Starting /dee2/code/volunteer_pipeline.sh ERR6133461 current disk space = 1545254899712 free memory = 1594132676 ERR6133461 SRAfilesize 4b7faf33b95e6abc3202f16794d0d5f1 ERR6133461.sra ERR6133461.sra file validated ERR6133461 is single end ERR6133461 is conventional basespace ERR6133461 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133461_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 34.897 37.0 33.0 37.0 33.0 37.0 2 36.31875 37.0 37.0 37.0 33.0 37.0 3 35.33375 37.0 33.0 37.0 33.0 37.0 4 34.96375 37.0 37.0 37.0 33.0 37.0 5 34.69675 37.0 33.0 37.0 27.0 37.0 6 35.308 37.0 37.0 37.0 33.0 37.0 7 36.786 37.0 37.0 40.0 33.0 40.0 8 36.91025 37.0 37.0 40.0 33.0 40.0 9 37.06925 37.0 37.0 40.0 33.0 40.0 10-11 36.977875 37.0 37.0 40.0 33.0 40.0 12-13 36.771625 37.0 37.0 40.0 33.0 40.0 14-15 36.708 37.0 37.0 40.0 33.0 40.0 16-17 36.573 37.0 37.0 40.0 33.0 40.0 18-19 36.2685 37.0 37.0 40.0 33.0 40.0 20-21 36.194625 37.0 37.0 40.0 33.0 40.0 22-23 35.95525 37.0 35.0 40.0 33.0 40.0 24-25 36.00425 37.0 33.0 40.0 33.0 40.0 26-27 36.316 37.0 37.0 40.0 33.0 40.0 28-29 36.10525 37.0 37.0 40.0 33.0 40.0 30-31 36.23175 37.0 37.0 40.0 33.0 40.0 32-33 36.14375 37.0 37.0 40.0 33.0 40.0 34-35 36.061125000000004 37.0 33.0 40.0 33.0 40.0 36-37 36.058125000000004 37.0 35.0 40.0 33.0 40.0 38-39 35.985625 37.0 33.0 40.0 33.0 40.0 40-41 35.84725 37.0 33.0 40.0 33.0 40.0 42-43 35.757125 37.0 33.0 40.0 33.0 40.0 44-45 35.39725 37.0 33.0 38.5 30.0 40.0 46-47 35.392125 37.0 33.0 37.0 30.0 40.0 48-49 35.320125 37.0 33.0 37.0 30.0 40.0 50-51 35.271125 37.0 33.0 37.0 33.0 40.0 52-53 35.061375 37.0 33.0 37.0 27.0 40.0 54-55 34.98225 37.0 33.0 37.0 33.0 40.0 56-57 34.702375 37.0 33.0 37.0 27.0 37.0 58-59 34.148875000000004 37.0 33.0 37.0 27.0 37.0 60-61 34.4415 37.0 33.0 37.0 27.0 37.0 62-63 34.3565 37.0 33.0 37.0 27.0 37.0 64-65 34.11025 37.0 33.0 37.0 27.0 37.0 66-67 34.091625 37.0 33.0 37.0 27.0 37.0 68-69 33.20975 35.0 33.0 37.0 27.0 37.0 70-71 33.45057215752567 35.0 33.0 37.0 27.0 37.0 72-73 33.73137568050835 37.0 33.0 37.0 27.0 37.0 74-75 33.707606479810075 37.0 33.0 37.0 27.0 37.0 76-77 33.77214337427698 37.0 33.0 37.0 27.0 37.0 78-79 33.80074857992542 37.0 33.0 37.0 27.0 37.0 80-81 33.785000759926206 37.0 33.0 37.0 27.0 37.0 82-83 33.68448204774819 37.0 33.0 37.0 27.0 37.0 84-85 33.381973178860335 35.0 33.0 37.0 27.0 37.0 86-87 33.31725032425422 33.0 33.0 37.0 27.0 37.0 88-89 33.452140077821014 37.0 33.0 37.0 27.0 37.0 90-91 33.02438391699092 33.0 33.0 37.0 27.0 37.0 92-93 33.106355382619974 33.0 33.0 37.0 27.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 10.0 21 11.0 22 28.0 23 18.0 24 30.0 25 29.0 26 40.0 27 49.0 28 71.0 29 93.0 30 123.0 31 134.0 32 190.0 33 190.0 34 285.0 35 493.0 36 857.0 37 886.0 38 445.0 39 18.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 87.075 2.3 3.075 7.55 2 71.39999999999999 17.575 7.049999999999999 3.975 3 34.825 40.775 13.700000000000001 10.7 4 31.574999999999996 29.475 20.775 18.175 5 26.974999999999998 28.375 26.950000000000003 17.7 6 18.224999999999998 35.925000000000004 27.725 18.125 7 38.6 28.625 18.2 14.575 8 30.2 31.674999999999997 22.55 15.575 9 25.025 29.099999999999998 29.425 16.45 10-11 24.712500000000002 28.1625 30.1375 16.9875 12-13 26.075 28.925 27.3 17.7 14-15 19.7 32.4375 29.8375 18.025 16-17 22.9875 32.0125 25.5 19.5 18-19 23.9 27.800000000000004 29.349999999999998 18.95 20-21 25.13134851138354 25.83187390542907 29.68476357267951 