Starting /dee2/code/volunteer_pipeline.sh ERR6133374 current disk space = 1547907768320 free memory = 1601978900 ERR6133374 SRAfilesize acfca1b135e8477e5d70f809ef3ee9fd ERR6133374.sra ERR6133374.sra file validated ERR6133374 is single end ERR6133374 is conventional basespace ERR6133374 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133374_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 35.5405 37.0 33.0 37.0 33.0 37.0 2 36.52175 37.0 37.0 37.0 37.0 37.0 3 36.23825 37.0 37.0 37.0 33.0 37.0 4 35.76475 37.0 37.0 37.0 33.0 37.0 5 35.5565 37.0 37.0 37.0 33.0 37.0 6 35.93175 37.0 37.0 37.0 33.0 37.0 7 37.78125 40.0 37.0 40.0 33.0 40.0 8 37.864 40.0 37.0 40.0 33.0 40.0 9 37.9795 40.0 37.0 40.0 33.0 40.0 10-11 37.894625000000005 40.0 37.0 40.0 33.0 40.0 12-13 37.845625 40.0 37.0 40.0 33.0 40.0 14-15 37.7635 40.0 37.0 40.0 33.0 40.0 16-17 37.636624999999995 38.5 37.0 40.0 33.0 40.0 18-19 37.612624999999994 40.0 37.0 40.0 33.0 40.0 20-21 37.468375 37.0 37.0 40.0 33.0 40.0 22-23 37.415375 37.0 37.0 40.0 33.0 40.0 24-25 37.620999999999995 38.5 37.0 40.0 33.0 40.0 26-27 37.501875 37.0 37.0 40.0 33.0 40.0 28-29 37.49925 37.0 37.0 40.0 33.0 40.0 30-31 37.336625 37.0 37.0 40.0 33.0 40.0 32-33 37.242875 37.0 37.0 40.0 33.0 40.0 34-35 37.084375 37.0 37.0 40.0 33.0 40.0 36-37 36.956 37.0 37.0 40.0 33.0 40.0 38-39 36.783 37.0 37.0 40.0 33.0 40.0 40-41 36.5615 37.0 37.0 40.0 33.0 40.0 42-43 36.489999999999995 37.0 37.0 40.0 33.0 40.0 44-45 36.141625000000005 37.0 35.0 40.0 33.0 40.0 46-47 35.947375 37.0 35.0 38.5 33.0 40.0 48-49 35.807 37.0 35.0 37.0 33.0 40.0 50-51 35.678875 37.0 33.0 37.0 33.0 40.0 52-53 35.335375 37.0 33.0 37.0 33.0 40.0 54-55 35.312 37.0 33.0 37.0 33.0 40.0 56-57 35.126 37.0 33.0 37.0 33.0 40.0 58-59 33.822374999999994 37.0 33.0 37.0 27.0 37.0 60-61 34.511125 37.0 33.0 37.0 30.0 37.0 62-63 34.56975 37.0 33.0 37.0 30.0 37.0 64-65 34.56 37.0 33.0 37.0 30.0 37.0 66-67 34.670500000000004 37.0 33.0 37.0 33.0 37.0 68-69 33.861625000000004 35.0 33.0 37.0 30.0 37.0 70-71 33.95141132264529 35.0 33.0 37.0 27.0 37.0 72-73 34.3332990098685 37.0 33.0 37.0 30.0 37.0 74-75 33.954525868099275 37.0 33.0 37.0 27.0 37.0 76-77 34.09096323860011 37.0 33.0 37.0 27.0 37.0 78-79 34.171519148792825 37.0 33.0 37.0 27.0 37.0 80-81 34.15957151192228 37.0 33.0 37.0 27.0 37.0 82-83 33.99239722363295 37.0 33.0 37.0 27.0 37.0 84-85 33.99322106798015 37.0 33.0 37.0 27.0 37.0 86-87 33.80844239158327 37.0 33.0 37.0 27.0 37.0 88-89 34.03579676674365 37.0 33.0 37.0 27.0 37.0 90-91 33.76225301513985 37.0 33.0 37.0 27.0 37.0 92-93 33.53695150115473 37.0 33.0 37.0 27.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 7.0 21 14.0 22 17.0 23 13.0 24 14.0 25 24.0 26 19.0 27 42.0 28 49.0 29 62.0 30 76.0 31 97.0 32 108.0 33 158.0 34 249.0 35 426.0 36 911.0 37 1041.0 38 660.0 39 13.