Starting /dee2/code/volunteer_pipeline.sh ERR6133376 current disk space = 1547447332864 free memory = 1604597204 ERR6133376 SRAfilesize ea62361a0d42cffade74de694acc39b9 ERR6133376.sra ERR6133376.sra file validated ERR6133376 is single end ERR6133376 is conventional basespace ERR6133376 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133376_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 46 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 35.387 37.0 33.0 37.0 33.0 37.0 2 36.4455 37.0 37.0 37.0 37.0 37.0 3 35.97225 37.0 37.0 37.0 33.0 37.0 4 35.5345 37.0 37.0 37.0 33.0 37.0 5 35.4225 37.0 37.0 37.0 33.0 37.0 6 35.556 37.0 37.0 37.0 33.0 37.0 7 37.55175 40.0 37.0 40.0 33.0 40.0 8 37.555 40.0 37.0 40.0 33.0 40.0 9 37.66525 40.0 37.0 40.0 33.0 40.0 10-11 37.648125 40.0 37.0 40.0 33.0 40.0 12-13 37.59925 38.5 37.0 40.0 33.0 40.0 14-15 37.54275 37.0 37.0 40.0 33.0 40.0 16-17 37.37875 37.0 37.0 40.0 33.0 40.0 18-19 37.3185 37.0 37.0 40.0 33.0 40.0 20-21 37.1505 37.0 37.0 40.0 33.0 40.0 22-23 37.19475 37.0 37.0 40.0 33.0 40.0 24-25 37.299875 37.0 37.0 40.0 33.0 40.0 26-27 37.31325 37.0 37.0 40.0 33.0 40.0 28-29 37.2615 37.0 37.0 40.0 33.0 40.0 30-31 37.111375 37.0 37.0 40.0 33.0 40.0 32-33 36.964625 37.0 37.0 40.0 33.0 40.0 34-35 36.821375 37.0 37.0 40.0 33.0 40.0 36-37 36.693124999999995 37.0 37.0 40.0 33.0 40.0 38-39 36.458749999999995 37.0 37.0 40.0 33.0 40.0 40-41 36.112125 37.0 37.0 40.0 33.0 40.0 42-43 36.12425 37.0 37.0 40.0 33.0 40.0 44-45 35.7115 37.0 35.0 38.5 33.0 40.0 46-47 35.55525 37.0 33.0 37.0 33.0 40.0 48-49 35.524625 37.0 33.0 37.0 33.0 40.0 50-51 35.451375 37.0 33.0 37.0 33.0 40.0 52-53 35.207375 37.0 33.0 37.0 33.0 40.0 54-55 35.148250000000004 37.0 33.0 37.0 33.0 40.0 56-57 34.73625 37.0 33.0 37.0 27.0 38.5 58-59 33.419 35.0 33.0 37.0 27.0 37.0 60-61 34.277625 37.0 33.0 37.0 27.0 37.0 62-63 34.391875 37.0 33.0 37.0 27.0 37.0 64-65 34.300250000000005 37.0 33.0 37.0 27.0 37.0 66-67 34.380750000000006 37.0 33.0 37.0 27.0 37.0 68-69 33.548625 35.0 33.0 37.0 27.0 37.0 70-71 33.64395322277847 35.0 33.0 37.0 27.0 37.0 72-73 34.016069760658795 37.0 33.0 37.0 27.0 37.0 74-75 33.8171605451987 37.0 33.0 37.0 27.0 37.0 76-77 33.994322619212554 37.0 33.0 37.0 27.0 37.0 78-79 33.871752172576876 37.0 33.0 37.0 27.0 37.0 80-81 33.843301578602066 37.0 33.0 37.0 27.0 37.0 82-83 33.67157783882928 37.0 33.0 37.0 27.0 37.0 84-85 33.83486575570231 37.0 33.0 37.0 27.0 37.0 86-87 33.692019628099175 37.0 33.0 37.0 27.0 37.0 88-89 33.88132747933884 37.0 33.0 37.0 27.0 37.0 90-91 33.340005165289256 37.0 33.0 37.0 27.0 37.0 92-93 33.295583677685954 37.0 33.0 37.0 27.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 6.0 21 18.0 22 17.0 23 14.0 24 17.0 25 31.0 26 42.0 27 51.0 28 58.0 29 65.0 30 84.0 31 110.0 32 150.0 33 189.0 34 239.0 35 409.0 36 912.0 37 954.0 38 615.0 39 19.