Starting /dee2/code/volunteer_pipeline.sh ERR6133563 current disk space = 1544515227648 free memory = 1421450084 ERR6133563 SRAfilesize 56b3d689bb68510a2a7d95a222b11962 ERR6133563.sra ERR6133563.sra file validated ERR6133563 is single end ERR6133563 is conventional basespace ERR6133563 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133563_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 35.05475 37.0 33.0 37.0 33.0 37.0 2 36.30625 37.0 37.0 37.0 33.0 37.0 3 36.35875 37.0 37.0 37.0 33.0 37.0 4 36.13825 37.0 37.0 37.0 33.0 37.0 5 36.19425 37.0 37.0 37.0 33.0 37.0 6 36.212 37.0 37.0 37.0 33.0 37.0 7 38.2045 40.0 37.0 40.0 33.0 40.0 8 38.233 40.0 37.0 40.0 33.0 40.0 9 38.26525 40.0 37.0 40.0 37.0 40.0 10-11 38.125 40.0 37.0 40.0 35.0 40.0 12-13 38.121125 40.0 37.0 40.0 33.0 40.0 14-15 38.02975 40.0 37.0 40.0 33.0 40.0 16-17 37.9935 40.0 37.0 40.0 33.0 40.0 18-19 37.945750000000004 40.0 37.0 40.0 33.0 40.0 20-21 37.81175 40.0 37.0 40.0 33.0 40.0 22-23 37.779875 40.0 37.0 40.0 33.0 40.0 24-25 37.950500000000005 40.0 37.0 40.0 33.0 40.0 26-27 37.872125 40.0 37.0 40.0 33.0 40.0 28-29 37.837500000000006 40.0 37.0 40.0 33.0 40.0 30-31 37.696375 40.0 37.0 40.0 33.0 40.0 32-33 37.59575 40.0 37.0 40.0 33.0 40.0 34-35 37.511250000000004 40.0 37.0 40.0 33.0 40.0 36-37 37.342625 40.0 37.0 40.0 33.0 40.0 38-39 37.149375 38.5 37.0 40.0 33.0 40.0 40-41 36.961749999999995 37.0 37.0 40.0 33.0 40.0 42-43 36.798875 37.0 37.0 40.0 33.0 40.0 44-45 36.577125 37.0 37.0 40.0 33.0 40.0 46-47 36.255875 37.0 37.0 40.0 33.0 40.0 48-49 36.107 37.0 37.0 40.0 33.0 40.0 50-51 36.0415 37.0 37.0 40.0 33.0 40.0 52-53 35.74275 37.0 35.0 38.5 33.0 40.0 54-55 35.495374999999996 37.0 33.0 37.0 33.0 40.0 56-57 35.382374999999996 37.0 33.0 37.0 33.0 40.0 58-59 34.1165 37.0 33.0 37.0 27.0 40.0 60-61 34.756 37.0 33.0 37.0 30.0 40.0 62-63 34.78 37.0 33.0 37.0 30.0 37.0 64-65 34.618125 37.0 33.0 37.0 27.0 37.0 66-67 34.6015 37.0 33.0 37.0 30.0 37.0 68-69 33.82925 35.0 33.0 37.0 30.0 37.0 70-71 33.82164787622889 35.0 33.0 37.0 27.0 37.0 72-73 34.2488594904853 37.0 33.0 37.0 27.0 37.0 74-75 34.05839663206449 37.0 33.0 37.0 27.0 37.0 76-77 34.08384373639416 37.0 33.0 37.0 27.0 37.0 78-79 33.99778812560143 37.0 33.0 37.0 27.0 37.0 80-81 33.9297249245099 37.0 33.0 37.0 27.0 37.0 82-83 33.60412696000065 37.0 33.0 37.0 27.0 37.0 84-85 33.6014350011356 37.0 33.0 37.0 27.0 37.0 86-87 33.66890348372358 37.0 33.0 37.0 27.0 37.0 88-89 33.52998286693318 37.0 33.0 37.0 27.0 37.0 90-91 33.34851513420902 37.0 33.0 37.0 27.0 37.0 92-93 33.238863506567675 37.0 33.0 37.0 27.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 12.0 21 8.0 22 8.0 23 23.0 24 17.0 25 26.0 26 26.0 27 29.0 28 41.0 29 65.0 30 72.0 31 99.0 32 139.0 33 180.0 34 212.0 35 298.0 36 666.0 37 1034.0 38 989.0 39 56.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 51.6 19.650000000000002 13.5 15.25 2 36.199999999999996 25.95 22.400000000000002 15.45 3 25.900000000000002 38.775 19.775000000000002 15.55 4 23.575 29.275000000000002 23.974999999999998 23.175 5 23.200000000000003 29.4 27.525 19.875 6 18.275 34.625 27.175 19.925 7 30.775000000000002 28.050000000000004 24.525 16.650000000000002 8 25.525 28.225 27.375 18.875 9 24.925 26.400000000000002 27.125 21.55 10-11 24.9375 27.975 28.349999999999998 18.7375 12-13 22.175 29.1125 27.712500000000002 21.0 14-15 24.675 27.5625 28.349999999999998 19.412499999999998 16-17 24.075 25.887500000000003 26.275 23.7625 18-19 23.5375 25.837500000000002 30.9 19.725 20-21 24.546705014380393 