Starting /dee2/code/volunteer_pipeline.sh SRR11445639 current disk space = 3051639963648 free memory = 1578472256 SRR11445639 SRAfilesize 97888f57c6e525642e1ad7d4ecdce4ba SRR11445639.sra SRR11445639.sra file validated SRR11445639 is paired end SRR11445639 is conventional basespace SRR11445639 read1 length is 150 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR11445639_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 150 %GC 37 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 23.95875 32.0 12.0 32.0 2.0 32.0 2 31.06875 32.0 32.0 32.0 32.0 32.0 3 34.445 37.0 32.0 37.0 32.0 37.0 4 34.99375 37.0 37.0 37.0 32.0 37.0 5 36.09125 37.0 37.0 37.0 32.0 37.0 6 39.57275 41.0 41.0 41.0 37.0 41.0 7 39.9275 41.0 41.0 41.0 37.0 41.0 8 39.57825 41.0 41.0 41.0 37.0 41.0 9 39.983 41.0 41.0 41.0 37.0 41.0 10-14 39.8377 41.0 41.0 41.0 37.0 41.0 15-19 38.92705 41.0 40.2 41.0 35.0 41.0 20-24 38.60645000000001 41.0 38.6 41.0 33.0 41.0 25-29 38.25940000000001 41.0 39.4 41.0 32.0 41.0 30-34 38.58579999999999 41.0 39.4 41.0 33.0 41.0 35-39 39.019149999999996 41.0 41.0 41.0 36.0 41.0 40-44 38.49355 41.0 38.6 41.0 33.0 41.0 45-49 37.9722 41.0 37.8 41.0 30.0 41.0 50-54 38.5002 41.0 38.6 41.0 33.0 41.0 55-59 38.153150000000004 41.0 37.0 41.0 31.0 41.0 60-64 38.0848 41.0 37.8 41.0 31.0 41.0 65-69 37.65695 41.0 37.0 41.0 30.0 41.0 70-74 36.6964 41.0 36.0 41.0 26.0 41.0 75-79 37.06365 41.0 37.0 41.0 28.0 41.0 80-84 36.46625000000001 40.2 36.0 41.0 22.0 41.0 85-89 34.52139999999999 38.6 32.0 41.0 19.0 41.0 90-94 35.45485000000001 40.2 34.0 41.0 19.0 41.0 95-99 35.26495 41.0 34.0 41.0 18.0 41.0 100-104 33.52035 39.4 28.0 41.0 14.0 41.0 105-109 35.3552 41.0 34.0 41.0 20.0 41.0 110-114 35.8791 41.0 37.0 41.0 20.0 41.0 115-119 35.2697 41.0 35.0 41.0 14.0 41.0 120-124 32.878750000000004 37.0 27.0 41.0 12.0 41.0 125-129 33.04535 37.8 29.0 41.0 12.0 41.0 130-134 32.58045 37.0 27.0 41.0 12.0 41.0 135-139 32.6408 37.0 27.0 41.0 12.0 41.0 140-144 31.5644 37.0 25.0 41.0 12.0 41.0 145-149 28.6646 33.0 18.0 39.4 12.0 41.0 150 30.258 32.0 22.0 41.0 12.0 41.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 19 4.0 20 5.0 21 15.0 22 18.0 23 33.0 24 38.0 25 43.0 26 59.0 27 82.0 28 98.0 29 122.0 30 88.0 31 126.0 32 134.0 33 155.0 34 194.0 35 236.0 36 338.0 37 443.0 38 615.0 39 683.0 40 471.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 25.916055962691537 25.51632245169887 24.98334443704197 23.584277148567622 2 25.05 25.85 22.975 26.125 3 22.7 29.925 23.7 23.674999999999997 4 23.95 28.799999999999997 21.6 25.650000000000002 5 24.725 29.225 23.25 22.8 6 26.8 28.4 22.35 22.45 7 28.4 26.85 23.225 21.525 8 27.575 29.15 26.35 16.925 9 28.775000000000002 28.549999999999997 27.450000000000003 15.225 10-14 26.765 30.509999999999998 27.05 15.675 15-19 22.935 31.619999999999997 29.575000000000003 15.870000000000001 20-24 21.57 32.33 30.220000000000002 15.879999999999999 25-29 22.39 30.86 30.37 16.38 30-34 21.805 30.98 30.259999999999998 16.955000000000002 35-39 21.12 30.825000000000003 30.714999999999996 17.34 40-44 20.785 30.98 31.52 16.715 45-49 20.435 30.9 30.975 17.69 50-54 20.349999999999998 30.64 31.324999999999996 17.685000000000002 55-59 19.794999999999998 31.8 31.319999999999997 17.085 60-64 19.979994998749685 31.762940735183797 30.85271317829457 17.404351087771943 65-69 