Starting /dee2/code/volunteer_pipeline.sh ERR6133421 current disk space = 1546902716416 free memory = 1421013044 ERR6133421 SRAfilesize ef57c0bdc92115a74109fc3af96cf35f ERR6133421.sra ERR6133421.sra file validated ERR6133421 is single end ERR6133421 is conventional basespace ERR6133421 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133421_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 fail #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 29.9335 33.0 27.0 33.0 15.0 37.0 2 33.7265 37.0 33.0 37.0 27.0 37.0 3 33.75725 37.0 33.0 37.0 27.0 37.0 4 33.95325 37.0 33.0 37.0 27.0 37.0 5 34.0265 37.0 33.0 37.0 27.0 37.0 6 34.1885 37.0 33.0 37.0 27.0 37.0 7 35.3105 37.0 33.0 40.0 27.0 40.0 8 35.07875 37.0 33.0 40.0 27.0 40.0 9 35.4185 37.0 33.0 40.0 33.0 40.0 10-11 35.3725 37.0 33.0 40.0 30.0 40.0 12-13 35.15725 37.0 33.0 38.5 27.0 40.0 14-15 35.181 37.0 33.0 37.0 27.0 40.0 16-17 34.890625 37.0 33.0 37.0 27.0 40.0 18-19 34.681 37.0 33.0 37.0 27.0 40.0 20-21 34.09425 37.0 33.0 37.0 27.0 40.0 22-23 33.968125 37.0 33.0 37.0 24.5 40.0 24-25 33.397999999999996 37.0 33.0 37.0 22.0 40.0 26-27 33.258875 37.0 33.0 37.0 22.0 40.0 28-29 32.8615 37.0 33.0 37.0 22.0 40.0 30-31 32.8485 37.0 33.0 37.0 22.0 40.0 32-33 32.388125 35.0 33.0 37.0 22.0 40.0 34-35 31.57125 33.0 27.0 37.0 18.5 40.0 36-37 31.179625 33.0 27.0 37.0 15.0 40.0 38-39 31.378999999999998 33.0 27.0 37.0 22.0 40.0 40-41 31.532874999999997 33.0 27.0 37.0 22.0 40.0 42-43 31.07525 33.0 27.0 37.0 15.0 40.0 44-45 30.838124999999998 33.0 27.0 37.0 15.0 40.0 46-47 30.33275 33.0 27.0 37.0 15.0 37.0 48-49 29.9155 33.0 27.0 37.0 15.0 37.0 50-51 29.569125 33.0 27.0 37.0 15.0 37.0 52-53 29.385875 33.0 27.0 37.0 15.0 37.0 54-55 29.25025 33.0 27.0 37.0 15.0 37.0 56-57 28.614625 33.0 27.0 35.0 15.0 37.0 58-59 28.4375 33.0 27.0 33.0 15.0 37.0 60-61 28.119500000000002 33.0 27.0 33.0 15.0 37.0 62-63 27.836875 33.0 22.0 33.0 15.0 37.0 64-65 27.3375 33.0 22.0 33.0 10.5 37.0 66-67 26.874375 33.0 22.0 33.0 10.5 37.0 68-69 26.411125 27.0 22.0 33.0 10.5 35.0 70-71 28.12970163316583 33.0 27.0 33.0 15.0 37.0 72-73 28.53911117551594 33.0 27.0 33.0 15.0 37.0 74-75 28.568913460300834 33.0 27.0 33.0 15.0 37.0 76-77 28.234239548602204 33.0 27.0 33.0 15.0 37.0 78-79 27.512508571399298 33.0 27.0 33.0 10.5 37.0 80-81 26.971760237223926 33.0 24.5 33.0 6.0 37.0 82-83 26.109012235149606 33.0 22.0 33.0 4.0 37.0 84-85 25.505819822310137 33.0 22.0 33.0 2.0 37.0 86-87 24.44701374207188 27.0 15.0 33.0 2.0 37.0 88-89 23.86139006342495 30.0 15.0 33.0 2.0 35.0 90-91 22.57729915433404 27.0 2.0 33.0 2.0 35.0 92-93 21.219344608879492 27.0 2.0 33.0 2.0 33.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 80.0 21 100.0 22 145.0 23 152.0 24 195.0 25 209.0 26 231.0 27 241.0 28 248.0 29 266.0 30 263.0 31 265.0 32 258.0 33 262.0 34 299.0 35 316.0 36 258.0 37 184.0 38 27.0 39 1.