Starting /dee2/code/volunteer_pipeline.sh SRR6031180 current disk space = 1523678068736 free memory = 1400119536 SRR6031180 SRAfilesize 793bdf822fd70c87b20192c80745d67f SRR6031180.sra SRR6031180.sra file validated SRR6031180 is paired end SRR6031180 is conventional basespace SRR6031180 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR6031180_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 47 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 23.9155 25.0 18.0 30.0 18.0 32.0 2 29.63975 31.0 29.0 33.0 25.0 33.0 3 31.22125 31.0 31.0 33.0 29.0 33.0 4 32.77125 33.0 33.0 33.0 32.0 33.0 5 33.0655 33.0 33.0 33.0 33.0 34.0 6 37.2525 38.0 37.0 38.0 36.0 38.0 7 37.706 38.0 38.0 38.0 38.0 38.0 8 37.7985 38.0 38.0 38.0 38.0 38.0 9 37.8745 38.0 38.0 38.0 38.0 38.0 10-14 37.858650000000004 38.0 38.0 38.0 38.0 38.0 15-19 37.879900000000006 38.0 38.0 38.0 38.0 38.0 20-24 37.91065 38.0 38.0 38.0 38.0 38.0 25-29 37.9009 38.0 38.0 38.0 38.0 38.0 30-34 37.90435 38.0 38.0 38.0 38.0 38.0 35-39 37.894 38.0 38.0 38.0 38.0 38.0 40-44 37.88045 38.0 38.0 38.0 38.0 38.0 45-49 37.8737 38.0 38.0 38.0 38.0 38.0 50-54 37.8429 38.0 38.0 38.0 38.0 38.0 55-59 37.8218 38.0 38.0 38.0 38.0 38.0 60-64 37.7937 38.0 38.0 38.0 38.0 38.0 65-69 37.78345 38.0 38.0 38.0 38.0 38.0 70-74 37.75065 38.0 38.0 38.0 38.0 38.0 75-79 37.7395 38.0 38.0 38.0 38.0 38.0 80-84 37.76365 38.0 38.0 38.0 38.0 38.0 85-89 37.716750000000005 38.0 38.0 38.0 38.0 38.0 90-94 37.68845 38.0 38.0 38.0 38.0 38.0 95-99 37.647400000000005 38.0 38.0 38.0 38.0 38.0 100-104 37.62050000000001 38.0 38.0 38.0 38.0 38.0 105-109 37.58385 38.0 38.0 38.0 38.0 38.0 110-114 37.5289 38.0 38.0 38.0 37.8 38.0 115-119 37.43205 38.0 38.0 38.0 37.0 38.0 120-124 37.30545 38.0 38.0 38.0 36.8 38.0 125-129 37.3157 38.0 38.0 38.0 36.6 38.0 130-134 37.188649999999996 38.0 38.0 38.0 36.0 38.0 135-139 37.095 38.0 38.0 38.0 36.0 38.0 140-144 37.011 38.0 38.0 38.0 35.6 38.0 145-149 36.76975 38.0 38.0 38.0 35.0 38.0 150-151 34.781875 38.0 36.0 38.0 29.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 19 1.0 20 2.0 21 1.0 22 1.0 23 1.0 24 1.0 25 5.0 26 1.0 27 2.0 28 7.0 29 4.0 30 3.0 31 8.0 32 11.0 33 21.0 34 37.0 35 55.0 36 301.0 37 3538.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 49.74974974974975 12.312312312312311 7.182182182182182 30.755755755755754 2 21.925 12.275 35.0 30.8 3 20.05 14.95 26.3 38.7 4 24.275 22.650000000000002 24.4 28.675 5 24.981245311327832 25.98149537384346 23.63090772693173 25.406351587896975 6 25.31962897969416 31.210829781900223 22.3614941087992 21.108047129606415 7 17.525 25.525 38.35 18.6 8 19.75 24.675 29.799999999999997 25.775 9 19.15 23.175 33.0 24.675 10-14 21.54 27.92 26.56 23.98 15-19 21.6 25.775 27.405 25.22 20-24 21.345 26.855 26.745 25.055 25-29 21.725 26.284999999999997 26.900000000000002 25.09 30-34 21.67 26.3 26.900000000000002 