Starting /dee2/code/volunteer_pipeline.sh SRR13695474 current disk space = 3050262024192 free memory = 1579067156 SRR13695474 SRAfilesize bf76f5a0c75b3f8f860058b62e3feebc SRR13695474.sra SRR13695474.sra file validated SRR13695474 is paired end SRR13695474 is conventional basespace SRR13695474 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR13695474_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 36.5405 37.0 37.0 37.0 37.0 37.0 2 36.335 37.0 37.0 37.0 37.0 37.0 3 36.561 37.0 37.0 37.0 37.0 37.0 4 36.6445 37.0 37.0 37.0 37.0 37.0 5 36.6865 37.0 37.0 37.0 37.0 37.0 6 36.6325 37.0 37.0 37.0 37.0 37.0 7 36.486 37.0 37.0 37.0 37.0 37.0 8 36.543 37.0 37.0 37.0 37.0 37.0 9 36.5555 37.0 37.0 37.0 37.0 37.0 10-14 36.55800000000001 37.0 37.0 37.0 37.0 37.0 15-19 36.5351 37.0 37.0 37.0 37.0 37.0 20-24 36.4705 37.0 37.0 37.0 37.0 37.0 25-29 36.47859999999999 37.0 37.0 37.0 37.0 37.0 30-34 36.4569 37.0 37.0 37.0 37.0 37.0 35-39 36.4336 37.0 37.0 37.0 37.0 37.0 40-44 36.3834 37.0 37.0 37.0 37.0 37.0 45-49 36.3774 37.0 37.0 37.0 37.0 37.0 50-54 36.3359 37.0 37.0 37.0 37.0 37.0 55-59 36.377599999999994 37.0 37.0 37.0 37.0 37.0 60-64 36.3478 37.0 37.0 37.0 37.0 37.0 65-69 36.314099999999996 37.0 37.0 37.0 37.0 37.0 70-74 36.251799999999996 37.0 37.0 37.0 37.0 37.0 75-79 36.243700000000004 37.0 37.0 37.0 37.0 37.0 80-84 36.1952 37.0 37.0 37.0 37.0 37.0 85-89 36.1946 37.0 37.0 37.0 37.0 37.0 90-94 36.13100000000001 37.0 37.0 37.0 37.0 37.0 95-99 36.1315 37.0 37.0 37.0 37.0 37.0 100-104 36.150099999999995 37.0 37.0 37.0 37.0 37.0 105-109 36.0946 37.0 37.0 37.0 37.0 37.0 110-114 36.101800000000004 37.0 37.0 37.0 37.0 37.0 115-119 36.1104 37.0 37.0 37.0 37.0 37.0 120-124 35.9842 37.0 37.0 37.0 37.0 37.0 125-129 35.913599999999995 37.0 37.0 37.0 37.0 37.0 130-134 35.9239 37.0 37.0 37.0 37.0 37.0 135-139 35.8707 37.0 37.0 37.0 37.0 37.0 140-144 35.8461 37.0 37.0 37.0 37.0 37.0 145-149 35.6854 37.0 37.0 37.0 37.0 37.0 150-151 35.41125 37.0 37.0 37.0 31.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 24 4.0 25 1.0 26 7.0 27 14.0 28 9.0 29 19.0 30 21.0 31 33.0 32 57.0 33 80.0 34 139.0 35 334.0 36 2932.0 37 350.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 32.85 11.25 9.85 46.050000000000004 2 19.09182137481184 13.49724034119418 38.18364274962368 29.227295534370295 3 19.55 15.9 25.575 38.975 4 23.674999999999997 25.674999999999997 22.675 27.975 5 25.2 30.2 24.15 20.45 6 20.275000000000002 34.5 25.3 19.925 7 15.075 27.450000000000003 41.75 15.725 8 18.6 27.125 32.35 21.925 9 17.5 24.474999999999998 33.900000000000006 24.125 10-14 19.0 29.625 28.439999999999998 22.935 15-19 19.3 27.279999999999998 28.79 24.63 20-24 19.689999999999998 28.23 28.485 23.595 25-29 19.945 28.389999999999997 27.73 23.935000000000002 30-34 19.375 28.585 27.485 24.555 35-39 20.575 27.58 27.705000000000002 24.14 40-44 20.075000000000003 27.884999999999998 28.294999999999998 23.745 45-49 20.59 28.410000000000004 28.01 22.99 50-54 20.22 28.349999999999998 27.905 23.525 55-59 20.185 28.549999999999997 28.499999999999996 22.765 60-64 20.615 28.475 27.805000000000003 23.105 65-69 20.125 28.07 28.12 23.685000000000002 70-74 20.150000000000002 28.63 27.555000000000003 23.665 75-79 20.415 27.965 27.85 23.77 80-84 20.415 28.595 27.589999999999996 23.400000000000002 85-89 20.28 27.400000000000002 28.73 23.59 90-94 20.43 27.925 27.689999999999998 