Starting /dee2/code/volunteer_pipeline.sh SRR21588386 current disk space = 1548807921664 free memory = 1599916320 SRR21588386 SRAfilesize 66ce8ea3738a48067e631273c3311c8d SRR21588386.sra SRR21588386.sra file validated SRR21588386 is paired end SRR21588386 is conventional basespace SRR21588386 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR21588386_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 43 >>END_MODULE >>Per base sequence quality fail #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 30.894 34.0 33.0 34.0 27.0 34.0 2 32.71225 34.0 33.0 34.0 28.0 34.0 3 32.932 34.0 33.0 34.0 32.0 34.0 4 32.9825 34.0 33.0 34.0 32.0 34.0 5 33.17 34.0 33.0 34.0 32.0 34.0 6 36.56975 38.0 37.0 38.0 34.0 38.0 7 36.70125 38.0 38.0 38.0 34.0 38.0 8 37.047 38.0 38.0 38.0 35.0 38.0 9 37.362 38.0 38.0 38.0 36.0 38.0 10-14 37.40735 38.0 38.0 38.0 37.2 38.0 15-19 37.47465 38.0 38.0 38.0 37.6 38.0 20-24 37.3762 38.0 38.0 38.0 37.0 38.0 25-29 37.243500000000004 38.0 38.0 38.0 37.0 38.0 30-34 37.19689999999999 38.0 38.0 38.0 37.0 38.0 35-39 37.051 38.0 38.0 38.0 36.6 38.0 40-44 35.15835 37.4 34.8 38.0 30.2 38.0 45-49 36.816700000000004 38.0 38.0 38.0 35.6 38.0 50-54 36.891149999999996 38.0 38.0 38.0 36.0 38.0 55-59 36.80105 38.0 38.0 38.0 35.4 38.0 60-64 36.61964999999999 38.0 38.0 38.0 35.0 38.0 65-69 35.987399999999994 38.0 37.6 38.0 32.2 38.0 70-74 32.3654 33.4 30.4 38.0 26.0 38.0 75-79 18.0845 4.4 2.0 38.0 2.0 38.0 80-84 18.167949999999998 2.0 2.0 38.0 2.0 38.0 85-89 17.98935 2.0 2.0 38.0 2.0 38.0 90-94 17.79535 2.0 2.0 38.0 2.0 38.0 95-99 17.502550000000003 2.0 2.0 38.0 2.0 38.0 100-104 17.070349999999998 2.0 2.0 38.0 2.0 38.0 105-109 16.8231 2.0 2.0 38.0 2.0 38.0 110-114 16.675850000000004 2.0 2.0 38.0 2.0 38.0 115-119 16.494999999999997 2.0 2.0 38.0 2.0 38.0 120-124 16.44325 2.0 2.0 38.0 2.0 38.0 125-129 16.3214 2.0 2.0 38.0 2.0 38.0 130-134 16.162200000000002 2.0 2.0 38.0 2.0 38.0 135-139 16.016600000000004 2.0 2.0 38.0 2.0 38.0 140-144 15.79995 2.0 2.0 38.0 2.0 38.0 145-149 15.4108 2.0 2.0 38.0 2.0 38.0 150-151 13.252875 2.0 2.0 33.0 2.0 38.0 >>END_MODULE >>Per sequence quality scores fail #Quality Count 6 1.0 7 8.0 8 8.0 9 0.0 10 0.0 11 0.0 12 3.0 13 3.0 14 10.0 15 30.0 16 50.0 17 92.0 18 651.0 19 1248.0 20 71.0 21 59.0 22 28.0 23 22.0 24 23.0 25 18.0 26 21.0 27 13.0 28 25.0 29 26.0 30 21.0 31 19.0 32 32.0 33 30.0 34 57.0 35 87.0 36 282.0 37 1062.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 76.8210127267804 5.578120769022475 5.117790414297319 12.48307608989981 2 10.05 65.3 13.225000000000001 11.425 3 9.65 9.775 68.475 12.1 4 11.450000000000001 12.25 8.575000000000001 67.72500000000001 5 68.425 13.600000000000001 9.25 8.725 6 66.475 14.374999999999998 10.775 8.375 7 7.5249999999999995 65.95 16.650000000000002 9.875 8 9.3 67.07499999999999 11.125 12.5 9 66.725 8.425 12.825000000000001 12.025 10-14 21.15 34.23 10.43 34.19 15-19 21.59 22.15 22.36 33.900000000000006 20-24 20.893133970095516 33.940091013652044 22.473371005650847 22.69340401060159 25-29 21.636372740473686 22.20219318011116 22.242251264333284 33.91918281508187 30-34 21.55751679871628 22.09908735332464 21.96870925684485 34.37468659111423 35-39 21.64182849114356 10.80335189924231 22.09343168247278 45.46138792714135 40-44 9.777264974415571 22.052774154710544 33.81157820808669 34.35838266278719 45-49 33.09746060423567 22.036535180166616 33.73481882966978 11.131185385927933 50-54 21.74524275744339 10.292714766280062 22.151930511623235 45.81011196465331 55-59 21.56016264243763 