Starting /dee2/code/volunteer_pipeline.sh SRR12919337 current disk space = 3051101306880 free memory = 992420272 SRR12919337 SRAfilesize daf522601beb92a50bee0962d567a828 SRR12919337.sra SRR12919337.sra file validated SRR12919337 is paired end SRR12919337 is conventional basespace SRR12919337 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12919337_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 pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.5775 37.0 37.0 37.0 37.0 37.0 2 36.1905 37.0 37.0 37.0 37.0 37.0 3 36.6985 37.0 37.0 37.0 37.0 37.0 4 36.693 37.0 37.0 37.0 37.0 37.0 5 36.615 37.0 37.0 37.0 37.0 37.0 6 36.687 37.0 37.0 37.0 37.0 37.0 7 36.58 37.0 37.0 37.0 37.0 37.0 8 36.706 37.0 37.0 37.0 37.0 37.0 9 36.6775 37.0 37.0 37.0 37.0 37.0 10-14 36.6838 37.0 37.0 37.0 37.0 37.0 15-19 36.6517 37.0 37.0 37.0 37.0 37.0 20-24 36.6168 37.0 37.0 37.0 37.0 37.0 25-29 36.5792 37.0 37.0 37.0 37.0 37.0 30-34 36.533899999999996 37.0 37.0 37.0 37.0 37.0 35-39 36.527100000000004 37.0 37.0 37.0 37.0 37.0 40-44 36.4964 37.0 37.0 37.0 37.0 37.0 45-49 36.5055 37.0 37.0 37.0 37.0 37.0 50-54 36.4577 37.0 37.0 37.0 37.0 37.0 55-59 36.485699999999994 37.0 37.0 37.0 37.0 37.0 60-64 36.410399999999996 37.0 37.0 37.0 37.0 37.0 65-69 36.443 37.0 37.0 37.0 37.0 37.0 70-74 36.346 37.0 37.0 37.0 37.0 37.0 75-79 36.352 37.0 37.0 37.0 37.0 37.0 80-84 36.3352 37.0 37.0 37.0 37.0 37.0 85-89 36.2654 37.0 37.0 37.0 37.0 37.0 90-94 36.2625 37.0 37.0 37.0 37.0 37.0 95-99 36.21040000000001 37.0 37.0 37.0 37.0 37.0 100-104 36.179199999999994 37.0 37.0 37.0 37.0 37.0 105-109 36.1391 37.0 37.0 37.0 37.0 37.0 110-114 36.1345 37.0 37.0 37.0 37.0 37.0 115-119 36.0967 37.0 37.0 37.0 37.0 37.0 120-124 36.1006 37.0 37.0 37.0 37.0 37.0 125-129 36.0093 37.0 37.0 37.0 37.0 37.0 130-134 35.935199999999995 37.0 37.0 37.0 37.0 37.0 135-139 35.9019 37.0 37.0 37.0 37.0 37.0 140-144 35.7807 37.0 37.0 37.0 37.0 37.0 145-149 35.8551 37.0 37.0 37.0 37.0 37.0 150-151 35.661 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 19 1.0 20 0.0 21 0.0 22 0.0 23 1.0 24 3.0 25 1.0 26 5.0 27 7.0 28 13.0 29 9.0 30 25.0 31 35.0 32 36.0 33 75.0 34 109.0 35 291.0 36 2954.0 37 435.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 39.0 11.600000000000001 7.175 42.225 2 20.17145738779627 13.993948562783661 35.07312153303076 30.76147251638931 3 17.974999999999998 18.0 28.349999999999998 35.675000000000004 4 21.325 25.7 23.549999999999997 29.425 5 22.625 31.324999999999996 23.95 22.1 6 20.200000000000003 35.025 23.075000000000003 21.7 7 14.399999999999999 25.8 42.525 17.275 8 18.275 26.325 31.6 23.799999999999997 9 16.275000000000002 25.15 34.375 24.2 10-14 19.705000000000002 29.62 27.655 23.02 15-19 19.28 28.16 28.33 24.23 20-24 20.225 28.810000000000002 27.994999999999997 22.97 25-29 19.689999999999998 29.125 27.79 23.395 30-34 19.52 28.455000000000002 28.235 23.79 35-39 19.53 28.294999999999998 28.249999999999996 23.925 40-44 19.27 