Starting /dee2/code/volunteer_pipeline.sh SRR8846488 current disk space = 1502850465792 free memory = 1351213808 SRR8846488 SRAfilesize db975733bd4f959fbd46f27cedb301dc SRR8846488.sra SRR8846488.sra file validated SRR8846488 is single end SRR8846488 is conventional basespace SRR8846488 read1 length is 101 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR8846488_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 fail #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 30.8105 34.0 33.0 34.0 27.0 34.0 2 32.842 34.0 33.0 34.0 28.0 34.0 3 33.01875 34.0 33.0 34.0 32.0 34.0 4 33.28225 34.0 33.0 34.0 32.0 34.0 5 33.28625 34.0 33.0 34.0 33.0 34.0 6 36.9765 38.0 37.0 38.0 36.0 38.0 7 37.23125 38.0 38.0 38.0 36.0 38.0 8 37.39575 38.0 38.0 38.0 37.0 38.0 9 37.5005 38.0 38.0 38.0 37.0 38.0 10-11 37.50075 38.0 38.0 38.0 37.5 38.0 12-13 37.5215 38.0 38.0 38.0 38.0 38.0 14-15 37.425 38.0 38.0 38.0 37.0 38.0 16-17 37.43325 38.0 38.0 38.0 37.0 38.0 18-19 37.52575 38.0 38.0 38.0 37.5 38.0 20-21 37.457125000000005 38.0 38.0 38.0 37.0 38.0 22-23 37.418625000000006 38.0 38.0 38.0 37.0 38.0 24-25 37.533875 38.0 38.0 38.0 37.5 38.0 26-27 37.425124999999994 38.0 38.0 38.0 37.0 38.0 28-29 37.435500000000005 38.0 38.0 38.0 37.0 38.0 30-31 37.4405 38.0 38.0 38.0 37.0 38.0 32-33 37.419624999999996 38.0 38.0 38.0 37.0 38.0 34-35 37.250125 38.0 38.0 38.0 37.0 38.0 36-37 37.141999999999996 38.0 38.0 38.0 36.5 38.0 38-39 37.036625 38.0 38.0 38.0 36.0 38.0 40-41 37.123000000000005 38.0 38.0 38.0 36.0 38.0 42-43 36.96525 38.0 38.0 38.0 36.0 38.0 44-45 36.961 38.0 38.0 38.0 36.0 38.0 46-47 37.04075 38.0 38.0 38.0 36.0 38.0 48-49 37.14175 38.0 38.0 38.0 36.0 38.0 50-51 37.0595 38.0 38.0 38.0 36.0 38.0 52-53 37.084374999999994 38.0 38.0 38.0 36.0 38.0 54-55 36.943125 38.0 38.0 38.0 36.0 38.0 56-57 36.733999999999995 38.0 38.0 38.0 35.5 38.0 58-59 36.654375 38.0 38.0 38.0 34.0 38.0 60-61 36.040875 38.0 37.0 38.0 32.0 38.0 62-63 36.077 38.0 37.0 38.0 32.0 38.0 64-65 35.891125 38.0 37.0 38.0 30.0 38.0 66-67 35.787375 38.0 37.0 38.0 29.5 38.0 68-69 35.74575 38.0 37.0 38.0 30.0 38.0 70-71 35.775000000000006 38.0 37.0 38.0 30.0 38.0 72-73 35.731750000000005 38.0 37.0 38.0 31.0 38.0 74-75 35.57525 38.0 37.0 38.0 30.0 38.0 76-77 35.2175 38.0 36.5 38.0 28.5 38.0 78-79 34.921375 38.0 36.0 38.0 27.5 38.0 80-81 34.73975 38.0 36.0 38.0 27.0 38.0 82-83 34.5965 38.0 35.5 38.0 26.0 38.0 84-85 34.53075 38.0 35.0 38.0 26.0 38.0 86-87 34.522875 38.0 35.5 38.0 26.0 38.0 88-89 34.925749999999994 38.0 36.0 38.0 27.5 38.0 90-91 34.4945 38.0 36.0 38.0 25.5 38.0 92-93 34.16325 38.0 35.5 38.0 25.0 38.0 94-95 32.839124999999996 38.0 34.0 38.0 14.5 38.0 96-97 30.917625 38.0 32.5 38.0 2.0 38.0 98-99 27.776875 37.5 15.0 38.0 2.0 38.0 100-101 24.01175 34.5 2.0 38.0 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 12 2.0 13 0.0 14 0.0 15 1.0 16 2.0 17 0.0 18 1.0 19 1.0 20 1.0 21 0.0 22 7.0 23 10.0 24 10.0 25 32.0 26 21.0 27 26.0 28 37.0 29 31.0 30 59.0 31 92.0 32 127.0 33 200.0 34 297.0 35 532.0 36 948.0 37 1563.