Starting /dee2/code/volunteer_pipeline.sh SRR6941537 current disk space = 1551545425920 free memory = 1607238584 SRR6941537 SRAfilesize fd3d7145ada097b2492c4c67493c93c4 SRR6941537.sra SRR6941537.sra file validated SRR6941537 is single end SRR6941537 is conventional basespace SRR6941537 read1 length is 101 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR6941537_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 46 >>END_MODULE >>Per base sequence quality fail #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 33.256 34.0 33.0 34.0 32.0 34.0 2 33.3905 34.0 33.0 34.0 33.0 34.0 3 33.118 34.0 33.0 34.0 31.0 34.0 4 33.2445 34.0 33.0 34.0 32.0 34.0 5 33.266 34.0 33.0 34.0 33.0 34.0 6 37.03925 38.0 37.0 38.0 36.0 38.0 7 37.31575 38.0 38.0 38.0 37.0 38.0 8 37.50325 38.0 38.0 38.0 37.0 38.0 9 37.55425 38.0 38.0 38.0 38.0 38.0 10-11 37.508 38.0 38.0 38.0 37.5 38.0 12-13 37.4475 38.0 38.0 38.0 38.0 38.0 14-15 37.5095 38.0 38.0 38.0 38.0 38.0 16-17 36.1245 38.0 37.0 38.0 31.5 38.0 18-19 36.862125000000006 38.0 37.5 38.0 33.5 38.0 20-21 36.181625 38.0 38.0 38.0 31.0 38.0 22-23 37.254999999999995 38.0 38.0 38.0 36.5 38.0 24-25 37.481875 38.0 38.0 38.0 37.5 38.0 26-27 37.44725 38.0 38.0 38.0 37.5 38.0 28-29 37.451375 38.0 38.0 38.0 38.0 38.0 30-31 37.407375 38.0 38.0 38.0 37.5 38.0 32-33 37.310875 38.0 38.0 38.0 37.0 38.0 34-35 37.236 38.0 38.0 38.0 37.0 38.0 36-37 37.15375 38.0 38.0 38.0 36.5 38.0 38-39 37.121125000000006 38.0 38.0 38.0 36.5 38.0 40-41 37.105 38.0 38.0 38.0 37.0 38.0 42-43 37.102375 38.0 38.0 38.0 36.5 38.0 44-45 37.197625 38.0 38.0 38.0 37.0 38.0 46-47 37.093875 38.0 38.0 38.0 36.5 38.0 48-49 37.177125000000004 38.0 38.0 38.0 36.5 38.0 50-51 36.949375 38.0 38.0 38.0 36.0 38.0 52-53 37.003125 38.0 38.0 38.0 36.0 38.0 54-55 37.1315 38.0 38.0 38.0 36.5 38.0 56-57 37.068 38.0 38.0 38.0 36.0 38.0 58-59 37.19125 38.0 38.0 38.0 37.0 38.0 60-61 37.040875 38.0 38.0 38.0 36.5 38.0 62-63 36.600625 38.0 38.0 38.0 34.5 38.0 64-65 36.331 38.0 37.0 38.0 33.0 38.0 66-67 35.82475 38.0 37.0 38.0 31.0 38.0 68-69 36.662625 38.0 38.0 38.0 34.5 38.0 70-71 36.23125 38.0 37.5 38.0 32.0 38.0 72-73 35.8395 38.0 37.0 38.0 30.0 38.0 74-75 35.683125000000004 38.0 37.0 38.0 29.0 38.0 76-77 35.90975 38.0 37.0 38.0 31.0 38.0 78-79 36.31975 38.0 38.0 38.0 33.5 38.0 80-81 36.637375 38.0 38.0 38.0 35.5 38.0 82-83 36.580124999999995 38.0 38.0 38.0 35.0 38.0 84-85 36.560375 38.0 38.0 38.0 34.5 38.0 86-87 36.380375 38.0 38.0 38.0 34.0 38.0 88-89 36.317375 38.0 38.0 38.0 34.0 38.0 90-91 36.204750000000004 38.0 38.0 38.0 34.0 38.0 92-93 35.978875 38.0 38.0 38.0 34.0 38.0 94-95 35.258375 38.0 37.5 38.0 31.5 38.0 96-97 32.798500000000004 38.0 34.5 38.0 8.5 38.0 98-99 29.319625000000002 37.5 24.5 38.0 2.0 38.0 100-101 25.242625 35.5 2.0 38.0 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 12 1.0 13 0.0 14 0.0 15 1.0 16 1.0 17 0.0 18 2.0 19 2.0 20 3.0 21 2.0 22 2.0 23 0.0 24 2.0 25 11.0 26 14.0 27 28.0 28 30.0 29 30.0 30 34.0 31 43.0 32 79.0 33 116.0 34 247.0 35 488.0 36 922.0 37 1942.