4.8875 0.0 0.0 0.0 0.0 80-81 5.262499999999999 0.0 0.0 0.0 0.0 82-83 6.05 0.0 0.0 0.0 0.0 84-85 6.55 0.0 0.0 0.0 0.0 86-87 7.05 0.0 0.0 0.0 0.0 88-89 7.8999999999999995 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE ERR3450075 read2 length is 101 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR3450075_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 36.0185 37.0 37.0 37.0 37.0 37.0 2 35.712 37.0 37.0 37.0 37.0 37.0 3 35.917 37.0 37.0 37.0 37.0 37.0 4 36.0165 37.0 37.0 37.0 37.0 37.0 5 36.107 37.0 37.0 37.0 37.0 37.0 6 36.1065 37.0 37.0 37.0 37.0 37.0 7 36.097 37.0 37.0 37.0 37.0 37.0 8 36.0185 37.0 37.0 37.0 37.0 37.0 9 36.0385 37.0 37.0 37.0 37.0 37.0 10-11 36.0345 37.0 37.0 37.0 37.0 37.0 12-13 36.05775 37.0 37.0 37.0 37.0 37.0 14-15 36.01175 37.0 37.0 37.0 37.0 37.0 16-17 36.042500000000004 37.0 37.0 37.0 37.0 37.0 18-19 36.117000000000004 37.0 37.0 37.0 37.0 37.0 20-21 36.05175 37.0 37.0 37.0 37.0 37.0 22-23 35.974999999999994 37.0 37.0 37.0 37.0 37.0 24-25 35.9225 37.0 37.0 37.0 37.0 37.0 26-27 35.91875 37.0 37.0 37.0 37.0 37.0 28-29 35.9375 37.0 37.0 37.0 37.0 37.0 30-31 35.864999999999995 37.0 37.0 37.0 37.0 37.0 32-33 35.90775 37.0 37.0 37.0 37.0 37.0 34-35 35.95525 37.0 37.0 37.0 37.0 37.0 36-37 35.894999999999996 37.0 37.0 37.0 37.0 37.0 38-39 35.83725 37.0 37.0 37.0 37.0 37.0 40-41 35.884 37.0 37.0 37.0 37.0 37.0 42-43 35.866 37.0 37.0 37.0 37.0 37.0 44-45 35.828 37.0 37.0 37.0 37.0 37.0 46-47 35.888999999999996 37.0 37.0 37.0 37.0 37.0 48-49 35.92375 37.0 37.0 37.0 37.0 37.0 50-51 35.878 37.0 37.0 37.0 37.0 37.0 52-53 35.9015 37.0 37.0 37.0 37.0 37.0 54-55 35.8635 37.0 37.0 37.0 37.0 37.0 56-57 35.911 37.0 37.0 37.0 37.0 37.0 58-59 35.896249999999995 37.0 37.0 37.0 37.0 37.0 60-61 35.85525 37.0 37.0 37.0 37.0 37.0 62-63 35.95725 37.0 37.0 37.0 37.0 37.0 64-65 35.93675 37.0 37.0 37.0 37.0 37.0 66-67 35.92575 37.0 37.0 37.0 37.0 37.0 68-69 35.86225 37.0 37.0 37.0 37.0 37.0 70-71 35.81 37.0 37.0 37.0 37.0 37.0 72-73 35.81675 37.0 37.0 37.0 37.0 37.0 74-75 35.817750000000004 37.0 37.0 37.0 37.0 37.0 76-77 35.74425 37.0 37.0 37.0 37.0 37.0 78-79 35.675749999999994 37.0 37.0 37.0 37.0 37.0 80-81 35.782 37.0 37.0 37.0 37.0 37.0 82-83 35.8555 37.0 37.0 37.0 37.0 37.0 84-85 35.756 37.0 37.0 37.0 37.0 37.0 86-87 35.80525 37.0 37.0 37.0 37.0 37.0 88-89 35.769999999999996 37.0 37.0 37.0 37.0 37.0 90-91 35.7345 37.0 37.0 37.0 37.0 37.0 92-93 35.7025 37.0 37.0 37.0 37.0 37.0 94-95 35.688500000000005 37.0 37.0 37.0 37.0 37.0 96-97 35.64125 37.0 37.0 37.0 37.0 37.0 98-99 35.627250000000004 37.0 37.0 37.0 37.0 37.0 100-101 35.65675 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 13 2.0 14 2.0 15 3.0 16 2.0 17 9.0 18 5.0 19 6.0 20 3.0 21 9.0 22 16.0 23 20.0 24 14.0 25 15.0 26 17.0 27 23.0 28 21.0 29 28.0 30 23.0 31 32.0 32 54.0 33 77.0 34 124.0 35 231.0 36 1968.0 37 1296.