Starting /dee2/code/volunteer_pipeline.sh SRR8846501 current disk space = 1500801675264 free memory = 1374411048 SRR8846501 SRAfilesize 9e8d1adc74b29b2233a3e5f7f2e6cc07 SRR8846501.sra SRR8846501.sra file validated SRR8846501 is single end SRR8846501 is conventional basespace SRR8846501 read1 length is 101 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR8846501_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 31.212 34.0 33.0 34.0 31.0 34.0 2 32.79075 34.0 33.0 34.0 30.0 34.0 3 33.0585 34.0 33.0 34.0 32.0 34.0 4 33.241 34.0 33.0 34.0 32.0 34.0 5 33.24275 34.0 33.0 34.0 33.0 34.0 6 36.994 38.0 37.0 38.0 36.0 38.0 7 37.34125 38.0 38.0 38.0 37.0 38.0 8 37.4305 38.0 38.0 38.0 37.0 38.0 9 37.45475 38.0 38.0 38.0 37.0 38.0 10-11 37.536625 38.0 38.0 38.0 38.0 38.0 12-13 37.569374999999994 38.0 38.0 38.0 38.0 38.0 14-15 37.510999999999996 38.0 38.0 38.0 37.5 38.0 16-17 37.49925 38.0 38.0 38.0 37.5 38.0 18-19 37.494625 38.0 38.0 38.0 37.5 38.0 20-21 37.5065 38.0 38.0 38.0 38.0 38.0 22-23 37.55025 38.0 38.0 38.0 38.0 38.0 24-25 37.58025 38.0 38.0 38.0 38.0 38.0 26-27 37.5385 38.0 38.0 38.0 38.0 38.0 28-29 37.55575 38.0 38.0 38.0 38.0 38.0 30-31 37.484750000000005 38.0 38.0 38.0 38.0 38.0 32-33 37.452625 38.0 38.0 38.0 37.5 38.0 34-35 37.357875 38.0 38.0 38.0 37.5 38.0 36-37 37.189499999999995 38.0 38.0 38.0 37.0 38.0 38-39 37.128125 38.0 38.0 38.0 36.0 38.0 40-41 37.241749999999996 38.0 38.0 38.0 37.0 38.0 42-43 37.190625 38.0 38.0 38.0 37.0 38.0 44-45 37.157625 38.0 38.0 38.0 37.0 38.0 46-47 37.127624999999995 38.0 38.0 38.0 37.0 38.0 48-49 37.2325 38.0 38.0 38.0 37.0 38.0 50-51 37.2795 38.0 38.0 38.0 37.0 38.0 52-53 37.231375 38.0 38.0 38.0 37.0 38.0 54-55 37.20675 38.0 38.0 38.0 37.0 38.0 56-57 37.086 38.0 38.0 38.0 37.0 38.0 58-59 37.138875 38.0 38.0 38.0 36.5 38.0 60-61 37.10825 38.0 38.0 38.0 37.0 38.0 62-63 36.674499999999995 38.0 38.0 38.0 35.5 38.0 64-65 36.416250000000005 38.0 38.0 38.0 33.0 38.0 66-67 36.29075 38.0 37.5 38.0 32.5 38.0 68-69 36.257374999999996 38.0 38.0 38.0 33.5 38.0 70-71 35.94525 38.0 37.5 38.0 31.0 38.0 72-73 35.965875 38.0 37.5 38.0 32.0 38.0 74-75 35.641125 38.0 37.5 38.0 28.5 38.0 76-77 35.175749999999994 38.0 36.5 38.0 27.5 38.0 78-79 35.264375 38.0 36.5 38.0 28.0 38.0 80-81 35.503125 38.0 37.0 38.0 29.0 38.0 82-83 34.93475 38.0 36.5 38.0 27.0 38.0 84-85 35.337125 38.0 37.0 38.0 28.5 38.0 86-87 35.487375 38.0 37.0 38.0 30.0 38.0 88-89 35.691375 38.0 38.0 38.0 32.0 38.0 90-91 35.681875 38.0 38.0 38.0 33.0 38.0 92-93 35.63175 38.0 38.0 38.0 33.0 38.0 94-95 35.274125 38.0 38.0 38.0 31.0 38.0 96-97 34.105125 38.0 36.5 38.0 24.0 38.0 98-99 32.784125 38.0 35.0 38.0 8.5 38.0 100-101 30.642625000000002 38.0 29.5 38.0 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 6 1.0 7 0.0 8 0.0 9 0.0 10 0.0 11 0.0 12 2.0 13 0.0 14 0.0 15 0.0 16 2.0 17 0.0 18 0.0 19 1.0 20 1.0 21 2.0 22 4.0 23 7.0 24 11.0 25 29.0 26 21.0 27 17.0 28 23.0 29 18.0 30 33.0 31 69.0 32 76.0 33 103.0 34 152.0 35 306.0 36 746.0 37 2376.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 27.908217716115264 25.773745997865525 20.97118463180363 25.34685165421558 2 25.95 31.624999999999996 15.675 26.75 3 25.1 19.3 22.25 33.35 4 28.175 29.599999999999998 17.349999999999998 24.875 5 31.5 25.4 19.875 23.225 6 25.025 27.400000000000002 25.224999999999998 22.35 7 38.625 24.099999999999998 19.1 18.175 8 20.575 22.875 35.325 21.224999999999998 9 25.4 34.75 22.325 17.525 10-11 31.087500000000002 25.0125 23.375 20.525 12-13 22.787499999999998 22.2625 19.6 35.35 14-15 22.875 37.2125 23.3 16.6125 16-17 