Starting /dee2/code/volunteer_pipeline.sh ERR10610834 current disk space = 1549391831040 free memory = 1596061084 ERR10610834 SRAfilesize 6c74bf46d1dedfac18bb2f4fcb61eb92 ERR10610834.sra ERR10610834.sra file validated ERR10610834 is paired end ERR10610834 is conventional basespace ERR10610834 read1 length is 101 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR10610834_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 101 %GC 48 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 24.2225 25.0 18.0 31.0 18.0 33.0 2 30.508 32.0 32.0 33.0 25.0 33.0 3 30.35775 31.0 29.0 33.0 25.0 33.0 4 31.86225 33.0 32.0 33.0 30.0 33.0 5 32.322 33.0 33.0 33.0 32.0 34.0 6 35.95075 38.0 36.0 38.0 32.0 38.0 7 36.3785 38.0 37.0 38.0 34.0 38.0 8 36.781 38.0 38.0 38.0 35.0 38.0 9 36.93025 38.0 38.0 38.0 36.0 38.0 10-11 37.00425 38.0 38.0 38.0 36.0 38.0 12-13 36.972375 38.0 38.0 38.0 36.0 38.0 14-15 37.06725 38.0 38.0 38.0 36.0 38.0 16-17 37.048 38.0 38.0 38.0 36.0 38.0 18-19 37.033500000000004 38.0 38.0 38.0 36.0 38.0 20-21 37.08425 38.0 38.0 38.0 36.5 38.0 22-23 37.063500000000005 38.0 38.0 38.0 36.5 38.0 24-25 37.02012499999999 38.0 38.0 38.0 36.0 38.0 26-27 37.025625000000005 38.0 38.0 38.0 36.0 38.0 28-29 37.018125 38.0 38.0 38.0 36.0 38.0 30-31 36.951125000000005 38.0 38.0 38.0 36.0 38.0 32-33 37.044375 38.0 38.0 38.0 36.0 38.0 34-35 36.96525 38.0 38.0 38.0 36.0 38.0 36-37 36.976124999999996 38.0 38.0 38.0 36.0 38.0 38-39 37.04025 38.0 38.0 38.0 36.0 38.0 40-41 36.995000000000005 38.0 38.0 38.0 36.5 38.0 42-43 37.0065 38.0 38.0 38.0 36.0 38.0 44-45 37.005125 38.0 38.0 38.0 36.0 38.0 46-47 37.008250000000004 38.0 38.0 38.0 36.0 38.0 48-49 36.908625 38.0 38.0 38.0 36.5 38.0 50-51 36.817875 38.0 38.0 38.0 36.0 38.0 52-53 36.565749999999994 38.0 38.0 38.0 35.5 38.0 54-55 36.676375 38.0 38.0 38.0 35.0 38.0 56-57 36.839625 38.0 38.0 38.0 35.5 38.0 58-59 36.810249999999996 38.0 38.0 38.0 35.5 38.0 60-61 36.932625 38.0 38.0 38.0 36.0 38.0 62-63 36.940375 38.0 38.0 38.0 36.0 38.0 64-65 36.775875 38.0 38.0 38.0 36.0 38.0 66-67 36.902874999999995 38.0 38.0 38.0 36.0 38.0 68-69 36.879374999999996 38.0 38.0 38.0 36.0 38.0 70-71 36.892875000000004 38.0 38.0 38.0 36.0 38.0 72-73 36.880375 38.0 38.0 38.0 35.5 38.0 74-75 36.895125 38.0 38.0 38.0 36.0 38.0 76-77 36.841750000000005 38.0 38.0 38.0 36.0 38.0 78-79 36.921 38.0 38.0 38.0 35.5 38.0 80-81 36.85125 38.0 38.0 38.0 35.5 38.0 82-83 36.872249999999994 38.0 38.0 38.0 36.0 38.0 84-85 36.8425 38.0 38.0 38.0 35.5 38.0 86-87 36.769875 38.0 38.0 38.0 35.0 38.0 88-89 36.74075 38.0 38.0 38.0 35.0 38.0 90-91 36.568 38.0 38.0 38.0 35.0 38.0 92-93 36.55375 38.0 38.0 38.0 35.0 38.0 94-95 36.51575 38.0 38.0 38.0 34.5 38.0 96-97 36.348375000000004 38.0 38.0 38.0 34.0 38.0 98-99 36.3085 38.0 38.0 38.0 34.0 38.0 100-101 36.075874999999996 38.0 37.0 38.0 33.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 16 3.0 17 0.0 18 2.0 19 11.0 20 8.0 21 10.0 22 15.0 23 3.0 24 13.0 25 9.0 26 18.0 27 29.0 28 21.0 29 32.0 30 31.0 31 38.0 32 51.0 33 74.0 34 102.0 35 171.0 36 396.0 37 2963.