Starting /dee2/code/volunteer_pipeline.sh SRR12670963 current disk space = 3053280382976 free memory = 1513268772 SRR12670963 SRAfilesize 328e796ecd006e8128db6cefbc70235b SRR12670963.sra SRR12670963.sra file validated SRR12670963 is paired end SRR12670963 is conventional basespace SRR12670963 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12670963_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 47 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.52275 37.0 37.0 37.0 37.0 37.0 2 36.5275 37.0 37.0 37.0 37.0 37.0 3 36.595 37.0 37.0 37.0 37.0 37.0 4 36.7015 37.0 37.0 37.0 37.0 37.0 5 36.6855 37.0 37.0 37.0 37.0 37.0 6 36.679 37.0 37.0 37.0 37.0 37.0 7 36.6365 37.0 37.0 37.0 37.0 37.0 8 36.6765 37.0 37.0 37.0 37.0 37.0 9 36.639 37.0 37.0 37.0 37.0 37.0 10-14 36.637600000000006 37.0 37.0 37.0 37.0 37.0 15-19 36.6484 37.0 37.0 37.0 37.0 37.0 20-24 36.569 37.0 37.0 37.0 37.0 37.0 25-29 36.5356 37.0 37.0 37.0 37.0 37.0 30-34 36.513099999999994 37.0 37.0 37.0 37.0 37.0 35-39 36.470800000000004 37.0 37.0 37.0 37.0 37.0 40-44 36.45550000000001 37.0 37.0 37.0 37.0 37.0 45-49 36.3925 37.0 37.0 37.0 37.0 37.0 50-54 36.3675 37.0 37.0 37.0 37.0 37.0 55-59 36.3717 37.0 37.0 37.0 37.0 37.0 60-64 36.319599999999994 37.0 37.0 37.0 37.0 37.0 65-69 36.249399999999994 37.0 37.0 37.0 37.0 37.0 70-74 36.257999999999996 37.0 37.0 37.0 37.0 37.0 75-79 36.2509 37.0 37.0 37.0 37.0 37.0 80-84 36.2063 37.0 37.0 37.0 37.0 37.0 85-89 36.1275 37.0 37.0 37.0 37.0 37.0 90-94 36.11 37.0 37.0 37.0 37.0 37.0 95-99 36.0921 37.0 37.0 37.0 37.0 37.0 100-104 36.0819 37.0 37.0 37.0 37.0 37.0 105-109 36.052499999999995 37.0 37.0 37.0 37.0 37.0 110-114 36.051 37.0 37.0 37.0 37.0 37.0 115-119 36.000800000000005 37.0 37.0 37.0 37.0 37.0 120-124 35.869600000000005 37.0 37.0 37.0 37.0 37.0 125-129 35.8677 37.0 37.0 37.0 37.0 37.0 130-134 35.7382 37.0 37.0 37.0 37.0 37.0 135-139 35.778999999999996 37.0 37.0 37.0 37.0 37.0 140-144 35.665200000000006 37.0 37.0 37.0 37.0 37.0 145-149 35.5219 37.0 37.0 37.0 37.0 37.0 150-151 35.1665 37.0 37.0 37.0 31.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 19 2.0 20 0.0 21 2.0 22 2.0 23 2.0 24 3.0 25 5.0 26 9.0 27 8.0 28 18.0 29 22.0 30 38.0 31 46.0 32 70.0 33 95.0 34 117.0 35 277.0 36 2471.0 37 813.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 42.885721430357584 10.777694423605903 5.126281570392599 41.21030257564391 2 13.725000000000001 6.2 38.875 41.199999999999996 3 11.700000000000001 7.5 28.675 52.125 4 18.8 13.525 26.625 41.05 5 22.8 20.175 26.900000000000002 30.125 6 23.0 24.525 26.450000000000003 26.025 7 18.65 23.150000000000002 38.525 19.675 8 17.1 23.325000000000003 35.025 24.55 9 17.275 22.95 37.075 22.7 10-14 20.23 26.545 29.365000000000002 23.86 15-19 21.735 24.765 28.51 24.990000000000002 20-24 20.745 26.21 26.555 26.490000000000002 25-29 22.255 24.945 27.125 25.674999999999997 30-34 22.35 23.87 26.995 26.784999999999997 35-39 21.68 25.81 26.985 25.525 40-44 21.345 26.21 26.875 25.569999999999997 45-49 22.21 24.95 26.695 26.145000000000003 50-54 22.335 24.445 27.725 25.495 55-59 21.21 26.340000000000003 27.765 24.685000000000002 60-64 22.585 24.75 26.77 25.895000000000003 65-69 20.685000000000002 25.81 27.29 26.215 70-74 21.515 25.585 26.740000000000002 26.16 75-79 20.29 26.895000000000003 27.07 25.745 80-84 20.215 27.67 26.150000000000002 25.965 85-89 20.990000000000002 26.38 25.759999999999998 26.87 90-94 21.395 26.21 26.729999999999997 25.665 95-99 19.99 25.965 28.1 25.945 100-104 20.605 26.895000000000003 26.889999999999997 25.61 105-109 21.165 26.634999999999998 25.715 26.484999999999996 110-114 21.654999999999998 25.485000000000003 27.529999999999998 25.330000000000002 115-119 21.59 25.540000000000003 26.889999999999997 25.979999999999997 120-124 21.625 26.705000000000002 26.305 25.365 125-129 21.345 26.575 25.56 26.52 130-134 21.555 26.179999999999996 26.445 25.82 135-139 22.06 27.005000000000003 25.03 25.905 140-144 23.09 26.640000000000004 24.42 25.85 145-149 22.755 26.515 25.105 25.624999999999996 