Starting /dee2/code/volunteer_pipeline.sh ERR3959300 current disk space = 1547754061824 free memory = 1476486812 ERR3959300 SRAfilesize c59f8cf496fc712e979bf3a0fadc045e ERR3959300.sra ERR3959300.sra file validated ERR3959300 is paired end ERR3959300 is conventional basespace ERR3959300 read1 length is 20-140 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR3959300_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 20-140 %GC 53 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.577 37.0 37.0 37.0 37.0 37.0 2 36.517 37.0 37.0 37.0 37.0 37.0 3 36.5425 37.0 37.0 37.0 37.0 37.0 4 36.4205 37.0 37.0 37.0 37.0 37.0 5 36.56 37.0 37.0 37.0 37.0 37.0 6 36.469 37.0 37.0 37.0 37.0 37.0 7 36.51 37.0 37.0 37.0 37.0 37.0 8 36.4035 37.0 37.0 37.0 37.0 37.0 9 36.6105 37.0 37.0 37.0 37.0 37.0 10-14 36.5044 37.0 37.0 37.0 37.0 37.0 15-19 36.4471 37.0 37.0 37.0 37.0 37.0 20-24 36.415119581753046 37.0 37.0 37.0 37.0 37.0 25-29 36.376612063265476 37.0 37.0 37.0 37.0 37.0 30-34 36.37257571663168 37.0 37.0 37.0 37.0 37.0 35-39 36.414071686193324 37.0 37.0 37.0 37.0 37.0 40-44 36.407170483256955 37.0 37.0 37.0 37.0 37.0 45-49 36.4000992910177 37.0 37.0 37.0 37.0 37.0 50-54 36.33999742522402 37.0 37.0 37.0 37.0 37.0 55-59 36.40058162800376 37.0 37.0 37.0 37.0 37.0 60-64 36.40704250829326 37.0 37.0 37.0 37.0 37.0 65-69 36.37539254918816 37.0 37.0 37.0 37.0 37.0 70-74 36.328957120825585 37.0 37.0 37.0 37.0 37.0 75-79 36.38944444108125 37.0 37.0 37.0 37.0 37.0 80-84 36.3537770900182 37.0 37.0 37.0 37.0 37.0 85-89 36.29020681424502 37.0 37.0 37.0 37.0 37.0 90-94 36.353548411823304 37.0 37.0 37.0 37.0 37.0 95-99 36.2936976694796 37.0 37.0 37.0 37.0 37.0 100-104 36.32314263119064 37.0 37.0 37.0 37.0 37.0 105-109 36.289983576797155 37.0 37.0 37.0 37.0 37.0 110-114 36.26411574086202 37.0 37.0 37.0 37.0 37.0 115-119 36.267386350672986 37.0 37.0 37.0 37.0 37.0 120-124 36.241901342919746 37.0 37.0 37.0 37.0 37.0 125-129 36.20920626340458 37.0 37.0 37.0 37.0 37.0 130-134 36.14416425058923 37.0 37.0 37.0 37.0 37.0 135-139 36.04774961103696 37.0 37.0 37.0 37.0 37.0 140 36.58573466476462 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 27 1.0 28 1.0 29 7.0 30 16.0 31 36.0 32 55.0 33 103.0 34 150.0 35 335.0 36 2897.0 37 399.0 >>END_MODULE >>Per base sequence content pass #Base G A T C 1 25.924999999999997 24.525 20.525 29.025000000000002 2 25.75 20.549999999999997 24.625 29.075 3 24.625 22.125 25.25 28.000000000000004 4 23.925 24.975 24.55 26.55 5 25.825 22.6 24.375 27.200000000000003 6 25.1 24.7 24.075 26.125 7 26.200000000000003 24.45 23.3 26.05 8 25.5 23.775 23.95 26.775 9 24.45 23.549999999999997 24.525 27.474999999999998 10-14 24.23 23.985 24.22 27.565 15-19 25.11 23.53 24.115000000000002 27.245 20-24 24.90118577075099 23.94556461700105 24.275779256516735 26.877470355731226 25-29 25.066386091487548 23.733653990680896 24.18958865674633 27.010371261085226 30-34 25.641411859215747 23.412160465933624 24.275744339006877 26.670683335843755 35-39 25.707535313929526 23.5560247323179 23.777208063137785 26.959231890614788 40-44 25.2088155378887 23.840193217268794 23.719432424272917 27.23155882056959 45-49 25.38930605251222 23.44907524063902 23.504510406692535 27.657108300156224 50-54 25.6775170325511 23.638657582639414 23.77491799142064 26.908907393388848 55-59 25.533744814327637 23.0446220783163 23.71243549529495 27.709197612061114 60-64 25.505703422053234 23.38149556400507 23.1128010139417 28.000000000000004 65-69 25.87416141492173 22.936572474080098 23.947956901809313 27.241309209188856 70-74 25.778185338020275 23.40414692546742 