Starting /dee2/code/volunteer_pipeline.sh SRR7171496 current disk space = 3087583547392 free memory = 1481508896 SRR7171496 SRAfilesize e976d35221e4475012965e981267980b SRR7171496.sra SRR7171496.sra file validated SRR7171496 is paired end SRR7171496 is conventional basespace SRR7171496 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR7171496_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 32.947 34.0 33.0 34.0 32.0 34.0 2 33.24 34.0 33.0 34.0 33.0 34.0 3 33.1655 34.0 33.0 34.0 31.0 34.0 4 32.8915 34.0 33.0 34.0 32.0 34.0 5 33.1165 34.0 33.0 34.0 32.0 34.0 6 36.76325 38.0 37.0 38.0 34.0 38.0 7 37.387 38.0 38.0 38.0 37.0 38.0 8 37.51875 38.0 38.0 38.0 37.0 38.0 9 37.5395 38.0 38.0 38.0 38.0 38.0 10-14 37.52735 38.0 38.0 38.0 37.8 38.0 15-19 37.504450000000006 38.0 38.0 38.0 37.6 38.0 20-24 37.404849999999996 38.0 38.0 38.0 37.2 38.0 25-29 37.442899999999995 38.0 38.0 38.0 37.6 38.0 30-34 37.487649999999995 38.0 38.0 38.0 37.6 38.0 35-39 36.3349 38.0 37.6 38.0 32.0 38.0 40-44 37.10865 38.0 38.0 38.0 35.0 38.0 45-49 37.3381 38.0 38.0 38.0 37.0 38.0 50-54 37.29905 38.0 38.0 38.0 37.0 38.0 55-59 37.2488 38.0 38.0 38.0 37.0 38.0 60-64 37.27875 38.0 38.0 38.0 36.8 38.0 65-69 37.2487 38.0 38.0 38.0 37.0 38.0 70-74 34.584250000000004 33.6 33.6 37.8 32.2 38.0 75-79 35.2937 36.2 35.0 38.0 31.8 38.0 80-84 37.1508 38.0 38.0 38.0 36.0 38.0 85-89 37.09250000000001 38.0 38.0 38.0 36.0 38.0 90-94 37.1254 38.0 38.0 38.0 36.0 38.0 95-99 37.03765 38.0 38.0 38.0 36.0 38.0 100-104 36.89545 38.0 38.0 38.0 35.4 38.0 105-109 36.85035 38.0 38.0 38.0 35.0 38.0 110-114 36.67595000000001 38.0 38.0 38.0 34.6 38.0 115-119 36.57075 38.0 38.0 38.0 34.4 38.0 120-124 36.37665 38.0 38.0 38.0 34.0 38.0 125-129 36.230450000000005 38.0 37.6 38.0 33.6 38.0 130-134 36.1863 38.0 37.0 38.0 33.0 38.0 135-139 36.1611 38.0 37.2 38.0 33.2 38.0 140-144 36.063 38.0 36.2 38.0 33.0 38.0 145-149 35.87235 38.0 36.0 38.0 32.6 38.0 150-151 33.52225 36.5 32.0 38.0 22.5 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 19 2.0 20 1.0 21 1.0 22 3.0 23 4.0 24 7.0 25 9.0 26 9.0 27 13.0 28 9.0 29 32.0 30 28.0 31 40.0 32 72.0 33 84.0 34 142.0 35 240.0 36 685.0 37 2619.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 41.75491679273828 10.842158345940495 10.337871911245587 37.065052950075646 2 21.55 15.1 33.300000000000004 30.049999999999997 3 19.075 20.549999999999997 26.05 34.325 4 23.400000000000002 27.6 22.675 26.325 5 21.45 31.674999999999997 25.45 21.425 6 20.1 34.325 26.200000000000003 19.375 7 14.549999999999999 24.875 42.05 18.525 8 17.775 25.95 29.525000000000002 26.75 9 16.575 23.724999999999998 35.85 23.849999999999998 10-14 19.495 29.425 27.884999999999998 23.195 15-19 19.63 28.294999999999998 27.875 24.2 20-24 19.8 28.349999999999998 28.49 23.36 25-29 20.013001950292544 28.724308646296944 27.659148872330853 23.603540531079663 30-34 19.801930675736507 28.955134297003955 