Starting /dee2/code/volunteer_pipeline.sh SRR3473009 current disk space = 3089038499840 free memory = 1523236400 SRR3473009 SRAfilesize 001822f0122ed9cc4e5b2211732c9185 SRR3473009.sra SRR3473009.sra file validated SRR3473009 is single end SRR3473009 is conventional basespace SRR3473009 read1 length is 100 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR3473009_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 100 %GC 12 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 31.9 33.0 31.0 34.0 30.0 34.0 2 32.261 33.0 31.0 34.0 30.0 34.0 3 30.21725 33.0 31.0 34.0 23.0 34.0 4 34.99075 37.0 35.0 37.0 32.0 37.0 5 35.63775 37.0 35.0 37.0 33.0 37.0 6 35.9175 37.0 35.0 37.0 35.0 37.0 7 36.03575 37.0 35.0 37.0 35.0 37.0 8 35.9935 37.0 35.0 37.0 35.0 37.0 9 38.029 39.0 38.0 39.0 35.0 39.0 10-11 38.065749999999994 39.0 38.5 39.0 36.0 39.0 12-13 38.2465 39.0 39.0 39.0 37.0 39.0 14-15 39.703500000000005 41.0 40.0 41.0 37.0 41.0 16-17 39.578125 41.0 39.0 41.0 37.0 41.0 18-19 39.17525 40.5 39.0 41.0 36.0 41.0 20-21 38.36175 39.5 36.5 41.0 35.0 41.0 22-23 37.447500000000005 38.0 35.0 40.0 35.0 41.0 24-25 36.621375 35.0 35.0 40.0 34.0 41.0 26-27 36.456125 35.0 35.0 40.0 33.5 41.0 28-29 36.332125 35.0 35.0 39.5 33.0 41.0 30-31 36.187 35.0 35.0 39.5 33.0 41.0 32-33 36.346375 35.0 35.0 40.0 33.5 41.0 34-35 35.866875 35.0 35.0 39.5 33.0 41.0 36-37 35.890875 35.0 35.0 39.5 33.0 41.0 38-39 35.975375 35.0 35.0 40.0 33.0 41.0 40-41 36.302499999999995 35.0 35.0 40.0 33.0 41.0 42-43 35.929874999999996 35.0 35.0 40.0 33.0 41.0 44-45 35.69725 35.0 35.0 39.0 33.0 41.0 46-47 35.785250000000005 35.0 35.0 39.0 33.0 41.0 48-49 35.658500000000004 35.0 35.0 38.0 33.0 41.0 50-51 35.381125 35.0 35.0 36.0 33.0 40.5 52-53 35.337375 35.0 35.0 35.5 33.0 40.0 54-55 34.977875 35.0 35.0 35.0 33.0 40.5 56-57 34.64775 35.0 35.0 35.0 33.0 38.0 58-59 34.040375 35.0 35.0 35.0 33.0 35.0 60-61 33.761375 35.0 35.0 35.0 33.0 35.0 62-63 33.456875 35.0 35.0 35.0 32.0 35.0 64-65 33.48075 35.0 35.0 35.0 33.0 35.0 66-67 33.38775 35.0 35.0 35.0 33.0 35.0 68-69 33.2855 35.0 35.0 35.0 33.0 35.0 70-71 33.195625 35.0 35.0 35.0 31.0 35.0 72-73 32.895375 35.0 35.0 35.0 31.0 35.0 74-75 32.765 35.0 35.0 35.0 30.5 35.0 76-77 31.50475 34.0 32.0 35.0 26.0 35.0 78-79 32.283249999999995 35.0 33.5 35.0 29.0 35.0 80-81 32.2355 35.0 35.0 35.0 29.0 35.0 82-83 31.980874999999997 35.0 34.5 35.0 29.0 35.0 84-85 31.717 35.0 34.0 35.0 27.0 35.0 86-87 31.455624999999998 35.0 34.0 35.0 24.5 35.0 88-89 31.153375 35.0 33.0 35.0 17.5 35.0 90-91 30.689375 35.0 33.0 35.0 2.0 35.0 92-93 30.409125 35.0 33.0 35.0 2.0 35.0 94-95 30.12675 35.0 33.0 35.0 2.0 35.0 96-97 29.8465 35.0 33.0 35.0 2.0 35.0 98-99 29.48075 35.0 33.0 35.0 2.0 35.0 100 29.0555 35.0 33.0 35.0 2.0 35.0 >>END_MODULE >>Per tile sequence quality pass #Tile Base Mean 1101 1 0.7170953858472622 1101 2 0.5915073566209585 1101 3 3.1131268141327197 1101 4 1.5876038434591138 1101 5 0.9392953658292456 1101 6 0.5494945450905817 1101 7 0.27322089880892975 1101 8 -0.10239215293763948 1101 9 0.02304574116704572 1101 10-11 0.3097662896606934 1101 12-13 0.10926083475127513 