Starting /dee2/code/volunteer_pipeline.sh SRR13165371 current disk space = 1541836050432 free memory = 1599105816 SRR13165371 SRAfilesize 874fd1806dd4f55dfecb61e5c5c05506 SRR13165371.sra SRR13165371.sra file validated SRR13165371 is paired end SRR13165371 is conventional basespace SRR13165371 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR13165371_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 50 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.647 37.0 37.0 37.0 37.0 37.0 2 36.1355 37.0 37.0 37.0 37.0 37.0 3 36.572 37.0 37.0 37.0 37.0 37.0 4 36.496 37.0 37.0 37.0 37.0 37.0 5 36.494 37.0 37.0 37.0 37.0 37.0 6 36.568 37.0 37.0 37.0 37.0 37.0 7 36.344 37.0 37.0 37.0 37.0 37.0 8 36.536 37.0 37.0 37.0 37.0 37.0 9 36.4725 37.0 37.0 37.0 37.0 37.0 10-14 36.5664 37.0 37.0 37.0 37.0 37.0 15-19 36.4953 37.0 37.0 37.0 37.0 37.0 20-24 36.5111 37.0 37.0 37.0 37.0 37.0 25-29 36.4602 37.0 37.0 37.0 37.0 37.0 30-34 36.4133 37.0 37.0 37.0 37.0 37.0 35-39 36.4131 37.0 37.0 37.0 37.0 37.0 40-44 36.41519999999999 37.0 37.0 37.0 37.0 37.0 45-49 36.3243 37.0 37.0 37.0 37.0 37.0 50-54 36.36129999999999 37.0 37.0 37.0 37.0 37.0 55-59 36.3541 37.0 37.0 37.0 37.0 37.0 60-64 36.2843 37.0 37.0 37.0 37.0 37.0 65-69 36.2993 37.0 37.0 37.0 37.0 37.0 70-74 36.296 37.0 37.0 37.0 37.0 37.0 75-79 36.2845 37.0 37.0 37.0 37.0 37.0 80-84 36.2649 37.0 37.0 37.0 37.0 37.0 85-89 36.2466 37.0 37.0 37.0 37.0 37.0 90-94 36.229200000000006 37.0 37.0 37.0 37.0 37.0 95-99 36.15070000000001 37.0 37.0 37.0 37.0 37.0 100-104 36.1486 37.0 37.0 37.0 37.0 37.0 105-109 36.1449 37.0 37.0 37.0 37.0 37.0 110-114 36.1079 37.0 37.0 37.0 37.0 37.0 115-119 36.0578 37.0 37.0 37.0 37.0 37.0 120-124 35.9504 37.0 37.0 37.0 37.0 37.0 125-129 35.8489 37.0 37.0 37.0 37.0 37.0 130-134 35.820100000000004 37.0 37.0 37.0 37.0 37.0 135-139 35.6371 37.0 37.0 37.0 37.0 37.0 140-144 35.368 37.0 37.0 37.0 37.0 37.0 145-149 35.0746 37.0 37.0 37.0 29.8 37.0 150-151 34.792500000000004 37.0 37.0 37.0 25.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 21 1.0 22 0.0 23 1.0 24 2.0 25 4.0 26 5.0 27 5.0 28 11.0 29 20.0 30 24.0 31 42.0 32 74.0 33 122.0 34 147.0 35 322.0 36 2814.0 37 406.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 56.699999999999996 10.95 5.125 27.224999999999998 2 25.85599194360524 10.045317220543806 33.93756294058409 30.16112789526687 3 20.5 17.825 26.674999999999997 35.0 4 27.425 22.45 22.275 27.85 5 27.275 29.2 20.95 22.575 6 24.7 30.525000000000002 21.45 23.325000000000003 7 18.7 23.45 39.475 18.375 8 20.75 23.724999999999998 29.525000000000002 26.0 9 22.075 20.3 31.424999999999997 26.200000000000003 10-14 24.884999999999998 24.98 25.03 25.105 15-19 24.585 24.84 24.815 25.759999999999998 20-24 24.349999999999998 24.825 25.195 25.629999999999995 25-29 24.474999999999998 24.905 24.97 25.650000000000002 30-34 24.125 24.66 25.205 26.009999999999998 35-39 24.135 25.169999999999998 24.505 26.19 40-44 23.765 25.55 24.685000000000002 26.0 45-49 23.805 24.94 24.91 26.345000000000002 50-54 23.89 24.97 25.285000000000004 25.855 55-59 23.215 24.435000000000002 25.900000000000002 26.450000000000003 60-64 24.255 24.675 24.415 26.655 65-69 24.515 25.545 24.175 25.765 70-74 24.990000000000002 