Starting /dee2/code/volunteer_pipeline.sh SRR12682216 current disk space = 1547427733504 free memory = 1600750380 SRR12682216 SRAfilesize fed6581d44961bea441c19dc8657c687 SRR12682216.sra SRR12682216.sra file validated SRR12682216 is single end SRR12682216 is conventional basespace SRR12682216 read1 length is 54-150 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12682216_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 54-150 %GC 52 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 31.519 32.0 32.0 32.0 32.0 32.0 2 31.538 32.0 32.0 32.0 32.0 32.0 3 31.5675 32.0 32.0 32.0 32.0 32.0 4 31.6575 32.0 32.0 32.0 32.0 32.0 5 31.62275 32.0 32.0 32.0 32.0 32.0 6 34.89925 36.0 36.0 36.0 36.0 36.0 7 35.28725 36.0 36.0 36.0 36.0 36.0 8 35.13375 36.0 36.0 36.0 36.0 36.0 9 35.12925 36.0 36.0 36.0 36.0 36.0 10-14 35.1219 36.0 36.0 36.0 36.0 36.0 15-19 35.09595 36.0 36.0 36.0 36.0 36.0 20-24 35.0027 36.0 36.0 36.0 36.0 36.0 25-29 34.85745 36.0 36.0 36.0 32.8 36.0 30-34 34.7996 36.0 36.0 36.0 33.6 36.0 35-39 34.781 36.0 36.0 36.0 32.8 36.0 40-44 34.68240000000001 36.0 36.0 36.0 32.0 36.0 45-49 34.58695 36.0 36.0 36.0 32.0 36.0 50-54 34.46175 36.0 36.0 36.0 32.0 36.0 55-59 34.41175293823456 36.0 36.0 36.0 32.0 36.0 60-64 34.21330665332666 36.0 36.0 36.0 32.0 36.0 65-69 34.07332332332332 36.0 36.0 36.0 31.0 36.0 70-74 34.11479422084612 36.0 36.0 36.0 32.0 36.0 75-79 33.94389847527828 36.0 36.0 36.0 30.0 36.0 80-84 33.932771357816456 36.0 36.0 36.0 30.0 36.0 85-89 33.75364667414864 36.0 36.0 36.0 28.0 36.0 90-94 33.82685003816293 36.0 36.0 36.0 29.0 36.0 95-99 33.707619478974905 36.0 36.0 36.0 27.0 36.0 100-104 33.670791273784936 36.0 36.0 36.0 27.0 36.0 105-109 33.25792839648813 36.0 32.8 36.0 27.0 36.0 110-114 33.17447020642035 36.0 32.8 36.0 27.0 36.0 115-119 32.78556827194518 36.0 32.0 36.0 27.0 36.0 120-124 32.2368553260307 34.4 32.0 36.0 24.6 36.0 125-129 31.993978842744877 34.4 32.0 36.0 23.4 36.0 130-134 31.507216293737503 32.0 32.0 36.0 21.0 36.0 135-139 31.562583728152084 33.6 32.0 36.0 21.0 36.0 140-144 31.684863533797927 34.4 32.0 36.0 21.0 36.0 145-149 31.525951153401234 32.0 32.0 36.0 21.0 36.0 150 26.085659898477157 27.0 14.0 32.0 14.0 36.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 18 4.0 19 1.0 20 1.0 21 6.0 22 13.0 23 11.0 24 12.0 25 37.0 26 42.0 27 59.0 28 90.0 29 90.0 30 133.0 31 200.0 32 228.0 33 348.0 34 960.0 35 1765.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 30.525000000000002 8.0 7.775 53.7 2 21.15 12.075 32.525 34.25 3 19.475 14.424999999999999 20.25 45.85 4 28.425 21.75 18.4 31.424999999999997 5 27.375 25.825 22.35 24.45 6 24.087591240875913 28.5426629750818 25.119557009816262 22.250188774226025 7 18.8 21.525 37.35 22.325 8 20.125 18.475 31.7 29.7 9 20.1 19.85 33.975 26.075 10-14 23.075000000000003 24.11 24.935 27.88 15-19 23.645 22.884999999999998 25.535000000000004 27.935 20-24 23.380000000000003 23.47 25.22 27.93 25-29 23.77 22.58 24.085 29.565 30-34 23.575 22.125 25.124999999999996 29.175 35-39 23.815 23.14 24.79 28.255000000000003 