Starting /dee2/code/volunteer_pipeline.sh ERR6133402 current disk space = 1547636817920 free memory = 1358981464 ERR6133402 SRAfilesize 1f81ac641bde5bd4edebd863e0f3291d ERR6133402.sra ERR6133402.sra file validated ERR6133402 is single end ERR6133402 is conventional basespace ERR6133402 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133402_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 fail #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 28.784 33.0 27.0 33.0 15.0 37.0 2 33.367 33.0 33.0 37.0 27.0 37.0 3 33.735 37.0 33.0 37.0 27.0 37.0 4 33.84775 37.0 33.0 37.0 27.0 37.0 5 33.9115 37.0 33.0 37.0 27.0 37.0 6 34.30475 37.0 33.0 37.0 27.0 37.0 7 35.18325 37.0 33.0 40.0 27.0 40.0 8 35.229 37.0 33.0 40.0 27.0 40.0 9 35.414 37.0 33.0 40.0 27.0 40.0 10-11 35.372125 37.0 33.0 40.0 30.0 40.0 12-13 35.262874999999994 37.0 33.0 38.5 27.0 40.0 14-15 35.181375 37.0 33.0 37.0 27.0 40.0 16-17 34.964749999999995 37.0 33.0 37.0 27.0 40.0 18-19 34.882625000000004 37.0 33.0 37.0 27.0 40.0 20-21 34.03375 37.0 33.0 37.0 24.5 40.0 22-23 33.748875 37.0 33.0 37.0 22.0 40.0 24-25 33.428 37.0 33.0 37.0 22.0 40.0 26-27 33.113749999999996 37.0 33.0 37.0 22.0 40.0 28-29 32.762625 37.0 33.0 37.0 22.0 40.0 30-31 32.599625 35.0 33.0 37.0 22.0 40.0 32-33 32.073625 33.0 30.0 37.0 22.0 40.0 34-35 31.193375 33.0 27.0 37.0 15.0 40.0 36-37 30.69525 33.0 27.0 37.0 15.0 37.0 38-39 31.20175 33.0 27.0 37.0 22.0 37.0 40-41 31.165625 33.0 27.0 37.0 22.0 38.5 42-43 31.016 33.0 27.0 37.0 15.0 40.0 44-45 30.5925 33.0 27.0 37.0 15.0 37.0 46-47 29.939500000000002 33.0 27.0 37.0 15.0 37.0 48-49 29.926625 33.0 27.0 37.0 15.0 37.0 50-51 29.500125 33.0 27.0 37.0 15.0 37.0 52-53 29.167375 33.0 27.0 37.0 15.0 37.0 54-55 29.08125 33.0 27.0 37.0 15.0 37.0 56-57 28.60275 33.0 27.0 35.0 15.0 37.0 58-59 28.3445 33.0 24.5 33.0 15.0 37.0 60-61 27.891624999999998 33.0 24.5 33.0 15.0 37.0 62-63 27.684625 33.0 22.0 33.0 15.0 37.0 64-65 26.918625 33.0 22.0 33.0 10.5 37.0 66-67 26.57175 27.0 22.0 33.0 6.0 37.0 68-69 26.133125 27.0 22.0 33.0 10.5 35.0 70-71 27.89316698089492 33.0 27.0 33.0 15.0 37.0 72-73 28.401498710400034 33.0 27.0 33.0 15.0 37.0 74-75 28.318526128563455 33.0 27.0 33.0 15.0 37.0 76-77 28.09884761076161 33.0 27.0 33.0 15.0 37.0 78-79 27.186722264813973 33.0 24.5 33.0 6.0 37.0 80-81 26.438814293145015 33.0 22.0 33.0 6.0 37.0 82-83 25.64372028343258 33.0 22.0 33.0 2.0 37.0 84-85 24.94493337322142 33.0 18.5 33.0 2.0 37.0 86-87 24.197508896797153 33.0 15.0 33.0 2.0 37.0 88-89 23.34464823432795 30.0 10.5 33.0 2.0 35.0 90-91 22.25554338899535 27.0 2.0 33.0 2.0 33.0 92-93 20.94032302217356 27.0 2.0 33.0 2.0 33.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 98.0 21 121.0 22 144.0 23 166.0 24 219.0 25 187.0 26 221.0 27 212.0 28 219.0 29 269.0 30 308.0 31 273.0 32 270.0 33 280.0 34 289.0 35 278.0 36 246.0 37 176.0 38 24.