Starting /dee2/code/volunteer_pipeline.sh ERR6133545 current disk space = 1544512442368 free memory = 1604183764 ERR6133545 SRAfilesize e08e1b478e71ef1b8fcf5f4170762aaa ERR6133545.sra ERR6133545.sra file validated ERR6133545 is single end ERR6133545 is conventional basespace ERR6133545 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133545_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 33.93525 37.0 33.0 37.0 27.0 37.0 2 36.00775 37.0 37.0 37.0 33.0 37.0 3 35.1335 37.0 33.0 37.0 33.0 37.0 4 35.25325 37.0 37.0 37.0 33.0 37.0 5 35.16975 37.0 37.0 37.0 33.0 37.0 6 35.45875 37.0 37.0 37.0 33.0 37.0 7 37.3225 37.0 37.0 40.0 33.0 40.0 8 37.3515 37.0 37.0 40.0 33.0 40.0 9 37.334 37.0 37.0 40.0 33.0 40.0 10-11 37.398125 37.0 37.0 40.0 33.0 40.0 12-13 37.40575 37.0 37.0 40.0 33.0 40.0 14-15 37.391 37.0 37.0 40.0 33.0 40.0 16-17 37.24375 37.0 37.0 40.0 33.0 40.0 18-19 37.200374999999994 37.0 37.0 40.0 33.0 40.0 20-21 37.11425 37.0 37.0 40.0 33.0 40.0 22-23 37.024125 37.0 37.0 40.0 33.0 40.0 24-25 37.093125 37.0 37.0 40.0 33.0 40.0 26-27 37.135374999999996 37.0 37.0 40.0 33.0 40.0 28-29 37.07925 37.0 37.0 40.0 33.0 40.0 30-31 36.955124999999995 37.0 37.0 40.0 33.0 40.0 32-33 36.739875 37.0 37.0 40.0 33.0 40.0 34-35 36.575874999999996 37.0 37.0 40.0 33.0 40.0 36-37 36.364000000000004 37.0 37.0 40.0 33.0 40.0 38-39 36.333875 37.0 37.0 40.0 33.0 40.0 40-41 36.064 37.0 37.0 40.0 33.0 40.0 42-43 36.019375 37.0 37.0 40.0 33.0 40.0 44-45 35.759875 37.0 35.0 38.5 33.0 40.0 46-47 35.395250000000004 37.0 33.0 37.0 33.0 40.0 48-49 35.516 37.0 33.0 37.0 33.0 40.0 50-51 35.424375 37.0 33.0 37.0 33.0 40.0 52-53 35.083749999999995 37.0 33.0 37.0 30.0 40.0 54-55 35.08 37.0 33.0 37.0 33.0 37.0 56-57 34.8635 37.0 33.0 37.0 30.0 37.0 58-59 34.116125 37.0 33.0 37.0 27.0 37.0 60-61 34.480374999999995 37.0 33.0 37.0 27.0 37.0 62-63 34.358875 37.0 33.0 37.0 27.0 37.0 64-65 34.320375 37.0 33.0 37.0 27.0 37.0 66-67 34.398624999999996 37.0 33.0 37.0 27.0 37.0 68-69 33.565 35.0 33.0 37.0 27.0 37.0 70-71 33.66159184184184 35.0 33.0 37.0 27.0 37.0 72-73 34.026435858437 37.0 33.0 37.0 27.0 37.0 74-75 33.95646227269037 37.0 33.0 37.0 27.0 37.0 76-77 33.904297273905506 37.0 33.0 37.0 27.0 37.0 78-79 34.02228841644766 37.0 33.0 37.0 27.0 37.0 80-81 33.974592007408596 37.0 33.0 37.0 27.0 37.0 82-83 33.821504584806924 37.0 33.0 37.0 27.0 37.0 84-85 33.794600085081726 37.0 33.0 37.0 27.0 37.0 86-87 33.68851419878296 37.0 33.0 37.0 27.0 37.0 88-89 33.74467545638945 37.0 33.0 37.0 27.0 37.0 90-91 33.617900608519264 37.0 33.0 37.0 27.0 37.0 92-93 33.60446247464503 37.0 33.0 37.0 27.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 8.0 21 17.0 22 23.0 23 26.0 24 25.0 25 37.0 26 39.0 27 57.0 28 43.0 29 83.0 30 82.0 31 104.0 32 136.0 33 144.0 34 213.0 35 445.0 36 983.0 37 941.0 38 582.0 39 12.