Starting /dee2/code/volunteer_pipeline.sh ERR6133500 current disk space = 1544444825600 free memory = 1424825408 ERR6133500 SRAfilesize f0b9b9739ac8073fbd38b86e93e929fb ERR6133500.sra ERR6133500.sra file validated ERR6133500 is single end ERR6133500 is conventional basespace ERR6133500 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133500_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 35.357 37.0 33.0 37.0 33.0 37.0 2 36.46925 37.0 37.0 37.0 37.0 37.0 3 35.933 37.0 37.0 37.0 33.0 37.0 4 35.4225 37.0 37.0 37.0 33.0 37.0 5 35.339 37.0 37.0 37.0 33.0 37.0 6 35.7165 37.0 37.0 37.0 33.0 37.0 7 37.61625 40.0 37.0 40.0 33.0 40.0 8 37.66025 40.0 37.0 40.0 33.0 40.0 9 37.66 40.0 37.0 40.0 33.0 40.0 10-11 37.650375 38.5 37.0 40.0 33.0 40.0 12-13 37.544 37.0 37.0 40.0 33.0 40.0 14-15 37.502250000000004 37.0 37.0 40.0 33.0 40.0 16-17 37.341875 37.0 37.0 40.0 33.0 40.0 18-19 37.1755 37.0 37.0 40.0 33.0 40.0 20-21 36.964375000000004 37.0 37.0 40.0 33.0 40.0 22-23 36.87675 37.0 37.0 40.0 33.0 40.0 24-25 36.829375 37.0 37.0 40.0 33.0 40.0 26-27 37.059375 37.0 37.0 40.0 33.0 40.0 28-29 37.03675 37.0 37.0 40.0 33.0 40.0 30-31 36.963 37.0 37.0 40.0 33.0 40.0 32-33 36.92375 37.0 37.0 40.0 33.0 40.0 34-35 36.901375 37.0 37.0 40.0 33.0 40.0 36-37 36.693875 37.0 37.0 40.0 33.0 40.0 38-39 36.5315 37.0 37.0 40.0 33.0 40.0 40-41 36.335375 37.0 37.0 40.0 33.0 40.0 42-43 36.41975 37.0 37.0 40.0 33.0 40.0 44-45 36.366875 37.0 37.0 40.0 33.0 40.0 46-47 36.195875 37.0 37.0 40.0 33.0 40.0 48-49 36.23725 37.0 37.0 38.5 33.0 40.0 50-51 36.083375000000004 37.0 37.0 37.0 33.0 40.0 52-53 35.816125 37.0 33.0 37.0 33.0 40.0 54-55 35.713125 37.0 33.0 37.0 33.0 40.0 56-57 35.541875000000005 37.0 33.0 37.0 33.0 40.0 58-59 34.511375 37.0 33.0 37.0 30.0 37.0 60-61 35.019875 37.0 33.0 37.0 33.0 37.0 62-63 34.885999999999996 37.0 33.0 37.0 33.0 37.0 64-65 34.8435 37.0 33.0 37.0 33.0 37.0 66-67 34.825625 37.0 33.0 37.0 33.0 37.0 68-69 34.037875 35.0 33.0 37.0 30.0 37.0 70-71 34.145766064257025 35.0 33.0 37.0 30.0 37.0 72-73 34.56037796424175 37.0 33.0 37.0 33.0 37.0 74-75 34.51166374028021 37.0 33.0 37.0 33.0 37.0 76-77 34.400304671415725 37.0 33.0 37.0 33.0 37.0 78-79 34.328045658424514 37.0 33.0 37.0 33.0 37.0 80-81 34.26882110149887 37.0 33.0 37.0 33.0 37.0 82-83 34.07461129678111 37.0 33.0 37.0 27.0 37.0 84-85 33.87764982116792 37.0 33.0 37.0 27.0 37.0 86-87 33.768088033012376 37.0 33.0 37.0 27.0 37.0 88-89 33.90220082530949 37.0 33.0 37.0 27.0 37.0 90-91 33.69339752407153 37.0 33.0 37.0 27.0 37.0 92-93 33.72613480055021 37.0 33.0 37.0 27.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 5.0 21 7.0 22 12.0 23 11.0 24 14.0 25 25.0 26 19.0 27 37.0 28 51.0 29 50.0 30 76.0 31 103.0 32 157.0 33 173.0 34 244.0 35 476.0 36 872.0 37 944.0 38 698.0 39 26.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 84.075 3.925 3.1 8.9 2 65.10000000000001 19.6 9.15 6.15 3 34.775 37.974999999999994 14.374999999999998 12.875 4 32.775 29.2 19.2 18.825 5 24.875 28.175 26.450000000000003 20.5 6 19.25 36.6 26.8 17.349999999999998 7 34.375 28.525 20.1 17.0 8 26.8 29.349999999999998 25.05 18.8 9 24.875 29.475 28.325 17.325 10-11 24.4875 28.725 27.775 19.0125 12-13 26.375 27.5875 27.650000000000002 18.387500000000003 14-15 21.4375 30.075000000000003 29.5875 18.9 16-17 25.2125 