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 67.525 8.375 8.225 15.875 2 50.775000000000006 23.525 15.75 9.950000000000001 3 34.0 34.699999999999996 17.0 14.299999999999999 4 26.625 32.074999999999996 21.025 20.275000000000002 5 28.625 24.925 26.55 19.900000000000002 6 18.45 39.025 25.650000000000002 16.875 7 37.225 24.75 20.65 17.375 8 24.575 26.700000000000003 25.624999999999996 23.1 9 22.275 31.175000000000004 27.450000000000003 19.1 10-11 22.5125 29.1125 29.5375 18.8375 12-13 22.0125 29.9625 26.674999999999997 21.349999999999998 14-15 21.175 33.2625 27.287499999999998 18.275 16-17 25.775 27.375 23.6625 23.1875 18-19 25.525 24.337500000000002 30.6875 19.45 20-21 26.85 24.1125 29.2 19.8375 22-23 29.875 22.8375 28.0625 19.225 24-25 22.8125 25.05 28.8625 23.275000000000002 26-27 27.05 23.6875 26.987499999999997 22.275 28-29 22.8625 28.787499999999998 28.875 19.475 30-31 30.525000000000002 24.725 25.2 19.55 32-33 27.237499999999997 23.200000000000003 26.387500000000003 23.175 34-35 22.025 33.7375 25.224999999999998 19.0125 36-37 26.724999999999998 26.0375 23.3625 23.875 38-39 31.912499999999998 22.725 25.4 19.9625 40-41 23.7125 24.25 32.0625 19.975 42-43 27.375 30.0 24.4875 18.1375 44-45 25.674999999999997 26.325 28.712500000000002 19.287499999999998 46-47 27.5875 25.137500000000003 24.5375 22.7375 48-49 25.937500000000004 25.2625 26.25 22.55 50-51 20.599999999999998 30.2625 26.237500000000004 22.900000000000002 52-53 23.474999999999998 25.8 25.0125 25.7125 54-55 22.175 25.912499999999998 29.299999999999997 22.6125 56-57 26.2875 28.812500000000004 25.0625 19.8375 58-59 23.1375 28.849999999999998 28.487499999999997 19.525000000000002 60-61 30.7625 25.087500000000002 25.1875 18.9625 62-63 21.512500000000003 27.325 29.6875 21.475 64-65 22.400000000000002 34.449999999999996 24.95 18.2 66-67 25.05 30.9375 24.6 19.412499999999998 68-69 20.825 28.050000000000004 28.375 22.75 70-71 22.75006267234896 29.7568312860366 25.47004261719729 22.023063424417145 72-73 26.507856056766343 25.60821084642676 29.92904206791688 17.954891028890017 74-75 26.522240738366875 28.94500705037816 26.20176900397385 18.33098320728112 76-77 21.704824731600052 24.485836243694216 25.869874531108522 27.939464493597203 78-79 26.077304779315746 29.381039435884045 25.84225646382868 18.699399320971533 80-81 22.49702420314773 35.56407882555217 25.03637085041661 16.902526120883483 82-83 25.016785282664163 26.279038539008997 24.425943332885723 24.278232845441117 84-85 21.50742810412975 27.29998637045114 30.952705465449093 20.239880059970012 86-87 21.03750342184506 31.084040514645494 24.56884752258418 23.309608540925268 88-89 19.572953736654807 29.49630440733644 28.77087325485902 22.15986860114974 90-91 24.993156309882288 31.631535724062417 24.199288256227756 19.17601970982754 92-93 19.12127018888585 32.507528059129484 27.01888858472488 21.352313167259787 >>END_MODULE >>Per sequence GC content fail #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 1.0 17 2.5 18 3.5 19 2.5 20 1.5 21 3.0 22 3.5 23 5.5 24 7.0 25 7.5 26 12.5 27 14.0 28 20.5 29 28.5 30 26.5 31 42.0 32 57.5 33 63.5 34 71.0 35 82.5 36 114.5 37 149.0 38 179.0 39 188.0 40 197.5 41 201.0 42 194.5 43 197.0 44 186.0 45 179.5 46 168.0 47 144.5 48 122.5 49 124.5 50 132.5 51 137.5 52 138.5 53 154.0 54 254.5 55 249.0 56 134.0 57 100.0 58 82.5 59 44.0 60 23.0 61 22.5 62 19.0 63 15.0 64 19.5 65 21.5 66 12.0 67 8.5 68 9.5 69 11.5 70 13.0 71 12.0 72 6.5 73 1.0 74 1.0 75 1.0 76 1.0 77 0.5 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 22.0 71 18.0 72 28.0 73 22.0 74 19.0 75 16.0 76 19.0 77 18.0 78 18.0 79 26.0 80 27.0 81 32.0 82 23.0 83 28.0 84 31.0 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 3653.