Starting /dee2/code/volunteer_pipeline.sh SRR8846563 current disk space = 1515254935552 free memory = 1570773352 SRR8846563 SRAfilesize 5a88a86834894ebbccec4fa58e598a57 SRR8846563.sra SRR8846563.sra file validated SRR8846563 is single end SRR8846563 is conventional basespace SRR8846563 read1 length is 101 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR8846563_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 30.8355 34.0 33.0 34.0 28.0 34.0 2 32.68675 34.0 33.0 34.0 28.0 34.0 3 32.9435 34.0 33.0 34.0 32.0 34.0 4 33.24275 34.0 33.0 34.0 32.0 34.0 5 33.2755 34.0 33.0 34.0 33.0 34.0 6 37.00225 38.0 37.0 38.0 36.0 38.0 7 37.32425 38.0 38.0 38.0 36.0 38.0 8 37.4765 38.0 38.0 38.0 37.0 38.0 9 37.5115 38.0 38.0 38.0 37.0 38.0 10-11 37.563625 38.0 38.0 38.0 38.0 38.0 12-13 37.578125 38.0 38.0 38.0 38.0 38.0 14-15 37.573125000000005 38.0 38.0 38.0 38.0 38.0 16-17 37.503125 38.0 38.0 38.0 38.0 38.0 18-19 37.563375 38.0 38.0 38.0 38.0 38.0 20-21 37.5155 38.0 38.0 38.0 38.0 38.0 22-23 37.554874999999996 38.0 38.0 38.0 38.0 38.0 24-25 37.584375 38.0 38.0 38.0 38.0 38.0 26-27 37.544250000000005 38.0 38.0 38.0 37.5 38.0 28-29 37.528375 38.0 38.0 38.0 38.0 38.0 30-31 37.4525 38.0 38.0 38.0 37.5 38.0 32-33 37.439625 38.0 38.0 38.0 37.0 38.0 34-35 37.33125 38.0 38.0 38.0 37.0 38.0 36-37 37.08525 38.0 38.0 38.0 36.5 38.0 38-39 37.0685 38.0 38.0 38.0 36.0 38.0 40-41 37.17575 38.0 38.0 38.0 37.0 38.0 42-43 37.22225 38.0 38.0 38.0 37.0 38.0 44-45 37.236000000000004 38.0 38.0 38.0 37.0 38.0 46-47 37.26325 38.0 38.0 38.0 37.0 38.0 48-49 37.277874999999995 38.0 38.0 38.0 37.0 38.0 50-51 37.295 38.0 38.0 38.0 37.0 38.0 52-53 37.3125 38.0 38.0 38.0 37.0 38.0 54-55 37.192125000000004 38.0 38.0 38.0 37.0 38.0 56-57 37.15975 38.0 38.0 38.0 37.0 38.0 58-59 37.065375 38.0 38.0 38.0 36.0 38.0 60-61 37.105999999999995 38.0 38.0 38.0 37.0 38.0 62-63 36.68675 38.0 38.0 38.0 34.5 38.0 64-65 36.563500000000005 38.0 37.5 38.0 34.5 38.0 66-67 36.343125 38.0 37.5 38.0 33.5 38.0 68-69 36.05625 38.0 37.0 38.0 32.0 38.0 70-71 35.931125 38.0 37.0 38.0 32.0 38.0 72-73 35.923625 38.0 37.5 38.0 32.0 38.0 74-75 35.63475 38.0 37.0 38.0 30.0 38.0 76-77 35.401875000000004 38.0 37.0 38.0 28.5 38.0 78-79 35.4755 38.0 37.0 38.0 30.0 38.0 80-81 35.736374999999995 38.0 37.0 38.0 31.5 38.0 82-83 35.418875 38.0 37.0 38.0 29.5 38.0 84-85 35.58525 38.0 37.0 38.0 30.5 38.0 86-87 35.501000000000005 38.0 37.0 38.0 31.0 38.0 88-89 35.553875000000005 38.0 37.5 38.0 31.5 38.0 90-91 35.475750000000005 38.0 38.0 38.0 31.5 38.0 92-93 35.12712500000001 38.0 38.0 38.0 30.0 38.0 94-95 34.296625000000006 38.0 37.0 38.0 25.5 38.0 96-97 32.428875 38.0 35.0 38.0 8.0 38.0 98-99 30.345625 38.0 30.5 38.0 2.0 38.0 100-101 27.672125 37.5 19.5 38.0 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 12 2.0 13 1.0 14 0.0 15 0.0 16 0.0 17 1.0 18 2.0 19 0.0 20 0.0 21 2.0 22 2.0 23 7.0 24 7.0 25 45.0 26 26.0 27 16.0 28 24.0 29 23.0 30 44.0 31 62.0 32 65.0 33 134.0 34 201.0 35 421.0 36 750.0 37 2165.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 33.91939410332702 23.289153367595347 22.180146064376522 20.61130646470111 2 25.575 28.449999999999996 17.8 28.175 3 25.624999999999996 21.15 18.35 34.875 4 26.125 34.975 16.725 22.175 5 27.425 25.575 22.375 24.625 6 26.275 26.825 25.05 21.85 7 36.675000000000004 26.375 18.675 18.275 8 19.7 22.1 35.725 22.475 9 24.85 35.975 21.224999999999998 17.95 10-11 30.4875 24.45 24.8625 20.200000000000003 12-13 22.3625 23.525 22.3125 31.8 14-15 25.174999999999997 37.225 20.4375 17.1625 16-17 23.2375 