23.419430434561107 27.398237301951195 75-79 25.633428688189618 22.73191663261136 24.177564364527992 27.457090314671024 80-84 25.643782317104385 22.776839195208108 23.800747453028208 27.778631034659295 85-89 26.06325533556184 23.162766778092053 23.92388788891746 26.850089997428643 90-94 26.14372312315424 23.309673073933993 23.522097300657997 27.02450650225377 95-99 26.043623460655397 23.298893759131705 22.573575453976204 28.083907326236695 100-104 25.772815840749907 23.40828900942651 23.79798830902101 27.02090684080257 105-109 26.060187888116342 22.902181412876175 23.533782707924207 27.503847991083276 110-114 25.76421547669944 23.06006840530141 22.766139375801625 28.40957674219752 115-119 26.311811703735692 22.867631181170374 23.2131289138415 27.607428201252432 120-124 26.880488736158842 22.42949871815851 23.329515082092403 27.36049746359025 125-129 27.145068553737282 22.9046881910659 22.67249004865104 27.277753206545775 130-134 25.96961771743364 22.280340548661734 23.79945467697958 27.95058705692505 135-139 26.65550906555091 22.97350069735007 22.895397489539747 27.475592747559276 140 27.16119828815977 22.624821683309555 22.653352353780313 27.560627674750354 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 1.0 1 1.0 2 1.0 3 0.5 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 0.0 25 0.0 26 0.0 27 1.0 28 3.5 29 3.0 30 4.0 31 8.0 32 11.5 33 15.5 34 22.0 35 34.0 36 40.5 37 48.0 38 62.0 39 79.0 40 98.5 41 120.5 42 143.5 43 160.5 44 172.5 45 177.5 46 171.0 47 170.0 48 172.0 49 159.5 50 140.5 51 128.5 52 124.0 53 114.5 54 107.5 55 110.0 56 95.5 57 68.5 58 63.5 59 71.0 60 74.0 61 73.5 62 83.5 63 88.5 64 80.5 65 77.0 66 69.5 67 68.0 68 65.5 69 70.5 70 72.0 71 69.0 72 69.0 73 52.0 74 39.5 75 35.5 76 34.0 77 27.0 78 18.0 79 14.0 80 9.0 81 6.5 82 6.0 83 5.5 84 4.5 85 2.5 86 1.5 87 0.5 88 0.5 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 10-14 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 0.005578489345085351 140 0.0 >>END_MODULE >>Sequence Length Distribution warn #Length Count 20-24 7.0 25-29 6.0 30-34 7.0 35-39 4.0 40-44 5.0 45-49 5.0 50-54 9.0 55-59 9.0 60-64 10.0 65-69 7.0 70-74 11.0 75-79 9.0 80-84 12.0 85-89 21.0 90-94 31.0 95-99 36.0 100-104 30.0 105-109 26.0 110-114 32.0 115-119 38.0 120-124 45.0 125-129 45.0 130-134 4.0 135-139 86.0 140-141 3505.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 95.675 #Duplication Level Percentage of deduplicated Percentage of total 1 95.7146590018291 91.57499999999999 2 4.102430101907499 7.85 3 0.1567807682257643 0.44999999999999996 4 0.0 0.0 5 0.026130128037627383 0.125 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 warn #Sequence Count Percentage Possible Source AGGAGATCACAGGGCCGACTGGATAGACCGTCGGGGCAGGGATTCCGGGC 5 0.125 No Hit >>END_MODULE >>Adapter Content pass #Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence SOLID Small RNA Adapter 1 0.0 0.0 0.0 0.0 0.0 2 0.0 0.0 0.0 0.0 0.0 3 0.0 0.0 0.0 0.0 0.0 4 0.0 0.0 0.0 0.0 0.0 5 0.0 0.0 0.0 0.0 0.0 6 0.0 0.0 0.0 0.0 0.0 7 0.0 0.0 0.0 0.0 0.0 8 0.0 0.0 0.0 0.0 0.0 9 0.0 0.0 0.0 0.0 0.0 10-11 0.0 0.0 0.0 0.0 0.0 12-13 0.0 0.0 0.0 0.0 0.0 14-15 0.0 0.0 0.0 0.0 0.0 16-17 0.0 0.0 0.0 0.0 0.0 18-19 0.0 0.0 0.0 0.0 0.0 20-21 0.0 0.0 0.0 0.0 0.0 22-23 0.0 0.0 0.0 0.0 0.0 24-25 0.0 0.0 0.0 0.0 0.0 26-27 0.0 0.0 0.0 0.0 0.0 28-29 0.0 0.0 0.0 0.0 0.0 30-31 0.0 0.0 0.0 0.0 0.0 32-33 0.0 0.0 0.0 0.0 0.0 34-35 0.0 0.0 0.0 0.0 0.0 36-37 0.0 0.0 0.0 0.0 0.0 38-39 0.0 0.0 0.0 0.0 0.0 40-41 0.0 0.0 0.0 0.0 0.0 42-43 0.0 0.0 0.0 0.0 0.0 44-45 0.0 0.0 0.0 0.0 0.0 46-47 0.0 0.0 0.0 0.0 0.0 48-49 0.0 0.0 0.0 0.0 