19.580000000000002 31.04 32.18 17.2 70-74 20.785 30.714999999999996 31.080000000000002 17.419999999999998 75-79 20.200000000000003 30.12 31.979999999999997 17.7 80-84 19.39 31.095 32.165 17.349999999999998 85-89 19.425 32.24 31.665 16.669999999999998 90-94 19.650000000000002 32.42 31.185000000000002 16.744999999999997 95-99 19.465 31.35 32.36 16.825000000000003 100-104 20.155 30.835 32.955 16.055 105-109 19.134999999999998 32.395 31.935000000000002 16.535 110-114 19.585 32.074999999999996 32.21 16.13 115-119 19.355 32.0 32.115 16.53 120-124 20.075000000000003 30.930000000000003 32.78 16.215 125-129 19.08 32.12 32.425 16.375 130-134 19.37 31.569999999999997 31.855 17.205000000000002 135-139 19.125 31.985000000000003 32.035000000000004 16.855 140-144 19.86 32.12 31.53 16.49 145-149 21.15 30.75 32.42 15.68 150 19.925 32.9 31.05 16.125 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 13.0 1 9.0 2 10.5 3 13.0 4 8.5 5 8.0 6 6.5 7 7.0 8 7.5 9 5.0 10 7.0 11 8.5 12 6.0 13 5.0 14 8.5 15 10.5 16 6.5 17 5.0 18 6.0 19 7.5 20 9.0 21 9.5 22 10.5 23 8.5 24 9.0 25 18.0 26 24.5 27 24.0 28 36.0 29 51.0 30 63.5 31 75.0 32 91.0 33 120.5 34 156.5 35 175.5 36 204.5 37 239.0 38 236.5 39 239.0 40 247.5 41 239.5 42 219.5 43 195.0 44 177.0 45 162.5 46 146.0 47 123.0 48 99.0 49 85.0 50 73.0 51 61.0 52 47.0 53 40.0 54 36.0 55 21.5 56 13.5 57 14.0 58 13.0 59 9.5 60 4.5 61 2.0 62 3.0 63 3.5 64 2.0 65 0.5 66 0.5 67 1.5 68 2.5 69 2.5 70 1.0 71 0.0 72 0.0 73 0.0 74 0.0 75 0.0 76 0.0 77 0.5 78 0.5 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 fail #Base N-Count 1 24.95 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 0.025 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 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 150 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 94.85 #Duplication Level Percentage of deduplicated Percentage of total 1 95.70374275171322 90.77499999999999 2 3.610964681075382 6.8500000000000005 3 0.42171850289931473 1.2 4 0.21085925144965736 0.8 5 0.02635740643120717 0.125 6 0.0 0.0 7 0.0 0.0 8 0.0 0.0 9 0.0 0.0 >10 0.02635740643120717 0.25 >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 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 10 0.25 No Hit CCAAAAAAAAAAAAAAAAAAAAGATCGGAAGAGCACACGTCTGAACTCCA 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 29bp) >>END_MODULE >>Adapter Content fail #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 0.05 0.0 0.0 0.0 0.0 7 0.05 0.0 0.0 0.0 0.0 8 0.075 0.0 0.0 0.0 0.0 9 0.075 0.0 0.0 0.0 0.0 10-11 0.1 0.0 0.0 0.0 0.0 12-13 0.1 0.0 0.0 0.0 0.0 14-15 0.1 0.0 0.0 0.0 0.0 16-17 0.1 0.0 0.0 0.0 0.0 18-19 0.2 0.0 0.0 0.0 0.0 20-21 0.9375 0.0 0.0 0.0 0.0 22-23 2.1875 0.0 0.0 0.0 0.0 24-25 2.8375000000000004 0.0 0.0 0.0 0.0 26-27 3.1875 0.0 0.0 0.0 0.0 28-29 3.4375 0.0 0.0 0.0 0.0 30-31 3.6125 0.0 0.0 0.0 0.0 32-33 3.85 0.0 0.0 0.0 0.0 34-35 4.1 0.0 0.0 0.0 0.0 36-37 4.2875 0.0 0.0 0.0 0.0 38-39 4.525 0.0 0.0 0.0 0.0 40-41 4.675 0.0 0.0 0.0 0.0 42-43 4.887499999999999 0.0 0.0 0.0 0.0 44-45 5.075 0.0 0.0 0.0 0.0 46-47 5.3 0.0 0.0 0.0 0.0 48-49 5.55 0.0 0.0 0.0 0.0 50-51 5.675 0.0 0.0 0.0 0.0 52-53 5.862500000000001 0.0 0.0 0.0 0.0 54-55 6.075 0.0 0.0 0.0 0.0 56-57 6.2625 0.0 0.0 0.0 0.0 58-59 6.325 0.0 0.0 0.0 0.0 60-61 6.487500000000001 0.0 0.0 0.0 0.0 62-63 6.625 0.0 