Starting /dee2/code/volunteer_pipeline.sh ERR6133574 current disk space = 1547581837312 free memory = 1364191912 ERR6133574 SRAfilesize c7209d45511a887e58b76d4a2767ce0b ERR6133574.sra ERR6133574.sra file validated ERR6133574 is single end ERR6133574 is conventional basespace ERR6133574 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133574_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 35.4655 37.0 33.0 37.0 33.0 37.0 2 36.53775 37.0 37.0 37.0 37.0 37.0 3 36.087 37.0 37.0 37.0 33.0 37.0 4 35.41325 37.0 37.0 37.0 33.0 37.0 5 35.171 37.0 37.0 37.0 33.0 37.0 6 35.5845 37.0 37.0 37.0 33.0 37.0 7 37.39275 40.0 37.0 40.0 33.0 40.0 8 37.477 37.0 37.0 40.0 33.0 40.0 9 37.56325 37.0 37.0 40.0 33.0 40.0 10-11 37.487 37.0 37.0 40.0 33.0 40.0 12-13 37.431625 37.0 37.0 40.0 33.0 40.0 14-15 37.422375 37.0 37.0 40.0 33.0 40.0 16-17 37.269125 37.0 37.0 40.0 33.0 40.0 18-19 37.2625 37.0 37.0 40.0 33.0 40.0 20-21 37.12825 37.0 37.0 40.0 33.0 40.0 22-23 36.99425 37.0 37.0 40.0 33.0 40.0 24-25 37.245875 37.0 37.0 40.0 33.0 40.0 26-27 37.204125 37.0 37.0 40.0 33.0 40.0 28-29 37.153999999999996 37.0 37.0 40.0 33.0 40.0 30-31 37.0305 37.0 37.0 40.0 33.0 40.0 32-33 36.895875000000004 37.0 37.0 40.0 33.0 40.0 34-35 36.723625 37.0 37.0 40.0 33.0 40.0 36-37 36.61025 37.0 37.0 40.0 33.0 40.0 38-39 36.3735 37.0 37.0 40.0 33.0 40.0 40-41 36.194874999999996 37.0 37.0 40.0 33.0 40.0 42-43 36.069 37.0 37.0 40.0 33.0 40.0 44-45 35.705375000000004 37.0 35.0 40.0 33.0 40.0 46-47 35.4955 37.0 33.0 37.0 33.0 40.0 48-49 35.459875 37.0 33.0 37.0 33.0 40.0 50-51 35.326 37.0 33.0 37.0 33.0 40.0 52-53 34.9705 37.0 33.0 37.0 27.0 40.0 54-55 34.898625 37.0 33.0 37.0 27.0 40.0 56-57 34.71525 37.0 33.0 37.0 27.0 37.0 58-59 33.60625 35.0 33.0 37.0 27.0 37.0 60-61 34.191500000000005 37.0 33.0 37.0 27.0 37.0 62-63 34.191874999999996 37.0 33.0 37.0 27.0 37.0 64-65 34.079499999999996 37.0 33.0 37.0 27.0 37.0 66-67 34.165625000000006 37.0 33.0 37.0 27.0 37.0 68-69 33.510625000000005 35.0 33.0 37.0 27.0 37.0 70-71 33.59276578156313 35.0 33.0 37.0 27.0 37.0 72-73 34.014278891952245 37.0 33.0 37.0 27.0 37.0 74-75 33.64670769528142 37.0 33.0 37.0 27.0 37.0 76-77 33.77405679566053 37.0 33.0 37.0 27.0 37.0 78-79 33.94719258360146 37.0 33.0 37.0 27.0 37.0 80-81 33.8021829413177 37.0 33.0 37.0 27.0 37.0 82-83 33.70060346295752 37.0 33.0 37.0 27.0 37.0 84-85 33.74655440755179 37.0 33.0 37.0 27.0 37.0 86-87 33.49280945043657 37.0 33.0 37.0 27.0 37.0 88-89 33.68888032871084 37.0 33.0 37.0 27.0 37.0 90-91 33.35631741140216 37.0 33.0 37.0 27.0 37.0 92-93 33.196456086286595 37.0 33.0 37.0 27.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 10.0 21 11.0 22 19.0 23 27.0 24 29.0 25 29.0 26 35.0 27 57.0 28 66.0 29 58.0 30 90.0 31 140.0 32 135.0 33 154.0 34 237.0 35 439.0 36 898.0 37 884.0 38 678.0 39 4.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 85.6 3.4750000000000005 3.875 7.049999999999999 2 70.875 17.45 6.825 4.8500000000000005 3 35.725 37.625 15.125 11.525 4 32.6 28.000000000000004 19.225 20.175 5 25.775 29.775000000000002 26.325 18.125 6 18.6 39.275 25.124999999999996 17.0 7 35.875 28.175 19.175 16.775000000000002 8 29.975 28.225 23.849999999999998 17.95 9 24.224999999999998 29.45 26.35 19.975 10-11 24.2625 28.349999999999998 27.400000000000002 19.9875 12-13 26.674999999999997 26.674999999999997 26.0125 20.6375 