24.484181568088033 27.622858571964485 23.34625484556709 22-23 25.5375 24.2375 29.125 21.099999999999998 24-25 23.846442415905962 24.171564336626236 29.873702638489437 22.10829060897837 26-27 22.975 26.275 29.912499999999998 20.837500000000002 28-29 21.858196823808928 27.160185069401027 27.76041015380768 23.22120795298237 30-31 23.974999999999998 25.2125 29.7125 21.099999999999998 32-33 24.349999999999998 26.200000000000003 27.750000000000004 21.7 34-35 24.55 29.262500000000003 25.637500000000003 20.549999999999997 36-37 23.7625 27.9125 25.5 22.825 38-39 24.01850462615654 25.95648912228057 28.132033008252062 21.892973243310827 40-41 25.268817204301076 27.306826706676667 27.294323580895224 20.130032508127034 42-43 25.390673834229275 30.366295786973375 26.740842605325664 17.502187773471682 44-45 22.35 29.625 27.8875 20.1375 46-47 26.5125 27.425 27.1 18.9625 48-49 25.0625 26.737499999999997 28.025 20.175 50-51 21.0125 30.9875 27.975 20.025000000000002 52-53 25.456821026282856 27.546933667083856 26.057571964956196 20.9386733416771 54-55 24.3625 25.95 28.462500000000002 21.224999999999998 56-57 25.4375 27.9125 28.3625 18.2875 58-59 22.662499999999998 31.1875 28.9875 17.1625 60-61 23.5375 28.6875 27.125 20.65 62-63 21.4 29.575000000000003 28.237499999999997 20.7875 64-65 22.85 30.112499999999997 27.6875 19.35 66-67 21.65 31.6875 27.4125 19.25 68-69 22.2125 29.462500000000002 27.8125 20.5125 70-71 22.216643655077192 30.086607254926573 28.14108196309778 19.555667126898456 72-73 24.58093410108765 27.575175943698017 29.328214971209217 18.515674984005116 74-75 22.58190836705391 29.330374624722623 29.721968411434542 18.36574859678893 76-77 20.815138282387192 26.505226941908166 29.48259891491333 23.197035860791317 78-79 26.730278188415536 25.13103077543341 28.920843972584333 19.217847063566726 80-81 24.71248630887185 29.21686746987952 26.793537787513692 19.27710843373494 82-83 22.7791701475912 29.19799498746867 28.195488721804512 19.827346143135614 84-85 20.042583392476935 26.88431511710433 34.22285308729596 18.850248403122784 86-87 21.858937749857223 28.498001142204455 27.198743575099943 22.44431753283838 88-89 20.145631067961165 32.80982295830954 28.569388920616788 18.475157053112508 90-91 21.159337521416333 31.410622501427753 28.769274700171334 18.66076527698458 92-93 19.23186750428327 35.13706453455169 27.869788692175902 17.76127926898915 >>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 1.5 17 1.0 18 1.0 19 2.5 20 3.0 21 4.0 22 5.0 23 10.0 24 13.5 25 15.0 26 21.0 27 27.5 28 36.5 29 47.5 30 50.5 31 56.5 32 71.5 33 96.5 34 119.0 35 129.0 36 150.0 37 197.0 38 212.0 39 188.5 40 191.5 41 201.5 42 219.5 43 229.5 44 189.5 45 164.0 46 146.0 47 127.5 48 128.5 49 107.5 50 115.0 51 172.0 52 173.0 53 175.5 54 196.0 55 118.5 56 57.5 57 59.5 58 48.5 59 34.0 60 22.5 61 19.5 62 16.0 63 11.0 64 11.5 65 5.5 66 3.5 67 3.5 68 4.5 69 7.0 70 5.5 71 3.0 72 2.0 73 1.5 74 1.0 75 1.0 76 1.0 77 0.5 78 0.5 79 0.0 80 0.0 81 0.0 82 0.0 83 0.5 84 0.5 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 0.0375 22-23 0.0 24-25 0.0375 26-27 0.0 28-29 0.0375 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 0.125 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 33.0 71 40.0 72 39.0 73 42.0 74 31.0 75 26.0 76 21.0 77 32.0 78 31.0 79 37.0 80 32.0 81 31.0 82 28.0 83 34.0 84 41.0 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 3502.