Starting /dee2/code/volunteer_pipeline.sh SRR8846498 current disk space = 1500442206208 free memory = 1372714884 SRR8846498 SRAfilesize 1b3330f7c2d0cf072694fb5ac3590a20 SRR8846498.sra SRR8846498.sra file validated SRR8846498 is single end SRR8846498 is conventional basespace SRR8846498 read1 length is 101 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR8846498_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 101 %GC 46 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 30.5515 34.0 33.0 34.0 25.0 34.0 2 32.737 34.0 33.0 34.0 28.0 34.0 3 32.8575 34.0 33.0 34.0 31.0 34.0 4 33.0805 34.0 33.0 34.0 32.0 34.0 5 33.10825 34.0 33.0 34.0 32.0 34.0 6 36.68075 38.0 37.0 38.0 35.0 38.0 7 37.068 38.0 38.0 38.0 36.0 38.0 8 37.26225 38.0 38.0 38.0 36.0 38.0 9 37.33475 38.0 38.0 38.0 37.0 38.0 10-11 37.346625 38.0 38.0 38.0 37.0 38.0 12-13 37.40712499999999 38.0 38.0 38.0 37.0 38.0 14-15 37.390874999999994 38.0 38.0 38.0 37.0 38.0 16-17 37.277874999999995 38.0 38.0 38.0 37.0 38.0 18-19 37.335375 38.0 38.0 38.0 37.0 38.0 20-21 37.259 38.0 38.0 38.0 37.0 38.0 22-23 37.3165 38.0 38.0 38.0 37.0 38.0 24-25 37.3555 38.0 38.0 38.0 37.0 38.0 26-27 37.381875 38.0 38.0 38.0 37.0 38.0 28-29 37.341625 38.0 38.0 38.0 37.0 38.0 30-31 37.316500000000005 38.0 38.0 38.0 37.0 38.0 32-33 37.160624999999996 38.0 38.0 38.0 37.0 38.0 34-35 36.92075 38.0 38.0 38.0 35.5 38.0 36-37 36.811875 38.0 38.0 38.0 35.5 38.0 38-39 36.680375 38.0 38.0 38.0 34.5 38.0 40-41 36.958375000000004 38.0 38.0 38.0 36.0 38.0 42-43 36.978875 38.0 38.0 38.0 36.0 38.0 44-45 36.845625 38.0 38.0 38.0 35.5 38.0 46-47 36.833375 38.0 38.0 38.0 35.5 38.0 48-49 36.985875 38.0 38.0 38.0 36.0 38.0 50-51 37.09325 38.0 38.0 38.0 36.0 38.0 52-53 37.09525 38.0 38.0 38.0 36.0 38.0 54-55 36.905125 38.0 38.0 38.0 35.5 38.0 56-57 36.765875 38.0 38.0 38.0 35.0 38.0 58-59 36.5945 38.0 38.0 38.0 34.0 38.0 60-61 36.711375000000004 38.0 38.0 38.0 34.0 38.0 62-63 36.142375 38.0 37.5 38.0 32.0 38.0 64-65 35.62287499999999 38.0 36.5 38.0 29.0 38.0 66-67 35.338125000000005 38.0 36.5 38.0 28.0 38.0 68-69 35.700125 38.0 37.0 38.0 29.0 38.0 70-71 35.413 38.0 37.0 38.0 28.0 38.0 72-73 35.47875 38.0 37.0 38.0 29.0 38.0 74-75 35.118750000000006 38.0 36.5 38.0 28.0 38.0 76-77 34.710375 38.0 36.0 38.0 27.0 38.0 78-79 34.917249999999996 38.0 36.0 38.0 27.0 38.0 80-81 34.6765 38.0 35.5 38.0 27.0 38.0 82-83 34.8775 38.0 36.0 38.0 27.0 38.0 84-85 34.97025 38.0 36.0 38.0 27.5 38.0 86-87 34.969375 38.0 36.0 38.0 27.5 38.0 88-89 35.077749999999995 38.0 36.0 38.0 29.0 38.0 90-91 34.69025 38.0 36.0 38.0 27.0 38.0 92-93 34.599375 38.0 36.0 38.0 27.0 38.0 94-95 34.196 38.0 35.5 38.0 26.0 38.0 96-97 32.55675 38.0 34.0 38.0 8.5 38.0 98-99 29.975375 38.0 28.5 38.0 2.0 38.0 100-101 27.279125 36.5 19.5 38.0 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 10 1.0 11 1.0 12 0.0 13 1.0 14 1.0 15 0.0 16 0.0 17 0.0 18 0.0 19 1.0 20 5.0 21 2.0 22 2.0 23 6.0 24 7.0 25 31.0 26 26.0 27 28.0 28 28.0 29 48.0 30 62.0 31 81.0 32 97.0 33 144.0 34 274.0 35 532.0 36 1009.0 37 1613.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 28.260277702150834 27.225701061802344 20.58263000272257 23.93139123332426 2 25.724999999999998 29.45 18.5 26.325 3 25.424999999999997 20.575 21.375 32.625 4 25.575 31.825 18.15 24.45 5 30.675 26.974999999999998 21.099999999999998 21.25 6 22.230557639409852 28.782195548887223 24.88122030507627 24.10602650662666 7 36.975 23.200000000000003 18.725 21.099999999999998 8 21.55 21.9 35.275 21.275 9 24.7 34.275 20.3 20.724999999999998 10-11 29.525000000000002 27.6625 22.6 20.2125 12-13 22.675 22.3 20.6625 34.362500000000004 14-15 22.1 36.575 23.875 17.45 16-17 25.124999999999996 26.125 