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 29.025000000000002 24.05 16.525000000000002 30.4 2 27.902902902902905 36.33633633633634 17.667667667667665 18.093093093093092 3 29.025000000000002 19.15 30.825000000000003 21.0 4 25.93148287071768 28.382095523880967 13.42835708927232 32.25806451612903 5 42.575 18.875 19.925 18.625 6 19.55 38.4 22.650000000000002 19.400000000000002 7 45.6 19.925 20.875 13.600000000000001 8 20.349999999999998 16.225 46.1 17.325 9 18.0 45.300000000000004 19.225 17.474999999999998 10-11 37.175000000000004 28.1 17.837500000000002 16.8875 12-13 17.825 15.812499999999998 21.4 44.9625 14-15 19.3875 34.6625 31.35 14.6 16-17 28.487499999999997 18.0 38.9125 14.6 18-19 35.6625 23.3875 26.387500000000003 14.5625 20-21 14.799999999999999 25.087500000000002 40.8 19.3125 22-23 32.5125 25.8125 25.8625 15.812499999999998 24-25 31.65 29.812499999999996 24.075 14.4625 26-27 40.925 26.700000000000003 18.787499999999998 13.5875 28-29 15.012500000000001 39.6125 25.2125 20.1625 30-31 18.337500000000002 10.5 47.6875 23.474999999999998 32-33 31.362499999999997 11.737499999999999 30.362499999999997 26.5375 34-35 37.487500000000004 21.2625 23.925 17.325 36-37 41.4375 18.1375 27.750000000000004 12.675 38-39 24.725 17.7875 34.6625 22.825 40-41 23.7125 15.475 22.125 38.6875 42-43 36.1375 28.749999999999996 16.3625 18.75 44-45 52.21249999999999 16.037499999999998 14.3625 17.3875 46-47 27.150000000000002 30.375000000000004 14.799999999999999 27.675 48-49 19.6375 26.025 18.512500000000003 35.825 50-51 27.700000000000003 25.825 8.799999999999999 37.675 52-53 29.15 42.5875 7.6 20.6625 54-55 18.725 26.325 22.175 32.775 56-57 11.3 28.512500000000003 20.575 39.6125 58-59 22.225 17.150000000000002 31.525 29.099999999999998 60-61 16.45 17.525 38.1375 27.8875 62-63 23.1375 19.5 22.287499999999998 35.075 64-65 16.0625 21.349999999999998 36.9125 25.674999999999997 66-67 16.375 9.275 44.3375 30.012499999999996 68-69 26.887499999999996 11.875 34.137499999999996 27.1 70-71 18.337500000000002 20.925 40.6875 20.05 72-73 23.8875 12.2875 35.8375 27.987499999999997 74-75 18.425 8.862499999999999 29.4125 43.3 76-77 22.1875 10.5625 44.7125 22.537499999999998 78-79 18.675 9.425 42.125 29.775000000000002 80-81 21.325 9.0625 34.1875 35.425000000000004 82-83 27.987499999999997 6.800000000000001 39.137499999999996 26.075 84-85 18.787499999999998 8.2875 38.7125 34.2125 86-87 19.25 16.3625 40.875 23.5125 88-89 13.6375 37.6375 30.4625 18.2625 90-91 10.487499999999999 43.125 28.825 17.5625 92-93 15.3625 48.449999999999996 23.375 12.812499999999998 94-95 11.0125 65.1875 16.8625 6.937500000000001 96-97 7.8875 78.2875 10.3875 3.4375000000000004 98-99 4.825 88.3125 4.425 2.4375 100-101 1.8624999999999998 89.1375 5.875 3.125 >>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 0.0 19 0.0 20 0.0 21 0.0 22 0.0 23 0.0 24 0.0 25 0.0 26 0.0 27 0.0 28 0.0 29 0.0 30 0.0 31 0.0 32 0.0 33 1.0 34 2.5 35 3.5 36 2.5 37 1.5 38 5.5 39 11.0 40 17.5 41 47.5 42 124.5 43 252.5 44 526.5 45 640.0 46 455.5 47 370.5 48 300.0 49 185.5 50 193.5 51 257.0 52 252.5 53 171.0 54 76.5 55 36.5 56 29.0 57 12.0 58 10.5 59 7.0 60 1.5 61 1.5 62 0.5 63 0.5 64 0.0 65 1.0 66 1.5 67 0.5 68 0.0 69 0.0 70 0.0 71 0.0 72 0.0 73 0.0 74 0.0 75 0.0 76 0.0 77 0.0 78 0.0 79 0.0 80 0.0 81 0.0 82 0.0 83 0.0 84 0.0 85 0.0 86 0.0 87 0.0 88 0.0 89 0.0 90 0.0 91 0.0 92 0.0 93 0.0 94 0.0 95 0.0 96 0.0 97 0.0 98 0.0 99 0.0 100 0.0 >>END_MODULE >>Per base N content pass #Base N-Count 1 0.0 2 0.1 3 0.0 4 0.025 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 warn #Total Deduplicated Percentage 50.64999999999999 #Duplication Level Percentage of deduplicated Percentage of total 1 88.45014807502469 44.800000000000004 2 4.1954590325765055 4.25 3 2.023692003948667 3.075 4 1.1846001974333662 2.4 5 0.7403751233958539 1.875 6 0.19743336623889435 0.6 7 0.3948667324777887 1.4000000000000001 8 0.24679170779861795 1.0 