Starting /dee2/code/volunteer_pipeline.sh SRR8846552 current disk space = 1528458842112 free memory = 1520331164 SRR8846552 SRAfilesize a9f9f1fb82c89c7e751d09c9d812f470 SRR8846552.sra SRR8846552.sra file validated SRR8846552 is single end SRR8846552 is conventional basespace SRR8846552 read1 length is 101 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR8846552_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 30.90075 34.0 33.0 34.0 27.0 34.0 2 32.78975 34.0 33.0 34.0 28.0 34.0 3 33.0035 34.0 33.0 34.0 32.0 34.0 4 33.04375 34.0 33.0 34.0 32.0 34.0 5 32.93625 34.0 33.0 34.0 32.0 34.0 6 36.52175 38.0 37.0 38.0 34.0 38.0 7 37.164 38.0 38.0 38.0 36.0 38.0 8 37.32725 38.0 38.0 38.0 37.0 38.0 9 37.366 38.0 38.0 38.0 37.0 38.0 10-11 37.449250000000006 38.0 38.0 38.0 37.0 38.0 12-13 37.473625 38.0 38.0 38.0 37.0 38.0 14-15 37.492 38.0 38.0 38.0 37.5 38.0 16-17 37.374875 38.0 38.0 38.0 37.0 38.0 18-19 37.458 38.0 38.0 38.0 37.0 38.0 20-21 37.484125000000006 38.0 38.0 38.0 38.0 38.0 22-23 37.435500000000005 38.0 38.0 38.0 37.0 38.0 24-25 37.518625 38.0 38.0 38.0 37.5 38.0 26-27 37.52375 38.0 38.0 38.0 38.0 38.0 28-29 37.53 38.0 38.0 38.0 38.0 38.0 30-31 37.508 38.0 38.0 38.0 38.0 38.0 32-33 37.407 38.0 38.0 38.0 37.0 38.0 34-35 37.220124999999996 38.0 38.0 38.0 36.5 38.0 36-37 37.234 38.0 38.0 38.0 37.0 38.0 38-39 37.15825 38.0 38.0 38.0 36.5 38.0 40-41 37.18575 38.0 38.0 38.0 37.0 38.0 42-43 37.098875 38.0 38.0 38.0 36.5 38.0 44-45 37.11725 38.0 38.0 38.0 36.5 38.0 46-47 37.150999999999996 38.0 38.0 38.0 36.0 38.0 48-49 37.16975 38.0 38.0 38.0 37.0 38.0 50-51 37.202375 38.0 38.0 38.0 36.5 38.0 52-53 37.25449999999999 38.0 38.0 38.0 37.0 38.0 54-55 37.147625000000005 38.0 38.0 38.0 36.5 38.0 56-57 36.961 38.0 38.0 38.0 36.0 38.0 58-59 36.968374999999995 38.0 38.0 38.0 36.0 38.0 60-61 36.982124999999996 38.0 38.0 38.0 36.0 38.0 62-63 36.7855 38.0 38.0 38.0 35.0 38.0 64-65 36.782 38.0 38.0 38.0 35.0 38.0 66-67 36.58475 38.0 38.0 38.0 34.5 38.0 68-69 36.437250000000006 38.0 38.0 38.0 34.5 38.0 70-71 36.050625 38.0 37.0 38.0 33.5 38.0 72-73 36.085625 38.0 38.0 38.0 34.0 38.0 74-75 35.999375 38.0 37.5 38.0 33.0 38.0 76-77 35.3775 38.0 37.0 38.0 29.0 38.0 78-79 35.077875000000006 38.0 36.5 38.0 27.5 38.0 80-81 35.150125 38.0 36.5 38.0 28.0 38.0 82-83 35.0945 38.0 36.0 38.0 28.0 38.0 84-85 35.2595 38.0 36.5 38.0 28.5 38.0 86-87 35.6545 38.0 37.0 38.0 31.5 38.0 88-89 35.658874999999995 38.0 37.0 38.0 31.0 38.0 90-91 35.557125 38.0 37.0 38.0 31.5 38.0 92-93 35.471625 38.0 37.5 38.0 31.5 38.0 94-95 35.116875 38.0 37.0 38.0 30.0 38.0 96-97 34.369 38.0 36.5 38.0 25.5 38.0 98-99 32.800124999999994 38.0 34.5 38.0 8.5 38.0 100-101 30.85725 38.0 32.5 38.0 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 8 1.0 9 0.0 10 0.0 11 0.0 12 0.0 13 0.0 14 0.0 15 0.0 16 1.0 17 0.0 18 0.0 19 3.0 20 2.0 21 1.0 22 3.0 23 5.0 24 11.0 25 34.0 26 25.0 27 12.0 28 19.0 29 26.0 30 30.0 31 71.0 32 85.0 33 114.0 34 164.0 35 307.0 36 773.0 37 2313.