40-44 24.66993398679736 23.32966593318664 23.954790958191637 28.045609121824366 45-49 24.568599009653376 22.592907517631172 24.908718051317962 27.92977542139749 50-54 23.36967393478696 22.754550910182036 25.2250450090018 28.650730146029208 55-59 24.02542160836711 22.589200820697595 24.385727868688384 28.99964970224691 60-64 23.395414038249722 21.287673976169017 26.234104335636328 29.082807649944932 65-69 22.993340343498073 23.51409543838566 25.21155675729808 28.281007460818188 70-74 23.890476906875282 22.18544706885312 25.339752269194122 28.584323755077477 75-79 24.904637622967275 22.766512748444086 23.705079301345112 28.623770327243527 80-84 24.125610185697752 21.740224447687584 24.72950530924463 29.404660057370037 85-89 23.75821952453212 21.947395042994437 24.613050075872533 29.68133535660091 90-94 25.0204206657137 22.2840514600776 24.178068205023486 28.517459669185214 95-99 22.993987144930543 22.579307484967863 25.549450549450547 28.87725482065105 100-104 24.38908283084735 22.521950703480375 24.955040727811276 28.133925737861 105-109 24.284479965439033 22.25942326385139 25.278107787018033 28.17798898369154 110-114 24.69735006973501 22.817294281729428 24.719665271966527 27.765690376569037 115-119 24.38129622081174 21.784196121819136 24.917020904908867 28.91748675246026 120-124 24.236525124711036 22.940747049519405 24.638033824066188 28.18469400170337 125-129 23.69226843582547 24.01760653227864 23.40520540954325 28.88491962235264 130-134 25.329726073723368 21.839702401082178 23.347987825498816 29.482583699695635 135-139 24.71609403254973 22.74864376130199 24.34719710669078 28.188065099457503 140-144 24.55947999060224 22.883546088182317 23.384759965541548 29.172213955673897 145-149 25.56598089007489 21.8817250581045 22.76835671860205 29.783937333218557 150 25.951776649746193 0.0 33.88324873096447 40.16497461928934 >>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 0.0 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 0.0 22 0.0 23 0.0 24 0.0 25 0.0 26 1.0 27 1.5 28 1.0 29 2.0 30 2.5 31 3.0 32 5.0 33 6.5 34 7.0 35 14.5 36 36.0 37 42.5 38 38.0 39 42.5 40 52.0 41 60.0 42 65.0 43 78.0 44 90.0 45 122.5 46 151.5 47 169.0 48 195.5 49 204.5 50 219.0 51 215.0 52 193.0 53 201.5 54 184.0 55 182.0 56 196.0 57 165.0 58 128.5 59 106.0 60 100.0 61 77.5 62 68.0 63 78.5 64 72.0 65 63.0 66 57.5 67 51.0 68 36.5 69 29.5 70 38.0 71 39.0 72 32.0 73 19.0 74 10.0 75 16.0 76 15.5 77 9.0 78 6.5 79 7.5 80 5.0 81 2.0 82 2.5 83 1.0 84 0.5 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 0.0 3 0.0 4 0.0 5 0.0 6 0.675 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 0.02 45-49 0.034999999999999996 50-54 0.02 55-59 0.06001500375093774 60-64 0.08004002001000501 65-69 0.04504504504504504 70-74 0.07015785517414182 75-79 0.025089066184956595 80-84 0.03018564169643306 85-89 0.04550280600637039 90-94 0.061224489795918366 95-99 0.1035625517812759 100-104 0.08983776356814459 105-109 0.08632782993417502 110-114 0.027886224205242612 115-119 0.05819705522900541 120-124 0.024327940639824838 125-129 