Starting /dee2/code/volunteer_pipeline.sh SRR6941535 current disk space = 1551902965760 free memory = 1607240952 SRR6941535 SRAfilesize 0661609092333108e6ee32d2d3dc41fc SRR6941535.sra SRR6941535.sra file validated SRR6941535 is single end SRR6941535 is conventional basespace SRR6941535 read1 length is 101 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR6941535_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 48 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 33.19125 34.0 33.0 34.0 32.0 34.0 2 33.218 34.0 33.0 34.0 32.0 34.0 3 33.0295 34.0 33.0 34.0 31.0 34.0 4 33.221 34.0 33.0 34.0 32.0 34.0 5 33.16525 34.0 33.0 34.0 31.0 34.0 6 36.922 38.0 37.0 38.0 36.0 38.0 7 37.2425 38.0 38.0 38.0 36.0 38.0 8 37.453 38.0 38.0 38.0 37.0 38.0 9 37.53625 38.0 38.0 38.0 37.0 38.0 10-11 37.46575 38.0 38.0 38.0 37.0 38.0 12-13 37.398875000000004 38.0 38.0 38.0 37.0 38.0 14-15 37.421499999999995 38.0 38.0 38.0 37.0 38.0 16-17 35.913375 38.0 37.0 38.0 26.5 38.0 18-19 36.75725 38.0 37.5 38.0 33.5 38.0 20-21 36.130125 38.0 38.0 38.0 30.0 38.0 22-23 37.176875 38.0 38.0 38.0 36.5 38.0 24-25 37.317625 38.0 38.0 38.0 37.0 38.0 26-27 37.21625 38.0 38.0 38.0 37.0 38.0 28-29 37.2845 38.0 38.0 38.0 37.0 38.0 30-31 37.300625 38.0 38.0 38.0 37.0 38.0 32-33 37.113625 38.0 38.0 38.0 36.5 38.0 34-35 37.025000000000006 38.0 38.0 38.0 36.0 38.0 36-37 36.987 38.0 38.0 38.0 36.5 38.0 38-39 37.000625 38.0 38.0 38.0 36.0 38.0 40-41 37.030625 38.0 38.0 38.0 36.0 38.0 42-43 36.97825 38.0 38.0 38.0 36.0 38.0 44-45 36.979 38.0 38.0 38.0 36.0 38.0 46-47 36.899125 38.0 38.0 38.0 35.5 38.0 48-49 37.078375 38.0 38.0 38.0 36.5 38.0 50-51 36.83925 38.0 38.0 38.0 35.5 38.0 52-53 36.94675 38.0 38.0 38.0 36.0 38.0 54-55 37.049625 38.0 38.0 38.0 36.0 38.0 56-57 37.005624999999995 38.0 38.0 38.0 36.0 38.0 58-59 37.1285 38.0 38.0 38.0 37.0 38.0 60-61 37.120000000000005 38.0 38.0 38.0 37.0 38.0 62-63 36.912875 38.0 38.0 38.0 36.0 38.0 64-65 36.6185 38.0 37.5 38.0 34.5 38.0 66-67 36.330124999999995 38.0 37.5 38.0 32.5 38.0 68-69 36.5815 38.0 38.0 38.0 34.0 38.0 70-71 36.373125 38.0 37.5 38.0 33.5 38.0 72-73 36.039375 38.0 37.0 38.0 32.0 38.0 74-75 35.638875 38.0 37.0 38.0 29.5 38.0 76-77 35.72825 38.0 37.0 38.0 31.5 38.0 78-79 36.06875 38.0 37.5 38.0 33.5 38.0 80-81 36.38725 38.0 38.0 38.0 34.5 38.0 82-83 36.413250000000005 38.0 38.0 38.0 35.0 38.0 84-85 36.407125 38.0 38.0 38.0 35.0 38.0 86-87 36.1325 38.0 38.0 38.0 34.0 38.0 88-89 36.1215 38.0 38.0 38.0 34.0 38.0 90-91 35.997125 38.0 38.0 38.0 34.0 38.0 92-93 35.770375 38.0 38.0 38.0 33.5 38.0 94-95 35.19825 38.0 37.5 38.0 30.5 38.0 96-97 33.294 38.0 35.5 38.0 19.0 38.0 98-99 31.096874999999997 38.0 33.0 38.0 2.0 38.0 100-101 28.187 38.0 24.0 38.0 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 3 1.0 4 0.0 5 0.0 6 0.0 7 1.0 8 0.0 9 1.0 10 1.0 11 0.0 12 1.0 13 0.0 14 0.0 15 1.0 16 0.0 17 2.0 18 1.0 19 2.0 20 1.0 21 5.0 22 1.0 23 2.0 24 2.0 25 10.0 26 18.0 27 39.0 28 33.0 29 32.0 30 48.0 31 46.0 32 79.0 33 108.0 34 188.0 35 416.0 36 796.0 37 2165.