27.62466863402191 23.618266393237633 35-39 19.739869934967484 29.03951975987994 27.018509254627315 24.20210105052526 40-44 20.38009502375594 28.00200050012503 28.052013003250813 23.565891472868216 45-49 19.971990196568797 27.81973690791777 28.15485419896964 24.05341869654379 50-54 20.292029202920293 28.497849784978495 27.012701270127014 24.197419741974198 55-59 20.01 28.73 27.43 23.830000000000002 60-64 19.97 28.275 27.88 23.875 65-69 19.75 28.349999999999998 28.375 23.525 70-74 20.645 29.659999999999997 25.779999999999998 23.915 75-79 20.145 27.98 27.76 24.115000000000002 80-84 19.765 28.249999999999996 27.700000000000003 24.285 85-89 20.165 28.18 27.500000000000004 24.154999999999998 90-94 19.375 28.189999999999998 28.065 24.37 95-99 20.3 28.725 26.995 23.98 100-104 20.165 28.904999999999998 27.455000000000002 23.474999999999998 105-109 20.580000000000002 28.125 27.55 23.745 110-114 20.474999999999998 28.27 27.875 23.380000000000003 115-119 20.27 27.985 28.13 23.615 120-124 20.085 28.98 26.875 24.060000000000002 125-129 20.544999999999998 28.384999999999998 27.22 23.849999999999998 130-134 20.96 28.435 26.995 23.61 135-139 20.885 27.744999999999997 27.200000000000003 24.169999999999998 140-144 21.0 28.16 27.3 23.54 145-149 20.525 29.115000000000002 26.355 24.005000000000003 150-151 21.637500000000003 27.0625 26.5625 24.7375 >>END_MODULE >>Per sequence GC content pass #GC Content Count 0 0.0 1 0.0 2 0.0 3 0.5 4 0.5 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10 0.0 11 0.5 12 0.5 13 0.0 14 0.0 15 0.0 16 0.5 17 0.5 18 0.5 19 0.5 20 0.5 21 1.0 22 1.0 23 1.0 24 0.5 25 1.0 26 3.5 27 4.5 28 6.5 29 12.5 30 14.5 31 19.5 32 29.5 33 38.0 34 51.5 35 66.0 36 83.0 37 100.0 38 133.0 39 163.5 40 189.0 41 231.0 42 256.5 43 256.0 44 271.5 45 285.0 46 271.0 47 252.5 48 233.0 49 199.5 50 173.0 51 149.0 52 120.0 53 100.5 54 67.0 55 47.0 56 37.0 57 30.5 58 25.5 59 16.0 60 12.5 61 9.5 62 8.5 63 6.5 64 5.0 65 4.5 66 2.0 67 2.0 68 2.0 69 0.5 70 0.5 71 0.5 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 0.8500000000000001 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 0.015 30-34 0.034999999999999996 35-39 0.05 40-44 0.025 45-49 0.034999999999999996 50-54 0.01 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 99.95 #Duplication Level Percentage of deduplicated Percentage of total 1 99.94997498749375 99.9 2 0.05002501250625312 0.1 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 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 0.0 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 0.0125 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 0.0625 0.0 0.0 0.0 0.0 82-83 0.0875 0.0 0.0 0.0 0.0 84-85 0.125 0.0 0.0 0.0 0.0 86-87 0.125 0.0 0.0 0.0 0.0 88-89 0.1375 0.0 0.0 0.0 0.0 90-91 0.2125 0.0 0.0 0.0 0.0 92-93 0.2625 0.0 0.0 0.0 0.0 94-95 0.375 0.0 0.0 0.0 0.0 96-97 0.5 0.0 0.0 0.0 0.0 98-99 0.5874999999999999 0.0 