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 70.75 7.35 7.199999999999999 14.7 2 52.925 23.724999999999998 14.549999999999999 8.799999999999999 3 32.35 36.775000000000006 17.125 13.750000000000002 4 27.925 29.725 21.099999999999998 21.25 5 25.874999999999996 25.275 29.45 19.400000000000002 6 17.150000000000002 36.3 28.7 17.849999999999998 7 34.849999999999994 27.025 20.674999999999997 17.45 8 23.95 26.075 28.349999999999998 21.625 9 22.3 33.1 26.224999999999998 18.375 10-11 22.3625 27.3 31.25 19.0875 12-13 21.6625 29.4 28.875 20.0625 14-15 19.900000000000002 31.1875 29.3375 19.575 16-17 23.724999999999998 29.062500000000004 24.587500000000002 22.625 18-19 24.5 24.637500000000003 31.3 19.5625 20-21 25.25 25.074999999999996 29.9 19.775000000000002 22-23 28.775000000000002 22.95 28.975 19.3 24-25 22.6875 25.974999999999998 29.525000000000002 21.8125 26-27 25.8 23.8875 29.25 21.0625 28-29 22.475 28.875 29.925 18.725 30-31 28.349999999999998 26.7625 26.2875 18.6 32-33 25.4625 24.2875 28.537499999999998 21.712500000000002 34-35 21.512500000000003 32.9625 26.3125 19.2125 36-37 25.362499999999997 26.400000000000002 25.025 23.2125 38-39 29.212500000000002 24.7 26.950000000000003 19.1375 40-41 24.087500000000002 24.2875 31.65 19.975 42-43 26.6 28.825 25.5625 19.0125 44-45 23.7625 25.5125 30.7125 20.0125 46-47 25.4375 25.775 26.325 22.4625 48-49 24.5625 25.0 28.0875 22.35 50-51 20.962500000000002 28.675 28.1875 22.175 52-53 23.125 27.3375 25.724999999999998 23.8125 54-55 21.55 26.7625 30.2625 21.425 56-57 26.474999999999998 27.725 26.687499999999996 19.112499999999997 58-59 22.3625 28.575 29.3875 19.675 60-61 28.6125 26.375 26.450000000000003 18.5625 62-63 20.849999999999998 27.750000000000004 31.4625 19.9375 64-65 20.5875 33.6 27.5875 18.224999999999998 66-67 24.587500000000002 29.599999999999998 26.700000000000003 19.112499999999997 68-69 21.2875 27.150000000000002 28.6375 22.925 70-71 22.24310776942356 28.345864661654137 26.829573934837093 22.581453634085214 72-73 25.463956571140006 25.640701931574295 29.768968564575182 19.126372932710517 74-75 25.616577676074243 28.14645308924485 27.536231884057973 18.700737350622934 76-77 21.743025339134885 25.223957000255954 27.732275403122603 25.300742257486565 78-79 25.14831054939386 27.98555584214599 28.3982460665463 18.467887541913854 80-81 21.350649350649352 33.42857142857143 27.844155844155843 17.376623376623375 82-83 23.36949418376683 26.140373807345448 26.36256698470788 24.127565024179844 84-85 21.755171959414945 25.74779285808407 31.82237448939254 20.674660693108446 86-87 19.70137420718816 30.88002114164905 27.048097251585624 22.370507399577168 88-89 20.031712473572938 27.906976744186046 30.377906976744185 21.68340380549683 90-91 24.947145877378436 29.92864693446089 25.34355179704017 19.780655391120508 92-93 20.65274841437632 30.64217758985201 27.048097251585624 21.656976744186046 >>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 2.0 18 3.5 19 2.5 20 3.5 21 6.5 22 6.5 23 5.0 24 7.0 25 12.0 26 11.0 27 13.0 28 18.5 29 17.5 30 28.0 31 43.5 32 58.5 33 75.5 34 77.0 35 85.0 36 118.5 37 176.0 38 220.0 39 210.5 40 208.0 41 220.0 42 224.0 43 232.5 44 214.0 45 178.5 46 156.5 47 145.0 48 126.0 49 123.0 50 125.5 51 128.0 52 131.5 53 137.0 54 201.0 55 187.0 56 105.0 57 85.0 58 62.5 59 33.0 60 23.5 61 23.5 62 17.5 63 11.0 64 8.0 65 8.0 66 10.0 67 8.0 68 6.0 69 8.0 70 11.0 71 11.0 72 7.0 73 1.5 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 0.0 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 0.0 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 >>END_MODULE >>Sequence Length Distribution warn #Length Count 70 20.0 71 12.0 72 15.0 73 16.0 74 8.0 75 14.0 76 16.0 77 16.0 78 12.0 79 14.0 80 14.0 81 10.0 82 15.0 83 13.0 84 21.0 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 3784.