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 42.05 16.875 11.525 29.549999999999997 2 27.450000000000003 23.0 26.125 23.425 3 24.825 24.325 27.800000000000004 23.05 4 31.374999999999996 26.375 17.175 25.074999999999996 5 30.8 30.349999999999998 18.725 20.125 6 24.575 32.275 20.424999999999997 22.725 7 24.95 19.375 31.85 23.825 8 25.4 21.775 23.95 28.875 9 26.525 22.400000000000002 25.074999999999996 26.0 10-11 28.375 27.462500000000002 18.975 25.1875 12-13 29.45 22.2125 22.412499999999998 25.924999999999997 14-15 26.4125 25.5375 22.85 25.2 16-17 27.487499999999997 24.474999999999998 22.625 25.412499999999998 18-19 28.449999999999996 24.45 22.2125 24.887500000000003 20-21 28.025 24.762500000000003 22.45 24.762500000000003 22-23 27.8875 24.725 21.0125 26.375 24-25 27.8625 23.7375 22.675 25.724999999999998 26-27 27.625 25.650000000000002 22.45 24.275 28-29 28.349999999999998 25.174999999999997 21.8625 24.6125 30-31 28.1875 25.1875 21.512500000000003 25.112499999999997 32-33 27.1125 24.6875 23.075000000000003 25.124999999999996 34-35 27.2625 25.924999999999997 21.837500000000002 24.975 36-37 26.4625 25.35 22.0625 26.125 38-39 27.6375 24.675 22.037499999999998 25.650000000000002 40-41 27.6875 25.137500000000003 21.45 25.724999999999998 42-43 28.125 25.4625 22.5125 23.9 44-45 27.375 25.275 22.6125 24.7375 46-47 27.737499999999997 24.0125 22.875 25.374999999999996 48-49 27.025 24.6 23.4125 24.962500000000002 50-51 27.787499999999998 24.95 23.2875 23.974999999999998 52-53 28.0875 23.575 23.25 25.087500000000002 54-55 27.175 25.912499999999998 21.075 25.837500000000002 56-57 27.5625 25.2875 23.1 24.05 58-59 28.725 24.3875 21.912499999999998 24.975 60-61 27.875 25.112499999999997 22.3125 24.7 62-63 28.725 23.962500000000002 22.662499999999998 24.65 64-65 28.0625 25.0125 22.112499999999997 24.8125 66-67 28.8375 24.65 21.637500000000003 24.875 68-69 28.1125 25.95 22.3125 23.625 70-71 28.262500000000003 25.45 21.6875 24.6 72-73 27.450000000000003 24.9375 22.7125 24.9 74-75 28.9125 24.462500000000002 22.037499999999998 24.587500000000002 76-77 28.050000000000004 25.874999999999996 21.375 24.7 78-79 27.537499999999998 25.4875 21.45 25.525 80-81 27.900000000000002 25.412499999999998 22.575 24.1125 82-83 27.487499999999997 25.9625 22.225 24.325 84-85 28.1125 25.4625 22.3125 24.1125 86-87 28.299999999999997 25.35 22.325 24.025 88-89 28.475 24.725 22.4875 24.3125 90-91 28.349999999999998 24.625 21.85 25.174999999999997 92-93 29.275000000000002 24.2625 22.412499999999998 24.05 94-95 29.062500000000004 24.95 22.1 23.8875 96-97 