0.0 50-51 0.0 0.0 0.0 0.0 0.0 52-53 0.0 0.0 0.0 0.0 0.0 54-55 0.0 0.0 0.0 0.0 0.0 56-57 0.0 0.0 0.0 0.0 0.0 58-59 0.0 0.0 0.0 0.0 0.0 60-61 0.0 0.0 0.0 0.0 0.0 62-63 0.0 0.0 0.0 0.0 0.0 64-65 0.0 0.0 0.0 0.0 0.0 66-67 0.0 0.0 0.0 0.0 0.0 68-69 0.0 0.0 0.0 0.0 0.0 70-71 0.0 0.0 0.0 0.0 0.0 72-73 0.0 0.0 0.0 0.0 0.0 74-75 0.0 0.0 0.0 0.0 0.0 76-77 0.0 0.0 0.0 0.0 0.0 78-79 0.0 0.0 0.0 0.0 0.0 80-81 0.0 0.0 0.0 0.0 0.0 82-83 0.0 0.0 0.0 0.0 0.0 84-85 0.0 0.0 0.0 0.0 0.0 86-87 0.0 0.0 0.0 0.0 0.0 88-89 0.0 0.0 0.0 0.0 0.0 90-91 0.0 0.0 0.0 0.0 0.0 92-93 0.0 0.0 0.0 0.0 0.0 94-95 0.0 0.0 0.0 0.0 0.0 96-97 0.0 0.0 0.0 0.0 0.0 98-99 0.0 0.0 0.0 0.0 0.0 100-101 0.0 0.0 0.0 0.0 0.0 102-103 0.0 0.0 0.0 0.0 0.0 104-105 0.0 0.0 0.0 0.0 0.0 106-107 0.0 0.0 0.0 0.0 0.0 108-109 0.0 0.0 0.0 0.0 0.0 110-111 0.0 0.0 0.0 0.0 0.0 112-113 0.0 0.0 0.0 0.0 0.0 114-115 0.0 0.0 0.0 0.0 0.0 116-117 0.0125 0.0 0.0 0.0 0.0 118-119 0.025 0.0 0.0 0.0 0.0 120-121 0.025 0.0 0.0 0.0 0.0 122-123 0.037500000000000006 0.0 0.0 0.0 0.0 124-125 0.05 0.0 0.0 0.0 0.0 126-127 0.05 0.0 0.0 0.0 0.0 128 0.05 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GTTCAGC 10 0.009143439 131.525 9 >>END_MODULE ERR3959300 read2 length is 20-140 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR3959300_2.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 20-140 %GC 54 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.4765 37.0 37.0 37.0 37.0 37.0 2 36.4265 37.0 37.0 37.0 37.0 37.0 3 36.4695 37.0 37.0 37.0 37.0 37.0 4 36.4065 37.0 37.0 37.0 37.0 37.0 5 36.431 37.0 37.0 37.0 37.0 37.0 6 36.4265 37.0 37.0 37.0 37.0 37.0 7 36.3305 37.0 37.0 37.0 37.0 37.0 8 36.3815 37.0 37.0 37.0 37.0 37.0 9 36.3855 37.0 37.0 37.0 37.0 37.0 10-14 36.3968 37.0 37.0 37.0 37.0 37.0 15-19 36.3609 37.0 37.0 37.0 37.0 37.0 20-24 36.288019499069875 37.0 37.0 37.0 37.0 37.0 25-29 36.325826462046585 37.0 37.0 37.0 37.0 37.0 30-34 36.28215134855727 37.0 37.0 37.0 37.0 37.0 35-39 36.306117555067146 37.0 37.0 37.0 37.0 37.0 40-44 36.29949307748589 37.0 37.0 37.0 37.0 37.0 45-49 36.17835653536562 37.0 37.0 37.0 37.0 37.0 50-54 36.22778743754506 37.0 37.0 37.0 37.0 37.0 55-59 36.26399900941571 37.0 37.0 37.0 37.0 37.0 60-64 36.22504672361203 37.0 37.0 37.0 37.0 37.0 65-69 36.15321982807543 37.0 37.0 37.0 37.0 37.0 70-74 36.22345486342154 37.0 37.0 37.0 37.0 37.0 75-79 36.20249477793359 37.0 37.0 37.0 37.0 37.0 80-84 36.1265806946328 37.0 37.0 37.0 37.0 37.0 85-89 36.178187157391434 37.0 37.0 37.0 37.0 37.0 90-94 36.16824490663204 37.0 37.0 37.0 37.0 37.0 95-99 36.16963075881407 37.0 37.0 37.0 37.0 37.0 100-104 36.05874593861654 37.0 37.0 37.0 37.0 37.0 105-109 36.10351868482344 37.0 37.0 37.0 37.0 37.0 110-114 36.04429745676923 37.0 37.0 37.0 37.0 37.0 115-119 35.956878355574176 37.0 37.0 37.0 37.0 37.0 120-124 35.98132954683103 37.0 37.0 37.0 37.0 37.0 125-129 35.86007915179154 37.0 37.0 37.0 37.0 37.0 130-134 35.97836314003395 37.0 37.0 37.0 37.0 37.0 135-139 35.826243695982924 37.0 37.0 37.0 37.0 37.0 140 36.38598442714127 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 27 2.0 28 6.0 29 6.0 30 25.0 31 34.0 32 55.0 33 96.0 34 191.0 35 635.0 36 2669.0 37 281.0 >>END_MODULE >>Per base sequence content pass #Base G A T C 1 28.425 22.05 19.05 30.475 2 29.475 19.05 21.925 29.549999999999997 3 26.450000000000003 20.925 22.900000000000002 29.725 4 26.125 23.474999999999998 23.599999999999998 26.8 5 27.925 23.724999999999998 20.45 27.900000000000002 6 27.400000000000002 21.65 22.275 28.675 7 27.85 24.025 22.725 25.4 8 28.275 22.25 22.650000000000002 26.825 9 27.150000000000002 21.625 