19.352014010507883 22-23 27.437499999999996 23.0 29.099999999999998 20.4625 24-25 24.6875 27.05 27.8875 20.375 26-27 24.25 24.55 32.7 18.5 28-29 25.0375 27.725 28.775000000000002 18.462500000000002 30-31 25.7875 26.1625 28.9875 19.0625 32-33 23.4875 24.8 30.2 21.512500000000003 34-35 22.6875 29.7125 27.4125 20.1875 36-37 24.962500000000002 26.5875 26.674999999999997 21.775 38-39 27.737499999999997 25.1875 28.825 18.25 40-41 27.0 23.974999999999998 27.150000000000002 21.875 42-43 25.118958176809414 28.049085900325572 28.136739293764084 18.695216629100926 44-45 22.377797224653083 26.59082385298162 31.19139892486561 19.839979997499686 46-47 24.2625 26.437500000000004 28.012500000000003 21.2875 48-49 24.6125 25.137500000000003 30.7375 19.5125 50-51 22.25 26.924999999999997 30.625000000000004 20.200000000000003 52-53 24.120665915633996 27.062210539491797 27.51283014144449 21.304293403429718 54-55 23.793448362090523 26.60665166291573 30.857714428607153 18.742185546386597 56-57 25.074999999999996 26.237500000000004 30.312499999999996 18.375 58-59 23.7 25.662499999999998 29.262500000000003 21.375 60-61 25.575 26.05 30.7 17.675 62-63 21.1875 28.3125 32.25 18.25 64-65 21.099999999999998 30.3875 30.7625 17.75 66-67 23.575 27.762500000000003 29.1125 19.55 68-69 20.175 27.800000000000004 28.075 23.95 70-71 22.945076942324533 28.975353434254973 28.850243963468035 19.22932565995246 72-73 24.64824120603015 25.201005025125628 30.3643216080402 19.786432160804022 74-75 24.649576966788736 26.392221240055562 30.44576335395883 18.512438439196867 76-77 22.91402485417195 25.62769464874461 29.558711640882578 21.89956885620086 78-79 23.458991339786042 25.85328578706062 31.39327559857361 19.294447274579724 80-81 22.0629639109291 31.63552597901203 28.794471461479397 17.507038648579474 82-83 21.688144329896907 28.13144329896907 28.827319587628864 21.353092783505154 84-85 22.433903576982893 23.872472783825817 33.190772420943496 20.502851218247798 86-87 22.153047989623865 27.561608300907913 30.86900129701686 19.416342412451364 88-89 19.429312581063556 27.80804150453956 32.64591439688716 20.116731517509727 90-91 24.863813229571985 26.835278858625163 29.481193255512324 18.819714656290532 92-93 21.50453955901427 29.208819714656293 30.168612191958495 19.118028534370946 >>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 0.0 14 0.0 15 0.5 16 0.5 17 5.5 18 6.0 19 1.0 20 2.5 21 2.0 22 2.0 23 4.5 24 5.5 25 6.0 26 10.0 27 16.0 28 20.5 29 23.0 30 33.0 31 51.0 32 78.0 33 98.0 34 85.0 35 87.5 36 115.0 37 158.0 38 222.0 39 223.5 40 223.0 41 220.5 42 224.5 43 258.0 44 213.5 45 203.5 46 201.5 47 179.5 48 172.5 49 141.5 50 131.0 51 143.0 52 126.5 53 95.5 54 124.5 55 107.5 56 49.0 57 40.5 58 41.0 59 27.0 60 17.5 61 22.5 62 21.0 63 16.0 64 12.5 65 14.0 66 11.5 67 9.0 68 9.5 69 10.5 70 12.5 71 13.0 72 7.5 73 3.0 74 2.0 75 0.5 76 2.0 77 2.0 78 0.5 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 0.075 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 0.17500000000000002 44-45 0.0125 46-47 0.0 48-49 0.0 50-51 0.0 52-53 0.13749999999999998 54-55 0.025 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 7.0 71 7.0 72 12.0 73 10.0 74 9.0 75 7.0 76 10.0 77 7.0 78 10.0 79 11.0 80 6.0 81 17.0 82 14.0 83 12.0 84 6.0 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 3855.