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 28.999999999999996 10.875 11.75 48.375 2 21.775 16.175 37.95 24.099999999999998 3 21.6 20.349999999999998 23.425 34.625 4 27.375 26.8 20.549999999999997 25.275 5 25.275 32.425 23.35 18.95 6 21.8 31.45 25.874999999999996 20.875 7 17.25 21.349999999999998 41.375 20.025000000000002 8 20.25 22.075 30.325000000000003 27.35 9 20.775 21.275 32.125 25.825 10-11 23.3125 29.012500000000003 22.475 25.2 12-13 22.025 23.925 27.6625 26.387500000000003 14-15 22.287499999999998 25.95 27.0875 24.675 16-17 23.05 26.5375 26.0125 24.4 18-19 22.127765970746342 25.078134766845857 26.378297287160894 26.415801975246904 20-21 22.440305038129765 26.115764470558823 26.415801975246904 25.028128516064506 22-23 23.474999999999998 24.9375 25.775 25.8125 24-25 22.8625 25.337500000000002 25.9625 25.837500000000002 26-27 22.05 25.775 26.5 25.674999999999997 28-29 22.6 25.775 26.0125 25.6125 30-31 22.2625 25.4375 26.137500000000003 26.1625 32-33 22.3375 24.962500000000002 27.05 25.650000000000002 34-35 23.6875 25.0125 25.650000000000002 25.650000000000002 36-37 21.85 25.1 26.924999999999997 26.125 38-39 22.5625 25.3 26.5375 25.6 40-41 23.0 25.162499999999998 25.900000000000002 25.937500000000004 42-43 23.140392549068633 25.21565195649456 26.290786348293537 25.353169146143266 44-45 22.852856607075882 25.86573321665208 25.740717589698715 25.54069258657332 46-47 22.525000000000002 26.375 25.2625 25.837500000000002 48-49 22.19298245614035 26.015037593984964 25.225563909774433 26.56641604010025 50-51 22.93105613462263 25.64360165766671 26.02034409142283 25.404998116287832 52-53 22.726699457686973 26.182368520620507 25.13557825703115 25.95535376466137 54-55 23.441427853192558 24.723479135243842 25.791855203619914 26.043237807943694 56-57 22.206931064681594 25.27211309896159 26.973601901663958 25.547353934692858 58-59 22.25 26.0625 25.4625 26.224999999999998 60-61 22.475 26.2625 25.75 25.5125 62-63 23.3 25.224999999999998 26.1125 25.362499999999997 64-65 23.746238716148447 24.686559679037114 26.10330992978937 25.463891675025074 66-67 23.705926481620406 25.168792198049513 26.081520380095025 25.04376094023506 68-69 22.703379224030037 25.281602002503128 26.395494367959948 25.619524405506883 70-71 23.5125 25.45 26.1125 24.925 72-73 23.35 24.9 25.900000000000002 25.85 74-75 22.3875 26.137500000000003 25.45 26.025 76-77 23.2875 25.1 25.4875 26.125 78-79 23.35 25.45 25.2125 25.9875 80-81 22.412499999999998 25.8625 25.887500000000003 25.837500000000002 82-83 23.6375 25.087500000000002 25.15 26.125 84-85 22.5875 25.074999999999996 25.837500000000002 26.5 86-87 23.25 25.35 25.4625 25.937500000000004 88-89 22.661330665332667 25.07503751875938 25.82541270635318 26.43821910955478 90-91 23.81790744466801 24.911971830985916 25.213782696177063 26.056338028169012 92-93 23.93463230672533 25.229415461973602 24.81458202388435 26.021370207416716 94-95 23.635906462157404 25.345737993462407 24.93085240130752 26.087503143072666 96-97 23.44853683148335 25.403632694248234 25.70635721493441 25.441473259334007 98-99 23.779408044523148 24.614217050341512 26.15734884897546 25.44902605615988 100-101 24.28787496849004 26.052432568691707 24.842450214267707 24.817242248550542 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 0.0 1 0.0 2 0.0 3 0.5 4 0.5 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 0.0 18 0.0 19 0.0 20 0.5 21 0.5 22 0.0 23 1.0 24 2.5 25 1.5 26 1.0 27 1.0 28 1.0 29 4.5 30 4.5 31 5.5 32 13.0 33 17.0 34 18.0 35 25.5 36 40.0 37 55.0 38 77.5 39 101.0 40 130.0 41 160.5 42 162.5 43 166.0 44 188.5 45 208.5 46 218.0 47 200.5 48 173.5 49 167.0 50 178.0 51 171.5 52 158.5 53 160.5 54 