14-15 22.0 31.3125 28.050000000000004 18.637500000000003 16-17 24.925 30.2875 24.637500000000003 20.150000000000002 18-19 23.962500000000002 25.724999999999998 28.5875 21.725 20-21 25.900000000000002 25.587500000000002 28.287499999999998 20.225 22-23 27.675 23.1625 27.025 22.1375 24-25 24.6 24.525 27.8375 23.0375 26-27 25.7875 24.5125 30.5375 19.162499999999998 28-29 24.212500000000002 25.9875 29.599999999999998 20.200000000000003 30-31 27.750000000000004 24.725 26.5375 20.9875 32-33 25.1 27.175 26.2875 21.4375 34-35 24.3 28.075 25.912499999999998 21.712500000000002 36-37 26.787499999999998 24.462500000000002 26.150000000000002 22.6 38-39 28.19454863715929 24.81870467616904 28.794698674668666 18.192048012003 40-41 26.694173543385848 25.506376594148538 26.86921730432608 20.930232558139537 42-43 25.453181647705964 29.128641080135015 25.86573321665208 19.55244405550694 44-45 24.675 25.7875 28.65 20.8875 46-47 25.1875 23.825 27.712500000000002 23.275000000000002 48-49 25.974999999999998 23.724999999999998 29.75 20.549999999999997 50-51 25.2375 26.05 28.1 20.6125 52-53 25.789473684210527 26.854636591478698 25.726817042606516 21.629072681704262 54-55 23.875 27.55 28.512500000000003 20.0625 56-57 27.625 25.624999999999996 26.387500000000003 20.3625 58-59 23.075000000000003 25.15 29.5375 22.237499999999997 60-61 26.8125 24.9125 27.85 20.424999999999997 62-63 20.65 28.575 32.125 18.65 64-65 22.912499999999998 28.3875 28.375 20.325 66-67 24.943735933983497 27.85696424106027 28.094523630907727 19.10477619404851 68-69 23.0 27.375 26.8375 22.787499999999998 70-71 24.524524524524523 26.363863863863862 27.102102102102105 22.00950950950951 72-73 26.556224899598398 24.1214859437751 28.413654618473892 20.908634538152608 74-75 24.077572094194686 27.90580531419217 28.76212063971792 19.25450195189523 76-77 22.03968153671174 25.502337924933656 28.547959054720078 23.910021483634523 78-79 24.265078560567662 25.30410542321338 30.00506842372022 20.425747592498734 80-81 22.968332697443724 29.53071346814193 29.047437364873456 18.453516469540887 82-83 22.909741754027102 25.543339299411915 29.915622602914855 21.631296343646124 84-85 23.023613963039015 22.535934291581107 32.340862422997944 22.09958932238193 86-87 21.725731895223422 27.966101694915253 30.059065228556754 20.24910118130457 88-89 21.302003081664097 28.49255264509502 30.17462763225475 20.03081664098613 90-91 25.924499229583976 26.938880328710834 28.40267077555213 18.733949666153055 92-93 21.610169491525426 29.699537750385208 29.51977401129944 19.170518746789934 >>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 0.5 14 0.5 15 0.0 16 0.0 17 8.5 18 9.0 19 1.0 20 1.5 21 1.0 22 2.5 23 7.5 24 8.0 25 5.0 26 8.5 27 11.5 28 18.0 29 26.0 30 34.0 31 42.0 32 57.5 33 69.5 34 72.5 35 83.5 36 95.5 37 124.0 38 165.0 39 176.5 40 173.0 41 181.5 42 186.0 43 188.0 44 178.5 45 174.0 46 197.5 47 184.5 48 148.5 49 150.5 50 164.5 51 158.0 52 147.5 53 168.0 54 185.5 55 132.5 56 72.5 57 65.5 58 64.0 59 53.5 60 44.5 61 40.0 62 34.5 63 33.0 64 30.0 65 20.5 66 15.0 67 15.0 68 12.5 69 14.5 70 15.0 71 12.0 72 10.5 73 8.0 74 6.0 75 3.5 76 1.5 77 0.5 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 0.0 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 0.025 40-41 0.025 42-43 0.0125 44-45 0.0 46-47 0.0 48-49 0.0 50-51 0.0 52-53 0.25 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 0.025 68-69 0.0 70-71 0.0 72-73 0.0 74-75 0.012591286829513975 76-77 0.0 78-79 0.0 80-81 0.012716174974567649 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 8.0 71 4.0 72 8.0 73 6.0 74 6.0 75 7.0 76 9.0 77 2.0 78 8.0 79 6.0 80 8.0 81 11.0 82 12.0 83 7.0 84 4.0 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 3894.