150-151 21.2875 26.174999999999997 25.837500000000002 26.700000000000003 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 0.0 1 0.5 2 0.5 3 0.5 4 0.5 5 1.0 6 1.0 7 0.0 8 0.0 9 0.0 10 0.0 11 0.0 12 0.0 13 0.5 14 0.5 15 0.0 16 0.5 17 0.5 18 0.5 19 2.0 20 1.5 21 0.5 22 2.0 23 5.0 24 5.0 25 3.0 26 6.0 27 12.0 28 13.0 29 14.0 30 15.5 31 18.5 32 19.5 33 26.5 34 35.5 35 46.5 36 58.0 37 73.0 38 79.0 39 95.0 40 136.0 41 152.5 42 155.5 43 168.0 44 170.5 45 186.5 46 204.5 47 197.0 48 177.5 49 171.0 50 154.0 51 120.5 52 126.5 53 137.5 54 142.5 55 193.0 56 202.5 57 146.5 58 120.5 59 135.0 60 96.5 61 35.5 62 37.5 63 30.0 64 19.0 65 15.5 66 11.5 67 6.5 68 4.0 69 3.5 70 0.5 71 0.0 72 0.0 73 2.5 74 2.5 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 0.025 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 73.52499999999999 #Duplication Level Percentage of deduplicated Percentage of total 1 84.01904114246855 61.775000000000006 2 10.23461407684461 15.049999999999999 3 2.380142808568514 5.25 4 1.292077524651479 3.8 5 0.6800408024481469 2.5 6 0.27201632097925876 1.2 7 0.17001020061203673 0.8750000000000001 8 0.27201632097925876 1.6 9 0.13600816048962938 0.8999999999999999 >10 0.5100306018361102 5.65 >50 0.034002040122407345 1.4000000000000001 >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 GTCCAGTCAACTGCTGCGCCTCAACGCATTTCGGGGAGAACCAGCTAGCT 56 1.4000000000000001 No Hit CCCCACTGCTGCCTCCCGTAGGAGTCTGGGCCGTGTCTCAGTCCCAGTGT 30 0.75 No Hit CCTCGCGGTACTTGTTTGCTATCGGTCTCTCGCCCGTATTTAGCCTTGGA 19 0.475 No Hit CCTCCTTTTGCTCCTCAGCCTACGGGGTATTAGCAGCCGTTTCCAGCTGT 18 0.44999999999999996 No Hit GTCCCTGTTAATCATTACTCCGATCCCGAAGGCCAACACAATAGGATCGA 17 0.42500000000000004 No Hit CCCGTCAATTCCTTTGAGTTTCATTCTTGCGAACGTACTCCCCAGGCGGG 15 0.375 No Hit CCCATCACGATGAAATTTCAAAGATTACCCGGGCCTGTCGGCCAAGGCTA 15 0.375 No Hit CCCACTGCTGCCTCCCGTAGGAGTCTGGGCCGTGTCTCAGTCCCAGTGTG 14 0.35000000000000003 No Hit ACCGCTTTAATGGGCGAACAGCCCAACCCTTGGAACATACTACAGCCCCA 13 0.325 No Hit GGCATGGGTTACTTCAGCGCCGTAGCGCCTGGTACTCGAACATTGGCTCG 13 0.325 No Hit GTCCTTGAACCGATAACCATCTTTCGGCTAACCTAGCCTCCTCCGTCCCT 13 0.325 No Hit GCTTTCTTTTCCTCTGGTTACTAAGATGTTTCAGTTCGCCAGGTTGTCTC 13 0.325 No Hit GTCTCTCAGTGTCAGTGTCGGCCCAGCAGAGTGCTTTCACCGTTGGTGTT 12 0.3 No Hit GTCCCTTCCAGAAGTCGGGGTTTGTTGCACGTATTAGCTCTAGAATTACT 12 0.3 No Hit CCCCTACCGATGCATTTTTACATCCCACAGCTTCGGCAGATCGCTTAGCC 11 0.27499999999999997 No Hit GTCTCTTGCCTGCCCATGGATTCGGCAGCAGTTTGAAAGGTTAACCTATT 11 0.27499999999999997 No Hit CTCCAGCTTGGCAGTTTCCACCGCCTGTCCAGGGTTGAGCCCTGGGATTT 9 0.22499999999999998 No Hit GCTCCTCAGCCTACGGGGTATTAGCAGCCGTTTCCAGCTGTTGTTCCCCT 9 0.22499999999999998 No Hit CTTTGAGTTTCATTCTTGCGAACGTACTCCCCAGGCGGGATACTTAACGC 9 0.22499999999999998 No Hit GTCCAACTACGAGCTTTTTAACTGCAACAACTTAAATATACGCTATTGGA 9 0.22499999999999998 No Hit CCCCAACTTTCGTTCTTGATTAATGAAAACATCCTTGGCAAATGCTTTCG 8 0.2 No Hit CTCCTACTCATCGGGGCCTGGCGCTTGCCCCGACGGCCGGGTATAGGTCG 8 0.2 No Hit CCAGTCAACTGCTGCGCCTCAACGCATTTCGGGGAGAACCAGCTAGCTCT 8 0.2 No Hit CCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAAT 8 0.2 No Hit CCCAACTTTCGTTCTTGATTAATGAAAACATCCTTGGCAAATGCTTTCGC 8 0.2 No Hit GTCCCTCTAAGAAGCTGGCCGCGGAGGGTCACCTCCGCATAGCTAGTTAG 8 0.2 No Hit CCCTAGAGTAACTTTTATCCGTTGAGCGACGGCCCTTCCACTCGGCACCG 8 0.2 No Hit CCCTAGATGTCCAGTCAACTGCTGCGCCTCAACGCATTTCGGGGAGAACC 8 0.2 No Hit GTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCT 7 0.17500000000000002 No Hit CCTAGAGTAACTTTTATCCGTTGAGCGACGGCCCTTCCACTCGGCACCGT 7 0.17500000000000002 No Hit GTCGGCATCGTTTATGGTTGAGACTAGGACGGTATCTGATCGTCTTCGAG 7 0.17500000000000002 No Hit GTCCCAGTGTGGCTGATCATCCTCTCGGACCAGCTACTGATCATCGCCTT 7 0.17500000000000002 No Hit GTCGCTATGAACGCTTGGCTGCCACAAGCCAGTTATCCCTGTGGTAACTT 7 0.17500000000000002 No Hit GCCTCAAACTTCCTTGGCCTGGAAGGCCATAGTCCCTCTAAGAAGCTGGC 6 0.15 No Hit CCCCGACTGTCCCTGTTAATCATTACTCCGATCCCGAAGGCCAACACAAT 6 0.15 No Hit GTCGCATCTAGCCCGGATTCTGACTTAGAGGCGTTCAGTCATAATCCAAC 6 0.15 No Hit CTCCCCTACCGATGCATTTTTACATCCCACAGCTTCGGCAGATCGCTTAG 6 0.15 No Hit CTCCACGCGGCATTGCTCCGTCAAGCTTTCGCCCATTGCGGAAAATTCCC 