139.5 55 130.0 56 136.0 57 125.5 58 105.0 59 93.5 60 93.5 61 89.5 62 72.0 63 48.5 64 45.0 65 38.0 66 26.0 67 19.5 68 13.0 69 6.5 70 1.0 71 1.5 72 1.5 73 0.0 74 0.0 75 0.0 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 0.0125 20-21 0.0125 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 0.0 42-43 0.0125 44-45 0.0125 46-47 0.0 48-49 0.25 50-51 0.46249999999999997 52-53 0.8875 54-55 0.5499999999999999 56-57 0.08750000000000001 58-59 0.0 60-61 0.0 62-63 0.0 64-65 0.3 66-67 0.025 68-69 0.125 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 0.05 90-91 0.6 92-93 0.5625 94-95 0.575 96-97 0.8999999999999999 98-99 1.175 100-101 0.8250000000000001 >>END_MODULE >>Sequence Length Distribution pass #Length Count 101 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 97.95 #Duplication Level Percentage of deduplicated Percentage of total 1 98.1368044920878 96.125 2 1.6590096988259317 3.25 3 0.17866258295048493 0.525 4 0.025523226135783564 0.1 5 0.0 0.0 6 0.0 0.0 7 0.0 0.0 8 0.0 0.0 9 0.0 0.0 >10 0.0 0.0 >50 0.0 0.0 >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 pass >>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 0.0125 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 0.05 0.0 0.0 0.0 0.0 62-63 0.0625 0.0 0.0 0.0 0.0 64-65 0.1 0.0 0.0 0.0 0.0 66-67 0.1 0.0 0.0 0.0 0.0 68-69 0.1 0.0 0.0 0.0 0.0 70-71 0.1 0.0 0.0 0.0 0.0 72-73 0.125 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 0.15 0.0 0.0 0.0 0.0 80-81 0.225 0.0 0.0 0.0 0.0 82-83 0.35 0.0 0.0 0.0 0.0 84-85 0.42500000000000004 0.0 0.0 0.0 0.0 86-87 0.5125 0.0 0.0 0.0 0.0 88-89 0.6499999999999999 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE ERR10610834 read2 length is 101 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR10610834_2.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 101 %GC 49 >>END_MODULE >>Per base sequence quality fail #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 32.368 33.0 33.0 34.0 31.0 34.0 2 32.24075 33.0 33.0 34.0 29.0 34.0 3 32.32 33.0 33.0 34.0 31.0 34.0 4 32.1605 33.0 33.0 34.0 31.0 34.0 5 32.2905 33.0 33.0 34.0 31.0 34.0 6 35.96275 38.0 38.0 38.0 33.0 38.0 7 35.755 38.0 38.0 38.0 31.0 38.0 8 2.0 2.0 2.0 2.0 2.0 2.0 9 28.605 30.0 30.0 31.0 26.0 31.0 10-11 23.069000000000003 22.5 22.5 23.0 20.5 29.5 12-13 30.816000000000003 32.5 31.0 34.0 26.0 34.0 14-15 34.639375 38.0 36.5 38.0 27.5 38.0 16-17 34.992000000000004 38.0 37.5 38.0 28.5 38.0 18-19 35.192750000000004 38.0 38.0 38.0 29.0 38.0 20-21 35.02275 38.0 38.0 38.0 28.0 38.0 22-23 35.10625 38.0 38.0 38.0 28.5 38.0 24-25 35.03175 38.0 38.0 38.0 28.5 38.0 26-27 35.03225 38.0 38.0 38.0 29.0 38.0 28-29 34.987125 38.0 38.0 38.0 28.5 38.0 30-31 34.875249999999994 38.0 38.0 38.0 28.0 38.0 32-33 34.813874999999996 38.0 38.0 38.0 28.0 38.0 34-35 35.022 38.0 38.0 38.0 28.0 38.0 36-37 35.175375 38.0 38.0 38.0 28.0 38.0 38-39 35.201625 38.0 38.0 38.0 28.5 38.0 40-41 35.17775 38.0 38.0 38.0 29.0 38.0 42-43 35.0025 38.0 38.0 38.0 28.0 38.0 44-45 35.051125 38.0 38.0 38.0 28.0 38.0 46-47 35.213875 38.0 38.0 38.0 29.0 38.0 48-49 35.253375000000005 38.0 38.0 38.0 29.0 38.0 50-51 35.471500000000006 38.0 38.0 38.0 28.5 38.0 52-53 35.738875 38.0 38.0 38.0 30.0 38.0 54-55 35.820125000000004 38.0 38.0 38.0 30.0 38.0 56-57 35.867625000000004 38.0 38.0 38.0 32.0 38.0 58-59 35.876875 38.0 38.0 38.0 31.0 38.0 60-61 35.853375 