0.08286060297023391 130-134 0.02704712962336872 135-139 0.028924723407332417 140-144 0.031316057308384875 145-149 0.07741269568209186 150 0.0 >>END_MODULE >>Sequence Length Distribution warn #Length Count 54-55 1.0 56-57 0.0 58-59 1.0 60-61 0.0 62-63 0.0 64-65 2.0 66-67 0.0 68-69 2.0 70-71 3.0 72-73 4.0 74-75 1.0 76-77 0.0 78-79 5.0 80-81 6.0 82-83 5.0 84-85 8.0 86-87 11.0 88-89 14.0 90-91 17.0 92-93 16.0 94-95 30.0 96-97 24.0 98-99 26.0 100-101 41.0 102-103 32.0 104-105 23.0 106-107 38.0 108-109 45.0 110-111 60.0 112-113 56.0 114-115 68.0 116-117 50.0 118-119 57.0 120-121 68.0 122-123 60.0 124-125 57.0 126-127 61.0 128-129 68.0 130-131 86.0 132-133 74.0 134-135 74.0 136-137 78.0 138-139 87.0 140-141 86.0 142-143 85.0 144-145 65.0 146-147 116.0 148-149 713.0 150-151 1576.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 70.05 #Duplication Level Percentage of deduplicated Percentage of total 1 82.08422555317631 57.49999999999999 2 8.458244111349037 11.85 3 3.640256959314775 7.6499999999999995 4 2.2840827980014278 6.4 5 1.284796573875803 4.5 6 0.9635974304068522 4.05 7 0.4996431120628123 2.45 8 0.32119914346895073 1.7999999999999998 9 0.10706638115631692 0.675 >10 0.35688793718772305 3.125 >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 CTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATT 17 0.42500000000000004 No Hit CCCGACTGTCCCTATTAATCATTACTCCGATCCCGAAGGCCAACACAATA 16 0.4 No Hit CCTCGCGGTACTTGTTCGCTATCGGTCTCTCGCCTGTATTTAGCCTTGGA 14 0.35000000000000003 No Hit CCCTTTTGTTCCACACGAGATTTCTGTTCTCGTTGAGCTCATCTTAGGAC 14 0.35000000000000003 No Hit CCTAATTCTCCGTCACCCGTCACCACCATGGTAGGCCCCTATCCTACCAT 12 0.3 No Hit ATCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCTATA 12 0.3 No Hit GTCGGGGCAGGCGGCGGGCGCAGGCGCCGCTTGCTAGCTTGGATTCTGAC 10 0.25 No Hit CTCCTACTCATCGGGGCATGGCGCTCGCCCAGATGGCCGGGTGTGGGTCG 10 0.25 No Hit GTCCTTTTCATCTTTCCCTCGCGGTACTTGTTCGCTATCGGTCTCTCGCC 10 0.25 No Hit CTCAGAGCCAATCCTTTTCCCGAAGTTACGGATCCGTTTTGCCGACTTCC 10 0.25 No Hit CTCCCACTTATCCTACACCTCTCAAGTCATTTCACAAAGTCGGACTAGAG 9 0.22499999999999998 No Hit GCCACGCTTTCACGGTTCGTATTCGTACTGGAAATCAGAATCAAACGAGC 9 0.22499999999999998 No Hit CCTGTGGTAACTTTTCTGACACCTCTAGCTTCAAACTCCGAAGATCTAAA 9 0.22499999999999998 No Hit CCCGCGTCAGCCTTTTATCTAATAAATGCGCCCCTCCCAGAAGTCGGGGT 8 0.2 No Hit GTTCGATTAGTCTTTCGCCCCTATACCCAAGTCAGACGAACGATTTGCAC 8 0.2 No Hit CTGACTATGAAATACGAATGCCCCCGACTGTCCCTATTAATCATTACTCC 8 0.2 No Hit CCCGAGCCCAGTCCTCAGAGCCAATCCTTTTCCCGAAGTTACGGATCCGT 8 0.2 No Hit CGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCAT 8 0.2 No Hit CTGCAAAGGATTCAGCCCGCCGCCCGTGGGGAAGGGAGCTTCGAGGCGGC 8 0.2 No Hit CCCATCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCT 8 0.2 No Hit CCCAACTTTCGTTCTTGATTAATGAAAACATCCTTGGCAAATGCTTTCGC 8 0.2 No Hit CTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGG 8 0.2 No Hit CTTTTGTTCCACACGAGATTTCTGTTCTCGTTGAGCTCATCTTAGGACAC 7 0.17500000000000002 No Hit CACCTCTCAAGTCATTTCACAAAGTCGGACTAGAGTCAAGCTCAACAGGG 7 0.17500000000000002 No Hit GTTCCATTGGCCAGAGGCTGTTCACCTTGGAGACCTGATGCGGTTATGAG 