6 0.15 No Hit GTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATT 6 0.15 No Hit CCTCTGGTTACTAAGATGTTTCAGTTCGCCAGGTTGTCTCTTGCCTGCCC 6 0.15 No Hit GGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGC 6 0.15 No Hit CCCGTATTTAGCCTTGGACGGAATTTACCGCCCGATTGGGGCTGCATTCC 5 0.125 No Hit CCTAGATGTCCAGTCAACTGCTGCGCCTCAACGCATTTCGGGGAGAACCA 5 0.125 No Hit ACCGTCATTGCTTCTTCTCCGGGAAAAGAAGTTCACGACCCGTAGGCCTT 5 0.125 No Hit GCTCCGCACTTGGCTACCCAGCGTTTACCGTGGGCACAATAACTGGTACA 5 0.125 No Hit CCTTGGAACATACTACAGCCCCAGGTGGCGAAGAGCCGACATCGAGGTGC 5 0.125 No Hit CTTGATTAATGAAAACATCCTTGGCAAATGCTTTCGCAGTTGTTCGTCTT 5 0.125 No Hit GCCCAATCATTCCGGATAACGCTTGCATCCTCTGTATTACCGCGGCTGCT 5 0.125 No Hit CCCGTTTTCACGGTTTAGGCTGCTCCCATTTCGCTCGCCGCTACTACGGG 5 0.125 No Hit CCCTTCCCTCACGGTACTACTTCGCTATCGGTCACCCAGGAGTATTTAGC 5 0.125 No Hit CCCCACCTGACAATGTCTTCCGCCCGGATCGGCCGCCGAAGCGGCCTTGG 5 0.125 No Hit GCTCCCCTAGCTTTCGTCTCTCAGTGTCAGTGTCGGCCCAGCAGAGTGCT 5 0.125 No Hit GTTCTTGATTAATGAAAACATCCTTGGCAAATGCTTTCGCAGTTGTTCGT 5 0.125 No Hit CCTCATAATGGCTGCACCCCCAGTTGGCATTTCAAATATTTGTTCCTTGG 5 0.125 No Hit CCTTCCCTCACGGTACTACTTCGCTATCGGTCACCCAGGAGTATTTAGCC 5 0.125 No Hit CTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATT 5 0.125 No Hit CCCGAGGTTACGGATCCATTTTGCCGACTTCCCTTGCCTACATTGTTCCA 5 0.125 No Hit GTTCCCTATTGGTGGGTGAACAATCCAACACTTGGTGAATTCTGCTTCAC 5 0.125 No Hit CTCTGGTTACTAAGATGTTTCAGTTCGCCAGGTTGTCTCTTGCCTGCCCA 5 0.125 No Hit CTCAGTGTCAGTGTCGGCCCAGCAGAGTGCTTTCACCGTTGGTGTTCTTT 5 0.125 No Hit CCCGACTGTCCCTGTTAATCATTACTCCGATCCCGAAGGCCAACACAATA 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 0.0 0.0 0.0 0.0 0.0 52-53 0.0 0.0 0.0 0.0 0.0 54-55 0.0125 0.0 0.0 0.0 0.0 56-57 0.037500000000000006 0.0 0.0 0.0 0.0 58-59 0.05 0.0 0.0 0.0 0.0 60-61 0.05 0.0 0.0 0.0 0.0 62-63 0.075 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 0.1125 0.0 0.0 0.0 0.0 70-71 0.15 0.0 0.0 0.0 0.0 72-73 0.175 0.0 0.0 0.0 0.0 74-75 0.175 0.0 0.0 0.0 0.0 76-77 0.2 0.0 0.0 0.0 0.0 78-79 0.3125 0.0 0.0 0.0 0.0 80-81 0.325 0.0 0.0 0.0 0.0 82-83 0.42500000000000004 0.0 0.0 0.0 0.0 84-85 0.5249999999999999 0.0 0.0 0.0 0.0 86-87 0.675 0.0 0.0 0.0 0.0 88-89 0.875 0.0 0.0 0.0 0.0 90-91 1.15 0.0 0.0 0.0 0.0 92-93 1.4125 0.0 0.0 0.0 0.0 94-95 1.6875 0.0 0.0 0.0 0.0 96-97 1.95 0.0 0.0 0.0 0.0 98-99 2.2 0.0 0.0 0.0 0.0 100-101 2.5125 0.0 0.0 0.0 0.0 102-103 2.875 0.0 0.0 0.0 0.0 104-105 3.075 0.0 0.0 0.0 0.0 106-107 3.5125 0.0 0.0 0.0 0.0 108-109 4.1 0.0 0.0 0.0 0.0 110-111 4.525 0.0 0.0 0.0 0.0 112-113 4.9 0.0 0.0 0.0 0.0 114-115 5.5375 0.0 0.0 0.0 0.0 116-117 6.325 0.0 0.0 0.0 0.0 118-119 6.9125 0.0 0.0 0.0 0.0 120-121 7.6625 0.0 0.0 0.0 0.0 122-123 8.3625 0.0 0.0 0.0 0.0 124-125 9.2625 0.0 0.0 0.0 0.0 126-127 10.025 0.0 0.0 0.0 0.0 128-129 11.1875 0.0 0.0 0.0 0.0 130-131 12.162500000000001 0.0 0.0 0.0 0.0 132-133 13.4 0.0 0.0 0.0 0.0 134-135 14.3625 0.0 0.0 0.0 0.0 136-137 15.350000000000001 0.0 0.0 0.0 0.0 138-139 16.7125 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TTGGGAA 10 0.006830828 145.0 7 CCTCAGA 10 0.006830828 145.0 1 >>END_MODULE SRR12670963 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12670963_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 47 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.381 37.0 37.0 37.0 37.0 37.0 2 36.436 37.0 37.0 37.0 37.0 37.0 3 36.448 37.0 37.0 37.0 37.0 37.0 4 36.473 37.0 37.0 37.0 37.0 37.0 5 36.4985 37.0 37.0 37.0 37.0 37.0 6 36.5505 37.0 37.0 37.0 37.0 37.0 7 36.479 37.0 37.0 37.0 37.0 37.0 8 36.581 37.0 37.0 37.0 37.0 37.0 9 36.4855 37.0 37.0 37.0 37.0 37.0 10-14 36.6148 37.0 37.0 37.0 37.0 37.0 15-19 36.5755 37.0 37.0 37.0 37.0 37.0 20-24 36.575599999999994 37.0 37.0 37.0 37.0 37.0 25-29 36.5361 37.0 37.0 37.0 37.0 37.0 30-34 36.543899999999994 37.0 37.0 37.0 37.0 37.0 35-39 36.5198 37.0 37.0 37.0 37.0 37.0 40-44 36.5067 37.0 37.0 37.0 37.0 37.0 45-49 36.5187 37.0 37.0 37.0 37.0 37.0 50-54 36.4842 37.0 37.0 37.0 37.0 37.0 55-59 36.478 37.0 37.0 37.0 37.0 37.0 60-64 36.4329 37.0 37.0 37.0 37.0 37.0 65-69 36.4821 