9 0.24679170779861795 1.125 >10 1.826258637709773 17.45 >50 0.3455083909180652 12.6 >100 0.14807502467917077 9.425 >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 CATCGAGTAGACCTTGTTATTGTGAGAATTTGGAATTCTCGGGTGCCAAG 141 3.5249999999999995 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGGAATTCTCGGGTGCC 133 3.325 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTGGAATTCTCGGGTGCCAAGG 103 2.5749999999999997 Illumina Small RNA Adapter 2 (100% over 21bp) CATCGAGTAGACCTTGTTATTGTGAGAATTCTGGAATTCTCGGGTGCCAA 95 2.375 No Hit CTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCA 82 2.0500000000000003 RNA PCR Primer, Index 1 (100% over 28bp) GAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAG 80 2.0 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTCTTGGAATTCTCGGGTGCCA 68 1.7000000000000002 No Hit GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGATTTGGAATTCTCGGGTG 66 1.6500000000000001 No Hit TCGGACCAGGCTTCATTCCCCTGGAATTCTCGGGTGCCAAGGAACTCCAG 61 1.525 RNA PCR Primer, Index 1 (100% over 29bp) TGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAA 52 1.3 No Hit TCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACTC 46 1.15 RNA PCR Primer, Index 1 (100% over 26bp) GGGATTGTAGTTCAATTGGTCAGAGCACCGCCTGGAATTCTCGGGTGCCA 39 0.975 No Hit CACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGAAGAACGTA 39 0.975 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTTGGAATTCTCGGGTGC 32 0.8 No Hit GTCAGGATAGCTCAGTTGGTAGAGCAGAGGACTTGGAATTCTCGGGTGCC 30 0.75 No Hit ATATTGGGTAGGTTGTGGTATTTCATTGCTTGGAATTCTCGGGTGCCAAG 30 0.75 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATATGGAATTCTCGGGTGCCAAG 30 0.75 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATGGAATTCTCGGGTGCCAAGGA 26 0.65 RNA PCR Primer, Index 1 (100% over 22bp) GCGAGCGTAGTTCAATGGTAAAACATCTCCTTTGGAATTCTCGGGTGCCA 26 0.65 No Hit TCCGTCGTAGTCTAGGTGGTTAGGATACTCTGGAATTCTCGGGTGCCAAG 25 0.625 No Hit GTCAGGATAGCTCAGTTGGTAGAGCAGAGGACTGGAATTCTCGGGTGCCA 23 0.575 No Hit ATATTGGGTAGGTTGTGGTATTTCATTGCTGGAATTCTCGGGTGCCAAGG 23 0.575 Illumina Small RNA Adapter 2 (100% over 21bp) GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCCTGGAATTCTCGGGTGC 21 0.525 No Hit TAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCAG 19 0.475 RNA PCR Primer, Index 1 (100% over 29bp) GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGAATTCTCGGGTGCCAAGG 16 0.4 Illumina Small RNA Adapter 2 (100% over 21bp) GGGTGTTTGGTCTAGTGGTATGATTCTCGCTTGGAATTCTCGGGTGCCAA 16 0.4 No Hit GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGATTGGAATTCTCGGGTGC 16 0.4 No Hit GGTGGCTGTAGTTTAGTGGTGAGAATTCCACGTTTGGAATTCTCGGGTGC 15 0.375 No Hit ACTTTGTATCGCGCGCATGACTTGGAATTCTCGGGTGCCAAGGAACTCCA 15 0.375 RNA PCR Primer, Index 1 (100% over 28bp) GGAGAGATGGCTGAGTGGACTAAAGCGGCGGATTTGGAATTCTCGGGTGC 14 0.35000000000000003 No Hit GACACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGAAGAACG 14 0.35000000000000003 No Hit TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTTTCGATCTCGTATGC 13 0.325 RNA PCR Primer, Index 21 (100% over 50bp) CATCGAGTAGACCTTGTTATTGTGAGAATTCTTAATGGAATTCTCGGGTG 13 0.325 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTATGGAATTCTCGGGTGCCAA 13 0.325 No Hit TGACAGAAGAGAGTGAGCACTGGAATTCTCGGGTGCCAAGGAACTCCAGT 12 0.3 RNA PCR Primer, Index 1 (100% over 30bp) TCCTCAGTAGCTCAGTGGTAGAGCGGTCGGCTTGGAATTCTCGGGTGCCA 12 0.3 No Hit AACTTTGTATCGCGCGCATGACTTGGAATTCTCGGGTGCCAAGGAACTCC 12 0.3 RNA PCR Primer, Index 1 (100% over 