25.979999999999997 23.585 25.445 75-79 24.575 24.755 24.615000000000002 26.055 80-84 24.865000000000002 24.195 24.9 26.040000000000003 85-89 24.175 24.905 24.349999999999998 26.57 90-94 25.21 25.169999999999998 24.15 25.47 95-99 25.069999999999997 24.610000000000003 24.26 26.06 100-104 25.215 25.19 23.865 25.729999999999997 105-109 25.22 24.625 23.845 26.31 110-114 25.36 25.155 23.995 25.490000000000002 115-119 23.96 25.75 23.21 27.08 120-124 24.73 25.6 23.055 26.615 125-129 25.295 25.965 22.82 25.919999999999998 130-134 24.98 25.435000000000002 23.9 25.685000000000002 135-139 25.080000000000002 24.815 23.150000000000002 26.955000000000002 140-144 25.245 26.040000000000003 22.595000000000002 26.119999999999997 145-149 25.174999999999997 25.385 23.335 26.105 150-151 26.137500000000003 24.8125 22.8625 26.187500000000004 >>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 0.5 7 0.5 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 0.5 26 0.5 27 2.0 28 3.0 29 2.0 30 4.0 31 7.0 32 8.0 33 18.0 34 31.0 35 38.5 36 52.0 37 61.0 38 61.0 39 86.0 40 124.0 41 130.0 42 138.5 43 158.0 44 178.5 45 199.0 46 196.0 47 193.0 48 192.5 49 173.0 50 151.5 51 144.5 52 138.0 53 133.0 54 122.0 55 95.5 56 84.0 57 81.0 58 76.0 59 89.5 60 81.5 61 57.0 62 54.5 63 56.5 64 58.5 65 64.0 66 68.5 67 58.0 68 41.0 69 46.0 70 46.0 71 28.5 72 29.5 73 35.0 74 29.0 75 20.0 76 19.5 77 14.5 78 3.5 79 4.0 80 4.5 81 2.5 82 3.0 83 2.0 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 0.7000000000000001 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 74.725 #Duplication Level Percentage of deduplicated Percentage of total 1 76.34660421545667 57.05 2 16.460354633656742 24.6 3 5.0853128136500505 11.4 4 1.5055202408832384 4.5 5 0.4014720642355303 1.5 6 0.16728002676480427 0.75 7 0.0 0.0 8 0.03345600535296086 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 GGCTGCTTCTGCGCCCTTCCGCCGTCTTCCTTCCCACCGCCGGCGGCTTC 8 0.2 No Hit AGCTAATTGGGTCCCCAGCAGCTGAGATACATGACCGTCCTCAGCCCCTC 6 0.15 No Hit TGGGGACACCGACCTGCTTGGCGAGCAGGATGTGCTCCTTGGTCTGCGGC 6 0.15 No Hit GGGGTGGCATCGGTTTGAAGAGCGGCAAGTTCTTGTCGAAGCTTGACGAT 6 0.15 No Hit AGGGGGAGAGAAAAAAAGGAGGCGAACAAGAACAAATCTTGGTGACACGA 6 0.15 No Hit CTTGACATTGTCAATGGTGTCTGACGACTCAACCTCAAGGGTGATGGTCT 6 0.15 No Hit GATAACTGTTTTGAATCCCTCATGGAGCTCCTGACGAACTTTGCACATGA 5 0.125 No Hit ACTCCTCAGTCCACAAACCAAAAAAGGAAAAACAGAAACAAAAAAATTGA 5 0.125 No Hit GGAGCACGTACTTCGAAATTGCGCGTGACTCGAAGAGAAGCAGATCCCCA 5 0.125 No Hit CTCCGTGGATGGTCCATGCTTGCCGACTTTGAATTTGAAGGATTGTCAGT 5 0.125 No Hit GTTCCTGTATATAGAAGTAATTAATTACGTAGCCACATCAAAATGTACAA 5 0.125 No Hit GCCTTGCTTATAGTTGAATTCATTGTCCAGGTCATCAACGTCTTCTTCCT 5 0.125 No Hit GTTGAGCAGGATGAGCTCCACGAGCGTGTCGGCCATGTCGCCGATGCTTG 5 0.125 No Hit GGACACCTGTACCACTGCCCACTTCTGGGGAAGAAGGTGAAGTTGATAAA 5 0.125 No Hit CTCCTCTGACGTATTTATCAGCCGTGGAAAATCACACACAAGGTGGTTTC 5 0.125 No Hit GGTCTTGTCACCAGGCATTTGTCCATCAGCCTGAATGCCATGCTCGAGGC 5 0.125 No Hit GTGGGTGGAGGGGCGCGCGGGCGATCCCACGACGAAGCCGCCGCCGTGGA 5 0.125 No Hit GTTTGTTAGGTAACTTGCCCTTAGGACTTGCTTCTGTTGAATTTGGTCTC 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 0.0 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 0.025 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 