0.0 0.0 0.0 64-65 6.7875 0.0 0.0 0.0 0.0 66-67 6.949999999999999 0.0 0.0 0.0 0.0 68-69 7.275 0.0 0.0 0.0 0.0 70-71 7.475 0.0 0.0 0.0 0.0 72-73 7.8125 0.0 0.0 0.0 0.0 74-75 8.025 0.0 0.0 0.0 0.0 76-77 8.225 0.0 0.0 0.0 0.0 78-79 8.3125 0.0 0.0 0.0 0.0 80-81 8.4375 0.0 0.0 0.0 0.0 82-83 8.625 0.0 0.0 0.0 0.0 84-85 8.9375 0.0 0.0 0.0 0.0 86-87 9.087499999999999 0.0 0.0 0.0 0.0 88-89 9.149999999999999 0.0 0.0 0.0 0.0 90-91 9.375 0.0 0.0 0.0 0.0 92-93 9.6375 0.0 0.0 0.0 0.0 94-95 9.7625 0.0 0.0 0.0 0.0 96-97 9.9375 0.0 0.0 0.0 0.0 98-99 10.1625 0.0 0.0 0.0 0.0 100-101 10.3125 0.0 0.0 0.0 0.0 102-103 10.4625 0.0 0.0 0.0 0.0 104-105 10.6375 0.0 0.0 0.0 0.0 106-107 10.8375 0.0 0.0 0.0 0.0 108-109 11.0125 0.0 0.0 0.0 0.0 110-111 11.1875 0.0 0.0 0.0 0.0 112-113 11.4125 0.0 0.0 0.0 0.0 114-115 11.649999999999999 0.0 0.0 0.0 0.0 116-117 11.9125 0.0 0.0 0.0 0.0 118-119 12.087499999999999 0.0 0.0 0.0 0.0 120-121 12.25 0.0 0.0 0.0 0.0 122-123 12.5375 0.0 0.0 0.0 0.0 124-125 12.875 0.0 0.0 0.0 0.0 126-127 13.1375 0.0 0.0 0.0 0.0 128-129 13.45 0.0 0.0 0.0 0.0 130-131 13.6375 0.0 0.0 0.0 0.0 132-133 13.875 0.0 0.0 0.0 0.0 134-135 14.0625 0.0 0.0 0.0 0.0 136-137 14.3125 0.0 0.0 0.0 0.0 138 14.425 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TATTAAA 10 0.0070081474 143.7625 8 ACAGGCA 10 0.0070081474 143.7625 3 >>END_MODULE SRR11445639 read2 length is 150 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR11445639_2.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 150 %GC 28 >>END_MODULE >>Per base sequence quality fail #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 19.42375 27.0 2.0 32.0 2.0 32.0 2 31.035 32.0 32.0 32.0 32.0 32.0 3 33.26 32.0 32.0 37.0 32.0 37.0 4 34.35 37.0 32.0 37.0 32.0 37.0 5 35.6975 37.0 37.0 37.0 32.0 37.0 6 38.68175 41.0 41.0 41.0 32.0 41.0 7 39.4275 41.0 41.0 41.0 37.0 41.0 8 38.98475 41.0 41.0 41.0 37.0 41.0 9 36.74325 41.0 37.0 41.0 27.0 41.0 10-14 39.2335 41.0 41.0 41.0 37.0 41.0 15-19 37.0129 40.2 36.6 41.0 28.0 41.0 20-24 27.330599999999997 29.0 16.0 38.6 12.0 41.0 25-29 30.66205 35.0 22.0 41.0 12.0 41.0 30-34 30.03345 34.0 18.0 41.0 12.0 41.0 35-39 28.82205 34.0 18.0 39.4 12.0 41.0 40-44 28.45525 32.0 12.0 41.0 12.0 41.0 45-49 27.862150000000003 30.0 16.0 39.4 12.0 41.0 50-54 26.36275 27.0 12.0 37.0 12.0 41.0 55-59 26.106600000000004 27.0 16.0 36.8 12.0 41.0 60-64 27.878549999999997 31.0 14.0 40.2 12.0 41.0 65-69 27.540699999999998 30.0 12.0 37.8 12.0 41.0 70-74 25.89625 26.0 12.0 36.8 12.0 41.0 75-79 24.9553 24.0 12.0 35.0 12.0 40.2 80-84 25.948 26.0 12.0 37.0 12.0 41.0 85-89 24.8601 22.0 12.0 37.0 12.0 41.0 90-94 23.98415 22.0 12.0 36.0 12.0 41.0 95-99 24.2131 22.0 12.0 36.0 12.0 40.2 100-104 22.7459 22.0 12.0 34.0 12.0 38.6 105-109 23.0169 22.0 12.0 34.0 12.0 40.2 110-114 21.3512 20.0 12.0 30.0 12.0 38.6 115-119 21.990450000000003 22.0 12.0 32.0 12.0 38.6 120-124 22.183349999999997 22.0 12.0 32.0 12.0 38.6 125-129 20.1059 16.0 12.0 28.0 12.0 36.0 130-134 20.0513 16.0 12.0 27.0 12.0 37.0 135-139 20.08585 14.0 12.0 28.0 12.0 37.0 140-144 19.376800000000003 14.0 12.0 27.0 12.0 35.0 145-149 19.078650000000003 14.0 12.0 26.0 12.0 35.0 150 19.55525 12.0 12.0 27.0 12.0 37.0 >>END_MODULE >>Per sequence quality scores warn #Quality Count 13 1.0 14 2.0 15 7.0 16 19.0 17 50.0 18 98.0 19 196.0 20 257.0 21 296.0 22 334.0 23 326.0 24 288.0 25 291.0 26 260.0 27 222.0 28 233.0 29 227.0 30 170.0 31 159.0 32 144.0 33 116.0 34 101.0 35 66.0 36 47.0 37 36.0 38 34.0 39 16.0 40 4.