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 73.97500000000001 #Duplication Level Percentage of deduplicated Percentage of total 1 92.05812774586009 68.10000000000001 2 3.8188577222034468 5.65 3 1.2842176410949644 2.85 4 0.9800608313619465 2.9000000000000004 5 0.33795201081446435 1.25 6 0.37174721189591076 1.6500000000000001 7 0.16897600540723218 0.8750000000000001 8 0.13518080432578572 0.8 9 0.16897600540723218 1.125 >10 0.6421088205474822 9.975000000000001 >50 0.0 0.0 >100 0.03379520108144643 4.825 >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 193 4.825 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 49 1.225 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 33 0.8250000000000001 No Hit CAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTG 30 0.75 No Hit CAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATAT 29 0.7250000000000001 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 29 0.7250000000000001 No Hit CAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCT 28 0.7000000000000001 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 27 0.675 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 23 0.575 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 20 0.5 No Hit GGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAA 16 0.4 No Hit GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 16 0.4 No Hit TCAAAAGAGGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGGA 16 0.4 No Hit GTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCT 15 0.375 No Hit GGAAAAGAAAGCAAAAGCGATTCCCGTAGTAGCGGCGAGCGAAATGGGAG 14 0.35000000000000003 No Hit GGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCTAAA 13 0.325 No Hit GCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCT 11 0.27499999999999997 No Hit GGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCTAAATGGATTC 10 0.25 No Hit GGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGC 10 0.25 No Hit GTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAG 10 0.25 No Hit CAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTT 9 0.22499999999999998 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 9 0.22499999999999998 No Hit GTACTATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTT 9 0.22499999999999998 No Hit GTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAA 9 0.22499999999999998 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 9 0.22499999999999998 No Hit GGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGC 8 0.2 No Hit GGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGG 8 0.2 No Hit AGTCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAA 8 0.2 No Hit GTATTAGTACTATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATCT 8 0.2 No Hit GGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAAC 7 0.17500000000000002 No Hit GGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTCCT 7 0.17500000000000002 No Hit GGGGTTGTGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTG 7 0.17500000000000002 No Hit GTGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCC 7 0.17500000000000002 No Hit GGGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTA 7 0.17500000000000002 No Hit GGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAA 6 0.15 No Hit GCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATC 6 0.15 No Hit GGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTG 6 0.15 No Hit GGTTGTGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAG 6 0.15 No Hit GATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAAT 6 0.15 No Hit GAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAAT 6 0.15 No Hit TCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATATCAT 6 0.15 No Hit GTCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAAT 6 0.15 No Hit CACGAACGTAATGCTCACAACTTCCCTCTAGATCTAGCTGCTCTTGAAGT 6 0.15 No Hit AACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGA 6 0.15 No Hit GGGTGAGAGCCCCGTCCGGCCCGGACCCTGTCGCCCCACGAGGCGCCGTC 6 0.15 No Hit CAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAACGAAGGG 5 0.125 No Hit TATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATA 5 0.125 No Hit CACCCTAGATGGCTAAAGTCCAGTAGCCGAAAGCATCACTAGCTTACGCT 5 0.125 No Hit GGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAAA 5 0.125 No Hit CTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGT 5 0.125 No Hit GCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAACGA 5 0.125 No Hit GGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTT 5 0.125 No Hit GGGTTGTGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGA 5 0.125 No Hit GGAGTATCCTTGATATATAAATATATAGATAAATAGATTTAAATGGAAAA 5 0.125 No Hit GAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGC 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 0.05 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 0.075 0.0 0.0 0.0 0.0 76-77 0.075 0.0 0.0 0.0 0.0 78-79 0.075 0.0 0.0 0.0 0.0 80-81 0.075 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GGAGAGC 40 1.135331E-5 53.710938 2 AGAGCAA 40 1.135331E-5 53.710938 4 GAGAGCA 40 1.135331E-5 53.710938 3 AGCAATA 40 1.135331E-5 53.710938 6 GCAATAC 45 2.280516E-5 47.743057 7 GGGAGAG 45 2.280516E-5 47.743057 1 CAATACA 45 2.280516E-5 47.743057 8 TGCCGCA 25 4.6680747E-5 42.968754 44-45 GAGCAAT 50 4.25181E-5 42.968754 5 AATACAA 55 7.463215E-5 39.062504 9 CATCACT 30 8.575485E-5 38.710587 82-83 ATCACTA 30 8.575485E-5 38.710587 84-85 CACTAGC 30 8.575485E-5 38.710587 86-87 TCACTAG 30 8.575485E-5 38.710587 84-85 ACTAGCT 30 8.575485E-5 38.710587 86-87 GCATCAC 30 8.575485E-5 38.710587 82-83 CCGAAAG 30 1.0060981E-4 37.691887 76-77 TCCAGTA 30 1.2683614E-4 36.26055 68-69 GATGGCT 30 1.3674125E-4 35.80729 56-57 GAGTGCC 30 1.3674125E-4 35.80729 42-43 >>END_MODULE Rejected 81965 READS because READLEN < 1 Read 81965 spots for ERR6133421.sra Written 81965 spots for ERR6133421.sra Rejected 81965 READS because READLEN < 1 Read 81965 spots for ERR6133421.sra Written 81965 spots for ERR6133421.sra Rejected 81965 READS because READLEN < 1 Read 81965 spots for ERR6133421.sra Written 81965 spots for ERR6133421.sra Rejected 81965 READS because READLEN < 1 Read 81965 spots for ERR6133421.sra Written 81965 spots for ERR6133421.sra Rejected 81965 READS because READLEN < 1 Read 81965 spots for ERR6133421.sra Written 81965 spots for ERR6133421.sra Rejected 81965 READS because READLEN < 1 Read 81965 spots for ERR6133421.sra Written 81965 spots for ERR6133421.sra Rejected 81965 READS because READLEN < 1 Read 81965 spots for ERR6133421.sra Written 81965 spots for ERR6133421.sra Rejected 81965 READS because READLEN < 1 Read 81965 spots for ERR6133421.sra