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 31.22646584185046 25.470683162990852 18.262506724045185 25.0403442711135 2 25.074999999999996 34.050000000000004 16.125 24.75 3 23.425 18.099999999999998 23.200000000000003 35.275 4 27.0 29.375 17.375 26.25 5 32.125 23.599999999999998 20.775 23.5 6 26.25 30.45 22.925 20.375 7 38.2 23.325000000000003 19.875 18.6 8 21.45 19.2 37.25 22.1 9 23.9 34.849999999999994 22.45 18.8 10-11 30.587500000000002 26.025 22.662499999999998 20.724999999999998 12-13 23.1 20.75 19.45 36.7 14-15 22.6 36.3125 24.625 16.4625 16-17 27.8375 26.2125 27.4125 18.5375 18-19 31.7875 26.825 21.1875 20.200000000000003 20-21 19.725 29.45 30.612499999999997 20.2125 22-23 26.0 28.8375 28.5625 16.6 24-25 27.6 26.8625 23.9125 21.625 26-27 33.074999999999996 28.012500000000003 19.9625 18.95 28-29 22.787499999999998 27.85 26.487500000000004 22.875 30-31 25.412499999999998 21.099999999999998 33.875 19.6125 32-33 23.5875 22.875 32.375 21.1625 34-35 24.525 23.5375 30.025000000000002 21.912499999999998 36-37 30.45 18.099999999999998 33.0875 18.3625 38-39 32.275 21.099999999999998 27.6375 18.987499999999997 40-41 30.862499999999997 19.3 27.8125 22.025 42-43 31.125000000000004 19.9375 28.225 20.7125 44-45 37.325 17.65 21.175 23.849999999999998 46-47 33.5 26.3625 16.75 23.3875 48-49 31.112499999999997 23.1875 21.9625 23.7375 50-51 28.65 21.5375 17.875 31.937500000000004 52-53 26.5625 29.9625 13.25 30.225 54-55 26.6625 26.7625 17.0875 29.4875 56-57 23.7625 30.012499999999996 15.0875 31.137500000000003 58-59 15.55 32.2625 19.662499999999998 32.525 60-61 11.662500000000001 29.175 22.575 36.5875 62-63 13.2875 29.4875 22.662499999999998 34.5625 64-65 10.4375 29.1625 29.9625 30.4375 66-67 6.175 23.4625 31.35 39.0125 68-69 8.387500000000001 23.8875 31.924999999999997 35.8 70-71 9.2375 22.525000000000002 37.75 30.4875 72-73 11.975 17.175 36.4625 34.387499999999996 74-75 12.0875 18.575 34.7125 34.625 76-77 14.0375 16.975 40.575 28.4125 78-79 16.162499999999998 10.625 38.324999999999996 34.887499999999996 80-81 17.525 11.2375 37.824999999999996 33.4125 82-83 18.85 11.7875 42.275 27.0875 84-85 18.925 8.3125 39.525 33.2375 86-87 21.825 9.825000000000001 37.775 30.575000000000003 88-89 19.05 19.35 38.0375 23.5625 90-91 15.75 24.5 37.225 22.525000000000002 92-93 17.0375 32.800000000000004 29.15 21.0125 94-95 14.2125 43.9625 25.8625 15.962499999999999 96-97 10.674999999999999 52.5 24.95 11.875 98-99 9.9625 63.5 17.299999999999997 9.2375 100-101 7.5249999999999995 73.6 12.15 6.7250000000000005 >>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 0.5 31 2.0 32 5.0 33 10.0 34 12.5 35 13.0 36 12.5 37 16.0 38 32.0 39 43.5 40 60.5 41 94.0 42 151.0 43 276.5 44 319.0 45 324.5 46 346.0 47 320.5 48 332.5 49 328.5 50 287.0 51 208.5 52 149.5 53 190.0 54 230.5 55 139.0 56 40.0 57 22.0 58 15.0 59 9.0 60 4.0 61 1.5 62 2.0 63 1.5 64 0.5 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 7.049999999999999 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 54.675 #Duplication Level Percentage of deduplicated Percentage of total 1 82.62459990855052 45.175 2 8.184727937814358 8.95 3 2.7892089620484684 4.575 4 1.4174668495656149 3.1 5 0.9602194787379973 2.625 6 0.6401463191586648 2.1 7 0.594421582075903 2.275 8 0.36579789666209417 1.6 9 0.3200731595793324 1.575 >10 1.9204389574759946 20.05 >50 0.18289894833104708 7.9750000000000005 >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 85 2.125 No Hit AGCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGC 81 2.025 No Hit GGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGA 78 1.95 RNA PCR