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 89.47500000000001 2.325 2.775 5.425 2 75.4 15.024999999999999 5.175 4.3999999999999995 3 39.1 37.025000000000006 12.775 11.1 4 32.824999999999996 30.349999999999998 17.65 19.175 5 27.224999999999998 31.474999999999998 24.7 16.6 6 19.55 41.8 23.200000000000003 15.45 7 39.825 28.449999999999996 17.575 14.149999999999999 8 29.075 29.849999999999998 21.625 19.45 9 26.950000000000003 31.3 24.775 16.975 10-11 24.4875 29.1625 27.737499999999997 18.6125 12-13 28.249999999999996 26.424999999999997 25.412499999999998 19.9125 14-15 21.7 32.875 27.2625 18.1625 16-17 26.087500000000002 30.049999999999997 23.962500000000002 19.900000000000002 18-19 24.712500000000002 27.237499999999997 27.150000000000002 20.9 20-21 25.912499999999998 25.2375 28.8875 19.9625 22-23 27.2625 23.549999999999997 26.987499999999997 22.2 24-25 25.35 22.787499999999998 29.099999999999998 22.7625 26-27 26.987499999999997 23.5875 29.15 20.275000000000002 28-29 24.587500000000002 28.4375 27.474999999999998 19.5 30-31 29.862499999999997 25.387500000000003 25.112499999999997 19.6375 32-33 24.762500000000003 27.325 25.937500000000004 21.975 34-35 24.96560350218887 28.21763602251407 25.916197623514698 20.900562851782365 36-37 26.787499999999998 23.0 26.9625 23.25 38-39 29.175 23.9375 27.987499999999997 18.9 40-41 26.50994122796049 24.884331624359135 28.598224334125298 20.007502813555085 42-43 25.944931163954944 29.7622027534418 24.593241551939926 19.69962453066333 44-45 25.296986369888707 24.696761285482054 29.06089783668876 20.94535450794048 46-47 26.1 23.075000000000003 26.5875 24.2375 48-49 26.5 24.05 28.475 20.974999999999998 50-51 24.7375 26.737499999999997 27.325 21.2 52-53 24.42776735459662 25.64102564102564 25.90368980612883 24.027517198248905 54-55 23.0125 27.425 28.5625 21.0 56-57 27.900000000000002 25.1 27.125 19.875 58-59 22.85 26.637499999999996 29.375 21.1375 60-61 28.1875 23.7625 27.3375 20.7125 62-63 20.9125 27.762500000000003 31.837500000000002 19.4875 64-65 22.662499999999998 30.662499999999998 27.8875 18.787499999999998 66-67 25.687500000000004 28.4375 27.325 18.55 68-69 23.175 24.625 28.4 23.799999999999997 70-71 25.15007503751876 25.625312656328163 26.638319159579787 22.586293146573286 72-73 27.784041087310534 23.02392584241513 29.02417637479644 20.16785669547789 74-75 24.81797639969872 27.793120763243785 27.516947024855636 19.871955812201858 76-77 21.700251889168765 26.007556675062972 27.38035264483627 24.911838790931988 78-79 25.31853160085783 25.12930490727892 28.888608553046552 20.663554938816702 80-81 23.019583070120024 31.4971572962729 28.477574226152875 17.0056854074542 82-83 24.275774826059457 24.073371283997467 28.690702087286528 22.960151802656547 84-85 23.314749113025847 23.808920425747594 31.322858590978203 21.55347187024835 86-87 21.703853955375255 27.789046653144016 30.324543610547668 20.18255578093306 88-89 20.14452332657201 28.372210953346855 31.44016227180527 20.04310344827586 90-91 27.497464503042597 26.495943204868155 27.345334685598377 18.66125760649087 92-93 20.841784989858013 27.67494929006085 29.95689655172414 21.526369168357 >>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 0.5 17 10.0 18 11.0 19 3.5 20 2.5 21 1.5 22 2.0 23 4.0 24 5.5 25 5.5 26 6.0 27 12.0 28 16.5 29 15.5 30 18.5 31 24.5 32 38.5 33 57.0 34 64.5 35 69.0 36 87.5 37 124.0 38 165.5 39 154.0 40 161.0 41 191.5 42 193.5 43 201.5 44 185.5 45 165.5 46 201.0 47 201.5 48 169.0 49 174.0 50 171.0 51 159.0 52 146.0 53 156.0 54 198.0 55 156.0 56 72.0 57 60.5 58 66.5 59 52.5 60 39.0 61 44.5 62 35.0 63 28.5 64 32.0 65 28.0 66 22.0 67 21.5 68 21.0 69 15.0 70 9.0 71 8.5 72 6.0 73 4.0 74 5.0 75 3.5 76 1.5 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 0.0625 36-37 0.0 38-39 0.0 40-41 0.0375 42-43 0.125 44-45 0.0375 46-47 0.0 48-49 0.0 50-51 0.0 52-53 0.0625 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 4.0 71 4.0 72 1.0 73 3.0 74 10.0 75 7.0 76 2.0 77 3.0 78 5.0 79 2.0 80 3.0 81 1.0 82 5.0 83 2.0 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 3944.