23.955000000000002 95-99 20.085 28.854999999999997 27.315 23.745 100-104 20.39 28.77 28.315 22.525000000000002 105-109 20.849999999999998 28.09 27.175 23.885 110-114 20.89 28.294999999999998 27.33 23.485 115-119 21.25 27.98 27.689999999999998 23.080000000000002 120-124 21.634999999999998 28.24 27.67 22.455 125-129 21.145 28.585 27.255000000000003 23.015 130-134 21.035 28.044999999999998 27.36 23.56 135-139 21.455 28.084999999999997 28.025 22.435 140-144 20.724999999999998 27.99 27.584999999999997 23.7 145-149 21.275 27.57 27.575 23.580000000000002 150-151 20.575 26.8625 28.8875 23.674999999999997 >>END_MODULE >>Per sequence GC content pass #GC Content Count 0 0.0 1 0.0 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10 0.0 11 0.0 12 0.0 13 0.0 14 0.0 15 0.0 16 0.0 17 0.0 18 0.0 19 0.0 20 0.0 21 0.5 22 0.5 23 1.0 24 2.0 25 3.0 26 3.5 27 6.0 28 13.5 29 14.0 30 23.0 31 29.5 32 30.5 33 35.5 34 44.0 35 65.0 36 91.0 37 116.0 38 141.5 39 169.0 40 189.0 41 224.0 42 244.5 43 237.5 44 267.0 45 273.0 46 266.5 47 275.0 48 234.5 49 194.0 50 162.5 51 138.0 52 111.0 53 82.5 54 64.5 55 58.0 56 50.0 57 30.5 58 30.5 59 26.5 60 14.5 61 8.5 62 8.5 63 8.0 64 2.5 65 2.5 66 2.5 67 0.5 68 0.5 69 0.0 70 1.0 71 2.0 72 1.0 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 0.0 2 0.35000000000000003 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 70.175 #Duplication Level Percentage of deduplicated Percentage of total 1 70.78731742073387 49.675000000000004 2 20.021375133594585 28.1 3 6.661916636978981 14.025000000000002 4 1.5675097969362308 4.3999999999999995 5 0.5700035625222657 2.0 6 0.21375133594584966 0.8999999999999999 7 0.14250089063056642 0.7000000000000001 8 0.035625222657641606 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 AAATAAAGAGGGCTCCCCAATAAAAGCATACAAGCGAGGACAACTTTTAC 8 0.2 No Hit ACCTGATAAATATGACAAGCCCATGGGTATGAATCTGGAGCAGACCAAAC 7 0.17500000000000002 No Hit GCGGTGATTACAGAATATGCTGAAAATAGCTTACTAGTGAGCAGCAAGGC 7 0.17500000000000002 No Hit CCTAGAGTTTTGTTCACCAAGCCATCTCTCACAAACGGGTAGGTTAGCAA 7 0.17500000000000002 No Hit CTCCCAGTGATGCATCACTTTACTCACAGCCACATTTCACCACTCTCTCT 7 0.17500000000000002 No Hit GCTAATACCAGCTGTGTCCTTGAAAGCTCATCCTAAGACAATGAATAAAC 6 0.15 No Hit CCTCCTCCCACCGCTGCTCTCTTCTCTGTTCTTCATCTCCACGTTGACTC 6 0.15 No Hit CTCCGAATAAAAAGACTACAAAACGTTCATAGGTAACATTTACAGGATTG 6 0.15 No Hit CTAAACTTACAAGAAATACAAAAGGAAGAACCTGGCATCAGGGACACTTA 6 0.15 No Hit TTCAACAGGGTTGTAGTTTAAGGGCCCATAGATGTAGACTGGTCTTATAG 6 0.15 No Hit CCCATCTTTGATAGCCTTTACTTGCTCGTACATGAGATCAAAGTTGTTGG 6 0.15 No Hit CATAAATCTTCTCAACCCCCGCGAAACCCTCTGGCCCAGAAATAGAAGCT 5 0.125 No Hit ATCCTTATTCCTTCAAGTTCAAAGATTGAATAATTAAAGATGAACTCAAA 5 0.125 No Hit CCAGATGACGAGTTCAGCTTCTAATTTTTCCCTATCTTCCAAACCAAGAA 5 0.125 No Hit GCTGGACCCGGTTACCCAACTCAGGGGAAACAGCCTCTACAATAGCGATG 5 0.125 No Hit ATCGGCATCATAAATCCGAACATTCTTAATCTTTGCTGCCCTGAGAAGTG 5 0.125 No Hit CTCAGTACGGGTCCCAATAATATCTCCAGCCAGATTCTTAGCCAAGTTTT 5 0.125 No Hit CTCAACTTTCTTTGGATAATTGACGACACCAGATCAATACTTGCATAGAT 5 0.125 No Hit GTTGGAGCAACTTGTTGTCCATTTCATCCGTTGCCACGGTTTGGAGCTGT 5 0.125 No Hit TAAGAGCATTAGCTCCTCCATCTGGTAGATCATCAATTTCAATATCTTGA 5 0.125 No Hit GTGCGCAAATTTTTTGCGGTTGGTCCTTTGCTAAAAGCATCTCCATTATG 5 0.125 No Hit TAGAGAGATCTCATTATCAAGCACCAAACAAACTTATTGAACTAGAAAAG 5 0.125 No Hit CTCTTCTTCTCGAGCTCTCCTCACTTTCTCTGCTTCCTCAAAGGCATCCT 5 0.125 No Hit ACAAAGATAAAGACACTCACGGACACTTTTGTTTGTTCACTCCACACCCA 