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 25.41049798115747 29.50201884253028 21.80349932705249 23.283983849259755 2 22.225 30.475 21.25 26.05 3 27.0 23.075000000000003 23.0 26.924999999999997 4 27.800000000000004 28.7 18.4 25.1 5 29.599999999999998 27.650000000000002 19.375 23.375 6 25.8 28.925 23.75 21.525 7 32.2 27.6 18.975 21.224999999999998 8 22.025 24.075 32.125 21.775 9 26.85 31.45 22.15 19.55 10-11 29.6625 26.787499999999998 23.225 20.325 12-13 23.7375 23.0375 22.5625 30.662499999999998 14-15 23.0375 32.5375 24.525 19.900000000000002 16-17 24.55 27.3625 29.2875 18.8 18-19 28.9875 26.0625 23.325000000000003 21.625 20-21 23.2625 27.3625 27.450000000000003 21.925 22-23 28.65 27.212500000000002 27.750000000000004 16.3875 24-25 27.712500000000002 25.8125 27.737499999999997 18.7375 26-27 35.1875 25.337500000000002 23.925 15.55 28-29 22.3125 32.2625 26.375 19.05 30-31 22.912499999999998 18.65 39.9125 18.525 32-33 27.462500000000002 16.2 33.5875 22.75 34-35 32.65 16.5625 28.5875 22.2 36-37 39.725 14.0875 28.012500000000003 18.175 38-39 33.4125 17.7375 27.700000000000003 21.15 40-41 29.2 19.525000000000002 21.15 30.125 42-43 30.8125 28.6375 18.875 21.675 44-45 39.137499999999996 22.0 15.5 23.3625 46-47 28.6125 30.862499999999997 14.5875 25.937500000000004 48-49 24.45 25.3125 18.8125 31.424999999999997 50-51 24.3625 23.375 14.649999999999999 37.6125 52-53 24.425 33.2125 12.4375 29.925 54-55 19.7375 25.662499999999998 18.7 35.9 56-57 19.45 31.0375 13.425 36.0875 58-59 23.25 24.7875 17.8125 34.150000000000006 60-61 16.8 28.6875 25.900000000000002 28.6125 62-63 20.8 22.9375 28.175 28.0875 64-65 17.25 25.424999999999997 30.887500000000003 26.437500000000004 66-67 16.7125 19.375 33.275 30.6375 68-69 22.175 19.125 29.799999999999997 28.9 70-71 20.4875 22.125 34.887499999999996 22.5 72-73 24.7 14.799999999999999 36.3625 24.1375 74-75 19.6 12.237499999999999 32.8125 35.35 76-77 21.3625 11.0375 41.112500000000004 26.487500000000004 78-79 18.25 8.1125 41.6875 31.95 80-81 19.2625 8.6375 39.6625 32.4375 82-83 22.6125 9.8375 42.4875 25.0625 84-85 19.3625 12.862499999999999 38.6125 29.1625 86-87 21.2875 20.6125 35.85 22.25 88-89 15.137500000000001 38.9 28.787499999999998 17.175 90-91 11.200000000000001 47.55 26.8625 14.387500000000001 92-93 11.637500000000001 55.900000000000006 20.5625 11.899999999999999 94-95 9.4 65.85 16.1 8.649999999999999 96-97 6.8875 73.275 14.387500000000001 5.45 98-99 6.075 80.4125 9.5 4.0125 100-101 4.5375 83.92500000000001 7.6625 3.875 >>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 1.0 32 1.5 33 2.0 34 3.0 35 5.5 36 9.0 37 10.5 38 15.0 39 45.0 40 76.5 41 127.5 42 210.5 43 271.0 44 379.5 45 428.0 46 396.5 47 385.0 48 348.5 49 300.0 50 264.5 51 206.5 52 140.0 53 102.0 54 72.0 55 80.0 56 61.5 57 19.5 58 11.5 59 9.5 60 6.5 61 5.5 62 3.5 63 1.0 64 0.0 65 0.0 66 0.5 67 0.5 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 7.124999999999999 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 65.525 #Duplication Level Percentage of deduplicated Percentage of total 1 86.57001144601297 56.725 2 6.4860740175505525 8.5 3 2.1365890881343 4.2 4 1.2590614269362839 3.3000000000000003 5 0.7249141549027089 2.375 6 0.5723006486074018 2.25 7 0.38153376573826786 1.7500000000000002 8 0.22892025944296068 1.2 9 0.22892025944296068 1.35 >10 1.3735215566577643 16.675 >50 0.03815337657382679 1.675 >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 TCGGACCAGGCTTCATTCCCCTGGAATTCTCGGGTGCCAAGGAACTCCAG 67 1.675 RNA PCR Primer, Index 1 (100% over 29bp) TCCACTGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGT 40 1.0 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTTGGAATTCTCGGGTGCCAAG 37 0.9249999999999999 No Hit AGCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGC 35 0.8750000000000001 No Hit AGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGG 33 0.8250000000000001 Illumina Small RNA Adapter 2 (100% over 21bp) CATCGAGTAGACCTTGTTATTGTGAGAATATGGAATTCTCGGGTGCCAAG 30 0.75 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGGAATTCTCGGGTGCC 28 0.7000000000000001 No Hit GACACGACTCTCGGCAACGGATATCTCTGGAATTCTCGGGTGCCAAGGAA 26 0.65 RNA PCR Primer, Index 1 (100% over 23bp) CTCTGATGATGATCAAACTAATACTTTCGTTCTTCTGGAATTCTCGGGTG 25 0.625 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTGGAATTCTCGGGTGCCAAGG 25 0.625 Illumina Small RNA Adapter 2 (100% over 21bp) ATATATTTCAAGTTATTTCGGATCTTGGAATTCTCGGGTGCCAAGGAACT 24 0.6 RNA PCR Primer, Index 1 (100% over 25bp) GGGATTGTAGTTCAATTGGTCAGAGCACCTGGAATTCTCGGGTGCCAAGG 22 0.5499999999999999 Illumina Small RNA Adapter 2 (100% over 21bp) GGGATTGTAGTTCAATTGGTCAGAGCACCGCCTGGAATTCTCGGGTGCCA 20 0.5 No Hit GACACGACTCTCGGCAACGGATATCTTGGAATTCTCGGGTGCCAAGGAAC 19 0.475 RNA PCR Primer, Index 1 (100% over 24bp) GGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGA 18 0.44999999999999996 RNA PCR Primer, Index 1 (100% over 22bp) GACACGACTCTCGGCAACGGATATCTGGAATTCTCGGGTGCCAAGGAACT 18 0.44999999999999996 RNA PCR Primer, Index 1 (100% over 25bp) TGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAA 18 0.44999999999999996 No Hit AATTCTCGGGTGCCAAGGAACTCCAGTCACCGATGTATCTCGTATGCCGT 17 0.42500000000000004 RNA PCR Primer, Index 2 (100% over 50bp) TTCGGACCAGGCTTCATTCCCTGGAATTCTCGGGTGCCAAGGAACTCCAG 16 0.4 RNA PCR Primer, Index 1 (100% over 29bp) GAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAG 15 0.375 No Hit TAATTCATGATCTGGCATGTGGAATTCTCGGGTGCCAAGGAACTCCAGTC 14 0.35000000000000003 RNA PCR Primer, Index 1 (100% over 31bp) GCACCAGTGGTCTAGTGGTAGAATAGTACCTGGAATTCTCGGGTGCCAAG 14 0.35000000000000003 No Hit CACGACTCTCGGCAACGGATATCTGGAATTCTCGGGTGCCAAGGAACTCC 14 0.35000000000000003 RNA PCR Primer, Index 1 (100% over 27bp) TCTCGGGTGCCAAGGAACTCCAGTCACCGATGTATCTCGTATGCCGTCTT 14 0.35000000000000003 RNA PCR Primer, Index 2 (100% over 50bp) CAGGGTTCGTTTCCCTGGATGCGCACCATGGAATTCTCGGGTGCCAAGGA 14 0.35000000000000003 RNA PCR Primer, Index 1 (100% over 22bp) CAGCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTG 13 0.325 No Hit ACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGGGTGC 13 0.325 No Hit AGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCCAAGGAACTCC 12 0.3 RNA PCR Primer, Index 1 (100% over 27bp) CGGATAACCGTAGTAATTCTAGAGCTAATACGTGGAATTCTCGGGTGCCA 11 0.27499999999999997 No Hit CTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCA 11 0.27499999999999997 RNA PCR Primer, Index 1 (100% over 28bp) CCAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTTGAATTCTCGG 11 0.27499999999999997 No Hit CAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGGG 10 0.25 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATGGAATTCTCGGGTGCCAAGGA 10 0.25 RNA PCR Primer, Index 1 (100% over 22bp) CATCGAGTAGACCTTGTTATTGTGAGATGGAATTCTCGGGTGCCAAGGAA 10 0.25 RNA PCR Primer, Index 1 (100% over 23bp) CCAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGG 10 0.25 No Hit GCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCC 10 0.25 No Hit ACTGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCC 10 0.25 No Hit GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGAATTCTCGGGTGCCAAGG 9 0.22499999999999998 Illumina Small RNA Adapter 2 (100% over 21bp) GACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGGGTG 9 0.22499999999999998 No Hit GGGGATATGGCGAAATCGGTAGACGCTACGGACTTTGGAATTCTCGGGTG 