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 79.85 3.9 9.325 6.925000000000001 2 62.075 22.325 10.125 5.475 3 34.949999999999996 32.2 15.45 17.4 4 27.650000000000002 31.15 18.475 22.725 5 27.775 26.924999999999997 29.275000000000002 16.025 6 16.575 43.575 24.15 15.7 7 40.575 26.05 19.125 14.249999999999998 8 29.775000000000002 26.55 22.375 21.3 9 21.825 30.075000000000003 26.325 21.775 10-11 20.7625 29.462500000000002 29.5 20.275000000000002 12-13 23.05 27.487499999999997 24.5 24.962500000000002 14-15 22.2625 35.5375 24.725 17.474999999999998 16-17 27.6125 29.875 21.462500000000002 21.05 18-19 24.349999999999998 26.6125 27.525 21.512500000000003 20-21 28.199999999999996 24.9125 28.4 18.4875 22-23 31.2625 21.1375 28.4 19.2 24-25 23.025000000000002 27.962500000000002 28.537499999999998 20.474999999999998 26-27 29.9875 23.05 27.700000000000003 19.2625 28-29 24.3875 27.537499999999998 28.487499999999997 19.5875 30-31 33.25 23.3625 25.374999999999996 18.0125 32-33 26.6125 26.85 25.7125 20.825 34-35 22.162499999999998 33.025 24.5125 20.3 36-37 27.5875 25.5125 23.825 23.075000000000003 38-39 32.874655991994 22.904678508881663 26.619964973730298 17.600700525394046 40-41 23.317488116087066 25.494120590442833 30.447835876907682 20.740555416562422 42-43 27.435288233087405 30.749030886582467 23.87145179442291 17.944229085907214 44-45 24.75 27.462500000000002 29.125 18.6625 46-47 27.3875 22.5125 26.887499999999996 23.2125 48-49 26.087500000000002 22.912499999999998 28.5875 22.412499999999998 50-51 20.6125 28.212500000000002 27.212500000000002 23.962500000000002 52-53 26.335543600650567 24.69660953334167 23.958463655698736 25.00938321030902 54-55 26.55 24.8 28.6375 20.0125 56-57 29.975 28.512500000000003 24.725 16.7875 58-59 21.775 25.7 32.800000000000004 19.725 60-61 30.875000000000004 24.2625 27.1375 17.724999999999998 62-63 20.6125 29.7 30.3875 19.3 64-65 20.9125 33.825 28.125 17.1375 66-67 23.6125 32.6875 26.825 16.875 68-69 21.3125 24.0625 28.6875 25.937500000000004 70-71 22.88930581613508 27.74233896185116 26.966854283927454 22.401500938086304 72-73 28.537350910232266 24.06779661016949 28.5247959824231 18.870056497175142 74-75 25.368620037807183 28.67044738500315 27.977315689981097 17.98361688720857 76-77 20.070913004938586 23.426617702925164 25.921235912371788 30.581233379764466 78-79 30.15752032520325 25.673272357723576 26.359247967479675 17.809959349593495 80-81 23.453641117204437 34.0390256344854 26.221145262083915 16.286187986226246 82-83 23.981030504998717 25.92924891053576 28.47987695462702 21.6098436298385 84-85 20.905339179778178 24.03920557131803 33.64714985813774 21.408305390766056 86-87 20.11880165289256 27.104855371900825 27.24690082644628 25.529442148760328 88-89 18.543388429752067 30.3073347107438 29.674586776859503 21.474690082644628 90-91 26.40754132231405 29.81663223140496 26.936983471074385 16.83884297520661 92-93 21.97830578512397 29.028925619834713 29.00309917355372 19.9896694214876 >>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 0.5 17 13.5 18 17.5 19 5.5 20 1.5 21 1.0 22 3.0 23 3.5 24 3.5 25 4.5 26 11.5 27 15.0 28 19.5 29 28.0 30 31.0 31 37.0 32 46.0 33 59.5 34 65.5 35 73.5 36 97.0 37 118.5 38 142.0 39 152.5 40 161.0 41 173.0 42 182.5 43 196.0 44 185.5 45 173.0 46 175.5 47 159.5 48 141.0 49 155.5 50 236.5 51 238.0 52 150.0 53 154.0 54 244.5 55 202.5 56 75.0 57 53.5 58 50.0 59 42.0 60 34.5 61 26.5 62 20.5 63 21.0 64 21.5 65 18.0 66 15.0 67 10.0 68 7.0 69 6.5 70 4.5 71 4.0 72 5.5 73 4.0 74 1.0 75 1.0 76 1.0 77 0.5 78 0.5 79 0.5 80 0.0 81 0.5 82 0.5 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 0.0 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 0.075 40-41 0.075 42-43 0.0375 44-45 0.0 46-47 0.0 48-49 0.0 50-51 0.0 52-53 0.08750000000000001 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 >>END_MODULE >>Sequence Length Distribution warn #Length Count 70 5.0 71 8.0 72 9.0 73 8.0 74 5.0 75 13.0 76 7.0 77 6.0 78 6.0 79 9.0 80 7.0 81 9.0 82 14.0 83 12.0 84 10.0 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 3872.