28.96 27.355 24.415 45-49 19.77 29.24 27.384999999999998 23.605 50-54 20.335 28.744999999999997 27.715 23.205000000000002 55-59 19.66 29.005 27.76 23.575 60-64 20.225 28.565 27.994999999999997 23.215 65-69 20.13 28.235 28.37 23.265 70-74 20.25 28.22 27.755000000000003 23.775 75-79 20.375 28.76 27.560000000000002 23.305 80-84 20.255000000000003 28.060000000000002 28.335 23.35 85-89 20.705000000000002 28.485 27.72 23.09 90-94 19.59 28.095 28.355000000000004 23.96 95-99 20.150000000000002 28.865000000000002 28.17 22.814999999999998 100-104 19.62 29.220000000000002 27.565 23.595 105-109 20.565 27.58 28.349999999999998 23.505000000000003 110-114 20.265 28.455000000000002 27.87 23.41 115-119 20.22 28.79 27.189999999999998 23.799999999999997 120-124 20.65 28.93 27.075 23.345 125-129 20.565 28.845 27.11 23.48 130-134 20.72 28.610000000000003 27.43 23.24 135-139 20.32 29.439999999999998 26.915 23.325000000000003 140-144 21.075 28.205000000000002 26.665 24.055 145-149 20.935000000000002 28.87 26.71 23.485 150-151 21.45 28.287499999999998 26.9125 23.35 >>END_MODULE >>Per sequence GC content pass #GC Content Count 0 0.0 1 0.0 2 0.5 3 0.5 4 0.0 5 0.0 6 0.0 7 0.0 8 0.5 9 0.5 10 0.0 11 0.5 12 0.5 13 0.0 14 0.0 15 0.0 16 0.0 17 0.5 18 0.5 19 0.0 20 0.5 21 1.5 22 1.5 23 1.5 24 3.5 25 6.0 26 6.0 27 6.0 28 6.0 29 9.0 30 15.0 31 27.5 32 39.5 33 46.5 34 58.0 35 65.5 36 77.0 37 111.0 38 141.0 39 160.5 40 188.5 41 235.0 42 274.0 43 280.5 44 265.0 45 265.5 46 270.5 47 247.5 48 213.0 49 191.0 50 176.0 51 138.5 52 103.5 53 91.0 54 77.5 55 54.5 56 40.0 57 31.5 58 22.5 59 12.0 60 6.5 61 7.5 62 7.0 63 4.5 64 3.0 65 2.0 66 1.5 67 1.0 68 1.0 69 0.5 70 0.0 71 0.0 72 0.0 73 0.5 74 0.5 75 0.0 76 0.0 77 0.0 78 0.0 79 0.0 80 0.0 81 0.0 82 0.0 83 0.0 84 0.0 85 0.0 86 0.0 87 0.0 88 0.0 89 0.0 90 0.0 91 0.0 92 0.0 93 0.0 94 0.0 95 0.0 96 0.0 97 0.0 98 0.0 99 0.0 100 0.0 >>END_MODULE >>Per base N content pass #Base N-Count 1 0.0 2 0.8500000000000001 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 0.0 140-144 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 90.45 #Duplication Level Percentage of deduplicated Percentage of total 1 90.6301824212272 81.975 2 8.208955223880597 14.85 3 1.1332227750138197 3.075 4 0.027639579878385848 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 0.0 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 0.025 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 0.075 0.0 0.0 0.0 0.0 66-67 0.075 0.0 0.0 0.0 0.0 68-69 0.075 0.0 0.0 0.0 0.0 70-71 0.075 0.0 0.0 0.0 0.0 72-73 0.1 0.0 0.0 0.0 0.0 74-75 0.1 0.0 0.0 0.0 0.0 76-77 0.1375 0.0 0.0 0.0 0.0 78-79 0.15 0.0 0.0 0.0 0.0 80-81 0.175 0.0 0.0 0.0 0.0 82-83 0.2 0.0 0.0 0.0 0.0 84-85 0.2625 0.0 0.0 0.0 0.0 86-87 0.275 0.0 0.0 0.0 0.0 88-89 0.4 0.0 0.0 0.0 0.0 90-91 0.5 0.0 0.0 0.0 0.0 92-93 0.525 0.0 0.0 0.0 0.0 94-95 0.55 0.0 0.0 0.0 0.0 96-97 0.625 0.0 0.0 0.0 0.0 98-99 0.7125 0.0 0.0 0.0 0.0 100-101 0.8875 0.0 0.0 0.0 0.0 102-103 