29.549999999999997 25.5 19.7375 18-19 25.087500000000002 26.5375 28.199999999999996 20.175 20-21 25.825 25.6 28.6875 19.8875 22-23 26.1625 24.837500000000002 27.474999999999998 21.525 24-25 24.45 26.025 28.512500000000003 21.0125 26-27 24.95 24.3875 30.112499999999997 20.549999999999997 28-29 24.962500000000002 27.487499999999997 28.249999999999996 19.3 30-31 28.199999999999996 25.45 26.687499999999996 19.662499999999998 32-33 24.7375 25.650000000000002 28.4375 21.175 34-35 23.3875 28.1875 27.6375 20.7875 36-37 24.95 25.087500000000002 27.05 22.912499999999998 38-39 27.350213085986464 25.156680872399097 28.866883930809728 18.62622211080471 40-41 25.431789737171464 26.057571964956196 29.386733416770966 19.123904881101378 42-43 24.66541588492808 29.368355222013758 26.49155722326454 19.474671669793622 44-45 23.1875 25.5125 30.55 20.75 46-47 24.8625 24.575 28.15 22.412499999999998 48-49 24.7 24.975 30.1375 20.1875 50-51 23.275000000000002 26.937499999999996 28.7375 21.05 52-53 23.867334167709636 27.521902377972467 26.68335419274093 21.927409261576972 54-55 23.5625 28.1125 28.8875 19.4375 56-57 25.21565195649456 26.940867608451057 28.30353794224278 19.5399424928116 58-59 23.7375 26.275 29.799999999999997 20.1875 60-61 25.3 26.674999999999997 27.737499999999997 20.2875 62-63 21.987499999999997 28.299999999999997 30.7875 18.925 64-65 22.975 29.4375 28.475 19.112499999999997 66-67 24.3625 28.875 27.425 19.3375 68-69 23.0875 27.1125 28.575 21.224999999999998 70-71 23.960420841683366 25.951903807615228 28.895290581162325 21.19238476953908 72-73 26.190476190476193 25.89918946301925 29.103343465045594 18.806990881458965 74-75 24.490841552452927 26.591520430382992 28.871525553990008 20.046112463174072 76-77 22.272609484322363 25.991189427312776 29.580202124902826 22.155998963462036 78-79 24.672088142707242 26.02308499475341 30.181007345225602 19.123819517313745 80-81 22.76595744680851 30.79787234042553 28.125 18.311170212765955 82-83 23.684920420825463 25.438359859724848 29.552198543296466 21.324521176153226 84-85 23.406879539536796 24.900644100315198 31.286830204193507 20.4056461559545 86-87 22.07702888583219 28.583218707015128 28.67950481430536 20.660247592847316 88-89 21.499312242090785 28.968363136176066 29.697386519944978 19.834938101788172 90-91 24.99312242090784 28.56946354883081 27.57909215955984 18.858321870701513 92-93 21.40302613480055 28.94085281980743 29.436038514442913 20.220082530949107 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 0.0 1 0.0 2 0.0 3 0.0 4 0.5 5 0.5 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 1.0 17 5.5 18 5.0 19 1.0 20 0.5 21 0.0 22 2.5 23 5.5 24 7.0 25 6.5 26 11.5 27 21.0 28 27.5 29 30.0 30 31.0 31 45.0 32 64.0 33 73.5 34 83.0 35 104.0 36 122.0 37 156.0 38 194.5 39 184.5 40 190.5 41 199.5 42 196.0 43 209.0 44 199.0 45 193.0 46 194.5 47 170.5 48 155.0 49 167.0 50 166.0 51 148.0 52 133.5 53 130.0 54 150.0 55 125.5 56 75.0 57 66.5 58 59.5 59 45.5 60 38.0 61 34.0 62 28.0 63 24.0 64 18.0 65 16.5 66 13.5 67 10.5 68 12.0 69 10.5 70 9.0 71 9.0 72 7.0 73 4.0 74 2.0 75 1.0 76 1.5 77 1.5 78 0.5 79 0.0 80 0.5 81 0.5 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 0.27499999999999997 40-41 0.125 42-43 0.0625 44-45 0.0 46-47 0.0 48-49 0.0 50-51 0.0 52-53 0.125 54-55 0.0 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 16.0 71 20.0 72 32.0 73 19.0 74 19.0 75 25.0 76 20.0 77 22.0 78 30.0 79 29.0 80 16.0 81 27.0 82 36.0 83 27.0 84 27.0 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 3635.