7 0.17500000000000002 No Hit CCCCGGAACCCAAAGACTTTGATTTCTCATAAGGTGCCGGCGGAGTCCTA 7 0.17500000000000002 No Hit CGGCAATTTCAAGCACTCTTTGACTCTCTTTTCAAAGTCCTTTTCATCTT 7 0.17500000000000002 No Hit CCGACATCGAAGGATCAAAAAGCAACGTCGCTATGAACGCTTGGCTGCCA 7 0.17500000000000002 No Hit CTTGTCCGTACCAGTTCTGAGTCGACTGTTCAGCGCTCGGGGAAAGCCCC 7 0.17500000000000002 No Hit GTCGGCATCGTTTATGGTTGAGACTAGGACGGTATCTGATCGTCTTCGAG 7 0.17500000000000002 No Hit CGGATGGGGAGCCCGCAGGCCGTTGCAGCGCAGTGCCCCGAGGGACACGC 7 0.17500000000000002 No Hit CATGAATCATCGGATCAGCGAGCAAAGCCCGCGTCAGCCTTTTATCTAAT 7 0.17500000000000002 No Hit CACGCTTTCACGGTTCGTATTCGTACTGGAAATCAGAATCAAACGAGCTT 7 0.17500000000000002 No Hit GTCGTCTGCAAAGGATTCAGCCCGCCGCCCGTGGGGAAGGGAGCTTCGAG 7 0.17500000000000002 No Hit GCCGCAGGCTCCACGCCTGGTGGTGCCCTTCCGTCAATTCCTTTAAGTTT 7 0.17500000000000002 No Hit CCCACTTATCCTACACCTCTCAAGTCATTTCACAAAGTCGGACTAGAGTC 7 0.17500000000000002 No Hit CACCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCA 6 0.15 No Hit GCCCGGTATTGTTATTTATTGTCACTACCTCCCCGTGTCAGGATTGGGTA 6 0.15 No Hit CTCTGACTATGAAATACGAATGCCCCCGACTGTCCCTATTAATCATTACT 6 0.15 No Hit GCATCGTTTATGGTTGAGACTAGGACGGTATCTGATCGTCTTCGAGCCCC 6 0.15 No Hit GTCACTACCTCCCCGTGTCAGGATTGGGTAATTTGCGCGCCTGCTGCCTT 6 0.15 No Hit CTTCCGTCAATTCCTTTAAGTTTCAGCCTTGCGACCATACTCCCCCCGGA 6 0.15 No Hit GTCGGATGGGGAGCCCGCAGGCCGTTGCAGCGCAGTGCCCCGAGGGACAC 6 0.15 No Hit CCGCTGATTCCGCCAAGCCCGTTCCCTTGGCTGTGGTTTCGCTGGATAGT 6 0.15 No Hit CCAACTACGAGCTTTTTAACTGCAACAACTTAAATATACGCTATTGGAGC 6 0.15 No Hit GTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACT 6 0.15 No Hit CCCGGCTTCCGGTTCATCCCGCATCGCCAGTTCTGCTTACCAAAAATGGC 6 0.15 No Hit CAGCCTTTTATCTAATAAATGCGCCCCTCCCAGAAGTCGGGGTTTGTTGC 6 0.15 No Hit CCCCCATCCGCTTCCCTCCCGGCAATTTCAAGCACTCTTTGACTCTCTTT 6 0.15 No Hit CCCAAGATTACCCGGGCCTGTCGGCCAAGGCTATATACTCGTTGAATACA 6 0.15 No Hit GTCAATTCCTTTAAGTTTCAGCCTTGCGACCATACTCCCCCCGGAACCCA 6 0.15 No Hit CTTGTTACGACTTCTCCTTCCTCTAAATGATAAGGTTCAATGGACTTCTC 6 0.15 No Hit GTCAGTATCGCTTCGAGCCTCCACCAGAGTTTCCTCTGGCTTCGCCCCGC 6 0.15 No Hit CCCGACTCGTTGACGGCGCCTCGTGGGGCGACAGGGTCCGGGCCGGACGG 6 0.15 No Hit GTGCGGTGCTCTTCCGGCCACTGGACCCTACCTCCGGCTGAACCGATTCC 6 0.15 No Hit CCGGTATTGTTATTTATTGTCACTACCTCCCCGTGTCAGGATTGGGTAAT 6 0.15 No Hit CCTATACCCAAGTCAGACGAACGATTTGCACGTCAGTATCGCTTCGAGCC 6 0.15 No Hit CCCGTGTCAGGATTGGGTAATTTGCGCGCCTGCTGCCTTCCTTGGATGTG 6 0.15 No Hit CCGCAGGCTCCACGCCTGGTGGTGCCCTTCCGTCAATTCCTTTAAGTTTC 6 0.15 No Hit CCGGAACCCAAAGACTTTGATTTCTCATAAGGTGCCGGCGGAGTCCTATA 6 0.15 No Hit CTGGAAATCAGAATCAAACGAGCTTTTACCCTTTTGTTCCACACGAGATT 6 0.15 No Hit CGCTGATTCCGCCAAGCCCGTTCCCTTGGCTGTGGTTTCGCTGGATAGTA 6 0.15 No Hit CGGTATTGTTATTTATTGTCACTACCTCCCCGTGTCAGGATTGGGTAATT 6 0.15 No Hit CCCGAAGTTACGGATCCGTTTTGCCGACTTCCCTTGCCTACATTGTTCCA 5 0.125 No Hit CCGCATACGGCCAGGACGCATCGCCGGCCCCCATCCGCTTCCCTCCCGGC 5 0.125 No Hit GAGCTTTTTAACTGCAACAACTTAAATATACGCTATTGGAGCTGGAATTA 5 0.125 No Hit GCAGAAATTTGAATGATGCGTCGCCGGCACGAGGGCCGTGCGATCCGTCG 5 0.125 No Hit CCCTGGTCGGCATCGTTTATGGTTGAGACTAGGACGGTATCTGATCGTCT 5 0.125 No Hit