Starting /dee2/code/volunteer_pipeline.sh ERR6133483 current disk space = 1515892498432 free memory = 1564420936 ERR6133483 SRAfilesize e7dd7407625820e1ab5ae40131fb7d7a ERR6133483.sra ERR6133483.sra file validated ERR6133483 is single end ERR6133483 is conventional basespace ERR6133483 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133483_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 70-93 %GC 44 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 35.4975 37.0 33.0 37.0 33.0 37.0 2 36.404 37.0 37.0 37.0 37.0 37.0 3 35.86325 37.0 37.0 37.0 33.0 37.0 4 35.28175 37.0 37.0 37.0 33.0 37.0 5 35.2385 37.0 37.0 37.0 33.0 37.0 6 35.548 37.0 37.0 37.0 33.0 37.0 7 37.31875 37.0 37.0 40.0 33.0 40.0 8 37.354 37.0 37.0 40.0 33.0 40.0 9 37.36525 37.0 37.0 40.0 33.0 40.0 10-11 37.429875 37.0 37.0 40.0 33.0 40.0 12-13 37.323875 37.0 37.0 40.0 33.0 40.0 14-15 37.274625 37.0 37.0 40.0 33.0 40.0 16-17 37.195 37.0 37.0 40.0 33.0 40.0 18-19 37.03 37.0 37.0 40.0 33.0 40.0 20-21 36.69025 37.0 37.0 40.0 33.0 40.0 22-23 36.668499999999995 37.0 37.0 40.0 33.0 40.0 24-25 36.6215 37.0 37.0 40.0 33.0 40.0 26-27 36.84162499999999 37.0 37.0 40.0 33.0 40.0 28-29 36.881125 37.0 37.0 40.0 33.0 40.0 30-31 36.7 37.0 37.0 40.0 33.0 40.0 32-33 36.70575 37.0 37.0 40.0 33.0 40.0 34-35 36.713125000000005 37.0 37.0 40.0 33.0 40.0 36-37 36.5625 37.0 37.0 40.0 33.0 40.0 38-39 36.455375000000004 37.0 37.0 40.0 33.0 40.0 40-41 36.314625 37.0 37.0 40.0 33.0 40.0 42-43 36.21725 37.0 37.0 40.0 33.0 40.0 44-45 36.230625 37.0 37.0 40.0 33.0 40.0 46-47 36.14075 37.0 37.0 40.0 33.0 40.0 48-49 36.087125 37.0 37.0 38.5 33.0 40.0 50-51 35.9775 37.0 37.0 37.0 33.0 40.0 52-53 35.79475 37.0 35.0 37.0 33.0 40.0 54-55 35.658125 37.0 33.0 37.0 33.0 40.0 56-57 35.409625 37.0 33.0 37.0 33.0 40.0 58-59 34.348749999999995 37.0 33.0 37.0 27.0 37.0 60-61 34.717 37.0 33.0 37.0 30.0 37.0 62-63 34.737375 37.0 33.0 37.0 33.0 37.0 64-65 34.706625 37.0 33.0 37.0 33.0 37.0 66-67 34.691500000000005 37.0 33.0 37.0 33.0 37.0 68-69 33.955875 35.0 33.0 37.0 30.0 37.0 70-71 34.02899386231334 35.0 33.0 37.0 27.0 37.0 72-73 34.454456690325074 37.0 33.0 37.0 33.0 37.0 74-75 34.35653533812197 37.0 33.0 37.0 33.0 37.0 76-77 34.249022930665106 37.0 33.0 37.0 30.0 37.0 78-79 34.12696550276597 37.0 33.0 37.0 27.0 37.0 80-81 34.118147528127764 37.0 33.0 37.0 27.0 37.0 82-83 34.00703937159696 37.0 33.0 37.0 27.0 37.0 84-85 33.6598518020122 37.0 33.0 37.0 27.0 37.0 86-87 33.602528945764774 37.0 33.0 37.0 27.0 37.0 88-89 33.80423522242535 37.0 33.0 37.0 27.0 37.0 90-91 33.57921998781231 37.0 33.0 37.0 27.0 37.0 92-93 33.49558196221816 35.0 33.0 37.0 27.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 4.0 21 13.0 22 10.0 23 17.0 24 26.0 25 26.0 26 28.0 27 34.0 28 59.0 29 63.0 30 89.0 31 94.0 32 132.0 33 181.0 34 261.0 35 464.0 36 850.0 37 899.0 38 685.0 39 65.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 81.10000000000001 7.8 3.8 7.3 2 65.60000000000001 20.0 9.4 5.0 3 37.05 36.4 16.025 10.525 4 31.4 28.849999999999998 21.349999999999998 18.4 5 26.625 30.4 25.5 17.474999999999998 6 19.725 38.324999999999996 25.624999999999996 16.325 7 36.7 29.349999999999998 19.275000000000002 14.674999999999999 8 29.375 28.15 25.650000000000002 16.825000000000003 9 26.450000000000003 30.475 26.85 16.225 10-11 24.4375 30.049999999999997 28.375 17.1375 12-13 26.05 28.1125 28.299999999999997 