1.0875 0.0 0.0 0.0 0.0 104-105 1.1875 0.0 0.0 0.0 0.0 106-107 1.4375 0.0 0.0 0.0 0.0 108-109 1.6875 0.0 0.0 0.0 0.0 110-111 1.875 0.0 0.0 0.0 0.0 112-113 2.0875000000000004 0.0 0.0 0.0 0.0 114-115 2.45 0.0 0.0 0.0 0.0 116-117 2.8375 0.0 0.0 0.0 0.0 118-119 3.0250000000000004 0.0 0.0 0.0 0.0 120-121 3.375 0.0 0.0 0.0 0.0 122-123 3.8 0.0 0.0 0.0 0.0 124-125 4.2125 0.0 0.0 0.0 0.0 126-127 4.475 0.0 0.0 0.0 0.0 128-129 4.875 0.0 0.0 0.0 0.0 130-131 5.262499999999999 0.0 0.0 0.0 0.0 132-133 5.637499999999999 0.0 0.0 0.0 0.0 134-135 6.275 0.0 0.0 0.0 0.0 136-137 6.9875 0.0 0.0 0.0 0.0 138-139 7.4 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position ACAGCAA 10 0.006830828 145.0 7 CAGCAAG 10 0.006830828 145.0 8 ATAAGAC 10 0.006830828 145.0 2 GATAAGA 10 0.006830828 145.0 1 AAGGGAC 10 0.006830828 145.0 8 GTCCTGT 10 0.006830828 145.0 1 TGCCATC 10 0.006830828 145.0 3 CCATCAA 10 0.006830828 145.0 5 GCCATCA 10 0.006830828 145.0 4 AAAATTC 10 0.006830828 145.0 3 AGCAAGA 10 0.006830828 145.0 9 TAAGGGA 10 0.006830828 145.0 7 TTGCCAT 10 0.006830828 145.0 2 >>END_MODULE SRR12919337 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12919337_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 36.216 37.0 37.0 37.0 37.0 37.0 2 36.345 37.0 37.0 37.0 37.0 37.0 3 36.34 37.0 37.0 37.0 37.0 37.0 4 36.27 37.0 37.0 37.0 37.0 37.0 5 36.3365 37.0 37.0 37.0 37.0 37.0 6 36.226 37.0 37.0 37.0 37.0 37.0 7 36.3315 37.0 37.0 37.0 37.0 37.0 8 36.2985 37.0 37.0 37.0 37.0 37.0 9 36.381 37.0 37.0 37.0 37.0 37.0 10-14 36.317 37.0 37.0 37.0 37.0 37.0 15-19 36.280899999999995 37.0 37.0 37.0 37.0 37.0 20-24 36.329899999999995 37.0 37.0 37.0 37.0 37.0 25-29 36.200599999999994 37.0 37.0 37.0 37.0 37.0 30-34 36.1461 37.0 37.0 37.0 37.0 37.0 35-39 36.137100000000004 37.0 37.0 37.0 37.0 37.0 40-44 36.098400000000005 37.0 37.0 37.0 37.0 37.0 45-49 36.080600000000004 37.0 37.0 37.0 37.0 37.0 50-54 35.98049999999999 37.0 37.0 37.0 37.0 37.0 55-59 36.054899999999996 37.0 37.0 37.0 37.0 37.0 60-64 36.0357 37.0 37.0 37.0 37.0 37.0 65-69 35.9717 37.0 37.0 37.0 37.0 37.0 70-74 35.9635 37.0 37.0 37.0 37.0 37.0 75-79 35.927499999999995 37.0 37.0 37.0 37.0 37.0 80-84 35.8914 37.0 37.0 37.0 37.0 37.0 85-89 35.891299999999994 37.0 37.0 37.0 37.0 37.0 90-94 35.794200000000004 37.0 37.0 37.0 37.0 37.0 95-99 35.8175 37.0 37.0 37.0 37.0 37.0 100-104 35.797 37.0 37.0 37.0 37.0 37.0 105-109 35.7716 37.0 37.0 37.0 37.0 37.0 110-114 35.78959999999999 37.0 37.0 37.0 37.0 37.0 115-119 35.6627 37.0 37.0 37.0 37.0 37.0 120-124 35.6785 37.0 37.0 37.0 37.0 37.0 125-129 35.5387 37.0 37.0 37.0 37.0 37.0 130-134 35.4732 37.0 37.0 37.0 37.0 37.0 135-139 35.3272 37.0 37.0 37.0 37.0 37.0 140-144 35.351099999999995 37.0 37.0 37.0 37.0 37.0 145-149 35.1305 37.0 37.0 37.0 29.8 37.0 150-151 34.9215 37.0 37.0 37.0 25.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 13 2.0 14 7.0 15 9.0 16 3.0 17 2.0 18 1.0 19 0.0 20 2.0 21 3.0 22 1.0 23 6.0 24 9.0 25 9.0 26 6.0 27 6.0 28 11.0 29 26.0 30 17.0 31 40.0 32 51.0 33 97.0 34 185.0 35 515.0 36 2683.0 37 309.