28.499999999999996 20.25 18-19 29.675 25.75 22.7125 21.8625 20-21 20.974999999999998 28.8875 28.349999999999998 21.7875 22-23 28.499999999999996 27.025 29.2375 15.2375 24-25 28.175 24.85 26.575 20.4 26-27 33.6625 28.725 20.8625 16.75 28-29 22.05 29.9375 27.5125 20.5 30-31 26.4625 19.85 36.662499999999994 17.025000000000002 32-33 23.7 20.4 33.375 22.525000000000002 34-35 30.112499999999997 17.0375 30.125 22.725 36-37 37.974999999999994 14.2 29.9875 17.837500000000002 38-39 35.4 17.925 27.150000000000002 19.525000000000002 40-41 29.9 19.400000000000002 22.7375 27.962500000000002 42-43 29.75 25.724999999999998 23.4375 21.087500000000002 44-45 39.0375 19.5 15.862499999999999 25.6 46-47 30.4375 31.2 14.1125 24.25 48-49 29.8375 23.175 18.725 28.262500000000003 50-51 24.4125 24.175 15.5 35.9125 52-53 24.587500000000002 32.5375 12.237499999999999 30.6375 54-55 23.3375 27.237499999999997 17.6875 31.7375 56-57 22.825 32.800000000000004 14.075 30.3 58-59 23.3875 29.025000000000002 20.8125 26.775 60-61 23.1 32.6 16.725 27.575 62-63 27.0625 30.9875 17.549999999999997 24.4 64-65 22.237499999999997 32.125 24.6875 20.95 66-67 22.025 24.75 26.35 26.875 68-69 25.35 25.8125 24.2875 24.55 70-71 24.4125 26.150000000000002 30.5375 18.9 72-73 29.099999999999998 21.8625 27.6875 21.349999999999998 74-75 22.75 18.712500000000002 27.187499999999996 31.35 76-77 23.0375 14.2875 38.45 24.224999999999998 78-79 19.825 9.4625 37.1 33.6125 80-81 21.0125 10.525 37.3875 31.075000000000003 82-83 21.9625 10.299999999999999 42.35 25.387500000000003 84-85 19.8875 10.4375 38.45 31.225 86-87 22.15 15.775 36.9125 25.162499999999998 88-89 16.45 32.4125 32.225 18.912499999999998 90-91 12.675 40.362500000000004 29.8375 17.125 92-93 12.9 50.887499999999996 22.15 14.0625 94-95 10.575 60.5 19.35 9.575 96-97 8.15 68.66250000000001 15.962499999999999 7.225 98-99 7.3 78.075 10.1875 4.4375 100-101 4.45 85.8 6.125 3.6249999999999996 >>END_MODULE >>Per sequence GC content warn #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 0.0 27 0.0 28 0.0 29 0.0 30 0.0 31 0.0 32 0.5 33 1.0 34 3.0 35 6.5 36 12.0 37 15.0 38 15.0 39 59.5 40 80.5 41 97.0 42 174.0 43 220.0 44 334.5 45 383.0 46 388.0 47 405.0 48 321.0 49 304.0 50 285.0 51 224.5 52 152.5 53 88.5 54 93.0 55 148.5 56 116.5 57 30.5 58 15.0 59 12.5 60 7.5 61 3.5 62 2.0 63 1.0 64 0.0 65 0.0 66 0.0 67 0.0 68 0.0 69 0.0 70 0.0 71 0.0 72 0.0 73 0.0 74 0.0 75 0.0 76 0.0 77 0.0 78 0.0 79 0.0 80 0.0 81 0.0 82 0.0 83 0.0 84 0.0 85 0.0 86 0.0 87 0.0 88 0.0 89 0.0 90 0.0 91 0.0 92 0.0 93 0.0 94 0.0 95 0.0 96 0.0 97 0.0 98 0.0 99 0.0 100 0.0 >>END_MODULE >>Per base N content warn #Base N-Count 1 8.175 2 0.0 3 0.0 4 0.0 5 0.0 6 0.025 7 0.0 8 0.0 9 0.0 10-11 0.0 12-13 0.0 14-15 0.0 16-17 0.0 18-19 0.0 20-21 0.0 22-23 0.0 24-25 0.0 26-27 0.0 28-29 0.0 30-31 0.0 32-33 0.0 34-35 0.0 36-37 0.0 38-39 0.0 40-41 0.0 42-43 0.0 44-45 0.0 46-47 0.0 48-49 0.0 50-51 0.0 52-53 0.0 54-55 0.0 56-57 0.0 58-59 0.0 60-61 0.0 62-63 0.0 64-65 0.0 66-67 0.0 68-69 0.0 70-71 0.0 72-73 0.0 74-75 0.0 76-77 0.0 78-79 0.0 80-81 0.0 82-83 0.0 84-85 0.0 86-87 0.0 88-89 0.0 90-91 0.0 92-93 0.0 94-95 0.0 96-97 0.0 98-99 0.0 100-101 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 101 4000.0 >>END_MODULE >>Sequence Duplication Levels warn #Total Deduplicated Percentage 58.775 #Duplication Level Percentage of deduplicated Percentage of total 1 86.55891110165886 50.875 2 5.487026797107614 6.45 3 2.3394300297745643 4.125 4 1.3185878349638451 3.1 5 0.8932369204593791 2.625 6 0.7656316461080391 2.7 7 0.340280731603573 1.4000000000000001 8 0.4253509145044662 2.0 9 0.38281582305401957 2.025 >10 1.3185878349638451 15.725 >50 0.12760527435133986 6.1 >100 