Starting /dee2/code/volunteer_pipeline.sh SRR7171419 current disk space = 3118657572864 free memory = 1580042920 SRR7171419 SRAfilesize 094ebec76e786221186e1aebdc837701 SRR7171419.sra SRR7171419.sra file validated SRR7171419 is paired end SRR7171419 is conventional basespace SRR7171419 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR7171419_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 151 %GC 44 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 33.02175 34.0 33.0 34.0 32.0 34.0 2 33.257 34.0 33.0 34.0 33.0 34.0 3 33.1175 34.0 33.0 34.0 31.0 34.0 4 33.3615 34.0 33.0 34.0 33.0 34.0 5 33.275 34.0 33.0 34.0 33.0 34.0 6 37.009 38.0 37.0 38.0 36.0 38.0 7 37.37275 38.0 38.0 38.0 37.0 38.0 8 37.44975 38.0 38.0 38.0 37.0 38.0 9 37.5905 38.0 38.0 38.0 38.0 38.0 10-14 37.58605 38.0 38.0 38.0 38.0 38.0 15-19 37.4986 38.0 38.0 38.0 37.8 38.0 20-24 37.425 38.0 38.0 38.0 37.2 38.0 25-29 37.45605 38.0 38.0 38.0 37.8 38.0 30-34 37.5172 38.0 38.0 38.0 38.0 38.0 35-39 36.22225 38.0 37.2 38.0 31.6 38.0 40-44 37.0175 38.0 38.0 38.0 33.8 38.0 45-49 37.406949999999995 38.0 38.0 38.0 37.2 38.0 50-54 37.3227 38.0 38.0 38.0 37.0 38.0 55-59 37.218650000000004 38.0 38.0 38.0 37.0 38.0 60-64 37.2689 38.0 38.0 38.0 37.0 38.0 65-69 37.28825 38.0 38.0 38.0 37.0 38.0 70-74 34.55585 33.6 33.6 37.8 32.4 38.0 75-79 35.24495 36.2 35.0 38.0 32.0 38.0 80-84 37.13994999999999 38.0 38.0 38.0 36.0 38.0 85-89 37.1485 38.0 38.0 38.0 36.0 38.0 90-94 37.1104 38.0 38.0 38.0 36.0 38.0 95-99 37.0985 38.0 38.0 38.0 36.0 38.0 100-104 36.9375 38.0 38.0 38.0 35.6 38.0 105-109 36.8469 38.0 38.0 38.0 35.0 38.0 110-114 36.726749999999996 38.0 38.0 38.0 35.0 38.0 115-119 36.669500000000006 38.0 38.0 38.0 34.2 38.0 120-124 36.42615 38.0 38.0 38.0 34.0 38.0 125-129 36.2999 38.0 38.0 38.0 33.6 38.0 130-134 36.2693 38.0 37.8 38.0 33.4 38.0 135-139 36.215250000000005 38.0 37.4 38.0 33.0 38.0 140-144 36.13875 38.0 37.4 38.0 33.0 38.0 145-149 35.871300000000005 38.0 36.0 38.0 32.4 38.0 150-151 33.6195 36.5 32.0 38.0 23.5 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 1.0 21 3.0 22 3.0 23 2.0 24 7.0 25 10.0 26 12.0 27 17.0 28 18.0 29 26.0 30 28.0 31 35.0 32 58.0 33 80.0 34 127.0 35 222.0 36 678.0 37 2673.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 40.849673202614376 10.85972850678733 10.180995475113122 38.10960281548517 2 22.575 13.25 34.1 30.075000000000003 3 20.025000000000002 17.5 24.3 38.175 4 22.725 27.275 21.224999999999998 28.775000000000002 5 22.900000000000002 30.599999999999998 24.05 22.45 6 20.200000000000003 33.675 24.575 21.55 7 15.299999999999999 26.575 40.475 17.65 8 17.075000000000003 26.875 30.45 25.6 9 17.075000000000003 24.349999999999998 34.075 24.5 10-14 19.785 29.38 27.169999999999998 23.665 15-19 19.73 28.035 27.839999999999996 24.395 20-24 20.200000000000003 28.410000000000004 27.41 23.98 25-29 19.725986299314965 28.691434571728585 27.67638381919096 23.906195309765486 30-34 20.065016254063515 28.02200550137534 27.806951737934483 