28.462500000000002 29.912499999999998 18.387500000000003 18-19 33.037499999999994 23.474999999999998 21.462500000000002 22.025 20-21 22.7375 29.812499999999996 25.525 21.925 22-23 26.7125 30.0375 28.212500000000002 15.037500000000001 24-25 28.025 27.025 25.1 19.85 26-27 28.325 28.499999999999996 24.125 19.05 28-29 25.0125 25.650000000000002 25.137500000000003 24.2 30-31 26.200000000000003 20.9 32.8625 20.0375 32-33 23.724999999999998 18.575 33.8375 23.8625 34-35 28.025 16.8625 32.05 23.0625 36-37 34.175 15.137500000000001 31.225 19.4625 38-39 34.9 19.475 25.9625 19.662499999999998 40-41 30.225 20.25 25.087500000000002 24.4375 42-43 30.75 21.1625 23.6375 24.45 44-45 35.112500000000004 21.925 16.6875 26.275 46-47 33.575 26.1 15.75 24.575 48-49 29.15 25.337500000000002 17.625 27.8875 50-51 24.3625 24.7375 16.287499999999998 34.612500000000004 52-53 22.3 30.675 12.9125 34.112500000000004 54-55 20.837500000000002 29.912499999999998 15.312500000000002 33.9375 56-57 19.125 30.862499999999997 13.625000000000002 36.3875 58-59 10.05 31.900000000000002 16.7625 41.2875 60-61 8.275 30.4 18.3625 42.9625 62-63 9.112499999999999 31.1 18.5375 41.25 64-65 9.025 30.9375 23.825 36.2125 66-67 7.2375 26.7625 25.5125 40.4875 68-69 9.2875 27.224999999999998 24.0125 39.475 70-71 11.6875 24.5125 28.775000000000002 35.025 72-73 15.312500000000002 21.875 30.612499999999997 32.2 74-75 13.975000000000001 21.2625 29.9375 34.825 76-77 16.7375 15.15 36.675000000000004 31.4375 78-79 18.025 10.5375 37.425000000000004 34.0125 80-81 19.3125 12.0625 37.3375 31.2875 82-83 19.0125 12.662499999999998 42.0 26.325 84-85 21.5 11.8875 36.662499999999994 29.95 86-87 20.3 17.65 34.7625 27.287499999999998 88-89 16.5625 29.15 35.3875 18.9 90-91 13.100000000000001 38.7125 30.775000000000002 17.4125 92-93 12.975 48.5875 22.9625 15.475 94-95 11.25 57.66250000000001 20.424999999999997 10.6625 96-97 8.4625 66.7625 17.3875 7.387499999999999 98-99 7.6625 77.17500000000001 10.75 4.4125 100-101 4.1875 85.175 6.3875 4.25 >>END_MODULE >>Per sequence GC content pass #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 2.0 32 2.0 33 3.0 34 10.0 35 11.5 36 10.5 37 12.0 38 15.0 39 32.5 40 57.5 41 123.0 42 174.5 43 216.0 44 289.5 45 326.0 46 386.0 47 411.0 48 371.0 49 329.5 50 308.5 51 273.5 52 175.5 53 98.0 54 84.0 55 128.0 56 97.0 57 19.5 58 10.0 59 8.0 60 4.5 61 4.0 62 3.5 63 2.5 64 1.0 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 7.575 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 56.39999999999999 #Duplication Level Percentage of deduplicated Percentage of total 1 84.04255319148936 47.4 2 7.801418439716312 8.799999999999999 3 1.950354609929078 3.3000000000000003 4 1.5070921985815602 3.4000000000000004 5 0.8865248226950355 2.5 6 0.7535460992907801 2.55 7 0.8421985815602837 3.325 8 0.22163120567375888 1.0 9 0.22163120567375888 1.125 >10 1.5070921985815602 16.275000000000002 >50 0.26595744680851063 10.325 >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 TCCACTGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGT 97 2.4250000000000003 No Hit GGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGA 76 1.9 RNA PCR Primer, Index 1 (100% over 22bp) GACACGACTCTCGGCAACGGATATCTCTGGAATTCTCGGGTGCCAAGGAA 64 1.6 RNA PCR Primer, Index 1 (100% over 23bp) GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGGAATTCTCGGGTGCC 60 1.5 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCTGGAATTCTCGGGTGCCA 59 1.4749999999999999 No Hit TCGGACCAGGCTTCATTCCCCTGGAATTCTCGGGTGCCAAGGAACTCCAG 57 1.425 RNA PCR Primer, Index 1 (100% over 