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 39.875 21.65 11.975 26.5 2 26.05 25.525 31.35 17.075000000000003 3 22.0 27.575 31.65 18.775 4 25.55 33.575 22.425 18.45 5 25.5 35.25 21.85 17.4 6 21.65 37.75 23.849999999999998 16.75 7 19.75 21.725 38.625 19.900000000000002 8 21.925 25.15 28.575 24.349999999999998 9 22.825 23.974999999999998 30.375000000000004 22.825 10-14 23.79 28.64 27.12 20.45 15-19 23.405 28.09 27.744999999999997 20.76 20-24 23.025000000000002 28.675 27.534999999999997 20.765 25-29 23.830000000000002 28.23 27.860000000000003 20.080000000000002 30-34 22.96 29.12 27.77 20.150000000000002 35-39 23.285 28.735 27.98 20.0 40-44 23.645 28.305000000000003 27.765 20.285 45-49 23.835 28.48 27.665 20.02 50-54 23.895 27.575 28.345 20.185 55-59 23.18 28.294999999999998 28.005000000000003 20.52 60-64 23.505000000000003 28.34 27.935 20.22 65-69 23.380000000000003 27.905 28.310000000000002 20.405 70-74 23.57 28.28 28.060000000000002 20.09 75-79 23.47 28.32 28.055000000000003 20.155 80-84 23.474999999999998 28.49 27.894999999999996 20.14 85-89 23.965 28.16 27.73 20.145 90-94 23.66 28.54 27.625 20.175 95-99 23.45 28.18 27.735 20.635 100-104 22.93 28.595 28.305000000000003 20.169999999999998 105-109 23.9 28.065 27.825 20.21 110-114 23.810000000000002 28.1 27.68 20.41 115-119 23.41 28.22 28.22 20.150000000000002 120-124 23.86 27.939999999999998 27.96 20.24 125-129 24.645 28.42 27.12 19.814999999999998 130-134 24.58 27.88 27.66 19.88 135-139 24.884999999999998 27.845 27.96 19.31 140-144 25.35 28.37 26.41 19.869999999999997 145-149 25.180000000000003 28.799999999999997 26.584999999999997 19.435 150-151 25.624999999999996 28.287499999999998 27.0 19.0875 >>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 0.5 7 1.0 8 0.5 9 0.0 10 0.0 11 0.0 12 1.0 13 1.0 14 1.0 15 1.0 16 0.5 17 0.5 18 0.5 19 0.5 20 0.5 21 2.0 22 1.5 23 1.5 24 3.0 25 3.5 26 5.0 27 6.5 28 9.5 29 14.5 30 18.5 31 20.0 32 26.5 33 48.5 34 60.0 35 67.0 36 86.5 37 106.5 38 135.0 39 170.5 40 206.0 41 232.0 42 248.0 43 286.0 44 301.5 45 279.5 46 255.0 47 245.0 48 238.5 49 190.0 50 155.5 51 126.0 52 91.5 53 81.5 54 61.5 55 45.5 56 35.5 57 27.5 58 22.5 59 15.0 60 11.0 61 9.5 62 6.5 63 3.5 64 4.5 65 3.0 66 1.0 67 0.0 68 0.0 69 0.5 70 1.0 71 1.5 72 3.0 73 2.0 74 0.0 75 1.0 76 1.0 77 0.0 78 0.0 79 0.0 80 0.5 81 1.0 82 0.5 83 1.0 84 1.0 85 0.0 86 0.0 87 0.0 88 0.5 89 0.5 90 0.5 91 0.5 92 0.5 93 0.5 94 0.0 95 0.0 96 0.0 97 0.0 98 0.0 99 0.0 100 3.0 >>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 0.0 140-144 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 90.275 #Duplication Level Percentage of deduplicated Percentage of total 1 90.61201883134866 81.8 2 8.197175297701467 14.799999999999999 3 1.1077263915812794 3.0 4 0.05538631957906397 0.2 5 0.0 0.0 6 0.0 0.0 7 0.0 0.0 8 0.027693159789531983 0.2 