Written 81965 spots for ERR6133421.sra Rejected 81965 READS because READLEN < 1 Read 81965 spots for ERR6133421.sra Written 81965 spots for ERR6133421.sra Rejected 81965 READS because READLEN < 1 Read 81965 spots for ERR6133421.sra Written 81965 spots for ERR6133421.sra Rejected 81965 READS because READLEN < 1 Read 81965 spots for ERR6133421.sra Written 81965 spots for ERR6133421.sra Rejected 81969 READS because READLEN < 1 Read 81969 spots for ERR6133421.sra Written 81969 spots for ERR6133421.sra Rejected 81965 READS because READLEN < 1 Read 81965 spots for ERR6133421.sra Written 81965 spots for ERR6133421.sra Rejected 81965 READS because READLEN < 1 Read 81965 spots for ERR6133421.sra Written 81965 spots for ERR6133421.sra Rejected 81965 READS because READLEN < 1 Read 81965 spots for ERR6133421.sra Written 81965 spots for ERR6133421.sra Rejected 81965 READS because READLEN < 1 Read 81965 spots for ERR6133421.sra Written 81965 spots for ERR6133421.sra Rejected 81965 READS because READLEN < 1 Read 81965 spots for ERR6133421.sra Written 81965 spots for ERR6133421.sra Rejected 81965 READS because READLEN < 1 Read 81965 spots for ERR6133421.sra Written 81965 spots for ERR6133421.sra Rejected 81965 READS because READLEN < 1 Read 81965 spots for ERR6133421.sra Written 81965 spots for ERR6133421.sra Rejected 81965 READS because READLEN < 1 Read 81965 spots for ERR6133421.sra Written 81965 spots for ERR6133421.sra SRR ids: ['ERR6133421.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_avlme0kv ERR6133421.sra spots: 1639304 blocks: [[1, 81965], [81966, 163930], [163931, 245895], [245896, 327860], [327861, 409825], [409826, 491790], [491791, 573755], [573756, 655720], [655721, 737685], [737686, 819650], [819651, 901615], [901616, 983580], [983581, 1065545], [1065546, 1147510], [1147511, 1229475], [1229476, 1311440], [1311441, 1393405], [1393406, 1475370], [1475371, 1557335], [1557336, 1639304]] ERR6133421 file size 359799 ERR6133421 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 ERR6133421 ERR6133421_1.fastq Input file: ERR6133421_1.fastq trimmed: ERR6133421-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 04:52:07 2024 >> started Sat Dec 7 04:52:12 2024 >> done (5.035s) 1639304 reads processed; of these: 32 ( 0.00%) short reads filtered out after trimming by size control 0 ( 0.00%) empty reads filtered out after trimming by size control 1639272 (100.00%) reads available; of these: 422946 (25.80%) trimmed reads available after processing 1216326 (74.20%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 9 0.00% 19 20 0.00% 20 5 0.00% 21 1 0.00% 22 6 0.00% 23 2 0.00% 24 2 0.00% 25 1 0.00% 26 1 0.00% 27 3 0.00% 28 4 0.00% 29 5 0.00% 30 1 0.00% 31 7 0.00% 32 11 0.00% 33 3 0.00% 34 0 0.00% 35 1 0.00% 36 3 0.00% 37 2 0.00% 38 16 0.00% 39 22 0.00% 40 25 0.00% 41 8 0.00% 42 14 0.00% 43 21 0.00% 44 22 0.00% 45 31 0.00% 46 45 0.00% 47 62 0.00% 48 94 0.01% 49 116 0.01% 50 184 0.01% 51 233 0.01% 52 288 0.02% 53 440 0.03% 54 639 0.04% 55 913 0.06% 56 1149 0.07% 57 1767 0.11% 58 1268 0.08% 59 1539 0.09% 60 1856 0.11% 61 2118 0.13% 62 2288 0.14% 63 2355 0.14% 64 2782 0.17% 65 2897 0.18% 66 2970 0.18% 67 3048 0.19% 68 2848 0.17% 69 2789 0.17% 70 9286 0.57% 71 9610 0.59% 72 11313 0.69% 73 11943 0.73% 74 12383 0.76% 75 13704 0.84% 76 14240 0.87% 77 16047 