0.11249999999999999 0.0 0.0 0.0 0.0 58-59 0.15 0.0 0.0 0.0 0.0 60-61 0.15 0.0 0.0 0.0 0.0 62-63 0.1875 0.0 0.0 0.0 0.0 64-65 0.25 0.0 0.0 0.0 0.0 66-67 0.3375 0.0 0.0 0.0 0.0 68-69 0.3625 0.0 0.0 0.0 0.0 70-71 0.45 0.0 0.0 0.0 0.0 72-73 0.5375 0.0 0.0 0.0 0.0 74-75 0.7124999999999999 0.0 0.0 0.0 0.0 76-77 0.85 0.0 0.0 0.0 0.0 78-79 0.9375 0.0 0.0 0.0 0.0 80-81 1.1 0.0 0.0 0.0 0.0 82-83 1.2875 0.0 0.0 0.0 0.0 84-85 1.4625 0.0 0.0 0.0 0.0 86-87 1.825 0.0 0.0 0.0 0.0 88-89 2.0375 0.0 0.0 0.0 0.0 90-91 2.5999999999999996 0.0 0.0 0.0 0.0 92-93 2.975 0.0 0.0 0.0 0.0 94-95 3.275 0.0 0.0 0.0 0.0 96-97 3.7249999999999996 0.0 0.0 0.0 0.0 98-99 4.0625 0.0 0.0 0.0 0.0 100-101 4.6625 0.0 0.0 0.0 0.0 102-103 5.112500000000001 0.0 0.0 0.0 0.0 104-105 5.574999999999999 0.0 0.0 0.0 0.0 106-107 5.9125 0.0 0.0 0.0 0.0 108-109 6.55 0.0 0.0 0.0 0.0 110-111 7.2125 0.0 0.0 0.0 0.0 112-113 7.9 0.0 0.0 0.0 0.0 114-115 8.600000000000001 0.0 0.0 0.0 0.0 116-117 9.274999999999999 0.0 0.0 0.0 0.0 118-119 10.05 0.0 0.0 0.0 0.0 120-121 11.0 0.0 0.0 0.0 0.0 122-123 11.787500000000001 0.0 0.0 0.0 0.0 124-125 12.8125 0.0 0.0 0.0 0.0 126-127 13.5125 0.0 0.0 0.0 0.0 128-129 14.05 0.0 0.0 0.0 0.0 130-131 14.875 0.0 0.0 0.0 0.0 132-133 15.587499999999999 0.0 0.0 0.0 0.0 134-135 16.262500000000003 0.0 0.0 0.0 0.0 136-137 16.9375 0.0 0.0 0.0 0.0 138-139 17.6375 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TGAACTC 60 0.004491891 14.500001 140-144 ACGTCTG 65 0.0076375785 13.384615 135-139 >>END_MODULE SRR13165371 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR13165371_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 51 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 35.98 37.0 37.0 37.0 37.0 37.0 2 36.1005 37.0 37.0 37.0 37.0 37.0 3 36.153 37.0 37.0 37.0 37.0 37.0 4 36.3115 37.0 37.0 37.0 37.0 37.0 5 36.374 37.0 37.0 37.0 37.0 37.0 6 36.2725 37.0 37.0 37.0 37.0 37.0 7 36.2645 37.0 37.0 37.0 37.0 37.0 8 36.2625 37.0 37.0 37.0 37.0 37.0 9 36.3105 37.0 37.0 37.0 37.0 37.0 10-14 36.336 37.0 37.0 37.0 37.0 37.0 15-19 36.2981 37.0 37.0 37.0 37.0 37.0 20-24 36.2753 37.0 37.0 37.0 37.0 37.0 25-29 36.2384 37.0 37.0 37.0 37.0 37.0 30-34 36.1967 37.0 37.0 37.0 37.0 37.0 35-39 36.2067 37.0 37.0 37.0 37.0 37.0 40-44 36.1614 37.0 37.0 37.0 37.0 37.0 45-49 36.1555 37.0 37.0 37.0 37.0 37.0 50-54 36.126099999999994 37.0 37.0 37.0 37.0 37.0 55-59 36.135000000000005 37.0 37.0 37.0 37.0 37.0 60-64 36.101099999999995 37.0 37.0 37.0 37.0 37.0 65-69 36.0338 37.0 37.0 37.0 37.0 37.0 70-74 36.0124 37.0 37.0 37.0 37.0 37.0 75-79 36.05485 37.0 37.0 37.0 37.0 37.0 80-84 36.002300000000005 37.0 37.0 37.0 37.0 37.0 85-89 35.934250000000006 37.0 37.0 37.0 37.0 37.0 90-94 35.88665 37.0 37.0 37.0 37.0 37.0 95-99 35.89365 37.0 37.0 37.0 37.0 37.0 100-104 35.8755 37.0 37.0 37.0 37.0 37.0 105-109 35.84310000000001 37.0 37.0 37.0 37.0 37.0 110-114 35.755900000000004 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 35.561499999999995 37.0 37.0 37.0 37.0 37.0 125-129 35.4995 37.0 37.0 37.0 37.0 37.0 130-134 35.2817 37.0 37.0 37.0 37.0 37.0 135-139 35.14915 37.0 37.0 37.0 34.6 37.0 140-144 34.961200000000005 37.0 37.0 37.0 25.0 37.0 145-149 34.77515 37.0 37.0 37.0 25.0 37.0 150-151 34.469 37.0 37.0 37.0 25.