Starting /dee2/code/volunteer_pipeline.sh ERR3317452 current disk space = 1525012295680 free memory = 1413558996 ERR3317452 SRAfilesize ba25021986f96f78a412e8a1a53e6caa ERR3317452.sra ERR3317452.sra file validated ERR3317452 is paired end ERR3317452 is conventional basespace ERR3317452 read1 length is 101 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR3317452_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 49 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 31.5005 34.0 31.0 34.0 31.0 34.0 2 32.29525 34.0 31.0 34.0 31.0 34.0 3 32.82475 34.0 31.0 34.0 31.0 34.0 4 36.36 37.0 37.0 37.0 35.0 37.0 5 36.378 37.0 37.0 37.0 35.0 37.0 6 36.388 37.0 37.0 37.0 35.0 37.0 7 36.394 37.0 37.0 37.0 35.0 37.0 8 36.418 37.0 37.0 37.0 35.0 37.0 9 38.2485 39.0 39.0 39.0 37.0 39.0 10-11 38.226124999999996 39.0 39.0 39.0 37.0 39.0 12-13 38.19325 39.0 39.0 39.0 37.0 39.0 14-15 39.672875 41.0 40.0 41.0 37.0 41.0 16-17 39.664 41.0 40.0 41.0 37.0 41.0 18-19 39.632875 41.0 40.0 41.0 37.0 41.0 20-21 39.588750000000005 41.0 40.0 41.0 37.0 41.0 22-23 39.49875 41.0 40.0 41.0 36.5 41.0 24-25 39.442750000000004 41.0 40.0 41.0 36.5 41.0 26-27 39.299375 41.0 39.0 41.0 36.0 41.0 28-29 39.12025 41.0 39.0 41.0 35.5 41.0 30-31 38.94475 40.5 39.0 41.0 35.0 41.0 32-33 38.617374999999996 40.0 38.0 41.0 34.5 41.0 34-35 38.33125 40.0 38.0 41.0 33.5 41.0 36-37 38.292875 40.0 38.0 41.0 34.0 41.0 38-39 37.9875 40.0 38.0 41.0 33.0 41.0 40-41 37.82425 40.0 37.0 41.0 33.0 41.0 42-43 37.908 40.0 37.0 41.0 33.0 41.0 44-45 37.478375 40.0 37.0 41.0 32.5 41.0 46-47 37.377875 40.0 36.0 41.0 32.5 41.0 48-49 37.048375 39.5 36.0 41.0 31.0 41.0 50-51 37.38675 39.5 36.0 41.0 33.0 41.0 52-53 37.21025 39.5 35.0 41.0 32.5 41.0 54-55 36.81275 39.0 35.0 41.0 31.5 41.0 56-57 36.469625 38.5 35.0 41.0 31.0 41.0 58-59 36.097625 37.5 35.0 41.0 31.0 41.0 60-61 35.807500000000005 37.0 35.0 40.0 31.0 41.0 62-63 35.492375 37.0 35.0 40.0 30.5 41.0 64-65 35.063875 36.0 35.0 39.0 30.0 41.0 66-67 34.72525 35.5 34.5 39.0 30.0 41.0 68-69 34.372 35.0 34.0 38.5 29.5 40.5 70-71 33.970875 35.0 34.0 37.0 29.0 39.5 72-73 33.438625 35.0 34.0 37.0 28.0 39.0 74-75 33.172 35.0 34.0 36.0 27.5 39.0 76-77 32.12825 34.5 32.5 35.0 26.0 37.0 78-79 32.3915 35.0 33.0 35.0 27.0 37.0 80-81 32.278999999999996 35.0 33.0 35.0 27.0 36.5 82-83 32.1245 35.0 33.0 35.0 26.5 36.0 84-85 31.74225 35.0 33.0 35.0 24.5 36.0 86-87 31.49925 35.0 33.0 35.0 24.0 36.0 88-89 31.29825 35.0 33.0 35.0 24.0 35.0 90-91 31.092 35.0 32.5 35.0 23.0 35.0 92-93 30.840874999999997 35.0 32.0 35.0 20.0 35.0 94-95 30.70025 35.0 32.0 35.0 20.0 35.0 96-97 30.42175 35.0 32.0 35.0 15.5 35.0 98-99 29.964875 35.0 31.5 35.0 2.0 35.0 100-101 27.563000000000002 33.0 26.5 34.5 2.0 35.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 4.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 1.0 9 2.0 10 7.0 11 9.0 12 6.0 13 7.0 14 4.0 15 10.0 16 10.0 17 9.0 18 8.0 19 10.0 20 16.0 21 23.0 22 18.0 23 15.0 24 17.0 25 29.0 26 35.0 27 36.0 28 47.0 29 49.0 30 56.0 31 82.0 32 112.0 33 126.0 34 188.0 35 314.0 36 602.0 37 1095.0 38 941.0 39 112.