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 81.27499999999999 #Duplication Level Percentage of deduplicated Percentage of total 1 93.66348815749001 76.125 2 3.3835742848354355 5.5 3 0.984312519224854 2.4 4 0.584435558289757 1.9 5 0.27683789603199016 1.125 6 0.2153183635804368 1.05 7 0.15379883112888343 0.8750000000000001 8 0.09227929867733005 0.6 9 0.06151953245155337 0.44999999999999996 >10 0.5536757920639803 7.6499999999999995 >50 0.030759766225776686 2.325 >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 GGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGC 93 2.325 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 31 0.775 No Hit GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 30 0.75 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 23 0.575 No Hit GGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGG 23 0.575 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 21 0.525 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 18 0.44999999999999996 No Hit GGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTCCT 18 0.44999999999999996 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 17 0.42500000000000004 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 16 0.4 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 15 0.375 No Hit GGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGC 14 0.35000000000000003 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 14 0.35000000000000003 No Hit GGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTT 13 0.325 No Hit GGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTT 11 0.27499999999999997 No Hit GGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAA 11 0.27499999999999997 No Hit GGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAA 11 0.27499999999999997 No Hit GGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAAGGCGATCAAATTC 10 0.25 No Hit GGGGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCT 10 0.25 No Hit GGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGC 9 0.22499999999999998 No Hit GGGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTG 9 0.22499999999999998 No Hit GGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAAA 8 0.2 No Hit GTATGGAAGGCGATCAAATTCGAGTTCGCGCCGGTAGATACTATCGATTA 8 0.2 No Hit GGGCCGGGTATCTCTCTGCATGTACGTATGCCTGTAATGTACGTAGCTAC 8 0.2 No Hit CAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATAT 7 0.17500000000000002 No Hit GGCCTGTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCG 7 0.17500000000000002 No Hit CAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCT 7 0.17500000000000002 No Hit GGAGTATCCTTGATATATAAATATATAGATAAATAGATTTAAATGGAAAA 7 0.17500000000000002 No Hit GGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGT 7 0.17500000000000002 No Hit GCAGCTTGCAAATGGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAA 6 0.15 No Hit GAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGC 6 0.15 No Hit GGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTTGAAATCGGA 6 0.15 No Hit GGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCTAAATGGATTC 6 0.15 No Hit GGAAGGCGATCAAATTCGAGTTCGCGCCGGTAGATACTATCGATTAATAG 6 0.15 No Hit GAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTA 6 0.15 No Hit CAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTG 6 0.15 No Hit GGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCG 5 0.125 No Hit GGTGGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGC 5 0.125 No Hit GAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAAT 5 0.125 No Hit GGGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGA 5 0.125 No Hit CAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAACGAAGGG 5 0.125 No Hit GGTATTAGTACTATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATC 5 0.125 No Hit GGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGGG 5 0.125 No Hit GTACAAGCTCGTAACGAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAAT 5 0.125 No Hit GGGGAAGTACACCAGCGACGGCGAGGCCGCCGCCGCCAAGGAAGGCATGT 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 0.0125 0.0 0.0 0.0 0.0 20-21 0.025 0.0 0.0 0.0 0.0 22-23 0.037500000000000006 0.0 0.0 0.0 0.0 24-25 0.05 0.0 0.0 0.0 0.0 26-27 0.05 0.0 0.0 0.0 0.0 28-29 0.05 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 0.05 0.0 0.0 0.0 0.0 36-37 0.05 0.0 0.0 0.0 0.0 38-39 0.05 0.0 0.0 0.0 0.0 40-41 0.05 0.0 0.0 0.0 0.0 42-43 0.075 0.0 0.0 0.0 0.0 44-45 0.075 0.0 0.0 0.0 0.0 46-47 0.075 0.0 0.0 0.0 0.0 48-49 0.075 0.0 0.0 0.0 0.0 50-51 0.075 0.0 0.0 0.0 0.0 52-53 0.075 0.0 0.0 0.0 0.0 54-55 0.075 0.0 0.0 0.0 0.0 56-57 0.075 0.0 0.0 0.0 0.0 58-59 0.075 0.0 0.0 0.0 0.0 60-61 0.075 0.0 0.0 0.0 0.0 62-63 0.075 0.0 0.0 0.0 0.0 64-65 0.075 0.0 0.0 0.0 0.0 66-67 0.075 0.0 0.0 0.0 0.0 68-69 0.075 0.0 0.0 0.0 0.0 70-71 0.075 0.0 0.0 0.0 0.0 72-73 0.1 0.0 0.0 0.0 0.0 74-75 0.1 0.0 0.0 0.0 0.0 76-77 0.1125 0.0 0.0 0.0 0.0 78-79 0.125 0.0 0.0 0.0 0.0 80-81 0.125 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position CAATACA 20 2.6719646E-5 85.012505 8 AGAGCAA 20 2.6719646E-5 85.012505 4 AGCAATA 20 2.6719646E-5 85.012505 6 GGAGAGC 25 8.079643E-5 68.01 2 GCAATAC 25 8.079643E-5 68.01 7 GAGAGCA 25 8.079643E-5 68.01 3 AATACAA 25 8.079643E-5 68.01 9 GGGAGAG 30 1.9920967E-4 56.675003 1 GAGCAAT 30 1.9920967E-4 56.675003 5 CATCACT 20 4.1875598E-4 49.28261 82-83 ATCACTA 20 4.1875598E-4 49.28261 84-85 AGCATCA 20 4.1875598E-4 49.28261 80-81 TCACTAG 20 4.1875598E-4 49.28261 84-85 ACTAGCT 20 4.1875598E-4 49.28261 86-87 GCATCAC 20 4.1875598E-4 49.28261 82-83 AAGCATC 20 4.1875598E-4 49.28261 80-81 CCGAAAG 20 5.941845E-4 45.952705 76-77 AGCCGAA 20 6.145152E-4 45.6443 74-75 GCCGAAA 20 6.145152E-4 45.6443 74-75 TAGCCGA 20 6.568331E-4 45.039738 72-73 >>END_MODULE Rejected 432434 READS because READLEN < 1 Read 432434 spots for ERR6133500.sra Written 432434 spots for ERR6133500.sra Rejected 432434 READS because READLEN < 1 Read 432434 spots for ERR6133500.sra Written 432434 spots for ERR6133500.sra Rejected 432434 READS because READLEN < 1 Read 432434 spots for ERR6133500.sra Written 432434 spots for ERR6133500.sra Rejected 432434 READS because READLEN < 1 Read 432434 spots for ERR6133500.sra Written 432434 spots for ERR6133500.sra Rejected 432434 READS because READLEN < 1 Read 432434 spots for ERR6133500.sra Written 432434 spots for ERR6133500.sra Rejected 432434 READS because READLEN < 1 Read 432434 spots for ERR6133500.sra