0.0 0.0 0.0 100-101 0.6375 0.0 0.0 0.0 0.0 102-103 0.7375 0.0 0.0 0.0 0.0 104-105 0.85 0.0 0.0 0.0 0.0 106-107 1.0499999999999998 0.0 0.0 0.0 0.0 108-109 1.325 0.0 0.0 0.0 0.0 110-111 1.6 0.0 0.0 0.0 0.0 112-113 1.8875 0.0 0.0 0.0 0.0 114-115 2.1 0.0 0.0 0.0 0.0 116-117 2.4125 0.0 0.0 0.0 0.0 118-119 2.7375 0.0 0.0 0.0 0.0 120-121 3.1875 0.0 0.0 0.0 0.0 122-123 3.6125 0.0 0.0 0.0 0.0 124-125 4.1125 0.0 0.0 0.0 0.0 126-127 4.6375 0.0 0.0 0.0 0.0 128-129 5.075 0.0 0.0 0.0 0.0 130-131 5.525 0.0 0.0 0.0 0.0 132-133 6.012499999999999 0.0 0.0 0.0 0.0 134-135 6.725 0.0 0.0 0.0 0.0 136-137 7.25 0.0 0.0 0.0 0.0 138-139 7.8375 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position CTTTAAT 10 0.0060887975 150.61038 1 AGCGCCA 10 0.006836113 144.9625 8 >>END_MODULE SRR7171496 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR7171496_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 33.0575 33.0 33.0 34.0 32.0 34.0 2 33.029 34.0 33.0 34.0 32.0 34.0 3 33.134 34.0 33.0 34.0 32.0 34.0 4 33.126 34.0 33.0 34.0 33.0 34.0 5 33.092 34.0 33.0 34.0 33.0 34.0 6 37.23875 38.0 38.0 38.0 37.0 38.0 7 37.244 38.0 38.0 38.0 37.0 38.0 8 37.17325 38.0 38.0 38.0 37.0 38.0 9 37.20325 38.0 38.0 38.0 37.0 38.0 10-14 37.218849999999996 38.0 38.0 38.0 37.0 38.0 15-19 37.19265 38.0 38.0 38.0 37.0 38.0 20-24 37.15474999999999 38.0 38.0 38.0 37.0 38.0 25-29 37.1703 38.0 38.0 38.0 37.0 38.0 30-34 37.169650000000004 38.0 38.0 38.0 37.0 38.0 35-39 37.110949999999995 38.0 38.0 38.0 36.8 38.0 40-44 36.967400000000005 38.0 38.0 38.0 36.2 38.0 45-49 36.9777 38.0 38.0 38.0 36.0 38.0 50-54 37.0475 38.0 38.0 38.0 36.6 38.0 55-59 37.0003 38.0 38.0 38.0 36.0 38.0 60-64 36.967600000000004 38.0 38.0 38.0 36.0 38.0 65-69 37.00025000000001 38.0 38.0 38.0 36.0 38.0 70-74 37.00695 38.0 38.0 38.0 36.0 38.0 75-79 36.9103 38.0 38.0 38.0 35.8 38.0 80-84 36.886100000000006 38.0 38.0 38.0 35.8 38.0 85-89 36.847150000000006 38.0 38.0 38.0 35.6 38.0 90-94 36.684799999999996 38.0 38.0 38.0 35.0 38.0 95-99 36.70715 38.0 38.0 38.0 35.2 38.0 100-104 36.5522 38.0 38.0 38.0 34.2 38.0 105-109 36.5043 38.0 38.0 38.0 34.2 38.0 110-114 36.428349999999995 38.0 38.0 38.0 34.2 38.0 115-119 36.361149999999995 38.0 38.0 38.0 34.0 38.0 120-124 36.168499999999995 38.0 38.0 38.0 33.4 38.0 125-129 36.07665 38.0 37.8 38.0 33.0 38.0 130-134 36.038050000000005 38.0 37.4 38.0 33.0 38.0 135-139 35.776300000000006 38.0 36.6 38.0 32.0 38.0 140-144 35.5265 38.0 36.0 38.0 31.0 38.0 145-149 35.1927 38.0 35.8 38.0 29.2 38.0 150-151 32.472625 35.5 29.5 38.0 20.5 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 2.0 3 0.0 4 0.0 5 0.0 6 1.0 7 0.0 8 0.0 9 0.0 10 0.0 11 1.0 12 2.0 13 0.0 14 0.0 15 1.0 16 3.0 17 3.0 18 6.0 19 3.0 20 4.0 21 3.0 22 4.0 23 7.0 24 13.0 25 14.0 26 13.0 27 15.0 28 20.0 29 43.0 30 45.0 31 46.0 32 67.0 33 90.0 34 122.0 35 192.0 36 431.0 37 2849.