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 25.268114046560292 27.72691603452786 20.193565262882554 26.811404656029296 2 27.625 25.025 19.05 28.299999999999997 3 28.000000000000004 26.05 17.424999999999997 28.525 4 27.525 25.650000000000002 16.25 30.575000000000003 5 28.000000000000004 25.424999999999997 15.950000000000001 30.625000000000004 6 29.75 27.775 17.925 24.55 7 32.425 22.6 20.525 24.45 8 33.575 25.174999999999997 23.175 18.075 9 33.875 26.6 23.200000000000003 16.325 10-11 34.2625 25.974999999999998 21.0625 18.7 12-13 30.9875 26.0625 23.962500000000002 18.987499999999997 14-15 27.450000000000003 26.9625 24.349999999999998 21.2375 16-17 27.5625 26.650000000000002 24.3 21.4875 18-19 27.0625 26.7625 24.9125 21.2625 20-21 25.45 27.237499999999997 25.2625 22.05 22-23 25.387500000000003 27.525 25.2 21.8875 24-25 25.575 26.75 25.087500000000002 22.5875 26-27 26.5875 26.6 24.0625 22.75 28-29 27.425 26.1125 23.5125 22.95 30-31 26.1 26.724999999999998 25.05 22.125 32-33 25.337500000000002 27.1125 25.162499999999998 22.3875 34-35 25.687500000000004 26.400000000000002 25.074999999999996 22.8375 36-37 25.8 26.474999999999998 24.887500000000003 22.8375 38-39 25.4 25.9625 25.674999999999997 22.9625 40-41 26.55 26.187500000000004 25.4375 21.825 42-43 26.25 25.2375 25.6125 22.900000000000002 44-45 25.45 26.7625 23.962500000000002 23.825 46-47 26.7125 25.7125 25.5125 22.0625 48-49 26.637499999999996 26.25 25.587500000000002 21.525 50-51 26.387500000000003 26.200000000000003 24.625 22.787499999999998 52-53 26.35 27.275 24.0625 22.3125 54-55 26.450000000000003 26.6125 25.4625 21.475 56-57 26.05 27.0625 24.9375 21.95 58-59 25.974999999999998 26.674999999999997 24.762500000000003 22.5875 60-61 24.474999999999998 26.7625 25.9875 22.775000000000002 62-63 25.337500000000002 27.700000000000003 24.7 22.2625 64-65 26.2125 26.437500000000004 24.6125 22.7375 66-67 25.0625 27.0 24.775 23.1625 68-69 25.337500000000002 27.6375 24.099999999999998 22.925 70-71 25.6125 27.500000000000004 23.9125 22.975 72-73 25.025 27.3 25.5375 22.1375 74-75 25.937500000000004 26.900000000000002 24.8625 22.3 76-77 25.75 28.3125 23.7125 22.225 78-79 25.112499999999997 27.525 25.4375 21.925 80-81 25.374999999999996 27.275 24.825 22.525000000000002 82-83 26.087500000000002 27.250000000000004 24.0125 22.650000000000002 84-85 24.95 27.6875 24.4125 22.95 86-87 26.3125 27.474999999999998 25.0125 21.2 88-89 25.3125 28.3375 24.725 21.625 90-91 26.150000000000002 27.525 23.525 22.8 92-93 25.8 27.925 23.599999999999998 22.675 94-95 26.0125 27.150000000000002 23.8625 22.975 96-97 25.25 28.0625 23.9125 22.775000000000002 98-99 25.9875 27.200000000000003 23.775 23.0375 100-101 26.3125 28.499999999999996 22.787499999999998 22.400000000000002 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 1.0 1 0.5 2 0.0 3 1.0 4 1.5 5 1.5 6 2.5 7 3.0 8 2.0 9 2.0 10 3.0 11 2.5 12 2.5 13 2.0 14 1.5 15 2.0 16 3.5 17 4.5 18 2.5 19 1.5 20 1.5 21 1.0 22 1.5 23 1.5 24 1.5 25 1.5 26 3.0 27 4.5 28 9.5 29 12.0 30 15.0 31 19.5 32 19.5 33 28.0 34 37.5 35 41.0 36 45.5 37 53.5 38 62.0 39 88.0 40 116.0 41 142.0 42 154.5 43 153.5 44 170.0 45 177.5 46 185.0 47 191.0 48 192.5 49 190.0 50 175.5 51 163.0 52 158.5 53 151.0 54 126.0 55 107.0 56 99.5 57 99.0 58 90.0 59 69.5 60 63.0 61 55.5 62 47.5 63 45.5 64 47.5 65 42.0 66 32.0 67 36.0 68 30.5 69 19.0 70 18.5 71 25.0 72 29.5 73 25.0 74 20.5 75 14.5 76 8.5 77 7.5 78 6.5 79 7.5 80 5.5 81 1.5 82 2.0 83 2.0 84 2.0 85 2.0 86 1.0 87 2.0 88 1.5 89 0.0 90 0.5 91 0.5 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 4.425 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 95.39999999999999 #Duplication Level Percentage of deduplicated Percentage of total 1 97.19601677148847 92.72500000000001 2 