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 75.14999999999999 #Duplication Level Percentage of deduplicated Percentage of total 1 90.8183632734531 68.25 2 4.1583499667332005 6.25 3 1.9627411842980707 4.425 4 0.8982035928143712 2.7 5 0.5988023952095809 2.25 6 0.5655355954757153 2.55 7 0.19960079840319359 1.05 8 0.166333998669328 1.0 9 0.1330671989354624 0.8999999999999999 >10 0.39920159680638717 4.125 >50 0.0665335994677312 3.6999999999999997 >100 0.0332667997338656 2.8000000000000003 >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 TCAAAAGAGGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGGA 112 2.8000000000000003 No Hit GGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGC 81 2.025 No Hit ATACACATCTCCTCACCACCCTCTCCACCCTCCAGCGATCGGAAGAGCAC 67 1.675 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 36 0.8999999999999999 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 18 0.44999999999999996 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 13 0.325 No Hit GGGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTT 12 0.3 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 12 0.3 No Hit ATATTGGGTAGGTTGTGGTATTTCATTGCTACAAACATGGGTTATTGTAA 11 0.27499999999999997 No Hit GTCAAAAGAGGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGG 11 0.27499999999999997 No Hit GTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAG 11 0.27499999999999997 No Hit TCTCATGGAGAGTTCGATCCTGGCTCAGGATGAACGCTGGCGGCATGCTT 11 0.27499999999999997 No Hit GTACTATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTT 10 0.25 No Hit GGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGC 10 0.25 No Hit AACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCG 10 0.25 No Hit GGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTTCGGGGA 9 0.22499999999999998 No Hit GTATTAGTACTATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATCT 9 0.22499999999999998 No Hit AGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTG 9 0.22499999999999998 No Hit GATTCAGTATTATCAGAATGCAAGTCTCACCCTTGAATTTACAGGATACC 9 0.22499999999999998 No Hit GCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGGTATG 8 0.2 No Hit GCACGAACGTAATGCTCACAACTTCCCTCTAGATCTAGCTGCTCTTGAAG 8 0.2 No Hit GTAATGCACGAACGTAATGCTCACAACTTCCCTCTAGATCTAGCTGCTCT 8 0.2 No Hit CAACCTTTTAAACTGCCTGCTGAATCCATGAGCAGGCAAGAGACAACCTG 8 0.2 No Hit CAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTG 8 0.2 No Hit GGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCTAAATGGATTC 7 0.17500000000000002 No Hit GGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGGAAGGGCGTA 7 0.17500000000000002 No Hit GTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAA 7 0.17500000000000002 No Hit AACGTAATGCTCACAACTTCCCTCTAGATCTAGCTGCTCTTGAAGTTCCC 7 0.17500000000000002 No Hit ACCCCATGGGGCTACACGACGCCCTTCTAGATCGGAAGAGCACACGTCTG 7 0.17500000000000002 Illumina Multiplexing PCR Primer 2.01 (100% over 22bp) GGGGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCT 7 0.17500000000000002 No Hit GGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAA 6 0.15 No Hit GGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAAGGCGATCAAATTC 6 0.15 No Hit CAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTT 6 0.15 No Hit GAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGGAAGGGCGTAG 6 0.15 No Hit GGAGATTCCCAAATAGGTCAACCTTTTAAACTGCCTGCTGAATCCATGAG 6 0.15 No Hit GGATACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATG 6 0.15 No Hit GGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTT 6 0.15 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 6 0.15 No Hit AGGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGGAAGGGCGT 6 0.15 No Hit CAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCT 6 0.15 No Hit GATACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGC 6 0.15 No Hit CGAACGTAATGCTCACAACTTCCCTCTAGATCTAGCTGCTCTTGAAGTTC 6 0.15 No Hit GTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGCTA 6 0.15 No Hit ATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAG 6 0.15 No Hit TAATGCTCACAACTTCCCTCTAGATCTAGCTGCTCTTGAAGTTCCCGCTA 6 0.15 No Hit ATACACATCTCCTCACCACCCTCTCCACCCTCCAGCGATCAAATTCGAGT 6 0.15 No Hit GAACGTAATGCTCACAACTTCCCTCTAGATCTAGCTGCTCTTGAAGTTCC 6 0.15 No Hit CGACGAAATGCTTCGGGGAGTTGAAAATAAGCATAGATCCGGAGATTCCC 5 0.125 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 5 0.125 No Hit AGGTCAACCTTTTAAACTGCCTGCTGAATCCATGAGCAGGCAAGAGACAA 5 0.125 No Hit GGGAAAAGAGGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTT 5 0.125 No Hit AAGAGGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGGAAGGG 5 0.125 No Hit GGTATTAGTACTATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATC 5 0.125 No Hit GGGGGTCGCAGTGACCAGGCCCGGGCGACTGTTTACCAAAAACACAGGTC 5 0.125 No Hit GGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGCTAAATACAG 5 0.125 No Hit GGCCTCCTCGGCGGCGGCGCCCTCCTCGTCTACAACACCAGCGCTCTCGC 5 0.125 No Hit GCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAAT 5 0.125 No Hit GTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTTTAA 5 0.125 No Hit GAAGTATGGAAGGCGATCAAATTCGAGTTCGCGCCGGTAGATACTATCGA 5 0.125 No Hit GATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAACGTAA 5 0.125 No Hit GCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCA 5 0.125 No Hit GGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGCA 5 0.125 No Hit ATAGGTCAACCTTTTAAACTGCCTGCTGAATCCATGAGCAGGCAAGAGAC 5 0.125 No Hit CGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAA 5 0.125 No Hit GGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGCT 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 0.025 0.0 0.0 0.0 0.0 8 0.025 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 0.037500000000000006 0.0 0.0 0.0 0.0 22-23 0.05 0.0 0.0 0.025 0.0 24-25 0.05 0.0 0.0 0.05 0.0 26-27 0.05 0.0 0.0 0.05 0.0 28-29 0.3625 0.0 0.0 0.05 0.0 30-31 0.675 0.0 0.0 0.07500000000000001 0.0 32-33 0.6875 0.0 0.0 0.1 0.0 34-35 0.825 0.0 0.0 0.1 0.0 36-37 0.9 0.0 0.0 0.1 0.0 38-39 0.9 0.0 0.0 0.1 0.0 40-41 0.9 0.0 0.0 0.1 0.0 42-43 0.9 0.0 0.0 0.1 0.0 44-45 0.9 0.0 0.0 0.1 0.0 46-47 0.9 0.0 0.0 0.1 0.0 48-49 0.9 0.0 0.0 0.1 0.0 50-51 0.9 0.0 0.0 0.1 0.0 52-53 0.9 0.0 0.0 0.1 0.0 54-55 0.9 0.0 0.0 0.1 0.0 56-57 0.9 0.0 0.0 0.1 0.0 58-59 0.9 0.0 0.0 0.1 0.0 60-61 0.9 0.0 0.0 0.1 0.0 62-63 0.9 0.0 0.0 0.1 0.0 64-65 0.9 0.0 0.0 0.1 0.0 66-67 0.9 0.0 0.0 0.1 0.0 68-69 0.9 0.0 0.0 0.1 0.0 70-71 0.9 0.0 0.0 0.1 0.0 72-73 0.9 0.0 0.0 0.1 0.0 74-75 0.9 0.0 0.0 0.1 0.0 76-77 0.9 0.0 0.0 0.1 0.0 78-79 0.9 0.0 0.0 0.1 0.0 80-81 0.925 0.0 0.0 0.1 0.0 >>END_MODULE >>Kmer Content fail #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position AAAGAGG 25 7.259605E-7 85.325005 4 AAGAGGA 20 2.6237458E-5 85.325 5 AGGAAAG 20 2.6237458E-5 85.325 8 TCAAAAG 20 2.6237458E-5 85.325 1 CAAAAGA 20 2.6237458E-5 85.325 2 AAAAGAG 30 2.1476626E-6 71.104164 3 GAGGAAA 25 7.9341014E-5 68.26 7 GGAAAGG 25 7.9341014E-5 68.26 9 AGAGGAA 30 1.9562777E-4 56.88333 6 GATACCT 20 8.611148E-4 42.6625 24-25 GCGGTGG 20 8.611148E-4 42.6625 18-19 GGATACC 20 8.611148E-4 42.6625 24-25 AGGCTTG 20 8.611148E-4 42.6625 12-13 CGGTGGA 20 8.611148E-4 42.6625 20-21 GGCTTGC 20 8.611148E-4 42.6625 14-15 GCTTGCG 