Primer, Index 1 (100% over 22bp) CACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGATGGAATTC 75 1.875 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATATGGAATTCTCGGGTGCCAAG 43 1.075 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGGAATTCTCGGGTGCC 40 1.0 No Hit GACACGACTCTCGGCAACGGATATCTCTGGAATTCTCGGGTGCCAAGGAA 39 0.975 RNA PCR Primer, Index 1 (100% over 23bp) AGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGG 34 0.8500000000000001 Illumina Small RNA Adapter 2 (100% over 21bp) CTCTGATGATGATCAAACTAATACTTTCGTTCTTCTGGAATTCTCGGGTG 30 0.75 No Hit GAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAG 29 0.7250000000000001 No Hit GCACCAGTGGTCTAGTGGTAGAATAGTACCTGGAATTCTCGGGTGCCAAG 27 0.675 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTTGGAATTCTCGGGTGCCAAG 26 0.65 No Hit TCGGACCAGGCTTCATTCCCCTGGAATTCTCGGGTGCCAAGGAACTCCAG 24 0.6 RNA PCR Primer, Index 1 (100% over 29bp) TCCGTCGTAGTCTAGGTGGTTAGGATACTCTGGAATTCTCGGGTGCCAAG 23 0.575 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCTGGAATTCTCGGGTGCCAAGG 23 0.575 Illumina Small RNA Adapter 2 (100% over 21bp) GCCTTGATGGTGAAATGGTAGACACGCGAGACTCATGGAATTCTCGGGTG 23 0.575 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTGGAATTCTCGGGTGCCAAGG 22 0.5499999999999999 Illumina Small RNA Adapter 2 (100% over 21bp) GCCCACCCCAAGATGAGTGCTCTCTCTGGAATTCTCGGGTGCCAAGGAAC 21 0.525 RNA PCR Primer, Index 1 (100% over 24bp) CTCGGGTGCCAAGGAACTCCAGTCACATTCCTATCTCGTATGCCGTCTTC 20 0.5 RNA PCR Primer, Index 27 (100% over 50bp) TCTCGGGTGCCAAGGAACTCCAGTCACATTCCTATCTCGTATGCCGTCTT 20 0.5 RNA PCR Primer, Index 27 (100% over 50bp) GGGATTGTAGTTCAATTGGTCAGAGCACCGCCTGGAATTCTCGGGTGCCA 18 0.44999999999999996 No Hit GACACGACTCTCGGCAACGGATATCTTGGAATTCTCGGGTGCCAAGGAAC 18 0.44999999999999996 RNA PCR Primer, Index 1 (100% over 24bp) ACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGATGGAATTCT 18 0.44999999999999996 No Hit TCCGTCGTAGTCTAGGTGGTTAGGATATGGAATTCTCGGGTGCCAAGGAA 17 0.42500000000000004 RNA PCR Primer, Index 1 (100% over 23bp) GACACGACTCTCGGCAACGGATATCTGGAATTCTCGGGTGCCAAGGAACT 17 0.42500000000000004 RNA PCR Primer, Index 1 (100% over 25bp) GACACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGATGGAAT 16 0.4 No Hit CAGCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTG 16 0.4 No Hit ACACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGATGGAATT 16 0.4 No Hit AATTCTCGGGTGCCAAGGAACTCCAGTCACATTCCTATCTCGTATGCCGT 16 0.4 RNA PCR Primer, Index 27 (100% over 50bp) AAGGGTGCTGAGAATACTTTGAATCTGACACTGGAATTCTCGGGTGCCAA 15 0.375 No Hit TGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAA 15 0.375 No Hit TCCTGTGGATGAGAAGGCATTTATATTCTGATGATATGGAATTCTCGGGT 14 0.35000000000000003 No Hit GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGATTGTGAATCTGGAATTC 14 0.35000000000000003 No Hit GCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCC 14 0.35000000000000003 No Hit GTCAGGATAGCTCAGTTGGTAGAGCAGAGGACTGATGGAATTCTCGGGTG 14 0.35000000000000003 No Hit ATATATTTCAAGTTATTTCGGATCTTGGAATTCTCGGGTGCCAAGGAACT 13 0.325 RNA PCR Primer, Index 1 (100% over 25bp) GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGAATTCTCGGGTGCCAAGG 12 0.3 Illumina Small RNA Adapter 2 (100% over 21bp) TTCTCGGGTGCCAAGGAACTCCAGTCACATTCCTATCTCGTATGCCGTCT 12 0.3 RNA PCR Primer, Index 27 (100% over 