10.546659304251795 45.16841524019878 22.72476281311179 60-64 21.596385542168676 22.299196787148595 33.90562248995984 22.19879518072289 65-69 10.220370463330154 68.45539882536016 10.45630239445811 10.867928316851563 70-74 10.311967098003812 67.89046042732471 10.472464640385194 11.325107834286287 75-79 13.153017781116954 55.17655897821187 13.774104683195592 17.89631855747558 80-84 16.977443609022554 43.26817042606516 19.57894736842105 20.175438596491226 85-89 22.3760092272203 33.90000501479364 20.5105059926784 23.213479765307657 90-94 19.694082246740223 26.860581745235706 28.09929789368104 25.346038114343028 95-99 20.5706835163733 29.12090667469034 27.65157213780653 22.656837671129836 100-104 16.640793229505736 47.68891782262507 17.87771045119936 17.79257849666984 105-109 13.666215470998145 56.610016543841176 13.480723918383717 16.24304406677696 110-114 14.91765414741916 52.35991162884114 15.133560956015263 17.58887326772444 115-119 16.516290726817044 46.421052631578945 17.11779448621554 19.94486215538847 120-124 17.78 43.955 17.474999999999998 20.79 125-129 19.24 41.21 18.385 21.165 130-134 18.745 41.02 17.424999999999997 22.81 135-139 18.385 40.125 18.785 22.705000000000002 140-144 19.29 39.255 18.515 22.939999999999998 145-149 19.35 39.1 18.855 22.695 150-151 19.1 40.875 17.75 22.275 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 0.0 1 0.0 2 0.5 3 1.5 4 1.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10 0.0 11 0.0 12 0.5 13 0.5 14 0.0 15 1.0 16 1.5 17 1.5 18 2.0 19 1.0 20 0.0 21 0.5 22 1.0 23 0.5 24 0.5 25 1.0 26 3.5 27 3.5 28 1.5 29 2.5 30 5.0 31 7.0 32 10.0 33 13.5 34 20.0 35 22.5 36 34.0 37 62.5 38 96.0 39 137.0 40 204.0 41 279.0 42 311.5 43 323.5 44 333.0 45 316.0 46 276.0 47 229.5 48 177.5 49 139.5 50 122.5 51 107.5 52 82.0 53 63.0 54 60.5 55 55.5 56 41.5 57 35.0 58 39.5 59 37.5 60 35.0 61 27.0 62 21.0 63 25.0 64 27.5 65 27.0 66 20.0 67 18.5 68 22.5 69 20.0 70 15.5 71 15.0 72 15.0 73 10.0 74 8.5 75 7.5 76 4.5 77 4.5 78 3.5 79 2.0 80 2.0 81 1.5 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 warn #Base N-Count 1 7.675 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 0.015 25-29 0.145 30-34 0.29 35-39 0.35500000000000004 40-44 0.33 45-49 0.37 50-54 0.415 55-59 0.395 60-64 0.4 65-69 0.395 70-74 0.31 75-79 0.17500000000000002 80-84 0.25 85-89 0.295 90-94 0.3 95-99 0.295 100-104 0.155 105-109 0.265 110-114 0.42 115-119 0.25 120-124 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 fail #Total Deduplicated Percentage 43.125 #Duplication Level Percentage of deduplicated Percentage of total 1 97.04347826086956 41.85 2 1.855072463768116 1.6 3 0.5797101449275363 0.75 4 0.2318840579710145 0.4 5 0.057971014492753624 0.125 6 0.0 0.0 7 0.0 0.0 8 0.0 0.0 9 0.0 0.0 >10 0.11594202898550725 0.6 >50 0.0 0.0 >100 0.057971014492753624 4.025 >500 0.0 0.0 >1k 0.057971014492753624 50.64999999999999 >5k 0.0 0.0 >10k+ 0.0 0.0 >>END_MODULE >>Overrepresented sequences fail #Sequence Count Percentage Possible Source GATCGGAAGAGCACACGTCTGAACTCCAGTCACGTCCGCATCTCGTATGC 2026 50.64999999999999 TruSeq Adapter, Index 18 (100% over 50bp) NATCGGAAGAGCACACGTCTGAACTCCAGTCACGTCCGCATCTCGTATGC 161 4.025 TruSeq Adapter, Index 18 (98% over 50bp) GATCGGAAGAGCACACGTCTGAACTCCAGTCACGTCCGCAGCTCGTATGC 13 0.325 TruSeq Adapter, Index 18 (98% over 50bp) GATCGGAAGAGCACACGTCTGAACTCCAGTCACGTCCGCATATCGTATGC 11 0.27499999999999997 TruSeq Adapter, Index 18 (98% over 50bp) TATCGGAAGAGCACACGTCTGAACTCCAGTCACGTCCGCATCTCGTATGC 5 0.125 TruSeq Adapter, Index 18 (98% over 50bp) >>END_MODULE >>Adapter Content warn #Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence SOLID Small RNA Adapter 1 0.025 0.0 0.0 0.0 0.0 2 0.025 0.0 0.0 0.0 0.0 3 0.025 0.0 0.0 0.0 0.0 4 0.025 0.0 0.0 0.0 0.0 5 0.025 0.0 0.0 0.0 0.0 6 0.025 0.0 0.0 0.0 0.0 7 0.025 0.0 0.0 0.0 0.0 8 0.025 0.0 0.0 0.0 0.0 9 0.025 0.0 0.0 0.0 0.0 10-11 0.025 0.0 0.0 0.0 0.0 12-13 0.025 0.0 0.0 0.0 0.0 14-15 0.025 0.0 0.0 0.0 0.0 16-17 0.025 0.0 0.0 0.0 0.0 18-19 0.025 0.0 0.0 0.0 0.0 20-21 0.025 0.0 0.0 0.0 0.0 22-23 0.025 0.0 0.0 0.0 0.0 24-25 0.025 0.0 0.0 0.0 0.0 26-27 0.025 0.0 0.0 0.0 0.0 28-29 0.025 0.0 0.0 0.0 0.0 30-31 0.025 0.0 0.0 0.0 0.0 32-33 0.025 0.0 0.0 0.0 0.0 34-35 0.025 0.0 0.0 0.0 0.0 36-37 0.025 0.0 0.0 0.0 0.0 38-39 0.025 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 0.025 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 0.07500000000000001 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 0.1 0.0 0.0 0.0 0.0 74-75 0.1125 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 0.21250000000000002 0.0 0.0 0.0 0.0 82-83 0.225 0.0 0.0 0.0 0.0 84-85 0.25 0.0 0.0 0.0 0.0 86-87 0.2875 0.0 0.0 0.0 0.0 88-89 0.44999999999999996 0.0 0.0 0.0 0.0 90-91 0.5125 0.0 0.0 0.0 0.0 92-93 0.6125 0.0 0.0 0.0 0.0 94-95 0.8 0.0 0.0 0.0 0.0 96-97 0.975 0.0 0.0 0.0 0.0 98-99 1.3 0.0 0.0 0.0 0.0 100-101 1.5125000000000002 0.0 0.0 0.0 0.0 102-103 1.6875 0.0 0.0 0.0 0.0 104-105 1.9 0.0 0.0 0.0 0.0 106-107 2.2125 0.0 0.0 0.0 0.0 108-109 2.5125 0.0 0.0 0.0 0.0 110-111 2.8125 0.0 0.0 0.0 0.0 112-113 3.075 0.0 0.0 0.0 0.0 114-115 3.3875 0.0 0.0 0.0 0.0 116-117 3.8875 0.0 0.0 0.0 0.0 118-119 4.1875 0.0 0.0 0.0 0.0 120-121 4.475 0.0 0.0 0.0 0.0 122-123 4.7875 0.0 0.0 0.0 0.0 124-125 5.112500000000001 0.0 0.0 0.0 0.0 126-127 5.4375 0.0 0.0 0.0 0.0 128-129 5.862500000000001 0.0 0.0 0.0 0.0 130-131 6.325 0.0 0.0 0.0 0.0 132-133 6.612500000000001 0.0 0.0 0.0 0.0 134-135 6.9 0.0 0.0 0.0 0.0 136-137 7.275 0.0 0.0 0.0 0.0 138-139 7.65 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GAGGCCC 10 0.006843168 144.91249 4 GATCGGA 285 0.0 128.16101 1 GAAGAGC 280 0.0 119.03526 6 TCGGAAG 280 0.0 119.03526 3 ATCGGAA 280 0.0 119.03526 2 GGAAGAG 280 0.0 119.03526 5 AAGAGCA 290 0.0 117.429085 7 GAGCACA 290 0.0 117.429085 9 AGAGCAC 290 0.0 117.429085 8 CGGAAGA 285 0.0 116.94692 4 CTGCTTG 245 0.0 27.799543 55-59 TGCTTGA 250 0.0 27.243551 55-59 CGTCTTC 250 0.0 27.243551 50-54 CTTCTGC 250 0.0 27.243551 50-54 TCTGCTT 255 0.0 26.709362 55-59 GCTTGAA 255 0.0 26.709362 55-59 TTCTGCT 250 0.0 26.6639 55-59 GTCTTCT 250 0.0 26.6639 50-54 GCCGTCT 250 0.0 26.6639 45-49 GTCCGCA 265 0.0 26.248302 30-34 >>END_MODULE SRR21588386 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR21588386_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 fail #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 32.599 33.0 33.0 34.0 32.0 34.0 2 32.4865 33.0 33.0 34.0 32.0 34.0 3 32.59575 33.0 33.0 34.0 32.0 34.0 4 32.4425 34.0 33.0 34.0 32.0 34.0 5 32.514 34.0 33.0 34.0 32.0 34.0 6 36.4795 38.0 38.0 38.0 34.0 38.0 7 36.0665 38.0 38.0 38.0 33.0 38.0 8 36.23275 38.0 38.0 38.0 33.0 38.0 9 36.43275 38.0 38.0 38.0 35.0 38.0 10-14 36.37985 38.0 38.0 38.0 34.6 38.0 15-19 36.40585 38.0 38.0 38.0 35.0 38.0 20-24 36.4699 38.0 38.0 38.0 35.6 38.0 25-29 36.14185 38.0 38.0 38.0 34.2 38.0 30-34 35.62955 38.0 37.0 38.0 30.0 38.0 35-39 34.8206 38.0 35.8 38.0 26.8 38.0 40-44 35.0643 38.0 36.4 38.0 27.4 38.0 45-49 32.7249 37.2 31.2 38.0 19.0 38.0 50-54 32.5673 37.2 30.6 38.0 17.4 38.0 55-59 