20 8.611148E-4 42.6625 14-15 CTTGCGG 20 8.611148E-4 42.6625 16-17 TTGCGGT 20 8.611148E-4 42.6625 16-17 GGTGGAT 20 8.611148E-4 42.6625 20-21 ATACCTA 20 8.611148E-4 42.6625 26-27 >>END_MODULE Rejected 22043 READS because READLEN < 1 Read 22043 spots for ERR6133563.sra Written 22043 spots for ERR6133563.sra Rejected 22043 READS because READLEN < 1 Read 22043 spots for ERR6133563.sra Written 22043 spots for ERR6133563.sra Rejected 22043 READS because READLEN < 1 Read 22043 spots for ERR6133563.sra Written 22043 spots for ERR6133563.sra Rejected 22043 READS because READLEN < 1 Read 22043 spots for ERR6133563.sra Written 22043 spots for ERR6133563.sra Rejected 22043 READS because READLEN < 1 Read 22043 spots for ERR6133563.sra Written 22043 spots for ERR6133563.sra Rejected 22043 READS because READLEN < 1 Read 22043 spots for ERR6133563.sra Written 22043 spots for ERR6133563.sra Rejected 22043 READS because READLEN < 1 Read 22043 spots for ERR6133563.sra Written 22043 spots for ERR6133563.sra Rejected 22043 READS because READLEN < 1 Read 22043 spots for ERR6133563.sra Written 22043 spots for ERR6133563.sra Rejected 22043 READS because READLEN < 1 Read 22043 spots for ERR6133563.sra Written 22043 spots for ERR6133563.sra Rejected 22043 READS because READLEN < 1 Read 22043 spots for ERR6133563.sra Written 22043 spots for ERR6133563.sra Rejected 22043 READS because READLEN < 1 Read 22043 spots for ERR6133563.sra Written 22043 spots for ERR6133563.sra Rejected 22043 READS because READLEN < 1 Read 22043 spots for ERR6133563.sra Written 22043 spots for ERR6133563.sra Rejected 22044 READS because READLEN < 1 Read 22044 spots for ERR6133563.sra Written 22044 spots for ERR6133563.sra Rejected 22043 READS because READLEN < 1 Read 22043 spots for ERR6133563.sra Written 22043 spots for ERR6133563.sra Rejected 22043 READS because READLEN < 1 Read 22043 spots for ERR6133563.sra Written 22043 spots for ERR6133563.sra Rejected 22043 READS because READLEN < 1 Read 22043 spots for ERR6133563.sra Written 22043 spots for ERR6133563.sra Rejected 22043 READS because READLEN < 1 Read 22043 spots for ERR6133563.sra Written 22043 spots for ERR6133563.sra Rejected 22043 READS because READLEN < 1 Read 22043 spots for ERR6133563.sra Written 22043 spots for ERR6133563.sra Rejected 22043 READS because READLEN < 1 Read 22043 spots for ERR6133563.sra Written 22043 spots for ERR6133563.sra Rejected 22043 READS because READLEN < 1 Read 22043 spots for ERR6133563.sra Written 22043 spots for ERR6133563.sra SRR ids: ['ERR6133563.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_w0c0oy1v ERR6133563.sra spots: 440861 blocks: [[1, 22043], [22044, 44086], [44087, 66129], [66130, 88172], [88173, 110215], [110216, 132258], [132259, 154301], [154302, 176344], [176345, 198387], [198388, 220430], [220431, 242473], [242474, 264516], [264517, 286559], [286560, 308602], [308603, 330645], [330646, 352688], [352689, 374731], [374732, 396774], [396775, 418817], [418818, 440861]] ERR6133563 file size 95269 ERR6133563 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 ERR6133563 ERR6133563_1.fastq Input file: ERR6133563_1.fastq trimmed: ERR6133563-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 08:42:39 2024 >> started Sat Dec 7 08:42:40 2024 >> done (0.465s) 440861 reads processed; of these: 166 ( 0.04%) short reads filtered out after trimming by size control 54 ( 0.01%) empty reads filtered out after trimming by size control 440641 (99.95%) reads available; of these: 18651 ( 