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 4.699453551912568 0.14571948998178508 90.34608378870675 4.808743169398907 2 0.525 0.22499999999999998 99.02499999999999 0.22499999999999998 3 0.375 0.17500000000000002 99.3 0.15 4 0.8750000000000001 0.05 98.75 0.325 5 0.075 0.17500000000000002 99.425 0.325 6 0.475 0.125 99.175 0.22499999999999998 7 0.2 0.2 99.375 0.22499999999999998 8 0.5 0.2 99.05000000000001 0.25 9 1.9754938734683671 0.2000500125031258 97.47436859214804 0.3500875218804701 10-14 0.3250975292587776 0.24507352205661698 99.18475542662799 0.24507352205661698 15-19 3.495 1.9449999999999998 92.635 1.925 20-24 19.189999999999998 29.17 35.735 15.905 25-29 12.8 42.325 33.295 11.58 30-34 14.26 33.465 37.54 14.735000000000001 35-39 13.375 27.750000000000004 44.095 14.78 40-44 13.184999999999999 28.515 45.43 12.870000000000001 45-49 13.469999999999999 32.11 41.78 12.64 50-54 15.36 32.875 38.375 13.389999999999999 55-59 16.195 32.255 37.57 13.98 60-64 16.495 32.085 35.47 15.950000000000001 65-69 17.29 32.33 33.684999999999995 16.695 70-74 17.485 32.31 33.155 17.05 75-79 16.275000000000002 32.86 34.42 16.445 80-84 15.761576157615762 34.83348334833483 33.71837183718372 15.686568656865688 85-89 16.035 34.394999999999996 33.505 16.064999999999998 90-94 16.465 33.31 34.35 15.875 95-99 16.885 34.365 33.07 15.68 100-104 17.06 33.7 33.23 16.009999999999998 105-109 17.169999999999998 33.595000000000006 33.06 16.175 110-114 17.195 33.995 32.71 16.1 115-119 17.49 34.275 31.929999999999996 16.305 120-124 16.76419104776194 34.303575893973495 31.487871967992 17.44436109027257 125-129 18.01090054502725 33.5966798339917 31.451572578628934 16.940847042352118 130-134 17.599999999999998 32.555 32.43 17.415 135-139 16.634999999999998 33.565 32.519999999999996 17.28 140-144 18.665000000000003 32.31 31.695 17.330000000000002 145-149 18.425 32.57 31.525 17.48 150 16.75 32.875 32.15 18.224999999999998 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 101.0 1 92.5 2 75.0 3 47.0 4 25.0 5 20.0 6 16.5 7 17.0 8 16.5 9 15.0 10 19.5 11 22.0 12 21.5 13 28.5 14 35.5 15 35.0 16 44.0 17 58.5 18 61.0 19 68.5 20 85.0 21 117.0 22 136.0 23 152.0 24 190.0 25 210.5 26 227.0 27 225.0 28 223.5 29 225.5 30 215.0 31 187.0 32 160.0 33 139.0 34 110.0 35 100.0 36 90.0 37 84.5 38 61.5 39 45.5 40 46.0 41 40.0 42 37.0 43 26.5 44 20.5 45 17.5 46 12.5 47 8.0 48 7.0 49 7.5 50 5.5 51 3.0 52 2.0 53 3.0 54 3.0 55 2.0 56 1.0 57 0.5 58 0.5 59 0.0 60 0.0 61 0.0 62 0.0 63 0.0 64 0.0 65 0.0 66 1.0 67 1.0 68 1.0 69 1.0 70 0.0 71 0.0 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 fail #Base N-Count 1 31.374999999999996 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.025 10-14 0.03 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 0.01 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 0.025 125-129 0.005 130-134 0.0 135-139 0.0 140-144 0.0 145-149 0.0 150 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 150 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 91.7 #Duplication Level Percentage of deduplicated Percentage of total 1 98.2824427480916 90.125 2 0.9814612868047983 1.7999999999999998 3 0.13631406761177753 