Written 432434 spots for ERR6133500.sra Rejected 432434 READS because READLEN < 1 Read 432434 spots for ERR6133500.sra Written 432434 spots for ERR6133500.sra Rejected 432434 READS because READLEN < 1 Read 432434 spots for ERR6133500.sra Written 432434 spots for ERR6133500.sra Rejected 432434 READS because READLEN < 1 Read 432434 spots for ERR6133500.sra Written 432434 spots for ERR6133500.sra Rejected 432434 READS because READLEN < 1 Read 432434 spots for ERR6133500.sra Written 432434 spots for ERR6133500.sra Rejected 432434 READS because READLEN < 1 Read 432434 spots for ERR6133500.sra Written 432434 spots for ERR6133500.sra Rejected 432434 READS because READLEN < 1 Read 432434 spots for ERR6133500.sra Written 432434 spots for ERR6133500.sra Rejected 432434 READS because READLEN < 1 Read 432434 spots for ERR6133500.sra Written 432434 spots for ERR6133500.sra Rejected 432434 READS because READLEN < 1 Read 432434 spots for ERR6133500.sra Written 432434 spots for ERR6133500.sra Rejected 432434 READS because READLEN < 1 Read 432434 spots for ERR6133500.sra Written 432434 spots for ERR6133500.sra Rejected 432434 READS because READLEN < 1 Read 432434 spots for ERR6133500.sra Written 432434 spots for ERR6133500.sra Rejected 432434 READS because READLEN < 1 Read 432434 spots for ERR6133500.sra Written 432434 spots for ERR6133500.sra Rejected 432434 READS because READLEN < 1 Read 432434 spots for ERR6133500.sra Written 432434 spots for ERR6133500.sra Rejected 432441 READS because READLEN < 1 Read 432441 spots for ERR6133500.sra Written 432441 spots for ERR6133500.sra Rejected 432434 READS because READLEN < 1 Read 432434 spots for ERR6133500.sra Written 432434 spots for ERR6133500.sra SRR ids: ['ERR6133500.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_wu4o3sml ERR6133500.sra spots: 8648687 blocks: [[1, 432434], [432435, 864868], [864869, 1297302], [1297303, 1729736], [1729737, 2162170], [2162171, 2594604], [2594605, 3027038], [3027039, 3459472], [3459473, 3891906], [3891907, 4324340], [4324341, 4756774], [4756775, 5189208], [5189209, 5621642], [5621643, 6054076], [6054077, 6486510], [6486511, 6918944], [6918945, 7351378], [7351379, 7783812], [7783813, 8216246], [8216247, 8648687]] ERR6133500 file size 1899524 ERR6133500 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 ERR6133500 ERR6133500_1.fastq Input file: ERR6133500_1.fastq trimmed: ERR6133500-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 07:25:34 2024 >> started Sat Dec 7 07:25:38 2024 >> done (4.037s) 8648687 reads processed; of these: 775 ( 0.01%) short reads filtered out after trimming by size control 76 ( 0.00%) empty reads filtered out after trimming by size control 8647836 (99.99%) reads available; of these: 134998 ( 1.56%) trimmed reads available after processing 8512838 (98.44%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 191 0.00% 19 364 0.00% 20 159 0.00% 21 96 0.00% 22 148 0.00% 23 46 0.00% 24 65 0.00% 25 47 0.00% 26 34 0.00% 27 67 0.00% 28 126 0.00% 29 83 0.00% 30 76 0.00% 31 91 0.00% 32 178 0.00% 33 82 0.00% 34 117 0.00% 35 682 0.01% 36 1083 0.01% 37 121 0.00% 38 216 0.00% 39 551 0.01% 40 615 0.01% 41 206 0.00% 42 74 0.00% 43 57 0.00% 44 100 0.00% 45 74 0.00% 46 45 0.00% 47 40 0.00% 48 42 0.00% 49 62 0.00% 50 68 0.00% 51 465 0.01% 52 