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 75.35 #Duplication Level Percentage of deduplicated Percentage of total 1 92.03715992037161 69.35 2 4.180491041804911 6.3 3 1.39349701393497 3.15 4 0.5972130059721301 1.7999999999999998 5 0.29860650298606506 1.125 6 0.232249502322495 1.05 7 0.16589250165892502 0.8750000000000001 8 0.13271400132714 0.8 9 0.13271400132714 0.8999999999999999 >10 0.7631055076310551 10.925 >50 0.06635700066357 3.7249999999999996 >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 GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 56 1.4000000000000001 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 42 1.05 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 35 0.8750000000000001 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 35 0.8750000000000001 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 33 0.8250000000000001 No Hit GGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGG 29 0.7250000000000001 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 24 0.6 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 21 0.525 No Hit GGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGGG 19 0.475 No Hit GGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTT 19 0.475 No Hit GGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAA 19 0.475 No Hit GGAAGAGCCCGAGCTGCTGCAGCAGGTTTTGAAAAGGGAATCGATCGTGA 18 0.44999999999999996 No Hit GGAGTATCCTTGATATATAAATATATAGATAAATAGATTTAAATGGAAAA 16 0.4 No Hit GGCCTGTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCG 14 0.35000000000000003 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 13 0.325 No Hit GGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCTAAATGGATTC 12 0.3 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 12 0.3 No Hit GGGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTG 12 0.3 No Hit GGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAA 11 0.27499999999999997 No Hit CAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCT 11 0.27499999999999997 No Hit GGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGC 11 0.27499999999999997 No Hit GGAAAAGAAAGCAAAAGCGATTCCCGTAGTAGCGGCGAGCGAAATGGGAG 11 0.27499999999999997 No Hit GGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCG 10 0.25 No Hit GGTTTTGAAAAGGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAA 10 0.25 No Hit GGAAAAGAGGGGTTACTTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTT 9 0.22499999999999998 No Hit GGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAAA 9 0.22499999999999998 No Hit GGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTT 9 0.22499999999999998 No Hit GGGGAAGTACACCAGCGACGGCGAGGCCGCCGCCGCCAAGGAAGGCATGT 9 0.22499999999999998 No Hit GAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTG 8 0.2 No Hit GTACAAGCTCGTAACGAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAAT 8 0.2 No Hit GGGTTGTGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGA 8 0.2 No Hit GAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGC 8 0.2 No Hit CAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAACGAAGGG 7 0.17500000000000002 No Hit GGGGTTACTTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTTGAAATCGG 7 0.17500000000000002 No Hit GTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAA 7 0.17500000000000002 No Hit GGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAACCCTCTTAACTA 7 0.17500000000000002 No Hit GGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAACCCTCTTAACT 7 0.17500000000000002 No Hit CAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATAT 6 0.15 No Hit GTACTATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTT 6 0.15 No Hit GGGAAAAGAGGGGTTACTTTTTTTTCATTTTTCCCTTAAAAGATAGGCTT 6 0.15 No Hit GGGCCGGGTATCTCTCTGCATGTACGTATGCCTGTAATGTACGTAGCTAC 6 0.15 No Hit GGAATAAGAATAAATCGCAACTCCTTTCCACTACACATAAAAATTGATTT 6 0.15 No Hit GGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTG 6 0.15 No Hit CAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTG 6 0.15 No Hit GGGAATTTGATCAACAAGTGTCTTCGTCTTCAGTTCAGTATGTTGATTTC 5 0.125 No Hit GGGTTACTTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTTGAAATCGGA 5 0.125 No Hit GGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGC 5 0.125 No Hit GGTGGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGC 5 0.125 No Hit GTATGGAAGGCGATCAAATTCGAGTTCGCGCCGGTAGATACTATCGATTA 5 0.125 No Hit GGAGTCCCATATATATATGTATAAGATGCCAGCCCGGTTTCGTCAACCAT 5 0.125 No Hit GTATTTAGCCTTGCAAGGTGGTCCTTGCTGATTCACACGGGATTCCACGT 5 0.125 No Hit GTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAG 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 0.0 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 0.0125 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 0.025 0.0 0.0 0.0 0.0 38-39 0.025 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 0.0625 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 0.0875 0.0 0.0 0.0 0.0 68-69 0.1 0.0 0.0 0.0 0.0 70-71 0.1 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 0.1 0.0 0.0 0.0 0.0 78-79 0.1 0.0 0.0 0.0 0.0 80-81 0.1 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GCAATAC 20 2.3823906E-5 87.0 7 GGGAGAG 20 2.3823906E-5 87.0 1 CAATACA 20 2.3823906E-5 87.0 8 GAGAGCA 20 2.3823906E-5 87.0 3 AATACAA 20 2.3823906E-5 87.0 9 GGAGAGC 25 7.205523E-5 69.6 2 AGCAATA 25 7.205523E-5 69.6 6 GAGCAAT 30 1.7769479E-4 58.0 5 AGAGCAA 30 1.7769479E-4 58.0 4 GTTGAGT 20 7.824886E-4 43.5 38-39 GCTAGGC 20 7.824886E-4 43.5 26-27 GAGTGCC 20 7.824886E-4 43.5 42-43 AGTAGCC 20 7.824886E-4 43.5 70-71 TGCCGCA 20 7.824886E-4 43.5 44-45 ATGGCTA 20 7.824886E-4 43.5 58-59 TAGCCGA 20 7.824886E-4 43.5 72-73 TTGAGTG 20 7.824886E-4 43.5 40-41 TCCAGTA 20 7.824886E-4 43.5 68-69 CCGCACC 20 7.824886E-4 43.5 46-47 CACCCTA 20 7.824886E-4 43.5 50-51 >>END_MODULE Rejected 153959 READS because READLEN < 1 Read 153959 spots for ERR6133574.sra Written 153959 spots for ERR6133574.sra Rejected 153959 READS because READLEN < 1 Read 153959 spots for ERR6133574.sra Written 153959 spots for ERR6133574.sra Rejected 153959 READS because READLEN < 1 Read 153959 spots for ERR6133574.sra Written 153959 spots for ERR6133574.sra Rejected 153959 READS because READLEN < 1 Read 153959 spots for ERR6133574.sra Written 153959 spots for ERR6133574.sra Rejected 153959 READS because READLEN < 1 Read 153959 spots for ERR6133574.sra Written 