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 74.125 #Duplication Level Percentage of deduplicated Percentage of total 1 92.17537942664418 68.325 2 3.406408094435076 5.050000000000001 3 1.585160202360877 3.5249999999999995 4 0.8431703204047217 2.5 5 0.6070826306913997 2.25 6 0.16863406408094433 0.75 7 0.2023608768971332 1.05 8 0.26981450252951095 1.6 9 0.16863406408094433 1.125 >10 0.5396290050590219 7.124999999999999 >50 0.0 0.0 >100 0.03372681281618887 6.7 >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 268 6.7 No Hit TCAAAAGAGGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGGA 30 0.75 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 27 0.675 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 24 0.6 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 23 0.575 No Hit CAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATAT 21 0.525 No Hit CAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTG 20 0.5 No Hit GGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGC 19 0.475 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 18 0.44999999999999996 No Hit GGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAA 17 0.42500000000000004 No Hit CAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCT 17 0.42500000000000004 No Hit GGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTCCT 15 0.375 No Hit GGGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTA 13 0.325 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 11 0.27499999999999997 No Hit GGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAAGGCGATCAAATTC 10 0.25 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 10 0.25 No Hit GTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTC 10 0.25 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 9 0.22499999999999998 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 9 0.22499999999999998 No Hit AACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGA 9 0.22499999999999998 No Hit GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 9 0.22499999999999998 No Hit GTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAG 9 0.22499999999999998 No Hit CAAATAGGTCAACCTTTTAAACTGCCTGCTGAATCCATGAGCAGGCAAGA 8 0.2 No Hit GGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCG 8 0.2 No Hit GGGAGGGTGAGAGCCCCGTCCGGCCCGGACCCTGTCGCCCCACGAGGCGC 8 0.2 No Hit GGGGTTGTGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTG 8 0.2 No Hit GTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAA 8 0.2 No Hit GTATTAGTACTATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATCT 8 0.2 No Hit GGGGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCT 8 0.2 No Hit GGGTGAGAGCCCCGTCCGGCCCGGACCCTGTCGCCCCACGAGGCGCCGTC 8 0.2 No Hit GGAGGGTGAGAGCCCCGTCCGGCCCGGACCCTGTCGCCCCACGAGGCGCC 7 0.17500000000000002 No Hit GTACTATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTT 7 0.17500000000000002 No Hit GCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCT 7 0.17500000000000002 No Hit GGACCCTGTCGCCCCACGAGGCGCCGTCAACGAGTCGGGTTGTTTGGGAA 7 0.17500000000000002 No Hit CGGGGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACC 7 0.17500000000000002 