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 74.52499999999999 #Duplication Level Percentage of deduplicated Percentage of total 1 91.78128144917814 68.4 2 4.495135860449514 6.7 3 1.442468970144247 3.225 4 0.5031868500503187 1.5 5 0.36900369003690037 1.375 6 0.4360952700436095 1.95 7 0.13418316001341832 0.7000000000000001 8 0.06709158000670916 0.4 9 0.10063737001006373 0.675 >10 0.6038242200603825 9.4 >50 0.03354579000335458 1.375 >100 0.03354579000335458 4.3 >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 172 4.3 No Hit GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 55 1.375 No Hit GGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGG 49 1.225 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 32 0.8 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 32 0.8 No Hit GGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTT 28 0.7000000000000001 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 24 0.6 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 23 0.575 No Hit GGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAA 20 0.5 No Hit GGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAA 18 0.44999999999999996 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 18 0.44999999999999996 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 18 0.44999999999999996 No Hit GGGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTG 18 0.44999999999999996 No Hit GGAGTATCCTTGATATATAAATATATAGATAAATAGATTTAAATGGAAAA 18 0.44999999999999996 No Hit GGAAAAGAAAGCAAAAGCGATTCCCGTAGTAGCGGCGAGCGAAATGGGAG 17 0.42500000000000004 No Hit GGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGGG 15 0.375 No Hit GGTGGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGC 14 0.35000000000000003 No Hit GGCCTGTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCG 12 0.3 No Hit GTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAA 10 0.25 No Hit GGGGATGGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACG 10 0.25 No Hit GGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCG 9 0.22499999999999998 No Hit GGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAACCCTCTTAACT 9 0.22499999999999998 No Hit GGTTTTGAAAAGGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAA 9 0.22499999999999998 No Hit GGGATGGAGATGGCCGCGGAGAACGGCGGCTGCGGCTGCAGCACCTGCAA 8 0.2 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 8 0.2 No Hit GGTGGGGCAATGGGCATTCCGTTGAGTTTGTATGGTGGGTGCTGTTTTGC 7 0.17500000000000002 No Hit CAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATAT 7 0.17500000000000002 No Hit GGAGAAGTACAAGTGCGGATCCAACGTCTTCTGGAAATGGTGAAGATGAT 7 0.17500000000000002 No Hit GGGCCATTTGTGGCATGCAGGAAGAGCCCGAGCTGCTGCAGCAGGTTTTG 7 0.17500000000000002 No Hit GGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGT 6 0.15 No Hit GGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAAA 6 0.15 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 6 0.15 No Hit CAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCT 6 0.15 No Hit GGGGTTGTGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTG 6 0.15 No Hit GGAAGAGCCCGAGCTGCTGCAGCAGGTTTTGAAAAGGGAATCGATCGTGA 6 0.15 No Hit GGAAATGGTGAAGATGATACGAATATGCCGGCCGGGTGCTGATATTGTGA 6 0.15 No Hit GGGCAAGGAGAAGTACAAGTGCGGATCCAACGTCTTCTGGAAATGGTGAA 6 0.15 No Hit GCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCA 6 0.15 No Hit GGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGCA 6 0.15 No Hit GAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGC 6 0.15 No Hit GGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGC 6 0.15 No Hit GGATTCTTCTTTTTTGTGGGCCATTTGTGGCATGCAGGAAGAGCCCGAGC 6 0.15 No Hit GGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCTAAATGGATTC 5 0.125 No Hit GGAGTGGGGGTGCCATACGCAAAAAGGAAGCGACTCATAGAATGGCAGAG 5 0.125 No Hit GTAACGAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCA 5 0.125 No Hit GGGATGGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACGA 5 0.125 No Hit GGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTT 5 0.125 No Hit GAGGAAAAGAAAGCAAAAGCGATTCCCGTAGTAGCGGCGAGCGAAATGGG 5 0.125 No Hit GGGAGTATTATGAAAGGAGATTAATCATAGATTATCAAAAACCCTAGAAA 5 0.125 No Hit GGAGAACGGCGGCTGCGGCTGCAGCACCTGCAAGTGCGGCACCAGCTGCG 5 0.125 No Hit GGGGTGCCATACGCAAAAAGGAAGCGACTCATAGAATGGCAGAGGCAAAT 5 0.125 No Hit GGAGCAGCCTAAACCGTGAAAACGGGGTTGTGGGAGAGCAATACAAGCGT 5 0.125 No Hit GGGCTTGGCTACAATTCCGAATACGCTATTACATGTTTGCGCTAGTTTTT 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 0.0125 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 0.025 0.0 0.0 0.0 0.0 50-51 0.025 0.0 0.0 0.0 0.0 52-53 0.025 0.0 0.0 0.0 0.0 54-55 0.025 0.0 0.0 0.0 0.0 56-57 0.025 0.0 0.0 0.0 0.0 58-59 0.025 0.0 0.0 0.0 0.0 60-61 0.025 0.0 0.0 0.0 0.0 62-63 0.025 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 warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GGAGAGC 15 8.889599E-4 86.5625 2 AGTAGGA 15 8.889599E-4 86.5625 8 GGGAGAG 15 8.889599E-4 86.5625 1 GGCCTGT 15 8.889599E-4 86.5625 1 TAGTAGG 15 8.889599E-4 86.5625 7 CCTGTAG 20 0.0027850142 64.921875 3 TGTAGTA 20 0.0027850142 64.921875 5 GTAGGAA 20 0.0027850142 64.921875 9 GCCTGTA 20 0.0027850142 64.921875 2 GTAGTAG 20 0.0027850142 64.921875 6 CTCGTGA 30 0.005514576 29.219412 82-83 AGGGCGC 30 0.0056895227 29.03564 68-69 GAAGGGC 30 0.005868829 28.854168 66-67 TGTGTAC 40 7.08738E-4 27.050781 48-49 >>END_MODULE Rejected 266086 READS because READLEN < 1 Read 266086 spots for ERR6133545.sra Written 266086 spots for ERR6133545.sra Rejected 266086 READS because READLEN < 1 Read 266086 spots for ERR6133545.sra Written 266086 spots for ERR6133545.sra Rejected 266086 READS because READLEN < 1 Read 266086 spots for ERR6133545.sra Written 266086 spots for ERR6133545.sra Rejected 266086 READS because READLEN < 1 Read 266086 spots for ERR6133545.sra Written 266086 spots for ERR6133545.sra Rejected 266086 READS because READLEN < 1 Read 266086 spots for ERR6133545.sra Written 266086 spots for ERR6133545.sra Rejected 266086 READS because READLEN < 1 Read 266086 spots for ERR6133545.sra Written 266086 spots for ERR6133545.sra Rejected 266086 READS because READLEN < 1 Read 266086 spots for ERR6133545.sra Written 266086 spots for ERR6133545.sra Rejected 266086 READS because READLEN < 1 Read 