27bp) CATCGAGTAGACCTTGTTATTGTGAGATGGAATTCTCGGGTGCCAAGGAA 12 0.3 RNA PCR Primer, Index 1 (100% over 23bp) GCGAGCGTAGTTCAATGGTAAAACATCTCCTTGCCAAGGATGGAATTCTC 12 0.3 No Hit ATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACT 12 0.3 RNA PCR Primer, Index 1 (100% over 25bp) GAAGATACGGGTTCGATTCCCGCCGCTCGCCCCATGGAATTCTCGGGTGC 11 0.27499999999999997 No Hit CATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAAC 11 0.27499999999999997 RNA PCR Primer, Index 1 (100% over 24bp) GAACTTTGTATCGCGCGCATGACTTGGAATTCTCGGGTGCCAAGGAACTC 10 0.25 RNA PCR Primer, Index 1 (100% over 26bp) GGGATTGTAGTTCAATTGGTCAGAGCACCTGGAATTCTCGGGTGCCAAGG 10 0.25 Illumina Small RNA Adapter 2 (100% over 21bp) CATCGAGTAGACCTTGTTATTGTGAGAATTCTTTGGAATTCTCGGGTGCC 10 0.25 No Hit TTGACAGAAGAGAGTGAGCACTGGAATTCTCGGGTGCCAAGGAACTCCAG 10 0.25 RNA PCR Primer, Index 1 (100% over 29bp) GCGAGCGTAGTTCAATGGTAAAACATCTCCTTGGAATTCTCGGGTGCCAA 10 0.25 No Hit AGAAGATACGGGTTCGATTCCCGCCGCTCGCCCCATGGAATTCTCGGGTG 9 0.22499999999999998 No Hit CGGTCGAGGGCACGCCTGCCTGGGCGTCACGCTGGAATTCTCGGGTGCCA 9 0.22499999999999998 No Hit GCGAGCGTAGTTCAATGGTAAAACATCTCCTTGTGGAATTCTCGGGTGCC 9 0.22499999999999998 No Hit TGTCGTGCCAATTCAACATAAACCCCTGGAATTCTCGGGTGCCAAGGAAC 9 0.22499999999999998 RNA PCR Primer, Index 1 (100% over 24bp) AGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGG 9 0.22499999999999998 Illumina Small RNA Adapter 2 (100% over 21bp) AGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCCAAGGAACTCC 8 0.2 RNA PCR Primer, Index 1 (100% over 27bp) CATCGAGTAGACCTTGTTATTGTGAGAATTCTATGGAATTCTCGGGTGCC 8 0.2 No Hit TCGGACCAGGCTTCGATCCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG 8 0.2 RNA PCR Primer, Index 1 (100% over 29bp) CATCGAGTAGACCTTGTTATTGTGAGAATTCAATGGAATTCTCGGGTGCC 8 0.2 No Hit TCGCTTGGTGCAGATCGGGACTGGAATTCTCGGGTGCCAAGGAACTCCAG 8 0.2 RNA PCR Primer, Index 1 (100% over 29bp) CGAACTTTGTATCGCGCGCATGACTTGGAATTCTCGGGTGCCAAGGAACT 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 25bp) TGAAGCTGCCAGCATGATCTGATGGAATTCTCGGGTGCCAAGGAACTCCA 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 28bp) GGGGATGTAGCTCAGATGGTAGATGGAATTCTCGGGTGCCAAGGAACTCC 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 27bp) CATCGAGTAGACCTTGTTATTGTGAGAATTCTAATGGAATTCTCGGGTGC 7 0.17500000000000002 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTAATGGAATTCTCGGGTGCCA 7 0.17500000000000002 No Hit GGTGGCTGTAGTTTAGTGGTGAGAATTCCACGTTGTTGGAATTCTCGGGT 7 0.17500000000000002 No Hit GAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 33bp) GGGATTGTAGTTCAATTGGACAGAGCACCGCCTGGAATTCTCGGGTGCCA 7 0.17500000000000002 No Hit CACCATGCGCGGGTTCAATTCCCGTCGTTCGCCCCATGGAATTCTCGGGT 6 0.15 No Hit GGGGATATGGCGAAATCGGTAGACGCTACGGACTTTGGAATTCTCGGGTG 6 0.15 No Hit TTTGGATTGAAGGGAGCTCTGTGGAATTCTCGGGTGCCAAGGAACTCCAG 6 0.15 RNA PCR Primer, Index 1 (100% over 29bp) ACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCAGTC 6 0.15 RNA PCR Primer, Index 1 (100% over 31bp) CATCGAGTAGACCTTGTTATTGTGAGAATAAATGGAATTCTCGGGTGCCA 5 0.125 No Hit TCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCCAAGGAAC 5 0.125 RNA PCR Primer, Index 1 (100% over 24bp) CATCGAGTAGACCTTGTTATTGTGAGAATTCTTAAATGGAATTCTCGGGT 5 0.125 No Hit GACACGACTCTCGGCAACGGATATCTCGGCTTGGAATTCTCGGGTGCCAA 5 0.125 No Hit CATCGAGTAGACCTTGTTATTGTGAGAAATGGAATTCTCGGGTGCCAAGG 5 0.125 Illumina Small RNA Adapter 2 (100% over 21bp) ACGTCGCACGGATTCGTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC 5 0.125 RNA PCR Primer, Index 1 (100% over 