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 12 1.0 13 3.0 14 2.0 15 4.0 16 5.0 17 6.0 18 1.0 19 1.0 20 4.0 21 4.0 22 4.0 23 5.0 24 5.0 25 6.0 26 8.0 27 11.0 28 12.0 29 18.0 30 15.0 31 40.0 32 68.0 33 109.0 34 194.0 35 459.0 36 2731.0 37 284.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 50.20080321285141 19.879518072289155 7.228915662650602 22.690763052208833 2 30.75 21.4 25.775 22.075 3 24.575 24.625 29.475 21.325 4 27.375 29.9 20.4 22.325 5 28.075 32.824999999999996 18.75 20.349999999999998 6 23.225 34.825 19.425 22.525000000000002 7 24.525 18.6 33.425 23.45 8 24.525 22.625 23.25 29.599999999999998 9 24.099999999999998 21.975 25.8 28.125 10-14 26.19 25.185000000000002 23.044999999999998 25.580000000000002 15-19 26.005 23.68 24.68 25.635 20-24 25.392539253925396 25.197519751975193 24.372437243724374 25.03750375037504 25-29 26.678339169584792 24.00200100050025 23.571785892946473 25.747873936968485 30-34 24.927478243473043 25.027508252475744 23.892167650295086 26.15284585375613 35-39 26.017601760176017 26.237623762376238 23.27232723272327 24.47244724472447 40-44 25.94778433530059 24.307292187656294 24.03220966289887 25.712713814144244 45-49 25.28005601120224 25.495099019803963 23.779755951190236 25.445089017803564 50-54 25.88758875887589 24.937493749374937 24.607460746074608 24.56745674567457 55-59 26.758379189594798 24.047023511755878 23.946973486743374 25.24762381190595 60-64 26.1976197619762 24.877487748774875 24.227422742274225 24.697469746974697 65-69 26.495 24.915000000000003 24.745 23.845 70-74 27.78389194597299 23.911955977988995 24.057028514257127 24.24712356178089 75-79 26.599309758415444 24.55859550842795 23.99839943980393 24.843695293352674 80-84 26.815 25.230000000000004 23.665 24.29 85-89 25.82662197989095 24.76114251413136 24.380971437146716 25.03126406883097 90-94 26.288943341501223 24.978746812021804 23.998599789968495 24.733710056508475 95-99 26.77133856692835 24.7862393119656 23.876193809690484 24.566228311415568 100-104 26.22311155577789 24.842421210605302 24.3671835917959 24.56728364182091 105-109 26.923461730865434 24.087043521760883 24.027013506753377 24.96248124062031 110-114 27.522752275227525 25.472547254725477 23.957395739573958 23.047304730473048 115-119 28.039019509754876 25.697848924462228 23.10655327663832 23.156578289144573 120-124 27.79889944972486 25.78789394697349 23.386693346673336 23.026513256628313 125-129 28.971588635454182 26.030412164865947 22.834133653461386 22.163865546218485 130-134 29.157494496698018 24.54472683610166 23.16890134080448 23.128877326395838 135-139 29.886437540647353 25.27890339686828 22.982640452248738 21.85201861023563 140-144 30.563056305630564 25.147514751475146 22.872287228722872 21.417141714171418 145-149 30.88198509180049 25.17884836660163 22.202211216168894 21.736955325428987 150-151 31.861396047035278 24.230673004753562 22.70452839629722 21.203402551913936 >>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 0.5 6 0.5 7 0.0 8 0.0 9 0.0 10 0.0 11 0.0 12 0.5 13 1.0 14 1.0 15 1.0 16 1.0 17 0.5 18 0.0 19 0.5 20 1.0 21 1.0 22 0.5 23 0.5 24 1.0 25 5.0 26 5.0 27 1.0 28 1.0 29 3.5 30 7.5 31 10.0 32 8.5 33 13.5 34 20.0 35 35.0 36 48.0 37 53.0 38 64.0 39 87.5 40 