153959 spots for ERR6133574.sra Rejected 153959 READS because READLEN < 1 Read 153959 spots for ERR6133574.sra Written 153959 spots for ERR6133574.sra Rejected 153959 READS because READLEN < 1 Read 153959 spots for ERR6133574.sra Written 153959 spots for ERR6133574.sra Rejected 153959 READS because READLEN < 1 Read 153959 spots for ERR6133574.sra Written 153959 spots for ERR6133574.sra Rejected 153959 READS because READLEN < 1 Read 153959 spots for ERR6133574.sra Written 153959 spots for ERR6133574.sra Rejected 153959 READS because READLEN < 1 Read 153959 spots for ERR6133574.sra Written 153959 spots for ERR6133574.sra Rejected 153959 READS because READLEN < 1 Read 153959 spots for ERR6133574.sra Written 153959 spots for ERR6133574.sra Rejected 153959 READS because READLEN < 1 Read 153959 spots for ERR6133574.sra Written 153959 spots for ERR6133574.sra Rejected 153959 READS because READLEN < 1 Read 153959 spots for ERR6133574.sra Written 153959 spots for ERR6133574.sra Rejected 153959 READS because READLEN < 1 Read 153959 spots for ERR6133574.sra Written 153959 spots for ERR6133574.sra Rejected 153960 READS because READLEN < 1 Read 153960 spots for ERR6133574.sra Written 153960 spots for ERR6133574.sra Rejected 153959 READS because READLEN < 1 Read 153959 spots for ERR6133574.sra Written 153959 spots for ERR6133574.sra Rejected 153959 READS because READLEN < 1 Read 153959 spots for ERR6133574.sra Written 153959 spots for ERR6133574.sra Rejected 153959 READS because READLEN < 1 Read 153959 spots for ERR6133574.sra Written 153959 spots for ERR6133574.sra Rejected 153959 READS because READLEN < 1 Read 153959 spots for ERR6133574.sra Written 153959 spots for ERR6133574.sra Rejected 153959 READS because READLEN < 1 Read 153959 spots for ERR6133574.sra Written 153959 spots for ERR6133574.sra SRR ids: ['ERR6133574.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_k9rurff0 ERR6133574.sra spots: 3079181 blocks: [[1, 153959], [153960, 307918], [307919, 461877], [461878, 615836], [615837, 769795], [769796, 923754], [923755, 1077713], [1077714, 1231672], [1231673, 1385631], [1385632, 1539590], [1539591, 1693549], [1693550, 1847508], [1847509, 2001467], [2001468, 2155426], [2155427, 2309385], [2309386, 2463344], [2463345, 2617303], [2617304, 2771262], [2771263, 2925221], [2925222, 3079181]] ERR6133574 file size 680707 ERR6133574 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 ERR6133574 ERR6133574_1.fastq Input file: ERR6133574_1.fastq trimmed: ERR6133574-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 Fri Dec 6 23:51:52 2024 >> started Fri Dec 6 23:51:54 2024 >> done (1.632s) 3079181 reads processed; of these: 212 ( 0.01%) short reads filtered out after trimming by size control 44 ( 0.00%) empty reads filtered out after trimming by size control 3078925 (99.99%) reads available; of these: 64251 ( 2.09%) trimmed reads available after processing 3014674 (97.91%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 52 0.00% 19 94 0.00% 20 47 0.00% 21 29 0.00% 22 25 0.00% 23 10 0.00% 24 13 0.00% 25 7 0.00% 26 15 0.00% 27 22 0.00% 28 22 0.00% 29 39 0.00% 30 12 0.00% 31 36 0.00% 32 38 0.00% 33 18 0.00% 34 32 0.00% 35 195 0.01% 36 445 0.01% 37 31 0.00% 38 46 0.00% 39 98 0.00% 40 141 0.00% 41 66 0.00% 42 18 0.00% 43 14 0.00% 44 17 0.00% 45 17 0.00% 46 4 0.00% 47 8 0.00% 48 7 