Starting /dee2/code/volunteer_pipeline.sh ERR6133459 current disk space = 1545457127424 free memory = 1603740420 ERR6133459 SRAfilesize f25b4b1f2dd93a1911a85c18799b6e81 ERR6133459.sra ERR6133459.sra file validated ERR6133459 is single end ERR6133459 is conventional basespace ERR6133459 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133459_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 45 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 35.0685 37.0 33.0 37.0 33.0 37.0 2 36.2725 37.0 37.0 37.0 33.0 37.0 3 35.34625 37.0 33.0 37.0 33.0 37.0 4 34.9475 37.0 33.0 37.0 33.0 37.0 5 34.8815 37.0 37.0 37.0 33.0 37.0 6 35.29425 37.0 37.0 37.0 33.0 37.0 7 36.77625 37.0 37.0 40.0 33.0 40.0 8 36.92175 37.0 37.0 40.0 33.0 40.0 9 37.0665 37.0 37.0 40.0 33.0 40.0 10-11 37.019125 37.0 37.0 40.0 33.0 40.0 12-13 36.96625 37.0 37.0 40.0 33.0 40.0 14-15 36.903625 37.0 37.0 40.0 33.0 40.0 16-17 36.727125 37.0 37.0 40.0 33.0 40.0 18-19 36.456875 37.0 37.0 40.0 33.0 40.0 20-21 36.270625 37.0 37.0 40.0 33.0 40.0 22-23 35.962374999999994 37.0 35.0 40.0 33.0 40.0 24-25 36.1465 37.0 35.0 40.0 33.0 40.0 26-27 36.402125 37.0 37.0 40.0 33.0 40.0 28-29 36.346875 37.0 37.0 40.0 33.0 40.0 30-31 36.298 37.0 37.0 40.0 33.0 40.0 32-33 36.285624999999996 37.0 37.0 40.0 33.0 40.0 34-35 36.202375 37.0 37.0 40.0 33.0 40.0 36-37 36.160624999999996 37.0 37.0 40.0 33.0 40.0 38-39 35.98025 37.0 33.0 40.0 33.0 40.0 40-41 35.933125000000004 37.0 33.0 40.0 33.0 40.0 42-43 35.848124999999996 37.0 33.0 40.0 33.0 40.0 44-45 35.587875 37.0 33.0 38.5 33.0 40.0 46-47 35.504125 37.0 33.0 37.0 33.0 40.0 48-49 35.526125 37.0 33.0 37.0 33.0 40.0 50-51 35.49375 37.0 33.0 37.0 33.0 40.0 52-53 35.22 37.0 33.0 37.0 33.0 40.0 54-55 35.1495 37.0 33.0 37.0 33.0 40.0 56-57 34.915125 37.0 33.0 37.0 33.0 38.5 58-59 34.2545 37.0 33.0 37.0 27.0 37.0 60-61 34.565125 37.0 33.0 37.0 27.0 37.0 62-63 34.50975 37.0 33.0 37.0 30.0 37.0 64-65 34.377875 37.0 33.0 37.0 30.0 37.0 66-67 34.21575 37.0 33.0 37.0 27.0 37.0 68-69 33.314499999999995 35.0 33.0 37.0 27.0 37.0 70-71 33.47512424547284 35.0 33.0 37.0 27.0 37.0 72-73 33.83355414311076 37.0 33.0 37.0 27.0 37.0 74-75 33.80883224458154 37.0 33.0 37.0 27.0 37.0 76-77 33.99922282821342 37.0 33.0 37.0 27.0 37.0 78-79 33.842157982682366 37.0 33.0 37.0 27.0 37.0 80-81 33.81540962501948 37.0 33.0 37.0 27.0 37.0 82-83 33.64602567035895 37.0 33.0 37.0 27.0 37.0 84-85 33.48157115940259 35.0 33.0 37.0 27.0 37.0 86-87 33.41999463950684 35.0 33.0 37.0 27.0 37.0 88-89 33.60024122219244 37.0 33.0 37.0 27.0 37.0 90-91 33.109086035915304 33.0 33.0 37.0 27.0 37.0 92-93 33.20369874028411 33.0 33.0 37.0 27.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 9.0 21 10.0 22 11.0 23 25.0 24 31.0 25 25.0 26 45.0 27 48.0 28 60.0 29 97.0 30 100.0 31 141.0 32 178.0 33 196.0 34 268.0 35 485.0 36 894.0 37 861.0 38 497.0 39 19.