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 83.175 4.675 5.775 6.375 2 63.5 21.275 9.925 5.3 3 33.675 35.9 16.0 14.424999999999999 4 30.7 29.775000000000002 18.85 20.674999999999997 5 24.675 29.75 28.249999999999996 17.325 6 19.650000000000002 40.65 24.625 15.075 7 36.525 27.975 20.7 14.799999999999999 8 29.75 25.525 24.125 20.599999999999998 9 23.175 29.049999999999997 27.474999999999998 20.3 10-11 22.775000000000002 28.625 28.849999999999998 19.75 12-13 25.4375 26.1125 26.125 22.325 14-15 22.4875 32.25 27.075 18.1875 16-17 25.7625 30.912499999999998 23.8625 19.4625 18-19 24.9375 25.674999999999997 27.675 21.712500000000002 20-21 26.7625 25.85 27.85 19.537499999999998 22-23 28.95 22.4375 27.712500000000002 20.9 24-25 25.25 25.637500000000003 27.900000000000002 21.212500000000002 26-27 26.9125 25.6125 28.299999999999997 19.175 28-29 25.4875 27.1375 27.85 19.525000000000002 30-31 30.5375 24.6 26.3625 18.5 32-33 25.7125 27.9125 25.75 20.625 34-35 24.775 29.7375 26.3 19.1875 36-37 26.075 24.725 25.874999999999996 23.325000000000003 38-39 28.526763381690845 23.21160580290145 28.87693846923462 19.384692346173086 40-41 24.349674837418707 26.21310655327664 28.264132066033014 21.173086543271637 42-43 25.681420355088775 31.345336334083523 24.99374843710928 17.97949487371843 44-45 24.95 25.912499999999998 29.599999999999998 19.537499999999998 46-47 26.437500000000004 22.912499999999998 26.6625 23.9875 48-49 25.412499999999998 24.5125 28.799999999999997 21.275 50-51 23.275000000000002 27.287499999999998 27.462500000000002 21.975 52-53 25.90829366073666 26.296667501879227 26.04610373340015 21.748935103983964 54-55 25.474999999999998 27.200000000000003 27.875 19.45 56-57 27.0875 26.737499999999997 27.474999999999998 18.7 58-59 24.15 24.7375 31.275 19.8375 60-61 28.1875 25.5 27.487499999999997 18.825 62-63 21.025 28.725 31.225 19.025 64-65 21.0375 30.5375 28.449999999999996 19.975 66-67 25.75 29.349999999999998 27.500000000000004 17.4 68-69 22.2625 26.3125 28.249999999999996 23.175 70-71 24.524524524524523 26.026026026026027 27.37737737737738 22.07207207207207 72-73 27.119708579324204 25.21040070342922 27.659841728426077 20.0100489888205 74-75 24.3727146639768 28.949691085613416 28.079687302988276 18.59790694742151 76-77 21.986084756483237 25.0853889943074 27.868437697659708 25.060088551549654 78-79 25.79868154158215 25.646551724137932 28.803245436105477 19.751521298174442 80-81 24.06512337827525 31.391503434240654 27.741032816077333 16.802340371406764 82-83 23.63450740173558 25.727411944869832 28.981623277182234 21.656457376212355 84-85 22.277735075582886 25.00640532923392 31.808864975659752 20.906994619523445 86-87 19.97690531177829 27.559661277906084 30.85706954067231 21.606363869643317 88-89 20.46445984090326 29.420066717988195 29.612522453169106 20.502950987939442 90-91 25.917372337695667 27.893251218886324 27.739286630741596 18.450089812676417 92-93 23.1075186040544 29.009494482935594 28.560431100846806 19.322555812163202 >>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 20.0 18 24.0 19 5.5 20 2.0 21 2.5 22 3.0 23 4.5 24 5.5 25 5.0 26 8.5 27 14.5 28 21.0 29 26.0 30 31.5 31 40.0 32 44.0 33 54.0 34 62.5 35 74.0 36 95.0 37 126.5 38 151.5 39 137.0 40 149.5 41 193.5 42 210.0 43 210.5 44 194.5 45 188.5 46 205.0 47 194.0 48 162.5 49 172.0 50 202.0 51 179.5 52 156.5 53 170.0 54 195.5 55 147.5 56 65.0 57 50.0 58 48.0 59 40.0 60 31.0 61 28.5 62 28.0 63 24.5 64 20.5 65 17.5 66 14.5 67 9.5 68 9.0 69 10.5 70 9.0 71 9.0 72 7.5 73 3.0 74 1.5 75 2.5 76 1.5 77 1.0 78 1.0 79 1.0 80 0.5 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 0.05 40-41 0.05 42-43 0.025 44-45 0.0 46-47 0.0 48-49 0.0 50-51 0.0 52-53 0.22499999999999998 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 8.0 71 7.0 72 9.0 73 5.0 74 11.0 75 7.0 76 1.0 77 6.0 78 4.0 79 8.0 80 6.0 81 6.0 82 8.0 83 5.0 84 12.0 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 3897.