5 0.125 No Hit CACCTGGAAGGCTTTAAAGCAATCCAGAATTCATTCAACTCCAATAAGAT 5 0.125 No Hit TCAGGACCAAGATCAATCTCATCTAGCAAAATTGCCTTGTTTGACTCAAG 5 0.125 No Hit TGAGGAAATTGTTGAGCCATGTAATCATAGAAAGGAAAGAGCGAAACAAT 5 0.125 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 0.0 0.0 0.0 0.0 0.0 58-59 0.07500000000000001 0.0 0.0 0.0 0.0 60-61 0.1 0.0 0.0 0.0 0.0 62-63 0.1 0.0 0.0 0.0 0.0 64-65 0.1 0.0 0.0 0.0 0.0 66-67 0.1375 0.0 0.0 0.0 0.0 68-69 0.15 0.0 0.0 0.0 0.0 70-71 0.15 0.0 0.0 0.0 0.0 72-73 0.15 0.0 0.0 0.0 0.0 74-75 0.15 0.0 0.0 0.0 0.0 76-77 0.175 0.0 0.0 0.0 0.0 78-79 0.225 0.0 0.0 0.0 0.0 80-81 0.225 0.0 0.0 0.0 0.0 82-83 0.275 0.0 0.0 0.0 0.0 84-85 0.30000000000000004 0.0 0.0 0.0 0.0 86-87 0.4125 0.0 0.0 0.0 0.0 88-89 0.6000000000000001 0.0 0.0 0.0 0.0 90-91 0.7125 0.0 0.0 0.0 0.0 92-93 0.775 0.0 0.0 0.0 0.0 94-95 0.875 0.0 0.0 0.0 0.0 96-97 0.9875 0.0 0.0 0.0 0.0 98-99 1.0625 0.0 0.0 0.0 0.0 100-101 1.25 0.0 0.0 0.0 0.0 102-103 1.4625 0.0 0.0 0.0 0.0 104-105 1.675 0.0 0.0 0.0 0.0 106-107 2.1 0.0 0.0 0.0 0.0 108-109 2.4749999999999996 0.0 0.0 0.0 0.0 110-111 2.7625 0.0 0.0 0.0 0.0 112-113 3.0625 0.0 0.0 0.0 0.0 114-115 3.5 0.0 0.0 0.0 0.0 116-117 3.975 0.0 0.0 0.0 0.0 118-119 4.2875 0.0 0.0 0.0 0.0 120-121 4.737500000000001 0.0 0.0 0.0 0.0 122-123 5.1 0.0 0.0 0.0 0.0 124-125 5.475 0.0 0.0 0.0 0.0 126-127 5.875 0.0 0.0 0.0 0.0 128-129 6.300000000000001 0.0 0.0 0.0 0.0 130-131 6.5375 0.0 0.0 0.0 0.0 132-133 7.0125 0.0 0.0 0.0 0.0 134-135 7.6375 0.0 0.0 0.0 0.0 136-137 8.125 0.0 0.0 0.0 0.0 138-139 8.775 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TTCATGC 10 0.006830828 145.0 8 GGTTCAT 10 0.006830828 145.0 6 TCATGCC 10 0.006830828 145.0 9 AGGTTCA 10 0.006830828 145.0 5 CAGGCTC 10 0.006830828 145.0 145 TGAATCC 10 0.006830828 145.0 3 GAGGTTC 10 0.006830828 145.0 4 >>END_MODULE SRR13695474 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR13695474_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 36.08625 37.0 37.0 37.0 37.0 37.0 2 36.1755 37.0 37.0 37.0 37.0 37.0 3 36.0235 37.0 37.0 37.0 37.0 37.0 4 36.2305 37.0 37.0 37.0 37.0 37.0 5 36.307 37.0 37.0 37.0 37.0 37.0 6 36.343 37.0 37.0 37.0 37.0 37.0 7 36.3425 37.0 37.0 37.0 37.0 37.0 8 36.378 37.0 37.0 37.0 37.0 37.0 9 36.335 37.0 37.0 37.0 37.0 37.0 10-14 36.3058 37.0 37.0 37.0 37.0 37.0 15-19 36.2977 37.0 37.0 37.0 37.0 37.0 20-24 36.219100000000005 37.0 37.0 37.0 37.0 37.0 25-29 36.15555 37.0 37.0 37.0 37.0 37.0 30-34 36.143950000000004 37.0 37.0 37.0 37.0 37.0 35-39 36.13445 37.0 37.0 37.0 37.0 37.0 40-44 36.109049999999996 37.0 37.0 37.0 37.0 37.0 45-49 36.14025 37.0 37.0 37.0 37.0 37.0 50-54 36.046749999999996 37.0 37.0 37.0 37.0 37.0 55-59 36.03865 37.0 37.0 37.0 37.0 37.0 60-64 36.01635 37.0 37.0 37.0 37.0 37.0 65-69 35.99425 37.0 37.0 37.0 37.0 37.0 70-74 35.910849999999996 37.0 37.0 37.0 37.0 37.0 75-79 35.86815 37.0 37.0 37.0 37.0 37.0 80-84 35.96005 37.0 37.0 37.0 37.0 37.0 85-89 35.777849999999994 37.0 37.0 37.0 37.0 37.0 90-94 35.806650000000005 37.0 37.0 37.0 37.0 37.0 95-99 35.8349 37.0 37.0 37.0 37.0 37.0 100-104 35.81745 37.0 37.0 37.0 37.0 37.0 105-109 35.80625 37.0 37.0 37.0 37.0 37.0 110-114 35.72425 37.0 37.0 37.0 37.0 37.0 115-119 35.69485 37.0 37.0 37.0 37.0 37.0 120-124 35.62564999999999 37.0 37.0 37.0 37.0 37.0 125-129 35.63445 37.0 37.0 37.0 37.0 37.0 130-134 35.53054999999999 37.0 37.0 37.0 34.6 37.0 135-139 35.459649999999996 37.0 37.0 37.0 37.0 37.0 140-144 35.426750000000006 37.0 37.0 37.0 34.6 37.0 145-149 35.2957 37.0 37.0 37.0 34.6 37.0 150-151 34.9245 37.0 37.0 37.0 31.