38.0 38.0 38.0 32.0 38.0 62-63 35.821 38.0 38.0 38.0 31.0 38.0 64-65 35.899249999999995 38.0 38.0 38.0 33.0 38.0 66-67 35.902375 38.0 38.0 38.0 32.0 38.0 68-69 35.667 38.0 38.0 38.0 31.0 38.0 70-71 35.631 38.0 38.0 38.0 31.0 38.0 72-73 35.570375 38.0 38.0 38.0 30.5 38.0 74-75 35.343625 38.0 37.0 38.0 29.0 38.0 76-77 35.3935 38.0 37.0 38.0 29.0 38.0 78-79 35.327124999999995 38.0 37.0 38.0 29.0 38.0 80-81 35.27075 38.0 37.0 38.0 28.5 38.0 82-83 35.2525 38.0 37.0 38.0 28.5 38.0 84-85 35.314625 38.0 37.5 38.0 29.0 38.0 86-87 35.295375 38.0 37.0 38.0 29.0 38.0 88-89 35.177499999999995 38.0 37.0 38.0 28.5 38.0 90-91 34.927 38.0 37.0 38.0 27.5 38.0 92-93 34.981125 38.0 37.0 38.0 27.5 38.0 94-95 34.929874999999996 38.0 37.0 38.0 27.0 38.0 96-97 34.815 38.0 37.0 38.0 26.5 38.0 98-99 34.75175 38.0 37.0 38.0 26.0 38.0 100-101 34.055375 38.0 35.5 38.0 20.5 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 12.0 3 1.0 4 1.0 5 6.0 6 10.0 7 6.0 8 13.0 9 10.0 10 7.0 11 8.0 12 4.0 13 2.0 14 5.0 15 4.0 16 7.0 17 10.0 18 27.0 19 31.0 20 21.0 21 25.0 22 20.0 23 29.0 24 28.0 25 34.0 26 33.0 27 22.0 28 41.0 29 45.0 30 62.0 31 76.0 32 91.0 33 114.0 34 175.0 35 342.0 36 2426.0 37 252.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 30.095142714071105 14.546820230345519 15.047571357035553 40.31046569854782 2 28.1774880922537 20.381047881674604 30.50889947355227 20.932564552519427 3 23.401053423626784 26.00953097567093 24.278906445949335 26.31050915475295 4 26.56132430398796 32.07925758715827 18.459994983697015 22.89942312515676 5 28.392274893403563 32.58088788562829 19.237521946325558 19.78931527464259 6 22.98356510745891 35.170670037926676 19.5448798988622 22.300884955752213 7 20.194026040336993 17.56446259892775 36.37988256318611 25.861628797549148 8 NaN NaN NaN NaN 9 24.508050089445437 22.54025044722719 27.16585739841554 25.785842064911833 10-11 23.570520965692506 29.237611181702665 20.78780177890724 26.404066073697585 12-13 27.085714285714285 22.615873015873017 24.1015873015873 26.196825396825396 14-15 25.48741123305358 25.7843770174306 24.648160103292447 24.080051646223367 16-17 26.67447002210951 25.347899596826633 23.540122252568604 24.437508128495253 18-19 26.0976557440746 25.152182359797955 24.426887708846003 24.32327418728144 20-21 26.540716612377853 25.52442996742671 23.635179153094462 24.299674267100976 22-23 25.941313944430018 25.850428460140222 23.59127499350818 24.616982601921578 24-25 25.618328560270765 26.008851861494403 24.48581098672221 23.887008591512625 26-27 26.083561108941822 25.614994142912924 24.703891708967852 23.597553039177406 28-29 27.245469951766392 25.003259027506193 23.73875635510364 24.012514665623776 30-31 24.87900588620013 26.344015696533685 25.219097449313278 23.55788096795291 32-33 26.880313930673644 25.899280575539567 24.041857423152386 23.178548070634402 34-35 25.697961303726792 25.360342812621738 24.51629658485911 24.425399298792364 36-37 26.491431516557146 26.220847828888026 23.695400077309625 23.5923205772452 38-39 26.205829249419654 26.721692029920042 23.910239876192932 23.16223884446737 40-41 26.857364742428164 25.873673310898265 23.763914056432824 23.505047890240746 42-43 25.1621271076524 25.65499351491569 25.1621271076524 24.020752269779507 44-45 26.070089227983967 25.85025216604164 24.531229794387688 23.548428811586707 46-47 25.993804852865253 26.122870418172432 