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 74.97500000000001 #Duplication Level Percentage of deduplicated Percentage of total 1 93.26442147382461 69.925 2 3.5678559519839945 5.35 3 1.1670556852284095 2.625 4 0.53351117039013 1.6 5 0.33344448149383127 1.25 6 0.16672224074691563 0.75 7 0.1333777925975325 0.7000000000000001 8 0.03334444814938312 0.2 9 0.03334444814938312 0.22499999999999998 >10 0.6668889629876625 9.75 >50 0.06668889629876625 3.85 >100 0.03334444814938312 3.775 >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 151 3.775 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 95 2.375 No Hit GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 59 1.4749999999999999 No Hit GGAGTATCCTTGATATATAAATATATAGATAAATAGATTTAAATGGAAAA 39 0.975 No Hit GGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGG 36 0.8999999999999999 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 31 0.775 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 29 0.7250000000000001 No Hit GGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAA 25 0.625 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 25 0.625 No Hit GGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTT 24 0.6 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 22 0.5499999999999999 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 21 0.525 No Hit GGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAA 16 0.4 No Hit GTATTTAGCCTTGCAAGGTGGTCCTTGCTGATTCACACGGGATTCCACGT 15 0.375 No Hit GGGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTG 15 0.375 No Hit GGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGC 15 0.375 No Hit GGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGGG 13 0.325 No Hit GTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAA 12 0.3 No Hit CAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCT 12 0.3 No Hit GGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCG 10 0.25 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 10 0.25 No Hit GGGAGTATTATGAAAGGAGATTAATCATAGATTATCAAAAACCCTAGAAA 10 0.25 No Hit GAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGC 10 0.25 No Hit CAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATAT 9 0.22499999999999998 No Hit GGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAAA 8 0.2 No Hit GCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATC 7 0.17500000000000002 No Hit GGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCG 7 0.17500000000000002 No Hit GAAATCTTTGGGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGG 7 0.17500000000000002 No Hit TCAAAAGAGGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGGA 7 0.17500000000000002 No Hit GGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAAGGCGATCAAATTC 6 0.15 No Hit CACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTTCGGGGAGT 6 0.15 No Hit GGCCTGTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCG 6 0.15 No Hit GATACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGC 6 0.15 No Hit GTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCT 6 0.15 No Hit GGCTTTAGAAGCCTGTGTACAAGCTCGTAACGAAGGGCGCGATCTTGCTC 5 0.125 No Hit GATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGGGG 5 0.125 No Hit GGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTG 5 0.125 No Hit GGGATGGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACGA 5 0.125 No Hit GGGAAAAGAGGGGTTACTTTTTTTTCATTTTTCCCTTAAAAGATAGGCTT 5 0.125 No Hit GAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAAT 5 0.125 No Hit GTACAAGCTCGTAACGAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAAT 5 0.125 No Hit GAAGGAACAAACGAGGATAAGATAAAATTGCTTTAAATTTATTTTGCCCA 5 0.125 No Hit CAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTG 5 0.125 No Hit GGAAAAGAAAGCAAAAGCGATTCCCGTAGTAGCGGCGAGCGAAATGGGAG 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 0.025 0.0 0.0 0.0 0.0 32-33 0.037500000000000006 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 0.075 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 0.1 0.0 0.0 0.0 0.0 48-49 0.1 0.0 0.0 0.0 0.0 50-51 0.1 0.0 0.0 0.0 0.0 52-53 0.1 0.0 0.0 0.0 0.0 54-55 0.1 0.0 0.0 0.0 0.0 56-57 0.1 0.0 0.0 0.0 0.0 58-59 0.1 0.0 0.0 0.0 0.0 60-61 0.1 0.0 0.0 0.0 0.0 62-63 0.1 0.0 0.0 0.0 0.0 64-65 0.1 0.0 0.0 0.0 0.0 66-67 0.1 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 TCGTGAA 25 4.3413726E-5 43.5 82-83 GCTCGTG 25 4.3413726E-5 43.5 80-81 TTGCTCG 25 4.3413726E-5 43.5 78-79 TGCACCT 60 1.15936775E-4 36.25 8 GCGATCT 30 1.2720095E-4 36.25 72-73 GCGCGAT 30 1.2720095E-4 36.25 70-71 GGGCGCG 30 1.2720095E-4 36.25 68-69 GAAGGTA 30 1.2720095E-4 36.25 86-87 TGCTCGT 25 0.0023441382 34.8 80-81 TGAAGGT 25 0.0023441382 34.8 86-87 ATGCACC 50 0.00220463 34.8 7 CGTGAAG 25 0.0023441382 34.8 84-85 CTCGTGA 25 0.0023441382 34.8 82-83 GCACCTG 65 1.8571172E-4 33.46154 9 AATGCAC 55 0.0035188831 31.636362 6 AGAAGCC 35 3.14738E-4 31.071426 40-41 AACGAAG 35 3.14738E-4 31.071426 62-63 GTGTACA 35 3.14738E-4 31.071426 48-49 CGAAGGG 35 3.14738E-4 31.071426 64-65 GCTCGTA 35 3.14738E-4 31.071426 56-57 >>END_MODULE Rejected 159258 READS because READLEN < 1 Read 159258 spots for ERR6133374.sra Written 159258 spots for ERR6133374.sra Rejected 159258 READS because READLEN < 1 Read 159258 spots for ERR6133374.sra Written 159258 spots for ERR6133374.sra Rejected 159258 READS because READLEN < 1 Read 159258 spots for ERR6133374.sra Written 159258 spots for ERR6133374.sra Rejected 159258 READS because READLEN < 1 Read 159258 spots for ERR6133374.sra Written 159258 spots for ERR6133374.sra Rejected 159258 READS because READLEN < 1 Read 159258 spots for ERR6133374.sra Written 159258 spots for ERR6133374.sra Rejected 159258 READS because READLEN < 1 Read 159258 spots for ERR6133374.sra Written 159258 spots for ERR6133374.sra Rejected 159258 READS because READLEN < 1 Read 159258 spots for ERR6133374.sra Written 159258 spots for ERR6133374.sra Rejected 159258 READS because READLEN < 1 Read 159258 spots for ERR6133374.sra Written 159258 spots for ERR6133374.sra Rejected 159258 READS because