0.04253509145044662 2.875 >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 TCCACTGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGT 115 2.875 No Hit GGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGA 99 2.475 RNA PCR Primer, Index 1 (100% over 22bp) AGCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGC 84 2.1 No Hit TCGGACCAGGCTTCATTCCCCTGGAATTCTCGGGTGCCAAGGAACTCCAG 61 1.525 RNA PCR Primer, Index 1 (100% over 29bp) GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGGAATTCTCGGGTGCC 50 1.25 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATATGGAATTCTCGGGTGCCAAG 44 1.0999999999999999 No Hit ATATATTTCAAGTTATTTCGGATCTTGGAATTCTCGGGTGCCAAGGAACT 42 1.05 RNA PCR Primer, Index 1 (100% over 25bp) CATCGAGTAGACCTTGTTATTGTGAGAATTTGGAATTCTCGGGTGCCAAG 36 0.8999999999999999 No Hit GACACGACTCTCGGCAACGGATATCTCTGGAATTCTCGGGTGCCAAGGAA 31 0.775 RNA PCR Primer, Index 1 (100% over 23bp) GCCCACCCCAAGATGAGTGCTCTCTCTGGAATTCTCGGGTGCCAAGGAAC 29 0.7250000000000001 RNA PCR Primer, Index 1 (100% over 24bp) CACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGATGGAATTC 26 0.65 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCTGGAATTCTCGGGTGCCA 23 0.575 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTGGAATTCTCGGGTGCCAAGG 22 0.5499999999999999 Illumina Small RNA Adapter 2 (100% over 21bp) CATCGAGTAGACCTTGTTATTGTGAGATGGAATTCTCGGGTGCCAAGGAA 20 0.5 RNA PCR Primer, Index 1 (100% over 23bp) AGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGG 20 0.5 Illumina Small RNA Adapter 2 (100% over 21bp) GACACGACTCTCGGCAACGGATATCTTGGAATTCTCGGGTGCCAAGGAAC 19 0.475 RNA PCR Primer, Index 1 (100% over 24bp) GACACGACTCTCGGCAACGGATATCTGGAATTCTCGGGTGCCAAGGAACT 19 0.475 RNA PCR Primer, Index 1 (100% over 25bp) TGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAA 19 0.475 No Hit GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGAATTCTCGGGTGCCAAGG 18 0.44999999999999996 Illumina Small RNA Adapter 2 (100% over 21bp) GGGATTGTAGTTCAATTGGTCAGAGCACCTGGAATTCTCGGGTGCCAAGG 18 0.44999999999999996 Illumina Small RNA Adapter 2 (100% over 21bp) CTCTGATGATGATCAAACTAATACTTTCGTTCTTCTGGAATTCTCGGGTG 18 0.44999999999999996 No Hit CTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCA 17 0.42500000000000004 RNA PCR Primer, Index 1 (100% over 28bp) GAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAG 16 0.4 No Hit TCTCGGGTGCCAAGGAACTCCAGTCACGTAGAGATCTCGTATGCCGTCTT 16 0.4 RNA PCR Primer, Index 17 (100% over 50bp) CCAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGG 15 0.375 No Hit GGGGATATGGCGAAATCGGTAGACGCTACGGACTTTGGAATTCTCGGGTG 14 0.35000000000000003 No Hit CTCGGGTGCCAAGGAACTCCAGTCACGTAGAGATCTCGTATGCCGTCTTC 13 0.325 RNA PCR Primer, Index 17 (100% over 50bp) GCACCAGTGGTCTAGTGGTAGAATAGTACCTGGAATTCTCGGGTGCCAAG 13 0.325 No Hit GCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCC 11 0.27499999999999997 No Hit CACGACTCTCGGCAACGGATATCTCTGGAATTCTCGGGTGCCAAGGAACT 10 0.25 RNA PCR Primer, Index 1 (100% over 25bp) CATCGAGTAGACCTTGTTATTGTGAGAATAAATGGAATTCTCGGGTGCCA 10 0.25 No Hit TTCGGACCAGGCTTCATTCCCTGGAATTCTCGGGTGCCAAGGAACTCCAG 10 0.25 RNA PCR Primer, Index 1 (100% over 29bp) CAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGGG 10 0.25 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATGGAATTCTCGGGTGCCAAGGA 10 0.25 RNA PCR Primer, Index 1 (100% over 22bp) CAGCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTG 10 0.25 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCCTGGAATTCTCGGGTGC 9 0.22499999999999998 No Hit NGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGA 9 0.22499999999999998 RNA PCR Primer, Index 1 (100% over 22bp) TCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACTC 9 