23.631905007743935 24.25141972121838 48-49 26.416795466254506 25.656877897990725 25.21895929933024 22.70736733642452 50-51 25.582876799592302 25.544655370110842 25.455472034654097 23.416995795642755 52-53 26.6944865958523 25.392008093070306 24.03894790085989 23.874557410217502 54-55 25.67073938783222 26.262753495402443 24.38594281395642 23.680564302808918 56-57 26.492819349962204 24.75434618291761 24.741748551272362 24.011085915847822 58-59 26.051902242378432 24.77954144620811 25.359032501889644 23.809523809523807 60-61 26.077097505668934 25.207860922146637 24.77954144620811 23.93550012597632 62-63 25.182665658856134 25.875535399344923 25.321239606953895 23.620559334845048 64-65 25.453629032258064 25.78125 25.12600806451613 23.639112903225808 66-67 26.600302419354836 25.315020161290324 24.584173387096776 23.500504032258064 68-69 25.148715352487027 25.553727376281483 25.832173142640176 23.465384128591317 70-71 26.256345177664976 25.888324873096447 24.428934010152282 23.426395939086294 72-73 25.082676163826 26.812515899262273 25.298906130755533 22.805901806156196 74-75 25.04143822516894 26.048705852352416 25.321943134004844 23.587912788473798 76-77 25.627948489098557 25.882952951676653 25.513196480938415 22.97590207828637 78-79 25.390125351752367 27.078536710156047 24.80173957533896 22.729598362752622 80-81 25.29689694802707 25.897075724683948 25.322436470438003 23.483590856850977 82-83 26.137377341659235 24.90123614120046 25.81878424875749 23.142602268382824 84-85 25.612244897959187 25.204081632653065 25.765306122448976 23.418367346938776 86-87 24.897854954034727 26.31511746680286 25.344739530132788 23.44228804902962 88-89 25.84485407066052 25.102406554019456 25.57603686635945 23.476702508960575 90-91 25.93641395288969 26.348307375466597 25.25421547174669 22.461063199897026 92-93 26.01282051282051 25.58974358974359 25.397435897435898 23.0 94-95 26.345609065155806 25.26397115632243 25.650270409477212 22.740149369044556 96-97 25.88098618820188 25.506647734606947 25.868077965664128 22.74428811152704 98-99 25.897700852492893 26.64686127615603 24.786876776026865 22.668561095324204 100-101 26.748545572074985 25.765998707175175 24.38267614738203 23.10277957336781 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 3.0 1 5.0 2 4.5 3 1.5 4 1.0 5 1.5 6 1.5 7 3.0 8 4.5 9 7.0 10 8.5 11 6.0 12 7.0 13 7.0 14 3.5 15 2.5 16 5.0 17 4.5 18 3.5 19 3.5 20 3.5 21 4.0 22 3.5 23 4.0 24 3.5 25 5.5 26 8.0 27 7.5 28 6.5 29 7.0 30 6.5 31 6.5 32 7.5 33 8.0 34 16.5 35 28.5 36 41.0 37 54.5 38 68.0 39 89.5 40 118.0 41 139.5 42 151.5 43 159.5 44 163.5 45 181.0 46 203.0 47 200.0 48 170.5 49 166.0 50 172.0 51 173.0 52 165.5 53 149.5 54 150.5 55 142.5 56 131.0 57 127.0 58 122.5 59 110.5 60 94.0 61 80.5 62 72.5 63 60.0 64 45.0 65 35.0 66 27.0 67 13.5 68 7.0 69 5.0 70 1.0 71 1.0 72 0.5 73 0.0 74 0.0 75 0.0 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 fail #Base N-Count 1 0.15 2 0.27499999999999997 3 0.325 4 0.325 5 0.325 6 1.125 7 2.075 8 100.0 9 2.175 10-11 1.625 12-13 1.5625 14-15 3.1875 16-17 3.8875 18-19 3.4875000000000003 20-21 4.0625 22-23 3.7249999999999996 24-25 3.975 26-27 3.9625 28-29 4.1125 30-31 4.4375 32-33 4.4375 34-35 3.7375 36-37 2.9875 38-39 3.075 40-41 3.4250000000000003 42-43 3.6249999999999996 44-45 3.3375000000000004 46-47 3.15 48-49 2.9499999999999997 50-51 1.8875 52-53 1.15 54-55 