50bp) GGAGAGATGGCTGAGTGGACTAAAGCGGCGGATTGCTAATCTGGAATTCT 11 0.27499999999999997 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATGGAATTCTCGGGTGCCAAGGA 11 0.27499999999999997 RNA PCR Primer, Index 1 (100% over 22bp) AGGGCTATAGCTCAGTTCGGTAGAGCAACTCGTTTACACCGAGATGGAAT 11 0.27499999999999997 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATAAATGGAATTCTCGGGTGCCA 10 0.25 No Hit GCAGCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGT 10 0.25 No Hit GACACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATTGGAATTC 10 0.25 No Hit TGTATGCAGCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCT 10 0.25 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTCTTAATGGAATTCTCGGGTG 10 0.25 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATAAAAAATGGAATTCTCGGGTG 9 0.22499999999999998 No Hit GCCTTGATGGTGAAATGGTAGACACGCGAGACTCAAAATCTTGGAATTCT 9 0.22499999999999998 No Hit CACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGGAATTCTCG 9 0.22499999999999998 No Hit GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGATTTGGAATTCTCGGGTG 9 0.22499999999999998 No Hit TGCCACGATCCACTGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAAT 9 0.22499999999999998 No Hit ACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGGGTGC 9 0.22499999999999998 No Hit CTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCA 9 0.22499999999999998 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCCTGGAATTCTCGGGTGC 8 0.2 No Hit CGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGATGGAATTCTC 8 0.2 No Hit CAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGGG 8 0.2 No Hit CAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTTGAATTCTCGGG 8 0.2 No Hit TATGCAGCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCG 8 0.2 No Hit TCCAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCG 8 0.2 No Hit CCAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGG 8 0.2 No Hit GACACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGTGGAATTCTC 8 0.2 No Hit GTCAGGATAGCTCAGTTGGTAGAGCAGAGGACTTGGAATTCTCGGGTGCC 7 0.17500000000000002 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATAAAATGGAATTCTCGGGTGCC 7 0.17500000000000002 No Hit TTCGGACCAGGCTTCATTCCCTGGAATTCTCGGGTGCCAAGGAACTCCAG 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 29bp) ACACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGGAATTCTC 7 0.17500000000000002 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATAAAAATGGAATTCTCGGGTGC 7 0.17500000000000002 No Hit ATAACCGTAGTAATTCTAGAGCTAATGGAATTCTCGGGTGCCAAGGAACT 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 25bp) NATCGAGTAGACCTTGTTATTGTGAGAATATGGAATTCTCGGGTGCCAAG 7 0.17500000000000002 No Hit GACACGACTCTCGGCAACGGATATCTCGGCTCTCGCTGGAATTCTCGGGT 7 0.17500000000000002 No Hit NGCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGC 7 0.17500000000000002 No Hit TCGTGCTGAAGAGCGTGGAGGTTCGAGTCCTCTTCAAGGCACCATGGAAT 7 0.17500000000000002 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTCAAGGCTGGAATTC 7 0.17500000000000002 No Hit TGCAGCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGG 7 0.17500000000000002 No Hit ATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCCAAGGAA 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 23bp) ATGCAGCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGG 6 0.15 No