22.625 28.599999999999998 10-14 27.134999999999998 23.05 22.634999999999998 27.18 15-19 26.955000000000002 23.115 22.285 27.644999999999996 20-24 27.105750462939792 23.232070466943597 22.241129072618985 27.421049997497622 25-29 26.899734162612226 23.137884335657322 22.290214174650146 27.672167327080306 30-34 27.79424323102426 22.705580951424125 22.183151655196664 27.317024162354954 35-39 27.060598441035953 22.992205179783756 22.368619562484284 27.578576816696003 40-44 27.43585866223096 23.65038560411311 22.213821261152276 26.699934472503656 45-49 28.029690971520903 22.68228640678651 22.702484346596645 26.58553827509594 50-54 27.880044502882573 22.82289875594215 22.327298472741987 26.969758268433296 55-59 27.698388567953785 23.38096685922773 22.49923989054424 26.421404682274247 60-64 27.569927407482613 23.092542768668462 22.381846794253516 26.955683029595413 65-69 27.69504447268107 22.500635324015246 22.86658195679797 26.937738246505717 70-74 27.44489130988138 23.260194471312936 22.28274703456702 27.01216718423866 75-79 27.920852669692486 23.33112346371564 21.740017338977 27.00800652761487 80-84 27.317297380113377 23.609621571931974 22.552474337367855 26.52060671058679 85-89 27.6379080953843 23.29853648551837 22.500255859175113 26.56329955992222 90-94 28.253512460260488 22.53615013844734 22.182340272792533 27.027997128499642 95-99 27.851676852755382 23.42971598787941 22.233064557547124 26.48554260181809 100-104 28.276748971193417 23.333333333333332 22.10390946502058 26.286008230452673 105-109 28.94506061387671 23.316997678617486 21.862264637606398 25.875677069899407 110-114 28.221302998965875 23.195449844881075 22.362978283350568 26.22026887280248 115-119 28.236757541204522 24.05411008603711 22.074219964755883 25.634912408002485 120-124 28.60041623309053 23.314255983350677 22.039542143600414 26.045785639958375 125-129 28.859975866953462 23.419547767693196 22.07124495042233 25.649231414931013 130-134 28.903601694915253 23.37923728813559 22.780720338983052 24.9364406779661 135-139 29.062383264848712 23.14424462351246 22.156998772613267 25.636373339025564 140 28.281423804226918 23.943270300333705 22.636262513904338 25.139043381535036 >>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 0.5 24 0.5 25 0.0 26 0.0 27 0.0 28 0.5 29 2.5 30 3.0 31 4.0 32 7.5 33 14.5 34 17.5 35 25.0 36 39.5 37 38.0 38 41.0 39 62.5 40 80.5 41 93.5 42 115.0 43 135.0 44 145.0 45 151.0 46 155.0 47 152.0 48 147.5 49 143.0 50 133.0 51 114.5 52 120.0 53 124.0 54 105.5 55 104.0 56 95.5 57 84.0 58 83.5 59 81.0 60 89.0 61 97.0 62 86.5 63 81.0 64 88.5 65 94.0 66 97.5 67 92.0 68 79.5 69 85.0 70 94.5 71 84.5 72 65.5 73 58.5 74 52.5 75 50.5 76 51.5 77 36.5 78 24.5 79 28.5 80 24.5 81 16.0 82 14.0 83 6.0 84 1.0 85 2.0 86 1.5 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 10-14 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 0.0 >>END_MODULE >>Sequence Length Distribution warn #Length Count 20-24 8.0 25-29 8.0 30-34 5.0 35-39 8.0 40-44 9.0 45-49 5.0 50-54 7.0 55-59 8.0 60-64 6.0 65-69 4.0 70-74 8.0 75-79 5.0 80-84 7.0 85-89 8.0 90-94 8.0 95-99 5.0 100-104 12.0 105-109 8.0 110-114 8.0 115-119 14.0 120-124 14.0 125-129 54.0 130-134 18.0 135-139 167.0 140-141 3596.