17.5375 14-15 21.975 31.574999999999996 29.5875 16.8625 16-17 24.474999999999998 31.6875 23.7875 20.05 18-19 24.4125 27.0125 28.9 19.675 20-21 25.459547330248846 25.747155183193698 28.223083656371138 20.570213830186322 22-23 27.900000000000002 24.224999999999998 27.6875 20.1875 24-25 25.025 25.587500000000002 29.2875 20.1 26-27 25.55 25.9625 28.799999999999997 19.6875 28-29 24.8 28.475 28.5875 18.1375 30-31 27.775 26.125 26.2125 19.8875 32-33 24.837500000000002 25.924999999999997 27.8625 21.375 34-35 24.762500000000003 28.749999999999996 27.3625 19.125 36-37 25.29066133266658 26.52831603950494 25.803225403175396 22.377797224653083 38-39 27.68538201825685 25.597098912092036 28.348130548955858 18.36938852069526 40-41 24.618654663665918 25.468867216804203 28.982245561390346 20.930232558139537 42-43 25.690711338917367 30.85385673209151 25.50318789848731 17.952244030503813 44-45 23.1375 28.487499999999997 29.5875 18.787499999999998 46-47 24.887500000000003 26.875 26.474999999999998 21.762500000000003 48-49 24.474999999999998 26.900000000000002 28.5875 20.0375 50-51 22.5 29.7125 27.025 20.7625 52-53 23.508069560865756 28.775178280995874 26.38558738896534 21.33116476917303 54-55 23.302912864108013 30.24128016002 28.166020752594072 18.28978622327791 56-57 24.978122265283158 29.366170771346418 27.103387923490434 18.552319039879986 58-59 22.7 28.000000000000004 29.425 19.875 60-61 26.9125 27.3 27.075 18.712500000000002 62-63 21.337500000000002 31.0375 30.099999999999998 17.525 64-65 22.7 31.387500000000003 27.700000000000003 18.212500000000002 66-67 24.575 30.5125 27.375 17.5375 68-69 21.0625 28.762500000000003 28.8625 21.3125 70-71 23.519054207017987 27.79524588102126 27.22927933593259 21.456420576028172 72-73 26.007231404958674 25.516528925619834 29.0676652892562 19.408574380165287 74-75 24.761273209549074 28.183023872679048 27.851458885941643 19.20424403183024 76-77 23.01738185768604 27.390005431830527 28.001086366105376 21.591526344378057 78-79 24.35968819599109 27.825723830734965 28.688752783964368 19.125835189309576 80-81 23.09343253684361 33.552725711832885 25.611675490055802 17.742166261267705 82-83 24.332257117698855 26.46022894041679 28.074552392133846 21.132961549750515 84-85 21.96820590461771 27.812263436790307 30.825132475397428 19.39439818319455 86-87 22.014015843997562 29.69226081657526 28.10786106032907 20.18586227909811 88-89 21.237050578915294 31.109079829372334 29.15904936014625 18.494820231566116 90-91 25.35039609993906 31.87081048141377 24.96953077391834 17.809262644728825 92-93 21.328458257160268 33.2114564290067 27.178549664838513 18.281535648994517 >>END_MODULE >>Per sequence GC content warn #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 0.5 14 1.0 15 0.5 16 1.5 17 5.5 18 7.0 19 5.5 20 3.5 21 2.5 22 4.0 23 5.5 24 7.5 25 7.5 26 13.0 27 22.5 28 33.5 29 41.0 30 41.0 31 50.0 32 66.0 33 87.0 34 112.5 35 134.0 36 153.5 37 189.5 38 210.5 39 192.5 40 196.5 41 205.5 42 208.0 43 217.0 44 201.5 45 196.0 46 191.5 47 163.5 48 150.0 49 161.0 50 151.5 51 131.5 52 124.0 53 127.5 54 166.0 55 132.5 56 61.0 57 49.5 58 36.5 59 25.5 60 23.5 61 20.5 62 21.5 63 22.0 64 21.5 65 21.0 66 14.0 67 9.0 68 12.0 69 13.0 70 10.0 71 9.0 72 5.5 73 2.5 74 2.0 75 0.5 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 0.0 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 0.0375 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 0.0125 38-39 0.0375 40-41 0.025 42-43 0.0125 44-45 0.0 46-47 0.0 48-49 0.0 50-51 0.0 52-53 0.08750000000000001 54-55 0.0125 56-57 0.0125 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 >>END_MODULE >>Sequence Length Distribution warn #Length Count 70 49.0 71 53.0 72 52.0 73 53.0 74 46.0 75 49.0 76 32.0 77 48.0 78 52.0 79 50.0 80 43.0 81 42.0 82 48.0 83 60.0 84 41.0 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 3282.