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 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 8 0.2 No Hit >>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 0.025 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 0.075 0.0 0.0 0.0 0.0 66-67 0.075 0.0 0.0 0.0 0.0 68-69 0.075 0.0 0.0 0.0 0.0 70-71 0.075 0.0 0.0 0.0 0.0 72-73 0.1 0.0 0.0 0.0 0.0 74-75 0.1 0.0 0.0 0.0 0.0 76-77 0.1375 0.0 0.0 0.0 0.0 78-79 0.175 0.0 0.0 0.0 0.0 80-81 0.2 0.0 0.0 0.0 0.0 82-83 0.225 0.0 0.0 0.0 0.0 84-85 0.2875 0.0 0.0 0.0 0.0 86-87 0.3 0.0 0.0 0.0 0.0 88-89 0.42500000000000004 0.0 0.0 0.0 0.0 90-91 0.525 0.0 0.0 0.0 0.0 92-93 0.55 0.0 0.0 0.0 0.0 94-95 0.575 0.0 0.0 0.0 0.0 96-97 0.65 0.0 0.0 0.0 0.0 98-99 0.7375 0.0 0.0 0.0 0.0 100-101 0.9125 0.0 0.0 0.0 0.0 102-103 1.1124999999999998 0.0 0.0 0.0 0.0 104-105 1.2125 0.0 0.0 0.0 0.0 106-107 1.4874999999999998 0.0 0.0 0.0 0.0 108-109 1.7375 0.0 0.0 0.0 0.0 110-111 1.9249999999999998 0.0 0.0 0.0 0.0 112-113 2.1375 0.0 0.0 0.0 0.0 114-115 2.5 0.0 0.0 0.0 0.0 116-117 2.8875 0.0 0.0 0.0 0.0 118-119 3.0999999999999996 0.0 0.0 0.0 0.0 120-121 3.4749999999999996 0.0 0.0 0.0 0.0 122-123 3.9000000000000004 0.0 0.0 0.0 0.0 124-125 4.3125 0.0 0.0 0.0 0.0 126-127 4.575 0.0 0.0 0.0 0.0 128-129 4.975 0.0 0.0 0.0 0.0 130-131 5.362500000000001 0.0 0.0 0.0 0.0 132-133 5.737500000000001 0.0 0.0 0.0 0.0 134-135 6.375 0.0 0.0 0.0 0.0 136-137 7.075 0.0 0.0 0.0 0.0 138-139 7.475 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position AACAAGG 10 0.006830828 145.0 3 AAACAAG 10 0.006830828 145.0 2 GCGGTGC 10 0.006830828 145.0 9 ACAAGGC 10 0.006830828 145.0 4 CAAACAA 10 0.006830828 145.0 1 >>END_MODULE Read 983665 spots for SRR12919337.sra Written 983665 spots for SRR12919337.sra Read 983665 spots for SRR12919337.sra Written 983665 spots for SRR12919337.sra Read 983665 spots for SRR12919337.sra Written 983665 spots for SRR12919337.sra Read 983665 spots for SRR12919337.sra Written 983665 spots for SRR12919337.sra Read 983665 spots for SRR12919337.sra Written 983665 spots for SRR12919337.sra Read 983665 spots for SRR12919337.sra Written 983665 spots for SRR12919337.sra Read 983665 spots for SRR12919337.sra Written 983665 spots for SRR12919337.sra Read 983665 spots for SRR12919337.sra Written 983665 spots for SRR12919337.sra Read 983665 spots for SRR12919337.sra Written 983665 spots for SRR12919337.sra Read 983665 spots for SRR12919337.sra Written 983665 spots for SRR12919337.sra Read 983665 spots for SRR12919337.sra Written 983665 spots for SRR12919337.sra Read 983665 spots for SRR12919337.sra Written 983665 spots for SRR12919337.sra Read 983665 spots for SRR12919337.sra Written 983665 spots for SRR12919337.sra Read 983665 spots for SRR12919337.sra Written 983665 spots for SRR12919337.sra Read 983670 spots for SRR12919337.sra Written 983670 spots for SRR12919337.sra Read 983665 spots for SRR12919337.sra Written 983665 spots for SRR12919337.sra Read 983665 spots for SRR12919337.sra Written 983665 spots for SRR12919337.sra Read 983665 spots for SRR12919337.sra Written 983665 spots for SRR12919337.sra Read 983665 spots for SRR12919337.sra Written 983665 spots for SRR12919337.sra Read 983665 spots for SRR12919337.sra Written 983665 spots for SRR12919337.sra SRR ids: ['SRR12919337.