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 95.45 #Duplication Level Percentage of deduplicated Percentage of total 1 95.46883184913567 91.125 2 4.32163436354112 8.25 3 0.18334206390780514 0.525 4 0.026191723415400735 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 warn #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 0.025 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 0.05 0.0 0.0 0.0 0.0 56-57 0.05 0.0 0.0 0.0 0.0 58-59 0.05 0.0 0.0 0.0 0.0 60-61 0.05 0.0 0.0 0.0 0.0 62-63 0.07500000000000001 0.0 0.0 0.0 0.0 64-65 0.125 0.0 0.0 0.0 0.0 66-67 0.125 0.0 0.0 0.0 0.0 68-69 0.125 0.0 0.0 0.0 0.0 70-71 0.15 0.0 0.0 0.0 0.0 72-73 0.175 0.0 0.0 0.0 0.0 74-75 0.2 0.0 0.0 0.0 0.0 76-77 0.275 0.0 0.0 0.0 0.0 78-79 0.3125 0.0 0.0 0.0 0.0 80-81 0.3625 0.0 0.0 0.0 0.0 82-83 0.48750000000000004 0.0 0.0 0.0 0.0 84-85 0.55 0.0 0.0 0.0 0.0 86-87 0.6375 0.0 0.0 0.0 0.0 88-89 0.7625 0.0 0.0 0.0 0.0 90-91 1.0375 0.0 0.0 0.0 0.0 92-93 1.275 0.0 0.0 0.0 0.0 94-95 1.3875000000000002 0.0 0.0 0.0 0.0 96-97 1.5875 0.0 0.0 0.0 0.0 98-99 1.9125 0.0 0.0 0.0 0.0 100-101 2.25 0.0 0.0 0.0 0.0 102-103 2.4625 0.0 0.0 0.0 0.0 104-105 2.7249999999999996 0.0 0.0 0.0 0.0 106-107 2.9625 0.0 0.0 0.0 0.0 108-109 3.15 0.0 0.0 0.0 0.0 110-111 3.45 0.0 0.0 0.0 0.0 112-113 3.7 0.0 0.0 0.0 0.0 114-115 4.1375 0.0 0.0 0.0 0.0 116-117 4.525 0.0 0.0 0.0 0.0 118-119 4.8625 0.0 0.0 0.0 0.0 120-121 5.175000000000001 0.0 0.0 0.0 0.0 122-123 5.675 0.0 0.0 0.0 0.0 124-125 6.125 0.0 0.0 0.0 0.0 126-127 6.275 0.0 0.0 0.0 0.0 128 6.3 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Read 2785961 spots for ERR3959300.sra Written 2785961 spots for ERR3959300.sra Read 2785961 spots for ERR3959300.sra Written 2785961 spots for ERR3959300.sra Read 2785961 spots for ERR3959300.sra Written 2785961 spots for ERR3959300.sra Read 2785961 spots for ERR3959300.sra Written 2785961 spots for ERR3959300.sra Read 2785961 spots for ERR3959300.sra Written 2785961 spots for ERR3959300.sra Read 2785961 spots for ERR3959300.sra Written 2785961 spots for ERR3959300.sra Read 2785961 spots for ERR3959300.sra Written 2785961 spots for ERR3959300.sra Read 2785961 spots for ERR3959300.sra Written 2785961 spots for ERR3959300.sra Read 2785961 spots for ERR3959300.sra Written 2785961 spots for ERR3959300.sra Read 2785961 spots for ERR3959300.sra Written 2785961 spots for ERR3959300.sra Read 2785961 spots for ERR3959300.sra Written 2785961 spots for ERR3959300.sra Read 2785961 spots for ERR3959300.sra Written 2785961 spots for ERR3959300.sra Read 2785961 spots for ERR3959300.sra Written 2785961 spots for ERR3959300.sra Read 2785961 spots for ERR3959300.sra Written 2785961 spots for ERR3959300.sra Read 2785961 spots for ERR3959300.sra Written 2785961 spots for ERR3959300.sra Read 2785961 spots for ERR3959300.sra Written 2785961 spots for ERR3959300.sra Read 2785961 spots for ERR3959300.sra Written 2785961 spots for ERR3959300.sra Read 2785961 spots for ERR3959300.sra Written 2785961 spots for ERR3959300.sra Read 2785967 spots for ERR3959300.sra Written 2785967 spots for ERR3959300.sra Read 2785961 spots for ERR3959300.sra Written 2785961 spots for ERR3959300.sra SRR ids: ['ERR3959300.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_069ttx4i ERR3959300.sra spots: 55719226 blocks: [[1, 2785961], [2785962, 5571922], [5571923, 8357883], [8357884, 11143844], [11143845, 13929805], [13929806, 16715766], [16715767, 19501727], [19501728, 22287688], [22287689, 25073649], [25073650, 27859610], [27859611, 30645571], [30645572, 33431532], [33431533, 36217493], [36217494, 39003454], [39003455, 41789415], [41789416, 44575376], [44575377, 47361337], [47361338, 50147298], [50147299, 52933259], [52933260, 55719226]] ERR3959300 file size 17207072 ERR3959300 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 ERR3959300 ERR3959300_1.fastq ERR3959300_2.fastq Input file: ERR3959300_1.fastq Paired file: ERR3959300_2.fastq trimmed: ERR3959300-trimmed-pair1.fastq, ERR3959300-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 Sat Dec 7 02:36:33 2024 >> started Sat Dec 7 02:46:21 2024 >> done (588.530s) 55719226 read pairs processed; of these: 0 ( 0.00%) short read pairs filtered out after trimming by size control 0 ( 0.00%) empty read pairs filtered out after trimming by size control 55719226 (100.00%) read pairs available; of these: 88875 ( 0.16%) trimmed read pairs available after processing 55630351 (99.84%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 20 478 0.00% 21 1084 0.00% 22 1555 0.00% 23 2147 0.00% 24 2411 0.00% 25 2717 0.00% 26 3153 0.01% 27 3512 0.01% 28 3697 0.01% 29 3956 0.01% 30 4380 0.01% 31 4513 0.01% 32 4741 0.01% 33 4821 0.01% 34 5026 0.01% 35 5046 0.01% 36 5349 0.01% 37 5229 0.01% 38 5595 0.01% 39 5638 0.01% 40 5664 0.01% 41 5768 0.01% 42 6091 0.01% 43 6240 0.01% 44 5965 0.01% 45 6426 0.01% 46 6311 0.01% 47 6249 0.01% 48 6502 0.01% 49 6747 0.01% 50 6599 0.01% 51 6793 0.01% 52 6696 0.01% 53 7094 0.01% 54 7093 0.01% 55 7196 0.01% 56 7301 0.01% 57 7362 0.01% 58 7499 0.01% 59 7561 0.01% 60 7881 0.01% 61 7841 0.01% 62 8010 0.01% 63 8173 0.01% 64 8256 0.01% 65 8457 0.02% 66 8595 0.02% 67 8651 0.02% 68 8918 0.02% 69 9175 0.02% 70 9488 0.02% 71 9727 0.02% 72 9841 0.02% 73 10270 0.02% 74 10550 0.02% 75 11002 0.02% 76 11023 0.02% 77 11547 0.02% 78 11685 0.02% 79 15042 0.03% 80 55984 0.10% 81 55915 0.10% 82 55788 0.10% 83 54641 0.10% 84 55248 0.10% 85 55578 0.10% 86 55818 0.10% 87 56334 0.10% 88 56376 0.10% 89 57473 0.10% 90 56837 0.10% 91 57618 0.10% 92 57722 0.10% 93 59150 0.11% 94 60102 0.11% 95 60091 0.11% 96 59966 0.11% 97 61234 0.11% 98 63097 0.11% 99 63253 0.11% 100 65685 0.12% 101 65804 0.12% 102 68800 0.12% 103 70642 0.13% 104 73929 0.13% 105 76139 0.14% 106 75637 0.14% 107 78913 0.14% 108 80777 0.14% 109 84158 0.15% 110 86673 0.16% 111 87984 0.16% 112 94653 0.17% 113 95180 0.17% 114 98196 0.18% 115 103191 0.19% 116 113555 0.20% 117 117851 0.21% 118 139493 0.25% 119 144028 0.26% 120 161135 0.29% 121 170655 0.31% 122 147738 0.27% 123 197453 0.35% 124 208512 0.37% 125 217373 0.39% 126 321001 0.58% 127 328561 0.59% 128 334506 0.60% 129 241426 0.43% 130 243815 0.44% 131 249817 0.45% 132 252137 0.45% 133 67994 0.12% 134 58266 0.10% 135 46528 0.08% 136 47987 0.09% 137 55333 0.10% 138 88037 0.16% 139 1944176 3.49% 140 46954926 84.27% 55719226 reads passed initial QC criterion=sequence-density sequence-density=0.20 sequence-density-rank=1 fanout-score=2.78 fanout-score-rank=23 prefix-density=0.23 prefix-fanout=2.4 sequence=TAGGCGTCCGGGTACTCCTTCTTGACCTCCTCCAGCTCCTTGAGCACCTG criterion=fanout-score sequence-density=0.05 sequence-density-rank=33 fanout-score=354.41 fanout-score-rank=1 prefix-density=0.90 prefix-fanout=18.8 sequence=GGCGGCGGCGAACCGCCCCCGTCGCCGCGATCCGAACACTTCACCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGCATTCCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCTATATACTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCAAACTTCCGTCGCCTAAACGGCGATAGTCCCTCTAAGAAGCTAGCTGCGGAGGGATGGCTCCGCATAGCTAGTTAGCAGGCTGAGGTCTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCATGCACCACCACCCATAGAATCAAGAAAGAGCTCTCAGTCTGTCAATCCTTGCTATGTCTGGACCTGGTAAG criterion=sequence-density sequence-density=5.32 sequence-density-rank=1 fanout-score=45.79 fanout-score-rank=2 prefix-density=6.06 prefix-fanout=40.2 sequence=AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTGGCTATTGGTGTAGATCTCGGTGGTCGCCGTATCATTAAA criterion=fanout-score sequence-density=0.16 sequence-density-rank=7 fanout-score=144.34 fanout-score-rank=1 prefix-density=1.16 