24.10602650662666 35-39 20.213085234093636 28.721488595438178 27.315926370548222 23.749499799919967 40-44 20.449089817963593 28.450690138027607 27.255451090218042 23.84476895379076 45-49 20.115028757189297 28.4671167791948 26.93173293323331 24.486121530382597 50-54 20.216010800540026 28.131406570328515 27.641382069103454 24.011200560028 55-59 19.79 28.095 27.91 24.205 60-64 19.805 27.92 27.61 24.665 65-69 20.365 27.955000000000002 27.500000000000004 24.18 70-74 20.785 28.799999999999997 26.235000000000003 24.18 75-79 19.994999999999997 28.18 27.224999999999998 24.6 80-84 20.57 27.58 27.700000000000003 24.15 85-89 20.544999999999998 27.815 27.584999999999997 24.055 90-94 20.57 28.38 27.12 23.93 95-99 20.51 28.055000000000003 27.37 24.065 100-104 20.585 28.105000000000004 27.250000000000004 24.060000000000002 105-109 20.64 27.96 26.845000000000002 24.555 110-114 20.775 27.92 27.3 24.005000000000003 115-119 20.705000000000002 28.205000000000002 27.345000000000002 23.745 120-124 20.915 27.55 27.060000000000002 24.474999999999998 125-129 21.060000000000002 27.765 26.884999999999998 24.29 130-134 21.29 28.315 26.52 23.875 135-139 21.105 27.63 26.810000000000002 24.455 140-144 21.59 27.77 26.224999999999998 24.415 145-149 21.335 28.499999999999996 25.979999999999997 24.185000000000002 150-151 20.9125 28.625 25.587500000000002 24.875 >>END_MODULE >>Per sequence GC content pass #GC Content Count 0 0.0 1 0.5 2 0.5 3 0.0 4 0.0 5 0.0 6 0.0 7 0.5 8 0.5 9 0.0 10 0.5 11 0.5 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 0.0 21 0.0 22 0.0 23 1.0 24 1.0 25 0.5 26 3.0 27 6.0 28 5.5 29 8.0 30 12.5 31 18.0 32 25.0 33 31.0 34 43.5 35 49.0 36 65.5 37 93.0 38 118.5 39 139.0 40 174.0 41 217.5 42 250.0 43 267.5 44 259.5 45 277.5 46 288.0 47 267.0 48 246.5 49 224.0 50 180.5 51 142.0 52 128.0 53 107.0 54 89.5 55 73.0 56 49.5 57 32.0 58 28.0 59 23.0 60 13.5 61 10.5 62 9.5 63 5.5 64 2.0 65 3.0 66 3.0 67 1.5 68 1.0 69 1.5 70 1.0 71 0.0 72 0.0 73 0.5 74 0.5 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 0.5499999999999999 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10-14 0.0 15-19 0.0 20-24 0.0 25-29 0.005 30-34 0.025 35-39 0.04 40-44 0.02 45-49 0.025 50-54 0.005 55-59 0.0 60-64 0.0 65-69 0.0 70-74 0.0 75-79 0.0 80-84 0.0 85-89 0.0 90-94 0.0 95-99 0.0 100-104 0.0 105-109 0.0 110-114 0.0 115-119 0.0 120-124 0.0 125-129 0.0 130-134 0.0 135-139 0.0 140-144 0.0 145-149 0.0 150-151 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 99.8 #Duplication Level Percentage of deduplicated Percentage of total 1 99.79959919839679 99.6 2 0.2004008016032064 0.4 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 fail #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 0.025 0.0 0.0 0.0 0.0 70-71 0.025 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 0.075 0.0 0.0 0.0 0.0 78-79 0.125 0.0 0.0 0.0 0.0 80-81 0.15 0.0 0.0 0.0 0.0 82-83 0.21250000000000002 0.0 0.0 0.0 0.0 84-85 0.275 0.0 0.0 0.0 0.0 86-87 0.3875 0.0 0.0 0.0 