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_ys6rjgqx SRR12919337.sra spots: 19673305 blocks: [[1, 983665], [983666, 1967330], [1967331, 2950995], [2950996, 3934660], [3934661, 4918325], [4918326, 5901990], [5901991, 6885655], [6885656, 7869320], [7869321, 8852985], [8852986, 9836650], [9836651, 10820315], [10820316, 11803980], [11803981, 12787645], [12787646, 13771310], [13771311, 14754975], [14754976, 15738640], [15738641, 16722305], [16722306, 17705970], [17705971, 18689635], [18689636, 19673305]] SRR12919337 file size 6664149 SRR12919337 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 SRR12919337 SRR12919337_1.fastq SRR12919337_2.fastq Input file: SRR12919337_1.fastq Paired file: SRR12919337_2.fastq trimmed: SRR12919337-trimmed-pair1.fastq, SRR12919337-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 Wed Feb 12 18:56:39 2025 >> started Wed Feb 12 18:57:04 2025 >> done (25.548s) 19673305 read pairs processed; of these: 32 ( 0.00%) short read pairs filtered out after trimming by size control 5824 ( 0.03%) empty read pairs filtered out after trimming by size control 19667449 (99.97%) read pairs available; of these: 2142763 (10.89%) trimmed read pairs available after processing 17524686 (89.11%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 3 0.00% 19 4 0.00% 20 5 0.00% 21 11 0.00% 22 12 0.00% 23 6 0.00% 24 6 0.00% 25 10 0.00% 26 7 0.00% 27 8 0.00% 28 12 0.00% 29 15 0.00% 30 18 0.00% 31 13 0.00% 32 13 0.00% 33 13 0.00% 34 12 0.00% 35 18 0.00% 36 28 0.00% 37 28 0.00% 38 28 0.00% 39 22 0.00% 40 42 0.00% 41 34 0.00% 42 41 0.00% 43 42 0.00% 44 46 0.00% 45 41 0.00% 46 53 0.00% 47 52 0.00% 48 67 0.00% 49 77 0.00% 50 98 0.00% 51 112 0.00% 52 108 0.00% 53 115 0.00% 54 144 0.00% 55 146 0.00% 56 122 0.00% 57 158 0.00% 58 218 0.00% 59 219 0.00% 60 272 0.00% 61 301 0.00% 62 376 0.00% 63 422 0.00% 64 409 0.00% 65 460 0.00% 66 464 0.00% 67 470 0.00% 68 608 0.00% 69 701 0.00% 70 831 0.00% 71 950 0.00% 72 1126 0.01% 73 1302 0.01% 74 1462 0.01% 75 1521 0.01% 76 1636 0.01% 77 1849 0.01% 78 2081 0.01% 79 2290 0.01% 80 2596 0.01% 81 2973 0.02% 82 3451 0.02% 83 3877 0.02% 84 4270 0.02% 85 4708 0.02% 86 5174 0.03% 87 5516 0.03% 88 5713 0.03% 89 6443 0.03% 90 7121 0.04% 91 7833 0.04% 92 8618 0.04% 93 9600 0.05% 94 10594 0.05% 95 11466 0.06% 96 12058 0.06% 97 12634 0.06% 98 13322 0.07% 99 13811 0.07% 100 14783 0.08% 101 15649 0.08% 102 17012 0.09% 103 18266 0.09% 104 19609 0.10% 105 20640 0.10% 106 21223 0.11% 107 21815 0.11% 108 22565 0.11% 109 23326 0.12% 110 23918 0.12% 111 24945 0.13% 112 26441 0.13% 113 27772 0.14% 114 28900 0.15% 115 30257 0.15% 116 31030 0.16% 117 32005 0.16% 