Hit NCCACTGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGT 6 0.15 No Hit CATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGGGTGCC 6 0.15 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTCTTAAATGGAATTCTCGGGT 6 0.15 No Hit ACTCGGATAACCGTAGTAATTCTAGAGCTAATACGTGGAATTCTCGGGTG 6 0.15 No Hit CCACTGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTG 6 0.15 No Hit GGGGATATGGCGAAATCGGTAGACGCTACGGACTTTGGAATTCTCGGGTG 6 0.15 No Hit GACACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGTGGAATT 6 0.15 No Hit ATGCAGTTACTAATTCATGATCTGGCTGGAATTCTCGGGTGCCAAGGAAC 6 0.15 RNA PCR Primer, Index 1 (100% over 24bp) GCGAGCGTAGTTCAATGGTAAAACATCTCCTTGCCAAGGATGGAATTCTC 6 0.15 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTAAAAAAAATGGAATTCTCGG 6 0.15 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTCTTAAAAAATGGAATTCTCG 6 0.15 No Hit ACTGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCC 6 0.15 No Hit GACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTTGAATTCTCGGGTG 6 0.15 No Hit CACGACTCTCGGCAACGGATATCTCTGGAATTCTCGGGTGCCAAGGAACT 5 0.125 RNA PCR Primer, Index 1 (100% over 25bp) TAAAAGGCTGACGCGGGCTTTGCTCGCTTGGAATTCTCGGGTGCCAAGGA 5 0.125 RNA PCR Primer, Index 1 (100% over 22bp) GCACCAGTGGTCTAGTGGTAGAATAGTATGGAATTCTCGGGTGCCAAGGA 5 0.125 RNA PCR Primer, Index 1 (100% over 22bp) ACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTTGATTTGGAATTCTC 5 0.125 No Hit CGACACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGATGGAA 5 0.125 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTCAAGGTGGAATTCT 5 0.125 No Hit GACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGGGTG 5 0.125 No Hit CATAGCAAGGATTGACAGACTGAGAGCTCTTTCTTGATTCTATGGAATTC 5 0.125 No Hit GCACCAGTAGTCTAGTGGTAGAATAGTACCTGGAATTCTCGGGTGCCAAG 5 0.125 No Hit GTCAGGATAGCTCAGTTGGTAGAGCAGATGGAATTCTCGGGTGCCAAGGA 5 0.125 RNA PCR Primer, Index 1 (100% over 22bp) ATATATTTCAAGTTATTTCGGATCTGGAATTCTCGGGTGCCAAGGAACTC 5 0.125 RNA PCR Primer, Index 1 (100% over 26bp) CATCGAGTAGACCTTGTTATTGTGAGAATAAAAAAAAATGGAATTCTCGG 5 0.125 No Hit GCAAGTATGAACTAATTTGAACTGTGAAACTTGGAATTCTCGGGTGCCAA 5 0.125 No Hit TGCAAGTATGAACTAATTTGAACTGTGAAACTTGGAATTCTCGGGTGCCA 5 0.125 No Hit GCCTTGATGGTGAAATGGTAGACACGCGAGACTTGGAATTCTCGGGTGCC 5 0.125 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTCTAATGGAATTCTCGGGTGC 5 0.125 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTAATGGAATTCTCGGGTGCCA 5 0.125 No Hit ATATTGGGTAGGTTGTGGTATTTCATTGCTGGAATTCTCGGGTGCCAAGG 5 0.125 Illumina Small RNA Adapter 2 (100% over 21bp) GACACGACTCTCGGCAACGGATATCTCGTGGAATTCTCGGGTGCCAAGGA 5 0.125 RNA PCR Primer, Index 1 (100% over 22bp) ATAACCGTAGTAATTCTAGAGCTAATATGGAATTCTCGGGTGCCAAGGAA 5 0.125 RNA PCR Primer, Index 1 (100% over 23bp) 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 0.025 0.0 0.0 0.0 7 0.0 0.025 0.0 0.0 0.0 8 0.0 0.025 0.0 0.0 0.0 9 0.0 0.075 0.0 0.0 0.0 10-11 0.0 0.125 0.0 0.0 0.0 12-13 0.0 0.16249999999999998 0.0 0.0 0.0 14-15 0.0 0.3 0.0 0.0 0.0 16-17 0.0 0.6375 0.0 0.0 0.0 18-19 0.0 0.9875 0.0 0.0 0.0 20-21 0.0 1.5375 0.0 0.0 0.0 22-23 0.0 4.0875 0.0 0.0 0.0 24-25 0.0 9.899999999999999 0.0 0.0 0.0 26-27 0.0 17.95 0.0 0.0 0.0 28-29 0.0 25.85 0.0 0.0 0.0 30-31 0.0 36.8875 0.0 0.0 0.0 32-33 0.0 46.125 0.0 0.0 0.0 34-35 0.0 56.125 0.0 0.0 0.0 36-37 0.0 68.0875 0.0 0.0 0.0 38-39 