No Hit TCTCATGGAGAGTTCGATCCTGGCTCAGGATGAACGCTGGCGGCATGCTT 7 0.17500000000000002 No Hit GATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAAT 6 0.15 No Hit GGCCTGTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCG 6 0.15 No Hit CGAACGTAATGCTCACAACTTCCCTCTAGATCTAGCTGCTCTTGAAGTTC 6 0.15 No Hit GGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGCA 6 0.15 No Hit GATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAG 6 0.15 No Hit GGAGTTTGGCTGGGGCGGCACATCTGTTAAAAGATAACGCAGGTGTCCTA 5 0.125 No Hit GTCAACGAGTCGGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACT 5 0.125 No Hit GGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGGG 5 0.125 No Hit GGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGCTAAATACAG 5 0.125 No Hit CGAGTCGGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTC 5 0.125 No Hit GTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAA 5 0.125 No Hit CAACGAGTCGGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCC 5 0.125 No Hit GGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGAGGTTGAGTGCCGC 5 0.125 No Hit GAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAAT 5 0.125 No Hit GTAATGCACGAACGTAATGCTCACAACTTCCCTCTAGATCTAGCTGCTCT 5 0.125 No Hit GTGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCC 5 0.125 No Hit CGAGGAAGGGCGTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAG 5 0.125 No Hit GTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGCTA 5 0.125 No Hit TATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAG 5 0.125 No Hit GGAGCAGCCTAAACCGTGAAAACGGGGTTGTGGGAGAGCAATACAAGCGT 5 0.125 No Hit GGAGTATCCTTGATATATAAATATATAGATAAATAGATTTAAATGGAAAA 5 0.125 No Hit GAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTCCTG 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 0.0 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 0.0 0.0 0.0 0.0 0.0 54-55 0.0 0.0 0.0 0.0 0.0 56-57 0.0 0.0 0.0 0.0 0.0 58-59 0.0 0.0 0.0 0.0 0.0 60-61 0.0 0.0 0.0 0.0 0.0 62-63 0.0125 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 0.025 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 GGAGAGC 40 1.1591048E-5 53.523438 2 GGGAGAG 40 1.1591048E-5 53.523438 1 GAGCAAT 40 1.1591048E-5 53.523438 5 AGAGCAA 40 1.1591048E-5 53.523438 4 GAGAGCA 40 1.1591048E-5 53.523438 3 AATACAA 40 1.1591048E-5 53.523438 9 GCAATAC 45 2.328195E-5 47.57639 7 CAATACA 45 2.328195E-5 47.57639 8 AGCAATA 45 2.328195E-5 47.57639 6 CACTAGC 20 5.73109E-4 46.29054 86-87 ACTAGCT 20 5.73109E-4 46.29054 86-87 AAAGCAT 30 9.114537E-5 38.316555 78-79 TAGCCGA 30 9.487198E-5 38.06111 72-73 AGCCGAA 30 9.487198E-5 38.06111 74-75 GCCGAAA 30 9.487198E-5 38.06111 74-75 CCGAAAG 30 9.487198E-5 38.06111 76-77 CATCACT 35 2.168639E-4 33.06467 82-83 AGCATCA 35 2.168639E-4 33.06467 80-81 GCATCAC 35 2.168639E-4 33.06467 82-83 GAAAGCA 35 2.2576572E-4 32.842762 78-79 >>END_MODULE Rejected 42372 READS because READLEN < 1 Read 42372 spots for ERR6133402.sra Written 42372 spots for ERR6133402.sra Rejected 42372 READS because READLEN < 1 Read 42372 spots for ERR6133402.sra Written 42372 spots for ERR6133402.sra Rejected 42372 READS because READLEN < 1 Read 42372 spots for ERR6133402.sra Written 42372 spots for ERR6133402.sra Rejected 42372 READS because READLEN < 1 