0.0 88-89 0.5 0.0 0.0 0.0 0.0 90-91 0.5874999999999999 0.0 0.0 0.0 0.0 92-93 0.6625 0.0 0.0 0.0 0.0 94-95 0.7875 0.0 0.0 0.0 0.0 96-97 0.95 0.0 0.0 0.0 0.0 98-99 1.2125 0.0 0.0 0.0 0.0 100-101 1.425 0.0 0.0 0.0 0.0 102-103 1.7125 0.0 0.0 0.0 0.0 104-105 2.0 0.0 0.0 0.0 0.0 106-107 2.175 0.0 0.0 0.0 0.0 108-109 2.6 0.0 0.0 0.0 0.0 110-111 2.8625 0.0 0.0 0.0 0.0 112-113 3.175 0.0 0.0 0.0 0.0 114-115 3.5625 0.0 0.0 0.0 0.0 116-117 4.0 0.0 0.0 0.0 0.0 118-119 4.425 0.0 0.0 0.0 0.0 120-121 4.975 0.0 0.0 0.0 0.0 122-123 5.375 0.0 0.0 0.0 0.0 124-125 6.05 0.0 0.0 0.0 0.0 126-127 6.6 0.0 0.0 0.0 0.0 128-129 7.15 0.0 0.0 0.0 0.0 130-131 7.9125 0.0 0.0 0.0 0.0 132-133 8.625 0.0 0.0 0.0 0.0 134-135 9.3625 0.0 0.0 0.0 0.0 136-137 10.2 0.0 0.0 0.0 0.0 138-139 10.95 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position AGCAGTG 10 0.006830828 145.0 6 TTTGCAG 10 0.006830828 145.0 5 CTCAAAT 10 0.006830828 145.0 1 >>END_MODULE SRR7171419 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR7171419_2.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 151 %GC 44 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 32.9765 33.0 33.0 34.0 32.0 34.0 2 33.0425 34.0 33.0 34.0 32.0 34.0 3 33.11725 34.0 33.0 34.0 33.0 34.0 4 33.10275 34.0 33.0 34.0 33.0 34.0 5 33.1095 34.0 33.0 34.0 33.0 34.0 6 37.26275 38.0 38.0 38.0 37.0 38.0 7 37.1775 38.0 38.0 38.0 37.0 38.0 8 37.2015 38.0 38.0 38.0 37.0 38.0 9 37.20275 38.0 38.0 38.0 37.0 38.0 10-14 37.2316 38.0 38.0 38.0 37.0 38.0 15-19 37.1805 38.0 38.0 38.0 37.0 38.0 20-24 37.1512 38.0 38.0 38.0 37.0 38.0 25-29 37.1143 38.0 38.0 38.0 37.0 38.0 30-34 37.189499999999995 38.0 38.0 38.0 37.0 38.0 35-39 37.164750000000005 38.0 38.0 38.0 37.0 38.0 40-44 36.947449999999996 38.0 38.0 38.0 36.2 38.0 45-49 37.01365 38.0 38.0 38.0 36.4 38.0 50-54 37.06699999999999 38.0 38.0 38.0 36.8 38.0 55-59 37.01885 38.0 38.0 38.0 36.4 38.0 60-64 37.0257 38.0 38.0 38.0 36.6 38.0 65-69 37.003150000000005 38.0 38.0 38.0 36.0 38.0 70-74 36.96470000000001 38.0 38.0 38.0 36.0 38.0 75-79 36.913050000000005 38.0 38.0 38.0 36.0 38.0 80-84 36.8928 38.0 38.0 38.0 36.0 38.0 85-89 36.83245 38.0 38.0 38.0 35.4 38.0 90-94 36.68 38.0 38.0 38.0 34.8 38.0 95-99 36.6915 38.0 38.0 38.0 35.0 38.0 100-104 36.5529 38.0 38.0 38.0 34.4 38.0 105-109 36.56145 38.0 38.0 38.0 34.6 38.0 110-114 36.38445 38.0 38.0 38.0 34.2 38.0 115-119 36.303599999999996 38.0 38.0 38.0 34.0 38.0 120-124 36.14 38.0 38.0 38.0 33.4 38.0 125-129 36.015100000000004 38.0 37.4 38.0 33.0 38.0 130-134 36.00155 38.0 37.4 38.0 32.8 38.0 135-139 35.68405 38.0 36.4 38.0 31.0 38.0 140-144 35.483399999999996 38.0 36.0 38.0 30.0 38.0 145-149 35.2166 38.0 35.6 38.0 28.6 38.0 150-151 32.3365 35.5 29.0 38.0 20.5 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 1.0 3 1.0 4 1.0 5 0.0 6 1.0 7 0.0 8 0.0 9 1.0 10 0.0 11 0.0 12 1.0 13 1.0 14 0.0 15 0.0 16 0.0 17 2.0 18 5.0 19 6.0 20 3.0 21 6.0 22 8.0 23 10.0 24 13.0 25 16.0 26 15.0 27 16.0 28 28.0 29 34.0 30 38.0 31 48.0 32 60.0 33 87.0 34 105.0 35 183.0 36 440.0 37 2870.