1101 14-15 0.06085476929236222 1101 16-17 0.029639175257734962 1101 18-19 0.158405064558103 1101 20-21 -0.20629816835151615 1101 22-23 0.1698653788409601 1101 24-25 0.16239615654088624 1101 26-27 0.15802972675408 1101 28-29 0.20000500450405667 1101 30-31 0.1738314483034742 1101 32-33 0.15425132619357385 1101 34-35 0.20573516164547812 1101 36-37 0.08417575818236855 1101 38-39 -0.06248123310979281 1101 40-41 0.005892803523167345 1101 42-43 0.525885797217498 1101 44-45 0.10878540686617555 1101 46-47 0.39214042638374735 1101 48-49 0.40496446802121255 1101 50-51 0.29874386948253573 1101 52-53 0.4291487338604725 1101 54-55 0.4508807927134413 1101 56-57 0.2876338704834325 1101 58-59 0.29181263136823077 1101 60-61 0.2658017215493942 1101 62-63 0.2643879491542336 1101 64-65 0.030602542288058032 1101 66-67 0.29315133620258393 1101 68-69 0.32086377739965855 1101 70-71 0.39350415373836967 1101 72-73 0.2873336002402169 1101 74-75 0.04198778901010769 1101 76-77 -0.07917125412871684 1101 78-79 0.11356470823741915 1101 80-81 0.2673781403262936 1101 82-83 0.3745120608547694 1101 84-85 0.40017265538985214 1101 86-87 0.4715118606746067 1101 88-89 0.492205484936445 1101 90-91 0.7508007206485843 1101 92-93 0.9035256731057935 1101 94-95 0.7048718846962245 1101 96-97 0.7341482334100675 1101 98-99 0.9664448003202857 1101 100 0.862601341207089 1104 1 -0.7170953858472622 1104 2 -0.5915073566209585 1104 3 -3.113126814132716 1104 4 -1.5876038434591138 1104 5 -0.9392953658292456 1104 6 -0.5494945450905817 1104 7 -0.27322089880892975 1104 8 0.10239215293764659 1104 9 -0.023045741167052824 1104 10-11 -0.3097662896607005 1104 12-13 -0.10926083475127513 1104 14-15 -0.06085476929236222 1104 16-17 -0.029639175257734962 1104 18-19 -0.158405064558103 1104 20-21 0.20629816835151615 1104 22-23 -0.16986537884095299 1104 24-25 -0.16239615654088624 1104 26-27 -0.15802972675408 1104 28-29 -0.20000500450404957 1104 30-31 -0.1738314483034742 1104 32-33 -0.15425132619357385 1104 34-35 -0.20573516164548522 1104 36-37 -0.08417575818236855 1104 38-39 0.062481233109799916 1104 40-41 -0.005892803523167345 1104 42-43 -0.5258857972174908 1104 44-45 -0.10878540686618265 1104 46-47 -0.39214042638374735 1104 48-49 -0.40496446802121966 1104 50-51 -0.29874386948253573 1104 52-53 -0.4291487338604725 1104 54-55 -0.4508807927134413 1104 56-57 -0.2876338704834325 1104 58-59 -0.29181263136823077 1104 60-61 -0.2658017215493942 1104 62-63 -0.2643879491542407 1104 64-65 -0.030602542288058032 1104 66-67 -0.29315133620257683 1104 68-69 -0.32086377739965855 1104 70-71 -0.39350415373836256 1104 72-73 -0.2873336002402169 1104 74-75 -0.04198778901010769 1104 76-77 0.07917125412871329 1104 78-79 -0.11356470823741205 1104 80-81 -0.2673781403262936 1104 82-83 -0.3745120608547765 1104 84-85 -0.4001726553898486 1104 86-87 -0.4715118606746067 1104 88-89 -0.492205484936445 1104 90-91 -0.7508007206485843 1104 92-93 -0.903525673105797 1104 94-95 -0.7048718846962281 1104 96-97 -0.7341482334100675 1104 98-99 -0.9664448003202892 1104 100 -0.8626013412070854 >>END_MODULE >>Per sequence quality scores pass #Quality Count 16 2.0 17 4.0 18 4.0 19 15.0 20 16.0 21 22.0 22 21.0 23 38.0 24 39.0 25 46.0 26 37.0 27 65.0 28 56.0 29 89.0 30 90.0 31 116.0 32 129.0 33 163.0 34 268.0 35 1368.0 36 774.0 37 616.0 38 19.0 39 3.