29bp) AGCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGC 47 1.175 No Hit CTCTGATGATGATCAAACTAATACTTTCGTTCTTCTGGAATTCTCGGGTG 47 1.175 No Hit GACACGACTCTCGGCAACGGATATCTTGGAATTCTCGGGTGCCAAGGAAC 40 1.0 RNA PCR Primer, Index 1 (100% over 24bp) GACACGACTCTCGGCAACGGATATCTGGAATTCTCGGGTGCCAAGGAACT 35 0.8750000000000001 RNA PCR Primer, Index 1 (100% over 25bp) GCACCAGTGGTCTAGTGGTAGAATAGTACCTGGAATTCTCGGGTGCCAAG 31 0.775 No Hit TCTCGGGTGCCAAGGAACTCCAGTCACCACTCAATCTCGTATGCCGTCTT 29 0.7250000000000001 RNA PCR Primer, Index 32 (100% over 50bp) GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCCTGGAATTCTCGGGTGC 22 0.5499999999999999 No Hit CAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGGG 22 0.5499999999999999 No Hit CTCGGGTGCCAAGGAACTCCAGTCACCACTCAATCTCGTATGCCGTCTTC 22 0.5499999999999999 RNA PCR Primer, Index 32 (100% over 50bp) CACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGATGGAATTC 20 0.5 No Hit GCCTTGATGGTGAAATGGTAGACACGCGAGACTCATGGAATTCTCGGGTG 20 0.5 No Hit GACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGGGTG 18 0.44999999999999996 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCTGGAATTCTCGGGTGCCAAGG 18 0.44999999999999996 Illumina Small RNA Adapter 2 (100% over 21bp) CATCGAGTAGACCTTGTTATTGTGAGAATATGGAATTCTCGGGTGCCAAG 18 0.44999999999999996 No Hit GCCCACCCCAAGATGAGTGCTCTCTCTGGAATTCTCGGGTGCCAAGGAAC 18 0.44999999999999996 RNA PCR Primer, Index 1 (100% over 24bp) CATCGAGTAGACCTTGTTATTGTGAGAATTTGGAATTCTCGGGTGCCAAG 17 0.42500000000000004 No Hit GCCTTGATGGTGAAATGGTAGACACGCGAGACTCAAAATCTTGGAATTCT 16 0.4 No Hit TCCGTCGTAGTCTAGGTGGTTAGGATATGGAATTCTCGGGTGCCAAGGAA 16 0.4 RNA PCR Primer, Index 1 (100% over 23bp) AGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGG 16 0.4 Illumina Small RNA Adapter 2 (100% over 21bp) AGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGGGT 15 0.375 No Hit GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGAATTCTCGGGTGCCAAGG 14 0.35000000000000003 Illumina Small RNA Adapter 2 (100% over 21bp) TTCGGACCAGGCTTCATTCCCTGGAATTCTCGGGTGCCAAGGAACTCCAG 14 0.35000000000000003 RNA PCR Primer, Index 1 (100% over 29bp) CCAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGG 14 0.35000000000000003 No Hit ACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGGGTGC 14 0.35000000000000003 No Hit ATATATTTCAAGTTATTTCGGATCTTGGAATTCTCGGGTGCCAAGGAACT 12 0.3 RNA PCR Primer, Index 1 (100% over 25bp) GCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCC 12 0.3 No Hit GTCAGGATAGCTCAGTTGGTAGAGCAGAGGACTTGGAATTCTCGGGTGCC 11 0.27499999999999997 No Hit ATAACCGTAGTAATTCTAGAGCTAATTGGAATTCTCGGGTGCCAAGGAAC 11 0.27499999999999997 RNA PCR Primer, Index 1 (100% over 24bp) TGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAA 11 0.27499999999999997 No Hit AATTCTCGGGTGCCAAGGAACTCCAGTCACCACTCAATCTCGTATGCCGT 11 0.27499999999999997 RNA PCR Primer, Index 32 (100% over 50bp) CACGACTCTCGGCAACGGATATCTCTGGAATTCTCGGGTGCCAAGGAACT 10 0.25 RNA PCR Primer, Index 1 (100% over 25bp) ATTCTCGGGTGCCAAGGAACTCCAGTCACCACTCAATCTCGTATGCCGTC 10 0.25 RNA PCR Primer, Index 32 (100% over 50bp) GCACCAGTAGTCTAGTGGTAGAATAGTACCTGGAATTCTCGGGTGCCAAG 10 0.25 No Hit TCAAAAGAGGAAAGGCTTGCGGTGGAATTCTCGGGTGCCAAGGAACTCCA 10 0.25 RNA PCR Primer, Index 1 (100% over 28bp) TCGGATAACCGTAGTAATTCTAGAGCTAATACGTGGAATTCTCGGGTGCC 9 0.22499999999999998 No Hit TCCAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCG 9 0.22499999999999998 No Hit GAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAG 9 0.22499999999999998 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTCTTAATGGAATTCTCGGGTG 9 0.22499999999999998 No Hit AGGGCTATAGCTCAGTTCGGTAGAGCAACTCGTTTACACCGAGATGGAAT 9 0.22499999999999998 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTCAAGGGTGGAATTC 8 0.2 No Hit CCACTGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTG 8 0.2 No Hit CAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTTGAATTCTCGGG 8 0.2 No Hit ATGCAGTTACTAATTCATGATCTGGCTGGAATTCTCGGGTGCCAAGGAAC 8 0.2 RNA PCR Primer, Index 1 (100% over 24bp) ACTGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCC 8 0.2 No Hit NCCACTGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGT 7 0.17500000000000002 No Hit NGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGGAATTCTCGGGTGCC 7 0.17500000000000002 No Hit CGGATAACCGTAGTAATTCTAGAGCTAATACGTGGAATTCTCGGGTGCCA 7 0.17500000000000002 No Hit GATGAGCTCAACGAGAACAGAAATCTCGTGTGGAATTCTCGGGTGCCAAG 7 0.17500000000000002 No Hit GTCAGGATAGCTCAGTTGGTAGAGCAGAGGACTGGAATTCTCGGGTGCCA 7 0.17500000000000002 No Hit CTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCA 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 28bp) CATCGAGTAGACCTTGTTATTGTGAGATGGAATTCTCGGGTGCCAAGGAA 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 23bp) CATCGAGTAGACCTTGTTATTGTGAGAATTGGAATTCTCGGGTGCCAAGG 7 0.17500000000000002 Illumina Small RNA Adapter 2 (100% over 21bp) GCCTTGATGGTGAAATGGTAGACACGCGAGACTTGGAATTCTCGGGTGCC 7 0.17500000000000002 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTCAAGGCGTGGAATT 7 0.17500000000000002 No Hit CACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGGAATTCTCG 7 0.17500000000000002 No Hit CACGACTCTCGGCAACGGATATCTGGAATTCTCGGGTGCCAAGGAACTCC 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 27bp) ACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTTGAATTCTCGGGTGC 7 0.17500000000000002 No Hit CACGACTCTCGGCAACGGATATCTCGTGGAATTCTCGGGTGCCAAGGAAC 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 24bp) AAGGGTGCTGAGAATACTTTGAATCTGACACTGGAATTCTCGGGTGCCAA 7 0.17500000000000002 No Hit CCAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTTGAATTCTCGG 7 0.17500000000000002 No Hit GGGGATATAGCTCAGTTGGTAGATGGAATTCTCGGGTGCCAAGGAACTCC 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 27bp) NACACGACTCTCGGCAACGGATATCTCTGGAATTCTCGGGTGCCAAGGAA 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 23bp) GACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTTGAATTCTCGGGTG 7 0.17500000000000002 No Hit CGACACGACTCTCGGCAACGGATATCTTGGAATTCTCGGGTGCCAAGGAA 6 0.15 RNA PCR Primer, Index 1 (100% over 23bp) AAGGGTGCTGAGAATACTTTGAATCTGACATGGAATTCTCGGGTGCCAAG 6 0.15 No Hit CATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGGGTGCC 6 0.15 No Hit GCGACCCCAGGTCAGGCGGGACTACCCGCTGATGGAATTCTCGGGTGCCA 6 0.15 No Hit TCCTGTGGATGAGAAGGCATTTATATTCTGATGATATGGAATTCTCGGGT 6 0.15 No Hit GTCCAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTTGAATTCTC 6 0.15 No Hit GGGATTGTAGTTCAATTGGTCAGAGCTGGAATTCTCGGGTGCCAAGGAAC 6 0.15 RNA PCR Primer, Index 1 (100% over 24bp) ACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTTGATTCTCGGGTGCC 6 0.15 No Hit CGACACGACTCTCGGCAACGGATATCTCTGGAATTCTCGGGTGCCAAGGA 6 0.15 RNA PCR Primer, Index 1 (100% over 22bp) GATAACCGTAGTAATTCTAGAGCTAATGGAATTCTCGGGTGCCAAGGAAC 6 0.15 RNA PCR Primer, Index 1 (100% over 24bp) TCTCGGACCAGGCTTCATTCCTGGAATTCTCGGGTGCCAAGGAACTCCAG 6 0.15 RNA PCR Primer, Index 1 (100% over 29bp) AGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTTGAATTCTCGGGT 6 0.15 No Hit ATAACCGTAGTAATTCTAGAGCTAATATGGAATTCTCGGGTGCCAAGGAA 6 0.15 RNA PCR Primer, Index 1 (100% over 