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 77.85 #Duplication Level Percentage of deduplicated Percentage of total 1 91.8111753371869 71.475 2 4.4958253050738595 7.000000000000001 3 1.5414258188824663 3.5999999999999996 4 0.5780346820809248 1.7999999999999998 5 0.2890173410404624 1.125 6 0.16056518946692355 0.75 7 0.2569043031470777 1.4000000000000001 8 0.03211303789338471 0.2 9 0.09633911368015415 0.675 >10 0.7064868336544637 9.049999999999999 >50 0.0 0.0 >100 0.03211303789338471 2.9250000000000003 >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 GGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGC 117 2.9250000000000003 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 30 0.75 No Hit GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 29 0.7250000000000001 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 24 0.6 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 23 0.575 No Hit GGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGG 20 0.5 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 20 0.5 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 17 0.42500000000000004 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 16 0.4 No Hit GGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTT 16 0.4 No Hit GGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAAGGCGATCAAATTC 15 0.375 No Hit GAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGC 15 0.375 No Hit GGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGC 15 0.375 No Hit GGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAA 15 0.375 No Hit GGGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTG 14 0.35000000000000003 No Hit GGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAA 13 0.325 No Hit GTATGGAAGGCGATCAAATTCGAGTTCGCGCCGGTAGATACTATCGATTA 13 0.325 No Hit GGATATCGTGTGTGTACATTTGAATGTACCGACATGGGCTCGAGGAGCAT 12 0.3 No Hit GGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTCCT 12 0.3 No Hit CAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCT 11 0.27499999999999997 No Hit GGAGTATCCTTGATATATAAATATATAGATAAATAGATTTAAATGGAAAA 11 0.27499999999999997 No Hit GGAAGGCGATCAAATTCGAGTTCGCGCCGGTAGATACTATCGATTAATAG 11 0.27499999999999997 No Hit GGGATGGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACGA 10 0.25 No Hit GGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTT 9 0.22499999999999998 No Hit GGGGATGGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACG 9 0.22499999999999998 No Hit GGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAA 9 0.22499999999999998 No Hit GGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGGG 8 0.2 No Hit GGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCG 7 0.17500000000000002 No Hit GGTGGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGC 7 0.17500000000000002 No Hit GGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAAA 7 0.17500000000000002 No Hit GGGCAAGGAGAAGTACAAGTGCGGATCCAACGTCTTCTGGAAATGGTGAA 