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 70.175 #Duplication Level Percentage of deduplicated Percentage of total 1 92.55432846455291 64.95 2 4.061275382971143 5.7 3 1.0331314570716068 2.175 4 0.7481296758104738 2.1 5 0.24937655860349126 0.8750000000000001 6 0.21375133594584966 0.8999999999999999 7 0.28500178126113285 1.4000000000000001 8 0.035625222657641606 0.2 9 0.035625222657641606 0.22499999999999998 >10 0.7125044531528322 10.375 >50 0.0 0.0 >100 0.07125044531528321 11.1 >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 266 6.65 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 178 4.45 No Hit GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 41 1.0250000000000001 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 37 0.9249999999999999 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 34 0.8500000000000001 No Hit GGAGTATCCTTGATATATAAATATATAGATAAATAGATTTAAATGGAAAA 30 0.75 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 28 0.7000000000000001 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 27 0.675 No Hit GGGAGTATTATGAAAGGAGATTAATCATAGATTATCAAAAACCCTAGAAA 25 0.625 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 24 0.6 No Hit GGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGG 22 0.5499999999999999 No Hit GGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTT 17 0.42500000000000004 No Hit GGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAA 15 0.375 No Hit GATACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGC 15 0.375 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 14 0.35000000000000003 No Hit GTATTTAGCCTTGCAAGGTGGTCCTTGCTGATTCACACGGGATTCCACGT 14 0.35000000000000003 No Hit GGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAA 14 0.35000000000000003 No Hit GGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGGG 13 0.325 No Hit TCAAAAGAGGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGGA 13 0.325 No Hit GGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAAA 11 0.27499999999999997 No Hit GGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGC 11 0.27499999999999997 No Hit GTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAA 10 0.25 No Hit GGGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTG 9 0.22499999999999998 No Hit GGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAAGGCGATCAAATTC 8 0.2 No Hit GGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCG 7 0.17500000000000002 No Hit CAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATAT 7 0.17500000000000002 No Hit GGATACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATG 7 0.17500000000000002 No Hit CACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTTCGGGGAGT 7 0.17500000000000002 No Hit GTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCT 7 0.17500000000000002 