0.22499999999999998 RNA PCR Primer, Index 1 (100% over 26bp) GAAGATACGGGTTCGATTCCCGCCGCTCGCCCCATGGAATTCTCGGGTGC 9 0.22499999999999998 No Hit GCCTTGATGGTGAAATGGTAGACACGCGAGACTCAAAATCTTGGAATTCT 9 0.22499999999999998 No Hit TGTATGCAGCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCT 9 0.22499999999999998 No Hit CCACTGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTG 9 0.22499999999999998 No Hit CACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGGAATTCTCG 9 0.22499999999999998 No Hit AAGGGTGCTGAGAATACTTTGAATCTGACACTGGAATTCTCGGGTGCCAA 9 0.22499999999999998 No Hit NCCACTGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGT 8 0.2 No Hit GTCAGGATAGCTCAGTTGGTAGAGCAGAGGACTTGGAATTCTCGGGTGCC 8 0.2 No Hit CATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGGGTGCC 8 0.2 No Hit TCCGTCGTAGTCTAGGTGGTTAGGATATGGAATTCTCGGGTGCCAAGGAA 8 0.2 RNA PCR Primer, Index 1 (100% over 23bp) TTCTCGGGTGCCAAGGAACTCCAGTCACGTAGAGATCTCGTATGCCGTCT 8 0.2 RNA PCR Primer, Index 17 (100% over 50bp) ATATATTTCAAGTTATTTCGGATCTGGAATTCTCGGGTGCCAAGGAACTC 8 0.2 RNA PCR Primer, Index 1 (100% over 26bp) GCGAGCGTAGTTCAATGGTAAAACATCTCCTTGTGGAATTCTCGGGTGCC 8 0.2 No Hit GCCTTGATGGTGAAATGGTAGACACGCGAGACTCATGGAATTCTCGGGTG 8 0.2 No Hit TCAAAAGAGGAAAGGCTTGCGGTGGAATTCTCGGGTGCCAAGGAACTCCA 8 0.2 RNA PCR Primer, Index 1 (100% over 28bp) CTGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCCA 8 0.2 No Hit CGGATAACCGTAGTAATTCTAGAGCTAATACGTGGAATTCTCGGGTGCCA 7 0.17500000000000002 No Hit TCCGTCGTAGTCTAGGTGGTTAGGATACTCTGGAATTCTCGGGTGCCAAG 7 0.17500000000000002 No Hit AGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGGGT 7 0.17500000000000002 No Hit AATTCTCGGGTGCCAAGGAACTCCAGTCACGTAGAGATCTCGTATGCCGT 7 0.17500000000000002 RNA PCR Primer, Index 17 (100% over 50bp) CACGACTCTCGGCAACGGATATCTGGAATTCTCGGGTGCCAAGGAACTCC 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 27bp) ACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGGGTGC 7 0.17500000000000002 No Hit ACTGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCC 7 0.17500000000000002 No Hit CAGGGTTCGTTTCCCTGGATGCGCACCATGGAATTCTCGGGTGCCAAGGA 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 22bp) TCCTGTGGATGAGAAGGCATTTATATTCTGATGATATGGAATTCTCGGGT 6 0.15 No Hit NACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGATGGAATTC 6 0.15 No Hit CGGTCGAGGGCACGCCTGCCTGGGCGTCACGCTGGAATTCTCGGGTGCCA 6 0.15 No Hit ACACGACTCTCGGCAACGGATATCTCTGGAATTCTCGGGTGCCAAGGAAC 6 0.15 RNA PCR Primer, Index 1 (100% over 24bp) CAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTTGAATTCTCGGG 6 0.15 No Hit TCCAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCG 6 0.15 No Hit NCGGACCAGGCTTCATTCCCCTGGAATTCTCGGGTGCCAAGGAACTCCAG 6 0.15 RNA PCR Primer, Index 1 (100% over 29bp) GCCTTGATGGTGAAATGGTAGACACGCGAGACTTGGAATTCTCGGGTGCC 6 0.15 No Hit TGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCCAA 6 0.15 No Hit AGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGGGTGCCAAG 6 0.15 No Hit CACGACTCTCGGCAACGGATATCTCGTGGAATTCTCGGGTGCCAAGGAAC 6 0.15 RNA PCR Primer, Index 1 (100% over 24bp) GCGAGCGTAGTTCAATGGTAAAACATCTCCTTGCCAAGGATGGAATTCTC 6 0.15 No Hit NGCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGC 6 0.15 No Hit ACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGATGGAATTCT 6 0.15 No Hit GCGAGCGTAGTTCAATGGTAAAACATCTCCTTTGGAATTCTCGGGTGCCA 6 0.15 No Hit CAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCCAAGGAACTC 6 0.15 RNA PCR Primer, Index 1 (100% over 26bp) TGCAGCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGG 6 0.15 No Hit CTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCA 6 0.15 No Hit NGGATTGTAGTTCAATTGGTCAGAGCACCTGGAATTCTCGGGTGCCAAGG 5 0.125 Illumina Small RNA