0.7625 56-57 0.775 58-59 0.775 60-61 0.775 62-63 0.775 64-65 0.8 66-67 0.8 68-69 1.2375 70-71 1.5 72-73 1.725 74-75 1.9625 76-77 1.9625 78-79 2.275 80-81 2.1125000000000003 82-83 1.9124999999999999 84-85 2.0 86-87 2.1 88-89 2.35 90-91 2.8875 92-93 2.5 94-95 2.9250000000000003 96-97 3.1625 98-99 3.225 100-101 3.3125 >>END_MODULE >>Sequence Length Distribution pass #Length Count 101 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 99.675 #Duplication Level Percentage of deduplicated Percentage of total 1 99.67394030599448 99.35000000000001 2 0.32605969400551793 0.65 3 0.0 0.0 4 0.0 0.0 5 0.0 0.0 6 0.0 0.0 7 0.0 0.0 8 0.0 0.0 9 0.0 0.0 >10 0.0 0.0 >50 0.0 0.0 >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 pass >>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 0.0125 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 0.05 0.0 0.0 0.0 0.0 62-63 0.0625 0.0 0.0 0.0 0.0 64-65 0.1 0.0 0.0 0.0 0.0 66-67 0.1 0.0 0.0 0.0 0.0 68-69 0.1 0.0 0.0 0.0 0.0 70-71 0.1 0.0 0.0 0.0 0.0 72-73 0.125 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 0.15 0.0 0.0 0.0 0.0 80-81 0.225 0.0 0.0 0.0 0.0 82-83 0.32499999999999996 0.0 0.0 0.0 0.0 84-85 0.375 0.0 0.0 0.0 0.0 86-87 0.4625 0.0 0.0 0.0 0.0 88-89 0.575 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Read 1122011 spots for ERR10610834.sra Written 1122011 spots for ERR10610834.sra Read 1122011 spots for ERR10610834.sra Written 1122011 spots for ERR10610834.sra Read 1122011 spots for ERR10610834.sra Written 1122011 spots for ERR10610834.sra Read 1122011 spots for ERR10610834.sra Written 1122011 spots for ERR10610834.sra Read 1122011 spots for ERR10610834.sra Written 1122011 spots for ERR10610834.sra Read 1122011 spots for ERR10610834.sra Written 1122011 spots for ERR10610834.sra Read 1122011 spots for ERR10610834.sra Written 1122011 spots for ERR10610834.sra Read 1122011 spots for ERR10610834.sra Written 1122011 spots for ERR10610834.sra Read 1122011 spots for ERR10610834.sra Written 1122011 spots for ERR10610834.sra Read 1122011 spots for ERR10610834.sra Written 1122011 spots for ERR10610834.sra Read 1122011 spots for ERR10610834.sra Written 1122011 spots for ERR10610834.sra Read 1122011 spots for ERR10610834.sra Written 1122011 spots for ERR10610834.sra Read 1122011 spots for ERR10610834.sra Written 1122011 spots for ERR10610834.sra Read 1122011 spots for ERR10610834.sra Written 1122011 spots for ERR10610834.sra Read 1122024 spots for ERR10610834.sra Written 1122024 spots for ERR10610834.sra Read 1122011 spots for ERR10610834.sra Written 1122011 spots for ERR10610834.sra Read 1122011 spots for ERR10610834.sra Written 1122011 spots for ERR10610834.sra Read 1122011 spots for ERR10610834.sra Written 1122011 spots for ERR10610834.sra Read 1122011 spots for ERR10610834.sra Written 1122011 spots for ERR10610834.sra Read 1122011 spots for ERR10610834.sra Written 1122011 spots for ERR10610834.sra SRR ids: ['ERR10610834.