114.5 41 115.5 42 124.5 43 137.0 44 154.0 45 196.0 46 204.0 47 176.0 48 168.0 49 177.5 50 165.0 51 137.5 52 120.0 53 117.0 54 119.0 55 109.0 56 96.0 57 78.5 58 84.0 59 89.0 60 71.0 61 70.0 62 76.0 63 71.0 64 74.0 65 69.0 66 54.0 67 66.0 68 62.5 69 56.0 70 64.5 71 54.5 72 34.5 73 25.0 74 21.5 75 15.0 76 17.0 77 15.5 78 6.5 79 3.0 80 3.0 81 3.0 82 1.5 83 1.0 84 1.0 85 0.0 86 0.5 87 1.0 88 0.5 89 0.0 90 0.5 91 0.5 92 0.0 93 0.5 94 0.5 95 0.0 96 0.0 97 0.0 98 0.0 99 1.0 100 2.5 >>END_MODULE >>Per base N content pass #Base N-Count 1 0.4 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 0.01 25-29 0.05 30-34 0.03 35-39 0.01 40-44 0.03 45-49 0.02 50-54 0.01 55-59 0.05 60-64 0.01 65-69 0.0 70-74 0.05 75-79 0.034999999999999996 80-84 0.0 85-89 0.045 90-94 0.015 95-99 0.005 100-104 0.05 105-109 0.05 110-114 0.01 115-119 0.05 120-124 0.05 125-129 0.04 130-134 0.06 135-139 0.055 140-144 0.01 145-149 0.055 150-151 0.075 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 75.3 #Duplication Level Percentage of deduplicated Percentage of total 1 77.29083665338645 58.199999999999996 2 15.803452855245684 23.799999999999997 3 4.648074369189907 10.5 4 1.593625498007968 4.8 5 0.4316069057104913 1.625 6 0.199203187250996 0.8999999999999999 7 0.033200531208499334 0.17500000000000002 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 TGGGTCTGGGTTCGGGTTCGGGTACAGCGGCAGCGGTAGCGGCGATGCAG 7 0.17500000000000002 No Hit GGCAAGACCATCACCCTTGAGGTGGAGTCATCTGACACCATCGACAATGT 6 0.15 No Hit CGGCCACGTCGACCACGGCAAGACCACCCTCACGGCGGCGCTCACCATGG 6 0.15 No Hit CCTTCACCATACACATTTCGCAGTCCATCCGCACCGATCCGCCACCATGA 6 0.15 No Hit GGAACTACGCTCTGAGGTCCATCCACCGGGCAGCCAAGGCCAACGTGCAG 6 0.15 No Hit TGGGCCGGATGGAGTCCGTGTGGGGGCGCGACTGCGGCGAGTTCAGGCCC 6 0.15 No Hit GACGAGCTCTTCTTCTCCGTCGCCAACCACACGCTCACAGTCGTTGAGGT 6 0.15 No Hit GTCTGTATGGGCACGATGCGGATCTGATAATGCTCGCTTTGGCATCTCAT 5 0.125 No Hit GGCGACGCGCCCGCGCCGGGTAAGCAGGCGAAAGGTGTGAATGGGCAGGT 5 0.125 No Hit CGTCTCCAAGGACATCCACGTCGGCGCCGCCCGCGCGCGCGTCTACCTCC 5 0.125 No Hit GTCATATGCTTGTCTCAAAGATTAAGCCATGCATGTGCAAGTATGAACTA 5 0.125 No Hit GGACAAACTGCAGATATATGCTGGGAGAAACTCAAGGGTGTCAGTGGCAT 5 0.125 No Hit CTGATAGCCTTGATGTCCCTTGTCGACTCCTGAAAGGAAGGCAGTACACA 5 0.125 No Hit TATTCATACACACACTCCCTGGTCTGTCTGTCTCTCTCGCCTGCAGAAAA 5 0.125 No Hit AAATTATTGTGTTGAGTTTTGCGGTTTTTTCTCGATCGATCAATTTTTTT 5 0.125 No Hit GCTAAAGCAAGCAAACTAGGTGATGGTACAAATGCAGTTAGCAAGTCAAC 5 0.125 No Hit ATTTGCTGCGGATTTTCCCACGGACGACACGCATTACTTCCTCTAATTAC 5 0.125 No Hit CACTTGGTTGCGGAATACAAGAGCTGCACGGGCATTGCCGTTCGATGACA 5 0.125 No Hit CGCCTTCCCGTCCTTCCTCACCTCGCTCCCTTCCCTCAAGTACCTCGACC 5 0.125 No Hit AATAAATTAAAGTGCGCATTCCATTTAATTGTTTTGTCTCGTTATGAATT 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 0.0 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 0.025 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 0.11249999999999999 0.0 0.0 0.0 0.0 58-59 0.15 0.0 0.0 0.0 0.0 60-61 0.15 0.0 0.0 0.0 0.0 62-63 0.1875 0.0 0.0 0.0 0.0 64-65 0.25 0.0 0.0 0.0 0.0 66-67 0.3375 0.0 0.0 0.0 0.0 68-69 0.3625 0.0 0.0 0.0 0.0 70-71 0.45 0.0 0.0 0.0 0.0 72-73 0.5375 0.0 0.0 0.0 0.0 74-75 0.7124999999999999 0.0 0.0 0.0 0.0 76-77 0.85 0.0 0.0 0.0 0.0 78-79 0.9375 0.0 0.0 0.0 0.0 80-81 1.1 0.0 0.0 