25.374999999999996 25.337500000000002 28.262500000000003 21.025 18-19 29.4875 25.874999999999996 22.85 21.7875 20-21 19.9375 27.775 29.8875 22.400000000000002 22-23 27.8875 28.325 27.287499999999998 16.5 24-25 28.15 25.35 23.7625 22.7375 26-27 32.9 26.674999999999997 20.45 19.975 28-29 21.987499999999997 28.675 25.412499999999998 23.925 30-31 25.55 23.0 32.625 18.825 32-33 24.1875 21.3125 32.65 21.85 34-35 25.8625 21.825 29.7 22.6125 36-37 32.237500000000004 17.0375 31.924999999999997 18.8 38-39 33.4875 22.5625 26.5625 17.3875 40-41 28.8875 20.625 26.737499999999997 23.75 42-43 29.4125 21.587500000000002 28.5625 20.4375 44-45 37.375 18.325 20.2875 24.0125 46-47 33.1875 26.924999999999997 16.6375 23.25 48-49 31.3 22.8 21.75 24.15 50-51 26.775 20.125 19.2125 33.887499999999996 52-53 26.200000000000003 30.45 12.125 31.225 54-55 26.337500000000002 26.85 16.8875 29.925 56-57 24.625 32.525 11.600000000000001 31.25 58-59 14.762500000000001 38.1625 13.1625 33.9125 60-61 13.2875 39.550000000000004 12.987499999999999 34.175 62-63 18.325 39.9375 10.95 30.7875 64-65 14.662500000000001 41.862500000000004 16.5125 26.9625 66-67 10.4 36.075 20.200000000000003 33.324999999999996 68-69 14.5375 36.6125 15.7625 33.0875 70-71 13.600000000000001 39.8375 21.337500000000002 25.224999999999998 72-73 18.8375 35.3125 22.1375 23.7125 74-75 17.95 27.787499999999998 22.8375 31.424999999999997 76-77 16.725 26.1 32.0125 25.162499999999998 78-79 18.462500000000002 19.787499999999998 31.324999999999996 30.425 80-81 20.6125 18.4125 31.7125 29.262500000000003 82-83 21.1375 15.137500000000001 40.1 23.625 84-85 19.8375 10.7 37.012499999999996 32.45 86-87 22.162499999999998 12.537499999999998 35.9875 29.312500000000004 88-89 18.525 23.875 36.5875 21.0125 90-91 14.787500000000001 28.1375 34.4125 22.662499999999998 92-93 16.7125 35.612500000000004 27.35 20.325 94-95 13.8875 45.2 25.324999999999996 15.587500000000002 96-97 10.7125 52.5 24.975 11.8125 98-99 9.7125 64.0 17.5 8.7875 100-101 7.5 74.7125 10.9625 6.825 >>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 0.5 26 0.5 27 0.0 28 0.0 29 0.0 30 1.0 31 4.5 32 6.5 33 7.0 34 10.0 35 9.5 36 9.5 37 12.0 38 30.0 39 45.0 40 82.0 41 134.0 42 172.0 43 288.0 44 326.5 45 317.5 46 323.0 47 294.0 48 297.0 49 297.5 50 291.0 51 204.5 52 133.0 53 168.0 54 240.5 55 178.0 56 54.5 57 24.0 58 11.0 59 8.0 60 6.0 61 4.5 62 4.5 63 2.0 64 1.0 65 1.0 66 0.0 67 0.0 68 0.5 69 0.5 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 6.3 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10-11 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 54.800000000000004 #Duplication Level Percentage of deduplicated Percentage of total 1 83.12043795620438 45.550000000000004 2 8.120437956204379 8.9 3 2.18978102189781 3.5999999999999996 4 1.551094890510949 3.4000000000000004 5 0.958029197080292 2.625 6 0.5474452554744526 1.7999999999999998 7 0.5018248175182481 1.925 8 0.45620437956204374 2.0 9 0.22810218978102187 1.125 >10 2.144160583941606 20.375 >50 0.13686131386861314 5.1 >100 0.04562043795620438 3.5999999999999996 >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 144 3.5999999999999996 No Hit AGCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGC 85 2.125 No Hit CACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGATGGAATTC 60 1.5 No Hit GGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGA 59 1.4749999999999999 RNA PCR Primer, Index 1 (100% over 22bp) TCGGACCAGGCTTCATTCCCCTGGAATTCTCGGGTGCCAAGGAACTCCAG 43 1.075 RNA PCR Primer, Index 1 (100% over 29bp) GACACGACTCTCGGCAACGGATATCTCTGGAATTCTCGGGTGCCAAGGAA 