CCCAAGTCAGACGAACGATTTGCACGTCAGTATCGCTTCGAGCCTCCACC 5 0.125 No Hit CTATGAAATACGAATGCCCCCGACTGTCCCTATTAATCATTACTCCGATC 5 0.125 No Hit CGGAAACCTTGTTACGACTTCTCCTTCCTCTAAATGATAAGGTTCAATGG 5 0.125 No Hit CCCCAACTTTCGTTCTTGATTAATGAAAACATCCTTGGCAAATGCTTTCG 5 0.125 No Hit CCCCTATACCCAAGTCAGACGAACGATTTGCACGTCAGTATCGCTTCGAG 5 0.125 No Hit CCAAGATTACCCGGGCCTGTCGGCCAAGGCTATATACTCGTTGAATACAT 5 0.125 No Hit CCCTTGTCCGTACCAGTTCTGAGTCGACTGTTCAGCGCTCGGGGAAAGCC 5 0.125 No Hit ACCGCGGCTGCTGGCACCAGACTTGCCCTCCAATGGATCCTCGTTAAGGG 5 0.125 No Hit GCTCATCTTAGGACACCTGCGTTATCTTTTAACAGATGTGCCGCCCCAGC 5 0.125 No Hit GGGAAACTTCGGAGGGAACCAGCTACTAGATGGTTCGATTAGTCTTTCGC 5 0.125 No Hit CCCGGAACCCAAAGACTTTGATTTCTCATAAGGTGCCGGCGGAGTCCTAT 5 0.125 No Hit CCGAAGATCTAAAGGATCGATAGGCCACGCTTTCACGGTTCGTATTCGTA 5 0.125 No Hit GTTACGACTTCTCCTTCCTCTAAATGATAAGGTTCAATGGACTTCTCGCG 5 0.125 No Hit GCTGTGGTTTCGCTGGATAGTAGACAGGGACAGTGGGAATCTCGTTAATC 5 0.125 No Hit GTCGAGTTATCATGAATCATCGGATCAGCGAGCAAAGCCCGCGTCAGCCT 5 0.125 No Hit CTCCCGGCAATTTCAAGCACTCTTTGACTCTCTTTTCAAAGTCCTTTTCA 5 0.125 No Hit CTAGAATTACTACGGTTATCCGAGTAGCACGTACCATCAAACAAACTATA 5 0.125 No Hit TAGAACTCGTAATGGGCTCCAGCTATCCTGAGGGAAACTTCGGAGGGAAC 5 0.125 No Hit GTTCGCTATCGGTCTCTCGCCTGTATTTAGCCTTGGACGGAGTCTACCGC 5 0.125 No Hit CGAAGATCTAAAGGATCGATAGGCCACGCTTTCACGGTTCGTATTCGTAC 5 0.125 No Hit CGGCAGGTGAGTTGTTACACACTCCTTAGCGGATTTCGACTTCCATGACC 5 0.125 No Hit GTCAGGATTGGGTAATTTGCGCGCCTGCTGCCTTCCTTGGATGTGGTAGC 5 0.125 No Hit GTTGAGACTAGGACGGTATCTGATCGTCTTCGAGCCCCCAACTTTCGTTC 5 0.125 No Hit CCCGCTCAGGCATAGTTCACCATCTTTCGGGTCCCGACAGGCGTGCTCCA 5 0.125 No Hit GCTGGAATTACCGCGGCTGCTGGCACCAGACTTGCCCTCCAATGGATCCT 5 0.125 No Hit CCCAGCCAAACTCCCCACCTGACAATGTCTTCCGCCCGGATCGGCCCGGT 5 0.125 No Hit CCCGGTATTGTTATTTATTGTCACTACCTCCCCGTGTCAGGATTGGGTAA 5 0.125 No Hit TGGAAATCAGAATCAAACGAGCTTTTACCCTTTTGTTCCACACGAGATTT 5 0.125 No Hit GTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGA 5 0.125 No Hit GTCCAACTACGAGCTTTTTAACTGCAACAACTTAAATATACGCTATTGGA 5 0.125 No Hit GGCATCGTTTATGGTTGAGACTAGGACGGTATCTGATCGTCTTCGAGCCC 5 0.125 No Hit >>END_MODULE >>Adapter Content pass #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 0.0 0.0 0.0 0.0 0.0 60-61 0.0 0.0 0.0 0.0 0.0 62-63 0.0 0.0 0.0 0.0 0.0 64-65 0.0 0.0 0.0 0.0 0.0 66-67 0.0 0.0 0.0 0.0 0.0 68-69 0.0 0.0 0.0 0.0 0.0 70-71 0.0 0.0 0.0 0.0 0.0 72-73 0.0 0.0 0.0 0.0 0.0 74-75 0.0 0.0 0.0 0.0 0.0 76-77 0.0 0.0 0.0 0.0 0.0 78-79 0.0 0.0 0.0 0.0 0.0 80-81 0.0 0.0 0.0 0.0 0.0 82-83 0.0 0.0 0.0 0.0 0.0 84-85 0.0 0.0 0.0 0.0 0.0 86-87 0.0 0.0 0.0 0.0 0.0 88-89 0.0 0.0 0.0 0.0 0.0 90-91 0.0 0.0 0.0 0.0 0.0 92-93 0.0 0.0 0.0 0.0 0.0 94-95 0.0 0.0 0.0 0.0 0.0 96-97 0.0 0.0 0.0 0.0 0.0 98-99 0.0 0.0 0.0 0.0 0.0 100-101 0.0 0.0 0.0 0.0 0.0 102-103 0.0 0.0 0.0 0.0 0.0 104-105 0.0 0.0 0.0 0.0 0.0 106-107 0.0 0.0 0.0 0.0 0.0 108-109 0.0 0.0 0.0 0.0 0.0 110-111 0.0 0.0 0.0 0.0 0.0 112-113 0.0 0.0 0.0 0.0 0.0 114-115 0.0 0.0 0.0 0.0 0.0 116-117 0.0 0.0 0.0 0.0 0.0 118-119 0.0 0.0 0.0 0.0 0.0 120-121 0.0 0.0 0.0 0.0 0.0 122-123 0.0 0.0 0.0 0.0 0.0 124-125 0.0 0.0 0.0 0.0 