Adapter 2 (100% over 21bp) AAGGGTGCTGAGAATACTTTGAATCTGACATGGAATTCTCGGGTGCCAAG 5 0.125 No Hit GATAACCGTAGTAATTCTAGAGCTAATTGGAATTCTCGGGTGCCAAGGAA 5 0.125 RNA PCR Primer, Index 1 (100% over 23bp) CACCATGCGCGGGTTCAATTCCCGTCGTTCGCCCCATGGAATTCTCGGGT 5 0.125 No Hit ATTCTCGGGTGCCAAGGAACTCCAGTCACGTAGAGATCTCGTATGCCGTC 5 0.125 RNA PCR Primer, Index 17 (100% over 50bp) GCGACCCCAGGTCAGGCGGGACTACCCGCTGATGGAATTCTCGGGTGCCA 5 0.125 No Hit GACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGGGTG 5 0.125 No Hit ATTGTATCCTTAACCATTTCTTTTTTGGAATTCTCGGGTGCCAAGGAACT 5 0.125 RNA PCR Primer, Index 1 (100% over 25bp) CATCGAGTAGACCTTGTTATTGTGAGAATTCTTAATTTGGAATTCTCGGG 5 0.125 No Hit AGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTTGAATTCTCGGGT 5 0.125 No Hit ACACGACTCTCGGCAACGGATATCTTGGAATTCTCGGGTGCCAAGGAACT 5 0.125 RNA PCR Primer, Index 1 (100% over 25bp) CACGACTCTCGGCAACGGATGGAATTCTCGGGTGCCAAGGAACTCCAGTC 5 0.125 RNA PCR Primer, Index 1 (100% over 31bp) ATATTGGGTAGGTTGTGGTATTTCATTGCTGGAATTCTCGGGTGCCAAGG 5 0.125 Illumina Small RNA Adapter 2 (100% over 21bp) GACACGACTCTCGGCAACGGATATCTCGTGGAATTCTCGGGTGCCAAGGA 5 0.125 RNA PCR Primer, Index 1 (100% over 22bp) NACACGACTCTCGGCAACGGATATCTCTGGAATTCTCGGGTGCCAAGGAA 5 0.125 RNA PCR Primer, Index 1 (100% over 23bp) CATCGAGTAGACCTTGTTATTGTGAGAATTCTTAATGGAATTCTCGGGTG 5 0.125 No Hit CGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCAGTCA 5 0.125 RNA PCR Primer, Index 1 (100% over 32bp) GACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTTGAATTCTCGGGTG 5 0.125 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTATGGAATTCTCGGGTGCCAA 5 0.125 No Hit ACACGACTCTCGGCAACGGATATCTGGAATTCTCGGGTGCCAAGGAACTC 5 0.125 RNA PCR Primer, Index 1 (100% over 26bp) GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTTGGAATTCTCGGGTGC 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 0.025 0.0 0.0 0.0 2 0.0 0.025 0.0 0.0 0.0 3 0.0 0.025 0.0 0.0 0.0 4 0.0 0.025 0.0 0.0 0.0 5 0.0 0.05 0.0 0.0 0.0 6 0.0 0.05 0.0 0.0 0.0 7 0.0 0.05 0.0 0.0 0.0 8 0.0 0.05 0.0 0.0 0.0 9 0.0 0.1 0.0 0.0 0.0 10-11 0.0 0.15 0.0 0.0 0.0 12-13 0.0 0.2375 0.0 0.0 0.0 14-15 0.0 0.44999999999999996 0.0 0.0 0.0 16-17 0.0 1.05 0.0 0.0 0.0 18-19 0.0 2.0875 0.0 0.0 0.0 20-21 0.0 4.1 0.0 0.0 0.0 22-23 0.0 10.462499999999999 0.0 0.0 0.0 24-25 0.0 21.5 0.0 0.0 0.0 26-27 0.0 34.6125 0.0 0.0 0.0 28-29 0.0 43.9125 0.0 0.0 0.0 30-31 0.0 54.625 0.0 0.0 0.0 32-33 0.0 62.912499999999994 0.0 0.0 0.0 34-35 0.0 72.4 0.0 0.0 0.0 36-37 0.0 82.0375 0.0 0.0 0.0 38-39 0.0 87.7875 0.0 0.0 0.0 40-41 0.0 90.4375 0.0 0.0 0.0 42-43 0.0 93.05 0.0 0.0 0.0 44-45 0.0 94.3375 0.0 0.0 0.0 46-47 0.0 94.86250000000001 0.0 0.0 0.0 48-49 0.0 94.95 0.0 0.0 0.0 50-51 0.0 95.0 0.0 0.0 0.0 52-53 0.0 95.025 0.0 0.0 0.0 54-55 0.0 95.05 0.0 0.0 0.0 56-57 0.0 95.0625 0.0 0.0 0.0 58-59 0.0 95.075 0.0 0.0 0.0 60-61 0.0 95.075 0.0 0.0 0.0 62-63 0.0 95.075 0.0 0.0 0.0 64-65 0.0 95.075 0.0 0.0 0.0 66-67 0.0 95.075 0.0 0.0 0.0 68-69 0.0 95.075 0.0 0.0 0.0 70-71 0.0 95.075 0.0 0.0 0.0 72-73 0.0 95.075 0.0 0.0 0.0 74-75 0.0 95.075 0.0 0.0 0.0 76-77 0.0 95.075 0.0 0.0 0.0 78-79 0.0 95.075 0.0 0.0 0.0 80-81 0.0 95.075 0.0 0.0 0.0 82-83 0.0 95.075 0.0 0.0 0.0 84-85 0.0 95.075 0.0 0.0 0.0 86-87 0.0 95.075 0.0 0.0 0.0 88-89 0.0 95.075 0.0 0.0 0.0 >>END_MODULE >>Kmer Content fail #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TCCACTG 20 8.418772E-6 106.9155 1 GGGATTG 20 8.418772E-6 106.9155 1 CATCGAG 25 1.8471837E-7 106.91549 1 GTAGACC 25 3.856112E-7 94.887505 7 CTGAGAT 25 3.856112E-7 94.887505 5 AGTAGAC 25 3.856112E-7 94.887505 6 CACTGAG 25 3.856112E-7 94.887505 3 TAGTTCA 25 3.856112E-7 94.887505 8 CCACTGA 25 3.856112E-7 94.887505 2 GAGTAGA 25 3.856112E-7 94.887505 