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 35.776832624468355 19.089316987740805 16.587440580435324 28.546409807355516 2 26.357947434292868 26.758448060075096 29.78723404255319 17.09637046307885 3 21.97197197197197 31.03103103103103 28.253253253253252 18.743743743743742 4 24.98122653316646 33.46683354192741 23.35419274092616 18.197747183979978 5 25.219133483596295 33.6839469070874 22.414224893563738 18.682694715752568 6 21.562734785875282 35.937891309792136 24.718256949661907 17.781116954670672 7 20.9366391184573 21.312296518908088 37.540696218382166 20.210368144252442 8 22.063611319809667 26.496368645128975 26.72176308539945 24.718256949661907 9 21.437515652391685 25.945404457801153 29.10092662158778 23.516153268219384 10-14 23.629896803927462 28.86985272016832 25.393247169622285 22.107003306281936 15-19 23.53353704353053 27.991784801883483 27.24540399739518 21.2292741571908 20-24 24.069528627961727 28.10699794620047 27.320543004558434 20.502930421279366 25-29 23.39594290007513 28.249436513899322 26.76684197345354 21.587778612572002 30-34 23.6371827601742 28.65795665014767 27.191269960454523 20.513590629223607 35-39 23.040736662996697 28.300470423381043 27.33960564508057 21.319187268541686 40-44 23.41810172206648 28.203844613536244 27.578093712454947 20.79995995194233 45-49 24.184905093404115 27.630590474282567 28.03125156508239 20.153252867230933 50-54 23.360881542699723 27.738542449286253 27.998998246932132 20.901577761081892 55-59 24.192174740744452 27.37337808727018 27.238114322929714 21.196332849055658 60-64 24.238476953907814 27.630260521042082 27.319639278557112 20.811623246492985 65-69 24.085946108384253 27.992587398577584 27.296403886607234 20.625062606430934 70-74 24.3931735148391 27.586206896551722 27.240878834893152 20.77974075371603 75-79 24.093432701445504 28.01980693242635 27.419596858900615 20.46716350722753 80-84 23.91739173917392 28.24282428242824 26.997699769976997 20.842084208420843 85-89 23.97178024617232 27.409186430501354 27.58430901631142 21.03472430701491 90-94 24.2814221331998 28.302453680520784 26.97045568352529 20.44566850275413 95-99 24.360066122326305 27.736312177528426 27.305515203125786 20.598106497019486 100-104 24.10320641282565 27.800601202404813 27.16432865731463 20.93186372745491 105-109 24.537848805170082 27.61885677070287 27.233104553880068 20.61018987024698 110-114 25.087684136687045 28.02886060727528 26.645956508668206 20.237498747369475 115-119 24.95490981963928 27.745490981963925 27.319639278557112 19.97995991983968 120-124 24.908590032556972 27.998998246932132 26.776859504132233 20.315552216378663 125-129 25.42551061273528 27.88346015218262 26.80716860232279 19.883860632759312 130-134 25.440528634361232 28.49919903884662 26.311573888666402 19.74869843812575 135-139 25.626127028651574 27.644760569024246 27.093768783810862 19.635343618513325 140-144 26.31789937863299 27.891360994187213 26.24273401483263 19.548005612347165 