0.0 126-127 0.0 0.0 0.0 0.0 0.0 128-129 0.0 0.0 0.0 0.0 0.0 130-131 0.0 0.0 0.0 0.0 0.0 132-133 0.0 0.0 0.0 0.0 0.0 134-135 0.0 0.0 0.0 0.0 0.0 136-137 0.0 0.0 0.0 0.0 0.0 138 0.0 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position CCACCAC 20 0.008867403 26.70886 85-89 GAACGGC 20 0.009431171 26.374998 70-74 >>END_MODULE Rejected 1388009 READS because READLEN < 1 Read 1388009 spots for SRR12682216.sra Written 1388009 spots for SRR12682216.sra Rejected 1388009 READS because READLEN < 1 Read 1388009 spots for SRR12682216.sra Written 1388009 spots for SRR12682216.sra Rejected 1388009 READS because READLEN < 1 Read 1388009 spots for SRR12682216.sra Written 1388009 spots for SRR12682216.sra Rejected 1388009 READS because READLEN < 1 Read 1388009 spots for SRR12682216.sra Written 1388009 spots for SRR12682216.sra Rejected 1388009 READS because READLEN < 1 Read 1388009 spots for SRR12682216.sra Written 1388009 spots for SRR12682216.sra Rejected 1388009 READS because READLEN < 1 Read 1388009 spots for SRR12682216.sra Written 1388009 spots for SRR12682216.sra Rejected 1388009 READS because READLEN < 1 Read 1388009 spots for SRR12682216.sra Written 1388009 spots for SRR12682216.sra Rejected 1388009 READS because READLEN < 1 Read 1388009 spots for SRR12682216.sra Written 1388009 spots for SRR12682216.sra Rejected 1388009 READS because READLEN < 1 Read 1388009 spots for SRR12682216.sra Written 1388009 spots for SRR12682216.sra Rejected 1388009 READS because READLEN < 1 Read 1388009 spots for SRR12682216.sra Written 1388009 spots for SRR12682216.sra Rejected 1388009 READS because READLEN < 1 Read 1388009 spots for SRR12682216.sra Written 1388009 spots for SRR12682216.sra Rejected 1388009 READS because READLEN < 1 Read 1388009 spots for SRR12682216.sra Written 1388009 spots for SRR12682216.sra Rejected 1388009 READS because READLEN < 1 Read 1388009 spots for SRR12682216.sra Written 1388009 spots for SRR12682216.sra Rejected 1388009 READS because READLEN < 1 Read 1388009 spots for SRR12682216.sra Written 1388009 spots for SRR12682216.sra Rejected 1388009 READS because READLEN < 1 Read 1388009 spots for SRR12682216.sra Written 1388009 spots for SRR12682216.sra Rejected 1388009 READS because READLEN < 1 Read 1388009 spots for SRR12682216.sra Written 1388009 spots for SRR12682216.sra Rejected 1388009 READS because READLEN < 1 Read 1388009 spots for SRR12682216.sra Written 1388009 spots for SRR12682216.sra Rejected 1388009 READS because READLEN < 1 Read 1388009 spots for SRR12682216.sra Written 1388009 spots for SRR12682216.sra Rejected 1388010 READS because READLEN < 1 Read 1388010 spots for SRR12682216.sra Written 1388010 spots for SRR12682216.sra Rejected 1388009 READS because READLEN < 1 Read 1388009 spots for SRR12682216.sra Written 1388009 spots for SRR12682216.sra SRR ids: ['SRR12682216.