25.130000000000003 35-39 21.925 26.040000000000003 26.545 25.490000000000002 40-44 22.36 26.07 26.88 24.69 45-49 21.37 26.435 27.155 25.040000000000003 50-54 21.795 25.685000000000002 26.825 25.695 55-59 21.765 26.314999999999998 26.415 25.505 60-64 21.66 26.36 26.495 25.485000000000003 65-69 21.78 26.279999999999998 26.875 25.064999999999998 70-74 21.995 26.615 26.505000000000003 24.884999999999998 75-79 21.755 26.284999999999997 26.8 25.16 80-84 22.295 26.005 26.465 25.235000000000003 85-89 21.93 27.005000000000003 26.185000000000002 24.88 90-94 22.545 26.595000000000002 26.515 24.345 95-99 22.21 26.205000000000002 26.615 24.97 100-104 22.17 25.575 26.765 25.490000000000002 105-109 22.785 25.485000000000003 26.765 24.965 110-114 22.259999999999998 25.814999999999998 27.155 24.77 115-119 21.990000000000002 26.029999999999998 26.68 25.3 120-124 22.46 25.64 26.61 25.290000000000003 125-129 22.355 25.765 26.695 25.185000000000002 130-134 22.57 26.275 26.43 24.725 135-139 22.28 25.929999999999996 26.090000000000003 25.7 140-144 21.75 26.005 26.875 25.369999999999997 145-149 22.375 25.650000000000002 26.71 25.264999999999997 150-151 22.25 25.650000000000002 26.687499999999996 25.412499999999998 >>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 0.0 17 0.0 18 0.0 19 0.5 20 0.5 21 0.0 22 0.0 23 0.0 24 0.5 25 1.0 26 2.0 27 3.0 28 3.0 29 3.5 30 9.0 31 14.0 32 15.0 33 27.0 34 36.5 35 39.0 36 59.0 37 76.0 38 81.5 39 111.5 40 159.0 41 178.0 42 200.0 43 220.0 44 207.5 45 210.0 46 216.0 47 201.0 48 201.0 49 208.5 50 203.0 51 180.0 52 151.5 53 128.5 54 116.0 55 106.0 56 93.0 57 77.0 58 69.5 59 66.5 60 52.0 61 49.0 62 36.5 63 28.5 64 30.5 65 21.5 66 15.5 67 15.0 68 15.0 69 15.5 70 11.5 71 11.0 72 10.0 73 5.0 74 3.0 75 1.5 76 1.0 77 1.0 78 1.5 79 1.0 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 0.1 2 0.0 3 0.0 4 0.0 5 0.025 6 0.27499999999999997 7 0.0 8 0.0 9 0.0 10-14 0.0 15-19 0.0 20-24 0.0 25-29 0.0 30-34 0.0 35-39 0.0 40-44 0.0 45-49 0.0 50-54 0.0 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 99.15 #Duplication Level Percentage of deduplicated Percentage of total 1 99.21835602622289 98.375 2 0.7060010085728694 1.4000000000000001 3 0.07564296520423601 0.22499999999999998 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 0.0 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 0.0125 0.0 0.0 0.0 0.0 52-53 0.025 0.0 0.0 0.0 0.0 54-55 0.025 0.0 0.0 0.0 0.0 56-57 0.025 0.0 0.0 0.0 0.0 58-59 0.025 0.0 0.0 0.0 0.0 60-61 0.025 0.0 0.0 0.0 0.0 62-63 0.025 0.0 0.0 0.0 0.0 64-65 0.025 0.0 0.0 0.0 0.0 66-67 0.025 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 0.025 0.0 0.0 0.025 0.0 74-75 0.025 0.0 0.0 0.025 0.0 76-77 0.025 0.0 0.0 0.025 0.0 78-79 0.025 0.0 0.0 0.025 0.0 80-81 0.037500000000000006 0.0 0.0 0.025 0.0 82-83 0.0625 0.0 0.0 0.025 0.0 84-85 0.1 0.0 0.0 0.025 0.0 86-87 0.1 0.0 