40 1.0 RNA PCR Primer, Index 1 (100% over 23bp) GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGGAATTCTCGGGTGCC 39 0.975 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTTGGAATTCTCGGGTGCCAAG 37 0.9249999999999999 No Hit GCCTTGATGGTGAAATGGTAGACACGCGAGACTCAAAATCTTGGAATTCT 33 0.8250000000000001 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATATGGAATTCTCGGGTGCCAAG 31 0.775 No Hit GACACGACTCTCGGCAACGGATATCTTGGAATTCTCGGGTGCCAAGGAAC 26 0.65 RNA PCR Primer, Index 1 (100% over 24bp) CTCTGATGATGATCAAACTAATACTTTCGTTCTTCTGGAATTCTCGGGTG 25 0.625 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTGGAATTCTCGGGTGCCAAGG 23 0.575 Illumina Small RNA Adapter 2 (100% over 21bp) AGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGG 22 0.5499999999999999 Illumina Small RNA Adapter 2 (100% over 21bp) GGAGAGATGGCTGAGTGGACTAAAGCGGCGGATTGCTAATCTGGAATTCT 20 0.5 No Hit AAGGGTGCTGAGAATACTTTGAATCTGACACTGGAATTCTCGGGTGCCAA 20 0.5 No Hit ACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGATGGAATTCT 20 0.5 No Hit AGGGCTATAGCTCAGTTCGGTAGAGCAACTCGTTTACACCGAGATGGAAT 19 0.475 No Hit TCCTGTGGATGAGAAGGCATTTATATTCTGATGATATGGAATTCTCGGGT 17 0.42500000000000004 No Hit GCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCC 17 0.42500000000000004 No Hit TCTCGGGTGCCAAGGAACTCCAGTCACCAAAAGATCTCGTATGCCGTCTT 16 0.4 RNA PCR Primer, Index 28 (100% over 50bp) CCACTGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTG 16 0.4 No Hit GAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAG 16 0.4 No Hit TGCCACGATCCACTGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAAT 16 0.4 No Hit TGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAA 16 0.4 No Hit CGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGATGGAATTCTC 15 0.375 No Hit CCAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGG 15 0.375 No Hit CTCGGGTGCCAAGGAACTCCAGTCACCAAAAGATCTCGTATGCCGTCTTC 14 0.35000000000000003 RNA PCR Primer, Index 28 (100% over 50bp) GGGATTGTAGTTCAATTGGTCAGAGCACCTGGAATTCTCGGGTGCCAAGG 14 0.35000000000000003 Illumina Small RNA Adapter 2 (100% over 21bp) AAGGGTGCTGAGAATACTTTGAATCTGACATGGAATTCTCGGGTGCCAAG 13 0.325 No Hit AATTCTCGGGTGCCAAGGAACTCCAGTCACCAAAAGATCTCGTATGCCGT 13 0.325 RNA PCR Primer, Index 28 (100% over 50bp) GCACCAGTGGTCTAGTGGTAGAATAGTACCTGGAATTCTCGGGTGCCAAG 13 0.325 No Hit GGGGATATGGCGAAATCGGTAGACGCTACGGACTTTGGAATTCTCGGGTG 13 0.325 No Hit GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGATTGTGAATCTGGAATTC 13 0.325 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCCTGGAATTCTCGGGTGC 12 0.3 No Hit GTCAGGATAGCTCAGTTGGTAGAGCAGAGGACTTGGAATTCTCGGGTGCC 12 0.3 No Hit NCCACTGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGT 11 0.27499999999999997 No Hit GACACGACTCTCGGCAACGGATATCTGGAATTCTCGGGTGCCAAGGAACT 11 0.27499999999999997 RNA PCR Primer, Index 1 (100% over 25bp) GCCCACCCCAAGATGAGTGCTCTCTCTGGAATTCTCGGGTGCCAAGGAAC 11 0.27499999999999997 RNA PCR Primer, Index 1 (100% over 24bp) TTCTCGGGTGCCAAGGAACTCCAGTCACCAAAAGATCTCGTATGCCGTCT 11 0.27499999999999997 RNA PCR Primer, Index 28 (100% over 50bp) CATCGAGTAGACCTTGTTATTGTGAGAATTCTTAATGGAATTCTCGGGTG 11 0.27499999999999997 No Hit CAGGGTTCGTTTCCCTGGATGCGCACCATGGAATTCTCGGGTGCCAAGGA 11 0.27499999999999997 RNA PCR Primer, Index 1 (100% over 22bp) CAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGGG 10 0.25 No Hit TGTATGCAGCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCT 10 0.25 No Hit ATATATTTCAAGTTATTTCGGATCTTGGAATTCTCGGGTGCCAAGGAACT 10 0.25 RNA PCR Primer, Index 1 (100% over 25bp) GATAACCGTAGTAATTCTAGAGCTAATGGAATTCTCGGGTGCCAAGGAAC 