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_uxzyaytq SRR12682216.sra spots: 27760181 blocks: [[1, 1388009], [1388010, 2776018], [2776019, 4164027], [4164028, 5552036], [5552037, 6940045], [6940046, 8328054], [8328055, 9716063], [9716064, 11104072], [11104073, 12492081], [12492082, 13880090], [13880091, 15268099], [15268100, 16656108], [16656109, 18044117], [18044118, 19432126], [19432127, 20820135], [20820136, 22208144], [22208145, 23596153], [23596154, 24984162], [24984163, 26372171], [26372172, 27760181]] SRR12682216 file size 8726592 SRR12682216 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 SRR12682216 SRR12682216_1.fastq Input file: SRR12682216_1.fastq trimmed: SRR12682216-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -- 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 -- minimum overlap length for adapter detection (-k): inf -- number of concurrent threads (-t): 20 Sat Dec 7 02:56:18 2024 >> started Sat Dec 7 02:56:33 2024 >> done (14.987s) 27760181 reads processed; of these: 0 ( 0.00%) short reads filtered out after trimming by size control 859 ( 0.00%) empty reads filtered out after trimming by size control 27759322 (100.00%) reads available; of these: 12640 ( 0.05%) trimmed reads available after processing 27746682 (99.95%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 22 6 0.00% 23 4 0.00% 24 14 0.00% 25 22 0.00% 26 14 0.00% 27 31 0.00% 28 38 0.00% 29 50 0.00% 30 68 0.00% 31 57 0.00% 32 94 0.00% 33 81 0.00% 34 94 0.00% 35 123 0.00% 36 142 0.00% 37 143 0.00% 38 211 0.00% 39 266 0.00% 40 294 0.00% 41 344 0.00% 42 356 0.00% 43 344 0.00% 44 387 0.00% 45 438 0.00% 46 437 0.00% 47 559 0.00% 48 734 0.00% 49 847 0.00% 50 1027 0.00% 51 1138 0.00% 52 1267 0.00% 53 1229 0.00% 54 1258 0.00% 55 1546 0.01% 56 1563 0.01% 57 1830 0.01% 58 2267 0.01% 59 2542 0.01% 60 2934 0.01% 61 3153 0.01% 62 3506 0.01% 63 3845 0.01% 64 3916 0.01% 65 4368 0.02% 66 4849 0.02% 67 5469 0.02% 68 5857 0.02% 69 6434 0.02% 70 6921 0.02% 71 8528 0.03% 72 9315 0.03% 73 10842 0.04% 74 11448 0.04% 75 12216 0.04% 76 13590 0.05% 77 14536 0.05% 78 15711 0.06% 79 17851 0.06% 80 19369 0.07% 81 21533 0.08% 82 23780 0.09% 83 25051 0.09% 84 27975 0.10% 85 32280 0.12% 86 36439 0.13% 87 38948 0.14% 88 41901 0.15% 89 44049 0.16% 90 47444 0.17% 91 50019 0.18% 92 57156 0.21% 93 63647 0.23% 94 66398 0.24% 95 73630 0.27% 96 81211 0.29% 97 84703 0.31% 98 99487 0.36% 99 99075 0.36% 100 101155 0.36% 101 103598 0.37% 102 112599 0.41% 103 120821 0.44% 104 128311 0.46% 105 128019 0.46% 106 137689 0.50% 107 147867 0.53% 108 139360 0.50% 109 155720 0.56% 110 157326 0.57% 111 168441 0.61% 112 185178 0.67% 113 177785 0.64% 114 193553 0.70% 115 209348 0.75% 116 213754 0.77% 117 208434 0.75% 118 204742 0.74% 119 218582 0.79% 120 233051 0.84% 121 219192 0.79% 122 245152 0.88% 123 253602 0.91% 124 240158 0.87% 125 242468 0.87% 126 252336 0.91% 127 246742 0.89% 128 251049 0.90% 129 276217 1.00% 130 253815 0.91% 131 254890 0.92% 132 258524 0.93% 133 264000 0.95% 134 251337 0.91% 135 258954 0.93% 136 262542 0.95% 137 270039 0.97% 138 258608 0.93% 139 267197 0.96% 140 259540 0.93% 141 255059 0.92% 142 255578 0.92% 143 250102 0.90% 144 261025 0.94% 145 249747 0.90% 146 308547 1.11% 147 483868 1.74% 