0.0 0.025 0.0 88-89 0.1125 0.0 0.0 0.025 0.0 90-91 0.125 0.0 0.0 0.025 0.0 92-93 0.125 0.0 0.0 0.025 0.0 94-95 0.125 0.0 0.0 0.025 0.0 96-97 0.125 0.0 0.0 0.025 0.0 98-99 0.125 0.0 0.0 0.025 0.0 100-101 0.125 0.0 0.0 0.025 0.0 102-103 0.16249999999999998 0.0 0.0 0.025 0.0 104-105 0.1875 0.0 0.0 0.025 0.0 106-107 0.2 0.0 0.0 0.025 0.0 108-109 0.225 0.0 0.0 0.025 0.0 110-111 0.225 0.0 0.0 0.025 0.0 112-113 0.225 0.0 0.0 0.025 0.0 114-115 0.25 0.0 0.0 0.025 0.0 116-117 0.2625 0.0 0.0 0.025 0.0 118-119 0.30000000000000004 0.0 0.0 0.025 0.0 120-121 0.3875 0.0 0.0 0.025 0.0 122-123 0.4 0.0 0.0 0.025 0.0 124-125 0.42500000000000004 0.0 0.0 0.025 0.0 126-127 0.45 0.0 0.0 0.025 0.0 128-129 0.475 0.0 0.0 0.025 0.0 130-131 0.525 0.0 0.0 0.025 0.0 132-133 0.525 0.0 0.0 0.025 0.0 134-135 0.6 0.0 0.0 0.025 0.0 136-137 0.6 0.0 0.0 0.025 0.0 138-139 0.6125 0.0 0.0 0.025 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GATACCA 10 0.006830828 145.0 145 >>END_MODULE SRR6031180 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR6031180_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 48 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 33.519 34.0 33.0 34.0 33.0 34.0 2 33.5835 34.0 33.0 34.0 33.0 34.0 3 33.63175 34.0 34.0 34.0 33.0 34.0 4 33.56925 34.0 34.0 34.0 33.0 34.0 5 33.593 34.0 34.0 34.0 33.0 34.0 6 37.6945 38.0 38.0 38.0 38.0 38.0 7 37.7115 38.0 38.0 38.0 38.0 38.0 8 37.6655 38.0 38.0 38.0 38.0 38.0 9 37.708 38.0 38.0 38.0 38.0 38.0 10-14 37.712450000000004 38.0 38.0 38.0 38.0 38.0 15-19 37.687949999999994 38.0 38.0 38.0 38.0 38.0 20-24 37.6565 38.0 38.0 38.0 38.0 38.0 25-29 37.71115 38.0 38.0 38.0 38.0 38.0 30-34 37.78485 38.0 38.0 38.0 38.0 38.0 35-39 37.7676 38.0 38.0 38.0 38.0 38.0 40-44 37.77155 38.0 38.0 38.0 38.0 38.0 45-49 37.75995 38.0 38.0 38.0 38.0 38.0 50-54 37.76795 38.0 38.0 38.0 38.0 38.0 55-59 37.72475 38.0 38.0 38.0 38.0 38.0 60-64 37.704249999999995 38.0 38.0 38.0 38.0 38.0 65-69 37.71485 38.0 38.0 38.0 38.0 38.0 70-74 37.634949999999996 38.0 38.0 38.0 38.0 38.0 75-79 37.7149 38.0 38.0 38.0 38.0 38.0 80-84 37.6756 38.0 38.0 38.0 38.0 38.0 85-89 37.64445 38.0 38.0 38.0 38.0 38.0 90-94 37.6094 38.0 38.0 38.0 38.0 38.0 95-99 37.55135 38.0 38.0 38.0 38.0 38.0 100-104 37.539 38.0 38.0 38.0 38.0 38.0 105-109 37.426100000000005 38.0 38.0 38.0 38.0 38.0 110-114 37.3414 38.0 38.0 38.0 38.0 38.0 115-119 37.2611 38.0 38.0 38.0 38.0 38.0 120-124 37.235949999999995 38.0 38.0 38.0 37.6 38.0 125-129 37.26425 38.0 38.0 38.0 37.0 38.0 130-134 37.200900000000004 38.0 38.0 38.0 36.6 38.0 135-139 37.094 38.0 38.0 38.0 36.0 38.0 140-144 37.0313 38.0 38.0 38.0 36.0 38.0 145-149 36.934000000000005 38.0 38.0 38.0 35.8 38.0 150-151 34.752250000000004 38.0 35.5 38.0 28.5 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 3 2.0 4 1.0 5 0.0 6 1.0 7 0.0 8 0.0 9 0.0 10 0.0 11 0.0 12 0.0 13 1.0 14 2.0 15 1.0 16 0.0 17 1.0 18 4.0 19 0.0 20 2.0 21 3.0 22 1.0 23 3.0 24 6.0 25 7.0 26 2.0 27 3.0 28 6.0 29 6.0 30 2.0 31 9.0 32 10.0 33 10.0 34 36.0 35 60.0 36 201.0 37 3620.