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 6 1.0 7 0.0 8 0.0 9 0.0 10 0.0 11 0.0 12 0.0 13 1.0 14 3.0 15 0.0 16 5.0 17 0.0 18 1.0 19 0.0 20 0.0 21 1.0 22 4.0 23 3.0 24 4.0 25 1.0 26 10.0 27 10.0 28 19.0 29 14.0 30 26.0 31 41.0 32 74.0 33 112.0 34 194.0 35 591.0 36 2688.0 37 197.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 35.038876348131424 19.38801103586657 16.629044394281415 28.944068221720592 2 27.575 23.075000000000003 31.4 17.95 3 20.4 30.0 30.099999999999998 19.5 4 23.25 33.575 24.5 18.675 5 24.9 35.85 22.475 16.775000000000002 6 19.75 40.925 22.525000000000002 16.8 7 20.525 21.575 38.725 19.175 8 21.175 27.450000000000003 27.200000000000003 24.175 9 22.45 25.374999999999996 29.925 22.25 10-14 22.835 29.945 25.66 21.560000000000002 15-19 23.025000000000002 27.339999999999996 28.405 21.23 20-24 22.94188256476943 28.50855256576973 28.148444533360006 20.40112033610083 25-29 22.326745058794096 28.256192144108084 28.246184638478862 21.170878158618965 30-34 22.22222222222222 29.216068837860824 27.75026264445445 20.811446295462506 35-39 23.183114089931475 27.02946031110889 28.7300555194318 21.057370079527836 40-44 21.87202961628896 27.895342438341086 28.8408624743609 21.391765471009055 45-49 21.919863938772448 27.917562903306486 28.97303786704017 21.189535290880894 50-54 22.332816485770017 27.90976841894663 28.32491371980193 21.43250137548142 55-59 23.222416812609456 27.78583937953465 27.68076057042782 21.310983237428072 60-64 23.073075576451757 28.755064272495375 27.284549592357326 20.887310558695543 65-69 23.278491773766067 28.594289143371505 27.24908736310447 20.878131719757963 70-74 23.572679509632223 28.936702526895168 26.46985238929197 21.020765574180636 75-79 22.53739556756216 28.50567812296763 28.58071939566762 20.37620691380259 80-84 22.290572643160793 29.08227056764191 27.131782945736433 21.495373843460865 85-89 23.590333716915996 28.583579326562266 27.627958172812328 20.19812878370941 90-94 22.80298104336518 27.709698394438053 28.449957485119793 21.037363077076975 95-99 23.03190957287186 29.24877463238972 27.28818645593678 20.43112933880164 100-104 23.2874655991994 28.396297222917187 27.340505379034276 20.975731798849136 105-109 22.71703777833375 29.482111583687765 27.400550412809604 20.400300225168877 110-114 23.888360926324214 29.26524283499225 26.554294002901013 20.292102235782526 115-119 23.96297222917188 28.89166875156367 26.349762321741306 20.79559669752314 120-124 24.0180135101326 28.591443582687013 26.78008506379785 20.610457843382537 125-129 23.690398759193478 28.513533796968026 26.982538650122578 20.813528793715914 130-134 24.72343194673875 28.582870300845975 26.745757621264453 19.947940131150823 135-139 24.67343976777939 27.82643511335769 27.23587408037636 20.26425103848656 140-144 25.6489771419997 27.174511078877607 27.149502325814034 20.027009453308658 145-149 25.618056250625564 27.329596636973275 27.004303873486137 20.04804323891502 150-151 25.482093663911847 28.136739293764084 27.172551965940393 19.208615076383673 >>END_MODULE >>Per sequence GC content pass #GC Content Count 0 0.0 1 0.0 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.5 8 0.5 9 0.0 10 0.0 11 0.0 12 0.5 13 0.5 14 0.0 15 0.0 16 