33bp) CATCGAGTAGACCTTGTTAATGTGAGAATTCTGGAATTCTCGGGTGCCAA 5 0.125 No Hit TCTCATGGAGAGTTCGATCCTGGCTTGGAATTCTCGGGTGCCAAGGAACT 5 0.125 RNA PCR Primer, Index 1 (100% over 25bp) GGTAGTTCGACCGCGGAATTGGAATTCTCGGGTGCCAAGGAACTCCAGTC 5 0.125 RNA PCR Primer, Index 1 (100% over 31bp) CATCGAGTAGACCTTGTTATTGTGAGAATTAAATGGAATTCTCGGGTGCC 5 0.125 No Hit ACACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGAAGAACGT 5 0.125 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTCAAGGCTGGAATTC 5 0.125 No Hit CAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCCAAGGAACTC 5 0.125 RNA PCR Primer, Index 1 (100% over 26bp) CATCGAGTAGACCTTGTTATTGTGAGAATTCTAAATGGAATTCTCGGGTG 5 0.125 No Hit TGAACCTTGGGGAAAAGCCGCCTTGGAATTCTCGGGTGCCAAGGAACTCC 5 0.125 RNA PCR Primer, Index 1 (100% over 27bp) >>END_MODULE >>Adapter Content fail #Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence SOLID Small RNA Adapter 1 0.0 0.4 0.0 0.0 0.0 2 0.0 0.4 0.0 0.0 0.0 3 0.0 0.4 0.0 0.0 0.0 4 0.0 0.4 0.0 0.0 0.0 5 0.0 0.4 0.0 0.0 0.0 6 0.0 0.4 0.0 0.0 0.0 7 0.0 0.425 0.0 0.0 0.0 8 0.0 0.45 0.0 0.0 0.0 9 0.0 0.475 0.0 0.0 0.0 10-11 0.0 0.5 0.0 0.0 0.0 12-13 0.0 0.5875 0.0 0.0 0.0 14-15 0.0 0.6875 0.0 0.0 0.0 16-17 0.0 0.8625 0.0 0.0 0.0 18-19 0.0 1.6 0.0 0.0 0.0 20-21 0.0 3.1375 0.0 0.0 0.0 22-23 0.0 11.5125 0.0 0.0 0.0 24-25 0.0 25.75 0.0 0.0 0.0 26-27 0.0 38.85 0.0 0.0 0.0 28-29 0.0 42.7625 0.0 0.0 0.0 30-31 0.0 54.587500000000006 0.0 0.0 0.0 32-33 0.0 70.0125 0.0 0.0 0.0 34-35 0.0 83.3125 0.0 0.0 0.0 36-37 0.0 90.825 0.0 0.0 0.0 38-39 0.0 92.6125 0.0 0.0 0.0 40-41 0.0 93.3 0.0 0.0 0.0 42-43 0.0 94.01249999999999 0.0 0.0 0.0 44-45 0.0 94.2875 0.0 0.0 0.0 46-47 0.0 94.45 0.0 0.0 0.0 48-49 0.0 94.475 0.0 0.0 0.0 50-51 0.0 94.4875 0.0 0.0 0.0 52-53 0.0 94.5 0.0 0.0 0.0 54-55 0.0 94.5 0.0 0.0 0.0 56-57 0.0 94.5 0.0 0.0 0.0 58-59 0.0 94.5 0.0 0.0 0.0 60-61 0.0 94.5 0.0 0.0 0.0 62-63 0.0 94.5 0.0 0.0 0.0 64-65 0.0 94.5 0.0 0.0 0.0 66-67 0.0 94.5 0.0 0.0 0.0 68-69 0.0 94.5 0.0 0.0 0.0 70-71 0.0 94.525 0.0 0.0 0.0 72-73 0.0 94.525 0.0 0.0 0.0 74-75 0.0 94.5625 0.0 0.0 0.0 76-77 0.0 94.625 0.0 0.0 0.0 78-79 0.0 94.75 0.0 0.0 0.0 80-81 0.0 94.8375 0.0 0.0 0.0 82-83 0.0 95.01249999999999 0.0 0.0 0.0 84-85 0.0 95.1125 0.0 0.0 0.0 86-87 0.0 95.125 0.0 0.0 0.0 88-89 0.0 95.2125 0.0 0.0 0.0 >>END_MODULE >>Kmer Content fail #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GTAGACC 65 0.0 95.0 7 GTGCAGA 15 6.142176E-4 95.0 8 AGCTCAG 15 6.142176E-4 95.0 9 TTGTAGT 25 3.8289727E-7 95.0 5 AGTAGAC 65 0.0 95.0 6 TAGCTCA 15 6.142176E-4 95.0 8 TAGCCAA 30 9.458745E-9 95.0 9 GGCTGTA 15 6.142176E-4 95.0 4 TAGTTTA 15 6.142176E-4 95.0 9 CGGATGT 30 9.458745E-9 95.0 3 GCGGATG 30 9.458745E-9 95.0 2 GATTGTA 25 3.8289727E-7 95.0 3 CTTGGTG 15 6.142176E-4 95.0 4 GCTGTAG 15 6.142176E-4 95.0 5 GAGTAGA 65 0.0 95.0 5 ATTGTAG 25 3.8289727E-7 95.0 4 TGTAGCC 30 9.458745E-9 95.0 7 GGGATTG 25 3.8289727E-7 95.0 1 GCTTGGT 15 6.142176E-4 95.0 3 TTGGTGC 15 6.142176E-4 95.0 5 >>END_MODULE Rejected 288584 READS because READLEN < 1 Read 288584 spots for SRR6941537.sra Written 288584 spots for SRR6941537.sra Rejected 288584 READS because READLEN < 1 Read 288584 spots for SRR6941537.sra Written 288584 spots for SRR6941537.sra Rejected 288584 READS because READLEN < 1 Read 288584 spots for SRR6941537.sra Written 288584 spots for SRR6941537.sra Rejected 288584 READS because READLEN < 1 Read 288584 spots for SRR6941537.sra Written 288584 spots for SRR6941537.sra Rejected 288584 READS because READLEN < 1 