Starting /dee2/code/volunteer_pipeline.sh ERR6133521 current disk space = 1544430514176 free memory = 1453620724 ERR6133521 SRAfilesize 686d65f6830e691e5f858e06e931c76b ERR6133521.sra ERR6133521.sra file validated ERR6133521 is single end ERR6133521 is conventional basespace ERR6133521 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133521_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 36.6205 37.0 37.0 37.0 37.0 37.0 2 36.863 37.0 37.0 37.0 37.0 37.0 3 36.571 37.0 37.0 37.0 37.0 37.0 4 35.8605 37.0 37.0 37.0 33.0 37.0 5 35.9205 37.0 37.0 37.0 33.0 37.0 6 36.25375 37.0 37.0 37.0 33.0 37.0 7 38.24125 40.0 37.0 40.0 37.0 40.0 8 38.25825 40.0 37.0 40.0 37.0 40.0 9 38.26825 40.0 37.0 40.0 37.0 40.0 10-11 38.28175 40.0 37.0 40.0 37.0 40.0 12-13 38.222624999999994 40.0 37.0 40.0 37.0 40.0 14-15 38.1835 40.0 37.0 40.0 37.0 40.0 16-17 38.045249999999996 40.0 37.0 40.0 37.0 40.0 18-19 37.994625 40.0 37.0 40.0 37.0 40.0 20-21 38.027 40.0 37.0 40.0 37.0 40.0 22-23 38.121624999999995 40.0 37.0 40.0 37.0 40.0 24-25 37.982124999999996 40.0 37.0 40.0 37.0 40.0 26-27 37.922 40.0 37.0 40.0 35.0 40.0 28-29 37.9255 40.0 37.0 40.0 37.0 40.0 30-31 37.990750000000006 40.0 37.0 40.0 37.0 40.0 32-33 38.017624999999995 40.0 37.0 40.0 37.0 40.0 34-35 37.948125000000005 38.5 37.0 40.0 37.0 40.0 36-37 37.86525 37.0 37.0 40.0 37.0 40.0 38-39 37.738749999999996 37.0 37.0 40.0 37.0 40.0 40-41 37.507374999999996 37.0 37.0 40.0 35.0 40.0 42-43 37.54475 37.0 37.0 40.0 37.0 40.0 44-45 37.266125 37.0 37.0 40.0 35.0 40.0 46-47 37.16075 37.0 37.0 40.0 33.0 40.0 48-49 37.039874999999995 37.0 37.0 38.5 33.0 40.0 50-51 36.8395 37.0 37.0 37.0 33.0 40.0 52-53 36.4125 37.0 37.0 37.0 33.0 40.0 54-55 36.411625 37.0 37.0 37.0 33.0 40.0 56-57 36.255875 37.0 37.0 37.0 33.0 38.5 58-59 35.805625 37.0 37.0 37.0 33.0 37.0 60-61 36.01625 37.0 37.0 37.0 33.0 37.0 62-63 35.904875000000004 37.0 37.0 37.0 33.0 37.0 64-65 35.774249999999995 37.0 37.0 37.0 33.0 37.0 66-67 35.808625 37.0 37.0 37.0 33.0 37.0 68-69 34.844125 35.0 35.0 37.0 33.0 37.0 70-71 35.06912756634952 37.0 33.0 37.0 33.0 37.0 72-73 35.54443346558683 37.0 33.0 37.0 33.0 37.0 74-75 35.59555174942719 37.0 35.0 37.0 33.0 37.0 76-77 35.57660508341934 37.0 33.0 37.0 33.0 37.0 78-79 35.49248618497776 37.0 33.0 37.0 33.0 37.0 80-81 35.410437380496504 37.0 33.0 37.0 33.0 37.0 82-83 35.272126020668324 37.0 33.0 37.0 33.0 37.0 84-85 35.13047511376354 37.0 33.0 37.0 33.0 37.0 86-87 35.037328855592875 37.0 33.0 37.0 33.0 37.0 88-89 35.00309997416689 37.0 33.0 37.0 33.0 37.0 90-91 34.97003358305348 37.0 33.0 37.0 33.0 37.0 92-93 34.935546370446914 37.0 33.0 37.0 33.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 3.0 21 5.0 22 0.0 23 4.0 24 5.0 25 6.0 26 9.0 27 6.0 28 23.0 29 22.0 30 29.0 31 39.0 32 51.0 33 71.0 34 111.0 35 307.0 36 1154.0 37 1394.0 38 750.0 39 11.