34.322849999999995 38.0 35.2 38.0 22.2 38.0 60-64 35.6 38.0 37.8 38.0 31.6 38.0 65-69 29.351300000000002 32.4 23.4 38.0 17.8 38.0 70-74 17.494899999999998 2.0 2.0 38.0 2.0 38.0 75-79 17.2801 2.0 2.0 38.0 2.0 38.0 80-84 17.03365 2.0 2.0 38.0 2.0 38.0 85-89 16.8367 2.0 2.0 38.0 2.0 38.0 90-94 16.729300000000002 2.0 2.0 38.0 2.0 38.0 95-99 16.6656 2.0 2.0 38.0 2.0 38.0 100-104 16.4797 2.0 2.0 38.0 2.0 38.0 105-109 16.3782 2.0 2.0 38.0 2.0 38.0 110-114 16.23165 2.0 2.0 38.0 2.0 38.0 115-119 16.13635 2.0 2.0 38.0 2.0 38.0 120-124 15.900900000000002 2.0 2.0 38.0 2.0 38.0 125-129 15.644349999999998 2.0 2.0 38.0 2.0 38.0 130-134 15.387799999999999 2.0 2.0 38.0 2.0 38.0 135-139 15.09375 2.0 2.0 38.0 2.0 38.0 140-144 14.668800000000001 2.0 2.0 37.6 2.0 38.0 145-149 14.18485 2.0 2.0 36.4 2.0 38.0 150-151 11.714125 2.0 2.0 28.0 2.0 37.0 >>END_MODULE >>Per sequence quality scores fail #Quality Count 2 45.0 3 9.0 4 1.0 5 9.0 6 3.0 7 8.0 8 7.0 9 6.0 10 17.0 11 15.0 12 23.0 13 49.0 14 90.0 15 164.0 16 467.0 17 1270.0 18 109.0 19 36.0 20 16.0 21 9.0 22 10.0 23 14.0 24 16.0 25 24.0 26 8.0 27 8.0 28 15.0 29 12.0 30 16.0 31 35.0 32 33.0 33 40.0 34 71.0 35 110.0 36 263.0 37 972.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 76.97500000000001 7.75 4.925 10.35 2 11.419984973703983 67.41798146756824 10.768845479589281 10.393188079138492 3 11.133350012509382 10.13259944958719 67.42556917688266 11.308481361020766 4 12.828207051762941 12.903225806451612 7.576894223555889 66.69167291822956 5 69.11911911911912 14.13913913913914 8.158158158158157 8.583583583583582 6 67.675 14.124999999999998 8.425 9.775 7 9.875 65.10000000000001 14.424999999999999 10.6 8 10.4 66.325 9.55 13.725000000000001 9 68.125 10.424999999999999 9.625 11.825 10-14 34.28 22.439999999999998 21.165 22.115000000000002 15-19 34.4 10.37 33.305 21.925 20-24 45.765 33.525 10.280000000000001 10.43 25-29 34.415 44.985 10.11 10.489999999999998 30-34 33.875 22.485 32.910000000000004 10.73 35-39 11.67 22.245 32.79 33.295 40-44 57.49999999999999 10.27 21.36 10.870000000000001 45-49 23.669999999999998 10.42 21.245 44.665 50-54 23.45 21.865000000000002 32.18 22.505 55-59 11.31 44.43 33.425 10.835 60-64 11.225 67.72500000000001 10.334999999999999 10.715 65-69 11.555 66.865 10.495000000000001 11.085 70-74 16.736673667366738 56.370637063706376 13.236323632363236 13.656365636563656 75-79 19.395 50.654999999999994 14.530000000000001 15.42 80-84 22.395 44.18 16.34 17.085 85-89 26.490000000000002 39.58 16.97 16.96 90-94 27.41 38.34 17.32 16.93 95-99 25.21 37.665 18.66 18.465 100-104 23.125 41.120000000000005 17.655 18.099999999999998 105-109 21.335 44.04 16.915 17.71 110-114 21.7 43.35 16.615 18.335 115-119 22.97 41.005 17.59 18.435000000000002 120-124 23.56 39.79 17.775 18.875 125-129 24.044999999999998 39.15 17.59 19.215 130-134 24.605 38.279999999999994 17.21 19.905 135-139 24.23984796959392 38.64772954590918 17.70354070814163 19.408881776355273 140-144 25.615 36.91 17.57 19.905 145-149 25.543940379132696 36.6228179862952 17.966288200870302 19.866953433701795 150-151 23.9375 38.550000000000004 17.95 19.5625 >>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 0.5 19 0.5 20 0.5 21 0.5 22 0.0 23 0.5 24 1.0 25 0.5 26 0.5 27 0.5 28 2.5 29 3.5 30 4.0 31 12.5 32 35.0 33 59.0 34 97.5 35 151.0 36 179.0 37 198.0 38 248.0 39 260.0 40 255.0 41 249.5 42 222.5 43 214.5 44 182.5 45 160.5 46 144.0 47 124.0 48 108.0 49 86.0 50 80.0 51 68.0 52 64.0 53 69.0 54 58.5 55 52.0 56 53.0 57 49.0 58 49.0 59 44.5 60 34.0 61 29.0 62 33.5 