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 35.199999999999996 23.35 16.075 25.374999999999996 2 31.990995497748877 31.765882941470736 17.2336168084042 19.009504752376188 3 33.375 18.575 25.174999999999997 22.875 4 25.775 32.35 14.674999999999999 27.200000000000003 5 41.05 18.55 23.175 17.224999999999998 6 19.650000000000002 36.175000000000004 25.025 19.15 7 45.074999999999996 19.8 20.5 14.625 8 20.75 16.175 44.425 18.65 9 17.599999999999998 44.525 21.475 16.400000000000002 10-11 37.8125 25.75 19.112499999999997 17.325 12-13 18.8375 15.275 22.95 42.9375 14-15 20.45 38.3125 26.337500000000002 14.899999999999999 16-17 27.250000000000004 18.875 39.2375 14.637500000000001 18-19 39.85 21.4375 24.6125 14.099999999999998 20-21 15.6 26.825 37.4 20.175 22-23 32.0125 28.9 23.1125 15.975 24-25 31.7125 30.125 21.65 16.5125 26-27 36.25 24.875 20.3375 18.5375 28-29 18.387500000000003 34.612500000000004 23.2375 23.7625 30-31 22.2625 11.924999999999999 41.85 23.962500000000002 32-33 29.099999999999998 13.65 30.312499999999996 26.937499999999996 34-35 36.1125 20.75 26.674999999999997 16.4625 36-37 38.7625 21.2625 28.025 11.95 38-39 23.8375 19.5875 35.5875 20.9875 40-41 22.75 14.762500000000001 26.8625 35.625 42-43 35.1875 22.525000000000002 19.625 22.662499999999998 44-45 52.1125 13.3125 15.937499999999998 18.637500000000003 46-47 32.0375 25.75 16.6875 25.525 48-49 23.425 24.5375 17.4625 34.575 50-51 26.474999999999998 28.212500000000002 8.1125 37.2 52-53 30.1875 41.5125 7.175 21.125 54-55 19.0 29.475 17.8875 33.637499999999996 56-57 12.5125 28.3625 13.175 45.95 58-59 13.212499999999999 19.225 16.75 50.81250000000001 60-61 18.3125 19.2125 23.200000000000003 39.275 62-63 12.55 19.475 18.7625 49.2125 64-65 9.9375 22.5125 22.162499999999998 45.387499999999996 66-67 13.8375 11.95 24.325 49.8875 68-69 20.0125 11.525 19.925 48.5375 70-71 13.575000000000001 19.3 30.662499999999998 36.4625 72-73 15.85 14.325 33.1875 36.6375 74-75 13.7625 10.7625 29.575000000000003 45.9 76-77 20.325 11.025 40.8125 27.8375 78-79 20.0625 10.174999999999999 40.8125 28.95 80-81 20.6625 10.3125 35.449999999999996 33.575 82-83 27.05 7.199999999999999 36.8375 28.9125 84-85 20.5625 7.3374999999999995 37.075 35.025 86-87 18.9625 13.05 41.0625 26.924999999999997 88-89 12.925 29.4875 37.1625 20.424999999999997 90-91 12.537499999999998 33.9375 33.6625 19.8625 92-93 16.725 40.5 26.8375 15.937499999999998 94-95 13.4 56.275 21.637500000000003 8.6875 96-97 9.4375 73.575 12.937499999999998 4.05 98-99 5.2749999999999995 86.2875 4.987500000000001 3.45 100-101 2.1624999999999996 90.675 3.325 3.8375 >>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 0.0 34 0.0 35 2.0 36 4.0 37 4.5 38 4.5 39 6.5 40 7.5 41 11.0 42 20.0 43 32.0 44 78.0 45 171.0 46 418.0 47 546.0 48 387.0 49 356.5 50 336.0 51 215.0 52 244.5 53 353.0 54 342.5 55 199.0 56 83.0 57 69.5 58 54.0 59 19.0 60 15.5 61 11.0 62 2.0 63 1.5 64 2.0 65 1.5 66 0.5 67 0.5 68 0.5 69 0.0 70 0.0 71 0.5 72 0.5 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 0.05 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 warn #Total Deduplicated Percentage 50.6 #Duplication Level Percentage of deduplicated Percentage of total 1 87.59881422924902 44.324999999999996 2 4.743083003952568 4.8 3 2.025691699604743 3.075 4 1.0375494071146245 2.1 5 0.7411067193675889 1.875 6 0.7905138339920948 2.4 7 0.3458498023715415 1.225 8 0.2964426877470355 1.2 9 0.14822134387351776 0.675 >10 1.7786561264822136 18.3 >50 0.3458498023715415 10.65 >100 0.14822134387351776 9.375 >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 GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGGAATTCTCGGGTGCC 150 3.75 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTTGGAATTCTCGGGTGCCAAG 116 2.9000000000000004 No Hit GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGATTTGGAATTCTCGGGTG 109 2.725 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTCTGGAATTCTCGGGTGCCAA 72 1.7999999999999998 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCTGGAATTCTCGGGTGCCA 70 1.7500000000000002 No Hit GAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAG 67 1.675 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTGGAATTCTCGGGTGCCAAGG 59 1.4749999999999999 Illumina Small RNA Adapter 2 (100% over 21bp) TGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAA 53 1.325 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTTGGAATTCTCGGGTGC 53 1.325 No Hit CTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCA 52 1.3 RNA PCR Primer, Index 1 (100% over 28bp) CATCGAGTAGACCTTGTTATTGTGAGAATTCTTGGAATTCTCGGGTGCCA 50 1.25 No Hit GCGAGCGTAGTTCAATGGTAAAACATCTCCTTTGGAATTCTCGGGTGCCA 49 1.225 No Hit GTCAGGATAGCTCAGTTGGTAGAGCAGAGGACTTGGAATTCTCGGGTGCC 44 1.0999999999999999 No Hit TCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACTC 41 1.0250000000000001 RNA PCR Primer, Index 1 (100% over 26bp) ATATTGGGTAGGTTGTGGTATTTCATTGCTTGGAATTCTCGGGTGCCAAG 38 0.95 No Hit TCGGACCAGGCTTCATTCCCCTGGAATTCTCGGGTGCCAAGGAACTCCAG 36 0.8999999999999999 RNA PCR Primer, Index 1 (100% over 29bp) TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCCGTCCATCTCGTATGC 35 0.8750000000000001 RNA PCR Primer, Index 16 (100% over 50bp) CATCGAGTAGACCTTGTTATTGTGAGAATATGGAATTCTCGGGTGCCAAG 27 0.675 No Hit GAAGATACGGGTTCGATTCCCGCCGCTCGCCCCATGGAATTCTCGGGTGC 26 0.65 No Hit AGAAGATACGGGTTCGATTCCCGCCGCTCGCCCCATGGAATTCTCGGGTG 23 0.575 No Hit TCCTCAGTAGCTCAGTGGTAGAGCGGTCGGCTTGGAATTCTCGGGTGCCA 23 0.575 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCCTGGAATTCTCGGGTGC 22 0.5499999999999999 No Hit ATATTGGGTAGGTTGTGGTATTTCATTGCTGGAATTCTCGGGTGCCAAGG 22 0.5499999999999999 Illumina Small RNA Adapter 2 (100% over 21bp) GTCAGGATAGCTCAGTTGGTAGAGCAGAGGACTGGAATTCTCGGGTGCCA 19 0.475 No Hit GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGATTGGAATTCTCGGGTGC 19 0.475 No Hit GCGAGCGTAGTTCAATGGTAAAACATCTCCTTGTGGAATTCTCGGGTGCC 16 0.4 No Hit GCGAGCGTAGTTCAATGGTAAAACATCTCCTTGCCAAGGATGGAATTCTC 14 0.35000000000000003 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTCTTAATGGAATTCTCGGGTG 14 0.35000000000000003 No Hit CAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCCAAGGAACTC 14 0.35000000000000003 RNA PCR Primer, Index 1 (100% over 26bp) CATCGAGTAGACCTTGTTATTGTGAGAATTATGGAATTCTCGGGTGCCAA 14 0.35000000000000003 No Hit TCCGTCGTAGTCTAGGTGGTTAGGATACTCTGGAATTCTCGGGTGCCAAG 13 0.325 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATGGAATTCTCGGGTGCCAAGGA 13 0.325 RNA PCR Primer, Index 1 (100% over 22bp) GGGATTGTAGTTCAATTGGTCAGAGCACCTGGAATTCTCGGGTGCCAAGG 13 0.325 Illumina Small RNA Adapter 2 (100% over 21bp) CACGACTCTCGGCAACGGATATCTCGGCTTGGAATTCTCGGGTGCCAAGG 13 0.325 Illumina Small RNA Adapter 2 (100% over 21bp) ACTTTGTATCGCGCGCATGACTTGGAATTCTCGGGTGCCAAGGAACTCCA 12 0.3 RNA PCR Primer, Index 1 (100% over 28bp) GCGAGCGTAGTTCAATGGTAAAACATCTCCTTGGAATTCTCGGGTGCCAA 12 0.3 No Hit GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGAATTCTCGGGTGCCAAGG 11 0.27499999999999997 Illumina Small RNA Adapter 2 (100% over 21bp) CGGTCGAGGGCACGCCTGCCTGGGCGTCACGCTGGAATTCTCGGGTGCCA 11 0.27499999999999997 No Hit AATATTGGGTAGGTTGTGGTATTTCATTGCTTGGAATTCTCGGGTGCCAA 11 0.27499999999999997 No Hit GGGTGTTTGGTCTAGTGGTATGATTCTCGCTTGGAATTCTCGGGTGCCAA 11 0.27499999999999997 No Hit TAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCAG 11 0.27499999999999997 RNA PCR Primer, Index 1 (100% over 29bp) CATCGAGTAGACCTTGTTATTGTGAGAATTCTTTGGAATTCTCGGGTGCC 11 0.27499999999999997 No Hit GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGATTGTGAATCTGGAATTC 11 0.27499999999999997 No Hit AGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGG 11 0.27499999999999997 Illumina Small RNA Adapter 2 (100% over 21bp) TTGACAGAAGAGAGTGAGCACTGGAATTCTCGGGTGCCAAGGAACTCCAG 11 0.27499999999999997 RNA PCR Primer, Index 1 (100% over 29bp) TCGCTTGGTGCAGATCGGGACTGGAATTCTCGGGTGCCAAGGAACTCCAG 11 0.27499999999999997 RNA PCR Primer, Index 1 (100% over 29bp) AACTTTGTATCGCGCGCATGACTTGGAATTCTCGGGTGCCAAGGAACTCC 9 0.22499999999999998 RNA PCR Primer, Index 1 (100% over 27bp) AAGATACGGGTTCGATTCCCGCCGCTCGCCCCATGGAATTCTCGGGTGCC 9 0.22499999999999998 No Hit ATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACT 9 0.22499999999999998 RNA PCR Primer, Index 1 (100% over 25bp) CATCGAGTAGACCTTGTTATTGTGAGAATAAATGGAATTCTCGGGTGCCA 8 0.2 No Hit GGAGAGATGGCTGAGTGGACTAAAGCGGCGGATTTGGAATTCTCGGGTGC 8 0.2 No Hit GACACGACTCTCGGCAACGGATATCTCTGGAATTCTCGGGTGCCAAGGAA 8 0.2 RNA PCR Primer, Index 1 (100% over 23bp) TGTCGTGCCAATTCAACATAAACCCTGGAATTCTCGGGTGCCAAGGAACT 8 0.2 RNA PCR Primer, Index 1 (100% over 25bp) CATCGAGTAGACCTTGTTATTGTGAGATGGAATTCTCGGGTGCCAAGGAA 8 0.2 RNA PCR Primer, Index 1 (100% over 23bp) GGTGGCTGTAGTTTAGTGGTGAGAATTCCACGTTTGGAATTCTCGGGTGC 8 0.2 No Hit GGGATTGTAGTTCAATTGGACAGAGCACCGCCCTGGAATTCTCGGGTGCC 7 0.17500000000000002 No Hit AGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCCAAGGAACTCC 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 27bp) TCGGACCAGGCTTCGATCCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 29bp) CATCGAGTAGACCTTGTTATTGTGAGAATTCAATGGAATTCTCGGGTGCC 7 0.17500000000000002 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTAATGGAATTCTCGGGTGCCA 7 0.17500000000000002 No Hit GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGATTGTGGAATTCTCGGGT 7 0.17500000000000002 No Hit CTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCA 7 0.17500000000000002 No Hit GGAGAGATGGCTGAGTGGACTAAAGCGGCGGATTGCTAATCTGGAATTCT 6 0.15 No Hit CACCATGCGCGGGTTCAATTCCCGTCGTTCGCCCCATGGAATTCTCGGGT 6 0.15 No Hit GACACGACTCTCGGCAACGGATATCTCGGCTTGGAATTCTCGGGTGCCAA 6 0.15 No Hit GACACGACTCTCGGCAACGGATATCTCGGCTGGAATTCTCGGGTGCCAAG 6 0.15 No Hit TTGTATCGCGCGCATGACTTGGAATTCTCGGGTGCCAAGGAACTCCAGTC 6 0.15 RNA PCR Primer, Index 1 (100% over 31bp) CATCGAGTAGACCTTGTTATTGTGAGAATTCTTAAAATGGAATTCTCGGG 6 0.15 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTCTTAATTGGAATTCTCGGGT 6 0.15 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTCTATGGAATTCTCGGGTGCC 6 0.15 No Hit AATATTGGGTAGGTTGTGGTATTTCATTGCTGGAATTCTCGGGTGCCAAG 6 0.15 No Hit GACACGACTCTCGGCAACGGATATCTGGAATTCTCGGGTGCCAAGGAACT 6 0.15 RNA PCR Primer, Index 1 (100% over 25bp) CATCGAGTAGACCTTGTTATTGTGAGAATTCTAATGGAATTCTCGGGTGC 6 0.15 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTAAATGGAATTCTCGGGTGCC 6 0.15 No Hit CACGACTCTCGGCAACGGATATCTCGTGGAATTCTCGGGTGCCAAGGAAC 6 0.15 RNA PCR Primer, Index 1 (100% over 24bp) TGTCGTGCCAATTCAACATAAACCCCTGGAATTCTCGGGTGCCAAGGAAC 6 0.15 RNA PCR Primer, Index 1 (100% over 24bp) GCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAA 6 0.15 RNA PCR Primer, Index 1 (100% over 23bp) ATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCCAAGGAA 6 0.15 RNA PCR Primer, Index 1 (100% over 23bp) GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTGGAATTCTCGGGTG 5 0.125 No Hit GACACGACTCTCGGCAACGGATATCTTGGAATTCTCGGGTGCCAAGGAAC 5 0.125 RNA PCR Primer, Index 1 (100% over 24bp) GGTGGCTGTAGTTTAGTGGTGAGAATTCCACGTTGTGGAATTCTCGGGTG 5 0.125 No Hit ATATTGGGTAGGTTGTGGTATTTCATTGCTATGGAATTCTCGGGTGCCAA 5 0.125 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGTGGAATTCTCGGGTGCCAAG 5 0.125 No Hit CAGCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTG 5 0.125 No Hit CATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAAC 5 0.125 RNA PCR Primer, Index 1 (100% over 24bp) GGGATTGTAGTTCAATTGGACAGAGCACCGCCTGGAATTCTCGGGTGCCA 5 0.125 No Hit GGGATTGTAGTTCAATGGGTCAGAGCACCGCCCTGGAATTCTCGGGTGCC 5 0.125 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTCAAGGCTGGAATTC 5 0.125 No Hit GTCAGGATAGCTCAGTTGGTAGAGCAGAGGACCTGGAATTCTCGGGTGCC 5 0.125 No Hit TGCAGCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGG 5 0.125 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTCTAAATGGAATTCTCGGGTG 5 0.125 No Hit CCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCCAAGGAACT 5 0.125 RNA PCR Primer, Index 1 (100% over 25bp) GGGATTGTAGTTCAATTGGTCAGAGCACCGCCATGGAATTCTCGGGTGCC 5 0.125 No Hit >>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 1.125 0.0 0.0 0.0 2 0.0 1.125 0.0 0.0 0.0 3 0.0 1.125 0.0 0.0 0.0 4 0.0 1.125 0.0 0.0 0.0 5 0.0 1.125 0.0 0.0 0.0 6 0.0 1.125 0.0 0.0 0.0 7 0.0 1.125 0.0 0.0 0.0 8 0.0 1.125 0.0 0.0 0.0 9 0.0 1.15 0.0 0.0 0.0 10-11 0.0 1.15 0.0 0.0 0.0 12-13 0.0 1.1875 0.0 0.0 0.0 14-15 0.0 1.2375 0.0 0.0 0.0 16-17 0.0 1.4125 0.0 0.0 0.0 18-19 0.0 1.8125 0.0 0.0 0.0 20-21 0.0 3.375 0.0 0.0 0.0 22-23 0.0 9.5875 0.0 0.0 0.0 24-25 0.0 20.475 0.0 0.0 0.0 26-27 0.0 30.9375 0.0 0.0 0.0 28-29 0.0 35.975 0.0 0.0 0.0 30-31 0.0 47.3625 0.0 0.0 0.0 32-33 0.0 63.775000000000006 0.0 0.0 0.0 34-35 0.0 81.17500000000001 0.0 0.0 0.0 36-37 0.0 91.2875 0.0 0.0 0.0 38-39 0.0 94.0625 0.0 0.0 0.0 40-41 0.0 95.13749999999999 0.0 0.0 0.0 42-43 0.0 96.475 0.0 0.0 0.0 44-45 0.0 97.15 0.0 0.0 0.0 46-47 0.0 97.3375 0.0 0.0 0.0 48-49 0.0 97.3875 0.0 0.0 0.0 50-51 0.0 97.425 0.0 0.0 0.0 52-53 0.0 97.425 0.0 0.0 0.0 54-55 0.0 97.425 0.0 0.0 0.0 56-57 0.0 97.425 0.0 0.0 0.0 58-59 0.0 97.425 0.0 0.0 0.0 60-61 0.0 97.425 0.0 0.0 0.0 62-63 0.0 97.425 0.0 0.0 0.0 64-65 0.0 97.425 0.0 0.0 0.0 66-67 0.0 97.425 0.0 0.0 0.0 68-69 0.0 97.425 0.0 0.0 0.0 70-71 0.0 97.425 0.0 0.0 0.0 72-73 0.0 97.425 0.0 0.0 0.0 74-75 0.0 97.425 0.0 0.0 0.0 76-77 0.0 97.425 0.0 0.0 0.0 78-79 0.0 97.45 0.0 0.0 0.0 80-81 0.0 97.475 0.0 0.0 0.0 82-83 0.0 97.475 0.0 0.0 0.0 84-85 0.0 97.475 0.0 0.0 0.0 86-87 0.0 97.475 0.0 0.0 0.0 88-89 0.0 97.475 0.0 0.0 0.0 >>END_MODULE >>Kmer Content fail #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TTGTAGT 40 5.456968E-12 95.00001 5 GGATTGT 40 5.456968E-12 95.00001 2 GATTGTA 40 5.456968E-12 95.00001 3 ATTGTAG 40 5.456968E-12 