5 GATCCAG 25 3.856112E-7 94.887505 9 CGAGTAG 25 3.856112E-7 94.887505 4 AGACCTT 25 3.856112E-7 94.887505 9 AGATCCA 25 3.856112E-7 94.887505 8 ATCGAGT 25 3.856112E-7 94.887505 2 TCGAGTA 25 3.856112E-7 94.887505 3 AGTTCAA 25 3.856112E-7 94.887505 9 GTAGTTC 25 3.856112E-7 94.887505 7 TAGACCT 25 3.856112E-7 94.887505 8 GAGATCC 25 3.856112E-7 94.887505 7 >>END_MODULE Rejected 1065148 READS because READLEN < 1 Read 1065148 spots for SRR8846498.sra Written 1065148 spots for SRR8846498.sra Rejected 1065148 READS because READLEN < 1 Read 1065148 spots for SRR8846498.sra Written 1065148 spots for SRR8846498.sra Rejected 1065148 READS because READLEN < 1 Read 1065148 spots for SRR8846498.sra Written 1065148 spots for SRR8846498.sra Rejected 1065148 READS because READLEN < 1 Read 1065148 spots for SRR8846498.sra Written 1065148 spots for SRR8846498.sra Rejected 1065148 READS because READLEN < 1 Read 1065148 spots for SRR8846498.sra Written 1065148 spots for SRR8846498.sra Rejected 1065148 READS because READLEN < 1 Read 1065148 spots for SRR8846498.sra Written 1065148 spots for SRR8846498.sra Rejected 1065148 READS because READLEN < 1 Read 1065148 spots for SRR8846498.sra Written 1065148 spots for SRR8846498.sra Rejected 1065148 READS because READLEN < 1 Read 1065148 spots for SRR8846498.sra Written 1065148 spots for SRR8846498.sra Rejected 1065148 READS because READLEN < 1 Read 1065148 spots for SRR8846498.sra Written 1065148 spots for SRR8846498.sra Rejected 1065148 READS because READLEN < 1 Read 1065148 spots for SRR8846498.sra Written 1065148 spots for SRR8846498.sra Rejected 1065148 READS because READLEN < 1 Read 1065148 spots for SRR8846498.sra Written 1065148 spots for SRR8846498.sra Rejected 1065154 READS because READLEN < 1 Read 1065154 spots for SRR8846498.sra Written 1065154 spots for SRR8846498.sra Rejected 1065148 READS because READLEN < 1 Read 1065148 spots for SRR8846498.sra Written 1065148 spots for SRR8846498.sra Rejected 1065148 READS because READLEN < 1 Read 1065148 spots for SRR8846498.sra Written 1065148 spots for SRR8846498.sra Rejected 1065148 READS because READLEN < 1 Read 1065148 spots for SRR8846498.sra Written 1065148 spots for SRR8846498.sra Rejected 1065148 READS because READLEN < 1 Read 1065148 spots for SRR8846498.sra Written 1065148 spots for SRR8846498.sra Rejected 1065148 READS because READLEN < 1 Read 1065148 spots for SRR8846498.sra Written 1065148 spots for SRR8846498.sra Rejected 1065148 READS because READLEN < 1 Read 1065148 spots for SRR8846498.sra Written 1065148 spots for SRR8846498.sra Rejected 1065148 READS because READLEN < 1 Read 1065148 spots for SRR8846498.sra Written 1065148 spots for SRR8846498.sra Rejected 1065148 READS because READLEN < 1 Read 1065148 spots for SRR8846498.sra Written 1065148 spots for SRR8846498.sra SRR ids: ['SRR8846498.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_zfwi8k3r SRR8846498.sra spots: 21302966 blocks: [[1, 1065148], [1065149, 2130296], [2130297, 3195444], [3195445, 4260592], [4260593, 5325740], [5325741, 6390888], [6390889, 7456036], [7456037, 8521184], [8521185, 9586332], [9586333, 10651480], [10651481, 11716628], [11716629, 12781776], [12781777, 13846924], [13846925, 14912072], [14912073, 15977220], [15977221, 17042368], [17042369, 18107516], [18107517, 19172664], [19172665, 20237812], [20237813, 21302966]] SRR8846498 file size 5116808 SRR8846498 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 SRR8846498 SRR8846498_1.fastq Input file: SRR8846498_1.fastq trimmed: SRR8846498-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 Sun Dec 8 23:45:03 2024 >> started Sun Dec 8 23:46:00 2024 >> done (56.588s) 21302966 reads