0.375 4 0.13631406761177753 0.5 5 0.08178844056706652 0.375 6 0.10905125408942204 0.6 7 0.02726281352235551 0.17500000000000002 8 0.0 0.0 9 0.0 0.0 >10 0.19083969465648853 2.7 >50 0.05452562704471102 3.35 >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 fail #Sequence Count Percentage Possible Source NTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 68 1.7000000000000002 No Hit TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 66 1.6500000000000001 No Hit TTTTTTTTTTTTTTTTTTTCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 28 0.7000000000000001 No Hit TTTTTTTTTTTTTTTTTTTATTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 19 0.475 No Hit TTTTTTTTTTTTTTTTTTTGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 14 0.35000000000000003 No Hit NTTTTTTTTTTTTTTTTTTGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 14 0.35000000000000003 No Hit TTTTTTTTTTTTTTTTTTTCCTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 12 0.3 No Hit NTTTTTTTTTTTTTTTTTTCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 11 0.27499999999999997 No Hit TTTTTTTTTTTTTTTTTTTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 10 0.25 No Hit TTTTTTTTTTTTTTTTTTGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 7 0.17500000000000002 No Hit NTTTTTTTTTTTTTTTTTTATTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 6 0.15 No Hit TTTTTTTTTTTTTTTTTTCCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 6 0.15 No Hit NTTTTTTTTTTTTTTTTTTTCTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 6 0.15 No Hit NTTTTTTTTTTTTTTTTTATTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 6 0.15 No Hit NTTTTTTTTTTTTTTTTTTCCTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 5 0.125 No Hit TTTTTTTTTTTTTTTTTTCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 5 0.125 No Hit TTTTTTTTTTTTTTTTTTTTGTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 5 0.125 No Hit >>END_MODULE >>Adapter Content fail #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 0.025 0.0 0.0 0.0 0.0 7 0.05 0.0 0.0 0.0 0.0 8 0.075 0.0 0.0 0.0 0.0 9 0.075 0.0 0.0 0.0 0.0 10-11 0.1 0.0 0.0 0.0 0.0 12-13 0.1 0.0 0.0 0.0 0.0 14-15 0.1 0.0 0.0 0.0 0.0 16-17 0.1 0.0 0.0 0.0 0.0 18-19 0.2125 0.0 0.0 0.0 0.0 20-21 0.8374999999999999 0.0 0.0 0.0 0.0 22-23 1.9249999999999998 0.0 0.0 0.0 0.0 24-25 2.4125 0.0 0.0 0.0 0.0 26-27 2.675 0.0 0.0 0.0 0.0 28-29 2.8499999999999996 0.0 0.0 0.0 0.0 30-31 3.05 0.0 0.0 0.0 0.0 32-33 3.3125 0.0 0.0 0.0 0.0 34-35 3.5875 0.0 0.0 0.0 0.0 36-37 3.7875 0.0 0.0 0.0 0.0 38-39 4.025 0.0 0.0 0.0 0.0 40-41 4.175 0.0 0.0 0.0 0.0 42-43 4.3375 0.0 0.0 0.0 0.0 44-45 4.55 0.0 0.0 0.0 0.0 46-47 4.725 0.0 0.0 0.0 0.0 48-49 4.9125 0.0 0.0 0.0 0.0 50-51 4.9875 0.0 0.0 0.0 0.0 52-53 5.0875 0.0 0.0 0.0 0.0 54-55 5.275 0.0 0.0 0.0 0.0 56-57 5.3875 0.0 0.0 0.0 0.0 58-59 5.425000000000001 0.0 0.0 0.0 0.0 60-61 5.512499999999999 0.0 0.0 0.0 0.0 62-63 5.7 0.0 0.0 0.0 0.0 64-65 5.887499999999999 0.0 0.0 0.0 0.0 66-67 6.0375 0.0 0.0 0.0 0.0 68-69 6.225 0.0 0.0 0.0 0.0 70-71 6.4125 0.0 0.0 0.0 0.0 72-73 6.6625 0.0 0.0 0.0 0.0 74-75 6.8375 0.0 0.0 0.0 0.0 76-77 6.975 0.0 0.0 0.0 0.0 78-79 7.15 0.0 0.0 0.0 0.0 80-81 7.3125 0.0 0.0 0.0 0.0 82-83 7.575 0.0 0.0 0.0 0.0 84-85 7.9375 0.0 0.0 0.0 0.0 86-87 8.0625 0.0 0.0 0.0 0.0 88-89 8.1125 0.0 0.0 0.0 0.0 90-91 8.2875 0.0 0.0 