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 88.075 3.35 3.3000000000000003 5.2749999999999995 2 74.925 14.399999999999999 6.45 4.2250000000000005 3 38.125 37.25 13.625000000000002 11.0 4 32.725 29.925 18.6 18.75 5 27.05 30.225 25.7 17.025000000000002 6 19.650000000000002 40.625 24.099999999999998 15.625 7 37.6 28.599999999999998 20.0 13.8 8 30.5 29.4 22.400000000000002 17.7 9 24.349999999999998 29.9 26.875 18.875 10-11 24.462500000000002 28.15 29.075 18.3125 12-13 27.875 26.6125 26.137500000000003 19.375 14-15 22.95 33.275 26.2625 17.5125 16-17 25.474999999999998 30.275000000000002 24.887500000000003 19.3625 18-19 24.212500000000002 27.3125 27.962500000000002 20.5125 20-21 25.35 26.0625 28.325 20.2625 22-23 27.962500000000002 23.3875 28.225 20.424999999999997 24-25 26.75 24.625 27.6375 20.9875 26-27 26.8 25.4375 29.6375 18.125 28-29 25.7875 27.762500000000003 27.150000000000002 19.3 30-31 29.625 24.587500000000002 26.174999999999997 19.6125 32-33 25.05 27.575 26.2875 21.087500000000002 34-35 25.3125 27.287499999999998 26.674999999999997 20.724999999999998 36-37 26.224999999999998 24.087500000000002 27.675 22.0125 38-39 28.449999999999996 24.025 29.725 17.8 40-41 26.985119419782418 25.984744279104667 27.64786795048143 19.382268350631488 42-43 25.803225403175396 31.25390673834229 24.54056757094637 18.40230028753594 44-45 24.224999999999998 26.525 28.6625 20.5875 46-47 24.762500000000003 22.825 28.599999999999998 23.8125 48-49 25.900000000000002 24.55 29.95 19.6 50-51 24.65 27.025 28.599999999999998 19.725 52-53 24.7491219267436 27.960361264425487 24.7491219267436 22.541394882087307 54-55 24.48112028007002 28.844711177794448 27.35683920980245 19.317329332333085 56-57 27.05 25.2375 27.800000000000004 19.9125 58-59 23.200000000000003 25.0625 29.8875 21.85 60-61 28.1625 24.625 27.525 19.6875 62-63 21.95 27.1 32.3625 18.587500000000002 64-65 24.224999999999998 29.925 26.687499999999996 19.162499999999998 66-67 25.2125 28.875 27.325 18.587500000000002 68-69 22.9875 26.137500000000003 27.1125 23.7625 70-71 23.980485364023014 26.257192894671004 27.820865649236925 21.94145609206905 72-73 26.539091023542742 24.461790255570943 28.70451970288304 20.29459901800327 74-75 24.42699759402305 28.909712549069265 28.162593389894898 18.50069646701279 76-77 21.646341463414632 26.07977642276423 27.210365853658537 25.0635162601626 78-79 25.394803871625065 26.464595007641368 28.757004584819157 19.383596535914414 80-81 24.262169413568415 30.803628465567908 28.12060815127124 16.813593969592436 82-83 24.62782340862423 24.743326488706366 28.8629363449692 21.765913757700204 84-85 24.584031987617696 23.681155681671612 30.38823681155682 21.346575519153877 86-87 21.46732110565745 27.69310255747869 30.71557737018858 20.123998966675277 88-89 21.57065357788685 28.171015241539653 30.560578661844485 19.69775251872901 90-91 27.86101782485146 27.11185740118832 27.75768535262206 17.269439421338156 92-93 22.113149057091192 30.457246189615088 28.51976233531387 18.90984241797985 >>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 0.0 17 4.5 18 5.0 19 1.5 20 2.5 21 3.5 22 2.0 23 4.0 24 7.5 25 6.0 26 5.0 27 8.0 28 16.5 29 22.0 30 24.0 31 25.0 32 28.5 33 39.5 34 45.0 35 54.5 36 82.0 37 122.5 38 172.0 39 175.5 40 168.0 41 176.5 42 224.5 43 279.5 44 224.5 45 188.5 46 251.5 47 239.5 48 174.0 49 169.5 50 178.0 51 186.5 52 186.5 53 189.5 54 210.0 55 154.0 56 68.5 57 51.5 58 48.0 59 31.5 60 18.0 61 17.5 62 16.5 63 16.0 64 17.5 65 13.5 66 6.0 67 4.0 68 4.5 69 5.0 70 4.5 71 3.0 72 1.5 73 1.5 74 2.0 75 0.5 76 0.0 77 0.0 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 0.0375 42-43 0.0125 44-45 0.0 46-47 0.0 48-49 0.0 50-51 0.0 52-53 0.35000000000000003 54-55 0.025 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 6.0 71 14.0 72 17.0 73 12.0 74 5.0 75 8.0 76 4.0 77 7.0 78 2.0 79 6.0 80 11.0 81 6.0 82 12.0 83 8.0 84 11.0 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 3871.