0.0 17 1.0 18 1.0 19 0.5 20 0.5 21 0.5 22 1.5 23 3.0 24 5.5 25 5.5 26 5.0 27 8.5 28 10.5 29 13.5 30 15.5 31 23.5 32 35.0 33 41.5 34 49.5 35 69.5 36 106.5 37 126.0 38 139.5 39 172.5 40 192.0 41 217.0 42 252.0 43 262.0 44 265.0 45 279.0 46 284.5 47 247.5 48 216.0 49 198.0 50 157.0 51 133.0 52 114.5 53 85.0 54 64.0 55 44.0 56 31.0 57 28.5 58 26.5 59 22.0 60 14.0 61 8.0 62 7.5 63 5.0 64 1.0 65 1.5 66 1.0 67 0.0 68 0.5 69 0.5 70 0.5 71 0.5 72 0.5 73 0.5 74 0.5 75 1.0 76 0.5 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 0.5 96 0.5 97 0.0 98 0.0 99 0.0 100 0.0 >>END_MODULE >>Per base N content pass #Base N-Count 1 0.325 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 0.03 25-29 0.075 30-34 0.055 35-39 0.034999999999999996 40-44 0.055 45-49 0.045 50-54 0.034999999999999996 55-59 0.075 60-64 0.034999999999999996 65-69 0.015 70-74 0.075 75-79 0.055 80-84 0.025 85-89 0.065 90-94 0.034999999999999996 95-99 0.03 100-104 0.075 105-109 0.075 110-114 0.034999999999999996 115-119 0.075 120-124 0.075 125-129 0.065 130-134 0.11499999999999999 135-139 0.095 140-144 0.034999999999999996 145-149 0.09 150-151 0.17500000000000002 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 70.15 #Duplication Level Percentage of deduplicated Percentage of total 1 71.06200997861724 49.85 2 19.672131147540984 27.6 3 6.486101211689238 13.65 4 1.8888096935138987 5.3 5 0.4632929436920884 1.625 6 0.21382751247327159 0.8999999999999999 7 0.1781895937277263 0.8750000000000001 8 0.03563791874554526 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 ATTTGATGTTTGCAGCTGCAGCTGCTGCTGCCTACTCCATTGCCAGAGTC 8 0.2 No Hit GTGGAATACATTGTGGTCATTGGACACAGCGCCTGTGGTGGAATTAAGGG 7 0.17500000000000002 No Hit GCTAAGGAAATGGCAGTTTGCACGGTATACACTACGCAGTCCCTCAATTC 7 0.17500000000000002 No Hit GATACAACCTCGATTCTCTTTCTTATTCAGTAACGGACTCCTTTCGAGCT 7 0.17500000000000002 No Hit TGCAAAGCATTGAAGATTCTCTGCCCCATTTGTTAAGAAGCAAACCTATT 7 0.17500000000000002 No Hit GCAGGTTACAGAAGACGGTGGAATAGGTAGCATTTGGAGACCCATTTGTC 7 0.17500000000000002 No Hit ATGGCATCCATAACCATGACAGCCTCATTCCTAACTGGTTCCGCCATGGC 6 0.15 No Hit GATTGTGGTCAAAGTCAACGGCAATCACTTATCTGGTATCCCTGCTAAGG 6 0.15 No Hit GTTGTTCAGACAGAGAAAGAGGAAAAGAGGAAAGCTAGAGCAAAAGAATT 6 0.15 No Hit GTTTATGTATAGTATGTTGACTTGGTGGTCCTGGAAATTCAAGCAAGAAA 6 0.15 No Hit ATTCATACTCCAAGTCTTTTAGTTCATCCATTTAAGCTTAATCAATCAAT 6 0.15 No Hit CTTGCATTTGAAAGGAGACAGGAAGGATTTTGAATTTGTGAAAACCAGTC 6 0.15 No Hit CACCTGAGTACCTAGATGGCAGTTTGGTTGGTGATTACGGGTTTGACCCA 5 0.125 No Hit CTCATGCTTGATAGCCTCCATGTATGCTGTATATTATAGATGTTCCTATA 5 0.125 No Hit TGGTAAATGAGGCGAAGAAGCCGAAGAAAGGGGATGTTGGGGATGAAGAT 5 0.125 No Hit AGTGGATCCGCTTTACTGGGAGGTGGGAGAGCATACGCTGATGAGCAAGG 5 0.125 No Hit GATGTGTACTGTTTTAGGCTGCTGTGGCTCAAGCAGGCCTAGCATACAAG 5 0.125 No Hit TGAATGAGTTTGACTCTTTGTAGAATGCACTAGCATGGTTGTGAAAGAAT 5 0.125 No Hit AGATATTGCAAGTGGTTCTGATGATTCAGGCAAGTCTGATGATGATTGTG 5 0.125 No Hit GTTGGGGAAAGGTCCGAGAATTAGAAGATGCGAGGTGACTTTGTTTACAA 5 0.125 No Hit CTATACTCCAAGCTGTTTTAACAAAAGAAAAAAGAAGGCAGTCAAATGGC 5 0.125 No Hit ACTTGACCTCTTCGTAGGCGAGTGACAAACACATCTAAAGCTACTGATAT 5 0.125 No Hit GCAATTGCTGATTCTGGAACCTCTTTGTTAGCTGGTCCTACGACTATTAT 5 0.125 No Hit GTTTCAGCTTGTCCTCGTGCTACGTACAGAAGATGGCAATGACCCAGGTC 5 0.125 No Hit GCTTCACCAAACATTATATGAGAGAATACAATCAGCAAAGGTTAATTCAT 5 0.125 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 0.0 0.0 0.0 0.0 0.0 58-59 0.07500000000000001 0.0 0.0 0.0 