Read 288584 spots for SRR6941537.sra Written 288584 spots for SRR6941537.sra Rejected 288584 READS because READLEN < 1 Read 288584 spots for SRR6941537.sra Written 288584 spots for SRR6941537.sra Rejected 288584 READS because READLEN < 1 Read 288584 spots for SRR6941537.sra Written 288584 spots for SRR6941537.sra Rejected 288584 READS because READLEN < 1 Read 288584 spots for SRR6941537.sra Written 288584 spots for SRR6941537.sra Rejected 288584 READS because READLEN < 1 Read 288584 spots for SRR6941537.sra Written 288584 spots for SRR6941537.sra Rejected 288584 READS because READLEN < 1 Read 288584 spots for SRR6941537.sra Written 288584 spots for SRR6941537.sra Rejected 288584 READS because READLEN < 1 Read 288584 spots for SRR6941537.sra Written 288584 spots for SRR6941537.sra Rejected 288584 READS because READLEN < 1 Read 288584 spots for SRR6941537.sra Written 288584 spots for SRR6941537.sra Rejected 288584 READS because READLEN < 1 Read 288584 spots for SRR6941537.sra Written 288584 spots for SRR6941537.sra Rejected 288584 READS because READLEN < 1 Read 288584 spots for SRR6941537.sra Written 288584 spots for SRR6941537.sra Rejected 288584 READS because READLEN < 1 Read 288584 spots for SRR6941537.sra Written 288584 spots for SRR6941537.sra Rejected 288584 READS because READLEN < 1 Read 288584 spots for SRR6941537.sra Written 288584 spots for SRR6941537.sra Rejected 288584 READS because READLEN < 1 Read 288584 spots for SRR6941537.sra Written 288584 spots for SRR6941537.sra Rejected 288584 READS because READLEN < 1 Read 288584 spots for SRR6941537.sra Written 288584 spots for SRR6941537.sra Rejected 288584 READS because READLEN < 1 Read 288584 spots for SRR6941537.sra Written 288584 spots for SRR6941537.sra Rejected 288584 READS because READLEN < 1 Read 288584 spots for SRR6941537.sra Written 288584 spots for SRR6941537.sra SRR ids: ['SRR6941537.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_boagrlx_ SRR6941537.sra spots: 5771680 blocks: [[1, 288584], [288585, 577168], [577169, 865752], [865753, 1154336], [1154337, 1442920], [1442921, 1731504], [1731505, 2020088], [2020089, 2308672], [2308673, 2597256], [2597257, 2885840], [2885841, 3174424], [3174425, 3463008], [3463009, 3751592], [3751593, 4040176], [4040177, 4328760], [4328761, 4617344], [4617345, 4905928], [4905929, 5194512], [5194513, 5483096], [5483097, 5771680]] SRR6941537 file size 1378750 SRR6941537 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 SRR6941537 SRR6941537_1.fastq Input file: SRR6941537_1.fastq trimmed: SRR6941537-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -- maximum error ratio allowed (-r): 0.100 -- maximum indel error ratio allowed (-d): 0.030 -- end quality threshold (-q): 10 -- minimum read length allowed after trimming (-l): 18 -- file format (-f): Sanger/Illumina 1.8+ FASTQ -- minimum overlap length for adapter detection (-k): inf -- number of concurrent threads (-t): 20 Fri Dec 6 10:31:32 2024 >> started Fri Dec 6 10:31:36 2024 >> done (3.814s) 5771680 reads processed; of these: 109 ( 0.00%) short reads filtered out after trimming by size control 21 ( 0.00%) empty reads filtered out after trimming by size control 5771550 (100.00%) reads available; of these: 1290582 (22.36%) trimmed reads available after processing 4480968 (77.64%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 5 0.00% 19 8 0.00% 20 12 0.00% 21 14 0.00% 22 18 0.00% 23 15 0.00% 24 17 0.00% 25 19 0.00% 26 18 0.00% 27 18 