23bp) GCCTTGATGGTGAAATGGTAGACACGCGAGACTGGAATTCTCGGGTGCCA 6 0.15 No Hit TCCAGAAAGGATGTAAGGAAGCTGAAGCGGAAATGGAATTCTCGGGTGCC 6 0.15 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTATGGAATTCTCGGGTGCCAA 6 0.15 No Hit GCCTTGATGGTGAAATGGTAGACACGCGAGACTCAAAATCTGGAATTCTC 6 0.15 No Hit NGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGA 5 0.125 RNA PCR Primer, Index 1 (100% over 22bp) GTCCAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTC 5 0.125 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATAAAATGGAATTCTCGGGTGCC 5 0.125 No Hit GACACGACTCTCGGCAACGGATATGGAATTCTCGGGTGCCAAGGAACTCC 5 0.125 RNA PCR Primer, Index 1 (100% over 27bp) CATCGAGTAGACCTTGTTATTGTGAGTGGAATTCTCGGGTGCCAAGGAAC 5 0.125 RNA PCR Primer, Index 1 (100% over 24bp) TTTGTTTTTATGTTATTTTGTGAAGGTGGAATTCTCGGGTGCCAAGGAAC 5 0.125 RNA PCR Primer, Index 1 (100% over 24bp) CATCGAGTAGACCTTGTTATTGTGAGAATAAAAAATGGAATTCTCGGGTG 5 0.125 No Hit GACACGACTCTCGGCAACGTGGAATTCTCGGGTGCCAAGGAACTCCAGTC 5 0.125 RNA PCR Primer, Index 1 (100% over 31bp) ACTCGGATAACCGTAGTAATTCTAGAGCTAATACGTGGAATTCTCGGGTG 5 0.125 No Hit ATAACCGTAGTAATTCTAGAGCTAATACTGGAATTCTCGGGTGCCAAGGA 5 0.125 RNA PCR Primer, Index 1 (100% over 22bp) TTCTCGGGTGCCAAGGAACTCCAGTCACCACTCAATCTCGTATGCCGTCT 5 0.125 RNA PCR Primer, Index 32 (100% over 50bp) GCACCAGTGGTCTAGTGGTAGAATATGGAATTCTCGGGTGCCAAGGAACT 5 0.125 RNA PCR Primer, Index 1 (100% over 25bp) CAGCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTG 5 0.125 No Hit AGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGGGTGCCAAG 5 0.125 No Hit AACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCAGT 5 0.125 RNA PCR Primer, Index 1 (100% over 30bp) GCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGGGTGCCAAGG 5 0.125 Illumina Small RNA Adapter 2 (100% over 21bp) TGCAGCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGG 5 0.125 No Hit ATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACT 5 0.125 RNA PCR Primer, Index 1 (100% over 25bp) TAACCGTAGTAATTCTAGAGCTAATGGAATTCTCGGGTGCCAAGGAACTC 5 0.125 RNA PCR Primer, Index 1 (100% over 26bp) CACTGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGC 5 0.125 No Hit >>END_MODULE >>Adapter Content fail #Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence SOLID Small RNA Adapter 1 0.0 0.0 0.0 0.0 0.0 2 0.0 0.0 0.0 0.0 0.0 3 0.0 0.0 0.0 0.0 0.0 4 0.0 0.0 0.0 0.0 0.0 5 0.0 0.0 0.0 0.0 0.0 6 0.0 0.0 0.0 0.0 0.0 7 0.0 0.0 0.0 0.0 0.0 8 0.0 0.075 0.0 0.0 0.0 9 0.0 0.275 0.0 0.0 0.0 10-11 0.0 0.35 0.0 0.0 0.0 12-13 0.0 0.5125 0.0 0.0 0.0 14-15 0.0 0.8 0.0 0.0 0.0 16-17 0.0 1.575 0.0 0.0 0.0 18-19 0.0 2.8375 0.0 0.0 0.0 20-21 0.0 4.95 0.0 0.0 0.0 22-23 0.0 11.85 0.0 0.0 0.0 24-25 0.0 20.4625 0.0 0.0 0.0 26-27 0.0 31.15 0.0 0.0 0.0 28-29 0.0 41.8375 0.0 0.0 0.0 30-31 0.0 51.5125 0.0 0.0 0.0 32-33 0.0 59.5375 0.0 0.0 0.0 34-35 0.0 69.7375 0.0 0.0 0.0 36-37 0.0 80.1 0.0 0.0 0.0 38-39 0.0 85.3125 0.0 0.0 0.0 40-41 0.0 88.01249999999999 0.0 0.0 0.0 42-43 0.0 90.725 0.0 0.0 0.0 44-45 0.0 92.4375 0.0 0.0 0.0 46-47 0.0 93.0875 0.0 0.0 0.0 48-49 0.0 93.2 0.0 0.0 0.0 50-51 0.0 93.30000000000001 0.0 0.0 0.0 52-53 0.0 93.3375 0.0 0.0 0.0 54-55 0.0 93.35 0.0 0.0 0.0 56-57 0.0 93.35 0.0 0.0 0.0 58-59 0.0 93.35 0.0 0.0 0.0 60-61 0.0 93.35 0.0 0.0 0.0 62-63 0.0 93.35 0.0 0.0 0.0 64-65 0.0 93.35 0.0 0.0 0.0 66-67 0.0 93.35 0.0 0.0 0.0 68-69 0.0 93.35 0.0 0.0 0.0 70-71 0.0 93.35 0.0 0.0 0.0 72-73 0.0 93.35 0.0 0.0 0.0 74-75 0.0 93.35 0.0 0.0 0.0 76-77 0.0 93.35 0.0 0.0 0.0 78-79 0.0 93.375 0.0 0.0 0.0 80-81 0.0 93.3875 0.0 0.0 0.0 82-83 0.0 93.4125 0.0 0.0 0.0 84-85 0.0 93.4375 0.0 0.0 0.0 