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_4wdgik_1 ERR10610834.sra spots: 22440233 blocks: [[1, 1122011], [1122012, 2244022], [2244023, 3366033], [3366034, 4488044], [4488045, 5610055], [5610056, 6732066], [6732067, 7854077], [7854078, 8976088], [8976089, 10098099], [10098100, 11220110], [11220111, 12342121], [12342122, 13464132], [13464133, 14586143], [14586144, 15708154], [15708155, 16830165], [16830166, 17952176], [17952177, 19074187], [19074188, 20196198], [20196199, 21318209], [21318210, 22440233]] ERR10610834 file size 5413043 ERR10610834 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 ERR10610834 ERR10610834_1.fastq ERR10610834_2.fastq Input file: ERR10610834_1.fastq Paired file: ERR10610834_2.fastq trimmed: ERR10610834-trimmed-pair1.fastq, ERR10610834-trimmed-pair2.fastq Parameters used: -- 3' end adapter sequence (-x): AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -- paired 3' end adapter sequence (-y): AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA -- 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 -- number of concurrent threads (-t): 20 Fri Dec 6 20:36:26 2024 >> started Fri Dec 6 20:36:56 2024 >> done (29.987s) 22440233 read pairs processed; of these: 88569 ( 0.39%) short read pairs filtered out after trimming by size control 7689 ( 0.03%) empty read pairs filtered out after trimming by size control 22343975 (99.57%) read pairs available; of these: 728494 ( 3.26%) trimmed read pairs available after processing 21615481 (96.74%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 19 2 0.00% 20 2 0.00% 21 3 0.00% 22 2 0.00% 23 5 0.00% 24 2 0.00% 25 4 0.00% 26 5 0.00% 27 7 0.00% 28 10 0.00% 29 15 0.00% 30 13 0.00% 31 21 0.00% 32 11 0.00% 33 36 0.00% 34 27 0.00% 35 29 0.00% 36 31 0.00% 37 50 0.00% 38 51 0.00% 39 65 0.00% 40 72 0.00% 41 105 0.00% 42 79 0.00% 43 124 0.00% 44 111 0.00% 45 142 0.00% 46 177 0.00% 47 196 0.00% 48 214 0.00% 49 247 0.00% 50 336 0.00% 51 361 0.00% 52 430 0.00% 53 467 0.00% 54 475 0.00% 55 565 0.00% 56 634 0.00% 57 727 0.00% 58 956 0.00% 59 3312 0.01% 60 44215 0.20% 61 1128 0.01% 62 1085 0.00% 63 1501 0.01% 64 1782 0.01% 65 2590 0.01% 66 2358 0.01% 67 4538 0.02% 68 3525 0.02% 69 2409 0.01% 70 2658 0.01% 71 3216 0.01% 72 3390 0.02% 73 4302 0.02% 74 4447 0.02% 75 5101 0.02% 76 5395 0.02% 77 6204 0.03% 78 6951 0.03% 79 8044 0.04% 80 9303 0.04% 81 9881 0.04% 82 11095 0.05% 83 13299 0.06% 84 14301 0.06% 85 15817 0.07% 86 16933 0.08% 87 18444 0.08% 88 20855 0.09% 89 22926 0.10% 90 24883 0.11% 91 27951 0.13% 92 30315 0.14% 93 33549 0.15% 94 36598 0.16% 95 39838 0.18% 96 42577 0.19% 97 47669 0.21% 98 51216 0.23% 99 55798 0.25% 100 60286 0.27% 101 21615481 96.74% 22343975 reads passed initial QC criterion=sequence-density sequence-density=0.54 sequence-density-rank=1 fanout-score=2.17 fanout-score-rank=25 prefix-density=0.55 prefix-fanout=2.1 sequence=GTGGCGTCGGTGCACCCGAACATGGGCAGCTTCCACATTGTCCAGTACCTGCCATCATAGTACCCAGGGGAGCTGTTGTG criterion=fanout-score sequence-density=0.01 sequence-density-rank=33 fanout-score=61.09 fanout-score-rank=1 prefix-density=0.17 prefix-fanout=2.0 sequence=TATATATATTACTGTTCACCAAATGAATATACTCAATATCTTTATATATGAACAAAAACTTTTCATGCCCAGCAATTGCTTGGATGCAATGCGGTACTTAGGTACAAAGAGTGAAACATCAGAATAATTAAAGTGGCATGCTTAAAAGGTGTAAAGGCAGCTGCCGTCGTCACTCCTTGCTGTTGGGTCGTAGTTCTCGGCATTCCGGTCAGTGCAACCTTCTGGGACGGGCAAATTACCTTGTTGTGCTCCTTTACCTCCTCCTATGCAGCTAGAGATGGTGTGTGTATGAAGAGTGTTCTAACCGTAGAAGGAACCAGTCTTCATGGCATCTGAGTTAGCATCTCCCAGAGCAGCCTCGCTCATGTACTTGTCAGCAAGCTGCACACGCTTGACATTGTCCTGCTCTTGGACGAGCATGTGGCCGTACTCCAGGAGCTTCTCGATTGTCATCTTTGGCTGCTCAAAGGACACCGGTCCATCCTTCGAGTTCACCAGCTTCTTGCCGATG criterion=sequence-density sequence-density=0.45 sequence-density-rank=1 fanout-score=3.29 fanout-score-rank=12 prefix-density=0.47 prefix-fanout=3.2 