READLEN < 1 Read 159258 spots for ERR6133374.sra Written 159258 spots for ERR6133374.sra Rejected 159258 READS because READLEN < 1 Read 159258 spots for ERR6133374.sra Written 159258 spots for ERR6133374.sra Rejected 159258 READS because READLEN < 1 Read 159258 spots for ERR6133374.sra Written 159258 spots for ERR6133374.sra Rejected 159258 READS because READLEN < 1 Read 159258 spots for ERR6133374.sra Written 159258 spots for ERR6133374.sra Rejected 159258 READS because READLEN < 1 Read 159258 spots for ERR6133374.sra Written 159258 spots for ERR6133374.sra Rejected 159273 READS because READLEN < 1 Read 159273 spots for ERR6133374.sra Written 159273 spots for ERR6133374.sra Rejected 159258 READS because READLEN < 1 Read 159258 spots for ERR6133374.sra Written 159258 spots for ERR6133374.sra Rejected 159258 READS because READLEN < 1 Read 159258 spots for ERR6133374.sra Written 159258 spots for ERR6133374.sra Rejected 159258 READS because READLEN < 1 Read 159258 spots for ERR6133374.sra Written 159258 spots for ERR6133374.sra Rejected 159258 READS because READLEN < 1 Read 159258 spots for ERR6133374.sra Written 159258 spots for ERR6133374.sra Rejected 159258 READS because READLEN < 1 Read 159258 spots for ERR6133374.sra Written 159258 spots for ERR6133374.sra Rejected 159258 READS because READLEN < 1 Read 159258 spots for ERR6133374.sra Written 159258 spots for ERR6133374.sra SRR ids: ['ERR6133374.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_r2zl7thp ERR6133374.sra spots: 3185175 blocks: [[1, 159258], [159259, 318516], [318517, 477774], [477775, 637032], [637033, 796290], [796291, 955548], [955549, 1114806], [1114807, 1274064], [1274065, 1433322], [1433323, 1592580], [1592581, 1751838], [1751839, 1911096], [1911097, 2070354], [2070355, 2229612], [2229613, 2388870], [2388871, 2548128], [2548129, 2707386], [2707387, 2866644], [2866645, 3025902], [3025903, 3185175]] ERR6133374 file size 704329 ERR6133374 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 ERR6133374 ERR6133374_1.fastq Input file: ERR6133374_1.fastq trimmed: ERR6133374-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 02:00:21 2024 >> started Sat Dec 7 02:00:23 2024 >> done (1.939s) 3185175 reads processed; of these: 225 ( 0.01%) short reads filtered out after trimming by size control 34 ( 0.00%) empty reads filtered out after trimming by size control 3184916 (99.99%) reads available; of these: 54270 ( 1.70%) trimmed reads available after processing 3130646 (98.30%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 14 0.00% 19 49 0.00% 20 38 0.00% 21 46 0.00% 22 43 0.00% 23 13 0.00% 24 16 0.00% 25 4 0.00% 26 13 0.00% 27 12 0.00% 28 44 0.00% 29 59 0.00% 30 17 0.00% 31 40 0.00% 32 25 0.00% 33 21 0.00% 34 23 0.00% 35 235 0.01% 36 252 0.01% 37 30 0.00% 38 22 0.00% 39 135 0.00% 40 52 0.00% 41 50 0.00% 42 5 0.00% 43 7 0.00% 44 7 0.00% 45 10 0.00% 46 2 0.00% 47 7 0.00% 48 2 0.00% 49 8 0.00% 50 4 0.00% 51 23 0.00% 52 9 0.00% 53 8 0.00% 54 1 0.00% 55 8 0.00% 56 3 0.00% 57 7 0.00% 58 7 0.00% 59 14 0.00% 60 13 0.00% 61 11 0.00% 62 3 0.00% 63 1 0.00% 64 2 0.00% 65 3 0.00% 66 4 0.00% 67 6 0.00% 68 22 0.00% 69 42 0.00% 70 5528 0.17% 71 5139 0.16% 72 6163 