95.00001 4 TGTAGTT 40 5.456968E-12 95.00001 6 GGGATTG 40 5.456968E-12 95.00001 1 GGATGTA 30 9.458745E-9 95.0 4 GTAGACC 65 0.0 95.0 7 AGCTCAG 15 6.142176E-4 95.0 9 AGTAGAC 65 0.0 95.0 6 GATGTAG 30 9.458745E-9 95.0 5 TAGCTCA 15 6.142176E-4 95.0 8 TAGCCAA 30 9.458745E-9 95.0 9 CGGATGT 30 9.458745E-9 95.0 3 TAGTTCA 50 0.0 95.0 8 GAGTAGA 65 0.0 95.0 5 TGTAGCC 30 9.458745E-9 95.0 7 CGAGTAG 65 0.0 95.0 4 TGAGGCA 15 6.142176E-4 95.0 1 AGACCTT 65 0.0 95.0 9 >>END_MODULE Rejected 308545 READS because READLEN < 1 Read 308545 spots for SRR6941535.sra Written 308545 spots for SRR6941535.sra Rejected 308545 READS because READLEN < 1 Read 308545 spots for SRR6941535.sra Written 308545 spots for SRR6941535.sra Rejected 308545 READS because READLEN < 1 Read 308545 spots for SRR6941535.sra Written 308545 spots for SRR6941535.sra Rejected 308545 READS because READLEN < 1 Read 308545 spots for SRR6941535.sra Written 308545 spots for SRR6941535.sra Rejected 308545 READS because READLEN < 1 Read 308545 spots for SRR6941535.sra Written 308545 spots for SRR6941535.sra Rejected 308545 READS because READLEN < 1 Read 308545 spots for SRR6941535.sra Written 308545 spots for SRR6941535.sra Rejected 308545 READS because READLEN < 1 Read 308545 spots for SRR6941535.sra Written 308545 spots for SRR6941535.sra Rejected 308545 READS because READLEN < 1 Read 308545 spots for SRR6941535.sra Written 308545 spots for SRR6941535.sra Rejected 308545 READS because READLEN < 1 Read 308545 spots for SRR6941535.sra Written 308545 spots for SRR6941535.sra Rejected 308545 READS because READLEN < 1 Read 308545 spots for SRR6941535.sra Written 308545 spots for SRR6941535.sra Rejected 308553 READS because READLEN < 1 Read 308553 spots for SRR6941535.sra Written 308553 spots for SRR6941535.sra Rejected 308545 READS because READLEN < 1 Read 308545 spots for SRR6941535.sra Written 308545 spots for SRR6941535.sra Rejected 308545 READS because READLEN < 1 Read 308545 spots for SRR6941535.sra Written 308545 spots for SRR6941535.sra Rejected 308545 READS because READLEN < 1 Read 308545 spots for SRR6941535.sra Written 308545 spots for SRR6941535.sra Rejected 308545 READS because READLEN < 1 Read 308545 spots for SRR6941535.sra Written 308545 spots for SRR6941535.sra Rejected 308545 READS because READLEN < 1 Read 308545 spots for SRR6941535.sra Written 308545 spots for SRR6941535.sra Rejected 308545 READS because READLEN < 1 Read 308545 spots for SRR6941535.sra Written 308545 spots for SRR6941535.sra Rejected 308545 READS because READLEN < 1 Read 308545 spots for SRR6941535.sra Written 308545 spots for SRR6941535.sra Rejected 308545 READS because READLEN < 1 Read 308545 spots for SRR6941535.sra Written 308545 spots for SRR6941535.sra Rejected 308545 READS because READLEN < 1 Read 308545 spots for SRR6941535.sra Written 308545 spots for SRR6941535.sra SRR ids: ['SRR6941535.