9 0.22499999999999998 No Hit TCCAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCG 9 0.22499999999999998 No Hit NCGGACCAGGCTTCATTCCCCTGGAATTCTCGGGTGCCAAGGAACTCCAG 9 0.22499999999999998 RNA PCR Primer, Index 1 (100% over 29bp) CTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCA 9 0.22499999999999998 No Hit CCACTGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTG 8 0.2 No Hit ACACGACTCTCGGCAACGGATATCTTGGAATTCTCGGGTGCCAAGGAACT 8 0.2 RNA PCR Primer, Index 1 (100% over 25bp) CTCGGGTGCCAAGGAACTCCAGTCACCGATGTATCTCGTATGCCGTCTTC 8 0.2 RNA PCR Primer, Index 2 (100% over 50bp) ACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTTGAATTCTCGGGTGC 8 0.2 No Hit GCCTTGATGGTGAAATGGTAGACACGCGAGACTCATGGAATTCTCGGGTG 8 0.2 No Hit GCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAA 8 0.2 RNA PCR Primer, Index 1 (100% over 23bp) CACGACTCTCGGCAACGGATATCTCTGGAATTCTCGGGTGCCAAGGAACT 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 25bp) TCCGTCGTAGTCTAGGTGGTTAGGATACTCTGGAATTCTCGGGTGCCAAG 7 0.17500000000000002 No Hit AGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGGGT 7 0.17500000000000002 No Hit TTCTCGGGTGCCAAGGAACTCCAGTCACCGATGTATCTCGTATGCCGTCT 7 0.17500000000000002 RNA PCR Primer, Index 2 (100% over 50bp) ATATATTTCAAGTTATTTCGGATCTGGAATTCTCGGGTGCCAAGGAACTC 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 26bp) CAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTTGAATTCTCGGG 7 0.17500000000000002 No Hit TGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCCAA 7 0.17500000000000002 No Hit TCAAAAGAGGAAAGGCTTGCGGTGGAATTCTCGGGTGCCAAGGAACTCCA 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 28bp) CCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCCAAGGAACT 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 25bp) ATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCCAAGGAA 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 23bp) NCCACTGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGT 6 0.15 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCCTGGAATTCTCGGGTGC 6 0.15 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATAAATGGAATTCTCGGGTGCCA 6 0.15 No Hit TCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACTC 6 0.15 RNA PCR Primer, Index 1 (100% over 26bp) AAGGGTGCTGAGAATACTTTGAATCTGACATGGAATTCTCGGGTGCCAAG 6 0.15 No Hit GATAACCGTAGTAATTCTAGAGCTAATTGGAATTCTCGGGTGCCAAGGAA 6 0.15 RNA PCR Primer, Index 1 (100% over 23bp) CATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGGGTGCC 6 0.15 No Hit CATCGAGTAGACCTTGTTATTGTGGAATTCTCGGGTGCCAAGGAACTCCA 6 0.15 RNA PCR Primer, Index 1 (100% over 28bp) TCGGATAACCGTAGTAATTCTAGAGCTAATACGTGGAATTCTCGGGTGCC 6 0.15 No Hit GACACGACTCTCGGCAACGGATATCTCGGCTTGGAATTCTCGGGTGCCAA 6 0.15 No Hit GACACGACTCTCGGCAACGTGGAATTCTCGGGTGCCAAGGAACTCCAGTC 6 0.15 RNA PCR Primer, Index 1 (100% over 31bp) GGGGATGTAGCTCAGATGGTAGATGGAATTCTCGGGTGCCAAGGAACTCC 6 0.15 RNA PCR Primer, Index 1 (100% over 27bp) AAGGGTGCTGAGAATACTTTGAATCTGACACTGGAATTCTCGGGTGCCAA 6 0.15 No Hit GCCCACCCCAAGATGAGTGCTCTCTCTGGAATTCTCGGGTGCCAAGGAAC 6 0.15 RNA PCR Primer, Index 1 (100% over 24bp) NACACGACTCTCGGCAACGGATATCTGGAATTCTCGGGTGCCAAGGAACT 6 0.15 RNA PCR Primer, Index 1 (100% over 25bp) ATGCAGCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGG 5 0.125 No Hit ATTCTCGGGTGCCAAGGAACTCCAGTCACCGATGTATCTCGTATGCCGTC 5 0.125 RNA PCR Primer, Index 2 (100% over 50bp) ATAACCGTAGTAATTCTAGAGCTAATGGAATTCTCGGGTGCCAAGGAACT 5 0.125 