37.0 37.0 37.0 37.0 37.0 70-74 36.4457 37.0 37.0 37.0 37.0 37.0 75-79 36.3832 37.0 37.0 37.0 37.0 37.0 80-84 36.381800000000005 37.0 37.0 37.0 37.0 37.0 85-89 36.3679 37.0 37.0 37.0 37.0 37.0 90-94 36.358000000000004 37.0 37.0 37.0 37.0 37.0 95-99 36.3577 37.0 37.0 37.0 37.0 37.0 100-104 36.338 37.0 37.0 37.0 37.0 37.0 105-109 36.2601 37.0 37.0 37.0 37.0 37.0 110-114 36.249900000000004 37.0 37.0 37.0 37.0 37.0 115-119 36.1776 37.0 37.0 37.0 37.0 37.0 120-124 36.0599 37.0 37.0 37.0 37.0 37.0 125-129 35.9462 37.0 37.0 37.0 37.0 37.0 130-134 35.8366 37.0 37.0 37.0 37.0 37.0 135-139 35.638600000000004 37.0 37.0 37.0 37.0 37.0 140-144 35.5253 37.0 37.0 37.0 37.0 37.0 145-149 35.262 37.0 37.0 37.0 37.0 37.0 150-151 35.0195 37.0 37.0 37.0 31.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 1.0 21 1.0 22 3.0 23 3.0 24 1.0 25 4.0 26 7.0 27 12.0 28 6.0 29 15.0 30 27.0 31 31.0 32 46.0 33 85.0 34 139.0 35 278.0 36 2606.0 37 735.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 41.675000000000004 28.15 4.825 25.35 2 25.224999999999998 29.275000000000002 30.175 15.325 3 21.2 26.424999999999997 29.099999999999998 23.275000000000002 4 25.05 31.825 23.875 19.25 5 29.65 32.300000000000004 21.3 16.75 6 24.325 37.25 20.075000000000003 18.35 7 22.875 24.425 33.275 19.425 8 22.325 25.575 27.025 25.074999999999996 9 24.5 22.425 29.45 23.625 10-14 26.365 27.38 24.43 21.825 15-19 25.61 27.79 25.019999999999996 21.58 20-24 26.779999999999998 27.16 24.675 21.385 25-29 26.595000000000002 27.05 24.705 21.65 30-34 27.05 26.68 24.34 21.93 35-39 25.61 27.675 25.174999999999997 21.54 40-44 26.31 26.915 25.635 21.14 45-49 25.945 27.66 25.490000000000002 20.905 50-54 26.334999999999997 27.034999999999997 25.14 21.490000000000002 55-59 25.855 27.32 25.674999999999997 21.15 60-64 25.840000000000003 26.58 25.935000000000002 21.645 65-69 26.369999999999997 26.865 25.39 21.375 70-74 25.955000000000002 27.189999999999998 25.47 21.385 75-79 26.3 27.55 25.205 20.945 80-84 26.38 27.450000000000003 25.305 20.865000000000002 85-89 25.935000000000002 27.200000000000003 25.555 21.310000000000002 90-94 26.68 26.57 25.615 21.135 95-99 25.945 26.495 25.945 21.615000000000002 100-104 26.21 27.935 24.965 20.89 105-109 27.05 27.125 25.290000000000003 20.535 110-114 27.04 27.26 25.369999999999997 20.330000000000002 115-119 26.47 27.894999999999996 24.925 20.71 120-124 27.400000000000002 27.295 24.715 20.59 125-129 28.405 26.965 24.46 20.169999999999998 130-134 28.93 27.055 24.415 19.6 135-139 29.13 27.32 23.915 19.634999999999998 140-144 30.18 27.67 23.62 18.529999999999998 145-149 31.195 26.735 23.7 18.37 150-151 33.475 26.224999999999998 23.2125 17.0875 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 0.0 1 0.0 2 0.0 3 0.0 4 0.5 5 0.5 6 0.0 7 0.0 8 0.0 9 0.0 10 0.5 11 1.0 12 0.5 13 0.5 14 0.5 15 0.0 16 0.0 17 0.5 18 0.5 19 0.0 20 1.0 21 2.0 22 2.0 23 2.0 24 2.5 25 3.0 26 2.5 27 6.5 28 11.0 29 8.0 30 8.0 31 11.0 32 15.0 33 22.0 34 38.5 35 58.0 36 69.0 37 81.0 38 96.5 39 121.0 40 141.5 41 158.0 42 169.0 43 182.0 44 204.0 45 212.0 46 189.5 47 171.0 48 166.0 49 162.5 50 146.0 51 138.5 52 146.0 53 149.5 54 170.5 55 168.0 56 154.5 57 146.0 58 113.5 59 79.5 60 61.0 61 42.0 62 32.0 63 26.5 64 14.0 65 7.5 66 5.5 67 4.0 68 9.0 69 13.0 70 10.5 71 15.0 72 12.0 73 5.0 74 4.5 75 1.5 76 1.0 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 1.5 >>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 80.95 #Duplication Level Percentage of deduplicated Percentage of total 1 84.74366893143916 68.60000000000001 2 11.179740580605312 18.099999999999998 3 2.53242742433601 6.15 4 0.7103150092649784 2.3 5 0.40148239654107476 1.625 6 0.1852995676343422 0.8999999999999999 7 0.06176652254478073 0.35000000000000003 8 0.0 0.0 9 0.030883261272390366 0.22499999999999998 >10 0.1544163063619518 1.7500000000000002 >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 GGCTTACGGTGGATACCTAGGCACCCAGAGACGAGGAAGGGCGTAGTAAG 20 0.5 No Hit GTTACTTTGAAGAAATTAGAGTGCTCAAAGCAAGCCTACGCTCTGGATAC 15 0.375 No Hit