145-149 26.25751503006012 27.24448897795591 26.988977955911825 19.509018036072145 150-151 26.390280561122243 27.542585170340683 26.052104208416832 20.01503006012024 >>END_MODULE >>Per sequence GC content pass #GC Content Count 0 0.0 1 0.5 2 0.5 3 1.0 4 1.0 5 0.0 6 0.0 7 0.0 8 0.5 9 0.5 10 0.0 11 0.0 12 0.0 13 0.5 14 0.5 15 0.0 16 0.0 17 0.0 18 0.5 19 0.5 20 0.0 21 0.5 22 1.0 23 1.0 24 0.5 25 0.5 26 2.0 27 3.0 28 3.5 29 4.5 30 3.5 31 6.5 32 15.0 33 19.0 34 27.5 35 48.0 36 62.5 37 79.5 38 111.5 39 152.0 40 203.5 41 244.5 42 267.0 43 277.5 44 295.0 45 300.0 46 292.5 47 269.5 48 238.0 49 219.0 50 191.5 51 153.5 52 110.5 53 88.5 54 76.0 55 54.5 56 42.0 57 37.0 58 26.0 59 17.5 60 13.0 61 9.0 62 4.5 63 3.0 64 4.5 65 4.0 66 2.5 67 2.0 68 1.0 69 1.5 70 1.0 71 0.0 72 0.5 73 0.5 74 0.0 75 1.0 76 1.0 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 0.075 2 0.125 3 0.1 4 0.125 5 0.17500000000000002 6 0.17500000000000002 7 0.17500000000000002 8 0.17500000000000002 9 0.17500000000000002 10-14 0.19 15-19 0.185 20-24 0.185 25-29 0.17500000000000002 30-34 0.11499999999999999 35-39 0.09 40-44 0.12 45-49 0.165 50-54 0.17500000000000002 55-59 0.19499999999999998 60-64 0.2 65-69 0.16999999999999998 70-74 0.095 75-79 0.034999999999999996 80-84 0.01 85-89 0.06999999999999999 90-94 0.15 95-99 0.185 100-104 0.2 105-109 0.19499999999999998 110-114 0.21 115-119 0.2 120-124 0.17500000000000002 125-129 0.12 130-134 0.12 135-139 0.18 140-144 0.22 145-149 0.2 150-151 0.2 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 99.675 #Duplication Level Percentage of deduplicated Percentage of total 1 99.79934788061199 99.47500000000001 2 0.15048908954100826 0.3 3 0.025081514923501375 0.075 4 0.0 0.0 5 0.0 0.0 6 0.025081514923501375 0.15 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 warn #Sequence Count Percentage Possible Source GTTAGGCTTGAGCAGATTCATTCGCCAACTAACCCTTTAATTTATCCTAT 6 0.15 No Hit >>END_MODULE >>Adapter Content fail #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 0.025 0.0 0.0 0.0 0.0 70-71 0.025 0.0 0.0 0.0 0.0 72-73 0.05 0.0 0.0 0.0 0.0 74-75 0.075 0.0 0.0 0.0 0.0 76-77 0.1 0.0 0.0 0.0 0.0 78-79 0.15 0.0 0.0 0.0 0.0 80-81 0.175 0.0 0.0 0.0 0.0 82-83 0.2375 0.0 0.0 0.0 0.0 84-85 0.30000000000000004 0.0 0.0 0.0 0.0 86-87 0.4125 0.0 0.0 0.0 0.0 88-89 0.5249999999999999 0.0 0.0 0.0 0.0 90-91 0.6125 0.0 0.0 0.0 0.0 92-93 0.6875 0.0 0.0 0.0 0.0 94-95 0.7875 0.0 0.0 0.0 0.0 96-97 0.95 0.0 0.0 0.0 0.0 98-99 1.225 0.0 0.0 0.0 0.0 100-101 1.45 0.0 0.0 0.0 0.0 102-103 1.7374999999999998 0.0 0.0 0.0 0.0 104-105 2.0 0.0 0.0 0.0 0.0 106-107 2.1625 0.0 0.0 0.0 0.0 108-109 2.575 0.0 0.0 0.0 0.0 110-111 2.8375 0.0 0.0 0.0 0.0 112-113 3.15 0.0 0.0 0.0 0.0 114-115 3.525 0.0 0.0 0.0 0.0 116-117 3.9375 0.0 0.0 0.0 0.0 118-119 4.362500000000001 0.0 0.0 0.0 0.0 120-121 4.9125 0.0 0.0 0.0 0.0 122-123 5.3 0.0 0.0 0.0 0.0 124-125 5.9625 0.0 0.0 0.0 0.0 126-127 6.5 0.0 0.0 0.0 0.0 128-129 7.025 0.0 0.0 0.0 0.0 130-131 7.7875 0.0 0.0 0.0 0.0 