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_kj7fyg0f SRR6941535.sra spots: 6170908 blocks: [[1, 308545], [308546, 617090], [617091, 925635], [925636, 1234180], [1234181, 1542725], [1542726, 1851270], [1851271, 2159815], [2159816, 2468360], [2468361, 2776905], [2776906, 3085450], [3085451, 3393995], [3393996, 3702540], [3702541, 4011085], [4011086, 4319630], [4319631, 4628175], [4628176, 4936720], [4936721, 5245265], [5245266, 5553810], [5553811, 5862355], [5862356, 6170908]] SRR6941535 file size 1474268 SRR6941535 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 SRR6941535 SRR6941535_1.fastq Input file: SRR6941535_1.fastq trimmed: SRR6941535-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 10:16:42 2024 >> started Fri Dec 6 10:16:46 2024 >> done (3.534s) 6170908 reads processed; of these: 139 ( 0.00%) short reads filtered out after trimming by size control 23 ( 0.00%) empty reads filtered out after trimming by size control 6170746 (100.00%) reads available; of these: 1119007 (18.13%) trimmed reads available after processing 5051739 (81.87%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 13 0.00% 19 13 0.00% 20 13 0.00% 21 26 0.00% 22 15 0.00% 23 22 0.00% 24 26 0.00% 25 24 0.00% 26 20 0.00% 27 30 0.00% 28 63 0.00% 29 78 0.00% 30 60 0.00% 31 45 0.00% 32 81 0.00% 33 105 0.00% 34 135 0.00% 35 147 0.00% 36 155 0.00% 37 120 0.00% 38 123 0.00% 39 111 0.00% 40 94 0.00% 41 87 0.00% 42 77 0.00% 43 81 0.00% 44 54 0.00% 45 89 0.00% 46 81 0.00% 47 80 0.00% 48 58 0.00% 49 61 0.00% 50 64 0.00% 51 80 0.00% 52 81 0.00% 53 83 0.00% 54 90 0.00% 55 86 0.00% 56 103 0.00% 57 103 0.00% 58 83 0.00% 59 115 0.00% 60 114 0.00% 61 122 0.00% 62 105 0.00% 63 104 0.00% 64 137 0.00% 65 174 0.00% 66 313 0.01% 67 376 0.01% 68 587 0.01% 69 621 0.01% 70 1058 0.02% 71 924 0.01% 72 1440 0.02% 73 3324 0.05% 74 18899 0.31% 75 10549 0.17% 76 3308 0.05% 77 1087 0.02% 78 1316 0.02% 79 1116 0.02% 80 1317 0.02% 81 1280 0.02% 82 1550 0.03% 83 2023 0.03% 84 3123 0.05% 85 3311 0.05% 86 3558 0.06% 87 3992 0.06% 88 4752 0.08% 89 6651 0.11% 90 9600 0.16% 91 14134 0.23% 92 18717 0.30% 93 32799 0.53% 94 53266 0.86% 95 115011 1.86% 96 112313 1.82% 97 123263 2.00% 98 220182 3.57% 99 226904 3.68% 100 112512 1.82% 101 5051739 81.87% 6170746 reads passed initial QC criterion=sequence-density sequence-density=97.44 sequence-density-rank=1 fanout-score=27.09 fanout-score-rank=3 prefix-density=96.85 prefix-fanout=27.1 sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCCGTCCATCTCGTATGCCGTCTTCTGCTTGAAAAAAA criterion=fanout-score sequence-density=0.01 sequence-density-rank=11 fanout-score=78.69 fanout-score-rank=1 prefix-density=0.50 prefix-fanout=1.0 sequence=CCATCGAGTAGACCTTGTTATTGTGAGAATT 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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCCGTCCATCTCGTATGCCGTCTTCTGCTTGAAAAAAA -o SRR6941535 - Input file: STDIN trimmed: SRR6941535-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCCGTCCATCTCGTATGCCGTCTTCTGCTTGA -- 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 10:17:05 2024 >> started Fri Dec 6 10:17:11 2024 >> done (6.839s) 6044813 reads processed; of these: 47536 ( 0.79%) short reads filtered out after trimming by size control 65480 ( 1.08%) empty reads filtered out after trimming by size control 5931797 (98.13%) reads available; of these: 5882949 (99.18%) trimmed reads available after processing 48848 ( 0.82%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 20501 0.35% 19 43461 0.73% 20 55644 0.94% 21 250399 4.22% 22 198857 3.35% 23 153660 2.59% 24 831092 14.01% 25 166413 2.81% 26 153951 2.60% 27 139487 2.35% 28 147128 2.48% 29 370711 6.25% 30 596680 10.06% 31 431825 7.28% 32 530887 8.95% 33 584139 9.85% 34 393297 6.63% 35 356563 