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 34.33962264150943 11.874213836477987 14.389937106918238 39.39622641509434 2 38.574999999999996 12.925 32.7 15.8 3 38.2 18.05 19.275000000000002 24.474999999999998 4 20.925 27.625 14.05 37.4 5 16.35408852213053 34.658664666166544 20.580145036259065 28.40710177544386 6 19.375 39.825 26.125 14.674999999999999 7 17.175 35.099999999999994 35.65 12.075 8 12.1 40.975 30.8 16.125 9 14.85 50.14999999999999 23.525 11.475 10-11 7.8125 70.025 16.662499999999998 5.5 12-13 7.425 56.2875 31.075000000000003 5.2124999999999995 14-15 14.325 56.574999999999996 20.0 9.1 16-17 8.0375 66.21249999999999 16.025 9.725 18-19 7.4624999999999995 59.62499999999999 24.075 8.8375 20-21 13.05 57.15 16.5875 13.212499999999999 22-23 8.575000000000001 58.3 21.6125 11.512500000000001 24-25 8.5 55.55 25.637500000000003 10.3125 26-27 13.5125 57.45 19.7 9.3375 28-29 13.0 58.037499999999994 25.900000000000002 3.0625 30-31 13.5625 57.16250000000001 25.587500000000002 3.6875 32-33 20.6125 49.975 24.7875 4.625 34-35 13.112499999999999 54.35 28.4125 4.125 36-37 10.75 54.862500000000004 31.175000000000004 3.2125 38-39 8.1625 46.650000000000006 37.6125 7.575 40-41 9.9625 47.175 38.3 4.5625 42-43 9.8 51.449999999999996 36.662499999999994 2.0875 44-45 9.425 45.324999999999996 42.35 2.9000000000000004 46-47 4.7375 45.4875 44.6875 5.0874999999999995 48-49 10.975 45.7375 42.575 0.7125 50-51 0.7250000000000001 45.637499999999996 53.025 0.6125 52-53 0.8999999999999999 45.6 52.862500000000004 0.6375 54-55 0.75 45.6875 52.87500000000001 0.6875 56-57 0.7625 45.5 52.97500000000001 0.7625 58-59 0.6875 45.637499999999996 52.93750000000001 0.7374999999999999 60-61 0.8999999999999999 45.45 52.887499999999996 0.7625 62-63 0.775 45.525 52.887499999999996 0.8125 64-65 0.9375 45.45 52.849999999999994 0.7625 66-67 0.8999999999999999 45.387499999999996 52.75 0.9625 68-69 0.8750000000000001 45.300000000000004 52.525 1.3 70-71 0.9249999999999999 45.1 52.887499999999996 1.0875 72-73 0.8625 45.025 52.849999999999994 1.2625000000000002 74-75 0.8375 44.925 52.837500000000006 1.4000000000000001 76-77 0.775 44.737500000000004 53.0 1.4874999999999998 78-79 0.8500000000000001 44.4375 52.912499999999994 1.7999999999999998 80-81 1.0375 43.8875 53.2125 1.8624999999999998 82-83 1.0999999999999999 43.824999999999996 52.925 2.15 84-85 1.5375 43.3875 53.2125 1.8624999999999998 86-87 1.4625000000000001 43.1875 52.9625 2.3875 88-89 1.5375 42.7875 53.325 2.35 90-91 1.6500000000000001 42.1875 53.525 2.6374999999999997 92-93 1.7500000000000002 41.9125 53.362500000000004 2.9749999999999996 94-95 2.1375 41.725 53.25 2.8875 96-97 2.0875 41.449999999999996 53.412499999999994 3.05 98-99 2.55 40.887499999999996 53.1375 3.4250000000000003 100 2.45 40.625 53.175 3.75 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 34.0 1 150.5 2 249.0 3 214.5 4 181.0 5 217.5 6 332.5 7 313.5 