ACCAGGCCCAAGTCCCCTGGAAAGGGGCGCCGGAGAGGGTGAGAGCCCCG 12 0.3 No Hit AAGGCTTACGGTGGATACCTAGGCACCCAGAGACGAGGAAGGGCGTAGTA 12 0.3 No Hit CCTGCCAGTAGTCATATGCTTGTCTCAAAGATTAAGCCATGCATGTGTAA 11 0.27499999999999997 No Hit GTTCGATCCTGGCTCAGGATGAACGCTGGCGGCATGCTTAACACATGCAA 9 0.22499999999999998 No Hit GGAGGGGCTCGCGTCTGATTAGCTAGTTGGTGAGGCAATAGCTTACCAAG 7 0.17500000000000002 No Hit GACCAGGCCCAAGTCCCCTGGAAAGGGGCGCCGGAGAGGGTGAGAGCCCC 7 0.17500000000000002 No Hit GGCCGTTCTTAGTTGGTGGAGCGATTTGTCTGGTTAATTCCGTTAACGAA 6 0.15 No Hit GAGGAATCCGCCCGAGGAGGGGCTCGCGTCTGATTAGCTAGTTGGTGAGG 6 0.15 No Hit ATTGTCACTGCTTATGGACCCGAACCTGGGTGATCTATCCATGACCAGGA 6 0.15 No Hit ATGGGATTAGATACCCCAGTAGTCCTAGCCGTAAACGATGGATACTGGGC 6 0.15 No Hit GGAAGTTTGAGGCAATAACAGGTCTGTGATGCCCTTAGATGTTCTGGGCC 6 0.15 No Hit GGATGAAGCTTGGGTGAAACTAAGTGGAGGTCCGAACCGACTGATGTTGA 6 0.15 No Hit GTGGGATTTACTCCACCGGAGTTGGACCCAAGTACCCCATCACCAATTTT 5 0.125 No Hit AGCAGTGGGAGGAGCCCGGGGCTCTGACCGCGTGCCTGTTGAAGAATGAG 5 0.125 No Hit CTTGAGAGGTGTAGGATAAGTGGGAGCTTCGGCGAAGGTGAAATACCACT 5 0.125 No Hit GTCAAATCCCAGGGCTCAACCCTGGACAGGCGGTGGAAACTGCCAAGCTG 5 0.125 No Hit GTATGTTCCAAGGGTTGGGCTGTTCGCCCATTAAAGCGGTACGTGAGCTG 5 0.125 No Hit GTAGCGAAAGCGAGTCTTCATAGGGCAATTGTCACTGCTTATGGACCCGA 5 0.125 No Hit GTAAGCTCCCAAGCAGTGGGAGGAGCCCGGGGCTCTGACCGCGTGCCTGT 5 0.125 No Hit GTCCAGTAGCCGAAAGCATCACTAGCTTACGCTCTGACCCGAGTAGCATG 5 0.125 No Hit ATCCGCCCGAGGAGGGGCTCGCGTCTGATTAGCTAGTTGGTGAGGCAATA 5 0.125 No Hit GTGGAAGGGCCGTCGCTCAACGGATAAAAGTTACTCTAGGGATAACAGGC 5 0.125 No Hit GAGGAACCGTTGATTCGCACAATTGGTCATCGCGCTTGGTTGAAAAGCCA 5 0.125 No Hit AGCGATTTGTCTGGTTAATTCCGTTAACGAACGAGACCTCAGCCTGCTAA 5 0.125 No Hit CCTTAACTGGCCGGGTCGTGCCTCCGGTGCTGTTACTTTGAAGAAATTAG 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 0.0 0.0 0.0 0.0 0.0 52-53 0.0 0.0 0.0 0.0 0.0 54-55 0.0125 0.0 0.0 0.0 0.0 56-57 0.037500000000000006 0.0 0.0 0.0 0.0 58-59 0.05 0.0 0.0 0.0 0.0 60-61 0.05 0.0 0.0 0.0 0.0 62-63 0.075 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 0.1125 0.0 0.0 0.0 0.0 70-71 0.15 0.0 0.0 0.0 0.0 72-73 0.175 0.0 0.0 0.0 0.0 74-75 0.175 0.0 0.0 0.0 0.0 76-77 0.2 0.0 0.0 0.0 0.0 78-79 0.3125 0.0 0.0 0.0 0.0 80-81 0.325 0.0 0.0 0.0 0.0 82-83 0.42500000000000004 0.0 0.0 0.0 0.0 84-85 0.5249999999999999 0.0 0.0 0.0 0.0 86-87 0.675 0.0 0.0 0.0 0.0 88-89 0.8500000000000001 0.0 0.0 0.0 0.0 90-91 1.125 0.0 0.0 0.0 0.0 92-93 1.3875000000000002 0.0 0.0 0.0 0.0 94-95 1.6625 0.0 0.0 0.0 0.0 96-97 1.95 0.0 0.0 0.0 0.0 98-99 2.2 0.0 0.0 0.0 0.0 100-101 2.5125 0.0 0.0 0.0 0.0 102-103 2.875 0.0 0.0 0.0 0.0 104-105 3.075 0.0 0.0 0.0 0.0 106-107 3.5250000000000004 0.0 0.0 0.0 0.0 108-109 4.125 0.0 0.0 0.0 0.0 110-111 4.550000000000001 0.0 0.0 0.0 0.0 112-113 4.925000000000001 0.0 0.0 0.0 0.0 114-115 5.6 0.0 0.0 0.0 0.0 116-117 6.4 0.0 0.0 0.0 0.0 118-119 6.987500000000001 0.0 0.0 0.0 0.0 120-121 7.7125 0.0 0.0 0.0 0.0 122-123 8.412500000000001 0.0 0.0 0.0 0.0 124-125 9.350000000000001 0.0 0.0 0.0 0.0 126-127 10.125 0.0 0.0 0.0 0.0 128-129 11.325 0.0 0.0 0.0 0.0 130-131 12.3125 0.0 0.0 0.0 0.0 132-133 13.5625 0.0 0.0 0.0 0.0 134-135 14.524999999999999 0.0 0.0 0.0 0.0 136-137 15.524999999999999 0.0 0.0 0.0 0.0 138-139 16.9 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position CTCTGAT 10 0.006830828 145.0 7 ACTTACT 10 0.006830828 145.0 7 GATTCCT 10 0.006830828 145.0 1 ATTCCTT 10 0.006830828 145.0 2 GGGGGGG 245 5.547354E-7 8.877551 140-144 >>END_MODULE Read 443269 spots for SRR12670963.sra Written 443269 spots for SRR12670963.sra Read 443269 spots for SRR12670963.sra Written 443269 spots for SRR12670963.sra Read 443269 spots for SRR12670963.sra Written 443269 spots for SRR12670963.sra Read 443269 spots for SRR12670963.sra Written 443269 spots for SRR12670963.sra Read 443269 spots for SRR12670963.sra Written 443269 spots for SRR12670963.sra Read 443269 spots for SRR12670963.sra Written 443269 spots for SRR12670963.sra Read 443269 spots for SRR12670963.sra Written 443269 spots for SRR12670963.sra Read 443269 spots for SRR12670963.sra Written 443269 spots for