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 75.575 #Duplication Level Percentage of deduplicated Percentage of total 1 92.9209394641085 70.22500000000001 2 4.035726099900761 6.1 3 0.9923916639100231 2.25 4 0.628514720476348 1.9 5 0.4300363876943433 1.625 6 0.09923916639100232 0.44999999999999996 7 0.09923916639100232 0.525 8 0.06615944426066822 0.4 9 0.03307972213033411 0.22499999999999998 >10 0.628514720476348 11.35 >50 0.03307972213033411 1.6 >100 0.03307972213033411 3.35 >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 134 3.35 No Hit GGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGG 64 1.6 No Hit GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 48 1.2 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 46 1.15 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 40 1.0 No Hit GGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTT 37 0.9249999999999999 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 35 0.8750000000000001 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 31 0.775 No Hit GGCCTGTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCG 25 0.625 No Hit GGGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTG 24 0.6 No Hit GGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGGG 22 0.5499999999999999 No Hit GGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAA 22 0.5499999999999999 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 21 0.525 No Hit GGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAA 18 0.44999999999999996 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 18 0.44999999999999996 No Hit GTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAA 14 0.35000000000000003 No Hit GGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCG 11 0.27499999999999997 No Hit GGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTT 11 0.27499999999999997 No Hit GGAGTATCCTTGATATATAAATATATAGATAAATAGATTTAAATGGAAAA 11 0.27499999999999997 No Hit GGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCTAAATGGATTC 10 0.25 No Hit GGAGCAGCCTAAACCGTGAAAACGGGGTTGTGGGAGAGCAATACAAGCGT 10 0.25 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 9 0.22499999999999998 No Hit GGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGT 8 0.2 No Hit CAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCT 8 0.2 No Hit GGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGC 7 0.17500000000000002 No Hit GGGAGTATTATGAAAGGAGATTAATCATAGATTATCAAAAACCCTAGAAA 7 0.17500000000000002 No Hit GTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCT 7 0.17500000000000002 No Hit GGAGAGGGTGAGCATATATATTTATACGACGAATAAAAGGCTGCCACGTG 6 0.15 No Hit GGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCTAAA 6 0.15 No Hit GGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGC 6 0.15 No Hit GGGAAAAGAGGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTT 5 0.125 No Hit GGAGTGGGGGTGCCATACGCAAAAAGGAAGCGACTCATAGAATGGCAGAG 5 0.125 No Hit CAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATAT 5 0.125 No Hit GGGATGGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACGA 5 0.125 No Hit GGGTCGAAATATGGCTTTCAAATTAAGTTCCGAATTAGTAGATGCTGCCA 5 0.125 No Hit GGGGATGGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACG 5 0.125 No Hit GGAGGAGAGCGGCGGCGGTCTGTTCAAGATGGCTCAGGGCTTCATGAAGT 5 0.125 No Hit GGGTGAGCATATATATTTATACGACGAATAAAAGGCTGCCACGTGGCGGG 5 0.125 No Hit GGAAGAGCCCGAGCTGCTGCAGCAGGTTTTGAAAAGGGAATCGATCGTGA 5 0.125 No Hit GGATTTGAAGAAAAAAAAGACTTCGATTCATTTTCTATTTATTTCGTTAG 5 0.125 No Hit GGGCCATTTGTGGCATGCAGGAAGAGCCCGAGCTGCTGCAGCAGGTTTTG 5 0.125 No Hit GGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTG 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 0.025 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 0.025 0.0 0.0 0.0 0.0 42-43 0.025 0.0 0.0 0.0 0.0 44-45 0.025 0.0 0.0 0.0 0.0 46-47 0.025 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 0.05 0.0 0.0 0.0 0.0 56-57 0.05 0.0 0.0 0.0 0.0 58-59 0.05 0.0 0.0 0.0 0.0 60-61 0.05 0.0 0.0 0.0 0.0 62-63 0.05 0.0 0.0 0.0 0.0 64-65 0.05 0.0 0.0 0.0 0.0 66-67 0.05 0.0 0.0 0.0 0.0 68-69 0.05 0.0 0.0 0.0 0.0 70-71 0.05 0.0 0.0 0.0 0.0 72-73 0.05 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 fail #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GCAATAC 25 6.6288885E-7 86.6375 7 GGGAGAG 30 1.7942511E-8 86.6375 1 CAATACA 25 6.6288885E-7 86.6375 8 GAGCAAT 25 6.6288885E-7 86.6375 5 GAGAGCA 25 6.6288885E-7 86.6375 3 AATACAA 25 6.6288885E-7 86.6375 9 AGCAATA 25 6.6288885E-7 86.6375 6 GGAGAGC 30 1.961349E-6 72.197914 2 AGAGCAA 30 1.961349E-6 72.197914 4 GGGTGTG 20 0.0027754677 64.97813 1 ATCACTA 25 3.822666E-5 44.429485 84-85 AGCATCA 25 3.822666E-5 44.429485 80-81 CACTAGC 25 3.822666E-5 44.429485 86-87 AAGCATC 25 3.822666E-5 44.429485 80-81 AAAGCAT 25 3.972107E-5 44.146496 78-79 GAAAGCA 25 3.972107E-5 44.146496 78-79 CCAGTAG 25 4.1263527E-5 43.867085 68-69 AGTAGCC 25 4.1263527E-5 43.867085 70-71 TAGCCGA 25 4.1263527E-5 43.867085 72-73 CGAAAGC 25 4.1263527E-5 43.867085 76-77 >>END_MODULE Rejected 118295 READS because READLEN < 1 Read 118295 spots for ERR6133521.sra Written 118295 spots for ERR6133521.sra Rejected 118295 READS because READLEN < 1 Read 118295 spots for ERR6133521.sra Written 118295 spots for ERR6133521.sra Rejected 118295 READS because READLEN < 1 Read 118295 spots for ERR6133521.sra Written 118295 spots for ERR6133521.sra Rejected 118295 READS because READLEN < 1 Read 118295 spots for ERR6133521.sra Written 118295 spots for ERR6133521.sra Rejected 118295 READS because READLEN < 1 Read 118295 spots for ERR6133521.sra Written 118295 spots for ERR6133521.sra Rejected 118295 READS because READLEN < 1 Read 118295 spots for ERR6133521.sra Written 118295 spots for ERR6133521.sra Rejected 118295 READS because READLEN < 1 Read 118295 spots for ERR6133521.sra Written 118295 spots for ERR6133521.sra