10 0.25 RNA PCR Primer, Index 1 (100% over 24bp) CACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGGAATTCTCG 10 0.25 No Hit GCCTTGATGGTGAAATGGTAGACACGCGAGACTCATGGAATTCTCGGGTG 10 0.25 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTCAAGGCTGGAATTC 10 0.25 No Hit ACTGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCC 10 0.25 No Hit TGCAGCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGG 10 0.25 No Hit CGGATAACCGTAGTAATTCTAGAGCTAATACGTGGAATTCTCGGGTGCCA 9 0.22499999999999998 No Hit GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGAATTCTCGGGTGCCAAGG 9 0.22499999999999998 Illumina Small RNA Adapter 2 (100% over 21bp) GGGATTGTAGTTCAATTGGTCAGAGCACCGCCTGGAATTCTCGGGTGCCA 9 0.22499999999999998 No Hit TCCGTCGTAGTCTAGGTGGTTAGGATATGGAATTCTCGGGTGCCAAGGAA 9 0.22499999999999998 RNA PCR Primer, Index 1 (100% over 23bp) GCGAGCGTAGTTCAATGGTAAAACATCTCCTTGCCAAGGATGGAATTCTC 9 0.22499999999999998 No Hit TCCGTCGTAGTCTAGGTGGTTAGGATACTCTGGAATTCTCGGGTGCCAAG 8 0.2 No Hit GAAGATACGGGTTCGATTCCCGCCGCTCGCCCCATGGAATTCTCGGGTGC 8 0.2 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTCAAGGTGGAATTCT 8 0.2 No Hit GCGAGCGTAGTTCAATGGTAAAACATCTCCTTGCCAAGGAGTGGAATTCT 8 0.2 No Hit CATCGAGTAGACCTTGTTATTGTGAGATGGAATTCTCGGGTGCCAAGGAA 8 0.2 RNA PCR Primer, Index 1 (100% over 23bp) CCAGGTCCAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAAT 8 0.2 No Hit TCCAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCG 8 0.2 No Hit ACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGGGTGC 8 0.2 No Hit CTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCA 8 0.2 No Hit GCCTTGATGGTGAAATGGTAGACACGCGAGACTCAAAATCTGGAATTCTC 8 0.2 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATAAATGGAATTCTCGGGTGCCA 7 0.17500000000000002 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATGGAATTCTCGGGTGCCAAGGA 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 22bp) CATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGGGTGCC 7 0.17500000000000002 No Hit NACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGATGGAATTC 7 0.17500000000000002 No Hit GACACGACTCTCGGCAACGGATATCTCGGCTCTCGCTGGAATTCTCGGGT 7 0.17500000000000002 No Hit TGCAAGTATGAACTAATTTGAACTGTGAAACTTGGAATTCTCGGGTGCCA 7 0.17500000000000002 No Hit NCGGACCAGGCTTCATTCCCCTGGAATTCTCGGGTGCCAAGGAACTCCAG 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 29bp) CACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGTGGAATTCTCGG 7 0.17500000000000002 No Hit ACACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGATGGAATT 7 0.17500000000000002 No Hit ATTCTCGGGTGCCAAGGAACTCCAGTCACCAAAAGATCTCGTATGCCGTC 7 0.17500000000000002 RNA PCR Primer, Index 28 (100% over 50bp) GACACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGTGGAATTCTC 7 0.17500000000000002 No Hit CACGACTCTCGGCAACGGATATCTCTGGAATTCTCGGGTGCCAAGGAACT 6 0.15 RNA PCR Primer, Index 1 (100% over 25bp) GACACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGATGGAAT 6 0.15 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATAAAAAATGGAATTCTCGGGTG 6 0.15 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATAAAAATGGAATTCTCGGGTGC 6 0.15 No Hit TCCCGTGCTGTAAAATAACTGATTTGCCTATCTGATCTGGAATTCTCGGG 6 0.15 No Hit CAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTTGAATTCTCGGG 6 0.15 No Hit TTCATGGACGTTGATAAGATCCTTCCTGGAATTCTCGGGTGCCAAGGAAC 6 0.15 RNA PCR Primer, Index 1 (100% over 24bp) CACGACTCTCGGCAACGGATATCTCGTGGAATTCTCGGGTGCCAAGGAAC 6 0.15 RNA PCR Primer, Index 1 (100% over 24bp) NGCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGC 6 0.15 No Hit TTTGGATTGAAGGGAGCTCTGTGGAATTCTCGGGTGCCAAGGAACTCCAG 