prefix-fanout=20.5 sequence=CCGCCGCCGCCG Potential 3prime adapter identified. Now checking if in reference sequence /dee2/code/volunteer_pipeline.sh: line 905: -f: command not found /dee2/code/volunteer_pipeline.sh: line 906: -f: command not found Adapter seq not found in reference. Now shuffling file before clipping skewer v0.2.2 [April 4, 2016] COMMAND LINE: skewer -f sanger -l 18 -t 20 -x TAGGCGTCCGGGTACTCCTTCTTGACCTCCTCCAGCTCCTTGAGCACCTG -y AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTGGCTATTGGTGTAGATCTCGGTGGTCGCCGTATCATTAAA -o ERR3959300 ERR3959300_1.fastq ERR3959300_2.fastq Input file: ERR3959300_1.fastq Paired file: ERR3959300_2.fastq trimmed: ERR3959300-trimmed-pair1.fastq, ERR3959300-trimmed-pair2.fastq Parameters used: -- 3' end adapter sequence (-x): TAGGCGTCCGGGTACTCCTTCTTGACCTCCTCCAGCTCCTTGAGCACCTG -- paired 3' end adapter sequence (-y): AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTGGCTATTGGTGTAGATCTCGGTGGTCGCCGT -- maximum error ratio allowed (-r): 0.100 -- maximum indel error ratio allowed (-d): 0.030 -- minimum read length allowed after trimming (-l): 18 -- file format (-f): Sanger/Illumina 1.8+ FASTQ -- number of concurrent threads (-t): 20 Sat Dec 7 03:15:19 2024 >> started Sat Dec 7 03:22:14 2024 >> done (414.475s) 27859613 read pairs processed; of these: 14 ( 0.00%) short read pairs filtered out after trimming by size control 665 ( 0.00%) empty read pairs filtered out after trimming by size control 27858934 (100.00%) read pairs available; of these: 24861 ( 0.09%) trimmed read pairs available after processing 27834073 (99.91%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 20 258 0.00% 21 558 0.00% 22 783 0.00% 23 1082 0.00% 24 1202 0.00% 25 1404 0.01% 26 1574 0.01% 27 1748 0.01% 28 1848 0.01% 29 1968 0.01% 30 2124 0.01% 31 2267 0.01% 32 2384 0.01% 33 2373 0.01% 34 2505 0.01% 35 2537 0.01% 36 2670 0.01% 37 2634 0.01% 38 2796 0.01% 39 2772 0.01% 40 2807 0.01% 41 2851 0.01% 42 3020 0.01% 43 3073 0.01% 44 2961 0.01% 45 3194 0.01% 46 3127 0.01% 47 3031 0.01% 48 3267 0.01% 49 3360 0.01% 50 3289 0.01% 51 3284 0.01% 52 3329 0.01% 53 3553 0.01% 54 3544 0.01% 55 3638 0.01% 56 3651 0.01% 57 3685 0.01% 58 3696 0.01% 59 3862 0.01% 60 3927 0.01% 61 3913 0.01% 62 3931 0.01% 63 4041 0.01% 64 4091 0.01% 65 4218 0.02% 66 4285 0.02% 67 4243 0.02% 68 4490 0.02% 69 4533 0.02% 70 4833 0.02% 71 4895 0.02% 72 4940 0.02% 73 5161 0.02% 74 5267 0.02% 75 5426 0.02% 76 5395 0.02% 77 5916 0.02% 78 5839 0.02% 79 7580 0.03% 80 27888 0.10% 81 27812 0.10% 82 28008 0.10% 83 27185 0.10% 84 27715 0.10% 85 28062 0.10% 86 27924 0.10% 87 28186 0.10% 88 28258 0.10% 89 28642 0.10% 90 28408 0.10% 91 28837 0.10% 92 28678 0.10% 93 29561 0.11% 94 30126 0.11% 95 30033 0.11% 96 30078 0.11% 97 30805 0.11% 98 31681 0.11% 99 31684 0.11% 100 32744 0.12% 101 32874 0.12% 102 34327 0.12% 103 35329 0.13% 104 36939 0.13% 105 38172 0.14% 106 37644 0.14% 107 39421 0.14% 108 40357 0.14% 109 42287 0.15% 110 43178 0.15% 111 43996 0.16% 112 47437 0.17% 113 47532 0.17% 114 49074 0.18% 115 51808 0.19% 116 56715 0.20% 117 58988 0.21% 118 69692 0.25% 119 72068 0.26% 120 80295 0.29% 121 85047 0.31% 122 73741 0.26% 123 98757 0.35% 124 104305 0.37% 125 108670 0.39% 126 160831 0.58% 127 164665 0.59% 128 167529 0.60% 129 120745 0.43% 130 121841 0.44% 131 125284 0.45% 132 126121 0.45% 133 33906 0.12% 134 29207 0.10% 135 23454 0.08% 136 24315 0.09% 137 29076 0.10% 138 47960 0.17% 139 991018 3.56% 140 23451381 84.18% criterion=sequence-density sequence-density=0.20 sequence-density-rank=1 fanout-score=2.76 fanout-score-rank=24 prefix-density=0.23 