0.0 0.0 82-83 1.2875 0.0 0.0 0.0 0.0 84-85 1.4625 0.0 0.0 0.0 0.0 86-87 1.825 0.0 0.0 0.0 0.0 88-89 2.05 0.0 0.0 0.0 0.0 90-91 2.5125 0.0 0.0 0.0 0.0 92-93 2.9 0.0 0.0 0.0 0.0 94-95 3.2 0.0 0.0 0.0 0.0 96-97 3.675 0.0 0.0 0.0 0.0 98-99 4.0125 0.0 0.0 0.0 0.0 100-101 4.6125 0.0 0.0 0.0 0.0 102-103 5.0625 0.0 0.0 0.0 0.0 104-105 5.525 0.0 0.0 0.0 0.0 106-107 5.8625 0.0 0.0 0.0 0.0 108-109 6.5 0.0 0.0 0.0 0.0 110-111 7.175 0.0 0.0 0.0 0.0 112-113 7.875 0.0 0.0 0.0 0.0 114-115 8.5875 0.0 0.0 0.0 0.0 116-117 9.2625 0.0 0.0 0.0 0.0 118-119 10.1125 0.0 0.0 0.0 0.0 120-121 11.1 0.0 0.0 0.0 0.0 122-123 11.8875 0.0 0.0 0.0 0.0 124-125 12.912500000000001 0.0 0.0 0.0 0.0 126-127 13.6125 0.0 0.0 0.0 0.0 128-129 14.15 0.0 0.0 0.0 0.0 130-131 14.9875 0.0 0.0 0.0 0.0 132-133 15.7 0.0 0.0 0.0 0.0 134-135 16.375 0.0 0.0 0.0 0.0 136-137 17.025 0.0 0.0 0.0 0.0 138-139 17.7125 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TTCATAC 10 0.006830828 145.0 3 TCATACA 10 0.006830828 145.0 4 CGTGTAG 50 0.0013298223 17.4 135-139 >>END_MODULE Read 1291236 spots for SRR13165371.sra Written 1291236 spots for SRR13165371.sra Read 1291236 spots for SRR13165371.sra Written 1291236 spots for SRR13165371.sra Read 1291236 spots for SRR13165371.sra Written 1291236 spots for SRR13165371.sra Read 1291236 spots for SRR13165371.sra Written 1291236 spots for SRR13165371.sra Read 1291236 spots for SRR13165371.sra Written 1291236 spots for SRR13165371.sra Read 1291254 spots for SRR13165371.sra Written 1291254 spots for SRR13165371.sra Read 1291236 spots for SRR13165371.sra Written 1291236 spots for SRR13165371.sra Read 1291236 spots for SRR13165371.sra Written 1291236 spots for SRR13165371.sra Read 1291236 spots for SRR13165371.sra Written 1291236 spots for SRR13165371.sra Read 1291236 spots for SRR13165371.sra Written 1291236 spots for SRR13165371.sra Read 1291236 spots for SRR13165371.sra Written 1291236 spots for SRR13165371.sra Read 1291236 spots for SRR13165371.sra Written 1291236 spots for SRR13165371.sra Read 1291236 spots for SRR13165371.sra Written 1291236 spots for SRR13165371.sra Read 1291236 spots for SRR13165371.sra Written 1291236 spots for SRR13165371.sra Read 1291236 spots for SRR13165371.sra Written 1291236 spots for SRR13165371.sra Read 1291236 spots for SRR13165371.sra Written 1291236 spots for SRR13165371.sra Read 1291236 spots for SRR13165371.sra Written 1291236 spots for SRR13165371.sra Read 1291236 spots for SRR13165371.sra Written 1291236 spots for SRR13165371.sra Read 1291236 spots for SRR13165371.sra Written 1291236 spots for SRR13165371.sra Read 1291236 spots for SRR13165371.sra Written 1291236 spots for SRR13165371.sra SRR ids: ['SRR13165371.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_53aqskry SRR13165371.sra spots: 25824738 blocks: [[1, 1291236], [1291237, 2582472], [2582473, 3873708], [3873709, 5164944], [5164945, 6456180], [6456181, 7747416], [7747417, 9038652], [9038653, 10329888], [10329889, 11621124], [11621125, 12912360], [12912361, 14203596], [14203597, 15494832], [15494833, 16786068], [16786069, 18077304], [18077305, 19368540], [19368541, 20659776], [20659777, 21951012], [21951013, 23242248], [23242249, 24533484], [24533485, 25824738]] SRR13165371 