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 7 0.17500000000000002 No Hit GAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGC 7 0.17500000000000002 No Hit GGAAAAGAAAGCAAAAGCGATTCCCGTAGTAGCGGCGAGCGAAATGGGAG 7 0.17500000000000002 No Hit GGCTTTAGAAGCCTGTGTACAAGCTCGTAACGAAGGGCGCGATCTTGCTC 6 0.15 No Hit GGCCTGTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCG 6 0.15 No Hit GGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTT 6 0.15 No Hit GGCATATGCCAGCTCTGACCGAAATCTTTGGGGATGATTCTGTATTACAA 6 0.15 No Hit GGAAAAGAGGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTTG 6 0.15 No Hit GGATTTGTTAAATCAAATCCTTGGTTTAATAACGAACGGTGTTAACTTAC 6 0.15 No Hit GGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCTAAATGGATTC 5 0.125 No Hit GGGAAAAGAGGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTT 5 0.125 No Hit GGGAGTATCCTTGATATATAAATATATAGATAAATAGATTTAAATGGAAA 5 0.125 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAATGCTTC 5 0.125 No Hit GGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGCA 5 0.125 No Hit GGGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGA 5 0.125 No Hit GGTGGATACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAA 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 0.0125 0.0 0.0 0.0 0.0 42-43 0.05 0.0 0.0 0.0 0.0 44-45 0.05 0.0 0.0 0.0 0.0 46-47 0.05 0.0 0.0 0.0 0.0 48-49 0.05 0.0 0.0 0.0 0.0 50-51 0.05 0.0 0.0 0.0 0.0 52-53 0.05 0.0 0.0 0.0 0.0 54-55 0.05 0.0 0.0 0.0 0.0 56-57 0.05 0.0 0.0 0.0 0.0 58-59 0.05 0.0 0.0 0.0 0.0 60-61 0.05 0.0 0.0 0.0 0.0 62-63 0.05 0.0 0.0 0.0 0.0 64-65 0.05 0.0 0.0 0.0 0.0 66-67 0.05 0.0 0.0 0.0 0.0 68-69 0.05 0.0 0.0 0.0 0.0 70-71 0.05 0.0 0.0 0.0 0.0 72-73 0.05 0.0 0.0 0.0 0.0 74-75 0.05 0.0 0.0 0.0 0.0 76-77 0.05 0.0 0.0 0.0 0.0 78-79 0.05 0.0 0.0 0.0 0.0 80-81 0.05 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content fail #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GGAGAGC 40 1.2732926E-11 87.0 2 GCAATAC 40 1.2732926E-11 87.0 7 GGGAGAG 40 1.2732926E-11 87.0 1 CAATACA 40 1.2732926E-11 87.0 8 GAGCAAT 40 1.2732926E-11 87.0 5 AGAGCAA 40 1.2732926E-11 87.0 4 GAGAGCA 40 1.2732926E-11 87.0 3 AATACAA 40 1.2732926E-11 87.0 9 AGCAATA 40 1.2732926E-11 87.0 6 CTAGGCA 25 7.205523E-5 69.6 4 CCTAGGC 25 7.205523E-5 69.6 3 TAGGCAC 25 7.205523E-5 69.6 5 CACCCAG 20 0.0027298967 65.25 9 GCACCCA 20 0.0027298967 65.25 8 GGCACCC 30 1.7769479E-4 58.0 7 AGGCACC 30 1.7769479E-4 58.0 6 ACCTAGG 30 1.7769479E-4 58.0 2 TACCTAG 35 3.8063803E-4 49.714283 1 GATGGCT 40 7.392373E-9 43.5 56-57 GAGTGCC 40 7.392373E-9 43.5 42-43 >>END_MODULE Rejected 218080 READS because READLEN < 1 Read 218080 spots for ERR6133376.sra Written 218080 spots for ERR6133376.sra Rejected 218080 READS because READLEN < 1 Read 218080 spots for ERR6133376.sra Written 218080 spots for ERR6133376.sra Rejected 218080 READS because READLEN < 1 Read 218080 spots for ERR6133376.sra Written 218080 spots for ERR6133376.sra Rejected 218080 READS because READLEN < 1 Read 218080 spots for ERR6133376.sra Written 218080 spots for ERR6133376.sra Rejected 218080 READS because READLEN < 1 Read 218080 spots for ERR6133376.sra Written 218080 spots for ERR6133376.sra Rejected 218080 READS because READLEN < 1 Read 218080 