148 1083090 3.90% 149 3741628 13.48% 150 11117734 40.05% 27759322 reads passed initial QC criterion=sequence-density sequence-density=0.94 sequence-density-rank=1 fanout-score=2.77 fanout-score-rank=36 prefix-density=2.55 prefix-fanout=1.0 sequence=CTTGGATGTGGCAGCCGTTTCTC criterion=fanout-score sequence-density=0.03 sequence-density-rank=35 fanout-score=55.78 fanout-score-rank=1 prefix-density=1.91 prefix-fanout=1.0 sequence=AAGTTACGGGGCTATTTTGCCGAGTTCCTTAGAGAGAGTTGTCTCGCGCCCCTAGGTATTCTCTACCTACCCACCTGTGTCGGTTTCGGGTACAGGTACCCTTTTGT Started job on | Dec 07 02:56:55 Started mapping on | Dec 07 02:56:55 Finished on | Dec 07 02:58:22 Mapping speed, Million of reads per hour | 1148.66 Number of input reads | 27759322 Average input read length | 138 UNIQUE READS: Uniquely mapped reads number | 7573172 Uniquely mapped reads % | 27.28% Average mapped length | 138.25 Number of splices: Total | 2799290 Number of splices: Annotated (sjdb) | 2633534 Number of splices: GT/AG | 2760804 Number of splices: GC/AG | 33788 Number of splices: AT/AC | 2093 Number of splices: Non-canonical | 2605 Mismatch rate per base, % | 0.25% Deletion rate per base | 0.01% Deletion average length | 1.68 Insertion rate per base | 0.00% Insertion average length | 1.13 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 1335846 % of reads mapped to multiple loci | 4.81% Number of reads mapped to too many loci | 16173822 % of reads mapped to too many loci | 58.26% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.33% % of reads unmapped: other | 8.32% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 18850304 18850304 18850304 N_multimapping 1335846 1335846 1335846 N_noFeature 559790 7376118 619511 N_ambiguous 171576 822 35504 UnstrandedReadsAssigned:6841806 PositiveStrandReadsAssigned:196232 NegativeStrandReadsAssigned:6918157 Dataset is classified negative stranded MeadianReadLen=149 20thPercentileLength=124 echo kmer=119 SRR12682216 Starting Kallisto single end mapping to ensembl reference transcriptome. kmer=31 [quant] fragment length distribution is truncated gaussian with mean = 100, sd = 20 [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 single-end mode [quant] will process file 1: SRR12682216-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 27,759,322 reads, 7,142,351 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,086 rounds 52973 SRR12682216.ke.tsv 35125 SRR12682216.se.tsv 88098 total ==> SRR12682216.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 837 0 0 PNS24247 1044 945 4.99136 1.03022 PNS24249 1928 1829 54.3432 5.79527 PNS24246 1044 945 4.99136 1.03022 PNS24248 1044 945 4.99136 1.03022 PNS24244 1471 1372 96.6828 13.7448 PNS24243 293 194 0 0 KQK14069 1603 1504 4541.74 589.003 KQK14071 474 375 165.939 86.3097 ==> SRR12682216.se.tsv <== BRADI_1g14170v3 4949 BRADI_1g53295v3 32 BRADI_1g59795v3 180 BRADI_1g07683v3 0 BRADI_1g00485v3 2 BRADI_1g20270v3 486 BRADI_1g74790v3 180 BRADI_1g09890v3 0 BRADI_1g77505v3 94 BRADI_1g48960v3 0 SRR12682216 completed mapping pipeline successfully