sequence=GAGTTCAGCAAGGTCGGCTT criterion=fanout-score sequence-density=0.02 sequence-density-rank=33 fanout-score=23.25 fanout-score-rank=1 prefix-density=0.11 prefix-fanout=3.9 sequence=AGAAGTTCAAGACCGAGGTCTACGACAAGAAGCCGGATGTCTTCGAGCCGCTCAAGGCCGGCCAGGCCCCCAAGTACATGGTGTTCGCCTGCGCCGACTCACGTGTGTGCCCGTCGGTGACCCTGGGCCTGGAGCCCGGTGAGGCCTTCACCGTCCGCAACATCGCCAACATGGTCCCGTCCTACTGCAAGAACAAGTACGCCGGTGTTGGGTCGGCCATCGAGTACGCCGTGTGTGCCCTCAAGGTTGAGGTCATCGTGGTGATTGGCCACAGCCGCTGCGGTGGAATCAAGGCACTCCTCTCGCTCAAGGATGGTGCAGATGACAGCTTCCACTTCGTCGAGGACTGGGTCAGGATCGGGTTCCCGGCCAAGAAGAAGGTGCAGACCGAGTGCGCCTCCATGCCTTTCGATGACCAATGCGCCGTCTTGGAAAAGGAGGCCGTGAACGTGTCCCTCGAGAACCTCAAGACCTACCCGTTCGTCAAGGAAGGCGTCGCCAACGGAACCCT ERR10610834 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 06 20:37:33 Started mapping on | Dec 06 20:37:33 Finished on | Dec 06 20:39:11 Mapping speed, Million of reads per hour | 820.80 Number of input reads | 22343975 Average input read length | 201 UNIQUE READS: Uniquely mapped reads number | 20479204 Uniquely mapped reads % | 91.65% Average mapped length | 200.62 Number of splices: Total | 13298455 Number of splices: Annotated (sjdb) | 12493494 Number of splices: GT/AG | 13115793 Number of splices: GC/AG | 165109 Number of splices: AT/AC | 3864 Number of splices: Non-canonical | 13689 Mismatch rate per base, % | 0.38% Deletion rate per base | 0.01% Deletion average length | 2.02 Insertion rate per base | 0.01% Insertion average length | 1.76 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 951814 % of reads mapped to multiple loci | 4.26% Number of reads mapped to too many loci | 59603 % of reads mapped to too many loci | 0.27% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 2.12% % of reads unmapped: other | 1.70% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 962097 962097 962097 N_multimapping 951814 951814 951814 N_noFeature 849065 19949049 956598 N_ambiguous 496485 1657 74836 UnstrandedReadsAssigned:19133654 PositiveStrandReadsAssigned:528498 NegativeStrandReadsAssigned:19447770 Dataset is classified negative stranded MeadianReadLen=101 20thPercentileLength=101 echo kmer=97 ERR10610834 Starting Kallisto paired end mapping to ensembl reference transcriptome [quant] fragment length distribution will be estimated from the data [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 paired-end mode [quant] will process pair 1: ERR10610834-trimmed-pair1.fastq ERR10610834-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 22,343,975 reads, 19,758,918 reads pseudoaligned [quant] estimated average fragment length: 179.049 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,189 rounds 52973 ERR10610834.ke.tsv 35125 ERR10610834.se.tsv 88098 total ==> ERR10610834.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 758.087 0 0 PNS24247 1044 865.951 64.8625 5.36695 PNS24249 1928 1749.95 22.0799 0.90406 PNS24246 1044 865.951 64.8625 5.36695 PNS24248 1044 865.951 64.8625 5.36695 PNS24244 1471 1292.95 80.3327 4.45182 PNS24243 293 125.116 0 0 KQK14069 1603 1424.95 223.05 11.2158 KQK14071 474 297.753 3.32065 0.799089 ==> ERR10610834.se.tsv <== BRADI_1g14170v3 260 BRADI_1g53295v3 49 BRADI_1g59795v3 478 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 224 BRADI_1g74790v3 168 BRADI_1g09890v3 0 BRADI_1g77505v3 355 BRADI_1g48960v3 0 ERR10610834 completed mapping pipeline successfully