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 38.594297148574285 19.834917458729365 14.882441220610303 26.688344172086044 2 25.293970477858394 26.720040030022517 29.321991493620214 18.663997998498875 3 20.690517888416313 29.39704778583938 31.573680260195147 18.33875406554916 4 25.375375375375377 34.209209209209206 22.347347347347345 18.06806806806807 5 24.912368552829246 35.878818227341014 21.75763645468202 17.45117676514772 6 20.61106937139995 37.34034560480842 23.59128474830954 18.457300275482094 7 20.18532431755572 21.26220886551465 39.318807913849234 19.233658903080393 8 22.70906359539309 24.812218327491237 27.916875312969452 24.56184276414622 9 22.61457550713749 24.843476083145504 29.42649636864513 23.115452041071876 10-14 23.725077647530306 28.754633804228035 26.314998497144575 21.205290051097084 15-19 23.67880579071282 28.096979411912038 27.76636778039373 20.457847016981415 20-24 23.294259092275325 27.862939585211905 27.166616571485825 21.676184751026952 25-29 23.51379776631442 28.742425001252066 27.750788801522514 19.992988430911005 30-34 23.227065712426807 27.8214303588409 28.211801211150593 20.739702717581704 35-39 22.989943463251112 27.57292239955971 28.19832891379397 21.238805223395207 40-44 23.27094384946452 28.49064157741968 27.544790311280153 20.69362426183565 45-49 24.02603905858788 28.637956935403103 27.57135703555333 19.764646970455686 50-54 23.44603055346857 27.803656398697722 27.908840470823943 20.841472577009768 55-59 23.915439334736 27.988177537320908 27.47720669271616 20.619176435226933 60-64 23.381763527054108 28.406813627254508 27.70541082164329 20.506012024048097 65-69 23.433665548154455 28.041268092352382 27.425251665247657 21.099814694245506 70-74 23.810476809926453 28.2883874518437 27.437834592485117 20.463301145744733 75-79 23.743310158555495 27.879757915270343 28.064822687940776 20.31210923823338 80-84 24.021005251312825 27.826956739184794 27.41685421355339 20.735183795948984 85-89 23.898143979188553 27.710240632347794 27.330031517334536 21.061583871129123 90-94 23.69343211854225 28.33400080096115 27.863436123348016 20.109130957148576 95-99 23.72270086155079 28.250851532758965 27.930274494089364 20.096173111600883 100-104 23.77229905792744 28.497694928843455 27.285027059530968 20.444978953698136 105-109 24.30726061031217 27.644435536403268 27.804780277596837 20.24352357568773 110-114 24.25821972734563 27.83179631114675 27.66138732959102 20.248596631916598 115-119 23.920232488225274 28.244313057420584 27.95871329792564 19.876741156428498 120-124 24.610607502378926 27.585516101567585 27.139780638052784 20.6640957580007 125-129 24.798558630699162 28.72228617186327 26.990641109053605 19.488514088383965 130-134 24.816093679627684 28.058850022519145 27.568433168192964 19.55662312966021 135-139 25.07136775679872 28.69234236490209 26.64396253818801 19.592327340111186 140-144 25.36213723622876 28.184050924765675 26.870833542178335 19.58297829682723 