RNA PCR Primer, Index 1 (100% over 25bp) TGTCGTGCCAATTCAACATAAACCCTGGAATTCTCGGGTGCCAAGGAACT 5 0.125 RNA PCR Primer, Index 1 (100% over 25bp) AACCGTAGTAATTCTAGAGCTAATTGGAATTCTCGGGTGCCAAGGAACTC 5 0.125 RNA PCR Primer, Index 1 (100% over 26bp) TCTCGGACCAGGCTTCATTCCTGGAATTCTCGGGTGCCAAGGAACTCCAG 5 0.125 RNA PCR Primer, Index 1 (100% over 29bp) GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGATTGTGAATCTGGAATTC 5 0.125 No Hit ATGCAGTTACTAATTCATGATCTGGCTGGAATTCTCGGGTGCCAAGGAAC 5 0.125 RNA PCR Primer, Index 1 (100% over 24bp) CACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGATGGAATTC 5 0.125 No Hit ATATTGGGTAGGTTGTGGTATTTCATTGCTGGAATTCTCGGGTGCCAAGG 5 0.125 Illumina Small RNA Adapter 2 (100% over 21bp) TTTGGATTGAAGGGAGCTCTGTGGAATTCTCGGGTGCCAAGGAACTCCAG 5 0.125 RNA PCR Primer, Index 1 (100% over 29bp) ATAACCGTAGTAATTCTAGAGCTAATATGGAATTCTCGGGTGCCAAGGAA 5 0.125 RNA PCR Primer, Index 1 (100% over 23bp) TCGTGACCCTGACCTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCGA 5 0.125 RNA PCR Primer, Index 2 (100% over 36bp) ACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGATGGAATTCT 5 0.125 No Hit AGCTGAGGCATCCTAACGAACGAACGATTTGAATGGAATTCTCGGGTGCC 5 0.125 No Hit GACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTTGAATTCTCGGGTG 5 0.125 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTATGGAATTCTCGGGTGCCAA 5 0.125 No Hit CTGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCCA 5 0.125 No Hit TCGCTTGGTGCAGATCGGGACTGGAATTCTCGGGTGCCAAGGAACTCCAG 5 0.125 RNA PCR Primer, Index 1 (100% over 29bp) >>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 0.05 0.0 0.0 0.0 2 0.0 0.05 0.0 0.0 0.0 3 0.0 0.05 0.0 0.0 0.0 4 0.0 0.05 0.0 0.0 0.0 5 0.0 0.05 0.0 0.0 0.0 6 0.0 0.075 0.0 0.0 0.0 7 0.0 0.075 0.0 0.0 0.0 8 0.0 0.075 0.0 0.0 0.0 9 0.0 0.1 0.0 0.0 0.0 10-11 0.0 0.23750000000000002 0.0 0.0 0.0 12-13 0.0 0.3875 0.0 0.0 0.0 14-15 0.0 0.725 0.0 0.0 0.0 16-17 0.0 1.5375 0.0 0.0 0.0 18-19 0.0 3.1375 0.0 0.0 0.0 20-21 0.0 6.1625 0.0 0.0 0.0 22-23 0.0 14.5625 0.0 0.0 0.0 24-25 0.0 27.825000000000003 0.0 0.0 0.0 26-27 0.0 41.9375 0.0 0.0 0.0 28-29 0.0 50.5 0.0 0.0 0.0 30-31 0.0 60.475 0.0 0.0 0.0 32-33 0.0 68.9375 0.0 0.0 0.0 34-35 0.0 77.025 0.0 0.0 0.0 36-37 0.0 85.025 0.0 0.0 0.0 38-39 0.0 89.23750000000001 0.0 0.0 0.0 40-41 0.0 91.5375 0.0 0.0 0.0 42-43 0.0 93.375 0.0 0.0 0.0 44-45 0.0 94.375 0.0 0.0 0.0 46-47 0.0 94.75 0.0 0.0 0.0 48-49 0.0 94.8375 0.0 0.0 0.0 50-51 0.0 94.9125 0.0 0.0 0.0 52-53 0.0 94.925 0.0 0.0 0.0 54-55 0.0 94.925 0.0 0.0 0.0 56-57 0.0 94.925 0.0 0.0 0.0 58-59 0.0 94.9375 0.0 0.0 0.0 60-61 0.0 94.95 0.0 0.0 0.0 62-63 0.0 94.95 0.0 0.0 0.0 64-65 0.0 94.95 0.0 0.0 0.0 66-67 0.0 94.95 0.0 0.0 0.0 68-69 0.0 94.95 0.0 0.0 0.0 70-71 0.0 94.95 0.0 0.0 0.0 72-73 0.0 94.95 0.0 0.0 0.0 74-75 0.0 94.95 0.0 0.0 0.0 76-77 0.0 94.95 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 94.975 0.0 0.0 0.0 84-85 0.0 94.975 0.0 0.0 0.0 86-87 0.0 94.975 0.0 0.0 0.0 88-89 0.0 94.975 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GCCTTGA 15 4.2518976E-4 104.0137 1 GGGATTG 15 4.2518976E-4 104.0137 1 GACACGA 20 9.691041E-6 104.013695 1 CATCGAG 20 9.691041E-6 104.013695 1 GTAGACC 20 1.5462934E-5 94.912506 7 ACACGAC 20 1.5462934E-5 94.912506 2 AGTAGAC 20 1.5462934E-5 94.912506 6 GAGTAGA 20 1.5462934E-5 94.912506 5 CGAGTAG 20 1.5462934E-5 94.912506 4 AGACCTT 20 1.5462934E-5 94.912506 9 ATCGAGT 20 1.5462934E-5 94.912506 2 TCGAGTA 20 1.5462934E-5 94.912506 