file size 8754675 SRR13165371 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 SRR13165371 SRR13165371_1.fastq SRR13165371_2.fastq Input file: SRR13165371_1.fastq Paired file: SRR13165371_2.fastq trimmed: SRR13165371-trimmed-pair1.fastq, SRR13165371-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 16:28:01 2024 >> started Sat Dec 7 16:28:30 2024 >> done (29.389s) 25824738 read pairs processed; of these: 718 ( 0.00%) short read pairs filtered out after trimming by size control 21279 ( 0.08%) empty read pairs filtered out after trimming by size control 25802741 (99.91%) read pairs available; of these: 5945271 (23.04%) trimmed read pairs available after processing 19857470 (76.96%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 33 0.00% 19 46 0.00% 20 41 0.00% 21 39 0.00% 22 59 0.00% 23 79 0.00% 24 74 0.00% 25 111 0.00% 26 107 0.00% 27 141 0.00% 28 158 0.00% 29 141 0.00% 30 185 0.00% 31 182 0.00% 32 181 0.00% 33 222 0.00% 34 172 0.00% 35 247 0.00% 36 280 0.00% 37 285 0.00% 38 302 0.00% 39 328 0.00% 40 387 0.00% 41 421 0.00% 42 451 0.00% 43 469 0.00% 44 500 0.00% 45 503 0.00% 46 589 0.00% 47 635 0.00% 48 869 0.00% 49 934 0.00% 50 1034 0.00% 51 1173 0.00% 52 1292 0.01% 53 1339 0.01% 54 1505 0.01% 55 1536 0.01% 56 1696 0.01% 57 1882 0.01% 58 2184 0.01% 59 2435 0.01% 60 2971 0.01% 61 3321 0.01% 62 3629 0.01% 63 4081 0.02% 64 4405 0.02% 65 4805 0.02% 66 5118 0.02% 67 5626 0.02% 68 6311 0.02% 69 7079 0.03% 70 8052 0.03% 71 9263 0.04% 72 10382 0.04% 73 11472 0.04% 74 12458 0.05% 75 13718 0.05% 76 15078 0.06% 77 16174 0.06% 78 17531 0.07% 79 19290 0.07% 80 21100 0.08% 81 23271 0.09% 82 25312 0.10% 83 28071 0.11% 84 30412 0.12% 85 32516 0.13% 86 34097 0.13% 87 35398 0.14% 88 37697 0.15% 89 38992 0.15% 90 41351 0.16% 91 43972 0.17% 92 46613 0.18% 93 50651 0.20% 94 52922 0.21% 95 55445 0.21% 96 57043 0.22% 97 58641 0.23% 98 59614 0.23% 99 61695 0.24% 100 63974 0.25% 101 65328 0.25% 102 67877 0.26% 103 70391 0.27% 104 73398 0.28% 105 74996 0.29% 106 75941 0.29% 107 78308 0.30% 108 79136 0.31% 109 80236 0.31% 110 80342 0.31% 111 83054 0.32% 112 84241 0.33% 113 85217 0.33% 114 88202 0.34% 115 89553 0.35% 116 92016 0.36% 117 92775 0.36% 118 92686 0.36% 119 93134 0.36% 120 94608 0.37% 121 95203 0.37% 122 95964 0.37% 123 98487 0.38% 124 99915 0.39% 125 100342 0.39% 126 102465 0.40% 127 101629 0.39% 128 102641 0.40% 129 103257 0.40% 130 102925 0.40% 131 103540 0.40% 132 105243 0.41% 133 106309 0.41% 134 106013 0.41% 135 108230 0.42% 136 109119 0.42% 137 107717 0.42% 138 108876 0.42% 139 108823 0.42% 140 107858 0.42% 141 108861 0.42% 142 110280 0.43% 143 110838 0.43% 144 111426 0.43% 145 114226 0.44% 146 114396 0.44% 147 116189 0.45% 148 112418 0.44% 149 113560 0.44% 150 112284 0.44% 151 19857470 76.96% 25802741 reads passed initial QC criterion=sequence-density sequence-density=0.22 sequence-density-rank=1 fanout-score=3.76 fanout-score-rank=24 prefix-density=0.32 prefix-fanout=2.5 sequence=GTGAGGGTCTTGACAAAGATCTGCATGCCACCACG criterion=fanout-score sequence-density=0.04 sequence-density-rank=26 fanout-score=243.78 fanout-score-rank=1 prefix-density=0.53 prefix-fanout=17.8 