Rejected 118295 READS because READLEN < 1 Read 118295 spots for ERR6133521.sra Written 118295 spots for ERR6133521.sra Rejected 118295 READS because READLEN < 1 Read 118295 spots for ERR6133521.sra Written 118295 spots for ERR6133521.sra Rejected 118295 READS because READLEN < 1 Read 118295 spots for ERR6133521.sra Written 118295 spots for ERR6133521.sra Rejected 118295 READS because READLEN < 1 Read 118295 spots for ERR6133521.sra Written 118295 spots for ERR6133521.sra Rejected 118311 READS because READLEN < 1 Read 118311 spots for ERR6133521.sra Written 118311 spots for ERR6133521.sra Rejected 118295 READS because READLEN < 1 Read 118295 spots for ERR6133521.sra Written 118295 spots for ERR6133521.sra Rejected 118295 READS because READLEN < 1 Read 118295 spots for ERR6133521.sra Written 118295 spots for ERR6133521.sra Rejected 118295 READS because READLEN < 1 Read 118295 spots for ERR6133521.sra Written 118295 spots for ERR6133521.sra Rejected 118295 READS because READLEN < 1 Read 118295 spots for ERR6133521.sra Written 118295 spots for ERR6133521.sra Rejected 118295 READS because READLEN < 1 Read 118295 spots for ERR6133521.sra Written 118295 spots for ERR6133521.sra Rejected 118295 READS because READLEN < 1 Read 118295 spots for ERR6133521.sra Written 118295 spots for ERR6133521.sra Rejected 118295 READS because READLEN < 1 Read 118295 spots for ERR6133521.sra Written 118295 spots for ERR6133521.sra Rejected 118295 READS because READLEN < 1 Read 118295 spots for ERR6133521.sra Written 118295 spots for ERR6133521.sra SRR ids: ['ERR6133521.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_91dfi8yt ERR6133521.sra spots: 2365916 blocks: [[1, 118295], [118296, 236590], [236591, 354885], [354886, 473180], [473181, 591475], [591476, 709770], [709771, 828065], [828066, 946360], [946361, 1064655], [1064656, 1182950], [1182951, 1301245], [1301246, 1419540], [1419541, 1537835], [1537836, 1656130], [1656131, 1774425], [1774426, 1892720], [1892721, 2011015], [2011016, 2129310], [2129311, 2247605], [2247606, 2365916]] ERR6133521 file size 522162 ERR6133521 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 ERR6133521 ERR6133521_1.fastq Input file: ERR6133521_1.fastq trimmed: ERR6133521-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 07:52:28 2024 >> started Sat Dec 7 07:52:29 2024 >> done (1.379s) 2365916 reads processed; of these: 292 ( 0.01%) short reads filtered out after trimming by size control 14 ( 0.00%) empty reads filtered out after trimming by size control 2365610 (99.99%) reads available; of these: 11008 ( 0.47%) trimmed reads available after processing 2354602 (99.53%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 56 0.00% 19 82 0.00% 20 35 0.00% 21 25 0.00% 22 27 0.00% 23 12 0.00% 24 15 0.00% 25 14 0.00% 26 10 0.00% 27 14 0.00% 28 27 0.00% 29 108 0.00% 30 23 0.00% 31 31 0.00% 32 37 0.00% 33 23 0.00% 34 23 0.00% 35 153 0.01% 36 285 0.01% 37 16 0.00% 38 38 0.00% 39 89 0.00% 40 94 0.00% 41 36 0.00% 42 11 0.00% 43 12 0.00% 44 17 0.00% 45 16 0.00% 46 13 0.00% 47 8 0.00% 48 9 0.00% 49 13 0.00% 50 6 0.00% 51 60 0.00% 52 12 0.00% 53 4 0.00% 54 5 0.00% 55 10 0.00% 56 3 0.00% 