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 73.575 #Duplication Level Percentage of deduplicated Percentage of total 1 91.36935100237852 67.225 2 4.17940876656473 6.15 3 1.529051987767584 3.375 4 0.9174311926605505 2.7 5 0.40774719673802245 1.5 6 0.27183146449201495 1.2 7 0.23785253143051308 1.225 8 0.13591573224600748 0.8 9 0.20387359836901123 1.35 >10 0.6455997281685355 8.5 >50 0.10193679918450561 5.975 >100 0.0 0.0 >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 GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 91 2.275 No Hit GGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGC 90 2.25 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 58 1.4500000000000002 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 38 0.95 No Hit GGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTT 27 0.675 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 27 0.675 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 25 0.625 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 25 0.625 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 22 0.5499999999999999 No Hit GGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAACCCTCTTAACT 20 0.5 No Hit CAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCT 19 0.475 No Hit GGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGG 18 0.44999999999999996 No Hit GGGATGGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACGA 15 0.375 No Hit GGTTTTGAAAAGGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAA 14 0.35000000000000003 No Hit GAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGC 13 0.325 No Hit GGGAAAAGAGGGGTTACTTTTTTTTCATTTTTCCCTTAAAAGATAGGCTT 12 0.3 No Hit GGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGGG 11 0.27499999999999997 No Hit GGAAAAGAGGGGTTACTTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTT 11 0.27499999999999997 No Hit GCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCT 11 0.27499999999999997 No Hit GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 11 0.27499999999999997 No Hit GGAAAAGAAAGCAAAAGCGATTCCCGTAGTAGCGGCGAGCGAAATGGGAG 11 0.27499999999999997 No Hit GGGGATGGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACG 10 0.25 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 9 0.22499999999999998 No Hit GGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGC 9 0.22499999999999998 No Hit GGGGGTGCCATACGCAAAAAGGAAGCGACTCATAGAATGGCAGAGGCAAA 9 0.22499999999999998 No Hit GGAGTATCCTTGATATATAAATATATAGATAAATAGATTTAAATGGAAAA 9 0.22499999999999998 No Hit GTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAG 9 0.22499999999999998 No Hit CAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTG 9 0.22499999999999998 No Hit GCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATC 8 0.2 No Hit GGGGTTACTTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTTGAAATCGG 8 0.2 No Hit GGATACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATG 8 0.2 No Hit GGGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTG 8 0.2 No Hit CAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATAT 7 0.17500000000000002 No Hit GGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTG 7 0.17500000000000002 No Hit GTATTTAGCCTTGCAAGGTGGTCCTTGCTGATTCACACGGGATTCCACGT 7 0.17500000000000002 No Hit GGGGTTGTGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTG 7 0.17500000000000002 No Hit CGAGGAAGGGCGTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAG 7 0.17500000000000002 No Hit GGGGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCT 7 0.17500000000000002 No Hit GGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAA 7 0.17500000000000002 No Hit GAGGAAGGGCGTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAGC 6 0.15 No Hit GGGAGTGGGGGTGCCATACGCAAAAAGGAAGCGACTCATAGAATGGCAGA 6 0.15 No Hit GGAGTGGGGGTGCCATACGCAAAAAGGAAGCGACTCATAGAATGGCAGAG 6 0.15 No Hit GTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAA 6 0.15 No Hit GGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACGAGCCGT 6 0.15 No Hit GGGCCGGGTATCTCTCTGCATGTACGTATGCCTGTAATGTACGTAGCTAC 6 0.15 No Hit GGGCACTGTAGCCAGTGTGTCAGTCGTTGTTAAATTACAGGTTGAGATCA 6 0.15 No Hit GGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGC 6 0.15 No Hit GAAGCTTATGCTATTTTCAACCCAATCGTGGATGTTATGCCTGTCATACC 5 0.125 No Hit GGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAA 5 0.125 No Hit GTAACGAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCA 5 0.125 No Hit GTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAGCATAGATCCGG 5 0.125 No Hit GTATGGAAGGCGATCAAATTCGAGTTCGCGCCGGTAGATACTATCGATTA 5 0.125 No Hit GGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAAA 5 0.125 No Hit GGATATCGTGTGTGTACATTTGAATGTACCGACATGGGCTCGAGGAGCAT 5 0.125 No Hit GGGAGGGTGAGAGCCCCGTCCGGCCCGGACCCTGTCGCCCCACGAGGCGC 5 0.125 No Hit GGAAGAGCCCGAGCTGCTGCAGCAGGTTTTGAAAAGGGAATCGATCGTGA 5 0.125 No Hit GAGGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGGAAGGGCG 5 0.125 No Hit GGAACAAACGAGGATAAGATAAAATTGCTTTAAATTTATTTTGCCCAAGT 5 0.125 No Hit GGATTCTTCTTTTTTGTGGGCCATTTGTGGCATGCAGGAAGAGCCCGAGC 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 0.025 0.0 0.0 0.0 0.0 10-11 0.025 0.0 0.0 0.0 0.0 12-13 0.025 0.0 0.0 0.0 0.0 14-15 0.025 0.0 0.0 0.0 0.0 16-17 0.025 0.0 0.0 0.0 0.0 18-19 0.025 0.0 0.0 0.0 0.0 20-21 0.025 0.0 0.0 0.0 0.0 22-23 0.025 0.0 0.0 0.0 0.0 24-25 0.025 0.0 0.0 0.0 0.0 26-27 0.025 0.0 0.0 0.0 0.0 28-29 0.025 0.0 0.0 0.0 0.0 30-31 0.025 0.0 0.0 0.0 0.0 32-33 0.025 0.0 0.0 0.0 0.0 34-35 0.025 0.0 0.0 0.0 0.0 36-37 0.05 0.0 0.0 0.0 0.0 38-39 0.075 0.0 0.0 0.0 0.0 40-41 0.1 0.0 0.0 0.0 0.0 42-43 0.1 0.0 0.0 0.0 0.0 44-45 0.1 0.0 0.0 0.0 0.0 46-47 0.1 0.0 0.0 0.0 0.0 48-49 0.1 0.0 0.0 0.0 0.0 50-51 0.125 0.0 0.0 0.0 0.0 52-53 0.125 0.0 0.0 0.0 0.0 54-55 0.125 0.0 0.0 0.0 0.0 56-57 0.125 0.0 0.0 0.0 0.0 58-59 0.125 0.0 0.0 0.0 0.0 60-61 0.125 0.0 0.0 0.0 0.0 62-63 0.125 0.0 0.0 0.0 0.0 64-65 0.125 0.0 0.0 0.0 0.0 66-67 0.125 0.0 0.0 0.0 0.0 68-69 0.125 0.0 0.0 0.0 0.0 70-71 0.125 0.0 0.0 0.0 0.0 72-73 0.125 0.0 0.0 0.0 0.0 74-75 0.125 0.0 0.0 0.0 0.0 76-77 0.125 0.0 0.0 0.0 0.0 78-79 0.125 0.0 0.0 0.0 0.0 80-81 0.1375 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GGATTCA 35 3.8280556E-4 49.657143 1 GATTCAA 35 3.8280556E-4 49.657143 2 ATTCAAT 40 7.3966914E-4 43.45 3 TTCAATT 45 0.0013209919 38.622223 4 TCAATTT 45 0.0013209919 38.622223 5 CCGTGCT 30 0.0057582413 28.966665 72-73 ATCTTGG 30 0.0057582413 28.966665 80-81 TGGTATG 30 0.0057582413 28.966665 84-85 CTTGGTA 30 0.0057582413 28.966665 82-83 GCTAATC 30 0.0057582413 28.966665 76-77 TAATCTT 30 0.0057582413 28.966665 78-79 CTAATCT 30 0.0057582413 28.966665 76-77 TCTTGGT 30 0.0057582413 28.966665 80-81 CGTGCTA 30 0.0057582413 28.966665 72-73 TGCTAAT 30 0.0057582413 28.966665 74-75 TTGGTAT 30 0.0057582413 28.966665 82-83 GTGCTAA 30 0.0057582413 28.966665 74-75 >>END_MODULE Rejected 312557 READS because READLEN < 1 Read 312557 spots for ERR6133461.sra Written 312557 spots for ERR6133461.sra Rejected 312557 READS because READLEN < 1 Read 312557 spots for ERR6133461.sra Written 312557 spots for