132-133 8.5125 0.0 0.0 0.0 0.0 134-135 9.274999999999999 0.0 0.0 0.0 0.0 136-137 10.125 0.0 0.0 0.0 0.0 138-139 10.837499999999999 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TGTCTCA 10 0.006843168 144.91249 6 GTCTCAT 10 0.006843168 144.91249 7 >>END_MODULE Read 799474 spots for SRR7171419.sra Written 799474 spots for SRR7171419.sra Read 799474 spots for SRR7171419.sra Written 799474 spots for SRR7171419.sra Read 799474 spots for SRR7171419.sra Written 799474 spots for SRR7171419.sra Read 799474 spots for SRR7171419.sra Written 799474 spots for SRR7171419.sra Read 799474 spots for SRR7171419.sra Written 799474 spots for SRR7171419.sra Read 799474 spots for SRR7171419.sra Written 799474 spots for SRR7171419.sra Read 799474 spots for SRR7171419.sra Written 799474 spots for SRR7171419.sra Read 799474 spots for SRR7171419.sra Written 799474 spots for SRR7171419.sra Read 799474 spots for SRR7171419.sra Written 799474 spots for SRR7171419.sra Read 799474 spots for SRR7171419.sra Written 799474 spots for SRR7171419.sra Read 799474 spots for SRR7171419.sra Written 799474 spots for SRR7171419.sra Read 799474 spots for SRR7171419.sra Written 799474 spots for SRR7171419.sra Read 799474 spots for SRR7171419.sra Written 799474 spots for SRR7171419.sra Read 799474 spots for SRR7171419.sra Written 799474 spots for SRR7171419.sra Read 799479 spots for SRR7171419.sra Written 799479 spots for SRR7171419.sra Read 799474 spots for SRR7171419.sra Written 799474 spots for SRR7171419.sra Read 799474 spots for SRR7171419.sra Written 799474 spots for SRR7171419.sra Read 799474 spots for SRR7171419.sra Written 799474 spots for SRR7171419.sra Read 799474 spots for SRR7171419.sra Written 799474 spots for SRR7171419.sra Read 799474 spots for SRR7171419.sra Written 799474 spots for SRR7171419.sra SRR ids: ['SRR7171419.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_cquv_46a SRR7171419.sra spots: 15989485 blocks: [[1, 799474], [799475, 1598948], [1598949, 2398422], [2398423, 3197896], [3197897, 3997370], [3997371, 4796844], [4796845, 5596318], [5596319, 6395792], [6395793, 7195266], [7195267, 7994740], [7994741, 8794214], [8794215, 9593688], [9593689, 10393162], [10393163, 11192636], [11192637, 11992110], [11992111, 12791584], [12791585, 13591058], [13591059, 14390532], [14390533, 15190006], [15190007, 15989485]] SRR7171419 file size 5396611 SRR7171419 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 SRR7171419 SRR7171419_1.fastq SRR7171419_2.fastq Input file: SRR7171419_1.fastq Paired file: SRR7171419_2.fastq trimmed: SRR7171419-trimmed-pair1.fastq, SRR7171419-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 Feb 14 08:01:43 2025 >> started Fri Feb 14 08:02:00 2025 >> done (16.834s) 15989485 read pairs processed; of these: 22 ( 0.00%) short read pairs filtered out after trimming by size control 1391 ( 0.01%) empty read pairs filtered out after trimming by size control 15988072 (99.99%) read pairs available; of these: 2624989 (16.42%) trimmed read pairs available after processing 13363083 (83.58%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 2 0.00% 19 0 0.00% 20 2 0.00% 21 0 0.00% 22 2 0.00% 23 0 0.00% 24 0 0.00% 25 0 0.00% 26 1 0.00% 27 2 0.00% 28 1 0.00% 29 1 0.00% 30 1 0.00% 31 1 0.00% 32 1 0.00% 33 3 0.00% 34 2 0.00% 35 2 0.00% 36 0 0.00% 37 3 0.00% 38 3 0.00% 39 4 0.00% 40 2 0.00% 41 1 0.00% 42 3 0.00% 43 5 0.00% 44 4 0.00% 45 5 0.00% 46 6 0.00% 47 5 0.00% 48 5 0.00% 49 12 0.00% 50 16 0.00% 51 18 0.00% 52 35 0.00% 53 26 0.00% 54 34 0.00% 55 34 0.00% 56 38 0.00% 57 68 0.00% 58 60 0.00% 59 67 0.00% 60 101 0.00% 61 96 0.00% 62 144 0.00% 63 159 0.00% 64 185 0.00% 65 186 0.00% 66 262 0.00% 67 303 0.00% 68 328 0.00% 69 384 0.00% 70 473 0.00% 71 554 0.00% 72 678 0.00% 73 708 0.00% 74 966 0.01% 75 1127 0.01% 76 1209 0.01% 77 1313 0.01% 78 1561 0.01% 79 1782 0.01% 80 2090 0.01% 81 2437 0.02% 82 2746 0.02% 83 3194 0.02% 84 3711 0.02% 85 4102 0.03% 86 4620 0.03% 87 5101 0.03% 88 5518 0.03% 89 6193 0.04% 90 6732 0.04% 91 7585 0.05% 92 8411 0.05% 93 9452 0.06% 94 10454 0.07% 95 11237 0.07% 96 12492 0.08% 97 13028 0.08% 98 14048 0.09% 99 14710 0.09% 100 16117 0.10% 101 17228 0.11% 102 18501 0.12% 103 19918 0.12% 104 21149 0.13% 105 22265 0.14% 106 23573 0.15% 107 25007 0.16% 108 25418 0.16% 109 26845 0.17% 110 27681 0.17% 111 29602 0.19% 112 30569 0.19% 113 31785 0.20% 114 33900 0.21% 115 36058 0.23% 116 37407 0.23% 117 41291 0.26% 118 43018 0.27% 119 41710 0.26% 120 41228 0.26% 121 41945 0.26% 122 44007 0.28% 123 45313 0.28% 124 47309 0.30% 125 48976 0.31% 126 50641 0.32% 127 51452 0.32% 128 52204 0.33% 129 53238 0.33% 130 54079 0.34% 131 54613 0.34% 132 57187 0.36% 133 58409 0.37% 134 59890 0.37% 135 61799 0.39% 136 63035 0.39% 137 64055 0.40% 138 64792 0.41% 139 65332 0.41% 140 67417 0.42% 141 71808 0.45% 142 71432 0.45% 143 73385 0.46% 144 73578 0.46% 145 76079 0.48% 146 73114 0.46% 147 74314 0.46% 148 77871 0.49% 149 75525 0.47% 150 81065 0.51% 151 13363083 83.58% 15988072 reads passed initial QC criterion=sequence-density sequence-density=0.36 sequence-density-rank=1 fanout-score=3.16 fanout-score-rank=19 prefix-density=0.57 prefix-fanout=2.0 sequence=CACTTGCAGCCATTCTCAGCACCAGAGTTCATCTCAGACC criterion=fanout-score sequence-density=0.04 sequence-density-rank=28 fanout-score=83.65 fanout-score-rank=1 prefix-density=0.22 prefix-fanout=14.4 sequence=TCTCCTTCCTCTAAATGATAAGGTTCAGTGGACTTCTCGCGACGTCGCCGGCGGCGAACCGCCCACGTCGCCGCGATCCGAACACTTCACCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGAATTCCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCAAAGATTACCCGGGCCTGTCGGCCAAGGCTATAGACTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCAAACTTCCTTGGCCTGGAAGGCCATAGTCCCTCTAAGAAGCTGGCCGCGGAGGGTCACCTCCGCATAGCTAGTTAGCAGGCTGAGGTCTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCATGCACCACCACCCATAGAATCAAGAA criterion=sequence-density sequence-density=0.46 sequence-density-rank=1 fanout-score=2.87 fanout-score-rank=25 prefix-density=0.47 