145-149 26.11397924916044 28.374517568041703 26.424740614505538 19.08676256829232 150-151 27.123527937860185 27.248809822099723 26.772738661989475 18.854923578050613 >>END_MODULE >>Per sequence GC content pass #GC Content Count 0 1.0 1 0.5 2 0.5 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 1.0 12 1.5 13 0.5 14 0.0 15 0.0 16 0.0 17 0.5 18 1.0 19 0.5 20 0.5 21 1.0 22 0.5 23 1.0 24 2.0 25 3.5 26 6.0 27 4.5 28 3.0 29 3.5 30 9.0 31 17.0 32 21.0 33 25.0 34 41.0 35 60.0 36 78.0 37 106.5 38 138.5 39 168.5 40 178.0 41 216.5 42 259.5 43 286.5 44 310.0 45 310.0 46 298.5 47 258.5 48 223.5 49 196.5 50 157.0 51 125.5 52 116.0 53 97.5 54 66.5 55 49.5 56 37.5 57 25.0 58 21.5 59 16.0 60 11.5 61 13.0 62 10.0 63 5.5 64 3.0 65 2.5 66 2.0 67 2.0 68 1.5 69 1.0 70 1.0 71 0.5 72 0.0 73 0.0 74 0.0 75 0.0 76 0.0 77 0.0 78 0.0 79 0.0 80 0.0 81 0.0 82 0.0 83 0.0 84 0.0 85 0.0 86 0.0 87 0.0 88 0.0 89 0.0 90 0.0 91 0.0 92 0.0 93 0.0 94 0.0 95 0.0 96 0.0 97 0.0 98 0.0 99 0.0 100 0.0 >>END_MODULE >>Per base N content pass #Base N-Count 1 0.05 2 0.075 3 0.075 4 0.1 5 0.15 6 0.17500000000000002 7 0.17500000000000002 8 0.15 9 0.17500000000000002 10-14 0.19 15-19 0.185 20-24 0.19 25-29 0.165 30-34 0.095 35-39 0.065 40-44 0.09 45-49 0.15 50-54 0.17500000000000002 55-59 0.19 60-64 0.2 65-69 0.165 70-74 0.065 75-79 0.034999999999999996 80-84 0.025 85-89 0.055 90-94 0.12 95-99 0.18 100-104 0.22 105-109 0.215 110-114 0.24 115-119 0.21 120-124 0.165 125-129 0.095 130-134 0.08499999999999999 135-139 0.165 140-144 0.245 145-149 0.245 150-151 0.22499999999999998 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 99.75 #Duplication Level Percentage of deduplicated Percentage of total 1 99.77443609022556 99.52499999999999 2 0.20050125313283207 0.4 3 0.02506265664160401 0.075 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 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 0.0 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 0.0125 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 0.0625 0.0 0.0 0.0 0.0 82-83 0.0875 0.0 0.0 0.0 0.0 84-85 0.125 0.0 0.0 0.0 0.0 86-87 0.125 0.0 0.0 0.0 0.0 88-89 0.1375 0.0 0.0 0.0 0.0 90-91 0.2125 0.0 0.0 0.0 0.0 92-93 0.2625 0.0 0.0 0.0 0.0 94-95 0.375 0.0 0.0 0.0 0.0 96-97 0.5125 0.0 0.0 0.0 0.0 98-99 0.6125 0.0 0.0 0.0 0.0 100-101 0.6625 0.0 0.0 0.0 0.0 102-103 0.7625 0.0 0.0 0.0 0.0 104-105 0.875 0.0 0.0 0.0 0.0 106-107 1.0750000000000002 0.0 0.0 0.0 0.0 108-109 1.3375 0.0 0.0 0.0 0.0 110-111 1.625 0.0 0.0 0.0 0.0 112-113 1.9375 0.0 0.0 0.0 0.0 114-115 2.125 0.0 0.0 0.0 0.0 116-117 2.4125 0.0 0.0 0.0 0.0 118-119 2.7 0.0 0.0 0.0 0.0 120-121 3.1125 0.0 0.0 0.0 0.0 122-123 3.5374999999999996 0.0 0.0 0.0 0.0 124-125 4.025 0.0 0.0 0.0 0.0 126-127 4.5375 0.0 0.0 0.0 0.0 128-129 4.975 0.0 0.0 0.0 0.0 130-131 5.4125 0.0 0.0 0.0 0.0 132-133 5.9125 0.0 0.0 0.0 0.0 134-135 6.625 0.0 0.0 0.0 0.0 136-137 7.15 0.0 0.0 0.0 0.0 