3 TAGACCT 20 1.5462934E-5 94.912506 8 TGATGGT 15 6.164719E-4 94.9125 5 GGTGAAA 15 6.164719E-4 94.9125 9 ATGGTGA 15 6.164719E-4 94.9125 7 CCTTGAT 15 6.164719E-4 94.9125 2 GATTGTA 15 6.164719E-4 94.9125 3 TAGTTCA 15 6.164719E-4 94.9125 8 TGTAGTT 15 6.164719E-4 94.9125 6 >>END_MODULE Rejected 981066 READS because READLEN < 1 Read 981066 spots for SRR8846488.sra Written 981066 spots for SRR8846488.sra Rejected 981066 READS because READLEN < 1 Read 981066 spots for SRR8846488.sra Written 981066 spots for SRR8846488.sra Rejected 981066 READS because READLEN < 1 Read 981066 spots for SRR8846488.sra Written 981066 spots for SRR8846488.sra Rejected 981066 READS because READLEN < 1 Read 981066 spots for SRR8846488.sra Written 981066 spots for SRR8846488.sra Rejected 981066 READS because READLEN < 1 Read 981066 spots for SRR8846488.sra Written 981066 spots for SRR8846488.sra Rejected 981066 READS because READLEN < 1 Read 981066 spots for SRR8846488.sra Written 981066 spots for SRR8846488.sra Rejected 981066 READS because READLEN < 1 Read 981066 spots for SRR8846488.sra Written 981066 spots for SRR8846488.sra Rejected 981066 READS because READLEN < 1 Read 981066 spots for SRR8846488.sra Written 981066 spots for SRR8846488.sra Rejected 981066 READS because READLEN < 1 Read 981066 spots for SRR8846488.sra Written 981066 spots for SRR8846488.sra Rejected 981066 READS because READLEN < 1 Read 981066 spots for SRR8846488.sra Written 981066 spots for SRR8846488.sra Rejected 981067 READS because READLEN < 1 Read 981067 spots for SRR8846488.sra Written 981067 spots for SRR8846488.sra Rejected 981066 READS because READLEN < 1 Read 981066 spots for SRR8846488.sra Written 981066 spots for SRR8846488.sra Rejected 981066 READS because READLEN < 1 Read 981066 spots for SRR8846488.sra Written 981066 spots for SRR8846488.sra Rejected 981066 READS because READLEN < 1 Read 981066 spots for SRR8846488.sra Written 981066 spots for SRR8846488.sra Rejected 981066 READS because READLEN < 1 Read 981066 spots for SRR8846488.sra Written 981066 spots for SRR8846488.sra Rejected 981066 READS because READLEN < 1 Read 981066 spots for SRR8846488.sra Written 981066 spots for SRR8846488.sra Rejected 981066 READS because READLEN < 1 Read 981066 spots for SRR8846488.sra Written 981066 spots for SRR8846488.sra Rejected 981066 READS because READLEN < 1 Read 981066 spots for SRR8846488.sra Written 981066 spots for SRR8846488.sra Rejected 981066 READS because READLEN < 1 Read 981066 spots for SRR8846488.sra Written 981066 spots for SRR8846488.sra Rejected 981066 READS because READLEN < 1 Read 981066 spots for SRR8846488.sra Written 981066 spots for SRR8846488.sra SRR ids: ['SRR8846488.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_cpghxi3n SRR8846488.sra spots: 19621321 blocks: [[1, 981066], [981067, 1962132], [1962133, 2943198], [2943199, 3924264], [3924265, 4905330], [4905331, 5886396], [5886397, 6867462], [6867463, 7848528], [7848529, 8829594], [8829595, 9810660], [9810661, 10791726], [10791727, 11772792], [11772793, 12753858], [12753859, 13734924], [13734925, 14715990], [14715991, 15697056], [15697057, 16678122], [16678123, 17659188], [17659189, 18640254], [18640255, 19621321]] SRR8846488 file size 4711176 SRR8846488 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 SRR8846488 SRR8846488_1.fastq Input file: SRR8846488_1.fastq trimmed: SRR8846488-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 