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 44.697348674337164 21.410705352676338 10.305152576288144 23.58679339669835 2 28.189094547273637 28.51425712856428 25.587793896948476 17.70885442721361 3 22.842131598699027 28.14610958218664 28.021015761821367 20.99074305729297 4 26.603206412825653 31.638276553106216 22.044088176352705 19.71442885771543 5 27.429859719438877 34.21843687374749 18.41182364729459 19.939879759519037 6 23.716503881793138 35.937891309792136 20.98672677185074 19.358878036563986 7 22.283425137706562 21.532298447671508 34.55182774161242 21.632448673009513 8 25.31328320802005 22.857142857142858 25.6140350877193 26.21553884711779 9 23.99198597545705 23.516153268219384 27.27272727272727 25.219133483596295 10-14 25.811460629132437 27.128831897415346 24.0833500300541 22.976357443398115 15-19 24.571514483311617 26.691390197454147 25.443520096221313 23.29357522301293 20-24 25.253285184070617 26.406861269936805 24.9724144849032 23.367439061089375 25-29 25.06008411776487 26.45703985579812 25.110154215902263 23.37272181053475 30-34 25.115 26.945000000000004 24.935 23.005 35-39 24.6 26.26 25.264999999999997 23.875 40-44 25.415 26.165 25.230000000000004 23.189999999999998 45-49 25.655 26.695 24.48 23.169999999999998 50-54 25.75 26.155 25.480000000000004 22.615 55-59 25.515618742490993 25.876051261513815 24.914897877452944 23.69343211854225 60-64 25.185000000000002 25.955000000000002 25.095 23.765 65-69 25.152515251525152 25.642564256425644 25.902590259025903 23.3023302330233 70-74 25.507086693043522 26.098061801973255 25.436971002153552 22.95788050282967 75-79 26.035000000000004 25.7 25.61 22.655 80-84 25.4 26.35 25.21 23.04 85-89 25.53 26.674999999999997 24.94 22.855 90-94 25.319999999999997 25.979999999999997 25.22 23.48 95-99 25.15 25.91 25.4 23.54 100-104 25.33506701340268 26.37027405481096 24.98499699939988 23.309661932386476 105-109 25.57894736842105 26.010025062656645 25.684210526315788 22.726817042606516 110-114 25.486850030114432 26.821923308572575 25.10038144950813 22.590845211804858 115-119 25.68028918566121 26.001606587006727 25.223416005623058 23.094688221709006 120-124 25.73776241294654 26.133573826344005 25.622526178666266 22.50613758204319 125-129 25.305 26.135 25.540000000000003 23.02 130-134 25.314999999999998 26.72 24.77 23.195 135-139 25.895000000000003 26.229999999999997 25.715 22.16 140-144 25.245 26.38 25.53 22.845 145-149 24.915000000000003 26.76 25.655 22.67 150-151 24.85 25.525 26.7625 22.8625 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 0.0 1 0.0 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10 0.0 11 0.0 12 0.0 13 0.0 14 0.0 15 0.0 16 0.0 17 0.0 18 0.0 19 0.0 20 0.0 21 0.0 