0.00% 28 28 0.00% 29 44 0.00% 30 56 0.00% 31 29 0.00% 32 50 0.00% 33 43 0.00% 34 47 0.00% 35 60 0.00% 36 44 0.00% 37 54 0.00% 38 58 0.00% 39 53 0.00% 40 65 0.00% 41 61 0.00% 42 84 0.00% 43 69 0.00% 44 75 0.00% 45 83 0.00% 46 102 0.00% 47 105 0.00% 48 75 0.00% 49 75 0.00% 50 73 0.00% 51 47 0.00% 52 74 0.00% 53 57 0.00% 54 52 0.00% 55 68 0.00% 56 90 0.00% 57 55 0.00% 58 75 0.00% 59 75 0.00% 60 94 0.00% 61 85 0.00% 62 98 0.00% 63 81 0.00% 64 83 0.00% 65 108 0.00% 66 128 0.00% 67 157 0.00% 68 271 0.00% 69 281 0.00% 70 511 0.01% 71 406 0.01% 72 675 0.01% 73 1733 0.03% 74 10117 0.18% 75 6283 0.11% 76 1751 0.03% 77 697 0.01% 78 1090 0.02% 79 1031 0.02% 80 1098 0.02% 81 1115 0.02% 82 1399 0.02% 83 1726 0.03% 84 2997 0.05% 85 3484 0.06% 86 4151 0.07% 87 4839 0.08% 88 5797 0.10% 89 8342 0.14% 90 11738 0.20% 91 18342 0.32% 92 22087 0.38% 93 37790 0.65% 94 60586 1.05% 95 143033 2.48% 96 139573 2.42% 97 153568 2.66% 98 259083 4.49% 99 273197 4.73% 100 108787 1.88% 101 4480968 77.64% 5771550 reads passed initial QC criterion=sequence-density sequence-density=95.63 sequence-density-rank=1 fanout-score=23.82 fanout-score-rank=2 prefix-density=95.61 prefix-fanout=23.8 sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTTTCGATCTCGTATGCCGTCTTCTGCTTGAAAAAA criterion=fanout-score sequence-density=3.73 sequence-density-rank=5 fanout-score=25.90 fanout-score-rank=1 prefix-density=95.64 prefix-fanout=1.0 sequence=CACGTTTCGATATCGTATGCCGT Potential 3prime adapter identified. Now checking if in reference sequence Warning: gzbuffer added in zlib v1.2.3.5. Unable to change buffer size from default of 8192. 1 reads; of these: 1 (100.00%) were unpaired; of these: 1 (100.00%) aligned 0 times 0 (0.00%) aligned exactly 1 time 0 (0.00%) aligned >1 times 0.00% overall alignment rate Adapter seq not found in reference. Now shuffling file before clipping skewer v0.2.2 [April 4, 2016] COMMAND LINE: skewer -f sanger -l 18 -t 20 -x TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTTTCGATCTCGTATGCCGTCTTCTGCTTGAAAAAA -o SRR6941537 - Input file: STDIN trimmed: SRR6941537-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTTTCGATCTCGTATGCCGTCTTCTGCTTGA -- maximum error ratio allowed (-r): 0.100 -- maximum indel error ratio allowed (-d): 0.030 -- minimum read length allowed after trimming (-l): 18 -- file format (-f): Sanger/Illumina 1.8+ FASTQ -- minimum overlap length for adapter detection (-k): 3 -- number of concurrent threads (-t): 20 Fri Dec 6 10:31:46 2024 >> started Fri Dec 6 10:31:54 2024 >> done (7.353s) 5651310 reads processed; of these: 76406 ( 1.35%) short reads filtered out after trimming by size control 33274 ( 0.59%) empty reads filtered out after trimming by size control 5541630 (98.06%) reads available; of these: 5400977 (97.46%) trimmed reads available after processing 140653 ( 2.54%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 23471 0.42% 19 55171 1.00% 20 69808 1.26% 21 333144 6.01% 22 261155 4.71% 23 162143 2.93% 24 1046687 18.89% 25 148626 2.68% 26 127767 2.31% 27 107140 1.93% 28 117395 2.12% 29 352588 6.36% 30 626094 11.30% 31 380366 6.86% 32 381402 6.88% 33 400820 7.23% 34 266466 4.81% 35 235864 4.26% 36 87569 1.58% 37 45575 0.82% 38 25845 0.47% 39 16927 0.31% 40 21952 0.40% 41 19841 0.36% 42 15523 0.28% 43 4150 0.07% 44 4897 0.09% 45 4421 0.08% 46 1471 0.03% 47 2306 0.04% 48 823 0.01% 49 435 0.01% 50 290 0.01% 51 274 0.00% 52 237 0.00% 53 226 0.00% 54 198 0.00% 55 207 0.00% 56 188 0.00% 57 338 