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 85.925 4.675 3.6999999999999997 5.7 2 71.22500000000001 16.950000000000003 7.9 3.925 3 37.05 37.55 14.6 10.8 4 30.575000000000003 30.599999999999998 19.275000000000002 19.55 5 28.125 28.050000000000004 26.650000000000002 17.175 6 18.175 39.45 24.725 17.65 7 40.0 27.125 18.575 14.299999999999999 8 27.675 30.2 23.275000000000002 18.85 9 23.425 31.95 27.700000000000003 16.925 10-11 22.7625 29.6875 31.2 16.35 12-13 24.7875 29.2 26.950000000000003 19.0625 14-15 19.1875 35.212500000000006 27.0625 18.5375 16-17 24.962500000000002 31.474999999999998 22.475 21.087500000000002 18-19 24.55 25.0625 32.15 18.2375 20-21 26.339509263895845 23.84827240861292 30.320480721081623 19.491737606409615 22-23 29.262500000000003 21.475 28.512500000000003 20.75 24-25 25.025 25.4875 27.875 21.6125 26-27 26.3625 22.9375 30.312499999999996 20.3875 28-29 24.15 28.512500000000003 28.775000000000002 18.5625 30-31 29.299999999999997 24.975 28.000000000000004 17.724999999999998 32-33 25.6 24.224999999999998 28.237499999999997 21.9375 34-35 22.2 32.6625 25.2875 19.85 36-37 26.365795724465556 25.30316289536192 25.17814726840855 23.15289411176397 38-39 30.31136676253595 24.046517444041516 27.98549456046017 17.65662123296236 40-41 25.656414103525883 23.293323330832706 30.145036259064767 20.905226306576644 42-43 25.322479649342515 29.730745147150905 26.086412022542266 18.860363180964306 44-45 22.97111416781293 26.79754908090534 31.561835688383145 18.669501062898586 46-47 25.3 23.3375 27.6875 23.674999999999997 48-49 25.587500000000002 25.025 28.799999999999997 20.5875 50-51 21.6625 28.15 28.925 21.2625 52-53 22.6072813711998 26.648317277617917 26.097835606155385 24.646565745026898 54-55 23.225 24.5625 31.837500000000002 20.375 56-57 27.150000000000002 28.212500000000002 26.625 18.0125 58-59 22.125 26.637499999999996 30.55 20.6875 60-61 28.812500000000004 25.3125 27.6 18.275 62-63 20.837500000000002 27.1625 31.837500000000002 20.1625 64-65 21.0125 33.2 27.787499999999998 18.0 66-67 24.75 29.762499999999996 26.2625 19.225 68-69 19.625 26.25 29.3875 24.7375 70-71 22.530090270812437 28.66098294884654 27.783350050150453 21.025576730190572 72-73 25.746835443037973 25.58227848101266 30.16455696202532 18.50632911392405 74-75 25.10214504596527 28.434627170582228 28.332482124616952 18.130745658835544 76-77 23.00167331702922 23.70961513708328 26.605740764577167 26.682970781310335 78-79 24.779564315352697 26.80238589211618 29.03267634854772 19.385373443983404 80-81 21.5135276434453 34.33538099594824 26.780812965625405 17.37027839498105 82-83 23.422827668297845 26.544107922232506 27.575717497685492 22.457346911784157 84-85 21.98154833533895 25.484690466639925 32.30378392833266 20.22997726968846 86-87 20.27606539801662 27.298311444652906 29.54971857410882 22.875904583221658 88-89 19.01634950415438 27.539533637094614 31.278477619941036 22.16563923880997 90-91 27.217904047172343 28.625033503082282 27.258107745912625 16.898954703832754 92-93 20.34307156258376 29.65692843741624 29.187885285446264 20.81211471455374 >>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 0.0 16 0.5 17 4.5 18 5.0 19 1.5 20 2.5 21 2.5 22 1.5 23 4.5 24 5.0 25 9.0 26 15.5 27 20.0 28 27.5 29 31.0 30 37.0 31 48.5 32 59.5 33 80.5 34 83.5 35 87.5 36 113.5 37 149.0 38 204.0 39 190.0 40 185.5 41 204.0 42 213.0 43 243.5 44 211.5 45 189.0 46 185.5 47 157.0 48 144.0 49 144.5 50 142.5 51 127.5 52 118.0 53 127.5 54 200.5 55 174.0 56 70.5 57 62.0 58 59.0 59 42.5 60 26.5 61 26.0 62 24.0 63 20.0 64 22.0 65 20.0 66 12.5 67 9.0 68 9.0 69 11.0 70 12.0 71 10.0 72 8.5 73 4.5 74 2.0 75 1.5 76 0.5 77 0.0 78 0.5 79 0.5 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 0.15 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 0.1875 44-45 0.0375 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 24.0 71 17.0 72 18.0 73 17.0 74 16.0 75 20.0 76 7.0 77 16.0 78 18.0 79 12.0 80 19.0 81 21.0 82 29.0 83 18.0 84 17.0 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 3731.