57 8 0.00% 58 8 0.00% 59 3 0.00% 60 14 0.00% 61 4 0.00% 62 1 0.00% 63 2 0.00% 64 1 0.00% 65 2 0.00% 66 3 0.00% 67 3 0.00% 68 7 0.00% 69 46 0.00% 70 5638 0.24% 71 4944 0.21% 72 5403 0.23% 73 4924 0.21% 74 4854 0.21% 75 4676 0.20% 76 4317 0.18% 77 4575 0.19% 78 4964 0.21% 79 5547 0.23% 80 5183 0.22% 81 6261 0.26% 82 6574 0.28% 83 6078 0.26% 84 5587 0.24% 85 36 0.00% 86 47 0.00% 87 101 0.00% 88 165 0.01% 89 317 0.01% 90 597 0.03% 91 1559 0.07% 92 6218 0.26% 93 2275471 96.19% 2365610 reads passed initial QC criterion=sequence-density sequence-density=0.67 sequence-density-rank=1 fanout-score=2.03 fanout-score-rank=28 prefix-density=0.68 prefix-fanout=2.0 sequence=CAAGGCTAAATAC criterion=fanout-score sequence-density=0.01 sequence-density-rank=31 fanout-score=123.78 fanout-score-rank=1 prefix-density=0.13 prefix-fanout=7.1 sequence=AAAAGAAGGGGTGTTCCATCTCCGGACGACGATCCTGCCTGCAGAGGAAGACATGCCGGCGATCATGTCGAGCTTCAAGAAGTTCAACGACTCATTCATGGAGCAATACCAAGACTACTCCAGGCTGTGATGTGAAGAGGGAAACAACGAGGTCATCATCGACATGATATATTGCTGCTATTTTCCACCAGCGATTAAAAGTTAAAAAATTTAGCTGTAAGCTGTAACTATCTTGAAGAAACTAAACTGGTTGCTGTGCTTGATATGTAT Started job on | Dec 07 07:52:48 Started mapping on | Dec 07 07:52:48 Finished on | Dec 07 07:52:53 Mapping speed, Million of reads per hour | 1703.24 Number of input reads | 2365610 Average input read length | 92 UNIQUE READS: Uniquely mapped reads number | 1549215 Uniquely mapped reads % | 65.49% Average mapped length | 92.05 Number of splices: Total | 93323 Number of splices: Annotated (sjdb) | 78562 Number of splices: GT/AG | 90772 Number of splices: GC/AG | 1684 Number of splices: AT/AC | 55 Number of splices: Non-canonical | 812 Mismatch rate per base, % | 0.36% Deletion rate per base | 0.04% Deletion average length | 1.78 Insertion rate per base | 0.02% Insertion average length | 1.84 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 750366 % of reads mapped to multiple loci | 31.72% Number of reads mapped to too many loci | 17787 % of reads mapped to too many loci | 0.75% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 2.00% % of reads unmapped: other | 0.03% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 66029 66029 66029 N_multimapping 750366 750366 750366 N_noFeature 97101 111141 1482963 N_ambiguous 60039 7797 246 UnstrandedReadsAssigned:1392075 PositiveStrandReadsAssigned:1430277 NegativeStrandReadsAssigned:66006 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=93 echo kmer=89 ERR6133521 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: ERR6133521-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 2,365,610 reads, 1,916,690 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,011 rounds 52973 ERR6133521.ke.tsv 35125 ERR6133521.se.tsv 88098 total ==> ERR6133521.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 85 42.0548 PNS24243 293 194 0 0 KQK14069 1603 1504 70 31.5937 KQK14071 474 375 0 0 ==> ERR6133521.se.tsv <== BRADI_1g14170v3 70 BRADI_1g53295v3 26 BRADI_1g59795v3 23 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 17 BRADI_1g74790v3 10 BRADI_1g09890v3 0 BRADI_1g77505v3 35 BRADI_1g48960v3 0 ERR6133521 completed mapping pipeline successfully