0.0 60-61 0.1 0.0 0.0 0.0 0.0 62-63 0.1 0.0 0.0 0.0 0.0 64-65 0.1 0.0 0.0 0.0 0.0 66-67 0.1375 0.0 0.0 0.0 0.0 68-69 0.15 0.0 0.0 0.0 0.0 70-71 0.15 0.0 0.0 0.0 0.0 72-73 0.15 0.0 0.0 0.0 0.0 74-75 0.15 0.0 0.0 0.0 0.0 76-77 0.175 0.0 0.0 0.0 0.0 78-79 0.225 0.0 0.0 0.0 0.0 80-81 0.225 0.0 0.0 0.0 0.0 82-83 0.275 0.0 0.0 0.0 0.0 84-85 0.30000000000000004 0.0 0.0 0.0 0.0 86-87 0.4125 0.0 0.0 0.0 0.0 88-89 0.6000000000000001 0.0 0.0 0.0 0.0 90-91 0.7125 0.0 0.0 0.0 0.0 92-93 0.775 0.0 0.0 0.0 0.0 94-95 0.875 0.0 0.0 0.0 0.0 96-97 0.9875 0.0 0.0 0.0 0.0 98-99 1.0625 0.0 0.0 0.0 0.0 100-101 1.25 0.0 0.0 0.0 0.0 102-103 1.4875 0.0 0.0 0.0 0.0 104-105 1.7 0.0 0.0 0.0 0.0 106-107 2.1125 0.0 0.0 0.0 0.0 108-109 2.4749999999999996 0.0 0.0 0.0 0.0 110-111 2.775 0.0 0.0 0.0 0.0 112-113 3.1125 0.0 0.0 0.0 0.0 114-115 3.55 0.0 0.0 0.0 0.0 116-117 4.0 0.0 0.0 0.0 0.0 118-119 4.3 0.0 0.0 0.0 0.0 120-121 4.737500000000001 0.0 0.0 0.0 0.0 122-123 5.1 0.0 0.0 0.0 0.0 124-125 5.4625 0.0 0.0 0.0 0.0 126-127 5.85 0.0 0.0 0.0 0.0 128-129 6.275 0.0 0.0 0.0 0.0 130-131 6.5125 0.0 0.0 0.0 0.0 132-133 7.0125 0.0 0.0 0.0 0.0 134-135 7.6625 0.0 0.0 0.0 0.0 136-137 8.15 0.0 0.0 0.0 0.0 138-139 8.825 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position AAAAAAA 120 2.3780814E-5 11.95625 3 >>END_MODULE Read 985758 spots for SRR13695474.sra Written 985758 spots for SRR13695474.sra Read 985758 spots for SRR13695474.sra Written 985758 spots for SRR13695474.sra Read 985758 spots for SRR13695474.sra Written 985758 spots for SRR13695474.sra Read 985758 spots for SRR13695474.sra Written 985758 spots for SRR13695474.sra Read 985758 spots for SRR13695474.sra Written 985758 spots for SRR13695474.sra Read 985758 spots for SRR13695474.sra Written 985758 spots for SRR13695474.sra Read 985758 spots for SRR13695474.sra Written 985758 spots for SRR13695474.sra Read 985758 spots for SRR13695474.sra Written 985758 spots for SRR13695474.sra Read 985758 spots for SRR13695474.sra Written 985758 spots for SRR13695474.sra Read 985758 spots for SRR13695474.sra Written 985758 spots for SRR13695474.sra Read 985758 spots for SRR13695474.sra Written 985758 spots for SRR13695474.sra Read 985758 spots for SRR13695474.sra Written 985758 spots for SRR13695474.sra Read 985758 spots for SRR13695474.sra Written 985758 spots for SRR13695474.sra Read 985758 spots for SRR13695474.sra Written 985758 spots for SRR13695474.sra Read 985758 spots for SRR13695474.sra Written 985758 spots for SRR13695474.sra Read 985758 spots for SRR13695474.sra Written 985758 spots for SRR13695474.sra Read 985758 spots for SRR13695474.sra Written 985758 spots for SRR13695474.sra Read 985761 spots for SRR13695474.sra Written 985761 spots for SRR13695474.sra Read 985758 spots for SRR13695474.sra Written 985758 spots for SRR13695474.sra Read 985758 spots for SRR13695474.sra Written 985758 spots for SRR13695474.sra SRR ids: ['SRR13695474.