0.00% 49 10 0.00% 50 6 0.00% 51 53 0.00% 52 13 0.00% 53 9 0.00% 54 7 0.00% 55 7 0.00% 56 8 0.00% 57 7 0.00% 58 15 0.00% 59 8 0.00% 60 17 0.00% 61 14 0.00% 62 3 0.00% 63 5 0.00% 64 3 0.00% 65 1 0.00% 66 7 0.00% 67 9 0.00% 68 19 0.00% 69 61 0.00% 70 6446 0.21% 71 5777 0.19% 72 5963 0.19% 73 5344 0.17% 74 5878 0.19% 75 5453 0.18% 76 4962 0.16% 77 5026 0.16% 78 5538 0.18% 79 6258 0.20% 80 5535 0.18% 81 5868 0.19% 82 6781 0.22% 83 6887 0.22% 84 6094 0.20% 85 133 0.00% 86 246 0.01% 87 340 0.01% 88 752 0.02% 89 1383 0.04% 90 2913 0.09% 91 8753 0.28% 92 46624 1.51% 93 2928071 95.10% 3078925 reads passed initial QC criterion=sequence-density sequence-density=0.29 sequence-density-rank=1 fanout-score=1.94 fanout-score-rank=36 prefix-density=0.30 prefix-fanout=1.9 sequence=GACCGATAGCGAA criterion=fanout-score sequence-density=0.02 sequence-density-rank=28 fanout-score=52.23 fanout-score-rank=1 prefix-density=0.12 prefix-fanout=7.3 sequence=AAAAGAAGGGGTGTTCCATCTCCGGACGACGATCCTGCCTGCGGAGGAAGACATGCCGGCGATCATGTCGAGCTTCAAGAAGTTCAACGACTCATTCATGGAGCAATACCAAGACTACTCCAGGCTGTGATGTGAAGAGGGAAACAACGACGTCATCATCGACATGATATATTGCTGCTATTTTCCACCAGCGATTAAAAGTTAAAAAATTTAGCTGTAAGCTGTAACTATCTTGAAGAAACTAAACTGGTTGCTGTGCTTGATATGTATAGGGAAAACATAATTTATGAGACAATCATACTGTGCAACTCTTGGCTCCATCGATTAATTAATACTCCTTGTTATTGCTTGC Started job on | Dec 06 23:52:11 Started mapping on | Dec 06 23:52:12 Finished on | Dec 06 23:52:17 Mapping speed, Million of reads per hour | 2216.83 Number of input reads | 3078925 Average input read length | 92 UNIQUE READS: Uniquely mapped reads number | 1971686 Uniquely mapped reads % | 64.04% Average mapped length | 92.04 Number of splices: Total | 104016 Number of splices: Annotated (sjdb) | 85714 Number of splices: GT/AG | 98680 Number of splices: GC/AG | 2035 Number of splices: AT/AC | 100 Number of splices: Non-canonical | 3201 Mismatch rate per base, % | 0.41% Deletion rate per base | 0.04% Deletion average length | 1.86 Insertion rate per base | 0.04% Insertion average length | 1.49 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 1039029 % of reads mapped to multiple loci | 33.75% Number of reads mapped to too many loci | 24045 % of reads mapped to too many loci | 0.78% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.39% % of reads unmapped: other | 0.05% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 68210 68210 68210 N_multimapping 1039029 1039029 1039029 N_noFeature 150340 170095 1885290 N_ambiguous 74107 7693 226 UnstrandedReadsAssigned:1747239 PositiveStrandReadsAssigned:1793898 NegativeStrandReadsAssigned:86170 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=93 echo kmer=89 ERR6133574 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: ERR6133574-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 3,078,925 reads, 2,500,889 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 989 rounds 52973 ERR6133574.ke.tsv 35125 ERR6133574.se.tsv 88098 total ==> ERR6133574.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 68 25.8401 PNS24243 293 194 0 0 KQK14069 1603 1504 127 44.0246 KQK14071 474 375 0 0 ==> ERR6133574.se.tsv <== BRADI_1g14170v3 127 BRADI_1g53295v3 26 BRADI_1g59795v3 13 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 19 BRADI_1g74790v3 18 BRADI_1g09890v3 0 BRADI_1g77505v3 59 BRADI_1g48960v3 0 ERR6133574 completed mapping pipeline successfully