1.939203354297694 3.6999999999999997 3 0.4454926624737945 1.275 4 0.1310272536687631 0.5 5 0.1310272536687631 0.625 6 0.026205450733752623 0.15 7 0.026205450733752623 0.17500000000000002 8 0.07861635220125787 0.6 9 0.0 0.0 >10 0.026205450733752623 0.25 >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 TGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTG 10 0.25 No Hit ACTTAACTGGGGGATTCACCGCAAATACTACTTTGGCTCATTATTGCCGC 8 0.2 No Hit TGCAAATGGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAAGGCGAT 8 0.2 No Hit AGCCGCAGCTTGTGAAGTATGGAAGGCGATCAAATTCGAGTTCGCGCCGG 8 0.2 No Hit AGGCGGAAGAGTCCTCTTAATATTTATCTAATCTTATATAGGTTTCAGTA 7 0.17500000000000002 No Hit ATGCCAGCTCTGACCGAAATCTTTGGGGATGATTCTGTATTACAATTTGG 6 0.15 No Hit TAGTAGCCAGAGGAAAAGAAAGCAAAAGCGATTCCCGTAGTAGCGGCGAG 5 0.125 No Hit AGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTTCGGGG 5 0.125 No Hit ATGCCAGGTGTTATACCAGTAGCTTCAGGTGGTATTCATGTTTGGCATAT 5 0.125 No Hit TTGGGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCT 5 0.125 No Hit ACGCCGGTACAGTAGTAGGTAAGTTAGAAGGGGAACGCGAAATCACTTTA 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 0.025 0.0 0.0 0.0 0.0 2 0.025 0.0 0.0 0.0 0.0 3 0.025 0.0 0.0 0.0 0.0 4 0.025 0.0 0.0 0.0 0.0 5 0.025 0.0 0.0 0.0 0.0 6 0.075 0.0 0.0 0.0 0.0 7 0.075 0.0 0.0 0.0 0.0 8 0.075 0.0 0.0 0.0 0.0 9 0.075 0.0 0.0 0.0 0.0 10-11 0.1 0.0 0.0 0.0 0.0 12-13 0.1 0.0 0.0 0.0 0.0 14-15 0.1125 0.0 0.0 0.0 0.0 16-17 0.125 0.0 0.0 0.0 0.0 18-19 0.125 0.0 0.0 0.0 0.0 20-21 0.125 0.0 0.0 0.0 0.0 22-23 0.125 0.0 0.0 0.0 0.0 24-25 0.125 0.0 0.0 0.0 0.0 26-27 0.1375 0.0 0.0 0.0 0.0 28-29 0.15 0.0 0.0 0.0 0.0 30-31 0.15 0.0 0.0 0.0 0.0 32-33 0.1875 0.0 0.0 0.0 0.0 34-35 0.225 0.0 0.0 0.0 0.0 36-37 0.2875 0.0 0.0 0.0 0.0 38-39 0.32499999999999996 0.0 0.0 0.0 0.0 40-41 0.4 0.0 0.0 0.0 0.0 42-43 0.4875 0.0 0.0 0.0 0.0 44-45 0.6000000000000001 0.0 0.0 0.0 0.0 46-47 0.725 0.0 0.0 0.0 0.0 48-49 0.7625 0.0 0.0 0.0 0.0 50-51 0.8125 0.0 0.0 0.0 0.0 52-53 0.9624999999999999 0.0 0.0 0.0 0.0 54-55 1.1125 0.0 0.0 0.0 0.0 56-57 1.225 0.0 0.0 0.0 0.0 58-59 1.3875 0.0 0.0 0.0 0.0 60-61 1.5499999999999998 0.0 0.0 0.0 0.0 62-63 1.75 0.0 0.0 0.0 0.0 64-65 1.875 0.0 0.0 0.0 0.0 66-67 2.0375 0.0 0.0 0.0 0.0 68-69 2.25 0.0 0.0 0.0 0.0 70-71 2.425 0.0 0.0 0.0 0.0 72-73 2.6375 0.0 0.0 0.0 0.0 74-75 2.8499999999999996 0.0 0.0 0.0 0.0 76-77 3.1875 0.0 0.0 0.0 0.0 78-79 3.5 0.0 0.0 0.0 0.0 80-81 3.9875 0.0 0.0 0.0 0.0 82-83 4.574999999999999 0.0 0.0 0.0 0.0 84-85 5.125 0.0 0.0 0.0 0.0 86-87 5.637499999999999 0.0 0.0 0.0 0.0 88-89 6.1875 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE ERR3317452 read2 length is 101 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR3317452_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 45 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 31.888 33.0 31.0 34.0 30.0 34.0 2 31.8045 34.0 31.0 34.0 30.0 34.0 3 31.748 34.0 31.0 34.0 30.0 34.0 4 35.132 37.0 35.0 37.0 32.0 37.0 5 35.36325 37.0 35.0 37.0 33.0 37.0 6 35.45725 37.0 35.0 37.0 33.0 37.0 7 35.55225 37.0 36.0 37.0 35.0 37.0 8 35.57475 37.0 37.0 37.0 35.0 37.0 9 37.34725 39.0 38.0 39.0 35.0 39.0 10-11 37.51575 39.0 39.0 39.0 35.0 39.0 12-13 37.460625 39.0 39.0 39.0 35.0 39.0 14-15 38.882125 41.0 40.0 41.0 36.0 41.0 16-17 38.8595 41.0 39.5 41.0 36.0 41.0 18-19 38.757999999999996 41.0 39.0 41.0 35.0 41.0 20-21 38.698125000000005 41.0 39.0 41.0 35.0 41.0 22-23 38.625125 41.0 39.0 41.0 35.0 