29.299999999999997 25.412499999999998 21.725 23.5625 98-99 28.999999999999996 24.9 22.35 23.75 100-101 30.8125 24.587500000000002 22.175 22.425 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 0.0 1 0.0 2 2.0 3 3.0 4 2.0 5 1.5 6 1.0 7 0.5 8 1.0 9 1.5 10 0.5 11 0.0 12 0.5 13 1.0 14 0.5 15 0.0 16 0.5 17 1.0 18 2.5 19 3.0 20 2.0 21 1.5 22 1.0 23 2.0 24 1.5 25 2.0 26 2.5 27 2.5 28 2.0 29 1.5 30 2.5 31 2.0 32 1.5 33 3.5 34 6.5 35 9.5 36 16.0 37 24.0 38 37.0 39 62.0 40 85.5 41 95.5 42 109.5 43 124.0 44 143.5 45 155.5 46 151.0 47 166.0 48 183.0 49 178.0 50 168.0 51 157.0 52 157.0 53 163.5 54 159.0 55 141.5 56 123.5 57 104.0 58 101.0 59 91.5 60 82.5 61 79.0 62 67.5 63 75.0 64 74.5 65 77.0 66 77.0 67 67.5 68 68.5 69 64.5 70 52.5 71 40.0 72 33.0 73 37.0 74 27.5 75 17.0 76 15.5 77 14.5 78 10.0 79 7.5 80 7.0 81 4.0 82 6.0 83 5.0 84 2.0 85 1.0 86 1.0 87 2.0 88 1.5 89 0.5 90 1.0 91 1.5 92 1.5 93 2.0 94 2.5 95 3.0 96 1.5 97 0.5 98 0.5 99 2.0 100 3.0 >>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 83.7 #Duplication Level Percentage of deduplicated Percentage of total 1 84.73715651135007 70.92500000000001 2 12.395459976105137 20.75 3 1.971326164874552 4.95 4 0.5675029868578256 1.9 5 0.2688172043010753 1.125 6 0.0 0.0 7 0.05973715651135006 0.35000000000000003 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 CAAATTTCTGCCCTATCAACTTTCGATGGTAGGATAGGGGCCTACCATGG 7 0.17500000000000002 No Hit CTTACCAGGTCCAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTT 7 0.17500000000000002 No Hit AGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTTGATTCTATGGGT 5 0.125 No Hit GATAACTCGACGGATCGCACGGCCCTCGTGCCGGCGACGCATCATTCAAA 5 0.125 No Hit GACGAACAACTGCGAAAGCATTTGCCAAGGATGTTTTCATTAATCAAGAA 5 0.125 No Hit ATAAAATAGAAGCTGCCCTGGGAAAGTTCACCGATGGTCCTTTCTTGCTT 5 0.125 No Hit GGTCGGCCGGTCCGCCTCACGGCGAGCACCGACCTACTCGACCCTTCAGC 5 0.125 No Hit CGAGGATCCATTGGAGGGCAAGTCTGGTGCCAGCAGCCGCGGTAATTCCA 5 0.125 No Hit GTTCTGGGCCGCACGCGCGCTACACTGATGTATTCAACGAGTATATAGCC 5 0.125 No Hit GTCGGGGGCATTCGTATTTCATAGTCAGAGGTGAAATTCTTGGATTTATG 5 0.125 No Hit ATTCATGATAACTCGACGGATCGCACGGCCCTCGTGCCGGCGACGCATCA 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 0.025 0.0 0.0 0.0 0.0 30-31 0.025 0.0 0.0 0.0 0.0 32-33 0.05 0.0 0.0 0.0 0.0 34-35 0.0875 0.0 0.0 0.0 0.0 36-37 0.125 0.0 0.0 0.0 0.0 38-39 0.125 0.0 0.0 0.0 0.0 40-41 0.125 0.0 0.0 0.0 0.0 42-43 0.2125 0.0 0.0 0.0 0.0 44-45 0.2625 0.0 0.0 0.0 0.0 46-47 0.4125 0.0 0.0 0.0 0.0 48-49 0.5375000000000001 0.0 0.0 0.0 0.0 50-51 0.625 0.0 0.0 0.0 0.0 52-53 0.85 0.0 0.0 0.0 0.0 54-55 0.9624999999999999 0.0 0.0 0.0 0.0 56-57 1.1375000000000002 0.0 0.0 0.0 0.0 58-59 1.3875 0.0 0.0 0.0 0.0 60-61 1.6125 0.0 0.0 0.0 0.0 62-63 1.9625000000000001 0.0 