spots for ERR6133376.sra Written 218080 spots for ERR6133376.sra Rejected 218080 READS because READLEN < 1 Read 218080 spots for ERR6133376.sra Written 218080 spots for ERR6133376.sra Rejected 218080 READS because READLEN < 1 Read 218080 spots for ERR6133376.sra Written 218080 spots for ERR6133376.sra Rejected 218080 READS because READLEN < 1 Read 218080 spots for ERR6133376.sra Written 218080 spots for ERR6133376.sra Rejected 218080 READS because READLEN < 1 Read 218080 spots for ERR6133376.sra Written 218080 spots for ERR6133376.sra Rejected 218080 READS because READLEN < 1 Read 218080 spots for ERR6133376.sra Written 218080 spots for ERR6133376.sra Rejected 218080 READS because READLEN < 1 Read 218080 spots for ERR6133376.sra Written 218080 spots for ERR6133376.sra Rejected 218080 READS because READLEN < 1 Read 218080 spots for ERR6133376.sra Written 218080 spots for ERR6133376.sra Rejected 218080 READS because READLEN < 1 Read 218080 spots for ERR6133376.sra Written 218080 spots for ERR6133376.sra Rejected 218090 READS because READLEN < 1 Read 218090 spots for ERR6133376.sra Written 218090 spots for ERR6133376.sra Rejected 218080 READS because READLEN < 1 Read 218080 spots for ERR6133376.sra Written 218080 spots for ERR6133376.sra Rejected 218080 READS because READLEN < 1 Read 218080 spots for ERR6133376.sra Written 218080 spots for ERR6133376.sra Rejected 218080 READS because READLEN < 1 Read 218080 spots for ERR6133376.sra Written 218080 spots for ERR6133376.sra Rejected 218080 READS because READLEN < 1 Read 218080 spots for ERR6133376.sra Written 218080 spots for ERR6133376.sra Rejected 218080 READS because READLEN < 1 Read 218080 spots for ERR6133376.sra Written 218080 spots for ERR6133376.sra SRR ids: ['ERR6133376.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_pav_jxkc ERR6133376.sra spots: 4361610 blocks: [[1, 218080], [218081, 436160], [436161, 654240], [654241, 872320], [872321, 1090400], [1090401, 1308480], [1308481, 1526560], [1526561, 1744640], [1744641, 1962720], [1962721, 2180800], [2180801, 2398880], [2398881, 2616960], [2616961, 2835040], [2835041, 3053120], [3053121, 3271200], [3271201, 3489280], [3489281, 3707360], [3707361, 3925440], [3925441, 4143520], [4143521, 4361610]] ERR6133376 file size 965182 ERR6133376 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 ERR6133376 ERR6133376_1.fastq Input file: ERR6133376_1.fastq trimmed: ERR6133376-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 Sat Dec 7 03:04:33 2024 >> started Sat Dec 7 03:04:35 2024 >> done (2.112s) 4361610 reads processed; of these: 383 ( 0.01%) short reads filtered out after trimming by size control 72 ( 0.00%) empty reads filtered out after trimming by size control 4361155 (99.99%) reads available; of these: 83464 ( 1.91%) trimmed reads available after processing 4277691 (98.09%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 40 0.00% 19 98 0.00% 20 68 0.00% 21 110 0.00% 22 95 0.00% 23 24 0.00% 24 40 0.00% 25 23 0.00% 26 22 0.00% 27 33 0.00% 28 107 0.00% 29 76 0.00% 30 57 0.00% 31 108 0.00% 32 39 0.00% 33 46 0.00% 34 70 0.00% 35 656 0.02% 36 518 0.01% 37 53 0.00% 38 55 0.00% 39 316 0.01% 40 105 0.00% 41 139 0.00% 42 9 0.00% 43 12 0.00% 44 18 0.00% 