41.0 24-25 38.554125 41.0 39.0 41.0 35.0 41.0 26-27 38.454750000000004 41.0 39.0 41.0 35.0 41.0 28-29 38.289500000000004 41.0 39.0 41.0 35.0 41.0 30-31 38.155125 40.5 38.0 41.0 35.0 41.0 32-33 38.049499999999995 40.0 38.0 41.0 34.5 41.0 34-35 37.92125 40.0 38.0 41.0 34.0 41.0 36-37 37.78375 40.0 38.0 41.0 33.5 41.0 38-39 37.73025 40.0 38.0 41.0 33.0 41.0 40-41 37.791125 40.0 38.0 41.0 34.0 41.0 42-43 37.73175 40.0 38.0 41.0 33.0 41.0 44-45 37.564 40.0 38.0 41.0 33.0 41.0 46-47 37.37575 40.0 37.0 41.0 33.0 41.0 48-49 37.211625 40.0 37.0 41.0 32.5 41.0 50-51 36.50025 39.5 35.5 40.5 31.5 41.0 52-53 36.363125 39.0 35.0 40.5 31.0 41.0 54-55 36.439375 39.0 35.0 41.0 31.5 41.0 56-57 36.20525 39.0 35.0 41.0 31.0 41.0 58-59 35.9315 39.0 35.0 41.0 31.0 41.0 60-61 35.677 38.0 35.0 41.0 30.5 41.0 62-63 35.1445 37.0 35.0 40.0 28.5 41.0 64-65 34.9065 37.0 35.0 40.0 29.0 41.0 66-67 34.817125000000004 36.5 35.0 40.0 29.0 41.0 68-69 34.57925 36.0 35.0 39.0 29.0 41.0 70-71 34.324375 36.0 35.0 39.0 30.0 41.0 72-73 33.951750000000004 35.0 35.0 38.5 29.5 40.5 74-75 33.558125000000004 35.0 34.5 37.0 29.0 39.0 76-77 33.15225 35.0 34.0 37.0 28.0 39.0 78-79 32.876625000000004 35.0 34.0 36.0 27.0 38.5 80-81 32.582125000000005 35.0 34.0 36.0 27.0 37.0 82-83 32.313875 35.0 34.0 35.5 27.0 37.0 84-85 32.06525 35.0 34.0 35.0 26.0 36.5 86-87 31.92875 35.0 34.0 35.0 26.0 36.0 88-89 31.758125 35.0 33.0 35.0 25.0 36.0 90-91 31.60325 35.0 33.0 35.0 24.5 36.0 92-93 31.405875 35.0 33.0 35.0 23.5 35.0 94-95 31.270625 35.0 33.0 35.0 24.0 35.0 96-97 31.033250000000002 35.0 33.0 35.0 21.5 35.0 98-99 30.789875 35.0 33.0 35.0 17.5 35.0 100-101 29.122500000000002 33.5 29.5 35.0 2.0 35.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 55.0 3 5.0 4 4.0 5 5.0 6 5.0 7 7.0 8 4.0 9 9.0 10 3.0 11 12.0 12 10.0 13 11.0 14 6.0 15 8.0 16 9.0 17 11.0 18 9.0 19 11.0 20 12.0 21 15.0 22 16.0 23 13.0 24 13.0 25 17.0 26 15.0 27 26.0 28 32.0 29 28.0 30 47.0 31 59.0 32 81.0 33 95.0 34 123.0 35 292.0 36 450.0 37 993.0 38 1238.0 39 251.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 26.900000000000002 11.25 32.925 28.925 2 24.175 11.425 26.875 37.525 3 20.65 12.875 32.4 34.075 4 22.325 11.600000000000001 29.675 36.4 5 23.200000000000003 13.975000000000001 26.724999999999998 36.1 6 22.45 19.075 32.85 25.624999999999996 7 17.525 23.35 41.55 17.575 8 17.05 24.725 37.9 20.325 9 16.975 27.500000000000004 37.974999999999994 17.549999999999997 10-11 16.9875 26.5875 35.75 20.674999999999997 12-13 19.2 26.85 33.725 20.225 14-15 19.35241905238155 26.003250406300786 33.90423802975372 20.740092511563944 16-17 19.817454363590898 25.406351587896975 32.195548887221804 22.58064516129032 18-19 18.982118294360383 26.647492809803673 31.361760660247594 23.008628235588347 20-21 19.507315243216205 25.697136426159812 31.27422783543829 23.521320495185694 22-23 20.165020627578446 25.015626953369168 31.078884860607577 23.740467558444806 24-25 18.825 26.137500000000003 31.8625 23.175 26-27 19.875 26.4625 29.4125 24.25 28-29 20.200000000000003 25.5625 28.525 25.7125 30-31 18.975 26.3 30.65 24.075 32-33 21.4875 25.637500000000003 29.5875 23.2875 34-35 20.875 25.624999999999996 28.4125 25.087500000000002 36-37 20.5 25.374999999999996 30.2875 23.8375 38-39 21.3 24.9375 28.775000000000002 24.9875 40-41 21.55 24.224999999999998 28.287499999999998 25.937500000000004 42-43 21.640205025628205 25.740717589698715 29.22865358169771 