7 0.17500000000000002 No Hit GGGGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCT 7 0.17500000000000002 No Hit AGGTCAACCTTTTGAACTGCCTGCTGAATCCATGAGCAGGCAAGAGACAA 7 0.17500000000000002 No Hit GGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGC 7 0.17500000000000002 No Hit GGAAAAGAGGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTTG 7 0.17500000000000002 No Hit GAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTG 6 0.15 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 6 0.15 No Hit GGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGT 6 0.15 No Hit GGGCTCGAGGAGCATATGTACATTTGAACCCTGACTACACATATACACAC 6 0.15 No Hit GGGTGAGAGCCCCGTCCGGCCCGGACCCTGTCGCCCCACGAGGCGCCGTC 6 0.15 No Hit GGAGAAGGGTCACATATATGCTGCAGGATTCGGTTGAGCACGTTGTAGTA 5 0.125 No Hit GCAGCTTGCAAATGGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAA 5 0.125 No Hit GGAGTCCCATATATATATGTATAAGATGCCAGCCCGGTTTCGTCAACCAT 5 0.125 No Hit GGGGTTGTGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTG 5 0.125 No Hit GTAACGAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCA 5 0.125 No Hit GGGAAATTAACAGTTGGAAAGGGCGATCGGTCTTGATCCCTCTGTGTTTC 5 0.125 No Hit AAAAGAGGAAAGGCTTGCGGTGGATACCTAGGTACCCAGAGACGAGGAAG 5 0.125 No Hit GGGCCGGGTATCTCTCTGCATGTACGTATGCCTGTAATGTACGTAGCTAC 5 0.125 No Hit GGAAAAGAAAGCAAAAGCGATTCCCGTAGTAGCGGCGAGCGAAATGGGAG 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 0.025 0.0 0.0 0.0 0.0 28-29 0.037500000000000006 0.0 0.0 0.0 0.0 30-31 0.05 0.0 0.0 0.0 0.0 32-33 0.05 0.0 0.0 0.0 0.0 34-35 0.0625 0.0 0.0 0.0 0.0 36-37 0.1 0.0 0.0 0.0 0.0 38-39 0.125 0.0 0.0 0.0 0.0 40-41 0.1875 0.0 0.0 0.0 0.0 42-43 0.2 0.0 0.0 0.0 0.0 44-45 0.2 0.0 0.0 0.0 0.0 46-47 0.2 0.0 0.0 0.0 0.0 48-49 0.2 0.0 0.0 0.0 0.0 50-51 0.2 0.0 0.0 0.0 0.0 52-53 0.2 0.0 0.0 0.0 0.0 54-55 0.2 0.0 0.0 0.0 0.0 56-57 0.2 0.0 0.0 0.0 0.0 58-59 0.2 0.0 0.0 0.0 0.0 60-61 0.2 0.0 0.0 0.0 0.0 62-63 0.2 0.0 0.0 0.0 0.0 64-65 0.2 0.0 0.0 0.0 0.0 66-67 0.2 0.0 0.0 0.0 0.0 68-69 0.2 0.0 0.0 0.0 0.0 70-71 0.2 0.0 0.0 0.0 0.0 72-73 0.21250000000000002 0.0 0.0 0.0 0.0 74-75 0.225 0.0 0.0 0.0 0.0 76-77 0.225 0.0 0.0 0.0 0.0 78-79 0.225 0.0 0.0 0.0 0.0 80-81 0.2375 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content fail #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GGAGAGC 25 8.759489E-7 82.675 2 GCAATAC 25 8.759489E-7 82.675 7 CAATACA 25 8.759489E-7 82.675 8 GAGCAAT 25 8.759489E-7 82.675 5 AGAGCAA 25 8.759489E-7 82.675 4 GAGAGCA 25 8.759489E-7 82.675 3 GGGTTGT 15 0.0010670066 82.674995 1 GGGAGAG 30 2.4834662E-8 82.674995 1 AATACAA 30 2.5906138E-6 68.89583 9 AGCAATA 30 2.5906138E-6 68.89583 6 CATCACT 25 9.371835E-6 56.05085 82-83 ATCACTA 25 9.371835E-6 56.05085 84-85 AAGCATC 25 9.371835E-6 56.05085 80-81 TCACTAG 30 3.9991755E-7 56.050846 84-85 AAAGCAT 25 9.863068E-6 55.579834 78-79 GAAAGCA 25 9.863068E-6 55.579834 78-79 CGAAAGC 25 1.3280471E-5 52.912003 76-77 CCGAAAG 25 1.3280471E-5 52.912003 76-77 AGCCGAA 25 1.3935472E-5 52.492065 74-75 GCCGAAA 25 1.3935472E-5 52.492065 74-75 >>END_MODULE Rejected 28656 READS because READLEN < 1 Read 28656 spots for ERR6133483.sra Written 28656 spots for ERR6133483.sra Rejected 28656 READS because READLEN < 1 Read 28656 spots for ERR6133483.sra Written 28656 spots for ERR6133483.sra Rejected 28656 READS because READLEN < 1 Read 28656 spots for ERR6133483.sra Written 28656 spots for ERR6133483.sra