6 0.15 RNA PCR Primer, Index 1 (100% over 29bp) CATCGAGTAGACCTTGTTATTGTGAGAATTCTAAAATGGAATTCTCGGGT 6 0.15 No Hit CACTGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGC 6 0.15 No Hit NGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGGAATTCTCGGGTGCC 5 0.125 No Hit GTCCAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTC 5 0.125 No Hit GATCCACTGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGG 5 0.125 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATAAAATGGAATTCTCGGGTGCC 5 0.125 No Hit ATAACCGTAGTAATTCTAGAGCTAATTGGAATTCTCGGGTGCCAAGGAAC 5 0.125 RNA PCR Primer, Index 1 (100% over 24bp) GACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGGGTG 5 0.125 No Hit AAGTATGAACTAATTTGAACTGTGAAACTTGGAATTCTCGGGTGCCAAGG 5 0.125 Illumina Small RNA Adapter 2 (100% over 21bp) GCAGTGATGTATGCAGCTGAGGCATCCTAACGAACGAACGATTTGAACTG 5 0.125 No Hit GCCTTGATGGTGAAATGGTAGACACGCGAGACTTGGAATTCTCGGGTGCC 5 0.125 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTCAAGGCGTGGAATT 5 0.125 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTCTAATGGAATTCTCGGGTGC 5 0.125 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATAAAAAAAATGGAATTCTCGGG 5 0.125 No Hit ATGCAGTTACTAATTCATGATCTGGCTGGAATTCTCGGGTGCCAAGGAAC 5 0.125 RNA PCR Primer, Index 1 (100% over 24bp) ACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTTGAATTCTCGGGTGC 5 0.125 No Hit CTGCCACGATCCACTGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAA 5 0.125 No Hit CCAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTTGAATTCTCGG 5 0.125 No Hit CCTCCTGGGAAGTCCTCGTGTTGCATTCCTTGGAATTCTCGGGTGCCAAG 5 0.125 No Hit CGGATAACCGTAGTAATTCTAGAGCTAATACTGGAATTCTCGGGTGCCAA 5 0.125 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTCTAAATGGAATTCTCGGGTG 5 0.125 No Hit TAACCGTAGTAATTCTAGAGCTAATGGAATTCTCGGGTGCCAAGGAACTC 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 0.1 0.0 0.0 0.0 2 0.0 0.1 0.0 0.0 0.0 3 0.0 0.1 0.0 0.0 0.0 4 0.0 0.1 0.0 0.0 0.0 5 0.0 0.1 0.0 0.0 0.0 6 0.0 0.1 0.0 0.0 0.0 7 0.0 0.125 0.0 0.0 0.0 8 0.0 0.125 0.0 0.0 0.0 9 0.0 0.15 0.0 0.0 0.0 10-11 0.0 0.225 0.0 0.0 0.0 12-13 0.0 0.36250000000000004 0.0 0.0 0.0 14-15 0.0 0.625 0.0 0.0 0.0 16-17 0.0 0.9625 0.0 0.0 0.0 18-19 0.0 1.2999999999999998 0.0 0.0 0.0 20-21 0.0 2.4 0.0 0.0 0.0 22-23 0.0 6.3 0.0 0.0 0.0 24-25 0.0 12.850000000000001 0.0 0.0 0.0 26-27 0.0 21.775 0.0 0.0 0.0 28-29 0.0 29.2875 0.0 0.0 0.0 30-31 0.0 38.6125 0.0 0.0 0.0 32-33 0.0 46.5 0.0 0.0 0.0 34-35 0.0 56.1875 0.0 0.0 0.0 36-37 0.0 68.1 0.0 0.0 0.0 38-39 0.0 75.75 0.0 0.0 0.0 40-41 0.0 80.35 0.0 0.0 0.0 42-43 0.0 87.225 0.0 0.0 0.0 44-45 0.0 91.3125 0.0 0.0 0.0 46-47 0.0 93.48750000000001 0.0 0.0 0.0 48-49 0.0 94.07499999999999 0.0 0.0 0.0 50-51 0.0 94.5375 0.0 0.0 0.0 52-53 0.0 94.6875 0.0 0.0 0.0 54-55 0.0 94.7375 0.0 0.0 0.0 56-57 0.0 94.8375 0.0 0.0 0.0 58-59 0.0 94.9 0.0 0.0 0.0 60-61 0.0 94.9 0.0 0.0 0.0 62-63 0.0 94.9 0.0 0.0 0.0 64-65 0.0 94.9 0.0 0.0 0.0 66-67 0.0 94.9 0.0 0.0 0.0 68-69 0.0 94.9 0.0 0.0 0.0 70-71 0.0 94.9 0.0 0.0 0.0 72-73 0.0 94.9 0.0 0.0 0.0 74-75 0.0 94.9 0.0 0.0 0.0 76-77 0.0 94.9 0.0 0.0 0.0 78-79 0.0 94.95 0.0 0.0 0.0 80-81 0.0 94.9625 0.0 0.0 0.0 82-83 0.0 94.9875 0.0 0.0 0.0 84-85 0.0 95.025 0.0 0.0 0.0 86-87 0.0 95.025 0.0 0.0 0.0 88-89 0.0 95.025 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GGAGAGA 15 5.268781E-4 98.66234 1 CATCGAG 30 7.195922E-9 98.66234 1 GTAGACC 35 2.3283064E-10 94.96251 7 AGTAGAC 35 2.3283064E-10 94.96251 6 GAGTAGA 35 2.3283064E-10 94.96251 5 CGAGTAG 35 2.3283064E-10 94.96251 4 AGACCTT 35 2.3283064E-10 94.96251 