6.01% 36 129053 2.18% 37 76765 1.29% 38 44056 0.74% 39 35625 0.60% 40 48817 0.82% 41 47521 0.80% 42 35300 0.60% 43 10202 0.17% 44 10181 0.17% 45 6617 0.11% 46 2913 0.05% 47 2719 0.05% 48 1245 0.02% 49 817 0.01% 50 459 0.01% 51 367 0.01% 52 239 0.00% 53 195 0.00% 54 179 0.00% 55 120 0.00% 56 95 0.00% 57 111 0.00% 58 73 0.00% 59 61 0.00% 60 54 0.00% 61 49 0.00% 62 61 0.00% 63 38 0.00% 64 37 0.00% 65 41 0.00% 66 53 0.00% 67 68 0.00% 68 99 0.00% 69 115 0.00% 70 103 0.00% 71 102 0.00% 72 88 0.00% 73 77 0.00% 74 115 0.00% 75 139 0.00% 76 201 0.00% 77 881 0.01% 78 120 0.00% 79 171 0.00% 80 1195 0.02% 81 335 0.01% 82 540 0.01% 83 446 0.01% 84 169 0.00% 85 160 0.00% 86 280 0.00% 87 391 0.01% 88 180 0.00% 89 175 0.00% 90 185 0.00% 91 335 0.01% 92 287 0.00% 93 309 0.01% 94 352 0.01% 95 495 0.01% 96 462 0.01% 97 528 0.01% 98 1012 0.02% 99 632 0.01% 100 743 0.01% 101 41549 0.70% criterion=sequence-density sequence-density=14.19 sequence-density-rank=1 fanout-score=0.00 fanout-score-rank=14 prefix-density=0.00 prefix-fanout=1.0 sequence=CATCGAGTAGACCTTGTTATTGTGAGAATTCTTAA criterion=fanout-score sequence-density=0.37 sequence-density-rank=12 fanout-score=37.36 fanout-score-rank=1 prefix-density=13.89 prefix-fanout=1.0 sequence=ATTGTGAGAATAAAAAA Started job on | Dec 06 10:17:25 Started mapping on | Dec 06 10:17:25 Finished on | Dec 06 10:17:45 Mapping speed, Million of reads per hour | 1090.39 Number of input reads | 6057730 Average input read length | 31 UNIQUE READS: Uniquely mapped reads number | 803291 Uniquely mapped reads % | 13.26% Average mapped length | 26.03 Number of splices: Total | 21239 Number of splices: Annotated (sjdb) | 3514 Number of splices: GT/AG | 20477 Number of splices: GC/AG | 623 Number of splices: AT/AC | 0 Number of splices: Non-canonical | 139 Mismatch rate per base, % | 0.98% Deletion rate per base | 0.01% Deletion average length | 1.31 Insertion rate per base | 0.00% Insertion average length | 1.32 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 3943806 % of reads mapped to multiple loci | 65.10% Number of reads mapped to too many loci | 1050354 % of reads mapped to too many loci | 17.34% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 3.70% % of reads unmapped: other | 0.60% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 1310633 1310633 1310633 N_multimapping 3943806 3943806 3943806 N_noFeature 517729 615639 701064 N_ambiguous 9487 4730 512 UnstrandedReadsAssigned:276075 PositiveStrandReadsAssigned:182922 NegativeStrandReadsAssigned:101715 Dataset is classified unstranded MeadianReadLen=30 20thPercentileLength=24 echo kmer=19 SRR6941535 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: SRR6941535-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 6,057,730 reads, 2,635,701 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 931 rounds 52973 SRR6941535.ke.tsv 35125 SRR6941535.se.tsv 88098 total ==> SRR6941535.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 0 0 PNS24243 293 194 3 2.61846 KQK14069 1603 1504 7.43883 0.837496 KQK14071 474 375 0 0 ==> SRR6941535.se.tsv <== BRADI_1g14170v3 20 BRADI_1g53295v3 2 BRADI_1g59795v3 0 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 2 BRADI_1g74790v3 5 BRADI_1g09890v3 15 BRADI_1g77505v3 0 BRADI_1g48960v3 0 SRR6941535 completed mapping pipeline successfully