0.01% 58 300 0.01% 59 211 0.00% 60 138 0.00% 61 134 0.00% 62 181 0.00% 63 130 0.00% 64 112 0.00% 65 104 0.00% 66 161 0.00% 67 144 0.00% 68 490 0.01% 69 498 0.01% 70 967 0.02% 71 501 0.01% 72 258 0.00% 73 369 0.01% 74 376 0.01% 75 793 0.01% 76 1297 0.02% 77 6883 0.12% 78 593 0.01% 79 1057 0.02% 80 9617 0.17% 81 3092 0.06% 82 5555 0.10% 83 4165 0.08% 84 898 0.02% 85 866 0.02% 86 1818 0.03% 87 3134 0.06% 88 1000 0.02% 89 670 0.01% 90 719 0.01% 91 2066 0.04% 92 1489 0.03% 93 773 0.01% 94 1012 0.02% 95 1691 0.03% 96 1361 0.02% 97 1260 0.02% 98 3210 0.06% 99 1317 0.02% 100 2607 0.05% 101 127813 2.31% criterion=sequence-density sequence-density=18.19 sequence-density-rank=1 fanout-score=0.00 fanout-score-rank=13 prefix-density=0.00 prefix-fanout=1.0 sequence=CATCGAGTAGACCTTGTTATTGTGAGAATTCTTAA criterion=fanout-score sequence-density=0.13 sequence-density-rank=26 fanout-score=135.65 fanout-score-rank=1 prefix-density=18.13 prefix-fanout=1.0 sequence=TATTGTGAGAAAAA Started job on | Dec 06 10:32:07 Started mapping on | Dec 06 10:32:07 Finished on | Dec 06 10:32:22 Mapping speed, Million of reads per hour | 1358.85 Number of input reads | 5661870 Average input read length | 32 UNIQUE READS: Uniquely mapped reads number | 947686 Uniquely mapped reads % | 16.74% Average mapped length | 27.21 Number of splices: Total | 23808 Number of splices: Annotated (sjdb) | 2078 Number of splices: GT/AG | 23026 Number of splices: GC/AG | 658 Number of splices: AT/AC | 6 Number of splices: Non-canonical | 118 Mismatch rate per base, % | 1.09% Deletion rate per base | 0.01% Deletion average length | 1.25 Insertion rate per base | 0.01% Insertion average length | 1.50 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 3649683 % of reads mapped to multiple loci | 64.46% Number of reads mapped to too many loci | 795348 % of reads mapped to too many loci | 14.05% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 3.96% % of reads unmapped: other | 0.79% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 1064501 1064501 1064501 N_multimapping 3649683 3649683 3649683 N_noFeature 638476 734656 846325 N_ambiguous 14235 8481 688 UnstrandedReadsAssigned:294975 PositiveStrandReadsAssigned:204549 NegativeStrandReadsAssigned:100673 Dataset is classified unstranded MeadianReadLen=29 20thPercentileLength=24 echo kmer=19 SRR6941537 Starting Kallisto single end mapping to ensembl reference transcriptome. kmer=19 [quant] fragment length distribution is truncated gaussian with mean = 100, sd = 20 [index] k-mer length: 19 [index] number of targets: 52,972 [index] number of k-mers: 65,492,969 [index] number of equivalence classes: 320,172 [quant] running in single-end mode [quant] will process file 1: SRR6941537-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 5,661,870 reads, 2,564,471 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 957 rounds 52973 SRR6941537.ke.tsv 35125 SRR6941537.se.tsv 88098 total ==> SRR6941537.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 837 0 0 PNS24247 1044 945 0 0 PNS24249 1928 1829 0 0 PNS24246 1044 945 0 0 PNS24248 1044 945 0 0 PNS24244 1471 1372 1 0.148727 PNS24243 293 194 0 0 KQK14069 1603 1504 7.23766 0.981964 KQK14071 474 375 0 0 ==> SRR6941537.se.tsv <== BRADI_1g14170v3 5 BRADI_1g53295v3 1 BRADI_1g59795v3 0 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 3 BRADI_1g74790v3 8 BRADI_1g09890v3 22 BRADI_1g77505v3 0 BRADI_1g48960v3 1 SRR6941537 completed mapping pipeline successfully