Read 42372 spots for ERR6133402.sra Written 42372 spots for ERR6133402.sra Rejected 42372 READS because READLEN < 1 Read 42372 spots for ERR6133402.sra Written 42372 spots for ERR6133402.sra Rejected 42372 READS because READLEN < 1 Read 42372 spots for ERR6133402.sra Written 42372 spots for ERR6133402.sra Rejected 42372 READS because READLEN < 1 Read 42372 spots for ERR6133402.sra Written 42372 spots for ERR6133402.sra Rejected 42372 READS because READLEN < 1 Read 42372 spots for ERR6133402.sra Written 42372 spots for ERR6133402.sra Rejected 42372 READS because READLEN < 1 Read 42372 spots for ERR6133402.sra Written 42372 spots for ERR6133402.sra Rejected 42372 READS because READLEN < 1 Read 42372 spots for ERR6133402.sra Written 42372 spots for ERR6133402.sra Rejected 42372 READS because READLEN < 1 Read 42372 spots for ERR6133402.sra Written 42372 spots for ERR6133402.sra Rejected 42372 READS because READLEN < 1 Read 42372 spots for ERR6133402.sra Written 42372 spots for ERR6133402.sra Rejected 42372 READS because READLEN < 1 Read 42372 spots for ERR6133402.sra Written 42372 spots for ERR6133402.sra Rejected 42372 READS because READLEN < 1 Read 42372 spots for ERR6133402.sra Written 42372 spots for ERR6133402.sra Rejected 42372 READS because READLEN < 1 Read 42372 spots for ERR6133402.sra Written 42372 spots for ERR6133402.sra Rejected 42388 READS because READLEN < 1 Read 42388 spots for ERR6133402.sra Written 42388 spots for ERR6133402.sra Rejected 42372 READS because READLEN < 1 Read 42372 spots for ERR6133402.sra Written 42372 spots for ERR6133402.sra Rejected 42372 READS because READLEN < 1 Read 42372 spots for ERR6133402.sra Written 42372 spots for ERR6133402.sra Rejected 42372 READS because READLEN < 1 Read 42372 spots for ERR6133402.sra Written 42372 spots for ERR6133402.sra Rejected 42372 READS because READLEN < 1 Read 42372 spots for ERR6133402.sra Written 42372 spots for ERR6133402.sra SRR ids: ['ERR6133402.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_r04xngcd ERR6133402.sra spots: 847456 blocks: [[1, 42372], [42373, 84744], [84745, 127116], [127117, 169488], [169489, 211860], [211861, 254232], [254233, 296604], [296605, 338976], [338977, 381348], [381349, 423720], [423721, 466092], [466093, 508464], [508465, 550836], [550837, 593208], [593209, 635580], [635581, 677952], [677953, 720324], [720325, 762696], [762697, 805068], [805069, 847456]] ERR6133402 file size 184462 ERR6133402 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 ERR6133402 ERR6133402_1.fastq Input file: ERR6133402_1.fastq trimmed: ERR6133402-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 03:14:18 2024 >> started Sat Dec 7 03:14:19 2024 >> done (0.854s) 847456 reads processed; of these: 39 ( 0.00%) short reads filtered out after trimming by size control 7 ( 0.00%) empty reads filtered out after trimming by size control 847410 (99.99%) reads available; of these: 217832 (25.71%) trimmed reads available after processing 629578 (74.29%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 1 0.00% 19 7 0.00% 20 4 0.00% 21 3 0.00% 22 7 0.00% 23 2 0.00% 24 3 0.00% 25 1 0.00% 26 0 0.00% 27 3 0.00% 28 25 0.00% 29 15 0.00% 30 3 0.00% 31 4 0.00% 32 8 0.00% 33 4 0.00% 34 6 0.00% 35 