63 37.5 64 33.5 65 35.5 66 30.0 67 20.5 68 21.5 69 24.0 70 20.0 71 13.5 72 14.0 73 15.0 74 12.0 75 7.5 76 6.5 77 7.0 78 6.0 79 5.5 80 2.5 81 1.0 82 1.5 83 0.5 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 0.17500000000000002 3 0.075 4 0.025 5 0.1 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 0.0 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 0.01 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 0.02 140-144 0.0 145-149 0.034999999999999996 150-151 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels fail #Total Deduplicated Percentage 45.550000000000004 #Duplication Level Percentage of deduplicated Percentage of total 1 97.03622392974754 44.2 2 1.920965971459934 1.7500000000000002 3 0.5488474204171241 0.75 4 0.10976948408342481 0.2 5 0.0 0.0 6 0.10976948408342481 0.3 7 0.054884742041712405 0.17500000000000002 8 0.0 0.0 9 0.0 0.0 >10 0.1646542261251372 1.25 >50 0.0 0.0 >100 0.0 0.0 >500 0.0 0.0 >1k 0.054884742041712405 51.37500000000001 >5k 0.0 0.0 >10k+ 0.0 0.0 >>END_MODULE >>Overrepresented sequences fail #Sequence Count Percentage Possible Source GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCG 2055 51.37500000000001 Illumina Single End PCR Primer 1 (100% over 50bp) GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGGCGCCG 21 0.525 Illumina Single End PCR Primer 1 (98% over 50bp) GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGGCG 15 0.375 Illumina Single End PCR Primer 1 (98% over 50bp) GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTGGCCG 14 0.35000000000000003 Illumina Single End PCR Primer 1 (98% over 50bp) GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTTGCCG 7 0.17500000000000002 Illumina Single End PCR Primer 1 (98% over 50bp) GCTGAAAGCCCTAACTTAATGGACGGGAGGTATCCCAATAGGAGGTTTCC 6 0.15 No Hit GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGGGGTCGCCG 6 0.15 Illumina Single End PCR Primer 1 (98% over 50bp) >>END_MODULE >>Adapter Content warn #Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence SOLID Small RNA Adapter 1 0.025 0.0 0.0 0.0 0.0 2 0.025 0.0 0.0 0.0 0.0 3 0.025 0.0 0.0 0.0 0.0 4 0.025 0.0 0.0 0.0 0.0 5 0.025 0.0 0.0 0.0 0.0 6 0.025 0.0 0.0 0.0 0.0 7 0.025 0.0 0.0 0.0 0.0 8 0.025 0.0 0.0 0.0 0.0 9 0.025 0.0 0.0 0.0 0.0 10-11 0.025 0.0 0.0 0.0 0.0 12-13 0.05 0.0 0.0 0.0 0.0 14-15 0.075 0.0 0.0 0.0 0.0 16-17 0.075 0.0 0.0 0.0 0.0 18-19 0.075 0.0 0.0 0.0 0.0 20-21 0.075 0.0 0.0 0.0 0.0 22-23 0.075 0.0 0.0 0.0 0.0 24-25 0.075 0.0 0.0 0.0 0.0 26-27 0.075 0.0 0.0 0.0 0.0 28-29 0.075 0.0 0.0 0.0 0.0 30-31 0.075 0.0 0.0 0.0 0.0 32-33 0.075 0.0 0.0 0.0 0.0 34-35 0.075 0.0 0.0 0.0 0.0 36-37 0.075 0.0 0.0 0.0 0.0 38-39 0.075 0.0 0.0 0.0 0.0 40-41 0.075 0.0 0.0 0.0 0.0 42-43 0.075 0.0 0.0 0.0 0.0 44-45 0.075 0.0 0.0 0.0 0.0 46-47 0.075 0.0 0.0 0.0 0.0 48-49 0.075 0.0 0.0 0.0 0.0 50-51 0.075 0.0 0.0 0.0 0.0 52-53 0.075 0.0 0.0 0.0 0.0 54-55 0.075 0.0 0.0 0.0 0.0 56-57 0.075 0.0 0.0 0.0 0.0 58-59 0.075 0.0 0.0 0.0 0.0 60-61 0.075 0.0 0.0 0.0 0.0 62-63 0.075 0.0 0.0 0.0 0.0 64-65 0.075 0.0 0.0 0.0 0.0 66-67 0.125 0.0 0.0 0.0 0.0 68-69 0.15 0.0 0.0 0.0 0.0 70-71 0.15 0.0 0.0 0.0 0.0 72-73 0.15 0.0 0.0 0.0 0.0 74-75 0.16249999999999998 0.0 0.0 0.0 0.0 76-77 0.175 0.0 0.0 0.0 0.0 78-79 0.2 0.0 0.0 0.0 0.0 80-81 0.2625 0.0 0.0 0.0 0.0 82-83 0.275 0.0 0.0 0.0 0.0 84-85 0.30000000000000004 0.0 0.0 0.0 0.0 86-87 0.3375 0.0 0.0 0.0 0.0 88-89 0.475 0.0 0.0 0.0 0.0 90-91 0.5625 0.0 0.0 0.0 0.0 92-93 0.6625 0.0 0.0 0.0 0.0 94-95 0.825 0.0 0.0 0.0 0.0 96-97 0.9875 0.0 0.0 