22 0.0 23 0.0 24 1.5 25 1.5 26 2.5 27 3.5 28 1.5 29 5.0 30 6.5 31 10.0 32 14.5 33 17.0 34 26.5 35 40.5 36 51.0 37 70.5 38 96.0 39 122.5 40 142.0 41 157.5 42 179.5 43 195.5 44 213.0 45 226.5 46 226.5 47 209.0 48 186.5 49 179.5 50 165.5 51 145.0 52 126.5 53 104.5 54 99.0 55 100.5 56 89.0 57 72.5 58 74.5 59 74.0 60 65.5 61 58.5 62 47.0 63 42.5 64 44.5 65 41.0 66 36.5 67 38.5 68 42.5 69 34.5 70 25.5 71 21.0 72 18.0 73 17.5 74 11.5 75 7.0 76 5.0 77 3.5 78 2.0 79 1.0 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 0.05 2 0.05 3 0.075 4 0.2 5 0.2 6 0.17500000000000002 7 0.15 8 0.25 9 0.17500000000000002 10-14 0.18 15-19 0.22999999999999998 20-24 0.31 25-29 0.13999999999999999 30-34 0.0 35-39 0.0 40-44 0.0 45-49 0.0 50-54 0.0 55-59 0.12 60-64 0.0 65-69 0.01 70-74 0.165 75-79 0.0 80-84 0.0 85-89 0.0 90-94 0.0 95-99 0.0 100-104 0.02 105-109 0.25 110-114 0.38 115-119 0.41000000000000003 120-124 0.20500000000000002 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 99.3 #Duplication Level Percentage of deduplicated Percentage of total 1 99.44612286002014 98.75 2 0.42799597180261834 0.8500000000000001 3 0.10070493454179255 0.3 4 0.025176233635448138 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 0.0 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 0.0125 0.0 0.0 0.0 0.0 52-53 0.025 0.0 0.0 0.0 0.0 54-55 0.025 0.0 0.0 0.0 0.0 56-57 0.025 0.0 0.0 0.0 0.0 58-59 0.025 0.0 0.0 0.0 0.0 60-61 0.025 0.0 0.0 0.0 0.0 62-63 0.025 0.0 0.0 0.0 0.0 64-65 0.025 0.0 0.0 0.0 0.0 66-67 0.025 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 0.025 0.0 0.0 0.0 0.0 74-75 0.025 0.0 0.0 0.0 0.0 76-77 0.025 0.0 0.0 0.0 0.0 78-79 0.025 0.0 0.0 0.0 0.0 80-81 0.037500000000000006 0.0 0.0 0.0 0.0 82-83 0.0625 0.0 0.0 0.0 0.0 84-85 0.1 0.0 0.0 0.0 0.0 86-87 0.1 0.0 0.0 0.0 0.0 88-89 0.1125 0.0 0.0 0.0 0.0 90-91 0.125 0.0 0.0 0.0 0.0 92-93 0.125 0.0 0.0 0.0 0.0 94-95 0.125 0.0 0.0 0.0 0.0 96-97 0.125 0.0 0.0 0.0 0.0 98-99 0.125 0.0 0.0 0.0 0.0 100-101 0.125 0.0 0.0 0.0 0.0 102-103 0.16249999999999998 0.0 0.0 0.0 0.0 104-105 0.1875 0.0 0.0 0.0 0.0 106-107 0.2 0.0 0.0 0.0 0.0 108-109 0.225 0.0 0.0 0.0 0.0 110-111 0.225 0.0 0.0 0.0 0.0 112-113 0.225 0.0 0.0 0.0 0.0 114-115 0.25 0.0 0.0 0.0 0.0 116-117 0.2625 0.0 0.0 0.0 0.0 118-119 0.30000000000000004 0.0 0.0 0.0 0.0 120-121 0.3875 0.0 0.0 0.0 0.0 122-123 0.4 0.0 0.0 0.0 0.0 124-125 0.42500000000000004 0.0 0.0 0.0 0.0 126-127 0.45 0.0 0.0 0.0 0.0 128-129 0.475 0.0 0.0 0.0 0.0 130-131 0.525 0.0 0.0 0.0 0.0 132-133 0.525 0.0 0.0 0.0 0.0 134-135 0.6 0.0 0.0 0.0 0.0 136-137 0.6 0.0 0.0 0.0 0.0 138-139 0.6125 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GACACCA 10 0.006830828 145.0 145 AAGCTGG 10 0.006830828 145.0 4 >>END_MODULE Read 425288 spots for SRR6031180.sra Written 425288 spots for SRR6031180.sra Read 425288 spots for SRR6031180.sra Written 425288 spots