19:28:03 2024 >> started Sun Dec 8 19:28:54 2024 >> done (51.126s) 19621321 reads processed; of these: 389 ( 0.00%) short reads filtered out after trimming by size control 100 ( 0.00%) empty reads filtered out after trimming by size control 19620832 (100.00%) reads available; of these: 5032039 (25.65%) trimmed reads available after processing 14588793 (74.35%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 50 0.00% 19 43 0.00% 20 34 0.00% 21 50 0.00% 22 59 0.00% 23 68 0.00% 24 79 0.00% 25 98 0.00% 26 112 0.00% 27 121 0.00% 28 145 0.00% 29 170 0.00% 30 163 0.00% 31 202 0.00% 32 195 0.00% 33 199 0.00% 34 242 0.00% 35 221 0.00% 36 206 0.00% 37 181 0.00% 38 190 0.00% 39 183 0.00% 40 223 0.00% 41 232 0.00% 42 201 0.00% 43 245 0.00% 44 309 0.00% 45 374 0.00% 46 326 0.00% 47 345 0.00% 48 341 0.00% 49 354 0.00% 50 325 0.00% 51 339 0.00% 52 301 0.00% 53 319 0.00% 54 314 0.00% 55 265 0.00% 56 304 0.00% 57 348 0.00% 58 363 0.00% 59 410 0.00% 60 545 0.00% 61 655 0.00% 62 906 0.00% 63 1247 0.01% 64 2038 0.01% 65 2524 0.01% 66 5404 0.03% 67 25393 0.13% 68 33446 0.17% 69 23888 0.12% 70 23496 0.12% 71 36685 0.19% 72 15246 0.08% 73 4254 0.02% 74 6157 0.03% 75 3848 0.02% 76 2721 0.01% 77 2761 0.01% 78 3298 0.02% 79 3699 0.02% 80 4225 0.02% 81 5065 0.03% 82 7255 0.04% 83 8441 0.04% 84 9568 0.05% 85 12761 0.07% 86 15186 0.08% 87 22414 0.11% 88 39388 0.20% 89 60493 0.31% 90 97559 0.50% 91 115245 0.59% 92 136105 0.69% 93 214823 1.09% 94 262235 1.34% 95 554550 2.83% 96 626868 3.19% 97 605136 3.08% 98 827978 4.22% 99 806292 4.11% 100 392992 2.00% 101 14588793 74.35% 19620832 reads passed initial QC criterion=sequence-density sequence-density=95.04 sequence-density-rank=1 fanout-score=38.41 fanout-score-rank=1 prefix-density=95.39 prefix-fanout=38.3 sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCGATGTATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAA criterion=fanout-score sequence-density=95.04 sequence-density-rank=1 fanout-score=38.41 fanout-score-rank=1 prefix-density=95.39 prefix-fanout=38.3 sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCGATGTATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAA 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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCGATGTATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAA -o SRR8846488 - Input file: STDIN trimmed: SRR8846488-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCGATGTATCTCGTATGCCGTCTTCTGCTTGA -- 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 19:32:14 2024 >> started Sun Dec 8 19:33:46 2024 >> done (91.960s) 19212065 reads processed; of these: 474992 ( 2.47%) short reads filtered out after trimming by size control 10451 ( 0.05%) empty reads filtered out after trimming by size control 18726622 (97.47%) reads available; of these: 18359623 (98.04%) trimmed reads available after processing 366999 ( 1.96%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 183093 0.98% 19 315431 1.68% 20 340852 1.82% 21 1207438 6.45% 22 675154 3.61% 23 874713 4.67% 24 2694703 14.39% 25 1025398 5.48% 26 854331 4.56% 27 812778 4.34% 28 802368 4.28% 29 941532 5.03% 30 1090269 5.82% 31 749909 4.00% 32 751561 4.01% 33 837613 4.47% 34 818082 4.37% 35 839253 4.48% 36 707117 3.78% 37 439849 2.35% 38 357408 1.91% 39 256231 1.37% 40 194004 1.04% 41 185261 0.99% 42 164192 0.88% 43 76256 0.41% 44 80112 0.43% 45 33445 0.18% 46 16016 0.09% 47 10197 0.05% 48 8032 0.04% 