138-139 7.737500000000001 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GGAGGCT 20 0.00593511 29.0 30-34 >>END_MODULE Read 889340 spots for SRR7171496.sra Written 889340 spots for SRR7171496.sra Read 889340 spots for SRR7171496.sra Written 889340 spots for SRR7171496.sra Read 889340 spots for SRR7171496.sra Written 889340 spots for SRR7171496.sra Read 889340 spots for SRR7171496.sra Written 889340 spots for SRR7171496.sra Read 889340 spots for SRR7171496.sra Written 889340 spots for SRR7171496.sra Read 889340 spots for SRR7171496.sra Written 889340 spots for SRR7171496.sra Read 889340 spots for SRR7171496.sra Written 889340 spots for SRR7171496.sra Read 889344 spots for SRR7171496.sra Written 889344 spots for SRR7171496.sra Read 889340 spots for SRR7171496.sra Written 889340 spots for SRR7171496.sra Read 889340 spots for SRR7171496.sra Written 889340 spots for SRR7171496.sra Read 889340 spots for SRR7171496.sra Written 889340 spots for SRR7171496.sra Read 889340 spots for SRR7171496.sra Written 889340 spots for SRR7171496.sra Read 889340 spots for SRR7171496.sra Written 889340 spots for SRR7171496.sra Read 889340 spots for SRR7171496.sra Written 889340 spots for SRR7171496.sra Read 889340 spots for SRR7171496.sra Written 889340 spots for SRR7171496.sra Read 889340 spots for SRR7171496.sra Written 889340 spots for SRR7171496.sra Read 889340 spots for SRR7171496.sra Written 889340 spots for SRR7171496.sra Read 889340 spots for SRR7171496.sra Written 889340 spots for SRR7171496.sra Read 889340 spots for SRR7171496.sra Written 889340 spots for SRR7171496.sra Read 889340 spots for SRR7171496.sra Written 889340 spots for SRR7171496.sra SRR ids: ['SRR7171496.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_5kialas3 SRR7171496.sra spots: 17786804 blocks: [[1, 889340], [889341, 1778680], [1778681, 2668020], [2668021, 3557360], [3557361, 4446700], [4446701, 5336040], [5336041, 6225380], [6225381, 7114720], [7114721, 8004060], [8004061, 8893400], [8893401, 9782740], [9782741, 10672080], [10672081, 11561420], [11561421, 12450760], [12450761, 13340100], [13340101, 14229440], [14229441, 15118780], [15118781, 16008120], [16008121, 16897460], [16897461, 17786804]] SRR7171496 file size 6005663 SRR7171496 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 SRR7171496 SRR7171496_1.fastq SRR7171496_2.fastq Input file: SRR7171496_1.fastq Paired file: SRR7171496_2.fastq trimmed: SRR7171496-trimmed-pair1.fastq, SRR7171496-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 Thu Feb 13 20:34:18 2025 >> started Thu Feb 13 20:34:38 2025 >> done (19.848s) 17786804 read pairs processed; of these: 14 ( 0.00%) short read pairs filtered out after trimming by size control 1461 ( 0.01%) empty read pairs filtered out after trimming by size control 17785329 (99.99%) read pairs available; of these: 2451915 (13.79%) trimmed read pairs available after