SRR12670963.sra Read 443269 spots for SRR12670963.sra Written 443269 spots for SRR12670963.sra Read 443269 spots for SRR12670963.sra Written 443269 spots for SRR12670963.sra Read 443269 spots for SRR12670963.sra Written 443269 spots for SRR12670963.sra Read 443269 spots for SRR12670963.sra Written 443269 spots for SRR12670963.sra Read 443269 spots for SRR12670963.sra Written 443269 spots for SRR12670963.sra Read 443269 spots for SRR12670963.sra Written 443269 spots for SRR12670963.sra Read 443269 spots for SRR12670963.sra Written 443269 spots for SRR12670963.sra Read 443269 spots for SRR12670963.sra Written 443269 spots for SRR12670963.sra Read 443286 spots for SRR12670963.sra Written 443286 spots for SRR12670963.sra Read 443269 spots for SRR12670963.sra Written 443269 spots for SRR12670963.sra Read 443269 spots for SRR12670963.sra Written 443269 spots for SRR12670963.sra Read 443269 spots for SRR12670963.sra Written 443269 spots for SRR12670963.sra SRR ids: ['SRR12670963.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_xeqzptw_ SRR12670963.sra spots: 8865397 blocks: [[1, 443269], [443270, 886538], [886539, 1329807], [1329808, 1773076], [1773077, 2216345], [2216346, 2659614], [2659615, 3102883], [3102884, 3546152], [3546153, 3989421], [3989422, 4432690], [4432691, 4875959], [4875960, 5319228], [5319229, 5762497], [5762498, 6205766], [6205767, 6649035], [6649036, 7092304], [7092305, 7535573], [7535574, 7978842], [7978843, 8422111], [8422112, 8865397]] SRR12670963 file size 2993365 SRR12670963 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 SRR12670963 SRR12670963_1.fastq SRR12670963_2.fastq Input file: SRR12670963_1.fastq Paired file: SRR12670963_2.fastq trimmed: SRR12670963-trimmed-pair1.fastq, SRR12670963-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 Tue Feb 11 10:26:05 2025 >> started Tue Feb 11 10:26:18 2025 >> done (13.526s) 8865397 read pairs processed; of these: 55 ( 0.00%) short read pairs filtered out after trimming by size control 2502 ( 0.03%) empty read pairs filtered out after trimming by size control 8862840 (99.97%) read pairs available; of these: 2387086 (26.93%) trimmed read pairs available after processing 6475754 (73.07%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 3 0.00% 19 4 0.00% 20 1 0.00% 21 2 0.00% 22 6 0.00% 23 3 0.00% 24 13 0.00% 25 10 0.00% 26 10 0.00% 27 9 0.00% 28 7 0.00% 29 8 0.00% 30 3 0.00% 31 8 0.00% 32 9 0.00% 33 12 0.00% 34 18 0.00% 35 22 0.00% 36 13 0.00% 37 29 0.00% 38 19 0.00% 39 23 0.00% 40 27 0.00% 41 29 0.00% 42 21 0.00% 43 30 0.00% 44 36 0.00% 45 49 0.00% 46 56 0.00% 47 40 0.00% 48 54 0.00% 49 62 0.00% 50 78 0.00% 51 76 0.00% 52 88 0.00% 53 140 0.00% 54 130 0.00% 55 154 0.00% 56 188 0.00% 57 203 0.00% 58 206 0.00% 59 221 0.00% 60 275 0.00% 61 296 0.00% 62 390 0.00% 63 388 0.00% 64 501 0.01% 65 567 0.01% 66 705 0.01% 67 787 0.01% 68 866 0.01% 69 996 0.01% 70 1070 0.01% 71 1141 0.01% 72 1323 0.01% 73 1669 0.02% 74 1934 0.02% 75 1878 0.02% 76 2206 0.02% 77 2432 0.03% 78 2680 0.03% 79 3319 0.04% 80 3690 0.04% 81 4242 0.05% 82 4073 0.05% 83 5020 0.06% 84 5292 0.06% 85 6681 0.08% 86 6659 0.08% 87 7572 0.09% 88 8071 0.09% 89 8351 0.09% 90 8739 0.10% 91 9359 0.11% 92 10558 0.12% 93 11730 0.13% 94 13508 0.15% 95 14164 0.16% 96 13800 0.16% 97 13756 0.16% 98 13388 0.15% 99 14353 0.16% 100 14777 0.17% 101 16073 0.18% 102 17597 0.20% 103 18200 0.21% 104 19577 0.22% 105 20631 0.23% 106 19971 0.23% 107 21262 0.24% 108 21697 0.24% 109 23303 0.26% 110 24674 0.28% 111 24365 0.27% 112 25328 0.29% 113 25990 0.29% 114 28524 0.32% 115 30473 0.34% 116 30177 0.34% 117 33183 0.37% 118 32740 0.37% 119 32460 0.37% 120 35307 0.40% 121 33704 0.38% 122 35010 0.40% 123 37806 0.43% 124 37810 0.43% 125 40228 0.45% 126 38670 0.44% 127 44800 0.51% 128 42046 0.47% 129 41554 0.47% 130 43871 0.49% 131 47363 0.53% 132 54031 0.61% 133 51174 0.58% 134 57333 0.65% 135 60072 0.68% 136 57989 0.65% 137 64111 0.72% 138 60433 0.68% 139 61261 0.69% 140 59046 0.67% 141 58218 0.66% 142 66344 0.75% 143 61629 0.70% 