49 3968 0.02% 50 2691 0.01% 51 2493 0.01% 52 1332 0.01% 53 974 0.01% 54 1015 0.01% 55 418 0.00% 56 402 0.00% 57 303 0.00% 58 241 0.00% 59 288 0.00% 60 375 0.00% 61 516 0.00% 62 692 0.00% 63 991 0.01% 64 1727 0.01% 65 2140 0.01% 66 4926 0.03% 67 24475 0.13% 68 32240 0.17% 69 22792 0.12% 70 22396 0.12% 71 35178 0.19% 72 13102 0.07% 73 2419 0.01% 74 1786 0.01% 75 1256 0.01% 76 1133 0.01% 77 1833 0.01% 78 1330 0.01% 79 1350 0.01% 80 1922 0.01% 81 1386 0.01% 82 1325 0.01% 83 1763 0.01% 84 958 0.01% 85 1048 0.01% 86 928 0.00% 87 826 0.00% 88 711 0.00% 89 763 0.00% 90 874 0.00% 91 1009 0.01% 92 1047 0.01% 93 1199 0.01% 94 1311 0.01% 95 1678 0.01% 96 2209 0.01% 97 3119 0.02% 98 4627 0.02% 99 4866 0.03% 100 6206 0.03% 101 157467 0.84% criterion=sequence-density sequence-density=5.31 sequence-density-rank=1 fanout-score=0.00 fanout-score-rank=19 prefix-density=0.00 prefix-fanout=1.0 sequence=CATCGAGTAGACCTTGTTATTGTGAGAATTCTTAA criterion=fanout-score sequence-density=0.01 sequence-density-rank=42 fanout-score=108.06 fanout-score-rank=1 prefix-density=0.59 prefix-fanout=1.0 sequence=GTAGCCAAGTGCGGAGAGGATAACTGCTGAAAGCATATAAGTAGTAAGCCCACCCCAAGATGAGTGCTCTCTCCTC Started job on | Dec 08 19:36:15 Started mapping on | Dec 08 19:36:16 Finished on | Dec 08 19:45:18 Mapping speed, Million of reads per hour | 127.10 Number of input reads | 19135389 Average input read length | 31 UNIQUE READS: Uniquely mapped reads number | 3371086 Uniquely mapped reads % | 17.62% Average mapped length | 26.02 Number of splices: Total | 47449 Number of splices: Annotated (sjdb) | 30221 Number of splices: GT/AG | 45128 Number of splices: GC/AG | 1663 Number of splices: AT/AC | 19 Number of splices: Non-canonical | 639 Mismatch rate per base, % | 0.15% Deletion rate per base | 0.00% Deletion average length | 1.34 Insertion rate per base | 0.00% Insertion average length | 1.02 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 6581883 % of reads mapped to multiple loci | 34.40% Number of reads mapped to too many loci | 8029973 % of reads mapped to too many loci | 41.96% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 5.31% % of reads unmapped: other | 0.71% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 9182420 9182420 9182420 N_multimapping 6581883 6581883 6581883 N_noFeature 2110981 2321940 3142563 N_ambiguous 46220 28025 808 UnstrandedReadsAssigned:1213885 PositiveStrandReadsAssigned:1021121 NegativeStrandReadsAssigned:227715 Dataset is classified unstranded MeadianReadLen=28 20thPercentileLength=24 echo kmer=19 SRR8846488 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: SRR8846488-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 19,135,389 reads, 5,758,389 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,105 rounds 52973 SRR8846488.ke.tsv 35125 SRR8846488.se.tsv 88098 total ==> SRR8846488.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 837 0 0 PNS24247 1044 945 0.333333 0.0607635 PNS24249 1928 1829 1.51484 0.142675 PNS24246 1044 945 0.333333 0.0607635 PNS24248 1044 945 0.333333 0.0607635 PNS24244 1471 1372 5.48516 0.688701 PNS24243 293 194 0 0 KQK14069 1603 1504 103.108 11.8097 KQK14071 474 375 11.5733 5.31645 ==> SRR8846488.se.tsv <== BRADI_1g14170v3 175 BRADI_1g53295v3 2 BRADI_1g59795v3 10 BRADI_1g07683v3 2 BRADI_1g00485v3 1 BRADI_1g20270v3 73 BRADI_1g74790v3 31 BRADI_1g09890v3 2 BRADI_1g77505v3 3 BRADI_1g48960v3 0 SRR8846488 completed mapping pipeline successfully