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_kqyi1d0o SRR13695474.sra spots: 19715163 blocks: [[1, 985758], [985759, 1971516], [1971517, 2957274], [2957275, 3943032], [3943033, 4928790], [4928791, 5914548], [5914549, 6900306], [6900307, 7886064], [7886065, 8871822], [8871823, 9857580], [9857581, 10843338], [10843339, 11829096], [11829097, 12814854], [12814855, 13800612], [13800613, 14786370], [14786371, 15772128], [15772129, 16757886], [16757887, 17743644], [17743645, 18729402], [18729403, 19715163]] SRR13695474 file size 6678374 SRR13695474 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 SRR13695474 SRR13695474_1.fastq SRR13695474_2.fastq Input file: SRR13695474_1.fastq Paired file: SRR13695474_2.fastq trimmed: SRR13695474-trimmed-pair1.fastq, SRR13695474-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 06:19:04 2025 >> started Wed Feb 12 06:19:26 2025 >> done (21.572s) 19715163 read pairs processed; of these: 159 ( 0.00%) short read pairs filtered out after trimming by size control 6768 ( 0.03%) empty read pairs filtered out after trimming by size control 19708236 (99.96%) read pairs available; of these: 2387640 (12.11%) trimmed read pairs available after processing 17320596 (87.89%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 2 0.00% 19 5 0.00% 20 11 0.00% 21 6 0.00% 22 1 0.00% 23 1 0.00% 24 2 0.00% 25 7 0.00% 26 1 0.00% 27 3 0.00% 28 3 0.00% 29 3 0.00% 30 6 0.00% 31 8 0.00% 32 5 0.00% 33 9 0.00% 34 10 0.00% 35 12 0.00% 36 8 0.00% 37 16 0.00% 38 15 0.00% 39 26 0.00% 40 21 0.00% 41 38 0.00% 42 36 0.00% 43 41 0.00% 44 51 0.00% 45 47 0.00% 46 51 0.00% 47 67 0.00% 48 61 0.00% 49 91 0.00% 50 92 0.00% 51 134 0.00% 52 148 0.00% 53 180 0.00% 54 155 0.00% 55 185 0.00% 56 246 0.00% 57 271 0.00% 58 265 0.00% 59 384 0.00% 60 398 0.00% 61 478 0.00% 62 555 0.00% 63 586 0.00% 64 664 0.00% 65 740 0.00% 66 844 0.00% 67 951 0.00% 68 1088 0.01% 69 1262 0.01% 70 1356 0.01% 71 1657 0.01% 72 1871 0.01% 73 2188 0.01% 74 2408 0.01% 75 2717 0.01% 76 2988 0.02% 77 3256 0.02% 78 3421 0.02% 79 3990 0.02% 80 4402 0.02% 81 4708 0.02% 82 5248 0.03% 83 5968 0.03% 84 6840 0.03% 85 7329 0.04% 86 7831 0.04% 87 8462 0.04% 88 8967 0.05% 89 9466 0.05% 90 10458 0.05% 91 10805 0.05% 92 11748 0.06% 93 12527 0.06% 94 13694 0.07% 95 14455 0.07% 96 15070 0.08% 97 15999 0.08% 98 16572 0.08% 99 17463 0.09% 100 18800 0.10% 101 18695 0.09% 102 19834 0.10% 103 20672 0.10% 104 21199 0.11% 105 22613 0.11% 106 23407 0.12% 107 24248 0.12% 108 25490 0.13% 109 26229 0.13% 110 26850 0.14% 111 27808 0.14% 112 28523 0.14% 113 29574 0.15% 114 30938 0.16% 115 31847 0.16% 116 33349 0.17% 117 33910 0.17% 118 35751 0.18% 119 36434 0.18% 120 36520 0.19% 121 38371 0.19% 122 38384 0.19% 123 39963 0.20% 124 41522 0.21% 125 41731 0.21% 126 43520 0.22% 127 44238 0.22% 128 45133 0.23% 129 45545 0.23% 130 47299 0.24% 131 48135 0.24% 132 49169 0.25% 133 49950 0.25% 134 51333 0.26% 135 51504 0.26% 136 53101 0.27% 137 54168 0.27% 138 54680 0.28% 139 56343 0.29% 140 56956 0.29% 141 58095 0.29% 142 58847 0.30% 143 59621 0.30% 144 60687 0.31% 145 61773 0.31% 146 62216 0.32% 147 62947 0.32% 148 64712 0.33% 149 64985 0.33% 150 65867 0.33% 151 17320596 87.89% 19708236 reads passed initial QC criterion=sequence-density sequence-density=0.35 sequence-density-rank=1 fanout-score=2.31 fanout-score-rank=22 prefix-density=0.37 prefix-fanout=2.2 sequence=TTAGCCTTTCTGGT criterion=fanout-score sequence-density=0.01 sequence-density-rank=30 fanout-score=619.18 fanout-score-rank=1 prefix-density=0.28 prefix-fanout=18.4 sequence=TGAAGAAGACACAAAGATAAAGACACTCACGGACACTTTTGTTTGTTCACTCCACACCCACAAGTACAGAAGAACACAGATTATTTATCAGAAATTACATTATTAATCCACTCCCAATCCCACATCAAACATGATAGTTGATGTGCTTGCTTAATGACCGCATGTGCAGGTAGTGCAAGTGCAGCCAGTACCGCAGTTGCACTTGCCATCGTTCTCAGCTGCTGGCACCTCCATGACTACGGAGGAGACATAGTTCTTCTCAGTCTCGACGATGCCAGCAGTGTAGCTGCTTCCCTTCTTGACACACTGGGTCTTGTCAGCGCAGTCGCAGTTGTCGCAGGTGCTAGACATGATGATTGATTGATTAAGCTTAAATGGATGAACTAAAAGACTTGGAGTATGAATGTGTTCTCTGTG