9 ATCGAGT 35 2.3283064E-10 94.96251 2 TCGAGTA 35 2.3283064E-10 94.96251 3 TAGACCT 35 2.3283064E-10 94.96251 8 TGGTCTA 15 6.1518257E-4 94.962494 8 GATGGCT 15 6.1518257E-4 94.962494 6 CCAGTGG 15 6.1518257E-4 94.962494 4 GGTCTAG 15 6.1518257E-4 94.962494 9 AGTGGTC 15 6.1518257E-4 94.962494 6 ATGGCTG 15 6.1518257E-4 94.962494 7 GGCTGAG 15 6.1518257E-4 94.962494 9 CACCAGT 15 6.1518257E-4 94.962494 2 AGATGGC 15 6.1518257E-4 94.962494 5 GAGAGAT 15 6.1518257E-4 94.962494 2 >>END_MODULE Rejected 786785 READS because READLEN < 1 Read 786785 spots for SRR8846501.sra Written 786785 spots for SRR8846501.sra Rejected 786785 READS because READLEN < 1 Read 786785 spots for SRR8846501.sra Written 786785 spots for SRR8846501.sra Rejected 786785 READS because READLEN < 1 Read 786785 spots for SRR8846501.sra Written 786785 spots for SRR8846501.sra Rejected 786785 READS because READLEN < 1 Read 786785 spots for SRR8846501.sra Written 786785 spots for SRR8846501.sra Rejected 786785 READS because READLEN < 1 Read 786785 spots for SRR8846501.sra Written 786785 spots for SRR8846501.sra Rejected 786785 READS because READLEN < 1 Read 786785 spots for SRR8846501.sra Written 786785 spots for SRR8846501.sra Rejected 786785 READS because READLEN < 1 Read 786785 spots for SRR8846501.sra Written 786785 spots for SRR8846501.sra Rejected 786785 READS because READLEN < 1 Read 786785 spots for SRR8846501.sra Written 786785 spots for SRR8846501.sra Rejected 786785 READS because READLEN < 1 Read 786785 spots for SRR8846501.sra Written 786785 spots for SRR8846501.sra Rejected 786785 READS because READLEN < 1 Read 786785 spots for SRR8846501.sra Written 786785 spots for SRR8846501.sra Rejected 786785 READS because READLEN < 1 Read 786785 spots for SRR8846501.sra Written 786785 spots for SRR8846501.sra Rejected 786785 READS because READLEN < 1 Read 786785 spots for SRR8846501.sra Written 786785 spots for SRR8846501.sra Rejected 786785 READS because READLEN < 1 Read 786785 spots for SRR8846501.sra Written 786785 spots for SRR8846501.sra Rejected 786785 READS because READLEN < 1 Read 786785 spots for SRR8846501.sra Written 786785 spots for SRR8846501.sra Rejected 786785 READS because READLEN < 1 Read 786785 spots for SRR8846501.sra Written 786785 spots for SRR8846501.sra Rejected 786785 READS because READLEN < 1 Read 786785 spots for SRR8846501.sra Written 786785 spots for SRR8846501.sra Rejected 786785 READS because READLEN < 1 Read 786785 spots for SRR8846501.sra Written 786785 spots for SRR8846501.sra Rejected 786785 READS because READLEN < 1 Read 786785 spots for SRR8846501.sra Written 786785 spots for SRR8846501.sra Rejected 786792 READS because READLEN < 1 Read 786792 spots for SRR8846501.sra Written 786792 spots for SRR8846501.sra Rejected 786785 READS because READLEN < 1 Read 786785 spots for SRR8846501.sra Written 786785 spots for SRR8846501.sra SRR ids: ['SRR8846501.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_eh9scndu SRR8846501.sra spots: 15735707 blocks: [[1, 786785], [786786, 1573570], [1573571, 2360355], [2360356, 3147140], [3147141, 3933925], [3933926, 4720710], [4720711, 5507495], [5507496, 6294280], [6294281, 7081065], [7081066, 7867850], [7867851, 8654635], [8654636, 9441420], [9441421, 10228205], [10228206, 11014990], [11014991, 11801775], [11801776, 12588560], [12588561, 13375345], [13375346, 14162130], [14162131, 14948915], [14948916, 15735707]] SRR8846501 file size 3773924 SRR8846501 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 SRR8846501 SRR8846501_1.fastq Input file: SRR8846501_1.fastq