0.0 0.0 0.0 64-65 2.2375 0.0 0.0 0.0 0.0 66-67 2.425 0.0 0.0 0.0 0.0 68-69 2.75 0.0 0.0 0.0 0.0 70-71 3.1125 0.0 0.0 0.0 0.0 72-73 3.4875 0.0 0.0 0.0 0.0 74-75 3.95 0.0 0.0 0.0 0.0 76-77 4.375 0.0 0.0 0.0 0.0 78-79 4.9375 0.0 0.0 0.0 0.0 80-81 5.3125 0.0 0.0 0.0 0.0 82-83 6.1 0.0 0.0 0.0 0.0 84-85 6.6125 0.0 0.0 0.0 0.0 86-87 7.0875 0.0 0.0 0.0 0.0 88-89 7.95 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Read 914089 spots for ERR3450075.sra Written 914089 spots for ERR3450075.sra Read 914089 spots for ERR3450075.sra Written 914089 spots for ERR3450075.sra Read 914089 spots for ERR3450075.sra Written 914089 spots for ERR3450075.sra Read 914089 spots for ERR3450075.sra Written 914089 spots for ERR3450075.sra Read 914089 spots for ERR3450075.sra Written 914089 spots for ERR3450075.sra Read 914089 spots for ERR3450075.sra Written 914089 spots for ERR3450075.sra Read 914089 spots for ERR3450075.sra Written 914089 spots for ERR3450075.sra Read 914089 spots for ERR3450075.sra Written 914089 spots for ERR3450075.sra Read 914089 spots for ERR3450075.sra Written 914089 spots for ERR3450075.sra Read 914089 spots for ERR3450075.sra Written 914089 spots for ERR3450075.sra Read 914089 spots for ERR3450075.sra Written 914089 spots for ERR3450075.sra Read 914089 spots for ERR3450075.sra Written 914089 spots for ERR3450075.sra Read 914089 spots for ERR3450075.sra Written 914089 spots for ERR3450075.sra Read 914089 spots for ERR3450075.sra Written 914089 spots for ERR3450075.sra Read 914089 spots for ERR3450075.sra Written 914089 spots for ERR3450075.sra Read 914089 spots for ERR3450075.sra Written 914089 spots for ERR3450075.sra Read 914089 spots for ERR3450075.sra Written 914089 spots for ERR3450075.sra Read 914089 spots for ERR3450075.sra Written 914089 spots for ERR3450075.sra Read 914089 spots for ERR3450075.sra Written 914089 spots for ERR3450075.sra Read 914089 spots for ERR3450075.sra Written 914089 spots for ERR3450075.sra SRR ids: ['ERR3450075.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd__7abqgpb ERR3450075.sra spots: 18281780 blocks: [[1, 914089], [914090, 1828178], [1828179, 2742267], [2742268, 3656356], [3656357, 4570445], [4570446, 5484534], [5484535, 6398623], [6398624, 7312712], [7312713, 8226801], [8226802, 9140890], [9140891, 10054979], [10054980, 10969068], [10969069, 11883157], [11883158, 12797246], [12797247, 13711335], [13711336, 14625424], [14625425, 15539513], [15539514, 16453602], [16453603, 17367691], [17367692, 18281780]] ERR3450075 file size 4388064 ERR3450075 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 ERR3450075 ERR3450075_1.fastq ERR3450075_2.fastq Input file: ERR3450075_1.fastq Paired file: ERR3450075_2.fastq