23.39042380297537 44-45 21.825 26.487500000000004 27.525 24.1625 46-47 20.599999999999998 26.6125 27.525 25.2625 48-49 20.325 27.375 28.175 24.125 50-51 22.0125 25.275 28.3125 24.4 52-53 21.987499999999997 24.5 27.175 26.337500000000002 54-55 20.6375 26.737499999999997 30.0875 22.537499999999998 56-57 21.55 24.85 28.875 24.725 58-59 20.625 24.5625 29.762499999999996 25.05 60-61 19.725 25.7375 30.0875 24.45 62-63 21.837500000000002 25.7375 27.987499999999997 24.4375 64-65 21.3875 24.375 28.9375 25.3 66-67 21.2875 25.137500000000003 29.299999999999997 24.275 68-69 22.0625 25.5125 27.212500000000002 25.2125 70-71 21.2875 26.137500000000003 26.9625 25.6125 72-73 20.575 25.900000000000002 27.85 25.674999999999997 74-75 21.475 24.4125 28.375 25.7375 76-77 22.45 25.1 27.037499999999998 25.412499999999998 78-79 21.55 26.25 27.150000000000002 25.05 80-81 22.425 26.575 27.237499999999997 23.7625 82-83 22.6 25.124999999999996 26.237500000000004 26.0375 84-85 23.35 26.0375 26.5125 24.099999999999998 86-87 23.9 26.0 26.650000000000002 23.45 88-89 22.3375 25.525 26.525 25.6125 90-91 23.200000000000003 25.637500000000003 27.3875 23.775 92-93 22.875 24.887500000000003 27.6375 24.6 94-95 22.6875 25.2875 26.7625 25.2625 96-97 24.3875 25.587500000000002 27.275 22.75 98-99 23.0875 26.5125 25.6 24.8 100-101 23.5125 25.2875 26.3125 24.887500000000003 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 45.0 1 32.0 2 16.0 3 9.0 4 6.0 5 5.5 6 5.0 7 5.5 8 3.5 9 2.5 10 3.0 11 3.0 12 3.0 13 3.0 14 3.0 15 2.5 16 2.0 17 3.0 18 5.0 19 5.5 20 3.0 21 1.5 22 3.0 23 4.5 24 5.0 25 8.0 26 9.5 27 8.5 28 10.0 29 12.5 30 12.0 31 20.0 32 30.0 33 38.0 34 47.0 35 56.5 36 70.0 37 96.0 38 109.0 39 126.0 40 153.5 41 175.5 42 197.0 43 186.0 44 182.5 45 180.0 46 174.0 47 165.5 48 141.5 49 143.5 50 159.0 51 153.0 52 141.0 53 120.5 54 101.5 55 83.5 56 68.5 57 71.5 58 66.0 59 61.5 60 59.5 61 56.5 62 47.0 63 39.5 64 33.0 65 29.5 66 32.0 67 24.5 68 22.0 69 21.5 70 16.5 71 13.0 72 13.0 73 12.0 74 8.0 75 10.0 76 8.5 77 3.5 78 4.0 79 4.0 80 2.5 81 0.5 82 0.0 83 0.5 84 0.5 85 0.5 86 0.5 87 0.5 88 0.5 89 0.0 90 0.0 91 0.0 92 0.0 93 0.0 94 0.5 95 0.5 96 0.0 97 0.0 98 0.0 99 0.0 100 0.0 >>END_MODULE >>Per base N content pass #Base N-Count 1 0.0 2 0.0 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 0.0125 16-17 0.025 18-19 0.0375 20-21 0.0375 22-23 0.0125 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 0.0125 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 94.45 #Duplication Level Percentage of deduplicated Percentage of total 1 97.96188459502382 92.525 2 1.2175754367390152 2.3 3 0.3440974060349391 0.975 4 0.18528321863419797 0.7000000000000001 5 0.07940709370037057 0.375 6 0.07940709370037057 0.44999999999999996 7 0.02646903123345686 0.17500000000000002 8 0.0 0.0 9 0.02646903123345686 0.22499999999999998 >10 0.05293806246691372 0.65 >50 0.02646903123345686 1.625 >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 fail #Sequence Count Percentage Possible Source TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 65 1.625 No Hit TCTTCATATTTAGTTTTATCTATTAATCGATAGTATCTACCGGCGCGAAC 15 0.375 No Hit TGGGGATGAAAAATAGAAAACTCAAAGCAATGTCAGAGTTGACAAAACTG 11 0.27499999999999997 No Hit TCTTTATATTTAGTTTTATCTATTAATCGATAGTATCTACCGGCGCGAAC 9 0.22499999999999998 No Hit TCTTCTTATTTAGTTTTATCTATTAATCGATAGTATCTACCGGCGCGAAC 7 0.17500000000000002 No Hit ATTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 