for SRR6031180.sra Read 425288 spots for SRR6031180.sra Written 425288 spots for SRR6031180.sra Read 425288 spots for SRR6031180.sra Written 425288 spots for SRR6031180.sra Read 425288 spots for SRR6031180.sra Written 425288 spots for SRR6031180.sra Read 425288 spots for SRR6031180.sra Written 425288 spots for SRR6031180.sra Read 425288 spots for SRR6031180.sra Written 425288 spots for SRR6031180.sra Read 425288 spots for SRR6031180.sra Written 425288 spots for SRR6031180.sra Read 425288 spots for SRR6031180.sra Written 425288 spots for SRR6031180.sra Read 425288 spots for SRR6031180.sra Written 425288 spots for SRR6031180.sra Read 425297 spots for SRR6031180.sra Written 425297 spots for SRR6031180.sra Read 425288 spots for SRR6031180.sra Written 425288 spots for SRR6031180.sra Read 425288 spots for SRR6031180.sra Written 425288 spots for SRR6031180.sra Read 425288 spots for SRR6031180.sra Written 425288 spots for SRR6031180.sra Read 425288 spots for SRR6031180.sra Written 425288 spots for SRR6031180.sra Read 425288 spots for SRR6031180.sra Written 425288 spots for SRR6031180.sra Read 425288 spots for SRR6031180.sra Written 425288 spots for SRR6031180.sra Read 425288 spots for SRR6031180.sra Written 425288 spots for SRR6031180.sra Read 425288 spots for SRR6031180.sra Written 425288 spots for SRR6031180.sra Read 425288 spots for SRR6031180.sra Written 425288 spots for SRR6031180.sra SRR ids: ['SRR6031180.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_dj1wqpk2 SRR6031180.sra spots: 8505769 blocks: [[1, 425288], [425289, 850576], [850577, 1275864], [1275865, 1701152], [1701153, 2126440], [2126441, 2551728], [2551729, 2977016], [2977017, 3402304], [3402305, 3827592], [3827593, 4252880], [4252881, 4678168], [4678169, 5103456], [5103457, 5528744], [5528745, 5954032], [5954033, 6379320], [6379321, 6804608], [6804609, 7229896], [7229897, 7655184], [7655185, 8080472], [8080473, 8505769]] SRR6031180 file size 2863544 SRR6031180 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 SRR6031180 SRR6031180_1.fastq SRR6031180_2.fastq Input file: SRR6031180_1.fastq Paired file: SRR6031180_2.fastq trimmed: SRR6031180-trimmed-pair1.fastq, SRR6031180-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 Tue Dec 10 00:44:46 2024 >> started Tue Dec 10 00:44:58 2024 >> done (12.091s) 8505769 read pairs processed; of these: 4811 ( 0.06%) short read pairs filtered out after trimming by size control 5590 ( 0.07%) empty read pairs filtered out after trimming by size control 8495368 (99.88%) read pairs available; of these: 1872106 (22.04%) trimmed read pairs available after processing 6623262 (77.96%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 11 0.00% 19 7 0.00% 20 2 0.00% 21 5 0.00% 22 2 0.00% 23 13 0.00% 24 6 0.00% 25 8 0.00% 26 6 0.00% 27 9 0.00% 28 7 0.00% 29 11 0.00% 30 7 0.00% 31 4 0.00% 32 6 0.00% 