trimmed: SRR8846501-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 Mon Dec 9 01:02:41 2024 >> started Mon Dec 9 01:03:23 2024 >> done (41.665s) 15735707 reads processed; of these: 284 ( 0.00%) short reads filtered out after trimming by size control 42 ( 0.00%) empty reads filtered out after trimming by size control 15735381 (100.00%) reads available; of these: 2009064 (12.77%) trimmed reads available after processing 13726317 (87.23%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 35 0.00% 19 33 0.00% 20 33 0.00% 21 25 0.00% 22 34 0.00% 23 44 0.00% 24 60 0.00% 25 72 0.00% 26 71 0.00% 27 101 0.00% 28 118 0.00% 29 141 0.00% 30 117 0.00% 31 123 0.00% 32 143 0.00% 33 169 0.00% 34 179 0.00% 35 155 0.00% 36 213 0.00% 37 166 0.00% 38 184 0.00% 39 242 0.00% 40 354 0.00% 41 463 0.00% 42 583 0.00% 43 608 0.00% 44 527 0.00% 45 509 0.00% 46 435 0.00% 47 352 0.00% 48 387 0.00% 49 509 0.00% 50 582 0.00% 51 609 0.00% 52 545 0.00% 53 462 0.00% 54 369 0.00% 55 224 0.00% 56 242 0.00% 57 233 0.00% 58 202 0.00% 59 267 0.00% 60 284 0.00% 61 525 0.00% 62 710 0.00% 63 920 0.01% 64 1897 0.01% 65 2770 0.02% 66 7607 0.05% 67 42149 0.27% 68 47192 0.30% 69 32870 0.21% 70 28270 0.18% 71 33362 0.21% 72 15133 0.10% 73 5508 0.04% 74 8518 0.05% 75 5511 0.04% 76 4246 0.03% 77 3711 0.02% 78 4732 0.03% 79 4905 0.03% 80 5577 0.04% 81 5903 0.04% 82 8659 0.06% 83 8090 0.05% 84 7662 0.05% 85 8296 0.05% 86 9003 0.06% 87 10273 0.07% 88 14760 0.09% 89 19066 0.12% 90 29522 0.19% 91 29054 0.18% 92 36166 0.23% 93 57152 0.36% 94 72993 0.46% 95 166417 1.06% 96 190881 1.21% 97 203110 1.29% 98 319592 2.03% 99 355551 2.26% 100 189597 1.20% 101 13726317 87.23% 15735381 reads passed initial QC criterion=sequence-density sequence-density=94.42 sequence-density-rank=1 fanout-score=31.50 fanout-score-rank=2 prefix-density=94.81 prefix-fanout=31.4 sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAAAAGATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAA criterion=fanout-score sequence-density=1.33 sequence-density-rank=6 fanout-score=74.43 fanout-score-rank=1 prefix-density=98.34 prefix-fanout=1.0 sequence=CACCAAAAGATATCGTATGCCGT 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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAAAAGATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAA -o SRR8846501 - Input file: STDIN trimmed: SRR8846501-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAAAAGATCTCGTATGCCGTCTTCTGCTTGA -- 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 Mon Dec 9 01:06:05 2024 >> started Mon Dec 9 01:07:19 2024 >> done (73.767s) 15404110 reads processed; of these: 159625 ( 1.04%) short reads filtered out after trimming by size control 15847 ( 0.10%) empty reads filtered out after trimming by size control 15228638 (98.86%) reads available; of these: 14771612 (97.00%) trimmed reads available after processing 457026 ( 3.00%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 42145 0.28% 19 75119 0.49% 20 93517 0.61% 21 395494 2.60% 22 211523 1.39% 23 330979 2.17% 24 1330270 8.74% 25 511268 3.36% 26 537297 3.53% 27 567079 3.72% 28 666197 4.37% 29 650535 4.27% 30 850728 5.59% 31 575731 3.78% 32 569635 3.74% 33 805893 5.29% 34 947937 6.22% 35 797238 5.24% 36 1092364 7.17% 37 461374 3.03% 38 409747 2.69% 39 390379 2.56% 40 381635 2.51% 41 552698 3.63% 42 578707 3.80% 43 232834 1.53% 44 283681 1.86% 45 140615 0.92% 46 88076 0.58% 47 50532 0.33% 48 47629 0.31% 49 25912 0.17% 50 19469 0.13% 51 17664 0.12% 52 8883 0.06% 53 5972 0.04% 54 8846 0.06% 55 2273 0.01% 56 2446 0.02% 57 1285 0.01% 58 898 0.01% 