118 32031 0.16% 119 33381 0.17% 120 33865 0.17% 121 34672 0.18% 122 35966 0.18% 123 37341 0.19% 124 38710 0.20% 125 39886 0.20% 126 40716 0.21% 127 41905 0.21% 128 42084 0.21% 129 42412 0.22% 130 43315 0.22% 131 43729 0.22% 132 45308 0.23% 133 46461 0.24% 134 47107 0.24% 135 49166 0.25% 136 49427 0.25% 137 50354 0.26% 138 51445 0.26% 139 51132 0.26% 140 51785 0.26% 141 51898 0.26% 142 53448 0.27% 143 54399 0.28% 144 56879 0.29% 145 57101 0.29% 146 57307 0.29% 147 58859 0.30% 148 59116 0.30% 149 58523 0.30% 150 59343 0.30% 151 17524686 89.11% 19667449 reads passed initial QC criterion=sequence-density sequence-density=0.26 sequence-density-rank=1 fanout-score=1.97 fanout-score-rank=41 prefix-density=0.25 prefix-fanout=2.0 sequence=TACAGTCCCCAACAAGTTCTCTCCATTCTCTGGATAATTGAAATCTCCAAATACCAGTTTACCTTTCTCCGATCCGAATTTCTTCCAGTTCCAAACTCCTGTGAAGGCAACAGCCTGCGGCACAGAAACATCACCTGGAACCATTGTTTTCTTATCCAAGCTTCCAGCATTCCCAAAATAGATGACTCCGTGAATGCTGAATCTAGCTAAAAGGATTTGCAAAGTTGTTGCCATATTTACTGAATGACTCCCTGTCTTGACATATACAATAGAAGAACCGTTTAGTGTCCCGCTATGGAACCTTCTGCCCGCAATGTCAACAGAAGAGTCTTCACTGTCAGGGCTATAGAGTCCAGAGTCTTGCAGAGCCCTTTCGTTGTTATCAGACGTAAAAACAAGCCCTAAGCGAAGGTGTGCGATTTTGCAGTTGCTTCTCTCGATTTCAGCAATGGGGTCTATCAAACTCGCTTGCATGGACTGCTGTGGCATAACCAGCAGCAGCCCAA criterion=fanout-score sequence-density=0.03 sequence-density-rank=39 fanout-score=174.65 fanout-score-rank=1 prefix-density=0.35 prefix-fanout=12.8 sequence=CATCACCATCCCTGATTGATCTTTGATTCACAACAAGACCAACCAACCGTACAATGTTTACATAACTTGGGATAATCTCACAAGAAAGAAAGATCAATACAAAACTAGTCAGCTCAGGATGTTCCAGGCACGGTAGAACCGTAGAACCATAACAACAAGAGACATATTGCAGATGAGTACTGAAAAACAAAACACAGTACGTATTTACATGGGCAACCTTGGTTGAAGGCAACCTCATCAACGATGCTCGCTCTTCGTCTCTCCACTGTACATCCAGTCATAGACAGTGGGTGTGTTAGGCTGTGGCTTGTCAAAAACATGAGCACCAATATTCTTAGTAGCAAGGTTGCTACCAGGGTGGAACACGCTCCTCCAAACATTGCTACGCGCCGACACTGGGGTTGTAGGGGTCACTGGTGTCGTCGGTGTCCCTGGAGTTCCTGGCATAGTCATGGACCTCTGAAACTTATTAACAGGACTGCTCCCCTCTCCGACGTCAATATCTTTGATG criterion=sequence-density sequence-density=0.31 sequence-density-rank=1 fanout-score=2.47 fanout-score-rank=32 prefix-density=0.40 prefix-fanout=1.9 sequence=TTGGGCTGCTGCTGGTTATGCCACAGCAGTCCATGCAAGCGAGTTTGATAGACCCCATTGCTGAAATCGAGAGAAGCAACTGCAAAATCGCACACCTTCGCTTAGGGCTTGTTTTTACGTCTGATAACAACGAAAGGGCTCTGCAAGACTCTGGACTCTATAGCCCTGACAGTGAAGACTCTTCTGTTGACATTGCGGGCAGAAGGTTCCATAGCGGGACACTAAACGGTTCTTCTATTGTATATGTCAAGACAGGGAGTCATTCAGTAAATATGGCAACAACTTTGCAAATCCTTTTAGCTAGATTCAGCATTCACGGAGTCATCTATTTTGGGAATGCTGGAAGCTTGGATAAGAAAACAATGGTTCCAGGTGATGTTTCTGTGCCGCAGGCTGTTGCCTTCACAGGAGTTTGGAACTGGAAGAAATTCGGATCGGAGAAAGGTAAACTGGTATTTGGAGATTTCAATTATCCAGAGAATGGAGAGAACTTGTTGGGGACTGTA criterion=fanout-score sequence-density=0.01 sequence-density-rank=35 fanout-score=67.65 fanout-score-rank=1 prefix-density=0.07 prefix-fanout=8.3 