0.0 75.44999999999999 0.0 0.0 0.0 40-41 0.0 80.8125 0.0 0.0 0.0 42-43 0.0 87.2125 0.0 0.0 0.0 44-45 0.0 91.75 0.0 0.0 0.0 46-47 0.0 93.5625 0.0 0.0 0.0 48-49 0.0 94.3125 0.0 0.0 0.0 50-51 0.0 94.725 0.0 0.0 0.0 52-53 0.0 94.94999999999999 0.0 0.0 0.0 54-55 0.0 95.07499999999999 0.0 0.0 0.0 56-57 0.0 95.1375 0.0 0.0 0.0 58-59 0.0 95.175 0.0 0.0 0.0 60-61 0.0 95.175 0.0 0.0 0.0 62-63 0.0 95.175 0.0 0.0 0.0 64-65 0.0 95.175 0.0 0.0 0.0 66-67 0.0 95.175 0.0 0.0 0.0 68-69 0.0 95.175 0.0 0.0 0.0 70-71 0.0 95.175 0.0 0.0 0.0 72-73 0.0 95.175 0.0 0.0 0.0 74-75 0.0 95.175 0.0 0.0 0.0 76-77 0.0 95.175 0.0 0.0 0.0 78-79 0.0 95.175 0.0 0.0 0.0 80-81 0.0 95.175 0.0 0.0 0.0 82-83 0.0 95.175 0.0 0.0 0.0 84-85 0.0 95.175 0.0 0.0 0.0 86-87 0.0 95.175 0.0 0.0 0.0 88-89 0.0 95.175 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GGGATTG 15 4.2518976E-4 104.0137 1 GTAGACC 40 5.456968E-12 94.912506 7 TTGTAGT 20 1.5462934E-5 94.912506 5 AGTAGAC 40 5.456968E-12 94.912506 6 TAGTTCA 20 1.5462934E-5 94.912506 8 CGAGTAG 40 5.456968E-12 94.912506 4 AGACCTT 40 5.456968E-12 94.912506 9 TCGAGTA 40 5.456968E-12 94.912506 3 AGTTCAA 20 1.5462934E-5 94.912506 9 GTAGTTC 20 1.5462934E-5 94.912506 7 TAGACCT 40 5.456968E-12 94.912506 8 GATTGTA 15 6.164719E-4 94.9125 3 GAGTAGA 45 0.0 94.9125 5 ATTGTAG 15 6.164719E-4 94.9125 4 TGTAGTT 15 6.164719E-4 94.9125 6 CATCGAG 35 1.43245416E-8 89.15461 1 AGCTGAG 30 6.489008E-7 86.678085 1 ATCGAGT 45 1.6370905E-11 84.36667 2 CTGAGGC 30 1.1400607E-6 79.09375 3 GCTGAGG 30 1.1400607E-6 79.09375 2 >>END_MODULE Rejected 927686 READS because READLEN < 1 Read 927686 spots for SRR8846552.sra Written 927686 spots for SRR8846552.sra Rejected 927686 READS because READLEN < 1 Read 927686 spots for SRR8846552.sra Written 927686 spots for SRR8846552.sra Rejected 927686 READS because READLEN < 1 Read 927686 spots for SRR8846552.sra Written 927686 spots for SRR8846552.sra Rejected 927686 READS because READLEN < 1 Read 927686 spots for SRR8846552.sra Written 927686 spots for SRR8846552.sra Rejected 927686 READS because READLEN < 1 Read 927686 spots for SRR8846552.sra Written 927686 spots for SRR8846552.sra Rejected 927686 READS because READLEN < 1 Read 927686 spots for SRR8846552.sra Written 927686 spots for SRR8846552.sra Rejected 927686 READS because READLEN < 1 Read 927686 spots for SRR8846552.sra Written 927686 spots for SRR8846552.sra Rejected 927688 READS because READLEN < 1 Read 927688 spots for SRR8846552.sra Written 927688 spots for SRR8846552.sra Rejected 927686 READS because READLEN < 1 Read 927686 spots for SRR8846552.sra Written 927686 spots for SRR8846552.sra Rejected 927686 READS because READLEN < 1 Read 927686 spots for SRR8846552.sra Written 927686 spots for SRR8846552.sra Rejected 927686 READS because READLEN < 1 Read 927686 spots for SRR8846552.sra Written 927686 spots for SRR8846552.sra Rejected 927686 READS because READLEN < 1 Read 927686 spots for SRR8846552.sra Written 927686 spots for SRR8846552.sra Rejected 927686 READS because READLEN < 1 Read 927686 spots for SRR8846552.sra Written 927686 spots for SRR8846552.sra Rejected 927686 READS because READLEN < 1 Read 927686 spots for SRR8846552.sra Written 927686 spots for SRR8846552.sra Rejected 927686 READS because READLEN < 1 Read 927686 spots for SRR8846552.sra