86-87 0.0 93.45 0.0 0.0 0.0 88-89 0.0 93.45 0.0 0.0 0.0 >>END_MODULE >>Kmer Content fail #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GGGATTG 35 1.09139364E-10 104.01371 1 AGCTGAG 15 4.2518976E-4 104.0137 1 CATCGAG 25 2.1896449E-7 104.0137 1 GTAGACC 25 3.8500548E-7 94.912506 7 TTGTAGT 35 2.3283064E-10 94.912506 5 AGTAGAC 25 3.8500548E-7 94.912506 6 GGATTGT 35 2.3283064E-10 94.912506 2 GATTGTA 35 2.3283064E-10 94.912506 3 TAGTTCA 35 2.3283064E-10 94.912506 8 GAGTAGA 25 3.8500548E-7 94.912506 5 ATTGTAG 35 2.3283064E-10 94.912506 4 TGTAGTT 35 2.3283064E-10 94.912506 6 CGAGTAG 25 3.8500548E-7 94.912506 4 AGACCTT 25 3.8500548E-7 94.912506 9 ATCGAGT 25 3.8500548E-7 94.912506 2 TCGAGTA 25 3.8500548E-7 94.912506 3 AGTTCAA 35 2.3283064E-10 94.912506 9 GTAGTTC 35 2.3283064E-10 94.912506 7 TAGACCT 25 3.8500548E-7 94.912506 8 GACACGA 20 0.0013340823 78.01028 1 >>END_MODULE Rejected 961566 READS because READLEN < 1 Read 961566 spots for SRR8846563.sra Written 961566 spots for SRR8846563.sra Rejected 961566 READS because READLEN < 1 Read 961566 spots for SRR8846563.sra Written 961566 spots for SRR8846563.sra Rejected 961566 READS because READLEN < 1 Read 961566 spots for SRR8846563.sra Written 961566 spots for SRR8846563.sra Rejected 961566 READS because READLEN < 1 Read 961566 spots for SRR8846563.sra Written 961566 spots for SRR8846563.sra Rejected 961566 READS because READLEN < 1 Read 961566 spots for SRR8846563.sra Written 961566 spots for SRR8846563.sra Rejected 961566 READS because READLEN < 1 Read 961566 spots for SRR8846563.sra Written 961566 spots for SRR8846563.sra Rejected 961566 READS because READLEN < 1 Read 961566 spots for SRR8846563.sra Written 961566 spots for SRR8846563.sra Rejected 961566 READS because READLEN < 1 Read 961566 spots for SRR8846563.sra Written 961566 spots for SRR8846563.sra Rejected 961566 READS because READLEN < 1 Read 961566 spots for SRR8846563.sra Written 961566 spots for SRR8846563.sra Rejected 961566 READS because READLEN < 1 Read 961566 spots for SRR8846563.sra Written 961566 spots for SRR8846563.sra Rejected 961582 READS because READLEN < 1 Read 961582 spots for SRR8846563.sra Written 961582 spots for SRR8846563.sra Rejected 961566 READS because READLEN < 1 Read 961566 spots for SRR8846563.sra Written 961566 spots for SRR8846563.sra Rejected 961566 READS because READLEN < 1 Read 961566 spots for SRR8846563.sra Written 961566 spots for SRR8846563.sra Rejected 961566 READS because READLEN < 1 Read 961566 spots for SRR8846563.sra Written 961566 spots for SRR8846563.sra Rejected 961566 READS because READLEN < 1 Read 961566 spots for SRR8846563.sra Written 961566 spots for SRR8846563.sra Rejected 961566 READS because READLEN < 1 Read 961566 spots for SRR8846563.sra Written 961566 spots for SRR8846563.sra Rejected 961566 READS because READLEN < 1 Read 961566 spots for SRR8846563.sra Written 961566 spots for SRR8846563.sra Rejected 961566 READS because READLEN < 1 Read 961566 spots for SRR8846563.sra Written 961566 spots for SRR8846563.sra Rejected 961566 READS because READLEN < 1 Read 961566 spots for SRR8846563.sra Written 961566 spots for SRR8846563.sra Rejected 961566 READS because READLEN < 1 Read 961566 spots for SRR8846563.sra Written 961566 spots for SRR8846563.sra SRR ids: ['SRR8846563.