prefix-fanout=2.4 sequence=TAGGCGTCCGGGTACTCCTTCTTGACCTCCTCCAGCTCCTTGAGCACCTG criterion=fanout-score sequence-density=0.05 sequence-density-rank=33 fanout-score=351.78 fanout-score-rank=1 prefix-density=0.90 prefix-fanout=18.4 sequence=GGCGGCGGCGAACCGCCCCCGTCGCCGCGATCCGAACACTTCACCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGCATTCCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCTATATACTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCAAACTTCCGTCGCCTAAACGGCGATAGTCCCTCTAAGAAGCTAGCTGCGGAGGGATGGCTCCGCATAGCTAGTTAGCAGGCTGAGGTCTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCATGCACCACCACCCATAGAATCAAGAAAGAGCTCTCAGTCTGTCAATCCTTGCTATGTCTGGACCTGGTAAG criterion=sequence-density sequence-density=5.49 sequence-density-rank=1 fanout-score=46.05 fanout-score-rank=2 prefix-density=6.27 prefix-fanout=40.3 sequence=AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTGGCTATTGGTGTAGATCTCGGTGGTCGCCGTATCATTAAAA criterion=fanout-score sequence-density=0.17 sequence-density-rank=6 fanout-score=140.66 fanout-score-rank=1 prefix-density=1.16 prefix-fanout=20.3 sequence=CCGCCGCCGCCG ERR3959300 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 07 03:31:10 Started mapping on | Dec 07 03:31:10 Finished on | Dec 07 04:10:16 Mapping speed, Million of reads per hour | 85.50 Number of input reads | 55718547 Average input read length | 273 UNIQUE READS: Uniquely mapped reads number | 47867220 Uniquely mapped reads % | 85.91% Average mapped length | 274.58 Number of splices: Total | 44353855 Number of splices: Annotated (sjdb) | 41952593 Number of splices: GT/AG | 43658009 Number of splices: GC/AG | 633726 Number of splices: AT/AC | 23895 Number of splices: Non-canonical | 38225 Mismatch rate per base, % | 0.07% Deletion rate per base | 0.00% Deletion average length | 1.50 Insertion rate per base | 0.00% Insertion average length | 1.15 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 584564 % of reads mapped to multiple loci | 1.05% Number of reads mapped to too many loci | 222576 % of reads mapped to too many loci | 0.40% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 11.18% % of reads unmapped: other | 1.47% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 7368934 7368934 7368934 N_multimapping 584564 584564 584564 N_noFeature 1486885 46606831 1930852 N_ambiguous 1110096 8042 302757 UnstrandedReadsAssigned:45270239 PositiveStrandReadsAssigned:1252347 NegativeStrandReadsAssigned:45633611 Dataset is classified negative stranded MeadianReadLen=140 20thPercentileLength=140 echo kmer=135 ERR3959300 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: ERR3959300-trimmed-pair1.fastq ERR3959300-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 55,718,547 reads, 51,684,463 reads pseudoaligned [quant] estimated average fragment length: 248.782 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,223 rounds 52973 ERR3959300.ke.tsv 35125 ERR3959300.se.tsv 88098 total ==> ERR3959300.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 688.693 0 0 PNS24247 1044 796.218 94.0213 3.22215 PNS24249 1928 1680.22 1038.45 16.8644 PNS24246 1044 796.218 94.0213 3.22215 PNS24248 1044 796.218 94.0213 3.22215 PNS24244 1471 1223.22 89.4856 1.99618 PNS24243 293 100.805 0 0 KQK14069 1603 1355.22 53720.9 1081.65 KQK14071 474 241.687 1784.27 201.446 ==> ERR3959300.se.tsv <== BRADI_1g14170v3 51368 BRADI_1g53295v3 491 BRADI_1g59795v3 642 BRADI_1g07683v3 0 BRADI_1g00485v3 41 BRADI_1g20270v3 2155 BRADI_1g74790v3 1780 BRADI_1g09890v3 4 BRADI_1g77505v3 625 BRADI_1g48960v3 0 ERR3959300 completed mapping pipeline successfully