6 0.15 No Hit GTTTCTTTTTATTTAGACCTTCTTCATATTTAGTTTTATCTATTAATCGA 6 0.15 No Hit TCCACCAAATTGTAATACAGAATCATCCCCAAAGATTTCGGTCAGAGCTG 6 0.15 No Hit TTTGTTTCTTTTTATTTAGACCTTCTTCATATTTAGTTTTATCTATTAAT 5 0.125 No Hit TCTTCGTATTTAGTTTTATCTATTAATCGATAGTATCTACCGGCGCGAAC 5 0.125 No Hit TGGGGTTGAAAAATAGAAAACTCAAAGCAATGTCAGAGTTGACAAAACTG 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 0.05 0.0 0.0 0.0 0.0 7 0.05 0.0 0.0 0.0 0.0 8 0.05 0.0 0.0 0.0 0.0 9 0.05 0.0 0.0 0.0 0.0 10-11 0.075 0.0 0.0 0.0 0.0 12-13 0.075 0.0 0.0 0.0 0.0 14-15 0.0875 0.0 0.0 0.0 0.0 16-17 0.1 0.0 0.0 0.0 0.0 18-19 0.1 0.0 0.0 0.0 0.0 20-21 0.1 0.0 0.0 0.0 0.0 22-23 0.1 0.0 0.0 0.0 0.0 24-25 0.1 0.0 0.0 0.0 0.0 26-27 0.1125 0.0 0.0 0.0 0.0 28-29 0.125 0.0 0.0 0.0 0.0 30-31 0.125 0.0 0.0 0.0 0.0 32-33 0.15 0.0 0.0 0.0 0.0 34-35 0.175 0.0 0.0 0.0 0.0 36-37 0.25 0.0 0.0 0.0 0.0 38-39 0.30000000000000004 0.0 0.0 0.0 0.0 40-41 0.375 0.0 0.0 0.0 0.0 42-43 0.475 0.0 0.0 0.0 0.0 44-45 0.5875 0.0 0.0 0.0 0.0 46-47 0.7 0.0 0.0 0.0 0.0 48-49 0.7375 0.0 0.0 0.0 0.0 50-51 0.7875 0.0 0.0 0.0 0.0 52-53 0.9875 0.0 0.0 0.0 0.0 54-55 1.1375 0.0 0.0 0.0 0.0 56-57 1.25 0.0 0.0 0.0 0.0 58-59 1.4125 0.0 0.0 0.0 0.0 60-61 1.5625 0.0 0.0 0.0 0.0 62-63 1.75 0.0 0.0 0.0 0.0 64-65 1.875 0.0 0.0 0.0 0.0 66-67 2.025 0.0 0.0 0.0 0.0 68-69 2.225 0.0 0.0 0.0 0.0 70-71 2.3875 0.0 0.0 0.0 0.0 72-73 2.625 0.0 0.0 0.0 0.0 74-75 2.825 0.0 0.0 0.0 0.0 76-77 3.1875 0.0 0.0 0.0 0.0 78-79 3.475 0.0 0.0 0.0 0.0 80-81 3.9875 0.0 0.0 0.0 0.0 82-83 4.574999999999999 0.0 0.0 0.0 0.0 84-85 5.15 0.0 0.0 0.0 0.0 86-87 5.7 0.0 0.0 0.0 0.0 88-89 6.25 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position CAGCAAG 15 0.009957196 47.5 62-63 TGACAAA 15 0.009957196 47.5 40-41 GTCCTTG 15 0.009957196 47.5 90-91 GACAAAA 15 0.009957196 47.5 40-41 >>END_MODULE Read 1883846 spots for ERR3317452.sra Written 1883846 spots for ERR3317452.sra Read 1883846 spots for ERR3317452.sra Written 1883846 spots for ERR3317452.sra Read 1883846 spots for ERR3317452.sra Written 1883846 spots for ERR3317452.sra Read 1883846 spots for ERR3317452.sra Written 1883846 spots for ERR3317452.sra Read 1883846 spots for ERR3317452.sra Written 1883846 spots for ERR3317452.sra Read 1883846 spots for ERR3317452.sra Written 1883846 spots for ERR3317452.sra Read 1883846 spots for ERR3317452.sra Written 1883846 spots for ERR3317452.sra Read 1883846 spots for ERR3317452.sra Written 1883846 spots for ERR3317452.sra Read 1883846 spots for ERR3317452.sra Written 1883846 spots for ERR3317452.sra Read 1883852 spots for ERR3317452.sra Written 1883852 spots for ERR3317452.sra Read 1883846 spots for ERR3317452.sra Written 1883846 spots for ERR3317452.sra Read 1883846 spots for ERR3317452.sra Written 1883846 spots for ERR3317452.sra Read 1883846 spots for ERR3317452.sra Written 1883846 spots for ERR3317452.sra Read 1883846 spots for ERR3317452.sra Written 1883846 spots for ERR3317452.sra Read 1883846 spots for ERR3317452.sra Written 1883846 spots for ERR3317452.sra Read 1883846 spots for ERR3317452.sra Written 1883846 spots for ERR3317452.sra Read 1883846 spots for ERR3317452.sra Written 1883846 spots for ERR3317452.sra Read 1883846 spots for ERR3317452.sra Written 1883846 spots for ERR3317452.sra Read 1883846 spots for ERR3317452.sra Written 1883846 spots for ERR3317452.sra Read 1883846 spots for ERR3317452.sra Written 1883846 spots for ERR3317452.sra SRR ids: ['ERR3317452.