sequence=GGCGGCGGCGAACCGCCCCCGTCGCCGCGATCCGAACACTTCACCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGCATTCCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCTATATACTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCAAACTTCCGTCGCCTAAACGGCGATAGTCCCTCTAAGAAGCTAGCTGCGGAGGGATGGCTCCGCATAGCTAGTTAGCAGGCTGAGGTCTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCATGCACCACCACCCATAGAATCAAGAAAGAGCTCTCAGTCTGTCAATCCTTGCTATGTCTGGACCTGGTAAG criterion=sequence-density sequence-density=0.29 sequence-density-rank=1 fanout-score=5.74 fanout-score-rank=20 prefix-density=0.39 prefix-fanout=4.3 sequence=GGCAAGACCATCACCCTTGAGGTGGAGTCATCTGACACCAT criterion=fanout-score sequence-density=0.12 sequence-density-rank=17 fanout-score=94.91 fanout-score-rank=1 prefix-density=0.81 prefix-fanout=13.9 sequence=CGGCGGCGGCGGAGCTGACGGGCAGCCACCTGGACGAGGTGAAGC SRR13165371 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 07 16:29:18 Started mapping on | Dec 07 16:29:18 Finished on | Dec 07 16:31:24 Mapping speed, Million of reads per hour | 737.22 Number of input reads | 25802741 Average input read length | 287 UNIQUE READS: Uniquely mapped reads number | 24275743 Uniquely mapped reads % | 94.08% Average mapped length | 286.37 Number of splices: Total | 22154475 Number of splices: Annotated (sjdb) | 20819955 Number of splices: GT/AG | 21881213 Number of splices: GC/AG | 220947 Number of splices: AT/AC | 11456 Number of splices: Non-canonical | 40859 Mismatch rate per base, % | 0.21% Deletion rate per base | 0.01% Deletion average length | 2.95 Insertion rate per base | 0.01% Insertion average length | 2.26 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 211136 % of reads mapped to multiple loci | 0.82% Number of reads mapped to too many loci | 82047 % of reads mapped to too many loci | 0.32% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 3.31% % of reads unmapped: other | 1.47% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 1316133 1316133 1316133 N_multimapping 211136 211136 211136 N_noFeature 832913 23601723 1091545 N_ambiguous 471693 2727 57694 UnstrandedReadsAssigned:22971137 PositiveStrandReadsAssigned:671293 NegativeStrandReadsAssigned:23126504 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=144 echo kmer=139 SRR13165371 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: SRR13165371-trimmed-pair1.fastq SRR13165371-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 25,802,741 reads, 23,368,219 reads pseudoaligned [quant] estimated average fragment length: 227.568 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,202 rounds 52973 SRR13165371.ke.tsv 35125 SRR13165371.se.tsv 88098 total ==> SRR13165371.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 709.777 0 0 PNS24247 1044 817.432 57.3344 4.7986 PNS24249 1928 1701.43 180.963 7.27653 PNS24246 1044 817.432 57.3344 4.7986 PNS24248 1044 817.432 57.3344 4.7986 PNS24244 1471 1244.43 54.0341 2.97062 PNS24243 293 115.078 0 0 KQK14069 1603 1376.43 271.71 13.5052 KQK14071 474 262.229 0 0 ==> SRR13165371.se.tsv <== BRADI_1g14170v3 286 BRADI_1g53295v3 334 BRADI_1g59795v3 465 BRADI_1g07683v3 0 BRADI_1g00485v3 6 BRADI_1g20270v3 568 BRADI_1g74790v3 404 BRADI_1g09890v3 1 BRADI_1g77505v3 338 BRADI_1g48960v3 0 SRR13165371 completed mapping pipeline successfully