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 74.3 #Duplication Level Percentage of deduplicated Percentage of total 1 93.3378196500673 69.35 2 3.1292059219380883 4.65 3 1.177658142664872 2.625 4 0.639300134589502 1.9 5 0.4374158815612382 1.625 6 0.23553162853297444 1.05 7 0.13458950201884254 0.7000000000000001 8 0.1009421265141319 0.6 9 0.1009421265141319 0.675 >10 0.6056527590847914 7.475 >50 0.06729475100942127 3.9 >100 0.033647375504710635 5.45 >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 218 5.45 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 87 2.175 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 69 1.725 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 41 1.0250000000000001 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 31 0.775 No Hit GGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTT 29 0.7250000000000001 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 21 0.525 No Hit GGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGG 19 0.475 No Hit GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 19 0.475 No Hit GGCCTGTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCG 15 0.375 No Hit GGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGC 14 0.35000000000000003 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 14 0.35000000000000003 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 13 0.325 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 12 0.3 No Hit GGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGGG 11 0.27499999999999997 No Hit GGGAAAAGAGGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTT 10 0.25 No Hit CAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATAT 10 0.25 No Hit GGGATGGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACGA 10 0.25 No Hit GGGAGGGTGAGAGCCCCGTCCGGCCCGGACCCTGTCGCCCCACGAGGCGC 10 0.25 No Hit GGAGCAGCCTAAACCGTGAAAACGGGGTTGTGGGAGAGCAATACAAGCGT 10 0.25 No Hit GGAGTATCCTTGATATATAAATATATAGATAAATAGATTTAAATGGAAAA 10 0.25 No Hit GGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTCCT 9 0.22499999999999998 No Hit CAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCT 9 0.22499999999999998 No Hit GGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAA 9 0.22499999999999998 No Hit GGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTT 8 0.2 No Hit GGAAGAGCCCGAGCTGCTGCAGCAGGTTTTGAAAAGGGAATCGATCGTGA 8 0.2 No Hit GGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGCA 8 0.2 No Hit GTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAA 7 0.17500000000000002 No Hit GGGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTT 7 0.17500000000000002 No Hit GGAACAAACGAGGATAAGATAAAATTGCTTTAAATTTATTTTGCCCAAGT 7 0.17500000000000002 No Hit GGAAAAGAAAGCAAAAGCGATTCCCGTAGTAGCGGCGAGCGAAATGGGAG 7 0.17500000000000002 No Hit GAGGAAGGGCGTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAGC 6 0.15 No Hit GCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATC 6 0.15 No Hit GGGGCAGAGGGAATTTCCGGTGGAGCGGTGAAATGCATTGAGATCGGAAA 6 0.15 No Hit GTATTTAGCCTTGCAAGGTGGTCCTTGCTGATTCACACGGGATTCCACGT 6 0.15 No Hit GGGGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCT 6 0.15 No Hit GGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGC 6 0.15 No Hit GGTTTTGAAAAGGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAA 6 0.15 No Hit GGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCTAAATGGATTC 5 0.125 No Hit GGATACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATG 5 0.125 No Hit GATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAAT 5 0.125 No Hit GGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAAA 5 0.125 No Hit GGGGATGGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACG 5 0.125 No Hit GGGGTTGTGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTG 5 0.125 No Hit CGAGGAAGGGCGTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAG 5 0.125 No Hit CACGAACGTAATGCTCACAACTTCCCTCTAGATCTAGCTGCTCTTGAAGT 5 0.125 No Hit GGAAAAGAGGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTTG 5 0.125 No Hit GTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAG 5 0.125 No Hit GGGTGAGAGCCCCGTCCGGCCCGGACCCTGTCGCCCCACGAGGCGCCGTC 5 0.125 No Hit CAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTG 5 0.125 No Hit GGGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTA 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 0.025 0.0 0.0 0.0 0.0 54-55 0.025 0.0 0.0 0.0 0.0 56-57 0.025 0.0 0.0 0.0 0.0 58-59 0.025 0.0 0.0 0.0 0.0 60-61 0.025 0.0 0.0 0.0 0.0 62-63 0.025 0.0 0.0 0.0 0.0 64-65 0.025 0.0 0.0 0.0 0.0 66-67 0.025 0.0 0.0 0.0 0.0 68-69 0.025 0.0 0.0 0.0 0.0 70-71 0.025 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 warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position CGTTCAA 15 8.758201E-4 86.8875 3 GGAGAGC 15 8.758201E-4 86.8875 2 GGCGTTC 15 8.758201E-4 86.8875 1 GTTCAAC 15 8.758201E-4 86.8875 4 GCAATAC 15 8.758201E-4 86.8875 7 GGGAGAG 15 8.758201E-4 86.8875 1 CAATACA 15 8.758201E-4 86.8875 8 GAGCAAT 15 8.758201E-4 86.8875 5 GCGTTCA 15 8.758201E-4 86.8875 2 AGCAATA 15 8.758201E-4 86.8875 6 TCAACCT 20 0.0027439385 65.16563 6 AGAGCAA 20 0.0027439385 65.16563 4 GAGAGCA 20 0.0027439385 65.16563 3 AATACAA 20 0.0027439385 65.16563 9 CAACCTA 25 0.0066407924 52.1325 7 AACCTAA 25 0.0066407924 52.1325 8 ACCTAAA 25 0.0066407924 52.1325 9 ATCTTGG 25 0.0022161324 35.194935 80-81 TGGTATG 25 0.0022161324 35.194935 84-85 CTTGGTA 25 0.0022161324 35.194935 82-83 >>END_MODULE Rejected 168150 READS because READLEN < 1 Read 168150 spots for ERR6133459.sra Written 168150 spots for ERR6133459.sra Rejected 168150 READS because READLEN < 1 Read 168150 spots for ERR6133459.sra Written 168150 spots for ERR6133459.sra Rejected 168150 READS because READLEN < 1 Read 168150 spots for ERR6133459.sra Written 168150 spots for ERR6133459.sra Rejected 168150 READS because READLEN < 1 Read 168150 spots for ERR6133459.sra Written 168150 spots for ERR6133459.sra Rejected 168150 READS because READLEN < 1 Read 168150 spots for ERR6133459.sra Written 168150 spots for ERR6133459.sra Rejected 168150 READS because READLEN < 1 Read 168150 spots for ERR6133459.sra Written 168150 spots for