59 713 0.00% 60 543 0.00% 61 841 0.01% 62 731 0.00% 63 922 0.01% 64 1869 0.01% 65 2624 0.02% 66 7386 0.05% 67 41175 0.27% 68 46055 0.30% 69 31962 0.21% 70 27478 0.18% 71 32286 0.21% 72 13562 0.09% 73 3765 0.02% 74 2606 0.02% 75 2118 0.01% 76 2704 0.02% 77 3596 0.02% 78 2861 0.02% 79 3058 0.02% 80 4980 0.03% 81 3774 0.02% 82 3388 0.02% 83 3636 0.02% 84 2039 0.01% 85 1957 0.01% 86 1677 0.01% 87 1416 0.01% 88 1127 0.01% 89 1222 0.01% 90 1115 0.01% 91 1062 0.01% 92 1157 0.01% 93 1480 0.01% 94 1453 0.01% 95 2013 0.01% 96 2768 0.02% 97 3851 0.03% 98 5438 0.04% 99 6053 0.04% 100 7242 0.05% 101 178431 1.17% criterion=sequence-density sequence-density=7.06 sequence-density-rank=1 fanout-score=0.00 fanout-score-rank=14 prefix-density=0.00 prefix-fanout=1.0 sequence=CATCGAGTAGACCTTGTTATTGTGAGAATTCTTAA criterion=fanout-score sequence-density=0.01 sequence-density-rank=40 fanout-score=163.47 fanout-score-rank=1 prefix-density=0.91 prefix-fanout=1.0 sequence=AGCCAAGTGCGGAGAGGATAACTGCTGAAAGCATATAAGTAGTAAGCCCACCCCAAGATGAGTGCTCTCTCCTCCGACTTC Started job on | Dec 09 01:09:41 Started mapping on | Dec 09 01:09:42 Finished on | Dec 09 01:17:30 Mapping speed, Million of reads per hour | 119.69 Number of input reads | 15559909 Average input read length | 35 UNIQUE READS: Uniquely mapped reads number | 2387854 Uniquely mapped reads % | 15.35% Average mapped length | 29.23 Number of splices: Total | 28042 Number of splices: Annotated (sjdb) | 17048 Number of splices: GT/AG | 24732 Number of splices: GC/AG | 2147 Number of splices: AT/AC | 23 Number of splices: Non-canonical | 1140 Mismatch rate per base, % | 0.15% Deletion rate per base | 0.00% Deletion average length | 1.27 Insertion rate per base | 0.00% Insertion average length | 1.03 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 5608009 % of reads mapped to multiple loci | 36.04% Number of reads mapped to too many loci | 6525692 % of reads mapped to too many loci | 41.94% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 6.12% % of reads unmapped: other | 0.55% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 7564046 7564046 7564046 N_multimapping 5608009 5608009 5608009 N_noFeature 1302268 1509757 2167669 N_ambiguous 51455 38527 421 UnstrandedReadsAssigned:1034131 PositiveStrandReadsAssigned:839570 NegativeStrandReadsAssigned:219764 Dataset is classified unstranded MeadianReadLen=33 20thPercentileLength=26 echo kmer=21 SRR8846501 Starting Kallisto single end mapping to ensembl reference transcriptome. kmer=21 [quant] fragment length distribution is truncated gaussian with mean = 100, sd = 20 [index] k-mer length: 21 [index] number of targets: 52,972 [index] number of k-mers: 65,978,135 [index] number of equivalence classes: 190,841 [quant] running in single-end mode [quant] will process file 1: SRR8846501-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 15,559,909 reads, 4,230,354 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,002 rounds 52973 SRR8846501.ke.tsv 35125 SRR8846501.se.tsv 88098 total ==> SRR8846501.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 837 6 1.44091 PNS24247 1044 945 0 0 PNS24249 1928 1829 0 0 PNS24246 1044 945 0 0 PNS24248 1044 945 0 0 PNS24244 1471 1372 0 0 PNS24243 293 194 0 0 KQK14069 1603 1504 246.514 32.9462 KQK14071 474 375 7.79898 4.1804 ==> SRR8846501.se.tsv <== BRADI_1g14170v3 290 BRADI_1g53295v3 1 BRADI_1g59795v3 7 BRADI_1g07683v3 0 BRADI_1g00485v3 4 BRADI_1g20270v3 24 BRADI_1g74790v3 9 BRADI_1g09890v3 0 BRADI_1g77505v3 8 BRADI_1g48960v3 0 SRR8846501 completed mapping pipeline successfully