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_q4xuv2hb ERR3317452.sra spots: 37676926 blocks: [[1, 1883846], [1883847, 3767692], [3767693, 5651538], [5651539, 7535384], [7535385, 9419230], [9419231, 11303076], [11303077, 13186922], [13186923, 15070768], [15070769, 16954614], [16954615, 18838460], [18838461, 20722306], [20722307, 22606152], [22606153, 24489998], [24489999, 26373844], [26373845, 28257690], [28257691, 30141536], [30141537, 32025382], [32025383, 33909228], [33909229, 35793074], [35793075, 37676926]] ERR3317452 file size 9066386 ERR3317452 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 ERR3317452 ERR3317452_1.fastq ERR3317452_2.fastq Input file: ERR3317452_1.fastq Paired file: ERR3317452_2.fastq trimmed: ERR3317452-trimmed-pair1.fastq, ERR3317452-trimmed-pair2.fastq Parameters used: -- 3' end adapter sequence (-x): AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -- paired 3' end adapter sequence (-y): AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA -- maximum error ratio allowed (-r): 0.100 -- maximum indel error ratio allowed (-d): 0.030 -- end quality threshold (-q): 10 -- minimum read length allowed after trimming (-l): 18 -- file format (-f): Sanger/Illumina 1.8+ FASTQ -- number of concurrent threads (-t): 20 Tue Dec 10 09:48:06 2024 >> started Tue Dec 10 09:48:50 2024 >> done (44.283s) 37676926 read pairs processed; of these: 271202 ( 0.72%) short read pairs filtered out after trimming by size control 638369 ( 1.69%) empty read pairs filtered out after trimming by size control 36767355 (97.59%) read pairs available; of these: 11109200 (30.21%) trimmed read pairs available after processing 25658155 (69.79%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 693 0.00% 19 773 0.00% 20 1111 0.00% 21 1230 0.00% 22 1562 0.00% 23 2118 0.01% 24 2682 0.01% 25 3235 0.01% 26 3680 0.01% 27 4335 0.01% 28 4537 0.01% 29 5249 0.01% 30 5776 0.02% 31 9106 0.02% 32 7336 0.02% 33 7975 0.02% 34 10196 0.03% 35 10341 0.03% 36 11222 0.03% 37 11697 0.03% 38 13472 0.04% 39 13871 0.04% 40 14918 0.04% 41 16417 0.04% 42 17765 0.05% 43 18638 0.05% 44 20399 0.06% 45 20947 0.06% 46 22328 0.06% 47 27182 0.07% 48 27270 0.07% 49 28132 0.08% 50 31250 0.08% 51 31287 0.09% 52 32106 0.09% 53 36560 0.10% 54 40216 0.11% 55 43120 0.12% 56 43035 0.12% 57 47194 0.13% 58 50452 0.14% 59 70208 0.19% 60 84101 0.23% 61 88363 0.24% 62 92915 0.25% 63 98937 0.27% 64 105254 0.29% 65 114379 0.31% 66 125128 0.34% 67 123858 0.34% 68 126083 0.34% 69 130419 0.35% 70 133633 0.36% 71 140872 0.38% 72 153337 0.42% 73 153326 0.42% 74 150693 0.41% 75 149275 0.41% 76 151291 0.41% 77 159949 0.44% 78 176227 0.48% 79 175120 0.48% 80 177798 0.48% 81 183726 0.50% 82 184329 0.50% 83 194734 0.53% 84 212003 0.58% 85 216415 0.59% 86 215648 0.59% 87 223521 0.61% 88 223677 0.61% 89 278298 0.76% 90 235319 0.64% 91 243711 0.66% 92 253238 0.69% 93 268756 0.73% 94 303785 0.83% 95 324212 0.88% 96 359682 0.98% 97 432791 1.18% 98 522189 1.42% 99 719647 1.96% 100 1930940 5.25% 101 25658155 69.79% 36767355 reads passed initial QC criterion=sequence-density sequence-density=0.72 sequence-density-rank=1 fanout-score=2.72 fanout-score-rank=17 prefix-density=0.77 prefix-fanout=2.5 sequence=AAGGAGCTGGAGGAGGTCAAGAAGGAGTACCC criterion=fanout-score sequence-density=0.15 sequence-density-rank=13 fanout-score=50.31 fanout-score-rank=1 prefix-density=0.64 prefix-fanout=12.1 