Rejected 28656 READS because READLEN < 1 Read 28656 spots for ERR6133483.sra Written 28656 spots for ERR6133483.sra Rejected 28656 READS because READLEN < 1 Read 28656 spots for ERR6133483.sra Written 28656 spots for ERR6133483.sra Rejected 28656 READS because READLEN < 1 Read 28656 spots for ERR6133483.sra Written 28656 spots for ERR6133483.sra Rejected 28656 READS because READLEN < 1 Read 28656 spots for ERR6133483.sra Written 28656 spots for ERR6133483.sra Rejected 28656 READS because READLEN < 1 Read 28656 spots for ERR6133483.sra Written 28656 spots for ERR6133483.sra Rejected 28656 READS because READLEN < 1 Read 28656 spots for ERR6133483.sra Written 28656 spots for ERR6133483.sra Rejected 28656 READS because READLEN < 1 Read 28656 spots for ERR6133483.sra Written 28656 spots for ERR6133483.sra Rejected 28656 READS because READLEN < 1 Read 28656 spots for ERR6133483.sra Written 28656 spots for ERR6133483.sra Rejected 28656 READS because READLEN < 1 Read 28656 spots for ERR6133483.sra Written 28656 spots for ERR6133483.sra Rejected 28656 READS because READLEN < 1 Read 28656 spots for ERR6133483.sra Written 28656 spots for ERR6133483.sra Rejected 28656 READS because READLEN < 1 Read 28656 spots for ERR6133483.sra Written 28656 spots for ERR6133483.sra Rejected 28656 READS because READLEN < 1 Read 28656 spots for ERR6133483.sra Written 28656 spots for ERR6133483.sra Rejected 28656 READS because READLEN < 1 Read 28656 spots for ERR6133483.sra Written 28656 spots for ERR6133483.sra Rejected 28670 READS because READLEN < 1 Read 28670 spots for ERR6133483.sra Written 28670 spots for ERR6133483.sra Rejected 28656 READS because READLEN < 1 Read 28656 spots for ERR6133483.sra Written 28656 spots for ERR6133483.sra Rejected 28656 READS because READLEN < 1 Read 28656 spots for ERR6133483.sra Written 28656 spots for ERR6133483.sra Rejected 28656 READS because READLEN < 1 Read 28656 spots for ERR6133483.sra Written 28656 spots for ERR6133483.sra SRR ids: ['ERR6133483.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_zazdfgyk ERR6133483.sra spots: 573134 blocks: [[1, 28656], [28657, 57312], [57313, 85968], [85969, 114624], [114625, 143280], [143281, 171936], [171937, 200592], [200593, 229248], [229249, 257904], [257905, 286560], [286561, 315216], [315217, 343872], [343873, 372528], [372529, 401184], [401185, 429840], [429841, 458496], [458497, 487152], [487153, 515808], [515809, 544464], [544465, 573134]] ERR6133483 file size 122840 ERR6133483 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 ERR6133483 ERR6133483_1.fastq Input file: ERR6133483_1.fastq trimmed: ERR6133483-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 Thu Dec 12 02:19:10 2024 >> started Thu Dec 12 02:19:10 2024 >> done (0.390s) 573134 reads processed; of these: 200 ( 0.03%) short reads filtered out after trimming by size control 30 ( 0.01%) empty reads filtered out after trimming by size control 572904 (99.96%) reads available; of these: 9597 ( 1.68%) trimmed reads available after processing 563307 (98.32%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 36 0.01% 19 52 0.01% 20 20 0.00% 21 25 0.00% 22 20 0.00% 23 14 0.00% 24 10 0.00% 25 15 0.00% 26 14 0.00% 27 21 0.00% 28 108 0.02% 29 36 0.01% 30 20 0.00% 31 14 0.00% 32 35 0.01% 33 31 0.01% 34 31 0.01% 35 144 0.03% 36 373 0.07% 37 17 0.00% 38 42 0.01% 39 75 0.01% 40 75 0.01% 41 39 0.01% 