33 3 0.00% 34 9 0.00% 35 8 0.00% 36 12 0.00% 37 7 0.00% 38 4 0.00% 39 10 0.00% 40 9 0.00% 41 8 0.00% 42 9 0.00% 43 7 0.00% 44 10 0.00% 45 6 0.00% 46 10 0.00% 47 10 0.00% 48 14 0.00% 49 9 0.00% 50 10 0.00% 51 10 0.00% 52 7 0.00% 53 13 0.00% 54 16 0.00% 55 15 0.00% 56 12 0.00% 57 12 0.00% 58 21 0.00% 59 17 0.00% 60 32 0.00% 61 33 0.00% 62 24 0.00% 63 32 0.00% 64 33 0.00% 65 44 0.00% 66 52 0.00% 67 52 0.00% 68 43 0.00% 69 53 0.00% 70 57 0.00% 71 70 0.00% 72 90 0.00% 73 74 0.00% 74 94 0.00% 75 119 0.00% 76 117 0.00% 77 147 0.00% 78 120 0.00% 79 139 0.00% 80 138 0.00% 81 183 0.00% 82 176 0.00% 83 224 0.00% 84 410 0.00% 85 603 0.01% 86 548 0.01% 87 604 0.01% 88 580 0.01% 89 553 0.01% 90 622 0.01% 91 649 0.01% 92 691 0.01% 93 692 0.01% 94 676 0.01% 95 702 0.01% 96 735 0.01% 97 787 0.01% 98 835 0.01% 99 896 0.01% 100 885 0.01% 101 923 0.01% 102 963 0.01% 103 1070 0.01% 104 1057 0.01% 105 1189 0.01% 106 1198 0.01% 107 1173 0.01% 108 1250 0.01% 109 1291 0.02% 110 1373 0.02% 111 1424 0.02% 112 1526 0.02% 113 1566 0.02% 114 1657 0.02% 115 1674 0.02% 116 1871 0.02% 117 1868 0.02% 118 2034 0.02% 119 2118 0.02% 120 2175 0.03% 121 2245 0.03% 122 2433 0.03% 123 2528 0.03% 124 2608 0.03% 125 2771 0.03% 126 2908 0.03% 127 3070 0.04% 128 3276 0.04% 129 3370 0.04% 130 3655 0.04% 131 3818 0.04% 132 4133 0.05% 133 4281 0.05% 134 4727 0.06% 135 4968 0.06% 136 5563 0.07% 137 5987 0.07% 138 6398 0.08% 139 6947 0.08% 140 7707 0.09% 141 8643 0.10% 142 9964 0.12% 143 11498 0.14% 144 13983 0.16% 145 17361 0.20% 146 23479 0.28% 147 34673 0.41% 148 61387 0.72% 149 158135 1.86% 150 1406194 16.55% 151 6623262 77.96% 8495368 reads passed initial QC criterion=sequence-density sequence-density=0.40 sequence-density-rank=1 fanout-score=1.99 fanout-score-rank=30 prefix-density=0.37 prefix-fanout=2.0 sequence=CCGTCAATTCCTTT criterion=fanout-score sequence-density=0.01 sequence-density-rank=35 fanout-score=204.25 fanout-score-rank=1 prefix-density=0.13 prefix-fanout=10.4 sequence=GCATCAATGATAATCCCAAAGTAGGAAGTGTGTACGTAGTAGCAAGTGTTATACATACATAAAATTAAGCGATGCGTTTCGATCAAGTACTTGGCATCATCGATCACATACGTACATTTCACAGCAGGTAGCTACGTACATTACAGGCATACGTACATGCAGAGAGATACCCGGCCCTGTGTTGTGTTTGCAATTGCATAGATGAGAATGAGATGACTTGATTCTTAATTAGCCGGCGAGAGCGCTGGTGTTGTAGACGAGGAGGGCGCCGCCGCCGAGGAGGCCGGCCAGGGTGACGGCCCAGATCAGGAGCCCCGTCGTCCCACCGGCGTAGCGGTCGCCAGATTCGGACCATACCTCCGGCGTGTAGATCGGGCTGTAGCCGTCGACGTTGGCGCCGTACTTGTCAACAAACT criterion=sequence-density sequence-density=0.25 sequence-density-rank=1 fanout-score=3.58 fanout-score-rank=29 prefix-density=0.43 prefix-fanout=2.1 sequence=TGGTGCATGGCCGTTCTTAGTTGGTGGAGCGATTTGTCTGGTTAATTCCGTTAACGAACGAGACCTCAGCCTGCTAACTAGCTATGCGGAGCCATCCCTCCGCAGCTAGCTTCTTAGAGGGACTATCGCCGTTTAGGCGACGGAAGTTTGAGGCAATAACAGGTCTGTGATGCCCTTAGATGTTCTGGGCCGCACGCGCGCTACACTGATGTATTCAACGAGTATATAGCCTTGGCCGACAGGCCCGGGTAATCTTGGGAAATTTCATCGTGATGGGGATAGATCATTGCAATTGTTGGTCTTCAACGAGGAATGCCTAGTAAGCGCGAGTCATCAGCTCGCGTTGACTACGTCCCTGCCCTTTGTACACACCGCCCGTC