processed; of these: 532 ( 0.00%) short reads filtered out after trimming by size control 81 ( 0.00%) empty reads filtered out after trimming by size control 21302353 (100.00%) reads available; of these: 4162086 (19.54%) trimmed reads available after processing 17140267 (80.46%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 60 0.00% 19 55 0.00% 20 53 0.00% 21 75 0.00% 22 68 0.00% 23 66 0.00% 24 81 0.00% 25 113 0.00% 26 110 0.00% 27 129 0.00% 28 170 0.00% 29 162 0.00% 30 168 0.00% 31 164 0.00% 32 193 0.00% 33 168 0.00% 34 231 0.00% 35 187 0.00% 36 199 0.00% 37 228 0.00% 38 223 0.00% 39 263 0.00% 40 285 0.00% 41 284 0.00% 42 310 0.00% 43 365 0.00% 44 369 0.00% 45 386 0.00% 46 456 0.00% 47 422 0.00% 48 443 0.00% 49 481 0.00% 50 452 0.00% 51 397 0.00% 52 421 0.00% 53 389 0.00% 54 352 0.00% 55 299 0.00% 56 375 0.00% 57 370 0.00% 58 440 0.00% 59 607 0.00% 60 809 0.00% 61 1096 0.01% 62 1566 0.01% 63 1814 0.01% 64 2935 0.01% 65 4113 0.02% 66 9428 0.04% 67 48005 0.23% 68 53613 0.25% 69 37519 0.18% 70 32238 0.15% 71 40073 0.19% 72 17874 0.08% 73 6209 0.03% 74 7003 0.03% 75 4356 0.02% 76 3532 0.02% 77 3879 0.02% 78 4220 0.02% 79 4718 0.02% 80 5068 0.02% 81 5535 0.03% 82 7335 0.03% 83 8110 0.04% 84 9295 0.04% 85 11150 0.05% 86 12777 0.06% 87 17436 0.08% 88 28100 0.13% 89 41752 0.20% 90 63559 0.30% 91 68465 0.32% 92 85954 0.40% 93 133498 0.63% 94 180968 0.85% 95 372543 1.75% 96 471618 2.21% 97 487843 2.29% 98 769898 3.61% 99 747822 3.51% 100 337291 1.58% 101 17140267 80.46% 21302353 reads passed initial QC criterion=sequence-density sequence-density=94.47 sequence-density-rank=1 fanout-score=30.52 fanout-score-rank=2 prefix-density=94.92 prefix-fanout=30.4 sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTAGAGATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAA criterion=fanout-score sequence-density=1.69 sequence-density-rank=5 fanout-score=58.84 fanout-score-rank=1 prefix-density=98.48 prefix-fanout=1.0 sequence=CACGTAGAGATATCGTATGCCGT Potential 3prime adapter identified. Now checking if in reference sequence Warning: gzbuffer added in zlib v1.2.3.5. Unable to change buffer size from default of 8192. 1 reads; of these: 1 (100.00%) were unpaired; of these: 1 (100.00%) aligned 0 times 0 (0.00%) aligned exactly 1 time 0 (0.00%) aligned >1 times 0.00% overall alignment rate 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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTAGAGATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAA -o SRR8846498 - Input file: STDIN trimmed: SRR8846498-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTAGAGATCTCGTATGCCGTCTTCTGCTTGA -- 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 -- minimum overlap length for adapter detection (-k): 3 -- number of concurrent threads (-t): 20 Sun Dec 8 23:49:34 2024 >> started Sun Dec 8 23:51:16 2024 >> done (102.172s) 20853883 reads processed; of these: 314245 ( 1.51%) short reads filtered out after trimming by size control 11078 ( 0.05%) empty reads filtered out after trimming by size control 20528560 (98.44%) reads available; of these: 19994625 (97.40%) trimmed reads available after processing 533935 ( 2.60%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 107417 0.52% 19 200557 0.98% 20 228165 1.11% 21 935392 4.56% 22 551565 2.69% 23 754949 3.68% 24 2667545 12.99% 25 1028938 5.01% 26 1019448 4.97% 27 1019729 4.97% 28 1212588 5.91% 29 1043016 5.08% 30 1177493 5.74% 31 767554 3.74% 32 813156 3.96% 33 1021630 4.98% 34 1154077 5.62% 35 983031 4.79% 36 1110007 5.41% 37 469581 2.29% 38 375360 1.83% 39 286055 1.39% 40 239191 1.17% 41 268479 1.31% 42 288502 1.41% 43 90853 0.44% 44 86032 0.42% 45 37851 0.18% 46 21171 0.10% 