ERR6133461.sra Rejected 312557 READS because READLEN < 1 Read 312557 spots for ERR6133461.sra Written 312557 spots for ERR6133461.sra Rejected 312557 READS because READLEN < 1 Read 312557 spots for ERR6133461.sra Written 312557 spots for ERR6133461.sra Rejected 312557 READS because READLEN < 1 Read 312557 spots for ERR6133461.sra Written 312557 spots for ERR6133461.sra Rejected 312557 READS because READLEN < 1 Read 312557 spots for ERR6133461.sra Written 312557 spots for ERR6133461.sra Rejected 312557 READS because READLEN < 1 Read 312557 spots for ERR6133461.sra Written 312557 spots for ERR6133461.sra Rejected 312557 READS because READLEN < 1 Read 312557 spots for ERR6133461.sra Written 312557 spots for ERR6133461.sra Rejected 312557 READS because READLEN < 1 Read 312557 spots for ERR6133461.sra Written 312557 spots for ERR6133461.sra Rejected 312557 READS because READLEN < 1 Read 312557 spots for ERR6133461.sra Written 312557 spots for ERR6133461.sra Rejected 312557 READS because READLEN < 1 Read 312557 spots for ERR6133461.sra Written 312557 spots for ERR6133461.sra Rejected 312557 READS because READLEN < 1 Read 312557 spots for ERR6133461.sra Written 312557 spots for ERR6133461.sra Rejected 312557 READS because READLEN < 1 Read 312557 spots for ERR6133461.sra Written 312557 spots for ERR6133461.sra Rejected 312557 READS because READLEN < 1 Read 312557 spots for ERR6133461.sra Written 312557 spots for ERR6133461.sra Rejected 312557 READS because READLEN < 1 Read 312557 spots for ERR6133461.sra Written 312557 spots for ERR6133461.sra Rejected 312557 READS because READLEN < 1 Read 312557 spots for ERR6133461.sra Written 312557 spots for ERR6133461.sra Rejected 312557 READS because READLEN < 1 Read 312557 spots for ERR6133461.sra Written 312557 spots for ERR6133461.sra Rejected 312575 READS because READLEN < 1 Read 312575 spots for ERR6133461.sra Written 312575 spots for ERR6133461.sra Rejected 312557 READS because READLEN < 1 Read 312557 spots for ERR6133461.sra Written 312557 spots for ERR6133461.sra Rejected 312557 READS because READLEN < 1 Read 312557 spots for ERR6133461.sra Written 312557 spots for ERR6133461.sra SRR ids: ['ERR6133461.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_5lv38d99 ERR6133461.sra spots: 6251158 blocks: [[1, 312557], [312558, 625114], [625115, 937671], [937672, 1250228], [1250229, 1562785], [1562786, 1875342], [1875343, 2187899], [2187900, 2500456], [2500457, 2813013], [2813014, 3125570], [3125571, 3438127], [3438128, 3750684], [3750685, 4063241], [4063242, 4375798], [4375799, 4688355], [4688356, 5000912], [5000913, 5313469], [5313470, 5626026], [5626027, 5938583], [5938584, 6251158]] ERR6133461 file size 1382551 ERR6133461 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 ERR6133461 ERR6133461_1.fastq Input file: ERR6133461_1.fastq trimmed: ERR6133461-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 06:33:22 2024 >> started Sat Dec 7 06:33:25 2024 >> done (2.950s) 6251158 reads processed; of these: 525 ( 0.01%) short reads filtered out after trimming by size control 72 ( 0.00%) empty reads filtered out after trimming by size control 6250561 (99.99%) reads available; of these: 90802 ( 1.45%) trimmed reads available after processing 6159759 (98.55%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 81 0.00% 19 251 0.00% 20 86 0.00% 21 76 0.00% 22 105 0.00% 23 29 0.00% 24 31 0.00% 25 26 0.00% 26 30 0.00% 27 59 0.00% 28 379 0.01% 29 88 