criterion=fanout-score sequence-density=0.02 sequence-density-rank=35 fanout-score=660.57 fanout-score-rank=1 prefix-density=0.51 prefix-fanout=20.4 sequence=GCCGCCGCCCCTCGTCCTCTGTGTTCCTTCTCCGAGTTTCAGCCATGGGTAAGGAGAAGACTCACATCAACATCGTGGTCATTGGCCATGTCGACTCTGGCAAGTCGACCACCACTGGCCACCTGATCTACAAGCTTGGAGGTATTGACAAGCGTGTGATCGAGAGGTTCGAGAAGGAGGCTGC SRR6031180 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 10 00:45:48 Started mapping on | Dec 10 00:45:48 Finished on | Dec 10 00:46:23 Mapping speed, Million of reads per hour | 873.81 Number of input reads | 8495368 Average input read length | 300 UNIQUE READS: Uniquely mapped reads number | 7827228 Uniquely mapped reads % | 92.14% Average mapped length | 300.24 Number of splices: Total | 8814618 Number of splices: Annotated (sjdb) | 8387417 Number of splices: GT/AG | 8703611 Number of splices: GC/AG | 100130 Number of splices: AT/AC | 4912 Number of splices: Non-canonical | 5965 Mismatch rate per base, % | 0.06% Deletion rate per base | 0.00% Deletion average length | 1.38 Insertion rate per base | 0.00% Insertion average length | 1.18 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 142488 % of reads mapped to multiple loci | 1.68% Number of reads mapped to too many loci | 34219 % of reads mapped to too many loci | 0.40% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 2.67% % of reads unmapped: other | 3.11% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 529219 529219 529219 N_multimapping 142488 142488 142488 N_noFeature 415507 7614622 471460 N_ambiguous 194921 1698 39204 UnstrandedReadsAssigned:7216800 PositiveStrandReadsAssigned:210908 NegativeStrandReadsAssigned:7316564 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=151 echo kmer=147 SRR6031180 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: SRR6031180-trimmed-pair1.fastq SRR6031180-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 8,495,368 reads, 7,397,453 reads pseudoaligned [quant] estimated average fragment length: 448.878 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,175 rounds 52973 SRR6031180.ke.tsv 35125 SRR6031180.se.tsv 88098 total ==> SRR6031180.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 489.469 0 0 PNS24247 1044 596.122 38.6442 12.4543 PNS24249 1928 1480.12 11.545 1.49854 PNS24246 1044 596.122 38.6442 12.4543 PNS24248 1044 596.122 38.6442 12.4543 PNS24244 1471 1023.12 32.5222 6.10691 PNS24243 293 59.8934 0 0 KQK14069 1603 1155.12 2139.37 355.817 KQK14071 474 123.757 11.8739 18.4328 ==> SRR6031180.se.tsv <== BRADI_1g14170v3 2484 BRADI_1g53295v3 26 BRADI_1g59795v3 239 BRADI_1g07683v3 0 BRADI_1g00485v3 24 BRADI_1g20270v3 575 BRADI_1g74790v3 64 BRADI_1g09890v3 0 BRADI_1g77505v3 98 BRADI_1g48960v3 0 SRR6031180 completed mapping pipeline successfully