0.0 0.0 92-93 8.55 0.0 0.0 0.0 0.0 94-95 8.6875 0.0 0.0 0.0 0.0 96-97 8.825 0.0 0.0 0.0 0.0 98-99 9.0375 0.0 0.0 0.0 0.0 100-101 9.1125 0.0 0.0 0.0 0.0 102-103 9.2625 0.0 0.0 0.0 0.0 104-105 9.425 0.0 0.0 0.0 0.0 106-107 9.625 0.0 0.0 0.0 0.0 108-109 9.775 0.0 0.0 0.0 0.0 110-111 9.875 0.0 0.0 0.0 0.0 112-113 10.0125 0.0 0.0 0.0 0.0 114-115 10.1875 0.0 0.0 0.0 0.0 116-117 10.3625 0.0 0.0 0.0 0.0 118-119 10.462499999999999 0.0 0.0 0.0 0.0 120-121 10.575 0.0 0.0 0.0 0.0 122-123 10.7625 0.0 0.0 0.0 0.0 124-125 11.0875 0.0 0.0 0.0 0.0 126-127 11.2625 0.0 0.0 0.0 0.0 128-129 11.4875 0.0 0.0 0.0 0.0 130-131 11.6375 0.0 0.0 0.0 0.0 132-133 11.7375 0.0 0.0 0.0 0.0 134-135 11.9 0.0 0.0 0.0 0.0 136-137 12.100000000000001 0.0 0.0 0.0 0.0 138 12.2 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TTCCTTT 20 0.006204759 28.7375 15-19 TTTTCGA 35 1.272894E-4 24.632143 15-19 TTTTTCG 55 1.9392974E-7 23.512499 15-19 TTTTAGA 45 2.6689282E-5 22.351389 15-19 TTTCTTT 55 1.2510967E-4 18.2875 15-19 TTTTGGG 40 0.008067169 17.960938 15-19 TTTTTAG 60 2.4349053E-4 16.763542 15-19 TTTTCTT 70 7.867457E-4 14.368751 15-19 TTTTTGG 85 2.1763614E-4 13.523529 15-19 TTTTTTC 200 1.2732926E-11 12.931874 10-14 TTTTTCT 85 0.0033970466 11.833088 15-19 TTTTTTA 295 0.0 10.715678 10-14 CTTTTTT 140 1.1281569E-4 10.263393 20-24 TTTTTTG 290 7.6397555E-11 9.909483 10-14 TTTTTTT 10455 0.0 5.428653 4 >>END_MODULE Read 961053 spots for SRR11445639.sra Written 961053 spots for SRR11445639.sra Read 961053 spots for SRR11445639.sra Written 961053 spots for SRR11445639.sra Read 961053 spots for SRR11445639.sra Written 961053 spots for SRR11445639.sra Read 961053 spots for SRR11445639.sra Written 961053 spots for SRR11445639.sra Read 961053 spots for SRR11445639.sra Written 961053 spots for SRR11445639.sra Read 961053 spots for SRR11445639.sra Written 961053 spots for SRR11445639.sra Read 961053 spots for SRR11445639.sra Written 961053 spots for SRR11445639.sra Read 961053 spots for SRR11445639.sra Written 961053 spots for SRR11445639.sra Read 961053 spots for SRR11445639.sra Written 961053 spots for SRR11445639.sra Read 961053 spots for SRR11445639.sra Written 961053 spots for SRR11445639.sra Read 961053 spots for SRR11445639.sra Written 961053 spots for SRR11445639.sra Read 961053 spots for SRR11445639.sra Written 961053 spots for SRR11445639.sra Read 961053 spots for SRR11445639.sra Written 961053 spots for SRR11445639.sra Read 961060 spots for SRR11445639.sra Written 961060 spots for SRR11445639.sra Read 961053 spots for SRR11445639.sra Written 961053 spots for SRR11445639.sra Read 961053 spots for SRR11445639.sra Written 961053 spots for SRR11445639.sra Read 961053 spots for SRR11445639.sra Written 961053 spots for SRR11445639.sra Read 961053 spots for SRR11445639.sra Written 961053 spots for SRR11445639.sra Read 961053 spots for SRR11445639.sra Written 961053 spots for SRR11445639.sra Read 961053 spots for SRR11445639.sra Written 961053 spots for SRR11445639.sra SRR ids: ['SRR11445639.