6 0.00% 36 2 0.00% 37 2 0.00% 38 13 0.00% 39 9 0.00% 40 13 0.00% 41 6 0.00% 42 11 0.00% 43 17 0.00% 44 11 0.00% 45 23 0.00% 46 32 0.00% 47 36 0.00% 48 72 0.01% 49 90 0.01% 50 125 0.01% 51 162 0.02% 52 189 0.02% 53 267 0.03% 54 406 0.05% 55 495 0.06% 56 666 0.08% 57 1025 0.12% 58 700 0.08% 59 794 0.09% 60 1020 0.12% 61 1134 0.13% 62 1197 0.14% 63 1409 0.17% 64 1523 0.18% 65 1534 0.18% 66 1624 0.19% 67 1608 0.19% 68 1507 0.18% 69 1568 0.19% 70 6004 0.71% 71 6419 0.76% 72 7438 0.88% 73 7743 0.91% 74 7922 0.93% 75 8512 1.00% 76 9140 1.08% 77 10080 1.19% 78 10292 1.21% 79 10923 1.29% 80 11424 1.35% 81 13188 1.56% 82 14095 1.66% 83 14195 1.68% 84 16183 1.91% 85 10834 1.28% 86 11174 1.32% 87 12588 1.49% 88 15004 1.77% 89 15463 1.82% 90 16702 1.97% 91 17815 2.10% 92 15273 1.80% 93 559607 66.04% 847410 reads passed initial QC criterion=sequence-density sequence-density=4.86 sequence-density-rank=1 fanout-score=2.07 fanout-score-rank=28 prefix-density=4.97 prefix-fanout=2.0 sequence=CAAGGCTAAATAC criterion=fanout-score sequence-density=0.10 sequence-density-rank=20 fanout-score=92.81 fanout-score-rank=1 prefix-density=9.26 prefix-fanout=1.0 sequence=GATGGCTAAAGGCCAGTAGCCGA 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 03:14:37 Started mapping on | Dec 07 03:14:38 Finished on | Dec 07 03:14:44 Mapping speed, Million of reads per hour | 508.45 Number of input reads | 847410 Average input read length | 89 UNIQUE READS: Uniquely mapped reads number | 360101 Uniquely mapped reads % | 42.49% Average mapped length | 88.06 Number of splices: Total | 13745 Number of splices: Annotated (sjdb) | 10939 Number of splices: GT/AG | 13009 Number of splices: GC/AG | 228 Number of splices: AT/AC | 14 Number of splices: Non-canonical | 494 Mismatch rate per base, % | 0.85% Deletion rate per base | 0.04% Deletion average length | 1.75 Insertion rate per base | 0.02% Insertion average length | 1.75 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 383865 % of reads mapped to multiple loci | 45.30% Number of reads mapped to too many loci | 46160 % of reads mapped to too many loci | 5.45% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 5.87% % of reads unmapped: other | 0.89% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 103444 103444 103444 N_multimapping 383865 383865 383865 N_noFeature 29997 33713 344503 N_ambiguous 14278 2383 60 UnstrandedReadsAssigned:315826 PositiveStrandReadsAssigned:324005 NegativeStrandReadsAssigned:15538 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=84 echo kmer=79 ERR6133402 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: ERR6133402-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 847,410 reads, 499,284 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 881 rounds 52973 ERR6133402.ke.tsv 35125 ERR6133402.se.tsv 88098 total ==> ERR6133402.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 15.5923 PNS24243 293 194 0 0 KQK14069 1603 1504 17 30.2257 KQK14071 474 375 0 0 ==> ERR6133402.se.tsv <== BRADI_1g14170v3 16 BRADI_1g53295v3 6 BRADI_1g59795v3 6 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 6 BRADI_1g74790v3 2 BRADI_1g09890v3 0 BRADI_1g77505v3 8 BRADI_1g48960v3 0 ERR6133402 completed mapping pipeline successfully