prefix-fanout=2.8 sequence=ATGTACCCTGACTT criterion=fanout-score sequence-density=0.12 sequence-density-rank=13 fanout-score=57.53 fanout-score-rank=1 prefix-density=0.44 prefix-fanout=15.5 sequence=TTGGTGCTGAGA SRR7171419 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 14 08:02:45 Started mapping on | Feb 14 08:02:45 Finished on | Feb 14 08:04:25 Mapping speed, Million of reads per hour | 575.57 Number of input reads | 15988072 Average input read length | 294 UNIQUE READS: Uniquely mapped reads number | 14856192 Uniquely mapped reads % | 92.92% Average mapped length | 293.33 Number of splices: Total | 14742404 Number of splices: Annotated (sjdb) | 14481369 Number of splices: GT/AG | 14518616 Number of splices: GC/AG | 174664 Number of splices: AT/AC | 11532 Number of splices: Non-canonical | 37592 Mismatch rate per base, % | 0.41% Deletion rate per base | 0.03% Deletion average length | 2.45 Insertion rate per base | 0.02% Insertion average length | 2.60 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 385751 % of reads mapped to multiple loci | 2.41% Number of reads mapped to too many loci | 211933 % of reads mapped to too many loci | 1.33% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 3.00% % of reads unmapped: other | 0.34% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 746129 746129 746129 N_multimapping 385751 385751 385751 N_noFeature 338200 14734654 383206 N_ambiguous 146141 880 69065 UnstrandedReadsAssigned:14371851 PositiveStrandReadsAssigned:120658 NegativeStrandReadsAssigned:14403921 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=151 echo kmer=147 SRR7171419 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: 52,400 [index] number of k-mers: 62,057,036 [index] number of equivalence classes: 130,681 [quant] running in paired-end mode [quant] will process pair 1: SRR7171419-trimmed-pair1.fastq SRR7171419-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 15,988,072 reads, 14,546,151 reads pseudoaligned [quant] estimated average fragment length: 214.162 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,068 rounds 52401 SRR7171419.ke.tsv 34699 SRR7171419.se.tsv 87100 total ==> SRR7171419.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1804.84 1187 39.8715 Potri.005G024800.1.v4.1 1035 821.838 840 61.9645 Potri.004G059700.1.v4.1 961 747.858 11 0.891709 Potri.007G009000.2.v4.1 1416 1202.84 0 0 Potri.003G141000.2.v4.1 2943 2729.84 708 15.7234 Potri.016G087400.1.v4.1 270 89.8075 1452.97 980.828 Potri.015G069301.1.v4.1 564 352.565 0 0 Potri.010G195200.1.v4.1 1773 1559.84 318.677 12.3857 Potri.012G127500.1.v4.1 977 763.853 2817 223.577 ==> SRR7171419.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 22 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 435 Potri.001G212900.v4.1 0 Potri.001G182400.v4.1 3 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 0 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 104 SRR7171419 completed mapping pipeline successfully