Starting /dee2/code/volunteer_pipeline.sh ERR6133486 current disk space = 1544678105088 free memory = 1421010408 ERR6133486 SRAfilesize 8d69c93dce855759de63f0eb546915b8 ERR6133486.sra ERR6133486.sra file validated ERR6133486 is single end ERR6133486 is conventional basespace ERR6133486 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133486_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 35.30225 37.0 33.0 37.0 33.0 37.0 2 36.34225 37.0 37.0 37.0 33.0 37.0 3 36.201 37.0 37.0 37.0 33.0 37.0 4 35.88175 37.0 37.0 37.0 33.0 37.0 5 35.72 37.0 37.0 37.0 33.0 37.0 6 35.91825 37.0 37.0 37.0 33.0 37.0 7 37.97825 40.0 37.0 40.0 33.0 40.0 8 38.07325 40.0 37.0 40.0 33.0 40.0 9 38.06775 40.0 37.0 40.0 33.0 40.0 10-11 38.015 40.0 37.0 40.0 33.0 40.0 12-13 37.94975 40.0 37.0 40.0 33.0 40.0 14-15 37.876000000000005 40.0 37.0 40.0 33.0 40.0 16-17 37.714749999999995 40.0 37.0 40.0 33.0 40.0 18-19 37.675375 40.0 37.0 40.0 33.0 40.0 20-21 37.5435 40.0 37.0 40.0 33.0 40.0 22-23 37.461749999999995 40.0 37.0 40.0 33.0 40.0 24-25 37.635374999999996 40.0 37.0 40.0 33.0 40.0 26-27 37.731 40.0 37.0 40.0 33.0 40.0 28-29 37.63375 40.0 37.0 40.0 33.0 40.0 30-31 37.494625 40.0 37.0 40.0 33.0 40.0 32-33 37.300625 40.0 37.0 40.0 33.0 40.0 34-35 37.187875000000005 40.0 37.0 40.0 33.0 40.0 36-37 37.053124999999994 37.0 37.0 40.0 33.0 40.0 38-39 36.790875 37.0 37.0 40.0 33.0 40.0 40-41 36.42075 37.0 37.0 40.0 33.0 40.0 42-43 36.321749999999994 37.0 37.0 40.0 33.0 40.0 44-45 35.961875 37.0 35.0 40.0 33.0 40.0 46-47 35.765249999999995 37.0 33.0 40.0 33.0 40.0 48-49 35.708625 37.0 35.0 37.0 33.0 40.0 50-51 35.6535 37.0 35.0 37.0 33.0 40.0 52-53 35.253 37.0 33.0 37.0 27.0 40.0 54-55 35.289500000000004 37.0 33.0 37.0 33.0 40.0 56-57 34.90475 37.0 33.0 37.0 27.0 40.0 58-59 33.40525 35.0 33.0 37.0 27.0 37.0 60-61 34.400375 37.0 33.0 37.0 27.0 37.0 62-63 34.564875 37.0 33.0 37.0 27.0 37.0 64-65 34.38325 37.0 33.0 37.0 27.0 37.0 66-67 34.48025 37.0 33.0 37.0 27.0 37.0 68-69 33.60425 35.0 33.0 37.0 27.0 37.0 70-71 33.70401333249875 35.0 33.0 37.0 27.0 37.0 72-73 34.14778031383307 37.0 33.0 37.0 27.0 37.0 74-75 33.7996216414532 37.0 33.0 37.0 27.0 37.0 76-77 34.042898224623286 37.0 33.0 37.0 27.0 37.0 78-79 34.03786104183041 37.0 33.0 37.0 27.0 37.0 80-81 33.89898124139884 37.0 33.0 37.0 27.0 37.0 82-83 33.73841273771937 37.0 33.0 37.0 27.0 37.0 84-85 33.8446502792187 37.0 33.0 37.0 27.0 37.0 86-87 33.672511603919546 37.0 33.0 37.0 27.0 37.0 88-89 33.90136668385766 37.0 33.0 37.0 27.0 37.0 90-91 33.62016503352244 37.0 33.0 37.0 27.0 37.0 92-93 33.46776689014956 37.0 33.0 37.0 27.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 6.0 21 12.0 22 18.0 23 22.0 24 29.0 25 22.0 26 35.0 27 39.0 28 60.0 29 83.0 30 72.0 31 99.0 32 121.0 33 149.0 34 225.0 35 346.0 36 791.0 37 1067.0 38 784.0 39 20.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 66.825 8.05 15.075 10.05 2 46.975 29.95 13.975000000000001 9.1 3 27.525 34.4 17.0 21.075 4 24.65 29.175 18.7 27.474999999999998 5 25.074999999999996 26.1 32.324999999999996 16.5 6 15.024999999999999 43.95 24.875 16.150000000000002 7 40.475 25.474999999999998 19.025 15.024999999999999 8 29.575000000000003 27.775 21.7 20.95 9 20.525 28.349999999999998 26.450000000000003 24.675 10-11 19.3875 30.125 28.625 21.8625 12-13 19.275000000000002 29.15 24.2875 27.287499999999998 14-15 22.8875 35.8375 23.625 17.65 16-17 27.150000000000002 30.5125 21.575 20.7625 18-19 23.5625 26.400000000000002 29.1625 20.875 20-21 27.528441055131893 25.84073009126141 27.453431678959873 19.17739717464683 22-23 33.225 20.75 28.262500000000003 17.7625 24-25 22.39029878734842 29.778722340292536 28.01600200025003 19.814976872109014 26-27 29.525000000000002 23.5375 27.712500000000002 19.225 28-29 24.381095273818453 27.981995498874717 25.318829707426854 22.31807951987997 30-31 29.025000000000002 23.962500000000002 27.825 19.1875 32-33 26.35 26.5875 26.7125 20.349999999999998 34-35 21.0625 35.1625 23.0 20.775 36-37 27.462500000000002 27.8875 21.675 22.975 38-39 30.342842842842842 21.90940940940941 26.08858858858859 21.65915915915916 40-41 23.954420235411973 27.42299023290759 28.149261207112446 20.473328324567994 42-43 28.40170085042521 31.4032016008004 23.23661830915458 16.95847923961981 44-45 22.400000000000002 31.1875 28.199999999999996 18.212500000000002 46-47 28.462500000000002 25.0375 26.5625 19.9375 48-49 25.174999999999997 23.2875 27.800000000000004 23.7375 50-51 18.637500000000003 28.037499999999998 28.625 24.7 52-53 29.101856497742094 23.95885599598595 22.742097340692425 24.197190165579528 54-55 28.762500000000003 23.200000000000003 27.725 20.3125 56-57 29.075 29.75 24.175 17.0 58-59 22.6125 26.1625 33.3125 17.9125 60-61 28.749999999999996 28.449999999999996 25.575 17.224999999999998 62-63 20.175 32.75 29.275000000000002 17.8 64-65 19.537499999999998 35.825 27.625 17.0125 66-67 22.405601400350086 34.93373343335834 25.04376094023506 17.616904226056516 68-69 21.5625 25.887500000000003 26.5 26.05 70-71 20.490367775831874 31.536152114085564 27.970978233675257 20.002501876407305 72-73 27.734570998494736 26.680883090817865 28.4746613146011 17.109884596086303 74-75 23.91194968553459 28.842767295597483 30.641509433962266 16.60377358490566 76-77 20.34134007585335 23.072060682680153 25.10745891276865 31.479140328697852 78-79 32.61393931699886 26.05052685032373 24.260505268503238 17.075028564174175 80-81 24.802648332060095 35.294117647058826 24.777183600713013 15.126050420168067 82-83 21.69183516764781 29.383158433580753 27.796263117481445 21.128743281289992 84-85 19.47449768160742 23.390005151983516 35.44564657393096 21.689850592478106 86-87 19.829809179989685 27.90097988653945 24.548736462093864 27.720474471377 88-89 16.761217122227954 33.62558019597731 27.346570397111915 22.266632284682828 90-91 23.272305312016503 30.42805569881382 28.82929345023208 17.470345538937597 92-93 22.08612686952037 31.31768953068592 27.037132542547702 19.559051057246002 >>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 19.0 18 21.0 19 4.0 20 4.0 21 6.0 22 6.5 23 6.5 24 5.5 25 6.5 26 11.0 27 13.0 28 20.0 29 29.0 30 29.5 31 33.5 32 41.0 33 54.5 34 71.5 35 78.0 36 98.0 37 150.5 38 191.5 39 168.5 40 189.0 41 210.5 42 193.0 43 202.0 44 170.5 45 154.0 46 159.5 47 141.5 48 114.0 49 128.0 50 257.0 51 293.0 52 184.0 53 133.5 54 205.5 55 184.0 56 60.5 57 35.0 58 32.5 59 26.5 60 25.5 61 26.5 62 20.5 63 14.0 64 9.5 65 9.5 66 9.5 67 7.0 68 7.0 69 7.0 70 5.0 71 4.0 72 2.5 73 0.5 74 1.0 75 2.5 76 1.5 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 0.0125 22-23 0.0 24-25 0.0125 26-27 0.0 28-29 0.025 30-31 0.0 32-33 0.0 34-35 0.0 36-37 0.0 38-39 0.1 40-41 0.17500000000000002 42-43 0.05 44-45 0.0 46-47 0.0 48-49 0.0 50-51 0.0 52-53 0.35000000000000003 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 0.025 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 0.012730744748567792 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 6.0 72 4.0 73 7.0 74 4.0 75 11.0 76 14.0 77 7.0 78 5.0 79 5.0 80 7.0 81 9.0 82 16.0 83 13.0 84 8.0 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 3878.0 >>END_MODULE >>Sequence Duplication Levels warn #Total Deduplicated Percentage 63.175000000000004 #Duplication Level Percentage of deduplicated Percentage of total 1 90.97744360902256 57.475 2 4.2342698852394145 5.35 3 1.780767708745548 3.375 4 0.8310249307479225 2.1 5 0.4352987732489117 1.375 6 0.19786307874950534 0.75 7 0.07914523149980214 0.35000000000000003 8 0.15829046299960428 0.8 9 0.2770083102493075 1.575 >10 0.8705975464978234 10.575 >50 0.07914523149980214 3.5249999999999995 >100 0.07914523149980214 12.75 >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 TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 275 6.875000000000001 No Hit GGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGC 235 5.875 No Hit TCAAAAGAGGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGGA 81 2.025 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 60 1.5 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 47 1.175 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 37 0.9249999999999999 No Hit GGAGTATCCTTGATATATAAATATATAGATAAATAGATTTAAATGGAAAA 34 0.8500000000000001 No Hit GGGAGTATTATGAAAGGAGATTAATCATAGATTATCAAAAACCCTAGAAA 26 0.65 No Hit CAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCT 25 0.625 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 24 0.6 No Hit GTATTTAGCCTTGCAAGGTGGTCCTTGCTGATTCACACGGGATTCCACGT 23 0.575 No Hit GATACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGC 20 0.5 No Hit GTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAG 19 0.475 No Hit TCTCATGGAGAGTTCGATCCTGGCTCAGGATGAACGCTGGCGGCATGCTT 18 0.44999999999999996 No Hit CAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATAT 16 0.4 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 15 0.375 No Hit GGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCG 14 0.35000000000000003 No Hit CAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTG 14 0.35000000000000003 No Hit CACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTTCGGGGAGT 13 0.325 No Hit GTACTATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTT 12 0.3 No Hit GTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAA 12 0.3 No Hit CAACATAGGTCATCGAAAAGATCTCGGACGACTCACCAAAGCACGAAAGC 12 0.3 No Hit GGGGGTCGCAGTGACCAGGCCCGGGCGACTGTTTACCAAAAACACAGGTC 11 0.27499999999999997 No Hit GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 11 0.27499999999999997 No Hit GGCCTGTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCG 10 0.25 No Hit AACAGTAAAGCTTCATAGGGTCTTTCTGTCCAGGTGCAGGTAGTCCGCAT 10 0.25 No Hit GTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAA 9 0.22499999999999998 No Hit GTATTAGTACTATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATCT 9 0.22499999999999998 No Hit GTCAAAAGAGGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGG 9 0.22499999999999998 No Hit CGAGGAAGGGCGTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAG 9 0.22499999999999998 No Hit GGGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTG 9 0.22499999999999998 No Hit AACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGA 9 0.22499999999999998 No Hit GGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGC 9 0.22499999999999998 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 8 0.2 No Hit AGGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGGAAGGGCGT 8 0.2 No Hit GGGCCATTCACAGACACACACAACTACACAAGAGCTCTCAGCTGCTGCCC 8 0.2 No Hit GAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGC 8 0.2 No Hit GCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCT 7 0.17500000000000002 No Hit GGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTT 7 0.17500000000000002 No Hit GAGGAAGGGCGTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAGC 6 0.15 No Hit GGATACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATG 6 0.15 No Hit ATATTGGGTAGGTTGTGGTATTTCATTGCTACAAACATGGGTTATTGTAA 6 0.15 No Hit GCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCA 6 0.15 No Hit GGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGCA 6 0.15 No Hit GGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAAGGCGATCAAATTC 5 0.125 No Hit GCAACATAGGTCATCGAAAAGATCTCGGACGACTCACCAAAGCACGAAAG 5 0.125 No Hit GGTCTTGATCCCTCTGTGTTTCCCGTGTAACGGCTACTGATCCAGTGGTT 5 0.125 No Hit GAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGGAAGGGCGTAG 5 0.125 No Hit GGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTT 5 0.125 No Hit GGAAGGGCGTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAGCAT 5 0.125 No Hit GGAGATTCCCAAATAGGTCAACCTTTTAAACTGCCTGCTGAATCCATGAG 5 0.125 No Hit GATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAAT 5 0.125 No Hit GATCCGGAGATTCCCAAATAGGTCAACCTTTTAAACTGCCTGCTGAATCC 5 0.125 No Hit GTACAAGCTCGTAACGAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAAT 5 0.125 No Hit AATCTCCGGATCTATGCTTATTTTCAACTCCCCGAAGCATTTCGTCGCTT 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 0.025 0.0 0.0 0.0 0.0 18-19 0.0625 0.0 0.0 0.0 0.0 20-21 0.075 0.0 0.0 0.0 0.0 22-23 0.075 0.0 0.0 0.0 0.0 24-25 0.075 0.0 0.0 0.0 0.0 26-27 0.075 0.0 0.0 0.0 0.0 28-29 0.075 0.0 0.0 0.0 0.0 30-31 0.0875 0.0 0.0 0.0 0.0 32-33 0.1 0.0 0.0 0.0 0.0 34-35 0.1 0.0 0.0 0.0 0.0 36-37 0.1 0.0 0.0 0.0 0.0 38-39 0.1 0.0 0.0 0.0 0.0 40-41 0.1 0.0 0.0 0.0 0.0 42-43 0.1 0.0 0.0 0.0 0.0 44-45 0.1 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 0.125 0.0 0.0 0.0 0.0 62-63 0.125 0.0 0.0 0.0 0.0 64-65 0.125 0.0 0.0 0.0 0.0 66-67 0.125 0.0 0.0 0.0 0.0 68-69 0.125 0.0 0.0 0.0 0.0 70-71 0.125 0.0 0.0 0.0 0.0 72-73 0.125 0.0 0.0 0.0 0.0 74-75 0.125 0.0 0.0 0.0 0.0 76-77 0.125 0.0 0.0 0.0 0.0 78-79 0.125 0.0 0.0 0.0 0.0 80-81 0.125 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content fail #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GGAGAGC 35 4.7475623E-10 86.787506 2 GCAATAC 35 4.7475623E-10 86.787506 7 GAGCAAT 35 4.7475623E-10 86.787506 5 AAAAGAG 15 8.7983714E-4 86.787506 3 AGAGCAA 35 4.7475623E-10 86.787506 4 GAGAGCA 35 4.7475623E-10 86.787506 3 AGCAATA 35 4.7475623E-10 86.787506 6 AAAGAGG 15 8.7983714E-4 86.787506 4 GGGAGAG 40 1.371518E-9 75.939064 1 CAATACA 45 3.4851837E-9 67.50139 8 AATACAA 45 3.4851837E-9 67.50139 9 TAAATGG 25 0.006671116 52.0725 6 ATGGATT 25 0.006671116 52.0725 9 CTAAATG 25 0.006671116 52.0725 5 ACCTAAA 25 0.006671116 52.0725 3 TAGCCGA 35 1.2302553E-7 43.94304 72-73 CATCACT 30 2.2424629E-6 43.94304 82-83 ATCACTA 30 2.2424629E-6 43.94304 84-85 CGAAAGC 35 1.2302553E-7 43.94304 76-77 AGCATCA 30 2.2424629E-6 43.94304 80-81 >>END_MODULE Rejected 217314 READS because READLEN < 1 Read 217314 spots for ERR6133486.sra Written 217314 spots for ERR6133486.sra Rejected 217314 READS because READLEN < 1 Read 217314 spots for ERR6133486.sra Written 217314 spots for ERR6133486.sra Rejected 217314 READS because READLEN < 1 Read 217314 spots for ERR6133486.sra Written 217314 spots for ERR6133486.sra Rejected 217314 READS because READLEN < 1 Read 217314 spots for ERR6133486.sra Written 217314 spots for ERR6133486.sra Rejected 217314 READS because READLEN < 1 Read 217314 spots for ERR6133486.sra Written 217314 spots for ERR6133486.sra Rejected 217314 READS because READLEN < 1 Read 217314 spots for ERR6133486.sra Written 217314 spots for ERR6133486.sra Rejected 217314 READS because READLEN < 1 Read 217314 spots for ERR6133486.sra Written 217314 spots for ERR6133486.sra Rejected 217314 READS because READLEN < 1 Read 217314 spots for ERR6133486.sra Written 217314 spots for ERR6133486.sra Rejected 217314 READS because READLEN < 1 Read 217314 spots for ERR6133486.sra Written 217314 spots for ERR6133486.sra Rejected 217314 READS because READLEN < 1 Read 217314 spots for ERR6133486.sra Written 217314 spots for ERR6133486.sra Rejected 217314 READS because READLEN < 1 Read 217314 spots for ERR6133486.sra Written 217314 spots for ERR6133486.sra Rejected 217314 READS because READLEN < 1 Read 217314 spots for ERR6133486.sra Written 217314 spots for ERR6133486.sra Rejected 217314 READS because READLEN < 1 Read 217314 spots for ERR6133486.sra Written 217314 spots for ERR6133486.sra Rejected 217314 READS because READLEN < 1 Read 217314 spots for ERR6133486.sra Written 217314 spots for ERR6133486.sra Rejected 217314 READS because READLEN < 1 Read 217314 spots for ERR6133486.sra Written 217314 spots for ERR6133486.sra Rejected 217314 READS because READLEN < 1 Read 217314 spots for ERR6133486.sra Written 217314 spots for ERR6133486.sra Rejected 217323 READS because READLEN < 1 Read 217323 spots for ERR6133486.sra Written 217323 spots for ERR6133486.sra Rejected 217314 READS because READLEN < 1 Read 217314 spots for ERR6133486.sra Written 217314 spots for ERR6133486.sra Rejected 217314 READS because READLEN < 1 Read 217314 spots for ERR6133486.sra Written 217314 spots for ERR6133486.sra Rejected 217314 READS because READLEN < 1 Read 217314 spots for ERR6133486.sra Written 217314 spots for ERR6133486.sra SRR ids: ['ERR6133486.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_7bj3t5xe ERR6133486.sra spots: 4346289 blocks: [[1, 217314], [217315, 434628], [434629, 651942], [651943, 869256], [869257, 1086570], [1086571, 1303884], [1303885, 1521198], [1521199, 1738512], [1738513, 1955826], [1955827, 2173140], [2173141, 2390454], [2390455, 2607768], [2607769, 2825082], [2825083, 3042396], [3042397, 3259710], [3259711, 3477024], [3477025, 3694338], [3694339, 3911652], [3911653, 4128966], [4128967, 4346289]] ERR6133486 file size 960945 ERR6133486 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 ERR6133486 ERR6133486_1.fastq Input file: ERR6133486_1.fastq trimmed: ERR6133486-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 07:06:58 2024 >> started Sat Dec 7 07:07:00 2024 >> done (2.284s) 4346289 reads processed; of these: 445 ( 0.01%) short reads filtered out after trimming by size control 87 ( 0.00%) empty reads filtered out after trimming by size control 4345757 (99.99%) reads available; of these: 85683 ( 1.97%) trimmed reads available after processing 4260074 (98.03%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 65 0.00% 19 125 0.00% 20 74 0.00% 21 102 0.00% 22 109 0.00% 23 22 0.00% 24 29 0.00% 25 33 0.00% 26 39 0.00% 27 58 0.00% 28 221 0.01% 29 72 0.00% 30 52 0.00% 31 100 0.00% 32 64 0.00% 33 123 0.00% 34 333 0.01% 35 4986 0.11% 36 625 0.01% 37 109 0.00% 38 75 0.00% 39 346 0.01% 40 112 0.00% 41 88 0.00% 42 24 0.00% 43 41 0.00% 44 30 0.00% 45 27 0.00% 46 14 0.00% 47 16 0.00% 48 23 0.00% 49 28 0.00% 50 26 0.00% 51 51 0.00% 52 28 0.00% 53 10 0.00% 54 23 0.00% 55 25 0.00% 56 22 0.00% 57 33 0.00% 58 44 0.00% 59 38 0.00% 60 22 0.00% 61 17 0.00% 62 2 0.00% 63 5 0.00% 64 7 0.00% 65 4 0.00% 66 7 0.00% 67 11 0.00% 68 25 0.00% 69 88 0.00% 70 9163 0.21% 71 8624 0.20% 72 9523 0.22% 73 8950 0.21% 74 9092 0.21% 75 9272 0.21% 76 8582 0.20% 77 9001 0.21% 78 9901 0.23% 79 10977 0.25% 80 9957 0.23% 81 12328 0.28% 82 13834 0.32% 83 11356 0.26% 84 11645 0.27% 85 152 0.00% 86 262 0.01% 87 476 0.01% 88 840 0.02% 89 1540 0.04% 90 3350 0.08% 91 9823 0.23% 92 58848 1.35% 93 4109608 94.57% 4345757 reads passed initial QC criterion=sequence-density sequence-density=6.82 sequence-density-rank=1 fanout-score=1.27 fanout-score-rank=25 prefix-density=0.33 prefix-fanout=1.3 sequence=GGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGCACCCTAGATGGCTAAAGTCCAGTAGCCGAAAGCATCACTAGCTTACGCTCTGACCCGAGTAGCATGGGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAAT criterion=fanout-score sequence-density=0.22 sequence-density-rank=9 fanout-score=51.84 fanout-score-rank=1 prefix-density=11.28 prefix-fanout=1.0 sequence=GGAGATTCCCATATAGATC 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: 1 (100.00%) aligned 0 times 0 (0.00%) aligned exactly 1 time 0 (0.00%) aligned >1 times 0.00% overall alignment rate Adapter seq not found in reference. Now shuffling file before clipping skewer v0.2.2 [April 4, 2016] COMMAND LINE: skewer -f sanger -l 18 -t 20 -x GGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGCACCCTAGATGGCTAAAGTCCAGTAGCCGAAAGCATCACTAGCTTACGCTCTGACCCGAGTAGCATGGGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAAT -o ERR6133486 - Input file: STDIN trimmed: ERR6133486-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): GGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGCACCCTAGATGGCTA -- maximum error ratio allowed (-r): 0.100 -- maximum indel error ratio allowed (-d): 0.030 -- minimum read length allowed after trimming (-l): 18 -- file format (-f): Sanger/Illumina 1.8+ FASTQ -- minimum overlap length for adapter detection (-k): 3 -- number of concurrent threads (-t): 20 Sat Dec 7 07:07:19 2024 >> started Sat Dec 7 07:07:24 2024 >> done (4.125s) 3104112 reads processed; of these: 10856 ( 0.35%) short reads filtered out after trimming by size control 201587 ( 6.49%) empty reads filtered out after trimming by size control 2891669 (93.16%) reads available; of these: 37826 ( 1.31%) trimmed reads available after processing 2853843 (98.69%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 61 0.00% 19 92 0.00% 20 79 0.00% 21 87 0.00% 22 175 0.01% 23 49 0.00% 24 32 0.00% 25 46 0.00% 26 39 0.00% 27 65 0.00% 28 164 0.01% 29 62 0.00% 30 78 0.00% 31 995 0.03% 32 102 0.00% 33 105 0.00% 34 244 0.01% 35 3573 0.12% 36 468 0.02% 37 248 0.01% 38 75 0.00% 39 256 0.01% 40 92 0.00% 41 84 0.00% 42 63 0.00% 43 35 0.00% 44 63 0.00% 45 63 0.00% 46 22 0.00% 47 16 0.00% 48 21 0.00% 49 109 0.00% 50 24 0.00% 51 41 0.00% 52 119 0.00% 53 23 0.00% 54 18 0.00% 55 19 0.00% 56 16 0.00% 57 24 0.00% 58 26 0.00% 59 46 0.00% 60 33 0.00% 61 18 0.00% 62 6 0.00% 63 10 0.00% 64 5 0.00% 65 5 0.00% 66 34 0.00% 67 186 0.01% 68 148 0.01% 69 283 0.01% 70 6590 0.23% 71 6228 0.22% 72 6625 0.23% 73 6339 0.22% 74 6436 0.22% 75 6602 0.23% 76 6243 0.22% 77 9932 0.34% 78 7737 0.27% 79 8882 0.31% 80 7179 0.25% 81 9297 0.32% 82 9115 0.32% 83 7997 0.28% 84 7624 0.26% 85 342 0.01% 86 696 0.02% 87 951 0.03% 88 2521 0.09% 89 6479 0.22% 90 21088 0.73% 91 6578 0.23% 92 38849 1.34% 93 2692592 93.12% criterion=sequence-density sequence-density=0.61 sequence-density-rank=1 fanout-score=1.99 fanout-score-rank=22 prefix-density=0.62 prefix-fanout=2.0 sequence=CAAGGCTAAATAC criterion=fanout-score sequence-density=0.12 sequence-density-rank=13 fanout-score=125.55 fanout-score-rank=1 prefix-density=15.15 prefix-fanout=1.0 sequence=GGGAGTTGAAATAAGCATA Started job on | Dec 07 07:07:41 Started mapping on | Dec 07 07:07:42 Finished on | Dec 07 07:07:49 Mapping speed, Million of reads per hour | 2125.70 Number of input reads | 4133314 Average input read length | 92 UNIQUE READS: Uniquely mapped reads number | 1821294 Uniquely mapped reads % | 44.06% Average mapped length | 91.53 Number of splices: Total | 83998 Number of splices: Annotated (sjdb) | 65956 Number of splices: GT/AG | 80131 Number of splices: GC/AG | 1565 Number of splices: AT/AC | 98 Number of splices: Non-canonical | 2204 Mismatch rate per base, % | 0.43% Deletion rate per base | 0.05% Deletion average length | 1.75 Insertion rate per base | 0.02% Insertion average length | 1.62 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 2173140 % of reads mapped to multiple loci | 52.58% Number of reads mapped to too many loci | 52558 % of reads mapped to too many loci | 1.27% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 2.01% % of reads unmapped: other | 0.08% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 138880 138880 138880 N_multimapping 2173140 2173140 2173140 N_noFeature 173674 197058 1742570 N_ambiguous 66520 11042 449 UnstrandedReadsAssigned:1581100 PositiveStrandReadsAssigned:1613194 NegativeStrandReadsAssigned:78275 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=93 echo kmer=89 ERR6133486 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: ERR6133486-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 4,133,314 reads, 2,730,710 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 938 rounds 52973 ERR6133486.ke.tsv 35125 ERR6133486.se.tsv 88098 total ==> ERR6133486.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 38 13.566 PNS24243 293 194 0 0 KQK14069 1603 1504 52 16.9347 KQK14071 474 375 0 0 ==> ERR6133486.se.tsv <== BRADI_1g14170v3 52 BRADI_1g53295v3 16 BRADI_1g59795v3 13 BRADI_1g07683v3 0 BRADI_1g00485v3 1 BRADI_1g20270v3 18 BRADI_1g74790v3 24 BRADI_1g09890v3 0 BRADI_1g77505v3 39 BRADI_1g48960v3 0 ERR6133486 completed mapping pipeline successfully