sequence=GAGCTTCAAAGCATGGTCAGTGACCTATAGTGAAGAAAAACAAAAAAGAAATGGATGCCAAAGCTCTCTTCTTCTTTGCCTTGTTGTCCTTCTCAGCTGTGTCGGTCAGGCCGGCATTAGCAGAAAATGAAGAAGACCCTGGTCTTGTTATGAACTTTTACAAGGATACATGCCCTCAAGCTGAGGACATTGTCAAAGAACAAGTTAGACTCCTTTACAAGAGACACAAAAACACTGCATTTTCTTGGCTAAGAAACATCTTCCATGACTGTGCTGTTCAGTCATGTGATGCTTCACTGCTGCTGGACTCAACAAGGAGGACCTTGTCCGAGAAGGAGACAGACAGGAGCTTTGGCCTCAGGAACTTTAGATACTTTGACGATATCAAAGAAGCTGTTGAAAGAGAGTGTCCTGGAGTCGTTTCCTGTGCTGATATTCTTGTCCTGTCTGCTAGAGATGGCATTGTTTCGCTAGGAGGACCTCATATCCCTCTCAAAACTGGAAGAAGGGA SRR12919337 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 12 18:58:15 Started mapping on | Feb 12 18:58:15 Finished on | Feb 12 19:00:19 Mapping speed, Million of reads per hour | 570.99 Number of input reads | 19667449 Average input read length | 284 UNIQUE READS: Uniquely mapped reads number | 16326058 Uniquely mapped reads % | 83.01% Average mapped length | 287.31 Number of splices: Total | 15337775 Number of splices: Annotated (sjdb) | 14982902 Number of splices: GT/AG | 15047114 Number of splices: GC/AG | 222704 Number of splices: AT/AC | 16966 Number of splices: Non-canonical | 50991 Mismatch rate per base, % | 0.38% Deletion rate per base | 0.03% Deletion average length | 2.90 Insertion rate per base | 0.02% Insertion average length | 2.47 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 426275 % of reads mapped to multiple loci | 2.17% Number of reads mapped to too many loci | 65113 % of reads mapped to too many loci | 0.33% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 14.33% % of reads unmapped: other | 0.16% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 2915116 2915116 2915116 N_multimapping 426275 426275 426275 N_noFeature 629013 16144689 711408 N_ambiguous 294011 2251 193429 UnstrandedReadsAssigned:15403034 PositiveStrandReadsAssigned:179118 NegativeStrandReadsAssigned:15421221 Dataset is classified negative stranded MeadianReadLen=147 20thPercentileLength=147 echo kmer=143 SRR12919337 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: SRR12919337-trimmed-pair1.fastq SRR12919337-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 19,667,449 reads, 17,470,618 reads pseudoaligned [quant] estimated average fragment length: 244.575 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,141 rounds 52401 SRR12919337.ke.tsv 34699 SRR12919337.se.tsv 87100 total ==> SRR12919337.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1774.42 765 27.6414 Potri.005G024800.1.v4.1 1035 791.425 181 14.6631 Potri.004G059700.1.v4.1 961 717.528 29 2.59128 Potri.007G009000.2.v4.1 1416 1172.42 0 0 Potri.003G141000.2.v4.1 2943 2699.42 588.593 13.9798 Potri.016G087400.1.v4.1 270 93.4015 857.126 588.365 Potri.015G069301.1.v4.1 564 332.071 0 0 Potri.010G195200.1.v4.1 1773 1529.42 98 4.10822 Potri.012G127500.1.v4.1 977 733.472 14095 1232.08 ==> SRR12919337.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 116 Potri.001G233950.v4.1 2 Potri.001G122700.v4.1 226 Potri.001G212900.v4.1 0 Potri.001G182400.v4.1 2 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 0 Potri.001G416900.v4.1 2 Potri.001G452600.v4.1 7 SRR12919337 completed mapping pipeline successfully