8 145.0 9 47.5 10 51.0 11 54.5 12 49.5 13 81.0 14 96.0 15 178.5 16 249.0 17 169.5 18 198.0 19 171.5 20 79.0 21 78.0 22 96.5 23 228.0 24 168.5 25 16.0 26 14.0 27 9.5 28 6.0 29 6.0 30 7.5 31 6.0 32 3.0 33 2.5 34 3.5 35 5.0 36 6.0 37 7.5 38 8.5 39 5.5 40 6.0 41 5.0 42 1.5 43 1.5 44 2.0 45 2.0 46 1.5 47 0.5 48 2.5 49 4.5 50 3.0 51 2.5 52 5.0 53 6.0 54 3.0 55 3.5 56 3.5 57 3.5 58 6.0 59 4.0 60 2.0 61 1.0 62 0.5 63 0.5 64 1.5 65 2.0 66 0.5 67 0.0 68 0.0 69 0.0 70 0.5 71 0.5 72 0.5 73 0.5 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 0.625 2 0.0 3 0.0 4 0.0 5 0.025 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 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 100 4000.0 >>END_MODULE >>Sequence Duplication Levels fail #Total Deduplicated Percentage 22.6 #Duplication Level Percentage of deduplicated Percentage of total 1 80.08849557522124 18.099999999999998 2 6.969026548672566 3.15 3 3.5398230088495577 2.4 4 1.3274336283185841 1.2 5 0.995575221238938 1.125 6 1.2168141592920354 1.6500000000000001 7 0.22123893805309736 0.35000000000000003 8 0.11061946902654868 0.2 9 0.33185840707964603 0.675 >10 2.9867256637168142 13.825000000000001 >50 1.3274336283185841 21.125 >100 0.8849557522123894 36.199999999999996 >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 CGGCCAGTGAATTGTAATACGACTCACTATAGGGAGATCTGTATGCTGGT 302 7.55 No Hit GTGAATTGTAATACGACTCACTATAGGGAGATCTGTATGCTGGTTTTTTT 210 5.25 No Hit GTCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 185 4.625 No Hit GCCGTCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 182 4.55 No Hit TGGCCGTCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 162 4.05 No Hit CAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 152 3.8 No Hit GGCCGTCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 151 3.775 No Hit CGGCCGTCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 104 2.6 No Hit CGTCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 94 2.35 No Hit CTGGCCGTCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 93 2.325 No Hit ATACGACTCACTATAGGGAGATCTGTATGCTGGTTTTTTTTTTTTTTTTT 85 2.125 No Hit GGCCAGTGAATTGTAATACGACTCACTATAGGGAGATCTGTATGCTGGTT 76 1.9 No Hit CCAGTGAATTGTAATACGACTCACTATAGGGAGATCTGTATGCTGGTTTT 73 1.825 No Hit TTGTAATACGACTCACTATAGGGAGATCTGTATGCTGGTTTTTTTTTTTT 73 1.825 No Hit GTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 66 1.6500000000000001 No Hit CGACTCACTATAGGGAGATCTGTATGCTGGTTTTTTTTTTTTTTTTTTTT 61 1.525 No Hit AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 60 1.5 No Hit CCGTCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 59 1.4749999999999999 No Hit CTCACTATAGGGAGATCTGTATGCTGGTTTTTTTTTTTTTTTTTTTTTTT 53 1.325 No Hit CTGGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 52 1.3 No Hit GAATTGTAATACGACTCACTATAGGGAGATCTGTATGCTGGTTTTTTTTT 50 1.25 No Hit TGTAATACGACTCACTATAGGGAGATCTGTATGCTGGTTTTTTTTTTTTT 45 1.125 No Hit AGTGAATTGTAATACGACTCACTATAGGGAGATCTGTATGCTGGTTTTTT 42 1.05 No Hit CGCCGTCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 36 0.8999999999999999 No Hit GCCAGTGAATTGTAATACGACTCACTATAGGGAGATCTGTATGCTGGTTT 31 0.775 No