Written 927686 spots for SRR8846552.sra Rejected 927686 READS because READLEN < 1 Read 927686 spots for SRR8846552.sra Written 927686 spots for SRR8846552.sra Rejected 927686 READS because READLEN < 1 Read 927686 spots for SRR8846552.sra Written 927686 spots for SRR8846552.sra Rejected 927686 READS because READLEN < 1 Read 927686 spots for SRR8846552.sra Written 927686 spots for SRR8846552.sra Rejected 927686 READS because READLEN < 1 Read 927686 spots for SRR8846552.sra Written 927686 spots for SRR8846552.sra Rejected 927686 READS because READLEN < 1 Read 927686 spots for SRR8846552.sra Written 927686 spots for SRR8846552.sra SRR ids: ['SRR8846552.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_c02v0jun SRR8846552.sra spots: 18553722 blocks: [[1, 927686], [927687, 1855372], [1855373, 2783058], [2783059, 3710744], [3710745, 4638430], [4638431, 5566116], [5566117, 6493802], [6493803, 7421488], [7421489, 8349174], [8349175, 9276860], [9276861, 10204546], [10204547, 11132232], [11132233, 12059918], [12059919, 12987604], [12987605, 13915290], [13915291, 14842976], [14842977, 15770662], [15770663, 16698348], [16698349, 17626034], [17626035, 18553722]] SRR8846552 file size 4453660 SRR8846552 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 SRR8846552 SRR8846552_1.fastq Input file: SRR8846552_1.fastq trimmed: SRR8846552-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 10:14:21 2024 >> started Mon Dec 9 10:14:42 2024 >> done (21.220s) 18553722 reads processed; of these: 354 ( 0.00%) short reads filtered out after trimming by size control 48 ( 0.00%) empty reads filtered out after trimming by size control 18553320 (100.00%) reads available; of these: 2308810 (12.44%) trimmed reads available after processing 16244510 (87.56%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 41 0.00% 19 47 0.00% 20 39 0.00% 21 37 0.00% 22 50 0.00% 23 59 0.00% 24 86 0.00% 25 61 0.00% 26 107 0.00% 27 87 0.00% 28 112 0.00% 29 143 0.00% 30 142 0.00% 31 157 0.00% 32 182 0.00% 33 218 0.00% 34 347 0.00% 35 315 0.00% 36 665 0.00% 37 784 0.00% 38 1025 0.01% 39 1196 0.01% 40 1093 0.01% 41 941 0.01% 42 728 0.00% 43 733 0.00% 44 630 0.00% 45 589 0.00% 46 431 0.00% 47 489 0.00% 48 506 0.00% 49 594 0.00% 50 774 0.00% 51 729 0.00% 52 606 0.00% 53 450 0.00% 54 304 0.00% 55 268 0.00% 56 284 0.00% 57 305 0.00% 58 344 0.00% 59 544 0.00% 60 712 0.00% 61 1332 0.01% 62 1843 0.01% 63 2645 0.01% 64 4022 0.02% 65 4271 0.02% 66 11219 0.06% 67 46052 0.25% 68 52459 0.28% 69 36946 0.20% 70 29360 0.16% 71 36907 0.20% 72 14752 0.08% 73 4385 0.02% 74 5482 0.03% 75 3659 0.02% 76 3441 0.02% 77 3488 0.02% 78 3998 0.02% 79 4461 0.02% 80 4904 0.03% 81 5802 0.03% 82 8234 0.04% 83 8262 0.04% 84 7861 0.04% 85 8200 0.04% 86 9110 0.05% 87 11670 0.06% 88 15762 0.08% 89 21079 0.11% 90 29534 0.16% 91 32107 0.17% 92 40235 0.22% 93 60596 0.33% 94 77479 0.42% 95 150840 0.81% 96 199782 1.08% 97 232794 1.25% 98 410186 2.21% 99 405024 2.18% 100 280673 1.51% 101 16244510 87.56% 18553320 reads passed initial QC criterion=sequence-density sequence-density=94.69 sequence-density-rank=1 fanout-score=30.37 fanout-score-rank=1 prefix-density=95.19 prefix-fanout=30.2 sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACATTCCTATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAA criterion=fanout-score sequence-density=94.69 sequence-density-rank=1 fanout-score=30.37 fanout-score-rank=1 prefix-density=95.19 prefix-fanout=30.2 sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACATTCCTATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAA 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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACATTCCTATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAA -o SRR8846552 - Input file: STDIN trimmed: SRR8846552-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACATTCCTATCTCGTATGCCGTCTTCTGCTTGA -- 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 10:17:16 2024 >> started Mon Dec 9 10:17:43 2024 >> done (26.555s) 18162724 reads processed; of these: 152172 ( 0.84%) short reads filtered out after trimming by size control 8808 ( 0.05%) empty reads filtered out after trimming by size control 18001744 (99.11%) reads available; of these: 17497160 (97.20%) trimmed reads available after processing 504584 ( 2.80%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 37505 0.21% 19 67834 0.38% 20 82883 0.46% 21 297709 1.65% 22 220123 1.22% 23 317587 1.76% 24 1113410 6.19% 25 546496 3.04% 26 635240 3.53% 27 738379 4.10% 28 959234 5.33% 29 939958 5.22% 30 1237558 6.87% 31 717309 3.98% 32 777900 4.32% 33 1011457 5.62% 34 1120703 6.23% 35 1035832 5.75% 36 1073166 5.96% 37 586524 3.26% 38 500617 2.78% 39 497656 2.76% 40 485023 2.69% 41 634283 3.52% 42 742237 4.12% 43 278515 1.55% 44 300985 1.67% 45 170219 0.95% 46 119642 0.66% 47 63567 0.35% 48 59177 0.33% 49 34288 0.19% 50 23950 0.13% 51 19943 0.11% 52 9635 0.05% 53 7002 0.04% 54 9674 0.05% 55 2544 0.01% 56 2646 0.01% 57 1429 0.01% 58 1030 0.01% 59 989 0.01% 60 969 0.01% 61 1610 0.01% 62 1814 0.01% 63 2631 0.01% 64 3924 0.02% 65 4099 0.02% 66 10830 0.06% 67 44964 0.25% 68 51130 0.28% 69 35823 0.20% 70 28480 0.16% 71 35647 0.20% 72 13020 0.07% 73 3017 0.02% 74 2116 0.01% 75 1627 0.01% 76 2047 0.01% 77 4373 0.02% 78 1962 0.01% 79 2294 0.01% 80 4826 0.03% 81 3244 0.02% 82 2913 0.02% 83 4136 0.02% 84 1759 0.01% 85 1646 0.01% 86 1683 0.01% 87 1604 0.01% 88 1168 0.01% 89 1635 0.01% 90 1364 0.01% 91 1355 0.01% 92 1351 0.01% 93 1790 0.01% 94 1768 0.01% 95 2236 0.01% 96 3023 0.02% 97 4475 0.02% 98 6844 0.04% 99 6752 0.04% 100 8469 0.05% 101 203468 1.13% criterion=sequence-density sequence-density=8.19 sequence-density-rank=1 fanout-score=0.00 fanout-score-rank=12 prefix-density=0.00 prefix-fanout=1.0 sequence=CATCGAGTAGACCTTGTTATTGTGAGAATTCTTAATTCAAGAGT criterion=fanout-score sequence-density=0.37 sequence-density-rank=14 fanout-score=20.68 fanout-score-rank=1 prefix-density=7.63 prefix-fanout=1.0 sequence=TTGTGAGAATTAAAAA Started job on | Dec 09 10:20:27 Started mapping on | Dec 09 10:20:27 Finished on | Dec 09 10:21:23 Mapping speed, Million of reads per hour | 1182.36 Number of input reads | 18392340 Average input read length | 35 UNIQUE READS: Uniquely mapped reads number | 2246481 Uniquely mapped reads % | 12.21% Average mapped length | 30.35 Number of splices: Total | 25618 Number of splices: Annotated (sjdb) | 15118 Number of splices: GT/AG | 22121 Number of splices: GC/AG | 2257 Number of splices: AT/AC | 17 Number of splices: Non-canonical | 1223 Mismatch rate per base, % | 0.15% Deletion rate per base | 0.00% