Starting /dee2/code/volunteer_pipeline.sh ERR6133538 current disk space = 1544515137536 free memory = 1425373928 ERR6133538 SRAfilesize 66dd3068519ab0b96c8c4424b20fdffa ERR6133538.sra ERR6133538.sra file validated ERR6133538 is single end ERR6133538 is conventional basespace ERR6133538 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133538_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 33.863 37.0 33.0 37.0 27.0 37.0 2 36.01575 37.0 37.0 37.0 33.0 37.0 3 35.2715 37.0 33.0 37.0 33.0 37.0 4 35.4595 37.0 37.0 37.0 33.0 37.0 5 35.337 37.0 37.0 37.0 33.0 37.0 6 35.71 37.0 37.0 37.0 33.0 37.0 7 37.54 37.0 37.0 40.0 33.0 40.0 8 37.624 40.0 37.0 40.0 33.0 40.0 9 37.5815 37.0 37.0 40.0 33.0 40.0 10-11 37.5995 37.0 37.0 40.0 33.0 40.0 12-13 37.52275 37.0 37.0 40.0 33.0 40.0 14-15 37.5275 37.0 37.0 40.0 33.0 40.0 16-17 37.417875 37.0 37.0 40.0 33.0 40.0 18-19 37.342625 37.0 37.0 40.0 33.0 40.0 20-21 37.288875 37.0 37.0 40.0 33.0 40.0 22-23 37.241875 37.0 37.0 40.0 33.0 40.0 24-25 37.281625 37.0 37.0 40.0 33.0 40.0 26-27 37.253125 37.0 37.0 40.0 33.0 40.0 28-29 37.204 37.0 37.0 40.0 33.0 40.0 30-31 37.119875 37.0 37.0 40.0 33.0 40.0 32-33 36.972750000000005 37.0 37.0 40.0 33.0 40.0 34-35 36.8625 37.0 37.0 40.0 33.0 40.0 36-37 36.64675 37.0 37.0 40.0 33.0 40.0 38-39 36.53175 37.0 37.0 40.0 33.0 40.0 40-41 36.33225 37.0 37.0 40.0 33.0 40.0 42-43 36.238625 37.0 37.0 40.0 33.0 40.0 44-45 35.95525000000001 37.0 37.0 38.5 33.0 40.0 46-47 35.570625 37.0 33.0 37.0 33.0 40.0 48-49 35.581374999999994 37.0 33.0 37.0 33.0 40.0 50-51 35.4935 37.0 33.0 37.0 33.0 40.0 52-53 35.1295 37.0 33.0 37.0 33.0 40.0 54-55 35.068124999999995 37.0 33.0 37.0 33.0 38.5 56-57 35.030249999999995 37.0 33.0 37.0 33.0 37.0 58-59 34.346500000000006 37.0 33.0 37.0 27.0 37.0 60-61 34.497 37.0 33.0 37.0 27.0 37.0 62-63 34.502375 37.0 33.0 37.0 27.0 37.0 64-65 34.479 37.0 33.0 37.0 30.0 37.0 66-67 34.565625 37.0 33.0 37.0 33.0 37.0 68-69 33.68025 35.0 33.0 37.0 30.0 37.0 70-71 33.807921843687375 35.0 33.0 37.0 27.0 37.0 72-73 34.231195393812826 37.0 33.0 37.0 27.0 37.0 74-75 34.19437322950756 37.0 33.0 37.0 27.0 37.0 76-77 34.1588824113728 37.0 33.0 37.0 27.0 37.0 78-79 34.11004431522269 37.0 33.0 37.0 27.0 37.0 80-81 34.042356222863006 37.0 33.0 37.0 27.0 37.0 82-83 33.92032976859435 37.0 33.0 37.0 27.0 37.0 84-85 33.96582191933786 37.0 33.0 37.0 27.0 37.0 86-87 33.95047230022977 37.0 33.0 37.0 27.0 37.0 88-89 34.002808271636454 37.0 33.0 37.0 27.0 37.0 90-91 33.665049782997194 37.0 33.0 37.0 27.0 37.0 92-93 33.56190962471279 37.0 33.0 37.0 27.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 10.0 21 11.0 22 15.0 23 25.0 24 16.0 25 29.0 26 48.0 27 33.0 28 60.0 29 65.0 30 74.0 31 96.0 32 145.0 33 158.0 34 241.0 35 426.0 36 907.0 37 1008.0 38 626.0 39 7.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 88.675 2.325 2.7 6.3 2 73.575 15.75 6.65 4.025 3 35.6 37.824999999999996 14.549999999999999 12.025 4 35.125 27.700000000000003 16.975 20.200000000000003 5 25.174999999999997 31.674999999999997 25.95 17.2 6 20.95 37.9 24.9 16.25 7 35.725 27.950000000000003 19.3 17.025000000000002 8 30.575000000000003 27.975 25.2 16.25 9 24.224999999999998 28.375 27.525 19.875 10-11 25.112499999999997 27.175 27.825 19.8875 12-13 27.712500000000002 25.662499999999998 27.224999999999998 19.400000000000002 14-15 21.95 30.025000000000002 30.2375 17.7875 16-17 24.325 30.2875 25.9875 19.400000000000002 18-19 23.19039879984998 28.378547318414803 26.89086135766971 21.540192524065507 20-21 25.318829707426854 26.85671417854464 27.219304826206553 20.605151287821954 22-23 27.4125 22.2625 27.3 23.025000000000002 24-25 27.55 23.0875 28.6625 20.7 26-27 27.0875 24.65 30.2375 18.025 28-29 26.003250406300786 28.20352544068008 25.99074884360545 19.802475309413676 30-31 29.025000000000002 26.224999999999998 24.375 20.375 32-33 23.0375 28.599999999999998 26.5875 21.775 34-35 25.647441511322405 25.59739772300763 26.83598148379832 21.919179281871635 36-37 24.725 23.525 29.275000000000002 22.475 38-39 27.0 25.0 29.762499999999996 18.2375 40-41 28.608956717538153 24.83112334250688 24.230673004753562 22.329246935201404 42-43 24.446113405933158 30.16647890849919 25.122042808862183 20.26536487670547 44-45 23.079809857393045 25.006254691018263 28.709031773830375 23.204903677758317 46-47 24.325 23.0125 27.925 24.7375 48-49 25.49387346836709 24.63115778944736 30.50762690672668 19.367341835458866 50-51 27.6 25.224999999999998 28.537499999999998 18.637500000000003 52-53 26.34610568494866 28.01152016028049 25.28174305033809 20.36063110443276 54-55 24.5625 29.8875 26.974999999999998 18.575 56-57 27.625 24.525 27.375 20.474999999999998 58-59 24.85 23.875 28.299999999999997 22.975 60-61 25.424999999999997 23.9 28.349999999999998 22.325 62-63 22.237499999999997 27.6875 32.6625 17.4125 64-65 24.3875 27.200000000000003 28.65 19.7625 66-67 25.112499999999997 27.650000000000002 26.7125 20.525 68-69 22.900000000000002 27.6375 26.787499999999998 22.675 70-71 26.351351351351347 24.974974974974977 26.063563563563562 22.61011011011011 72-73 26.580531861515304 23.79578524836929 27.972905168088307 21.650777722027094 74-75 23.3232856066315 27.882441597588546 28.48530519969857 20.308967596081388 76-77 22.85210380448476 26.35424540186445 28.634416729654827 22.15923406399597 78-79 24.772497472194136 23.90040444893832 30.182002022244692 21.14509605662285 80-81 24.863699759097248 28.578673766958286 28.794218333967287 17.763408139977177 82-83 25.21617497456765 25.979145473041708 27.822990844354017 20.98168870803662 84-85 24.164327634600664 21.906098494513905 31.576932891043636 22.352640979841794 86-87 21.700280827163645 26.525402093438856 33.09931069696196 18.675006382435537 88-89 20.793974980852695 29.7676793464386 30.21444983405668 19.22389583865203 90-91 27.50829716619862 25.453152923155475 27.112586162879754 19.925963747766147 92-93 22.810824610671432 29.333673729895327 28.46566249680878 19.389839162624458 >>END_MODULE >>Per sequence GC content warn #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 7.5 18 8.5 19 2.5 20 1.0 21 3.0 22 3.5 23 2.5 24 5.0 25 5.5 26 7.0 27 9.0 28 15.0 29 21.0 30 27.5 31 40.0 32 43.5 33 43.5 34 49.0 35 71.0 36 93.0 37 119.0 38 142.0 39 146.5 40 169.0 41 177.5 42 199.5 43 230.0 44 199.0 45 161.5 46 236.5 47 241.5 48 179.0 49 185.0 50 185.5 51 183.5 52 161.0 53 171.0 54 148.0 55 84.5 56 66.0 57 66.5 58 60.0 59 51.5 60 48.0 61 41.0 62 33.0 63 30.5 64 33.5 65 29.5 66 22.5 67 18.5 68 15.0 69 12.5 70 7.5 71 6.0 72 5.5 73 6.0 74 5.5 75 3.5 76 1.5 77 0.5 78 0.5 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 0.0125 20-21 0.025 22-23 0.0 24-25 0.0 26-27 0.0 28-29 0.0125 30-31 0.0 32-33 0.0 34-35 0.08750000000000001 36-37 0.0 38-39 0.0 40-41 0.075 42-43 0.13749999999999998 44-45 0.075 46-47 0.0 48-49 0.025 50-51 0.0 52-53 0.17500000000000002 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 5.0 72 2.0 73 0.0 74 8.0 75 5.0 76 6.0 77 7.0 78 6.0 79 7.0 80 5.0 81 4.0 82 10.0 83 6.0 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 3917.0 >>END_MODULE >>Sequence Duplication Levels warn #Total Deduplicated Percentage 69.72500000000001 #Duplication Level Percentage of deduplicated Percentage of total 1 90.24740050197202 62.925 2 4.94801003944066 6.9 3 1.6493366798135531 3.45 4 0.8605234851201148 2.4 5 0.5378271782000718 1.875 6 0.35855145213338113 1.5 7 0.2151308712800287 1.05 8 0.17927572606669057 1.0 9 0.07171029042667623 0.44999999999999996 >10 0.8605234851201148 14.424999999999999 >50 0.07171029042667623 4.025 >100 0.0 0.0 >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 GGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGG 94 2.35 No Hit GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 67 1.675 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 46 1.15 No Hit GGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGGG 44 1.0999999999999999 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 42 1.05 No Hit GGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGC 41 1.0250000000000001 No Hit GGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTT 36 0.8999999999999999 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 32 0.8 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 31 0.775 No Hit GGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAA 31 0.775 No Hit GGGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTG 28 0.7000000000000001 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 27 0.675 No Hit GGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAA 26 0.65 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 22 0.5499999999999999 No Hit GGTGGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGC 20 0.5 No Hit GTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAA 17 0.42500000000000004 No Hit GGAGTCCCATATATATATGTATAAGATGCCAGCCCGGTTTCGTCAACCAT 17 0.42500000000000004 No Hit GGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAAA 16 0.4 No Hit GGAGTATCCTTGATATATAAATATATAGATAAATAGATTTAAATGGAAAA 15 0.375 No Hit GGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGC 15 0.375 No Hit GGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCG 14 0.35000000000000003 No Hit CAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCT 14 0.35000000000000003 No Hit GGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAACCCTCTTAACT 12 0.3 No Hit GGCCTGTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCG 11 0.27499999999999997 No Hit GGAAGAGCCCGAGCTGCTGCAGCAGGTTTTGAAAAGGGAATCGATCGTGA 10 0.25 No Hit GTACAAGCTCGTAACGAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAAT 10 0.25 No Hit GGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAAGGCGATCAAATTC 9 0.22499999999999998 No Hit GGAAAAGAAAGCAAAAGCGATTCCCGTAGTAGCGGCGAGCGAAATGGGAG 9 0.22499999999999998 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 8 0.2 No Hit GGCATATGCCAGCTCTGACCGAAATCTTTGGGGATGATTCTGTATTACAA 8 0.2 No Hit GGGGAAGTACACCAGCGACGGCGAGGCCGCCGCCGCCAAGGAAGGCATGT 8 0.2 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 8 0.2 No Hit GAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGC 8 0.2 No Hit GGTGGGGCAATGGGCATTCCGTTGAGTTTGTATGGTGGGTGCTGTTTTGC 7 0.17500000000000002 No Hit GGGGATGGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACG 7 0.17500000000000002 No Hit GGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTT 7 0.17500000000000002 No Hit GGAGCAGCCTAAACCGTGAAAACGGGGTTGTGGGAGAGCAATACAAGCGT 7 0.17500000000000002 No Hit GGGCCATTTGTGGCATGCAGGAAGAGCCCGAGCTGCTGCAGCAGGTTTTG 7 0.17500000000000002 No Hit GGTTTTGAAAAGGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAA 7 0.17500000000000002 No Hit GGGAAAAGAGGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTT 6 0.15 No Hit GGCTTTAGAAGCCTGTGTACAAGCTCGTAACGAAGGGCGCGATCTTGCTC 6 0.15 No Hit GGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGT 6 0.15 No Hit GGAGTGGGGGTGCCATACGCAAAAAGGAAGCGACTCATAGAATGGCAGAG 6 0.15 No Hit CAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATAT 6 0.15 No Hit GGGATGGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACGA 6 0.15 No Hit GGAGAAGTACAAGTGCGGATCCAACGTCTTCTGGAAATGGTGAAGATGAT 6 0.15 No Hit GTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAG 6 0.15 No Hit GGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTG 6 0.15 No Hit GGATTCTTCTTTTTTGTGGGCCATTTGTGGCATGCAGGAAGAGCCCGAGC 6 0.15 No Hit GGGTATCCATGCCAGGTGTTATACCAGTAGCTTCAGGTGGTATTCATGTT 5 0.125 No Hit GAAGGAACAAACGAGGATAAGATAAAATTTCTTTAAATTTATTTTGCCCA 5 0.125 No Hit GATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGGGG 5 0.125 No Hit GGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTG 5 0.125 No Hit GCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGA 5 0.125 No Hit GGATTCCGGCGGAACAAACTAAAATCTAGTACTGCTCTTGGATTGGATCT 5 0.125 No Hit GGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACGAGCCGT 5 0.125 No Hit GGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAACCCTCTTAACTA 5 0.125 No Hit GAAGCCTGTGTACAAGCTCGTAACGAAGGGCGCGATCTTGCTCGTGAAGG 5 0.125 No Hit GGATATCGTGTGTGTACATTTGAATGTACCGACATGGGCTCGAGGAGCAT 5 0.125 No Hit GGGAGTATTATGAAAGGAGATTAATCATAGATTATCAAAAACCCTAGAAA 5 0.125 No Hit GAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTG 5 0.125 No Hit GTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCT 5 0.125 No Hit GGAAAAGAGGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTTG 5 0.125 No Hit GGGCTTTTTTAGTATTTATCTAAAGGAAGGAACAAACGAGGATAAGATAA 5 0.125 No Hit >>END_MODULE >>Adapter Content pass #Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence SOLID Small RNA Adapter 1 0.0 0.0 0.0 0.0 0.0 2 0.0 0.0 0.0 0.0 0.0 3 0.0 0.0 0.0 0.0 0.0 4 0.0 0.0 0.0 0.0 0.0 5 0.0 0.0 0.0 0.0 0.0 6 0.0 0.0 0.0 0.0 0.0 7 0.0 0.0 0.0 0.0 0.0 8 0.0 0.0 0.0 0.0 0.0 9 0.0 0.0 0.0 0.0 0.0 10-11 0.0 0.0 0.0 0.0 0.0 12-13 0.0 0.0 0.0 0.0 0.0 14-15 0.0 0.0 0.0 0.0 0.0 16-17 0.0 0.0 0.0 0.0 0.0 18-19 0.0 0.0 0.0 0.0 0.0 20-21 0.0 0.0 0.0 0.0 0.0 22-23 0.0 0.0 0.0 0.0 0.0 24-25 0.0 0.0 0.0 0.0 0.0 26-27 0.0 0.0 0.0 0.0 0.0 28-29 0.0 0.0 0.0 0.0 0.0 30-31 0.0 0.0 0.0 0.0 0.0 32-33 0.0 0.0 0.0 0.0 0.0 34-35 0.0 0.0 0.0 0.0 0.0 36-37 0.0 0.0 0.0 0.0 0.0 38-39 0.0 0.0 0.0 0.0 0.0 40-41 0.0 0.0 0.0 0.0 0.0 42-43 0.0 0.0 0.0 0.0 0.0 44-45 0.0 0.0 0.0 0.0 0.0 46-47 0.0 0.0 0.0 0.0 0.0 48-49 0.0 0.0 0.0 0.0 0.0 50-51 0.0 0.0 0.0 0.0 0.0 52-53 0.0 0.0 0.0 0.0 0.0 54-55 0.0 0.0 0.0 0.0 0.0 56-57 0.0 0.0 0.0 0.0 0.0 58-59 0.0 0.0 0.0 0.0 0.0 60-61 0.0 0.0 0.0 0.0 0.0 62-63 0.0 0.0 0.0 0.0 0.0 64-65 0.0 0.0 0.0 0.0 0.0 66-67 0.0 0.0 0.0 0.0 0.0 68-69 0.0 0.0 0.0 0.0 0.0 70-71 0.0 0.0 0.0 0.0 0.0 72-73 0.0 0.0 0.0 0.0 0.0 74-75 0.0 0.0 0.0 0.0 0.0 76-77 0.0 0.0 0.0 0.0 0.0 78-79 0.0 0.0 0.0 0.0 0.0 80-81 0.0 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Rejected 213290 READS because READLEN < 1 Read 213290 spots for ERR6133538.sra Written 213290 spots for ERR6133538.sra Rejected 213290 READS because READLEN < 1 Read 213290 spots for ERR6133538.sra Written 213290 spots for ERR6133538.sra Rejected 213290 READS because READLEN < 1 Read 213290 spots for ERR6133538.sra Written 213290 spots for ERR6133538.sra Rejected 213290 READS because READLEN < 1 Read 213290 spots for ERR6133538.sra Written 213290 spots for ERR6133538.sra Rejected 213290 READS because READLEN < 1 Read 213290 spots for ERR6133538.sra Written 213290 spots for ERR6133538.sra Rejected 213290 READS because READLEN < 1 Read 213290 spots for ERR6133538.sra Written 213290 spots for ERR6133538.sra Rejected 213290 READS because READLEN < 1 Read 213290 spots for ERR6133538.sra Written 213290 spots for ERR6133538.sra Rejected 213290 READS because READLEN < 1 Read 213290 spots for ERR6133538.sra Written 213290 spots for ERR6133538.sra Rejected 213299 READS because READLEN < 1 Read 213299 spots for ERR6133538.sra Written 213299 spots for ERR6133538.sra Rejected 213290 READS because READLEN < 1 Read 213290 spots for ERR6133538.sra Written 213290 spots for ERR6133538.sra Rejected 213290 READS because READLEN < 1 Read 213290 spots for ERR6133538.sra Written 213290 spots for ERR6133538.sra Rejected 213290 READS because READLEN < 1 Read 213290 spots for ERR6133538.sra Written 213290 spots for ERR6133538.sra Rejected 213290 READS because READLEN < 1 Read 213290 spots for ERR6133538.sra Written 213290 spots for ERR6133538.sra Rejected 213290 READS because READLEN < 1 Read 213290 spots for ERR6133538.sra Written 213290 spots for ERR6133538.sra Rejected 213290 READS because READLEN < 1 Read 213290 spots for ERR6133538.sra Written 213290 spots for ERR6133538.sra Rejected 213290 READS because READLEN < 1 Read 213290 spots for ERR6133538.sra Written 213290 spots for ERR6133538.sra Rejected 213290 READS because READLEN < 1 Read 213290 spots for ERR6133538.sra Written 213290 spots for ERR6133538.sra Rejected 213290 READS because READLEN < 1 Read 213290 spots for ERR6133538.sra Written 213290 spots for ERR6133538.sra Rejected 213290 READS because READLEN < 1 Read 213290 spots for ERR6133538.sra Written 213290 spots for ERR6133538.sra Rejected 213290 READS because READLEN < 1 Read 213290 spots for ERR6133538.sra Written 213290 spots for ERR6133538.sra SRR ids: ['ERR6133538.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_u07fj31t ERR6133538.sra spots: 4265809 blocks: [[1, 213290], [213291, 426580], [426581, 639870], [639871, 853160], [853161, 1066450], [1066451, 1279740], [1279741, 1493030], [1493031, 1706320], [1706321, 1919610], [1919611, 2132900], [2132901, 2346190], [2346191, 2559480], [2559481, 2772770], [2772771, 2986060], [2986061, 3199350], [3199351, 3412640], [3412641, 3625930], [3625931, 3839220], [3839221, 4052510], [4052511, 4265809]] ERR6133538 file size 944526 ERR6133538 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 ERR6133538 ERR6133538_1.fastq Input file: ERR6133538_1.fastq trimmed: ERR6133538-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 08:10:24 2024 >> started Sat Dec 7 08:10:27 2024 >> done (2.661s) 4265809 reads processed; of these: 51 ( 0.00%) short reads filtered out after trimming by size control 14 ( 0.00%) empty reads filtered out after trimming by size control 4265744 (100.00%) reads available; of these: 80242 ( 1.88%) trimmed reads available after processing 4185502 (98.12%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 8 0.00% 19 11 0.00% 20 3 0.00% 21 3 0.00% 22 7 0.00% 23 4 0.00% 24 0 0.00% 25 4 0.00% 26 2 0.00% 27 4 0.00% 28 3 0.00% 29 9 0.00% 30 0 0.00% 31 2 0.00% 32 7 0.00% 33 10 0.00% 34 5 0.00% 35 31 0.00% 36 455 0.01% 37 12 0.00% 38 15 0.00% 39 13 0.00% 40 22 0.00% 41 10 0.00% 42 8 0.00% 43 7 0.00% 44 9 0.00% 45 6 0.00% 46 3 0.00% 47 5 0.00% 48 5 0.00% 49 4 0.00% 50 5 0.00% 51 5 0.00% 52 5 0.00% 53 3 0.00% 54 7 0.00% 55 9 0.00% 56 6 0.00% 57 3 0.00% 58 9 0.00% 59 9 0.00% 60 3 0.00% 61 6 0.00% 62 1 0.00% 63 2 0.00% 64 4 0.00% 65 10 0.00% 66 5 0.00% 67 9 0.00% 68 36 0.00% 69 83 0.00% 70 7471 0.18% 71 5786 0.14% 72 6320 0.15% 73 5498 0.13% 74 6220 0.15% 75 6399 0.15% 76 5187 0.12% 77 5247 0.12% 78 6687 0.16% 79 8365 0.20% 80 6675 0.16% 81 7555 0.18% 82 8564 0.20% 83 9657 0.23% 84 7069 0.17% 85 182 0.00% 86 280 0.01% 87 577 0.01% 88 1011 0.02% 89 2102 0.05% 90 4876 0.11% 91 13891 0.33% 92 54920 1.29% 93 4084298 95.75% 4265744 reads passed initial QC criterion=sequence-density sequence-density=0.35 sequence-density-rank=1 fanout-score=3.17 fanout-score-rank=28 prefix-density=0.39 prefix-fanout=2.8 sequence=GTGTTGTGTTGT criterion=fanout-score sequence-density=0.01 sequence-density-rank=40 fanout-score=99.61 fanout-score-rank=1 prefix-density=0.57 prefix-fanout=1.0 sequence=GGCATTTTGGATTTCAGGGCTTTTAGCCCCGATTAGTGAAGGACCCGAAAAGCTTTCTAGTTATGAATCGGGTATAGAACCCATGGGAGGGGCTTGGCTACAATTCCGAATACGCTATTACATGTTTGCGCTAGTTTTTGTTGTTTTTGATGTGGAAACCGTCTTTCTCTACCCTTGGGCAATGAGTTTCGACGTATTGGGTGTATCCGTTTTTATCGAAGCTTTCATTTTCGTGCTTATCCTAGTTGTTGGTTTAGTTTATGCATGGCGAAAAGGAGCCTTGGAATGGTCTTAA Started job on | Dec 07 08:10:51 Started mapping on | Dec 07 08:10:51 Finished on | Dec 07 08:10:57 Mapping speed, Million of reads per hour | 2559.45 Number of input reads | 4265744 Average input read length | 92 UNIQUE READS: Uniquely mapped reads number | 2612163 Uniquely mapped reads % | 61.24% Average mapped length | 92.14 Number of splices: Total | 116005 Number of splices: Annotated (sjdb) | 94415 Number of splices: GT/AG | 110874 Number of splices: GC/AG | 2552 Number of splices: AT/AC | 78 Number of splices: Non-canonical | 2501 Mismatch rate per base, % | 0.48% Deletion rate per base | 0.04% Deletion average length | 1.92 Insertion rate per base | 0.02% Insertion average length | 1.89 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 1573085 % of reads mapped to multiple loci | 36.88% Number of reads mapped to too many loci | 21727 % of reads mapped to too many loci | 0.51% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.34% % of reads unmapped: other | 0.04% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 80496 80496 80496 N_multimapping 1573085 1573085 1573085 N_noFeature 175083 204954 2488064 N_ambiguous 105800 11851 363 UnstrandedReadsAssigned:2331280 PositiveStrandReadsAssigned:2395358 NegativeStrandReadsAssigned:123736 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=93 echo kmer=89 ERR6133538 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: ERR6133538-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 4,265,744 reads, 3,586,659 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 958 rounds 52973 ERR6133538.ke.tsv 35125 ERR6133538.se.tsv 88098 total ==> ERR6133538.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 76 20.3627 PNS24243 293 194 0 0 KQK14069 1603 1504 80.0787 19.5725 KQK14071 474 375 0 0 ==> ERR6133538.se.tsv <== BRADI_1g14170v3 86 BRADI_1g53295v3 21 BRADI_1g59795v3 20 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 45 BRADI_1g74790v3 32 BRADI_1g09890v3 0 BRADI_1g77505v3 38 BRADI_1g48960v3 0 ERR6133538 completed mapping pipeline successfully