0.00% 30 47 0.00% 31 60 0.00% 32 145 0.00% 33 96 0.00% 34 59 0.00% 35 270 0.00% 36 679 0.01% 37 50 0.00% 38 92 0.00% 39 297 0.00% 40 339 0.01% 41 101 0.00% 42 27 0.00% 43 53 0.00% 44 42 0.00% 45 27 0.00% 46 15 0.00% 47 14 0.00% 48 16 0.00% 49 24 0.00% 50 21 0.00% 51 127 0.00% 52 35 0.00% 53 17 0.00% 54 9 0.00% 55 10 0.00% 56 16 0.00% 57 20 0.00% 58 26 0.00% 59 11 0.00% 60 27 0.00% 61 14 0.00% 62 4 0.00% 63 5 0.00% 64 6 0.00% 65 9 0.00% 66 7 0.00% 67 15 0.00% 68 47 0.00% 69 184 0.00% 70 16792 0.27% 71 13673 0.22% 72 14602 0.23% 73 13780 0.22% 74 14863 0.24% 75 13814 0.22% 76 12496 0.20% 77 13043 0.21% 78 14954 0.24% 79 16213 0.26% 80 15525 0.25% 81 18629 0.30% 82 20297 0.32% 83 17712 0.28% 84 16808 0.27% 85 195 0.00% 86 355 0.01% 87 603 0.01% 88 1182 0.02% 89 2372 0.04% 90 4890 0.08% 91 15689 0.25% 92 58582 0.94% 93 5929188 94.86% 6250561 reads passed initial QC criterion=sequence-density sequence-density=0.78 sequence-density-rank=1 fanout-score=2.00 fanout-score-rank=31 prefix-density=0.78 prefix-fanout=2.0 sequence=CAAGGCTAAATAC criterion=fanout-score sequence-density=0.02 sequence-density-rank=22 fanout-score=44.37 fanout-score-rank=1 prefix-density=0.54 prefix-fanout=1.5 sequence=TGCTGCAGCAGCTTAATTTGCATGCCAGGGACGCATGCAACGACCATCTACATATAGCTACTCGATCTACCGCTACCATGAACCGATCCAAGGCTAGCTGCACAAGCTAGGCCCTTATTTCCCTTTGTACGGGTGCATGCATGCCATCCCATGCCATGCTTGTAACCCCCCATAAATAAAATCGCCCTGGTTTAAC Started job on | Dec 07 06:33:41 Started mapping on | Dec 07 06:33:41 Finished on | Dec 07 06:33:49 Mapping speed, Million of reads per hour | 2812.75 Number of input reads | 6250561 Average input read length | 92 UNIQUE READS: Uniquely mapped reads number | 3777047 Uniquely mapped reads % | 60.43% Average mapped length | 91.87 Number of splices: Total | 120107 Number of splices: Annotated (sjdb) | 96839 Number of splices: GT/AG | 113551 Number of splices: GC/AG | 3181 Number of splices: AT/AC | 125 Number of splices: Non-canonical | 3250 Mismatch rate per base, % | 0.45% Deletion rate per base | 0.04% Deletion average length | 1.86 Insertion rate per base | 0.04% Insertion average length | 1.28 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 2289075 % of reads mapped to multiple loci | 36.62% Number of reads mapped to too many loci | 87572 % of reads mapped to too many loci | 1.40% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.44% % of reads unmapped: other | 0.11% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 184439 184439 184439 N_multimapping 2289075 2289075 2289075 N_noFeature 404555 443630 3612621 N_ambiguous 150209 24762 720 UnstrandedReadsAssigned:3222283 PositiveStrandReadsAssigned:3308655 NegativeStrandReadsAssigned:163706 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=93 echo kmer=89 ERR6133461 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: ERR6133461-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 6,250,561 reads, 4,778,018 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,039 rounds 52973 ERR6133461.ke.tsv 35125 ERR6133461.se.tsv 88098 total ==> ERR6133461.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 84 16.9318 PNS24243 293 194 0 0 KQK14069 1603 1504 94 17.2846 KQK14071 474 375 0 0 ==> ERR6133461.se.tsv <== BRADI_1g14170v3 94 BRADI_1g53295v3 17 BRADI_1g59795v3 34 BRADI_1g07683v3 0 BRADI_1g00485v3 1 BRADI_1g20270v3 44 BRADI_1g74790v3 41 BRADI_1g09890v3 0 BRADI_1g77505v3 115 BRADI_1g48960v3 0 ERR6133461 completed mapping pipeline successfully