ERR6133459.sra Rejected 168150 READS because READLEN < 1 Read 168150 spots for ERR6133459.sra Written 168150 spots for ERR6133459.sra Rejected 168150 READS because READLEN < 1 Read 168150 spots for ERR6133459.sra Written 168150 spots for ERR6133459.sra Rejected 168150 READS because READLEN < 1 Read 168150 spots for ERR6133459.sra Written 168150 spots for ERR6133459.sra Rejected 168150 READS because READLEN < 1 Read 168150 spots for ERR6133459.sra Written 168150 spots for ERR6133459.sra Rejected 168150 READS because READLEN < 1 Read 168150 spots for ERR6133459.sra Written 168150 spots for ERR6133459.sra Rejected 168164 READS because READLEN < 1 Read 168164 spots for ERR6133459.sra Written 168164 spots for ERR6133459.sra Rejected 168150 READS because READLEN < 1 Read 168150 spots for ERR6133459.sra Written 168150 spots for ERR6133459.sra Rejected 168150 READS because READLEN < 1 Read 168150 spots for ERR6133459.sra Written 168150 spots for ERR6133459.sra Rejected 168150 READS because READLEN < 1 Read 168150 spots for ERR6133459.sra Written 168150 spots for ERR6133459.sra Rejected 168150 READS because READLEN < 1 Read 168150 spots for ERR6133459.sra Written 168150 spots for ERR6133459.sra Rejected 168150 READS because READLEN < 1 Read 168150 spots for ERR6133459.sra Written 168150 spots for ERR6133459.sra Rejected 168150 READS because READLEN < 1 Read 168150 spots for ERR6133459.sra Written 168150 spots for ERR6133459.sra Rejected 168150 READS because READLEN < 1 Read 168150 spots for ERR6133459.sra Written 168150 spots for ERR6133459.sra Rejected 168150 READS because READLEN < 1 Read 168150 spots for ERR6133459.sra Written 168150 spots for ERR6133459.sra SRR ids: ['ERR6133459.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_mknnz1ah ERR6133459.sra spots: 3363014 blocks: [[1, 168150], [168151, 336300], [336301, 504450], [504451, 672600], [672601, 840750], [840751, 1008900], [1008901, 1177050], [1177051, 1345200], [1345201, 1513350], [1513351, 1681500], [1681501, 1849650], [1849651, 2017800], [2017801, 2185950], [2185951, 2354100], [2354101, 2522250], [2522251, 2690400], [2690401, 2858550], [2858551, 3026700], [3026701, 3194850], [3194851, 3363014]] ERR6133459 file size 738528 ERR6133459 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 ERR6133459 ERR6133459_1.fastq Input file: ERR6133459_1.fastq trimmed: ERR6133459-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 06:28:18 2024 >> started Sat Dec 7 06:28:20 2024 >> done (1.688s) 3363014 reads processed; of these: 307 ( 0.01%) short reads filtered out after trimming by size control 28 ( 0.00%) empty reads filtered out after trimming by size control 3362679 (99.99%) reads available; of these: 47985 ( 1.43%) trimmed reads available after processing 3314694 (98.57%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 40 0.00% 19 56 0.00% 20 34 0.00% 21 30 0.00% 22 39 0.00% 23 18 0.00% 24 21 0.00% 25 32 0.00% 26 21 0.00% 27 28 0.00% 28 114 0.00% 29 40 0.00% 30 18 0.00% 31 28 0.00% 32 43 0.00% 33 41 0.00% 34 35 0.00% 35 192 0.01% 36 577 0.02% 37 36 0.00% 38 49 0.00% 39 115 0.00% 40 92 0.00% 41 61 0.00% 42 27 0.00% 43 15 0.00% 44 33 0.00% 45 21 0.00% 46 23 0.00% 47 21 0.00% 48 12 0.00% 49 12 0.00% 50 25 0.00% 51 75 0.00% 52 15 0.00% 