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_2fsy9dny SRR11445639.sra spots: 19221067 blocks: [[1, 961053], [961054, 1922106], [1922107, 2883159], [2883160, 3844212], [3844213, 4805265], [4805266, 5766318], [5766319, 6727371], [6727372, 7688424], [7688425, 8649477], [8649478, 9610530], [9610531, 10571583], [10571584, 11532636], [11532637, 12493689], [12493690, 13454742], [13454743, 14415795], [14415796, 15376848], [15376849, 16337901], [16337902, 17298954], [17298955, 18260007], [18260008, 19221067]] SRR11445639 file size 6472917 SRR11445639 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 SRR11445639 SRR11445639_1.fastq SRR11445639_2.fastq Input file: SRR11445639_1.fastq Paired file: SRR11445639_2.fastq trimmed: SRR11445639-trimmed-pair1.fastq, SRR11445639-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 15:42:07 2025 >> started Wed Feb 12 15:42:28 2025 >> done (20.839s) 19221067 read pairs processed; of these: 26287 ( 0.14%) short read pairs filtered out after trimming by size control 1496 ( 0.01%) empty read pairs filtered out after trimming by size control 19193284 (99.86%) read pairs available; of these: 4603935 (23.99%) trimmed read pairs available after processing 14589349 (76.01%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 24842 0.13% 19 70675 0.37% 20 77719 0.40% 21 117824 0.61% 22 84321 0.44% 23 50172 0.26% 24 39010 0.20% 25 32010 0.17% 26 29140 0.15% 27 24623 0.13% 28 22126 0.12% 29 21584 0.11% 30 19880 0.10% 31 20206 0.11% 32 20922 0.11% 33 20822 0.11% 34 22262 0.12% 35 21419 0.11% 36 21393 0.11% 37 21127 0.11% 38 21316 0.11% 39 20794 0.11% 40 20212 0.11% 41 20157 0.11% 42 19857 0.10% 43 19501 0.10% 44 18618 0.10% 45 18085 0.09% 46 18471 0.10% 47 17876 0.09% 48 17450 0.09% 49 17685 0.09% 50 17247 0.09% 51 16966 0.09% 52 17425 0.09% 53 17450 0.09% 54 17136 0.09% 55 17479 0.09% 56 17450 0.09% 57 17699 0.09% 58 18023 0.09% 59 18631 0.10% 60 18979 0.10% 61 19388 0.10% 62 20151 0.10% 63 19186 0.10% 64 18853 0.10% 65 19371 0.10% 66 19927 0.10% 67 20576 0.11% 68 19388 0.10% 69 19094 0.10% 70 18671 0.10% 71 18511 0.10% 72 18813 0.10% 73 18726 0.10% 74 19453 0.10% 75 19279 0.10% 76 19616 0.10% 77 20115 0.10% 78 19611 0.10% 79 20032 0.10% 80 20581 0.11% 81 20266 0.11% 82 20156 0.11% 83 19484 0.10% 84 19450 0.10% 85 19888 0.10% 86 20011 0.10% 87 19679 0.10% 88 20059 0.10% 89 19977 0.10% 90 20016 0.10% 91 19285 0.10% 92 19223 0.10% 93 19030 0.10% 94 19259 0.10% 95 19304 0.10% 96 19359 0.10% 97 19854 0.10% 98 19504 0.10% 99 19756 0.10% 100 19748 0.10% 101 19677 0.10% 102 19476 0.10% 103 19594 0.10% 104 19015 0.10% 105 19032 0.10% 106 19133 0.10% 107 19360 0.10% 108 19229 0.10% 109 19528 0.10% 110 19695 0.10% 111 20061 0.10% 112 20248 0.11% 113 19186 0.10% 114 19209 0.10% 115 19948 0.10% 116 19734 0.10% 117 19961 0.10% 118 20272 0.11% 119 20936 0.11% 120 21228 0.11% 121 20455 0.11% 122 20601 0.11% 123 20873 0.11% 124 21017 0.11% 125 21447 0.11% 126 21010 0.11% 127 21592 0.11% 128 21126 0.11% 129 21206 0.11% 130 21345 0.11% 131 21572 0.11% 132 21885 0.11% 133 21766 0.11% 134 21418 0.11% 135 21557 0.11% 136 21508 0.11% 137 21794 0.11% 138 22281 0.12% 139 21897 0.11% 140 22211 0.12% 141 23296 0.12% 142 23868 0.12% 143 24725 0.13% 144 26363 0.14% 145 32041 0.17% 146 48498 0.25% 147 98026 0.51% 148 266935 1.39% 149 1267866 6.61% 150 14589349 76.01% 19193284 reads passed initial QC criterion=sequence-density sequence-density=0.54 sequence-density-rank=1 fanout-score=2.04 fanout-score-rank=28 prefix-density=0.53 prefix-fanout=2.0 sequence=TGTACTAGAATAAATTATATGT criterion=fanout-score sequence-density=0.01 sequence-density-rank=34 