0.0 0.0 98-99 1.2625000000000002 0.0 0.0 0.0 0.0 100-101 1.4874999999999998 0.0 0.0 0.0 0.0 102-103 1.6625 0.0 0.0 0.0 0.0 104-105 1.95 0.0 0.0 0.0 0.0 106-107 2.2249999999999996 0.0 0.0 0.0 0.0 108-109 2.5125 0.0 0.0 0.0 0.0 110-111 2.825 0.0 0.0 0.0 0.0 112-113 3.1125 0.0 0.0 0.0 0.0 114-115 3.3875 0.0 0.0 0.0 0.0 116-117 3.85 0.0 0.0 0.0 0.0 118-119 4.175 0.0 0.0 0.0 0.0 120-121 4.45 0.0 0.0 0.0 0.0 122-123 4.75 0.0 0.0 0.0 0.0 124-125 5.05 0.0 0.0 0.0 0.0 126-127 5.3625 0.0 0.0 0.0 0.0 128-129 5.775 0.0 0.0 0.0 0.0 130-131 6.137499999999999 0.0 0.0 0.0 0.0 132-133 6.425 0.0 0.0 0.0 0.0 134-135 6.7375 0.0 0.0 0.0 0.0 136-137 7.1625 0.0 0.0 0.0 0.0 138-139 7.5125 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content fail #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GAGCGTC 270 0.0 123.51851 9 TCGGAAG 270 0.0 123.51851 3 CGGAAGA 270 0.0 123.51851 4 GGAAGAG 270 0.0 123.51851 5 AGAGCGT 275 0.0 121.27272 8 ATCGGAA 275 0.0 121.27272 2 GATCGGA 285 0.0 119.56141 1 AAGAGCG 280 0.0 119.107155 7 GAAGAGC 285 0.0 117.017555 6 CATTAAA 235 0.0 27.765959 50-54 TCATTAA 235 0.0 27.765959 50-54 GGTCGCC 230 0.0 27.739132 40-44 TGGTCGC 225 0.0 27.711113 40-44 TATCATT 225 0.0 27.711113 50-54 GGTGGTC 225 0.0 27.711113 40-44 GTGGTCG 225 0.0 27.711113 40-44 CGCCGTA 225 0.0 27.711113 45-49 TCGCCGT 215 0.0 27.651165 45-49 ATCTCGG 245 0.0 27.22449 35-39 GATCTCG 245 0.0 27.22449 30-34 >>END_MODULE Read 1242251 spots for SRR21588386.sra Written 1242251 spots for SRR21588386.sra Read 1242251 spots for SRR21588386.sra Written 1242251 spots for SRR21588386.sra Read 1242251 spots for SRR21588386.sra Written 1242251 spots for SRR21588386.sra Read 1242251 spots for SRR21588386.sra Written 1242251 spots for SRR21588386.sra Read 1242251 spots for SRR21588386.sra Written 1242251 spots for SRR21588386.sra Read 1242251 spots for SRR21588386.sra Written 1242251 spots for SRR21588386.sra Read 1242251 spots for SRR21588386.sra Written 1242251 spots for SRR21588386.sra Read 1242251 spots for SRR21588386.sra Written 1242251 spots for SRR21588386.sra Read 1242251 spots for SRR21588386.sra Written 1242251 spots for SRR21588386.sra Read 1242251 spots for SRR21588386.sra Written 1242251 spots for SRR21588386.sra Read 1242251 spots for SRR21588386.sra Written 1242251 spots for SRR21588386.sra Read 1242251 spots for SRR21588386.sra Written 1242251 spots for SRR21588386.sra Read 1242251 spots for SRR21588386.sra Written 1242251 spots for SRR21588386.sra Read 1242262 spots for SRR21588386.sra Written 1242262 spots for SRR21588386.sra Read 1242251 spots for SRR21588386.sra Written 1242251 spots for SRR21588386.sra Read 1242251 spots for SRR21588386.sra Written 1242251 spots for SRR21588386.sra Read 1242251 spots for SRR21588386.sra Written 1242251 spots for SRR21588386.sra Read 1242251 spots for SRR21588386.sra Written 1242251 spots for SRR21588386.sra Read 1242251 spots for SRR21588386.sra Written 1242251 spots for SRR21588386.sra Read 1242251 spots for SRR21588386.sra Written 1242251 spots for SRR21588386.sra SRR ids: ['SRR21588386.