Hit AGGCCGTCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 24 0.6 No Hit AATAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 23 0.575 No Hit AATTGTAATACGACTCACTATAGGGAGATCTGTATGCTGGTTTTTTTTTT 22 0.5499999999999999 No Hit TACGACTCACTATAGGGAGATCTGTATGCTGGTTTTTTTTTTTTTTTTTT 22 0.5499999999999999 No Hit TCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 21 0.525 No Hit CAGTGAATTGTAATACGACTCACTATAGGGAGATCTGTATGCTGGTTTTT 20 0.5 No Hit ACTCACTATAGGGAGATCTGTATGCTGGTTTTTTTTTTTTTTTTTTTTTT 19 0.475 No Hit ATTGTAATACGACTCACTATAGGGAGATCTGTATGCTGGTTTTTTTTTTT 19 0.475 No Hit GTAATACGACTCACTATAGGGAGATCTGTATGCTGGTTTTTTTTTTTTTT 17 0.42500000000000004 No Hit GCTGGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 15 0.375 No Hit ACGACTCACTATAGGGAGATCTGTATGCTGGTTTTTTTTTTTTTTTTTTT 14 0.35000000000000003 No Hit AATACGACTCACTATAGGGAGATCTGTATGCTGGTTTTTTTTTTTTTTTT 14 0.35000000000000003 No Hit CGTCCAGTGAATTGTAATACGACTCACTATAGGGAGATCTGTATGCTGGT 14 0.35000000000000003 No Hit CTATAGGGAGATCTGTATGCTGGTTTTTTTTTTTTTTTTTTTTTTTTTTT 13 0.325 No Hit GTTAATTGTAATACGACTCACTATAGGGAGATCTGTATGCTGGTTTTTTT 13 0.325 No Hit GGGAGATCTGTATGCTGGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 13 0.325 No Hit GGTCGTCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 13 0.325 No Hit TGTCCGTCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 12 0.3 No Hit CATAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 11 0.27499999999999997 No Hit GCTGTCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 10 0.25 No Hit GTCGTCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 10 0.25 No Hit GGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 10 0.25 No Hit CTTGCCGTCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 9 0.22499999999999998 No Hit TGCCGTCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 9 0.22499999999999998 No Hit GGGCCGTCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 9 0.22499999999999998 No Hit GACTCACTATAGGGAGATCTGTATGCTGGTTTTTTTTTTTTTTTTTTTTT 8 0.2 No Hit TGGTCGTCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 7 0.17500000000000002 No Hit TCCGTCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 7 0.17500000000000002 No Hit TAGGGAGATCTGTATGCTGGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 6 0.15 No Hit CTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 6 0.15 No Hit CGGCCAGTGAATTGTAATACGACTCACTATAGGGAATCTGTATGCTGGTT 6 0.15 No Hit GTTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 6 0.15 No Hit CTGGTCGTCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 6 0.15 No Hit CGGGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 6 0.15 No Hit CCTGTGAATTGTAATACGACTCACTATAGGGAGATCTGTATGCTGGTTTT 6 0.15 No Hit CGTCCGTCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 6 0.15 No Hit TTTGGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 6 0.15 No Hit TGGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 6 0.15 No Hit ATTCGACTCACTATAGGGAGATCTGTATGCTGGTTTTTTTTTTTTTTTTT 6 0.15 No Hit ATAGGGAGATCTGTATGCTGGTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 5 0.125 No Hit CCTGGCCGTCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 5 0.125 No Hit TAATACGACTCACTATAGGGAGATCTGTATGCTGGTTTTTTTTTTTTTTT 5 0.125 No Hit CACTATAGGGAGATCTGTATGCTGGTTTTTTTTTTTTTTTTTTTTTTTTT 5 0.125 No Hit CGGCCAGTGAATTGTAATACGACTCACTATAGGAGATCTGTATGCTGGTT 5 0.125 No Hit GAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 5 0.125 No Hit CGGGCCGTCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 5 0.125 No Hit TTTTAATACGACTCACTATAGGGAGATCTGTATGCTGGTTTTTTTTTTTT 5 0.125 No Hit NAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 5 0.125 No Hit >>END_MODULE >>Adapter Content pass #Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence SOLID Small RNA Adapter 1 0.0 0.0 0.0 0.0 0.0 2 0.0 0.0 0.0 0.0 0.0 3 0.0 0.0 0.0 0.0 0.0 4 0.0 0.0 0.0 0.0 0.0 5 0.0 0.0 0.0 0.0 0.0 6 0.0 0.0 0.0 0.0 0.0 7 0.0 0.0 0.0 0.0 0.0 8 0.0 0.0 0.0 0.0 0.0 9 0.0 0.0 0.0 0.0 0.0 10-11 0.0 0.0 0.0 0.0 0.0 12-13 0.0 0.0 0.0 0.0 0.0 14-15 0.0 0.0 0.0 0.0 0.0 16-17 0.0 0.0 0.0 0.0 0.0 18-19 0.0 0.0 0.0 0.0 0.0 20-21 0.0 0.0 0.0 0.0 0.0 22-23 0.0 0.0 0.0 0.0 0.0 24-25 0.0 0.0 0.0 0.0 0.0 26-27 0.0 0.0 0.0 0.0 0.0 28-29 0.0 0.0 0.0 0.0 0.0 30-31 0.0 0.0 0.0 0.0 0.0 32-33 0.0 0.0 0.0 0.0 0.0 34-35 0.0 0.0 0.0 0.0 0.0 36-37 0.0 0.0 0.0 0.0 0.0 38-39 0.0 0.0 0.0 0.0 0.0 40-41 0.0 0.0 0.0 0.0 0.0 42-43 0.0 0.0 0.0 0.0 0.0 44-45 0.0 0.0 0.0 0.0 0.0 46-47 0.0 0.0 0.0 0.0 0.0 48-49 0.0 0.0 0.0 0.0 0.0 50-51 0.0 0.0 0.0 0.0 0.0 52-53 0.0 0.0 0.0 0.0 0.0 54-55 0.0 0.0 0.0 0.0 0.0 56-57 0.0 0.0 0.0 0.0 0.0 58-59 0.0 0.0 0.0 0.0 0.0 60-61 0.0 0.0 0.0 0.0 0.0 62-63 0.0 0.0 0.0 0.0 0.0 64-65 0.0 0.0 0.0 0.0 0.0 66-67 0.0 0.0 0.0 0.0 0.0 68-69 0.0 0.0 0.0 0.0 0.0 70-71 0.0 0.0 0.0 0.0 0.0 72-73 0.0 0.0 0.0 0.0 0.0 74-75 0.0 0.0 0.0 0.0 0.0 76-77 0.0 0.0 0.0 0.0 0.0 78-79 0.0 0.0 0.0 0.0 0.0 80-81 0.0 0.0 0.0 0.0 0.0 82-83 0.0 0.0 0.0 0.0 0.0 84-85 0.0 0.0 0.0 0.0 0.0 86-87 0.0 0.0 0.0 0.0 0.0 88 0.0 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content fail #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position CGGCCAG 30 9.30595E-9 95.17722 1 TAAAAAA 15 6.409497E-4 93.9875 3 ATAAAAA 15 6.409497E-4 93.9875 2 TGGCCGT 40 6.566552E-10 83.28006 1 GGCCAGT 40 7.505696E-8 70.49062 2 GGCCGTC 90 0.0 62.658337 2 GCCAGTG 45 1.6973536E-7 62.658337 3 GCCGTCA 105 0.0 53.70714 3 CCAGTGA 55 6.799037E-7 51.265907 4 CCGTCAA 120 0.0 50.909897 4 CGTCAAA 135 0.0 45.25324 5 GTCAAAA 140 0.0 43.637054 6 TCAAAAA 140 0.0 43.637054 7 CAGTGAA 65 2.1524083E-6 43.378845 5 AGTGAAT 70 3.5853282E-6 40.280357 6 GAATTGT 80 8.976271E-6 35.24531 9 GTGAATT 80 8.976271E-6 35.24531 7 TGAATTG 80 8.976271E-6 35.24531 8 CAAAAAA 180 0.0 33.939934 8 ATTGTAA 90 4.6030527E-6 20.886112 10-11 >>END_MODULE Read 704934 spots for SRR3473009.sra Written 704934 spots for SRR3473009.sra Read 704934 spots for SRR3473009.sra Written 704934 spots for SRR3473009.sra Read 704934 spots for SRR3473009.sra Written 704934 spots for SRR3473009.sra Read 704934 spots for SRR3473009.sra Written 704934 spots for SRR3473009.sra Read 704934 spots for SRR3473009.sra Written 704934 spots for SRR3473009.sra Read 704934 spots for SRR3473009.sra Written 