processing 15333414 (86.21%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 20 2 0.00% 21 0 0.00% 22 0 0.00% 23 0 0.00% 24 2 0.00% 25 2 0.00% 26 1 0.00% 27 1 0.00% 28 2 0.00% 29 2 0.00% 30 1 0.00% 31 1 0.00% 32 2 0.00% 33 3 0.00% 34 0 0.00% 35 2 0.00% 36 3 0.00% 37 4 0.00% 38 2 0.00% 39 2 0.00% 40 4 0.00% 41 6 0.00% 42 4 0.00% 43 5 0.00% 44 4 0.00% 45 10 0.00% 46 12 0.00% 47 13 0.00% 48 15 0.00% 49 18 0.00% 50 27 0.00% 51 26 0.00% 52 21 0.00% 53 37 0.00% 54 34 0.00% 55 46 0.00% 56 54 0.00% 57 68 0.00% 58 54 0.00% 59 74 0.00% 60 96 0.00% 61 101 0.00% 62 117 0.00% 63 150 0.00% 64 174 0.00% 65 194 0.00% 66 208 0.00% 67 261 0.00% 68 336 0.00% 69 311 0.00% 70 435 0.00% 71 494 0.00% 72 581 0.00% 73 726 0.00% 74 797 0.00% 75 880 0.00% 76 1032 0.01% 77 1148 0.01% 78 1354 0.01% 79 1470 0.01% 80 1802 0.01% 81 2020 0.01% 82 2423 0.01% 83 2681 0.02% 84 3101 0.02% 85 3531 0.02% 86 3895 0.02% 87 4296 0.02% 88 4646 0.03% 89 5105 0.03% 90 5734 0.03% 91 6239 0.04% 92 7050 0.04% 93 7988 0.04% 94 8958 0.05% 95 9643 0.05% 96 10670 0.06% 97 11119 0.06% 98 11765 0.07% 99 12707 0.07% 100 13606 0.08% 101 14979 0.08% 102 16070 0.09% 103 17570 0.10% 104 18464 0.10% 105 19831 0.11% 106 20956 0.12% 107 21869 0.12% 108 22846 0.13% 109 23573 0.13% 110 24479 0.14% 111 25823 0.15% 112 27457 0.15% 113 28949 0.16% 114 30761 0.17% 115 32753 0.18% 116 34518 0.19% 117 38345 0.22% 118 40127 0.23% 119 38360 0.22% 120 37699 0.21% 121 38784 0.22% 122 40244 0.23% 123 41950 0.24% 124 43755 0.25% 125 45146 0.25% 126 46839 0.26% 127 47935 0.27% 128 48561 0.27% 129 49363 0.28% 130 50703 0.29% 131 51072 0.29% 132 52848 0.30% 133 54758 0.31% 134 56791 0.32% 135 58505 0.33% 136 60174 0.34% 137 60450 0.34% 138 61511 0.35% 139 61989 0.35% 140 64145 0.36% 141 70049 0.39% 142 68964 0.39% 143 71417 0.40% 144 71606 0.40% 145 75097 0.42% 146 71260 0.40% 147 72629 0.41% 148 76233 0.43% 149 73347 0.41% 150 79953 0.45% 151 15333414 86.21% 17785329 reads passed initial QC criterion=sequence-density sequence-density=0.37 sequence-density-rank=1 fanout-score=6.34 fanout-score-rank=14 prefix-density=0.74 prefix-fanout=3.2 sequence=TTGCAGCCATTCTCAGCACCAAAGTTCATCTCAGAGCTCTCGTAGAACATCCTAACTGGAGCTACACCAGCAATGATTGT criterion=fanout-score sequence-density=0.02 sequence-density-rank=31 fanout-score=115.17 fanout-score-rank=1 prefix-density=0.17 prefix-fanout=13.5 sequence=CTCCTTCCTCTAAATGATAAGGTTCAGTGGACTTCTCGCGACGTCGCCGGCGGCGAACCGCCCACGTCGCCGCGATCCGAACACTTCACCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGAATTCCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCAAAGATTACCCGGGCCTGTCGGCCAAGGCTATAGACTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCAAACTTCCTTGGCCTGGAAGGCCATAGTCCCTCTAAGAAGCTGGCCGCGGAGGGTCACCTCCGCATAGCTAGTTAGCAGGCTGAGGTCTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCATGCACCACCACCCATAGAATCAAGAAA criterion=sequence-density sequence-density=0.48 sequence-density-rank=1 