53 18 0.00% 54 13 0.00% 55 21 0.00% 56 13 0.00% 57 23 0.00% 58 21 0.00% 59 11 0.00% 60 25 0.00% 61 23 0.00% 62 6 0.00% 63 9 0.00% 64 6 0.00% 65 6 0.00% 66 9 0.00% 67 21 0.00% 68 48 0.00% 69 204 0.01% 70 19272 0.57% 71 17551 0.52% 72 17264 0.51% 73 16393 0.49% 74 16454 0.49% 75 17039 0.51% 76 14909 0.44% 77 15330 0.46% 78 16654 0.50% 79 16094 0.48% 80 16336 0.49% 81 19299 0.57% 82 20807 0.62% 83 19843 0.59% 84 17511 0.52% 85 109 0.00% 86 222 0.01% 87 351 0.01% 88 607 0.02% 89 1218 0.04% 90 2458 0.07% 91 7945 0.24% 92 29924 0.89% 93 3056573 90.90% 3362679 reads passed initial QC criterion=sequence-density sequence-density=1.55 sequence-density-rank=1 fanout-score=2.02 fanout-score-rank=31 prefix-density=1.55 prefix-fanout=2.0 sequence=CAAGGCTAAATAC criterion=fanout-score sequence-density=0.02 sequence-density-rank=26 fanout-score=223.94 fanout-score-rank=1 prefix-density=0.55 prefix-fanout=7.3 sequence=GAAGAAGAAAAGTTTTCTCAACATGGGGAGGAAGTCCCTCCGAAATTTGATTTGTTATTGTATTGTAAGGGGCTTTTTTAGTATTTATCTAAAGGAAGGAACAAACGAGGATAAGATAAAATTGCTTTAAATTTATTTTGCCCAAGTGGGATATATGGCATACTATTCTTTCCATTTTCATCTTTTTTTCTATTCCACTCCATCTAGATATAAGAAAGAACCCAATGCAATGAAATTCCACTAATATACAATACAAAAAAGAAGAATAGATACAGGGTCTCAAACC Started job on | Dec 07 06:28:35 Started mapping on | Dec 07 06:28:35 Finished on | Dec 07 06:28:44 Mapping speed, Million of reads per hour | 1345.07 Number of input reads | 3362679 Average input read length | 91 UNIQUE READS: Uniquely mapped reads number | 1853448 Uniquely mapped reads % | 55.12% Average mapped length | 91.67 Number of splices: Total | 77790 Number of splices: Annotated (sjdb) | 64630 Number of splices: GT/AG | 74102 Number of splices: GC/AG | 1986 Number of splices: AT/AC | 47 Number of splices: Non-canonical | 1655 Mismatch rate per base, % | 0.47% Deletion rate per base | 0.04% Deletion average length | 1.85 Insertion rate per base | 0.02% Insertion average length | 1.87 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 1210473 % of reads mapped to multiple loci | 36.00% Number of reads mapped to too many loci | 70548 % of reads mapped to too many loci | 2.10% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 6.61% % of reads unmapped: other | 0.18% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 298758 298758 298758 N_multimapping 1210473 1210473 1210473 N_noFeature 167894 186140 1772760 N_ambiguous 72676 10056 367 UnstrandedReadsAssigned:1612878 PositiveStrandReadsAssigned:1657252 NegativeStrandReadsAssigned:80321 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=93 echo kmer=89 ERR6133459 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: ERR6133459-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 3,362,679 reads, 2,311,674 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,017 rounds 52973 ERR6133459.ke.tsv 35125 ERR6133459.se.tsv 88098 total ==> ERR6133459.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 46 19.2118 PNS24243 293 194 0 0 KQK14069 1603 1504 6 2.28595 KQK14071 474 375 0 0 ==> ERR6133459.se.tsv <== BRADI_1g14170v3 6 BRADI_1g53295v3 18 BRADI_1g59795v3 16 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 31 BRADI_1g74790v3 25 BRADI_1g09890v3 0 BRADI_1g77505v3 59 BRADI_1g48960v3 0 ERR6133459 completed mapping pipeline successfully