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_7ibi0ho9 SRR8846563.sra spots: 19231336 blocks: [[1, 961566], [961567, 1923132], [1923133, 2884698], [2884699, 3846264], [3846265, 4807830], [4807831, 5769396], [5769397, 6730962], [6730963, 7692528], [7692529, 8654094], [8654095, 9615660], [9615661, 10577226], [10577227, 11538792], [11538793, 12500358], [12500359, 13461924], [13461925, 14423490], [14423491, 15385056], [15385057, 16346622], [16346623, 17308188], [17308189, 18269754], [18269755, 19231336]] SRR8846563 file size 4617108 SRR8846563 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 SRR8846563 SRR8846563_1.fastq Input file: SRR8846563_1.fastq trimmed: SRR8846563-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 Thu Dec 12 03:07:10 2024 >> started Thu Dec 12 03:07:21 2024 >> done (11.238s) 19231336 reads processed; of these: 372 ( 0.00%) short reads filtered out after trimming by size control 43 ( 0.00%) empty reads filtered out after trimming by size control 19230921 (100.00%) reads available; of these: 4149483 (21.58%) trimmed reads available after processing 15081438 (78.42%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 32 0.00% 19 23 0.00% 20 40 0.00% 21 61 0.00% 22 46 0.00% 23 51 0.00% 24 72 0.00% 25 92 0.00% 26 127 0.00% 27 171 0.00% 28 237 0.00% 29 264 0.00% 30 237 0.00% 31 250 0.00% 32 284 0.00% 33 317 0.00% 34 314 0.00% 35 310 0.00% 36 302 0.00% 37 280 0.00% 38 239 0.00% 39 244 0.00% 40 209 0.00% 41 184 0.00% 42 194 0.00% 43 230 0.00% 44 233 0.00% 45 205 0.00% 46 171 0.00% 47 153 0.00% 48 193 0.00% 49 162 0.00% 50 187 0.00% 51 180 0.00% 52 223 0.00% 53 232 0.00% 54 264 0.00% 55 225 0.00% 56 343 0.00% 57 368 0.00% 58 459 0.00% 59 570 0.00% 60 786 0.00% 61 1472 0.01% 62 2368 0.01% 63 2496 0.01% 64 4646 0.02% 65 5961 0.03% 66 15945 0.08% 67 74667 0.39% 68 85881 0.45% 69 55964 0.29% 70 39709 0.21% 71 40369 0.21% 72 17668 0.09% 73 6563 0.03% 74 7847 0.04% 75 5617 0.03% 76 5206 0.03% 77 4734 0.02% 78 5930 0.03% 79 5799 0.03% 80 7822 0.04% 81 10013 0.05% 82 22974 0.12% 83 19706 0.10% 84 15186 0.08% 85 15531 0.08% 86 18508 0.10% 87 21931 0.11% 88 38003 0.20% 89 60064 0.31% 90 87975 0.46% 91 89070 0.46% 92 113842 0.59% 93 177277 0.92% 94 210124 1.09% 95 394037 2.05% 96 448862 2.33% 97 464545 2.42% 98 546109 2.84% 99 606431 3.15% 100 382867 1.99% 101 15081438 78.42% 19230921 reads passed initial QC criterion=sequence-density sequence-density=93.18 sequence-density-rank=1 fanout-score=35.66 fanout-score-rank=1 prefix-density=93.56 prefix-fanout=35.5 sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCACTCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAA criterion=fanout-score sequence-density=93.18 sequence-density-rank=1 fanout-score=35.66 fanout-score-rank=1 prefix-density=93.56 prefix-fanout=35.5 sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCACTCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAA 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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCACTCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAA -o SRR8846563 - Input file: STDIN trimmed: SRR8846563-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCACTCAATCTCGTATGCCGTCTTCTGCTTGA -- 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 Thu Dec 12 03:08:01 2024 >> started Thu Dec 12 03:08:25 2024 >> done (23.508s) 18821753 reads processed; of these: 506476 ( 2.69%) short reads filtered out after trimming by size control 9708 ( 0.05%) empty reads filtered out after trimming by size control 18305569 (97.26%) reads available; of these: 17634663 (96.33%) trimmed reads available after processing 670906 ( 3.67%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 149739 0.82% 19 262676 1.43% 20 280696 1.53% 21 858455 4.69% 22 524367 2.86% 23 678298 3.71% 24 