704934 spots for SRR3473009.sra Read 704934 spots for SRR3473009.sra Written 704934 spots for SRR3473009.sra Read 704934 spots for SRR3473009.sra Written 704934 spots for SRR3473009.sra Read 704934 spots for SRR3473009.sra Written 704934 spots for SRR3473009.sra Read 704934 spots for SRR3473009.sra Written 704934 spots for SRR3473009.sra Read 704934 spots for SRR3473009.sra Written 704934 spots for SRR3473009.sra Read 704934 spots for SRR3473009.sra Written 704934 spots for SRR3473009.sra Read 704934 spots for SRR3473009.sra Written 704934 spots for SRR3473009.sra Read 704934 spots for SRR3473009.sra Written 704934 spots for SRR3473009.sra Read 704938 spots for SRR3473009.sra Written 704938 spots for SRR3473009.sra Read 704934 spots for SRR3473009.sra Written 704934 spots for SRR3473009.sra Read 704934 spots for SRR3473009.sra Written 704934 spots for SRR3473009.sra Read 704934 spots for SRR3473009.sra Written 704934 spots for SRR3473009.sra Read 704934 spots for SRR3473009.sra Written 704934 spots for SRR3473009.sra Read 704934 spots for SRR3473009.sra Written 704934 spots for SRR3473009.sra SRR ids: ['SRR3473009.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_gg6tl_hs SRR3473009.sra spots: 14098684 blocks: [[1, 704934], [704935, 1409868], [1409869, 2114802], [2114803, 2819736], [2819737, 3524670], [3524671, 4229604], [4229605, 4934538], [4934539, 5639472], [5639473, 6344406], [6344407, 7049340], [7049341, 7754274], [7754275, 8459208], [8459209, 9164142], [9164143, 9869076], [9869077, 10574010], [10574011, 11278944], [11278945, 11983878], [11983879, 12688812], [12688813, 13393746], [13393747, 14098684]] SRR3473009 file size 3672011 SRR3473009 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 SRR3473009 SRR3473009_1.fastq Input file: SRR3473009_1.fastq trimmed: SRR3473009-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 Feb 14 01:04:50 2025 >> started Fri Feb 14 01:04:58 2025 >> done (7.339s) 14098684 reads processed; of these: 0 ( 0.00%) short reads filtered out after trimming by size control 0 ( 0.00%) empty reads filtered out after trimming by size control 14098684 (100.00%) reads available; of these: 2334670 (16.56%) trimmed reads available after processing 11764014 (83.44%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 47 1 0.00% 48 0 0.00% 49 0 0.00% 50 0 0.00% 51 10939 0.08% 52 13907 0.10% 53 15625 0.11% 54 16980 0.12% 55 18806 0.13% 56 21091 0.15% 57 22097 0.16% 58 23469 0.17% 59 24816 0.18% 60 27427 0.19% 61 28913 0.21% 62 29367 0.21% 63 31126 0.22% 64 33690 0.24% 65 36470 0.26% 66 37280 0.26% 67 39321 0.28% 68 38230 0.27% 69 41183 0.29% 70 42198 0.30% 71 44659 0.32% 72 45371 0.32% 73 47026 0.33% 74 49792 0.35% 75 55684 0.39% 76 39206 0.28% 77 47110 0.33% 78 52730 0.37% 79 53383 0.38% 80 55032 0.39% 81 57741 0.41% 82 61785 0.44% 83 60867 0.43% 84 60227 0.43% 85 66257 0.47% 86 66226 0.47% 87 65784 0.47% 88 69154 0.49% 89 69346 0.49% 90 72682 0.52% 91 74757 0.53% 92 73361 0.52% 93 77078 0.55% 94 78405 0.56% 95 78225 0.55% 96 77509 0.55% 97 73816 0.52% 98 61633 0.44% 99 46888 0.33% 100 11764014 83.44% 14098684 