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_8kzhdl7m SRR21588386.sra spots: 24845031 blocks: [[1, 1242251], [1242252, 2484502], [2484503, 3726753], [3726754, 4969004], [4969005, 6211255], [6211256, 7453506], [7453507, 8695757], [8695758, 9938008], [9938009, 11180259], [11180260, 12422510], [12422511, 13664761], [13664762, 14907012], [14907013, 16149263], [16149264, 17391514], [17391515, 18633765], [18633766, 19876016], [19876017, 21118267], [21118268, 22360518], [22360519, 23602769], [23602770, 24845031]] SRR21588386 file size 8421728 SRR21588386 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 SRR21588386 SRR21588386_1.fastq SRR21588386_2.fastq Input file: SRR21588386_1.fastq Paired file: SRR21588386_2.fastq trimmed: SRR21588386-trimmed-pair1.fastq, SRR21588386-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 21:56:41 2024 >> started Fri Dec 6 21:57:28 2024 >> done (46.400s) 24845031 read pairs processed; of these: 68017 ( 0.27%) short read pairs filtered out after trimming by size control 14383000 (57.89%) empty read pairs filtered out after trimming by size control 10394014 (41.84%) read pairs available; of these: 6411262 (61.68%) trimmed read pairs available after processing 3982752 (38.32%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 31 0.00% 19 23 0.00% 20 35 0.00% 21 54 0.00% 22 35 0.00% 23 32 0.00% 24 30 0.00% 25 27 0.00% 26 42 0.00% 27 62 0.00% 28 56 0.00% 29 52 0.00% 30 35 0.00% 31 51 0.00% 32 47 0.00% 33 49 0.00% 34 53 0.00% 35 89 0.00% 36 84 0.00% 37 84 0.00% 38 105 0.00% 39 139 0.00% 40 381 0.00% 41 154 0.00% 42 181 0.00% 43 333 0.00% 44 686 0.01% 45 1189 0.01% 46 1589 0.02% 47 1528 0.01% 48 1403 0.01% 49 1395 0.01% 50 1470 0.01% 51 1527 0.01% 52 1741 0.02% 53 1718 0.02% 54 2538 0.02% 55 1810 0.02% 56 1916 0.02% 57 1923 0.02% 58 1972 0.02% 59 1898 0.02% 60 1868 0.02% 61 1897 0.02% 62 1945 0.02% 63 2105 0.02% 64 2520 0.02% 65 3416 0.03% 66 4789 0.05% 67 7737 0.07% 68 17185 0.17% 69 39788 0.38% 70 37607 0.36% 71 19850 0.19% 72 13304 0.13% 73 10044 0.10% 74 8544 0.08% 75 7897 0.08% 76 7466 0.07% 77 7687 0.07% 78 7728 0.07% 79 7981 0.08% 80 8643 0.08% 81 9796 0.09% 82 10635 0.10% 83 11627 0.11% 84 13668 0.13% 85 14946 0.14% 86 15987 0.15% 87 16730 0.16% 88 17707 0.17% 89 19262 0.19% 90 19978 0.19% 91 21190 0.20% 92 22717 0.22% 93 24115 0.23% 94 24976 0.24% 95 25929 0.25% 96 27147 0.26% 97 27978 0.27% 98 28692 0.28% 99 30102 0.29% 100 31203 0.30% 101 32954 0.32% 102 35319 0.34% 103 37074 0.36% 104 39016 0.38% 105 38835 0.37% 106 38868 0.37% 107 39530 0.38% 108 40536 0.39% 109 40793 0.39% 110 41719 0.40% 111 43455 0.42% 112 45558 0.44% 113 47171 0.45% 114 48574 0.47% 115 49702 0.48% 116 50456 0.49% 117 49000 0.47% 118 49332 0.47% 119 50229 0.48% 120 51050 0.49% 121 52180 0.50% 122 53713 0.52% 123 56354 0.54% 124 57959 0.56% 125 58284 0.56% 126 58968 0.57% 127 58634 0.56% 128 58053 0.56% 129 59433 0.57% 130 59438 0.57% 131 60823 0.59% 132 63659 0.61% 133 64975 0.63% 134 65406 0.63% 135 67996 0.65% 136 69743 0.67% 137 69967 0.67% 138 72068 0.69% 139 72961 0.70% 140 74268 0.71% 141 76955 0.74% 142 82763 0.80% 143 87814 0.84% 144 95894 0.92% 145 106278 1.02% 146 124478 1.20% 147 155160 1.49% 148 219457 2.11% 149 426445 4.10% 150 2249012 21.64% 151 3982752 38.32% 10394014 reads passed initial QC criterion=sequence-density sequence-density=0.57 sequence-density-rank=1 fanout-score=3.42 fanout-score-rank=13 prefix-density=0.61 prefix-fanout=3.2 sequence=AGGCAAGGAACCCACTTGGAGCGGATCAGGTACTCGATCTGCTTCAGGAGAGACTCCACGGAGAGAGGGGGCAGGTACGAGAGGGTCTCGAACTTCTT criterion=fanout-score sequence-density=0.01 sequence-density-rank=33 fanout-score=20.72 fanout-score-rank=1 prefix-density=0.05 prefix-fanout=5.1 