sequence=TGCTGCTGCTAG criterion=sequence-density sequence-density=0.33 sequence-density-rank=1 fanout-score=2.29 fanout-score-rank=31 prefix-density=0.32 prefix-fanout=2.3 sequence=GTATTTAGCCTTGGACGGAGTCTACCGCCCGATTTGGGCTGCATTCCCAAACAACCCGACTCGTTGACGGCGCCTCGTGGGGCGACAGGGTCCGGGCCGGACG criterion=fanout-score sequence-density=0.01 sequence-density-rank=33 fanout-score=94.22 fanout-score-rank=1 prefix-density=0.81 prefix-fanout=1.4 sequence=TCTTTTCCTTTTTGTTTGTTTCGAGAAAGATATCGTCCGATTCTCCTTCTATTGATTCTTTTCCGATCGAGATGTATGGATCCATGTGTCTACATACCTAGATTCTGTTCATGGATTAACGAAAATGTGCAAGAGCTCTATTTGCCTCTGCCATTCTATGAGTCGCTTCCTTTTTGCGTATGGCACCCCCACTCCCTTTGGCAGCATCTACTAATTCGGAACTTAATTTGAAAGCCATATTTCGACCCGGACGCTTTTGGGATGCTTCTAATAACCAACGAATGGCAAGTGCTCTTCCTTGTTTAGATCCTATTTCAATCGGAACTTTCCGCGTCGATCCTTTTTTATTACGTCTTGTTTTTACTCCTATATTGGGAGTTACTCTACGTATTGCTTGACGTAAAACCAATAGTGGATTTGTTTCTGTCTTTTGTTGAATCTTTTTGACGGCTCGATAGAGAATTTGATAAGCCAATGATTTTTTTCCGTCTTTCATA ERR3317452 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 10 09:49:50 Started mapping on | Dec 10 09:49:51 Finished on | Dec 10 09:53:14 Mapping speed, Million of reads per hour | 652.03 Number of input reads | 36767355 Average input read length | 192 UNIQUE READS: Uniquely mapped reads number | 30003859 Uniquely mapped reads % | 81.60% Average mapped length | 191.53 Number of splices: Total | 15633152 Number of splices: Annotated (sjdb) | 14867188 Number of splices: GT/AG | 15410765 Number of splices: GC/AG | 196209 Number of splices: AT/AC | 11205 Number of splices: Non-canonical | 14973 Mismatch rate per base, % | 0.39% Deletion rate per base | 0.00% Deletion average length | 1.22 Insertion rate per base | 0.00% Insertion average length | 1.25 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 4054088 % of reads mapped to multiple loci | 11.03% Number of reads mapped to too many loci | 179220 % of reads mapped to too many loci | 0.49% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 3.66% % of reads unmapped: other | 3.22% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 2992223 2992223 2992223 N_multimapping 4054088 4054088 4054088 N_noFeature 1190008 2238516 28158688 N_ambiguous 1197028 506658 20661 UnstrandedReadsAssigned:27616823 PositiveStrandReadsAssigned:27258685 NegativeStrandReadsAssigned:1824510 Dataset is classified positive stranded MeadianReadLen=101 20thPercentileLength=100 echo kmer=95 ERR3317452 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: ERR3317452-trimmed-pair1.fastq ERR3317452-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 36,767,355 reads, 30,568,085 reads pseudoaligned [quant] estimated average fragment length: 191.445 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,152 rounds 52973 ERR3317452.ke.tsv 35125 ERR3317452.se.tsv 88098 total ==> ERR3317452.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 745.72 0 0 PNS24247 1044 853.555 17.4259 0.924498 PNS24249 1928 1737.55 39.5553 1.03088 PNS24246 1044 853.555 17.4259 0.924498 PNS24248 1044 853.555 17.4259 0.924498 PNS24244 1471 1280.55 292.167 10.3318 PNS24243 293 130.123 0 0 KQK14069 1603 1412.55 337.008 10.8038 KQK14071 474 290.246 0 0 ==> ERR3317452.se.tsv <== BRADI_1g14170v3 358 BRADI_1g53295v3 39 BRADI_1g59795v3 210 BRADI_1g07683v3 0 BRADI_1g00485v3 47 BRADI_1g20270v3 1792 BRADI_1g74790v3 720 BRADI_1g09890v3 14 BRADI_1g77505v3 442 BRADI_1g48960v3 2 ERR3317452 completed mapping pipeline successfully