144 69047 0.78% 145 68072 0.77% 146 66502 0.75% 147 78663 0.89% 148 72276 0.82% 149 74428 0.84% 150 76737 0.87% 151 6475754 73.07% 8862840 reads passed initial QC criterion=sequence-density sequence-density=2.62 sequence-density-rank=1 fanout-score=2.08 fanout-score-rank=23 prefix-density=2.63 prefix-fanout=2.1 sequence=GTATTTAGCCTTG criterion=fanout-score sequence-density=0.12 sequence-density-rank=22 fanout-score=17.94 fanout-score-rank=1 prefix-density=1.69 prefix-fanout=1.3 sequence=CTGCTGGCACCTCCATGACTACGGAGGAGACATAGTTCTTCTCAGTCTCGACGATGCCAGCAGTGTAGCTGCTTCCCTTCTTGACACACTGGGTCTTGTCAGCGCAGTCGCAGGTGTCGCAGGTGCTAGACATGATGATTGATTGATTAAGCTTAAATGGATGAACTAAAAGACTTGGAGTATGAATGTGTTCTCTG criterion=sequence-density sequence-density=1.98 sequence-density-rank=1 fanout-score=2.12 fanout-score-rank=23 prefix-density=2.07 prefix-fanout=2.0 sequence=CAAGGCTAAATAC criterion=fanout-score sequence-density=0.15 sequence-density-rank=19 fanout-score=24.62 fanout-score-rank=1 prefix-density=1.73 prefix-fanout=2.1 sequence=GTGCCAGCAGCTGAGAACGATGGCAAGTGCAACTGCGGTACTGGCTGCACTTGCACTACCTGCACATGCGGTCATTAAGCAAGCACATCAACTATCATGTTTGATGTGGGATTGGGAGTGGATTAATAATGTAATTTCTGATAAATAATCTGTGTTCTTCTGTACTTGTGGGTGT Potential 3prime adapter identified. Now checking if in reference sequence /dee2/code/volunteer_pipeline.sh: line 905: -f: command not found /dee2/code/volunteer_pipeline.sh: line 906: -f: command not found Adapter seq not found in reference. Now shuffling file before clipping skewer v0.2.2 [April 4, 2016] COMMAND LINE: skewer -f sanger -l 18 -t 20 -x GTATTTAGCCTTG -y CAAGGCTAAATAC -o SRR12670963 SRR12670963_1.fastq SRR12670963_2.fastq Input file: SRR12670963_1.fastq Paired file: SRR12670963_2.fastq trimmed: SRR12670963-trimmed-pair1.fastq, SRR12670963-trimmed-pair2.fastq Parameters used: -- 3' end adapter sequence (-x): GTATTTAGCCTTG -- paired 3' end adapter sequence (-y): CAAGGCTAAATAC -- maximum error ratio allowed (-r): 0.100 -- maximum indel error ratio allowed (-d): 0.030 -- minimum read length allowed after trimming (-l): 18 -- file format (-f): Sanger/Illumina 1.8+ FASTQ -- number of concurrent threads (-t): 20 Tue Feb 11 10:27:14 2025 >> started Tue Feb 11 10:27:19 2025 >> done (4.968s) 2954280 read pairs processed; of these: 337 ( 0.01%) short read pairs filtered out after trimming by size control 33 ( 0.00%) empty read pairs filtered out after trimming by size control 2953910 (99.99%) read pairs available; of these: 21 ( 0.00%) trimmed read pairs available after processing 2953889 (100.00%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 3 0.00% 19 1 0.00% 20 0 0.00% 21 1 0.00% 22 2 0.00% 23 1 0.00% 24 6 0.00% 25 0 0.00% 26 2 0.00% 27 1 0.00% 28 2 0.00% 29 1 0.00% 30 1 0.00% 31 1 0.00% 32 1 0.00% 33 8 0.00% 34 5 0.00% 35 7 0.00% 36 4 0.00% 37 10 0.00% 38 5 0.00% 39 6 0.00% 40 7 0.00% 41 8 0.00% 42 8 0.00% 43 14 0.00% 44 15 0.00% 45 11 0.00% 46 14 0.00% 47 13 0.00% 48 15 0.00% 49 19 0.00% 50 33 0.00% 51 33 0.00% 52 24 0.00% 53 50 0.00% 54 47 0.00% 55 42 0.00% 56 59 0.00% 57 67 0.00% 58 61 0.00% 59 71 0.00% 60 91 0.00% 61 89 0.00% 62 145 0.00% 63 125 0.00% 64 150 0.01% 65 204 0.01% 66 221 0.01% 67 263 0.01% 68 308 0.01% 69 337 0.01% 70 362 0.01% 71 388 0.01% 72 418 0.01% 73 573 0.02% 74 651 0.02% 75 615 0.02% 76 730 0.02% 77 828 0.03% 78 878 0.03% 79 1122 0.04% 80 1300 0.04% 81 1404 0.05% 82 1351 0.05% 83 1628 0.06% 84 1807 0.06% 85 2265 0.08% 86 2215 0.07% 87 2535 0.09% 88 2731 0.09% 89 2738 0.09% 90 2922 0.10% 91 3106 0.11% 92 3534 0.12% 93 3841 0.13% 94 4528 0.15% 95 4665 0.16% 96 4562 0.15% 97 4570 0.15% 98 4471 0.15% 99 4783 0.16% 100 4896 0.17% 101 5390 0.18% 102 5918 0.20% 103 6076 0.21% 104 6465 0.22% 105 6911 0.23% 106 6758 0.23% 107 7130 0.24% 108 7393 0.25% 109 7660 0.26% 110 8102 0.27% 111 8163 0.28% 112 8505 0.29% 113 8630 0.29% 114 9451 0.32% 115 10262 0.35% 116 9964 0.34% 117 10923 0.37% 118 10977 0.37% 119 10900 0.37% 120 11746 0.40% 121 11159 0.38% 122 11760 0.40% 123 12650 0.43% 124 12560 0.43% 125 13414 0.45% 126 12887 0.44% 127 