fanout-score=29.90 fanout-score-rank=1 prefix-density=0.08 prefix-fanout=4.2 sequence=AAGGGCAAGATACCTGGGGGTGGCGGTGGCAGTGGCGTCCGTGGTGAAGGAGGAGAGAAAAAGAAGAAAAAGGACAAGAAGAAGAATGAAGATGGCCATAGCAGCAGCAGTGACAGCGACTAAAAATCTTGCACTGCTTCCATGCATTAGGTGTGGAGGAGGTCGAGGTCCTGTCTACCAGTGTTGCTGATTATCACTAGAAAAAAAAAGA criterion=sequence-density sequence-density=0.13 sequence-density-rank=1 fanout-score=2.17 fanout-score-rank=22 prefix-density=0.02 prefix-fanout=2.2 sequence=TTTTTTTTTTGG criterion=fanout-score sequence-density=0.01 sequence-density-rank=46 fanout-score=4.44 fanout-score-rank=1 prefix-density=0.02 prefix-fanout=2.2 sequence=TTTTTTTTTGAT SRR11445639 testing PE reads STAR mapping to Ensembl genome Unpaired reads removal Started job on | Feb 12 15:54:13 Started mapping on | Feb 12 15:54:13 Finished on | Feb 12 16:00:40 Mapping speed, Million of reads per hour | 171.45 Number of input reads | 18431207 Average input read length | 266 UNIQUE READS: Uniquely mapped reads number | 8046099 Uniquely mapped reads % | 43.65% Average mapped length | 247.68 Number of splices: Total | 737291 Number of splices: Annotated (sjdb) | 668248 Number of splices: GT/AG | 695309 Number of splices: GC/AG | 8714 Number of splices: AT/AC | 977 Number of splices: Non-canonical | 32291 Mismatch rate per base, % | 2.77% Deletion rate per base | 0.03% Deletion average length | 2.10 Insertion rate per base | 0.02% Insertion average length | 2.08 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 609775 % of reads mapped to multiple loci | 3.31% Number of reads mapped to too many loci | 18451 % of reads mapped to too many loci | 0.10% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 52.14% % of reads unmapped: other | 0.79% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 9775608 9775608 9775608 N_multimapping 609775 609775 609775 N_noFeature 441006 518094 7835554 N_ambiguous 211729 78030 1350 UnstrandedReadsAssigned:7393364 PositiveStrandReadsAssigned:7449975 NegativeStrandReadsAssigned:209195 Dataset is classified positive stranded MeadianReadLen=150 20thPercentileLength=150 echo kmer=145 SRR11445639 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: SRR11445639-trimmed-pair1.fastq SRR11445639-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 18,431,207 reads, 13,906,434 reads pseudoaligned [quant] estimated average fragment length: 188.195 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,126 rounds 52401 SRR11445639.ke.tsv 34699 SRR11445639.se.tsv 87100 total ==> SRR11445639.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1830.8 846.483 31.2538 Potri.005G024800.1.v4.1 1035 847.805 890 70.9611 Potri.004G059700.1.v4.1 961 773.805 8 0.698852 Potri.007G009000.2.v4.1 1416 1228.8 0 0 Potri.003G141000.2.v4.1 2943 2755.8 472 11.5776 Potri.016G087400.1.v4.1 270 102.021 113 74.8713 Potri.015G069301.1.v4.1 564 377.138 0 0 Potri.010G195200.1.v4.1 1773 1585.8 142 6.05292 Potri.012G127500.1.v4.1 977 789.805 9844 842.516 ==> SRR11445639.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 15 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 236 Potri.001G212900.v4.1 0 Potri.001G182400.v4.1 4 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 36 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 18 SRR11445639 completed mapping pipeline successfully