1549382 8.46% 25 838941 4.58% 26 952470 5.20% 27 999990 5.46% 28 958259 5.23% 29 821143 4.49% 30 1049037 5.73% 31 672262 3.67% 32 950353 5.19% 33 1037768 5.67% 34 960017 5.24% 35 909396 4.97% 36 910181 4.97% 37 426899 2.33% 38 356842 1.95% 39 282235 1.54% 40 266430 1.46% 41 279817 1.53% 42 266751 1.46% 43 123949 0.68% 44 112709 0.62% 45 49843 0.27% 46 24795 0.14% 47 13803 0.08% 48 10996 0.06% 49 6343 0.03% 50 4419 0.02% 51 3522 0.02% 52 2308 0.01% 53 1705 0.01% 54 2144 0.01% 55 806 0.00% 56 1357 0.01% 57 614 0.00% 58 664 0.00% 59 766 0.00% 60 831 0.00% 61 1595 0.01% 62 2317 0.01% 63 2408 0.01% 64 4497 0.02% 65 5726 0.03% 66 15472 0.08% 67 72970 0.40% 68 83852 0.46% 69 54456 0.30% 70 38512 0.21% 71 38955 0.21% 72 15722 0.09% 73 4952 0.03% 74 4223 0.02% 75 3084 0.02% 76 3613 0.02% 77 5056 0.03% 78 3401 0.02% 79 3334 0.02% 80 7682 0.04% 81 5981 0.03% 82 4926 0.03% 83 8027 0.04% 84 2981 0.02% 85 2975 0.02% 86 2837 0.02% 87 2274 0.01% 88 1701 0.01% 89 2053 0.01% 90 1685 0.01% 91 1629 0.01% 92 1858 0.01% 93 2306 0.01% 94 2222 0.01% 95 3124 0.02% 96 4302 0.02% 97 5850 0.03% 98 7972 0.04% 99 9318 0.05% 100 11450 0.06% 101 244293 1.33% criterion=sequence-density sequence-density=3.90 sequence-density-rank=1 fanout-score=0.00 fanout-score-rank=14 prefix-density=0.00 prefix-fanout=1.0 sequence=CATCGAGTAGACCTTGTTATTGTGAGAAT criterion=fanout-score sequence-density=0.01 sequence-density-rank=42 fanout-score=147.27 fanout-score-rank=1 prefix-density=0.79 prefix-fanout=1.0 sequence=GTAGCCAAGTGCGGAGAGGATAACTGCTGAAAGCATATAAGTAGTAAGCCCACCCCAAGATGAGTGCTCTCTCCTCCGACT Started job on | Dec 12 03:08:47 Started mapping on | Dec 12 03:08:47 Finished on | Dec 12 03:09:54 Mapping speed, Million of reads per hour | 1005.57 Number of input reads | 18714737 Average input read length | 33 UNIQUE READS: Uniquely mapped reads number | 2633597 Uniquely mapped reads % | 14.07% Average mapped length | 28.17 Number of splices: Total | 38315 Number of splices: Annotated (sjdb) | 23090 Number of splices: GT/AG | 35136 Number of splices: GC/AG | 2486 Number of splices: AT/AC | 19 Number of splices: Non-canonical | 674 Mismatch rate per base, % | 0.18% 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 | 6156282 % of reads mapped to multiple loci | 32.90% Number of reads mapped to too many loci | 8506842 % of reads mapped to too many loci | 45.46% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 7.12% % of reads unmapped: other | 0.46% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 9924858 9924858 9924858 N_multimapping 6156282 6156282 6156282 N_noFeature 1384531 1540700 2459838 N_ambiguous 51803 33843 558 UnstrandedReadsAssigned:1197263 PositiveStrandReadsAssigned:1059054 NegativeStrandReadsAssigned:173201 Dataset is classified positive stranded MeadianReadLen=30 20thPercentileLength=24 echo kmer=19 SRR8846563 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: SRR8846563-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 18,714,737 reads, 2,765,477 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 962 rounds 52973 SRR8846563.ke.tsv 35125 SRR8846563.se.tsv 88098 total ==> SRR8846563.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 7 2.32205 PNS24243 293 194 0 0 KQK14069 1603 1504 368.104 111.391 KQK14071 474 375 5.35934 6.5044 ==> SRR8846563.se.tsv <== BRADI_1g14170v3 483 BRADI_1g53295v3 3 BRADI_1g59795v3 2 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 18 BRADI_1g74790v3 20 BRADI_1g09890v3 0 BRADI_1g77505v3 5 BRADI_1g48960v3 0 SRR8846563 completed mapping pipeline successfully