0.98% 78 16851 1.03% 79 17946 1.09% 80 19102 1.17% 81 21928 1.34% 82 23674 1.44% 83 23890 1.46% 84 26795 1.63% 85 21527 1.31% 86 22002 1.34% 87 24710 1.51% 88 29545 1.80% 89 31458 1.92% 90 33068 2.02% 91 36146 2.21% 92 31035 1.89% 93 1126135 68.70% 1639272 reads passed initial QC criterion=sequence-density sequence-density=2.75 sequence-density-rank=1 fanout-score=2.07 fanout-score-rank=23 prefix-density=2.82 prefix-fanout=2.0 sequence=CAAGGCTAAATAC criterion=fanout-score sequence-density=0.01 sequence-density-rank=30 fanout-score=12.80 fanout-score-rank=1 prefix-density=0.04 prefix-fanout=2.5 sequence=GAAGAAATTAGAGTGCTCAAAGCAAGCCATCGCTCTGGATACATTAGCATGGGATAACATCATAGGATTCCGGTCCTATTGTGTTGGCCTTCGGGATCGGAGTAATGATTAATAGGGACAGTCGGGGGCATTCGTATTTCATAGTCAGAGGTGAAATTCTTGGATTTATGAAAGACGAACAACTGCGAAAGCATTTGCCAAGGATGTTTTCATTAATCAAGAACGAAAGTTGGGGGCTCGAAGACGATCAGATACCGT Potential 3prime adapter identified. Now checking if in reference sequence Warning: gzbuffer added in zlib v1.2.3.5. Unable to change buffer size from default of 8192. 1 reads; of these: 1 (100.00%) were unpaired; of these: 0 (0.00%) aligned 0 times 0 (0.00%) aligned exactly 1 time 1 (100.00%) aligned >1 times 100.00% overall alignment rate Potential adapter found in reference sequence. Continuing without clipping. Started job on | Dec 07 04:53:48 Started mapping on | Dec 07 04:53:49 Finished on | Dec 07 04:54:35 Mapping speed, Million of reads per hour | 128.29 Number of input reads | 1639272 Average input read length | 89 UNIQUE READS: Uniquely mapped reads number | 702384 Uniquely mapped reads % | 42.85% Average mapped length | 88.78 Number of splices: Total | 27042 Number of splices: Annotated (sjdb) | 21133 Number of splices: GT/AG | 25553 Number of splices: GC/AG | 577 Number of splices: AT/AC | 36 Number of splices: Non-canonical | 876 Mismatch rate per base, % | 0.81% Deletion rate per base | 0.04% Deletion average length | 1.73 Insertion rate per base | 0.02% Insertion average length | 1.42 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 826063 % of reads mapped to multiple loci | 50.39% Number of reads mapped to too many loci | 48376 % of reads mapped to too many loci | 2.95% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 3.29% % of reads unmapped: other | 0.52% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 110825 110825 110825 N_multimapping 826063 826063 826063 N_noFeature 65087 72191 671196 N_ambiguous 28843 4717 177 UnstrandedReadsAssigned:608454 PositiveStrandReadsAssigned:625476 NegativeStrandReadsAssigned:31011 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=85 echo kmer=81 ERR6133421 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: ERR6133421-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 1,639,272 reads, 1,112,378 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 902 rounds 52973 ERR6133421.ke.tsv 35125 ERR6133421.se.tsv 88098 total ==> ERR6133421.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 22 18.8136 PNS24243 293 194 0 0 KQK14069 1603 1504 6 4.68066 KQK14071 474 375 0 0 ==> ERR6133421.se.tsv <== BRADI_1g14170v3 6 BRADI_1g53295v3 4 BRADI_1g59795v3 5 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 6 BRADI_1g74790v3 3 BRADI_1g09890v3 0 BRADI_1g77505v3 12 BRADI_1g48960v3 0 ERR6133421 completed mapping pipeline successfully