47 10511 0.05% 48 9763 0.05% 49 4462 0.02% 50 3130 0.02% 51 2667 0.01% 52 1427 0.01% 53 1095 0.01% 54 1209 0.01% 55 455 0.00% 56 605 0.00% 57 359 0.00% 58 320 0.00% 59 464 0.00% 60 595 0.00% 61 868 0.00% 62 1228 0.01% 63 1484 0.01% 64 2534 0.01% 65 3735 0.02% 66 8873 0.04% 67 46685 0.23% 68 52005 0.25% 69 36135 0.18% 70 30877 0.15% 71 38489 0.19% 72 15468 0.08% 73 4126 0.02% 74 2605 0.01% 75 1713 0.01% 76 1580 0.01% 77 2429 0.01% 78 2015 0.01% 79 2036 0.01% 80 2343 0.01% 81 1790 0.01% 82 1555 0.01% 83 1614 0.01% 84 1268 0.01% 85 1234 0.01% 86 1081 0.01% 87 938 0.00% 88 979 0.00% 89 991 0.00% 90 922 0.00% 91 1028 0.01% 92 1182 0.01% 93 1426 0.01% 94 1849 0.01% 95 2659 0.01% 96 3302 0.02% 97 4326 0.02% 98 6978 0.03% 99 7486 0.04% 100 9199 0.04% 101 223131 1.09% criterion=sequence-density sequence-density=6.64 sequence-density-rank=1 fanout-score=0.00 fanout-score-rank=14 prefix-density=0.00 prefix-fanout=1.0 sequence=CATCGAGTAGACCTTGTTATTGTGAGAATTCTTAATTCAAGAG criterion=fanout-score sequence-density=0.25 sequence-density-rank=19 fanout-score=21.95 fanout-score-rank=1 prefix-density=5.55 prefix-fanout=1.0 sequence=TTGTGAGAATTAAAAA Started job on | Dec 08 23:53:49 Started mapping on | Dec 08 23:53:50 Finished on | Dec 09 00:02:49 Mapping speed, Million of reads per hour | 140.11 Number of input reads | 20977030 Average input read length | 32 UNIQUE READS: Uniquely mapped reads number | 3583164 Uniquely mapped reads % | 17.08% Average mapped length | 26.53 Number of splices: Total | 37591 Number of splices: Annotated (sjdb) | 24277 Number of splices: GT/AG | 34502 Number of splices: GC/AG | 2358 Number of splices: AT/AC | 14 Number of splices: Non-canonical | 717 Mismatch rate per base, % | 0.12% Deletion rate per base | 0.00% Deletion average length | 1.33 Insertion rate per base | 0.00% Insertion average length | 1.02 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 8238610 % of reads mapped to multiple loci | 39.27% Number of reads mapped to too many loci | 7876993 % of reads mapped to too many loci | 37.55% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 5.42% % of reads unmapped: other | 0.67% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 9155256 9155256 9155256 N_multimapping 8238610 8238610 8238610 N_noFeature 2284255 2501723 3348349 N_ambiguous 55750 37851 740 UnstrandedReadsAssigned:1243159 PositiveStrandReadsAssigned:1043590 NegativeStrandReadsAssigned:234075 Dataset is classified unstranded MeadianReadLen=29 20thPercentileLength=24 echo kmer=19 SRR8846498 Starting Kallisto single end mapping to ensembl reference transcriptome. kmer=19 [quant] fragment length distribution is truncated gaussian with mean = 100, sd = 20 [index] k-mer length: 19 [index] number of targets: 52,972 [index] number of k-mers: 65,492,969 [index] number of equivalence classes: 320,172 [quant] running in single-end mode [quant] will process file 1: SRR8846498-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 20,977,030 reads, 6,240,384 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,115 rounds 52973 SRR8846498.ke.tsv 35125 SRR8846498.se.tsv 88098 total ==> SRR8846498.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 837 0 0 PNS24247 1044 945 0 0 PNS24249 1928 1829 0 0 PNS24246 1044 945 0 0 PNS24248 1044 945 0 0 PNS24244 1471 1372 4 0.420592 PNS24243 293 194 1 0.743624 KQK14069 1603 1504 81.6634 7.83312 KQK14071 474 375 6.62447 2.54844 ==> SRR8846498.se.tsv <== BRADI_1g14170v3 109 BRADI_1g53295v3 2 BRADI_1g59795v3 12 BRADI_1g07683v3 0 BRADI_1g00485v3 1 BRADI_1g20270v3 38 BRADI_1g74790v3 43 BRADI_1g09890v3 4 BRADI_1g77505v3 3 BRADI_1g48960v3 0 SRR8846498 completed mapping pipeline successfully