266086 spots for ERR6133545.sra Written 266086 spots for ERR6133545.sra Rejected 266086 READS because READLEN < 1 Read 266086 spots for ERR6133545.sra Written 266086 spots for ERR6133545.sra Rejected 266086 READS because READLEN < 1 Read 266086 spots for ERR6133545.sra Written 266086 spots for ERR6133545.sra Rejected 266097 READS because READLEN < 1 Read 266097 spots for ERR6133545.sra Written 266097 spots for ERR6133545.sra Rejected 266086 READS because READLEN < 1 Read 266086 spots for ERR6133545.sra Written 266086 spots for ERR6133545.sra Rejected 266086 READS because READLEN < 1 Read 266086 spots for ERR6133545.sra Written 266086 spots for ERR6133545.sra Rejected 266086 READS because READLEN < 1 Read 266086 spots for ERR6133545.sra Written 266086 spots for ERR6133545.sra Rejected 266086 READS because READLEN < 1 Read 266086 spots for ERR6133545.sra Written 266086 spots for ERR6133545.sra Rejected 266086 READS because READLEN < 1 Read 266086 spots for ERR6133545.sra Written 266086 spots for ERR6133545.sra Rejected 266086 READS because READLEN < 1 Read 266086 spots for ERR6133545.sra Written 266086 spots for ERR6133545.sra Rejected 266086 READS because READLEN < 1 Read 266086 spots for ERR6133545.sra Written 266086 spots for ERR6133545.sra Rejected 266086 READS because READLEN < 1 Read 266086 spots for ERR6133545.sra Written 266086 spots for ERR6133545.sra Rejected 266086 READS because READLEN < 1 Read 266086 spots for ERR6133545.sra Written 266086 spots for ERR6133545.sra SRR ids: ['ERR6133545.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_twv3pu2d ERR6133545.sra spots: 5321731 blocks: [[1, 266086], [266087, 532172], [532173, 798258], [798259, 1064344], [1064345, 1330430], [1330431, 1596516], [1596517, 1862602], [1862603, 2128688], [2128689, 2394774], [2394775, 2660860], [2660861, 2926946], [2926947, 3193032], [3193033, 3459118], [3459119, 3725204], [3725205, 3991290], [3991291, 4257376], [4257377, 4523462], [4523463, 4789548], [4789549, 5055634], [5055635, 5321731]] ERR6133545 file size 1179970 ERR6133545 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 ERR6133545 ERR6133545_1.fastq Input file: ERR6133545_1.fastq trimmed: ERR6133545-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 08:21:02 2024 >> started Sat Dec 7 08:21:05 2024 >> done (2.880s) 5321731 reads processed; of these: 158 ( 0.00%) short reads filtered out after trimming by size control 31 ( 0.00%) empty reads filtered out after trimming by size control 5321542 (100.00%) reads available; of these: 97926 ( 1.84%) trimmed reads available after processing 5223616 (98.16%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 23 0.00% 19 37 0.00% 20 15 0.00% 21 12 0.00% 22 11 0.00% 23 2 0.00% 24 6 0.00% 25 5 0.00% 26 7 0.00% 27 7 0.00% 28 12 0.00% 29 25 0.00% 30 7 0.00% 31 14 0.00% 32 21 0.00% 33 14 0.00% 34 16 0.00% 35 79 0.00% 36 754 0.01% 37 17 0.00% 38 23 0.00% 39 49 0.00% 40 53 0.00% 41 29 0.00% 42 13 0.00% 43 13 0.00% 44 11 0.00% 45 9 0.00% 46 13 0.00% 47 11 0.00% 48 4 0.00% 49 13 0.00% 50 13 0.00% 51 21 0.00% 52 8 0.00% 53 6 0.00% 54 5 0.00% 55 4 0.00% 56 6 0.00% 57 8 0.00% 58 8 0.00% 59 6 0.00% 60 8 0.00% 61 3 0.00% 62 2 0.00% 63 1 0.00% 64 7 0.00% 65 4 0.00% 66 9 0.00% 67 16 0.00% 68 16 0.00% 69 82 0.00% 70 6080 0.11% 71 5291 0.10% 72 5505 0.10% 73 5225 0.10% 74 5512 0.10% 75 5482 0.10% 76 4900 0.09% 77 5342 0.10% 78 5988 0.11% 79 7095 0.13% 80 6339 0.12% 81 6742 0.13% 82 7677 0.14% 83 7979 0.15% 84 6589 0.12% 85 179 0.00% 86 445 0.01% 87 688 0.01% 88 1236 0.02% 89 2495 0.05% 90 5587 0.10% 91 16274 0.31% 92 67915 1.28% 93 5133419 96.46% 5321542 reads passed initial QC criterion=sequence-density sequence-density=0.32 sequence-density-rank=1 fanout-score=6.20 fanout-score-rank=23 prefix-density=0.77 prefix-fanout=2.6 sequence=GCCGCCGCCGCCAAGGAAGGCATGTTCGTCAAGAACTACAGCTACTGATCCTAATCGCATCAAGCTTCAACGCCTGTGAGTGAAAACCAGTGATGAGAGTGCTGCTGCTAGCTAGCGCCGGCATTGATGAGCTTGAGAGGGCACTGTAGCCAGTGTGTCAGTCGTTGTTAAATTACAGGTTGAGATCATCAGCGTACTCCGATGGGAGGTGGACATCAGAAAGTATACTGTGTTTTACCACCCTAATTAAGTAAACAACTTTTGGAATGGTGATCATCTTACTGTTTTAAATAAATCTGTTTC criterion=fanout-score sequence-density=0.01 sequence-density-rank=39 fanout-score=126.63 fanout-score-rank=1 prefix-density=0.14 prefix-fanout=7.1 sequence=AGAGGAAGAGACTTATAATATTGTGGCTGCTCATGGTTATTTTGGCCGATTAATCTTCCAATATGCTAGTTTCAACAACTCTCGTTCTTTACACTTCTTCTTGGCTGCTTGGCCTGTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAACGTAATGCTCACAACTTCCCTCTAGATCTAGCTGCTCTTGAAGTTCCCGCTATTAATGGATAAGGTTTTTCCGCTAACATA Started job on | Dec 07 08:21:18 Started mapping on | Dec 07 08:21:18 Finished on | Dec 07 08:21:25 Mapping speed, Million of reads per hour | 2736.79 Number of input reads | 5321542 Average input read length | 92 UNIQUE READS: Uniquely mapped reads number | 3594053 Uniquely mapped reads % | 67.54% Average mapped length | 92.32 Number of splices: Total | 184391 Number of splices: Annotated (sjdb) | 151949 Number of splices: GT/AG | 176500 Number of splices: GC/AG | 4446 Number of splices: AT/AC | 95 Number of splices: Non-canonical | 3350 Mismatch rate per base, % | 0.43% Deletion rate per base | 0.04% Deletion average length | 1.80 Insertion rate per base | 0.03% Insertion average length | 2.06 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 1635378 % of reads mapped to multiple loci | 30.73% Number of reads mapped to too many loci | 25940 % of reads mapped to too many loci | 0.49% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.21% % of reads unmapped: other | 0.04% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 92111 92111 92111 N_multimapping 1635378 1635378 1635378 N_noFeature 232045 267813 3429693 N_ambiguous 144626 16049 478 UnstrandedReadsAssigned:3217382 PositiveStrandReadsAssigned:3310191 NegativeStrandReadsAssigned:163882 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=93 echo kmer=89 ERR6133545 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: ERR6133545-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 5,321,542 reads, 4,312,938 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,058 rounds 52973 ERR6133545.ke.tsv 35125 ERR6133545.se.tsv 88098 total ==> ERR6133545.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 137 30.4242 PNS24243 293 194 0 0 KQK14069 1603 1504 91 18.4352 KQK14071 474 375 0 0 ==> ERR6133545.se.tsv <== BRADI_1g14170v3 91 BRADI_1g53295v3 22 BRADI_1g59795v3 20 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 52 BRADI_1g74790v3 54 BRADI_1g09890v3 0 BRADI_1g77505v3 66 BRADI_1g48960v3 0 ERR6133545 completed mapping pipeline successfully