45 19 0.00% 46 16 0.00% 47 15 0.00% 48 13 0.00% 49 13 0.00% 50 13 0.00% 51 25 0.00% 52 9 0.00% 53 10 0.00% 54 8 0.00% 55 23 0.00% 56 5 0.00% 57 9 0.00% 58 7 0.00% 59 4 0.00% 60 19 0.00% 61 15 0.00% 62 1 0.00% 63 4 0.00% 64 4 0.00% 65 6 0.00% 66 9 0.00% 67 12 0.00% 68 18 0.00% 69 80 0.00% 70 7822 0.18% 71 7254 0.17% 72 8928 0.20% 73 7551 0.17% 74 7512 0.17% 75 7551 0.17% 76 7011 0.16% 77 6927 0.16% 78 7805 0.18% 79 8806 0.20% 80 7983 0.18% 81 8769 0.20% 82 10719 0.25% 83 10331 0.24% 84 9036 0.21% 85 162 0.00% 86 299 0.01% 87 497 0.01% 88 882 0.02% 89 1689 0.04% 90 3605 0.08% 91 10660 0.24% 92 60846 1.40% 93 4155216 95.28% 4361155 reads passed initial QC criterion=sequence-density sequence-density=0.81 sequence-density-rank=1 fanout-score=1.40 fanout-score-rank=28 prefix-density=0.04 prefix-fanout=1.4 sequence=GGGAGTATTATGAAAGGAGATTAATCATAGATTATCAAAAACCCTAGAAAAAATTCTTCCTGGGTCGATGCCCGAGCGGTTAATGGGGACGGACTGTAAATTCGTTGACAAAATGTCTACGCTGGTTCAAATCCAGCTCGGCCCAAAAATCTGGGGCTTCGTGAATATGAACTAAATCTTTTTAT criterion=fanout-score sequence-density=0.12 sequence-density-rank=11 fanout-score=64.12 fanout-score-rank=1 prefix-density=7.51 prefix-fanout=1.0 sequence=GGAGATTCCCAGATAGA Started job on | Dec 07 03:05:55 Started mapping on | Dec 07 03:05:55 Finished on | Dec 07 03:06:14 Mapping speed, Million of reads per hour | 826.32 Number of input reads | 4361155 Average input read length | 92 UNIQUE READS: Uniquely mapped reads number | 2329014 Uniquely mapped reads % | 53.40% Average mapped length | 91.91 Number of splices: Total | 121308 Number of splices: Annotated (sjdb) | 98749 Number of splices: GT/AG | 115311 Number of splices: GC/AG | 2554 Number of splices: AT/AC | 42 Number of splices: Non-canonical | 3401 Mismatch rate per base, % | 0.46% Deletion rate per base | 0.05% Deletion average length | 1.71 Insertion rate per base | 0.03% Insertion average length | 1.71 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 1920299 % of reads mapped to multiple loci | 44.03% Number of reads mapped to too many loci | 44936 % of reads mapped to too many loci | 1.03% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.46% % of reads unmapped: other | 0.08% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 111842 111842 111842 N_multimapping 1920299 1920299 1920299 N_noFeature 164016 190892 2221976 N_ambiguous 92569 12343 350 UnstrandedReadsAssigned:2072429 PositiveStrandReadsAssigned:2125779 NegativeStrandReadsAssigned:106688 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=93 echo kmer=89 ERR6133376 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: ERR6133376-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 4,361,155 reads, 3,058,090 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 993 rounds 52973 ERR6133376.ke.tsv 35125 ERR6133376.se.tsv 88098 total ==> ERR6133376.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 39 12.1528 PNS24243 293 194 0 0 KQK14069 1603 1504 11 3.12687 KQK14071 474 375 0 0 ==> ERR6133376.se.tsv <== BRADI_1g14170v3 11 BRADI_1g53295v3 90 BRADI_1g59795v3 14 BRADI_1g07683v3 0 BRADI_1g00485v3 1 BRADI_1g20270v3 32 BRADI_1g74790v3 30 BRADI_1g09890v3 0 BRADI_1g77505v3 79 BRADI_1g48960v3 0 ERR6133376 completed mapping pipeline successfully