fanout-score=2.13 fanout-score-rank=30 prefix-density=0.49 prefix-fanout=2.1 sequence=GGCAGTGGCTGCAA criterion=fanout-score sequence-density=0.07 sequence-density-rank=28 fanout-score=41.35 fanout-score-rank=1 prefix-density=0.23 prefix-fanout=13.0 sequence=GAGAAGGCAATGAGAGATGC SRR7171496 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 13 20:35:25 Started mapping on | Feb 13 20:35:26 Finished on | Feb 13 20:38:14 Mapping speed, Million of reads per hour | 381.11 Number of input reads | 17785329 Average input read length | 295 UNIQUE READS: Uniquely mapped reads number | 16069514 Uniquely mapped reads % | 90.35% Average mapped length | 294.62 Number of splices: Total | 16030752 Number of splices: Annotated (sjdb) | 15708294 Number of splices: GT/AG | 15763190 Number of splices: GC/AG | 208812 Number of splices: AT/AC | 12868 Number of splices: Non-canonical | 45882 Mismatch rate per base, % | 0.41% Deletion rate per base | 0.03% Deletion average length | 2.35 Insertion rate per base | 0.02% Insertion average length | 2.61 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 461686 % of reads mapped to multiple loci | 2.60% Number of reads mapped to too many loci | 124463 % of reads mapped to too many loci | 0.70% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 6.15% % of reads unmapped: other | 0.20% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 1254129 1254129 1254129 N_multimapping 461686 461686 461686 N_noFeature 445028 15923390 503255 N_ambiguous 172278 887 83810 UnstrandedReadsAssigned:15452208 PositiveStrandReadsAssigned:145237 NegativeStrandReadsAssigned:15482449 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=151 echo kmer=147 SRR7171496 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: SRR7171496-trimmed-pair1.fastq SRR7171496-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 17,785,329 reads, 15,589,709 reads pseudoaligned [quant] estimated average fragment length: 223.131 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,090 rounds 52401 SRR7171496.ke.tsv 34699 SRR7171496.se.tsv 87100 total ==> SRR7171496.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1795.87 1159 40.5551 Potri.005G024800.1.v4.1 1035 812.869 245 18.9401 Potri.004G059700.1.v4.1 961 738.874 49 4.16737 Potri.007G009000.2.v4.1 1416 1193.87 0 0 Potri.003G141000.2.v4.1 2943 2720.87 507.148 11.7129 Potri.016G087400.1.v4.1 270 85.6896 1307 958.483 Potri.015G069301.1.v4.1 564 344.525 0 0 Potri.010G195200.1.v4.1 1773 1550.87 503 20.3812 Potri.012G127500.1.v4.1 977 754.874 6270 521.951 ==> SRR7171496.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 67 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 614 Potri.001G212900.v4.1 0 Potri.001G182400.v4.1 0 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 0 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 387 SRR7171496 completed mapping pipeline successfully