4.23%) trimmed reads available after processing 421990 (95.77%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 24 0.01% 19 51 0.01% 20 46 0.01% 21 26 0.01% 22 62 0.01% 23 19 0.00% 24 11 0.00% 25 21 0.00% 26 58 0.01% 27 211 0.05% 28 2516 0.57% 29 274 0.06% 30 71 0.02% 31 65 0.01% 32 266 0.06% 33 494 0.11% 34 396 0.09% 35 5894 1.34% 36 180 0.04% 37 62 0.01% 38 46 0.01% 39 92 0.02% 40 48 0.01% 41 37 0.01% 42 7 0.00% 43 11 0.00% 44 19 0.00% 45 37 0.01% 46 20 0.00% 47 10 0.00% 48 16 0.00% 49 9 0.00% 50 18 0.00% 51 30 0.01% 52 13 0.00% 53 10 0.00% 54 19 0.00% 55 21 0.00% 56 18 0.00% 57 17 0.00% 58 71 0.02% 59 26 0.01% 60 24 0.01% 61 12 0.00% 62 0 0.00% 63 0 0.00% 64 0 0.00% 65 0 0.00% 66 1 0.00% 67 3 0.00% 68 10 0.00% 69 42 0.01% 70 4008 0.91% 71 4395 1.00% 72 3924 0.89% 73 3703 0.84% 74 3528 0.80% 75 3570 0.81% 76 3526 0.80% 77 3707 0.84% 78 3585 0.81% 79 3994 0.91% 80 3643 0.83% 81 4157 0.94% 82 4239 0.96% 83 3930 0.89% 84 4216 0.96% 85 15 0.00% 86 19 0.00% 87 55 0.01% 88 79 0.02% 89 146 0.03% 90 306 0.07% 91 877 0.20% 92 5124 1.16% 93 364461 82.71% 440641 reads passed initial QC criterion=sequence-density sequence-density=2.95 sequence-density-rank=1 fanout-score=1.95 fanout-score-rank=19 prefix-density=2.97 prefix-fanout=1.9 sequence=CAAGGCTAAATAC criterion=fanout-score sequence-density=0.15 sequence-density-rank=16 fanout-score=16.55 fanout-score-rank=1 prefix-density=2.53 prefix-fanout=1.0 sequence=CCGCTAACATACAAAA 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 08:43:08 Started mapping on | Dec 07 08:43:08 Finished on | Dec 07 08:43:13 Mapping speed, Million of reads per hour | 317.26 Number of input reads | 440641 Average input read length | 81 UNIQUE READS: Uniquely mapped reads number | 209048 Uniquely mapped reads % | 47.44% Average mapped length | 79.11 Number of splices: Total | 5492 Number of splices: Annotated (sjdb) | 4173 Number of splices: GT/AG | 5162 Number of splices: GC/AG | 100 Number of splices: AT/AC | 38 Number of splices: Non-canonical | 192 Mismatch rate per base, % | 0.51% Deletion rate per base | 0.04% Deletion average length | 1.69 Insertion rate per base | 0.02% Insertion average length | 1.69 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 200721 % of reads mapped to multiple loci | 45.55% Number of reads mapped to too many loci | 17194 % of reads mapped to too many loci | 3.90% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 2.86% % of reads unmapped: other | 0.24% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 30872 30872 30872 N_multimapping 200721 200721 200721 N_noFeature 30428 33773 200006 N_ambiguous 6748 1021 54 UnstrandedReadsAssigned:171872 PositiveStrandReadsAssigned:174254 NegativeStrandReadsAssigned:8988 Dataset is classified positive stranded MeadianReadLen=85 20thPercentileLength=85 echo kmer=81 ERR6133563 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: ERR6133563-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 440,641 reads, 264,567 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 728 rounds 52973 ERR6133563.ke.tsv 35125 ERR6133563.se.tsv 88098 total ==> ERR6133563.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 8 29.8804 PNS24243 293 194 0 0 KQK14069 1603 1504 1 3.40724 KQK14071 474 375 0 0 ==> ERR6133563.se.tsv <== BRADI_1g14170v3 1 BRADI_1g53295v3 0 BRADI_1g59795v3 0 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 0 BRADI_1g74790v3 4 BRADI_1g09890v3 0 BRADI_1g77505v3 5 BRADI_1g48960v3 0 ERR6133563 completed mapping pipeline successfully