42 11 0.00% 43 13 0.00% 44 31 0.01% 45 14 0.00% 46 22 0.00% 47 15 0.00% 48 13 0.00% 49 10 0.00% 50 22 0.00% 51 49 0.01% 52 12 0.00% 53 9 0.00% 54 8 0.00% 55 7 0.00% 56 10 0.00% 57 24 0.00% 58 17 0.00% 59 9 0.00% 60 12 0.00% 61 13 0.00% 62 3 0.00% 63 1 0.00% 64 2 0.00% 65 6 0.00% 66 3 0.00% 67 4 0.00% 68 10 0.00% 69 55 0.01% 70 9011 1.57% 71 7897 1.38% 72 7543 1.32% 73 7085 1.24% 74 7060 1.23% 75 7420 1.30% 76 6277 1.10% 77 6434 1.12% 78 6881 1.20% 79 7107 1.24% 80 6303 1.10% 81 7044 1.23% 82 7892 1.38% 83 8629 1.51% 84 6231 1.09% 85 11 0.00% 86 28 0.00% 87 47 0.01% 88 83 0.01% 89 158 0.03% 90 330 0.06% 91 940 0.16% 92 4833 0.84% 93 455988 79.59% 572904 reads passed initial QC criterion=sequence-density sequence-density=1.85 sequence-density-rank=1 fanout-score=1.96 fanout-score-rank=27 prefix-density=1.85 prefix-fanout=2.0 sequence=CAAGGCTAAATAC criterion=fanout-score sequence-density=0.02 sequence-density-rank=30 fanout-score=19.24 fanout-score-rank=1 prefix-density=0.19 prefix-fanout=2.3 sequence=TGCTGCAGCAGCTTAATTTGCATGCCAGGGACGCATGCAACGACCATCTACATATAGCTACTCGATCTACCGCTACCATGAACCGATCCAAGGCTAGCTGCACAAGCTAGGCCCTTATTTCCCTTTGTACGGGTGCATGCATGCCATCCCATGCCATGCTTGTAACCCCCCATAAATAAAATCGCCCTGGT Started job on | Dec 12 02:19:28 Started mapping on | Dec 12 02:19:28 Finished on | Dec 12 02:19:36 Mapping speed, Million of reads per hour | 257.81 Number of input reads | 572904 Average input read length | 89 UNIQUE READS: Uniquely mapped reads number | 295137 Uniquely mapped reads % | 51.52% Average mapped length | 90.00 Number of splices: Total | 9990 Number of splices: Annotated (sjdb) | 8149 Number of splices: GT/AG | 9343 Number of splices: GC/AG | 356 Number of splices: AT/AC | 6 Number of splices: Non-canonical | 285 Mismatch rate per base, % | 0.60% Deletion rate per base | 0.05% Deletion average length | 1.85 Insertion rate per base | 0.02% Insertion average length | 1.96 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 170216 % of reads mapped to multiple loci | 29.71% Number of reads mapped to too many loci | 12411 % of reads mapped to too many loci | 2.17% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 16.42% % of reads unmapped: other | 0.19% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 107551 107551 107551 N_multimapping 170216 170216 170216 N_noFeature 23328 26813 280225 N_ambiguous 12972 1544 53 UnstrandedReadsAssigned:258837 PositiveStrandReadsAssigned:266780 NegativeStrandReadsAssigned:14859 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=92 echo kmer=87 ERR6133483 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: 52,972 [index] number of k-mers: 66,720,672 [index] number of equivalence classes: 111,837 [quant] running in single-end mode [quant] will process file 1: ERR6133483-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 572,904 reads, 357,771 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 824 rounds 52973 ERR6133483.ke.tsv 35125 ERR6133483.se.tsv 88098 total ==> ERR6133483.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 4 11.5254 PNS24243 293 194 0 0 KQK14069 1603 1504 18 47.3123 KQK14071 474 375 0 0 ==> ERR6133483.se.tsv <== BRADI_1g14170v3 18 BRADI_1g53295v3 3 BRADI_1g59795v3 2 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 0 BRADI_1g74790v3 3 BRADI_1g09890v3 0 BRADI_1g77505v3 3 BRADI_1g48960v3 0 ERR6133483 completed mapping pipeline successfully