85 0.00% 53 35 0.00% 54 41 0.00% 55 24 0.00% 56 37 0.00% 57 85 0.00% 58 76 0.00% 59 37 0.00% 60 94 0.00% 61 56 0.00% 62 16 0.00% 63 10 0.00% 64 14 0.00% 65 19 0.00% 66 39 0.00% 67 57 0.00% 68 115 0.00% 69 397 0.00% 70 49810 0.58% 71 48342 0.56% 72 53762 0.62% 73 48212 0.56% 74 47777 0.55% 75 48881 0.57% 76 42137 0.49% 77 44775 0.52% 78 51467 0.60% 79 56121 0.65% 80 50692 0.59% 81 59699 0.69% 82 64546 0.75% 83 62858 0.73% 84 53796 0.62% 85 305 0.00% 86 472 0.01% 87 778 0.01% 88 1401 0.02% 89 2721 0.03% 90 5583 0.06% 91 17520 0.20% 92 87149 1.01% 93 7741324 89.52% 8647836 reads passed initial QC criterion=sequence-density sequence-density=1.43 sequence-density-rank=1 fanout-score=1.96 fanout-score-rank=31 prefix-density=1.44 prefix-fanout=2.0 sequence=CAAGGCTAAATAC criterion=fanout-score sequence-density=0.02 sequence-density-rank=23 fanout-score=196.53 fanout-score-rank=1 prefix-density=0.52 prefix-fanout=7.1 sequence=GAAGAAGAAAAGTTTTCTCAACATGGGGAGGAAGTCCCTCCGAAATTTGATTTGTTATTGTATTGTAAGGGGCTTTTTTAGTATTTATCTAAAGGAAGGAACAAACGAGGATAAGATAAAATTTCTTTAAATTTATTTTGCCCAAGTGGGATATATGGCATACTATTCTTTCCATTTTCATCTTTTTTTCTATTCCACTCCATCTAGATATAAGAAAGAACCCAATGCAATGAAATTCCACTAATATACAATACAAAAAAGAAGAATAGATACAGGGTCTCAAACCTTGCTATAGAGTTTTTGCTT Started job on | Dec 07 07:25:58 Started mapping on | Dec 07 07:25:58 Finished on | Dec 07 07:26:12 Mapping speed, Million of reads per hour | 2223.73 Number of input reads | 8647836 Average input read length | 91 UNIQUE READS: Uniquely mapped reads number | 5712569 Uniquely mapped reads % | 66.06% Average mapped length | 90.85 Number of splices: Total | 242979 Number of splices: Annotated (sjdb) | 198655 Number of splices: GT/AG | 230148 Number of splices: GC/AG | 6353 Number of splices: AT/AC | 123 Number of splices: Non-canonical | 6355 Mismatch rate per base, % | 0.52% Deletion rate per base | 0.05% Deletion average length | 1.88 Insertion rate per base | 0.03% Insertion average length | 1.85 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 2621590 % of reads mapped to multiple loci | 30.31% Number of reads mapped to too many loci | 152311 % of reads mapped to too many loci | 1.76% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.76% % of reads unmapped: other | 0.10% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 313677 313677 313677 N_multimapping 2621590 2621590 2621590 N_noFeature 406653 462987 5448362 N_ambiguous 236600 28546 1171 UnstrandedReadsAssigned:5069316 PositiveStrandReadsAssigned:5221036 NegativeStrandReadsAssigned:263036 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=93 echo kmer=89 ERR6133500 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: ERR6133500-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 8,647,836 reads, 6,876,859 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,133 rounds 52973 ERR6133500.ke.tsv 35125 ERR6133500.se.tsv 88098 total ==> ERR6133500.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 141 20.181 PNS24243 293 194 0 0 KQK14069 1603 1504 66 8.61737 KQK14071 474 375 0 0 ==> ERR6133500.se.tsv <== BRADI_1g14170v3 65 BRADI_1g53295v3 135 BRADI_1g59795v3 28 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 121 BRADI_1g74790v3 69 BRADI_1g09890v3 0 BRADI_1g77505v3 201 BRADI_1g48960v3 1 ERR6133500 completed mapping pipeline successfully