14966 0.51% 128 13892 0.47% 129 13801 0.47% 130 14695 0.50% 131 15833 0.54% 132 17848 0.60% 133 17160 0.58% 134 19259 0.65% 135 19735 0.67% 136 19465 0.66% 137 21399 0.72% 138 20323 0.69% 139 20520 0.69% 140 19522 0.66% 141 19214 0.65% 142 22177 0.75% 143 20551 0.70% 144 22847 0.77% 145 22653 0.77% 146 22249 0.75% 147 26181 0.89% 148 24350 0.82% 149 24729 0.84% 150 25659 0.87% 151 2158099 73.06% criterion=sequence-density sequence-density=2.59 sequence-density-rank=1 fanout-score=2.09 fanout-score-rank=29 prefix-density=2.60 prefix-fanout=2.1 sequence=GTATTTAGCCTTG criterion=fanout-score sequence-density=0.12 sequence-density-rank=22 fanout-score=18.03 fanout-score-rank=1 prefix-density=1.69 prefix-fanout=1.3 sequence=CTGCTGGCACCTCCATGACTACGGAGGAGACATAGTTCTTCTCAGTCTCGACGATGCCAGCAGTGTAGCTGCTTCCCTTCTTGACACACTGGGTCTTGTCAGCGCAGTCGCAGGTGTCGCAGGTGCTAGACATGATGATTGATTGATTAAGCTTAAATGGATGAACTAAAAGACTTGGAGTATGAATGTGTTCTCTG criterion=sequence-density sequence-density=1.93 sequence-density-rank=1 fanout-score=2.12 fanout-score-rank=26 prefix-density=2.02 prefix-fanout=2.0 sequence=CAAGGCTAAATAC criterion=fanout-score sequence-density=0.15 sequence-density-rank=22 fanout-score=24.62 fanout-score-rank=1 prefix-density=1.71 prefix-fanout=2.1 sequence=GTGCCAGCAGCTGAGAACGATGGCAAGTGCAACTGCGGTACTGGCTGCACTTGCACTACCTGCACATGCGGTCATTAAGCAAGCACATCAACTATCATGTTTGATGTGGGATTGGGAGTGGATTAATAATGTAATTTCTGATAAATAATCTGTGTTCTTCTGTACTTGTGGGTGT SRR12670963 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 11 10:28:10 Started mapping on | Feb 11 10:28:11 Finished on | Feb 11 10:29:58 Mapping speed, Million of reads per hour | 298.18 Number of input reads | 8862470 Average input read length | 289 UNIQUE READS: Uniquely mapped reads number | 6350983 Uniquely mapped reads % | 71.66% Average mapped length | 289.77 Number of splices: Total | 4401359 Number of splices: Annotated (sjdb) | 4308144 Number of splices: GT/AG | 4315219 Number of splices: GC/AG | 67759 Number of splices: AT/AC | 4004 Number of splices: Non-canonical | 14377 Mismatch rate per base, % | 0.59% Deletion rate per base | 0.02% Deletion average length | 2.93 Insertion rate per base | 0.08% Insertion average length | 2.81 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 665695 % of reads mapped to multiple loci | 7.51% Number of reads mapped to too many loci | 1470865 % of reads mapped to too many loci | 16.60% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 2.99% % of reads unmapped: other | 1.24% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 1845792 1845792 1845792 N_multimapping 665695 665695 665695 N_noFeature 1371445 6199596 1413966 N_ambiguous 139763 1045 30071 UnstrandedReadsAssigned:4839775 PositiveStrandReadsAssigned:150342 NegativeStrandReadsAssigned:4906946 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=142 echo kmer=137 SRR12670963 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: SRR12670963-trimmed-pair1.fastq SRR12670963-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 8,862,470 reads, 5,780,705 reads pseudoaligned [quant] estimated average fragment length: 176.55 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,053 rounds 52401 SRR12670963.ke.tsv 34699 SRR12670963.se.tsv 87100 total ==> SRR12670963.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1842.45 481 20.5685 Potri.005G024800.1.v4.1 1035 859.45 47 4.30855 Potri.004G059700.1.v4.1 961 785.45 0 0 Potri.007G009000.2.v4.1 1416 1240.45 0 0 Potri.003G141000.2.v4.1 2943 2767.45 390.676 11.1222 Potri.016G087400.1.v4.1 270 97.4724 139 112.353 Potri.015G069301.1.v4.1 564 388.509 0 0 Potri.010G195200.1.v4.1 1773 1597.45 77 3.79767 Potri.012G127500.1.v4.1 977 801.45 43 4.22713 ==> SRR12670963.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 77 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 54 Potri.001G212900.v4.1 5 Potri.001G182400.v4.1 0 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 0 Potri.001G416900.v4.1 1 Potri.001G452600.v4.1 0 SRR12670963 completed mapping pipeline successfully