sequence=TTTTTTTTTCGCATATAACCACATTCAAATTGACCTCCCTCAGGAAGCTAAGAAATACTATCTCGGCAATAGGATTGTAGCCCAGGATGAGTCCCTCAGCGTGACGCAGTAAACTAGTAGCATCCCGATCTTTTCCCTATCTAATTCACCTCCTATTAGGAGCCGATCGTGCTTGTGCGCCGGCAAAACTTTTCAGGCGAATTTCCGCCCCTGGCGCTCTAGGCTACTACGTGCGCGATATGACAAGTTAACAAGACGGCGCAGGTTGATGCTTCCAATAAACATGATCTTTCTGCTCCGCTGAGAAGTACACCTTTTTGCTAGCATCTCGCACGGCAAGAGCGATTGCCGAGCTTAGAGCGTATCTTCCGGGATCGGGCAAAGGGGCAACTCGAGCTAATCTCCCCAGCGGCTAGCATGTGTAGTGCGCCATATCATATCCAAGATAGTGTAGGACTCGTCGCATTGGATGACGATGCCTAGTACTGTGCGCCAATTAGGTCGTCATTGC criterion=sequence-density sequence-density=0.66 sequence-density-rank=1 fanout-score=3.86 fanout-score-rank=13 prefix-density=0.73 prefix-fanout=3.5 sequence=GAGTTCAGCAAGGTCGGCTT criterion=fanout-score sequence-density=0.01 sequence-density-rank=31 fanout-score=33.83 fanout-score-rank=1 prefix-density=0.06 prefix-fanout=5.0 sequence=GGAGATTGTCTCGTACGGTTAAGAGCCTCCGCCCGTCTCTGGGACTATGGACGGGCACGCTCATATCAGGCTATATTTGGTCCGGGTTATTATCGTCGCGGTTACCGTAATACTTCAGATCAGTTAAGTAGGGCCATATGCCTCGGGAATAAGCTGACGGTGACAAGGTTTCCCCCTAATCGAGACGCTGCAATAACACAGGGGCATACAGTAACCAGGCAAGAGTTCAATCGCTTAGTTTCGTGGCGGGATTTGAGGAAAACTGCGACTGTTCTTTAACCAAACATCCGTGCGATTCGTGCCACTCGTAGACGGCATCTCACAGTCACTGAAGGCTATTAAAGAGTTAGCACCCACCATTGGATGAAGCCCAGGATAAGTGACCCCCCCGGACCTTGGAGTTTCATGCTAATCAAAGAAGAGCTAATCCGACGTAAAGTTGCGGCGTTGATTACGCAGGATTGCGAC SRR21588386 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 06 21:58:32 Started mapping on | Dec 06 21:58:32 Finished on | Dec 06 22:05:02 Mapping speed, Million of reads per hour | 95.94 Number of input reads | 10394014 Average input read length | 280 UNIQUE READS: Uniquely mapped reads number | 8149950 Uniquely mapped reads % | 78.41% Average mapped length | 282.82 Number of splices: Total | 7785452 Number of splices: Annotated (sjdb) | 7260886 Number of splices: GT/AG | 7684045 Number of splices: GC/AG | 90685 Number of splices: AT/AC | 4385 Number of splices: Non-canonical | 6337 Mismatch rate per base, % | 0.11% Deletion rate per base | 0.00% Deletion average length | 1.36 Insertion rate per base | 0.00% Insertion average length | 1.28 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 179555 % of reads mapped to multiple loci | 1.73% Number of reads mapped to too many loci | 24413 % of reads mapped to too many loci | 0.23% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 18.43% % of reads unmapped: other | 1.20% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 2080809 2080809 2080809 N_multimapping 179555 179555 179555 N_noFeature 275293 7865557 368799 N_ambiguous 240364 1145 49508 UnstrandedReadsAssigned:7634293 PositiveStrandReadsAssigned:283248 NegativeStrandReadsAssigned:7731643 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=132 echo kmer=127 SRR21588386 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: SRR21588386-trimmed-pair1.fastq SRR21588386-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 10,394,014 reads, 7,831,921 reads pseudoaligned [quant] estimated average fragment length: 206.554 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,136 rounds 52973 SRR21588386.ke.tsv 35125 SRR21588386.se.tsv 88098 total ==> SRR21588386.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 730.658 0 0 PNS24247 1044 838.446 14.5299 2.43519 PNS24249 1928 1722.45 19.5433 1.5944 PNS24246 1044 838.446 14.5299 2.43519 PNS24248 1044 838.446 14.5299 2.43519 PNS24244 1471 1265.45 52.867 5.87066 PNS24243 293 118.268 0 0 KQK14069 1603 1397.45 3521.94 354.154 KQK14071 474 275.969 116.554 59.3488 ==> SRR21588386.se.tsv <== BRADI_1g14170v3 3901 BRADI_1g53295v3 14 BRADI_1g59795v3 181 BRADI_1g07683v3 0 BRADI_1g00485v3 14 BRADI_1g20270v3 1188 BRADI_1g74790v3 156 BRADI_1g09890v3 0 BRADI_1g77505v3 247 BRADI_1g48960v3 1 SRR21588386 completed mapping pipeline successfully