trimmed: ERR3450075-trimmed-pair1.fastq, ERR3450075-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 14:38:17 2024 >> started Sat Dec 7 14:38:33 2024 >> done (15.455s) 18281780 read pairs processed; of these: 271 ( 0.00%) short read pairs filtered out after trimming by size control 134251 ( 0.73%) empty read pairs filtered out after trimming by size control 18147258 (99.26%) read pairs available; of these: 2344596 (12.92%) trimmed read pairs available after processing 15802662 (87.08%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 43 0.00% 19 76 0.00% 20 212 0.00% 21 546 0.00% 22 655 0.00% 23 296 0.00% 24 309 0.00% 25 410 0.00% 26 634 0.00% 27 837 0.00% 28 1133 0.01% 29 1481 0.01% 30 1883 0.01% 31 2485 0.01% 32 2567 0.01% 33 2607 0.01% 34 2876 0.02% 35 2611 0.01% 36 3030 0.02% 37 3073 0.02% 38 3737 0.02% 39 4468 0.02% 40 5027 0.03% 41 6227 0.03% 42 7373 0.04% 43 7635 0.04% 44 6326 0.03% 45 6208 0.03% 46 6323 0.03% 47 7293 0.04% 48 8055 0.04% 49 8713 0.05% 50 9715 0.05% 51 10794 0.06% 52 11970 0.07% 53 12357 0.07% 54 13063 0.07% 55 13710 0.08% 56 14392 0.08% 57 15063 0.08% 58 16232 0.09% 59 17521 0.10% 60 18975 0.10% 61 21042 0.12% 62 23041 0.13% 63 24380 0.13% 64 25442 0.14% 65 26251 0.14% 66 27168 0.15% 67 28467 0.16% 68 30028 0.17% 69 31004 0.17% 70 33057 0.18% 71 35848 0.20% 72 37737 0.21% 73 39563 0.22% 74 41072 0.23% 75 42333 0.23% 76 43476 0.24% 77 44526 0.25% 78 45956 0.25% 79 47926 0.26% 80 49172 0.27% 81 50852 0.28% 82 54023 0.30% 83 55597 0.31% 84 57327 0.32% 85 59156 0.33% 86 60093 0.33% 87 62200 0.34% 88 63657 0.35% 89 66076 0.36% 90 67089 0.37% 91 70554 0.39% 92 73614 0.41% 93 75029 0.41% 94 77637 0.43% 95 78143 0.43% 96 79402 0.44% 97 82051 0.45% 98 82235 0.45% 99 82909 0.46% 100 90522 0.50% 101 15802662 87.08% 18147258 reads passed initial QC criterion=sequence-density sequence-density=0.32 sequence-density-rank=1 fanout-score=3.47 fanout-score-rank=27 prefix-density=0.55 prefix-fanout=2.0 sequence=CGCTATCGGTCACCCAGGAGTATTTAGCCTTGCAAGGTGGTCCTTGCTGATTCACACGGGATTCCACGTGCCCCATGCTACTCGGGTCAGAGCGTAAGCTAGTGATGCTTTCGGCTACTGGACTTTAGCCATCTAGGGTGCGGCACTCAACCGCTTCGCCTAGCAGCACAACGCTTGTATTGCTCTCCCACAACCCCGTTTTCACGGTTTAGGCTGCTCCCATTTCGCTCGCCGCTACTACGGGAATCGCTTTTGCTTTCTTTTCCTCTGGCTACTAAGATGTTTCAGTTCGCCAGGTTGTCTCTTGCCTGCTCATGGATTCAGCAGGCAGTTTAAAAGGTTGACCTATTTGGGAATCTCCGGATCTATGCTTATTTTCAACTCCCCGAAGCATTTCGTCGCTTGCTACGCCCTTCCTCGTCTCTGGGTGCCTAGGTATCCACCGCAAGCCT criterion=fanout-score sequence-density=0.07 sequence-density-rank=17 fanout-score=166.77 fanout-score-rank=1 prefix-density=0.63 prefix-fanout=19.9 sequence=CGCCGCCGCCGA criterion=sequence-density sequence-density=0.32 sequence-density-rank=1 fanout-score=2.09 fanout-score-rank=35 prefix-density=0.34 prefix-fanout=2.0 sequence=CAAGGCTAAATAC criterion=fanout-score sequence-density=0.08 sequence-density-rank=21 fanout-score=239.88 fanout-score-rank=1 prefix-density=0.83 prefix-fanout=22.8 sequence=CGGCGGCGGCGA ERR3450075 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 07 14:39:07 Started mapping on | Dec 07 14:39:07 Finished on | Dec 07 14:40:40 Mapping speed, Million of reads per hour | 702.47 Number of input reads | 18147258 Average input read length | 196 UNIQUE READS: Uniquely mapped reads number | 13103500 Uniquely mapped reads % | 72.21% Average mapped length | 196.62 Number of splices: Total | 7302525 Number of splices: Annotated (sjdb) | 6902220 Number of splices: GT/AG | 7207117 Number of splices: GC/AG | 81565 Number of splices: AT/AC | 4409 Number of splices: Non-canonical | 9434 Mismatch rate per base, % | 0.23% Deletion rate per base | 0.01% Deletion average length | 2.13 Insertion rate per base | 0.01% Insertion average length | 1.96 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 1125561 % of reads mapped to multiple loci | 6.20% Number of reads mapped to too many loci | 730328 % of reads mapped to too many loci | 4.02% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 3.03% % of reads unmapped: other | 14.54% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 3918197 3918197 3918197 N_multimapping 1125561 1125561 1125561 N_noFeature 426374 12508370 825685 N_ambiguous 238820 1971 44259 UnstrandedReadsAssigned:12438306 PositiveStrandReadsAssigned:593159 NegativeStrandReadsAssigned:12233556 Dataset is classified negative stranded MeadianReadLen=101 20thPercentileLength=101 echo kmer=97 ERR3450075 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: ERR3450075-trimmed-pair1.fastq ERR3450075-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 18,147,258 reads, 13,017,821 reads pseudoaligned [quant] estimated average fragment length: 180.382 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,242 rounds 52973 ERR3450075.ke.tsv 35125 ERR3450075.se.tsv 88098 total ==> ERR3450075.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 756.746 6.68637e-07 1.06232e-07 PNS24247 1044 864.618 24.212 3.36683 PNS24249 1928 1748.62 174.584 12.004 PNS24246 1044 864.618 24.212 3.36683 PNS24248 1044 864.618 24.212 3.36683 PNS24244 1471 1291.62 9.77963 0.910339 PNS24243 293 133.725 0 0 KQK14069 1603 1423.62 4437.04 374.727 KQK14071 474 298.258 86.8057 34.9922 ==> ERR3450075.se.tsv <== BRADI_1g14170v3 4582 BRADI_1g53295v3 44 BRADI_1g59795v3 110 BRADI_1g07683v3 0 BRADI_1g00485v3 14 BRADI_1g20270v3 750 BRADI_1g74790v3 175 BRADI_1g09890v3 18 BRADI_1g77505v3 102 BRADI_1g48960v3 1 ERR3450075 completed mapping pipeline successfully