criterion=sequence-density sequence-density=0.29 sequence-density-rank=1 fanout-score=6.83 fanout-score-rank=17 prefix-density=0.71 prefix-fanout=2.8 sequence=ATGGCTTCCTCCTCTATGATCTCATCGGCAGCCGTTGCCACCGTCAACCGCACCCCGGCACAAGCCAACATGGTGGCACCATTCAATGGTCTCAAGTCTGCCGCAGCTTTCCCAGTCAGTACCAGAAAGGCTAATGACATTACTTCCATTGCAAGCAATGG criterion=fanout-score sequence-density=0.07 sequence-density-rank=31 fanout-score=63.57 fanout-score-rank=1 prefix-density=0.45 prefix-fanout=10.3 sequence=AGAAAAGAAAACAGATTATCAAGCTTACTAGAATTATGGAAGGAATGAGTGTGGAGAACATGCACAAGATAGTGGTGGCAGTGGATGAGAGTGAGGAGAGCATGCATGCTCTTTCATGGTGTCTCAGCAACCTTATTTCTCACAACTCCACCGCCACGTTAGTCCTCCTCTAT SRR13695474 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 12 06:20:05 Started mapping on | Feb 12 06:20:06 Finished on | Feb 12 06:22:21 Mapping speed, Million of reads per hour | 525.55 Number of input reads | 19708236 Average input read length | 295 UNIQUE READS: Uniquely mapped reads number | 18546914 Uniquely mapped reads % | 94.11% Average mapped length | 294.56 Number of splices: Total | 18187872 Number of splices: Annotated (sjdb) | 17771145 Number of splices: GT/AG | 17817259 Number of splices: GC/AG | 294022 Number of splices: AT/AC | 10519 Number of splices: Non-canonical | 66072 Mismatch rate per base, % | 0.37% Deletion rate per base | 0.03% Deletion average length | 2.82 Insertion rate per base | 0.02% Insertion average length | 2.40 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 460175 % of reads mapped to multiple loci | 2.33% Number of reads mapped to too many loci | 58315 % of reads mapped to too many loci | 0.30% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 3.14% % of reads unmapped: other | 0.13% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 701410 701410 701410 N_multimapping 460175 460175 460175 N_noFeature 783074 18166479 1021916 N_ambiguous 251649 1930 108846 UnstrandedReadsAssigned:17512191 PositiveStrandReadsAssigned:378505 NegativeStrandReadsAssigned:17416152 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=151 echo kmer=147 SRR13695474 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: SRR13695474-trimmed-pair1.fastq SRR13695474-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 19,708,236 reads, 17,469,423 reads pseudoaligned [quant] estimated average fragment length: 247.881 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,100 rounds 52401 SRR13695474.ke.tsv 34699 SRR13695474.se.tsv 87100 total ==> SRR13695474.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1771.12 645 20.5888 Potri.005G024800.1.v4.1 1035 788.119 318 22.8115 Potri.004G059700.1.v4.1 961 714.276 0 0 Potri.007G009000.2.v4.1 1416 1169.12 0 0 Potri.003G141000.2.v4.1 2943 2696.12 1256 26.3372 Potri.016G087400.1.v4.1 270 85.8017 830 546.891 Potri.015G069301.1.v4.1 564 326.911 0 0 Potri.010G195200.1.v4.1 1773 1526.12 77 2.85247 Potri.012G127500.1.v4.1 977 730.196 66 5.11003 ==> SRR13695474.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 131 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 299 Potri.001G212900.v4.1 2 Potri.001G182400.v4.1 0 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 2 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 1 SRR13695474 completed mapping pipeline successfully