0.19% 73 5405 0.17% 74 5514 0.17% 75 5486 0.17% 76 5034 0.16% 77 5093 0.16% 78 5674 0.18% 79 6478 0.20% 80 6026 0.19% 81 6115 0.19% 82 6971 0.22% 83 7408 0.23% 84 6277 0.20% 85 132 0.00% 86 198 0.01% 87 387 0.01% 88 669 0.02% 89 1117 0.04% 90 2284 0.07% 91 6566 0.21% 92 40376 1.27% 93 3043384 95.56% 3184916 reads passed initial QC criterion=sequence-density sequence-density=0.41 sequence-density-rank=1 fanout-score=5.34 fanout-score-rank=25 prefix-density=0.58 prefix-fanout=3.8 sequence=ATGCATGCATGC criterion=fanout-score sequence-density=0.01 sequence-density-rank=32 fanout-score=87.10 fanout-score-rank=1 prefix-density=0.12 prefix-fanout=7.2 sequence=AAAAGAAGGGGTGTTCCATCTCCGGACGACGATCCTGCCTGCGGAGGAAGACATGCCGGCGATCATGTCGAGCTTCAAGAAGTTCAACGACTCATTCATGGAGCAATACCAAGACTACTCCAGGCTGTGATGTGAAGAGGGAAACAACGACGTCATCATCGACATGATATATTGCTGCTATTTTCCACCAGCGATTAAAAGTTAAAAAATTTAGCTGTAAGCTGTAACTATCTTGAAGAAACTAAACTGGTTGCTGTGCTTGATATGTATAGGGAAAACATAATTTATGAGACAATCATACTGTGCAACTCTTGGCTCCATCGATTAATTAATACTCCTTGTTATTGCTTGC Started job on | Dec 07 02:00:40 Started mapping on | Dec 07 02:00:40 Finished on | Dec 07 02:00:46 Mapping speed, Million of reads per hour | 1910.95 Number of input reads | 3184916 Average input read length | 92 UNIQUE READS: Uniquely mapped reads number | 1979722 Uniquely mapped reads % | 62.16% Average mapped length | 92.03 Number of splices: Total | 107264 Number of splices: Annotated (sjdb) | 87752 Number of splices: GT/AG | 102008 Number of splices: GC/AG | 2304 Number of splices: AT/AC | 50 Number of splices: Non-canonical | 2902 Mismatch rate per base, % | 0.42% Deletion rate per base | 0.05% Deletion average length | 1.73 Insertion rate per base | 0.03% Insertion average length | 1.62 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 1132000 % of reads mapped to multiple loci | 35.54% Number of reads mapped to too many loci | 25860 % of reads mapped to too many loci | 0.81% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.42% % of reads unmapped: other | 0.07% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 73194 73194 73194 N_multimapping 1132000 1132000 1132000 N_noFeature 133131 153987 1889262 N_ambiguous 78863 9214 265 UnstrandedReadsAssigned:1767728 PositiveStrandReadsAssigned:1816521 NegativeStrandReadsAssigned:90195 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=93 echo kmer=89 ERR6133374 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: ERR6133374-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 3,184,916 reads, 2,522,093 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,020 rounds 52973 ERR6133374.ke.tsv 35125 ERR6133374.se.tsv 88098 total ==> ERR6133374.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 837 0 0 PNS24247 1044 945 0 0 PNS24249 1928 1829 4.00219 1.1425 PNS24246 1044 945 0 0 PNS24248 1044 945 0 0 PNS24244 1471 1372 42.9978 16.3631 PNS24243 293 194 0 0 KQK14069 1603 1504 29 10.0675 KQK14071 474 375 0 0 ==> ERR6133374.se.tsv <== BRADI_1g14170v3 29 BRADI_1g53295v3 48 BRADI_1g59795v3 8 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 39 BRADI_1g74790v3 16 BRADI_1g09890v3 0 BRADI_1g77505v3 73 BRADI_1g48960v3 0 ERR6133374 completed mapping pipeline successfully