reads passed initial QC criterion=sequence-density sequence-density=0.87 sequence-density-rank=1 fanout-score=42.96 fanout-score-rank=23 prefix-density=35.55 prefix-fanout=1.1 sequence=CTCACTATAGGAGATCTGTA criterion=fanout-score sequence-density=0.01 sequence-density-rank=34 fanout-score=2224.11 fanout-score-rank=1 prefix-density=16.69 prefix-fanout=1.1 sequence=GAATTGTAATATGACTCACTATA Started job on | Feb 14 01:05:36 Started mapping on | Feb 14 01:05:36 Finished on | Feb 14 01:07:12 Mapping speed, Million of reads per hour | 528.70 Number of input reads | 14098684 Average input read length | 92 UNIQUE READS: Uniquely mapped reads number | 6231215 Uniquely mapped reads % | 44.20% Average mapped length | 91.32 Number of splices: Total | 56223 Number of splices: Annotated (sjdb) | 8633 Number of splices: GT/AG | 51448 Number of splices: GC/AG | 417 Number of splices: AT/AC | 19 Number of splices: Non-canonical | 4339 Mismatch rate per base, % | 0.64% Deletion rate per base | 0.00% Deletion average length | 1.89 Insertion rate per base | 0.00% Insertion average length | 1.67 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 2241459 % of reads mapped to multiple loci | 15.90% Number of reads mapped to too many loci | 1443110 % of reads mapped to too many loci | 10.24% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 29.07% % of reads unmapped: other | 0.60% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 5626010 5626010 5626010 N_multimapping 2241459 2241459 2241459 N_noFeature 6066366 6133035 6162476 N_ambiguous 2918 540 317 UnstrandedReadsAssigned:161931 PositiveStrandReadsAssigned:97640 NegativeStrandReadsAssigned:68422 Dataset is classified unstranded MeadianReadLen=96 20thPercentileLength=96 echo kmer=91 SRR3473009 Starting Kallisto single end mapping to ensembl reference transcriptome. kmer=31 [quant] fragment length distribution is truncated gaussian with mean = 100, sd = 20 [index] k-mer length: 31 [index] number of targets: 52,400 [index] number of k-mers: 62,057,036 [index] number of equivalence classes: 130,681 [quant] running in single-end mode [quant] will process file 1: SRR3473009-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 14,098,684 reads, 13,015,471 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 817 rounds 52401 SRR3473009.ke.tsv 34699 SRR3473009.se.tsv 87100 total ==> SRR3473009.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1919 13 0.240053 Potri.005G024800.1.v4.1 1035 936 0 0 Potri.004G059700.1.v4.1 961 862 0 0 Potri.007G009000.2.v4.1 1416 1317 0 0 Potri.003G141000.2.v4.1 2943 2844 0 0 Potri.016G087400.1.v4.1 270 171 1 0.207226 Potri.015G069301.1.v4.1 564 465 0 0 Potri.010G195200.1.v4.1 1773 1674 11 0.23285 Potri.012G127500.1.v4.1 977 878 10 0.403594 ==> SRR3473009.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 60 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 0 Potri.001G212900.v4.1 0 Potri.001G182400.v4.1 0 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 0 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 0 SRR3473009 completed mapping pipeline successfully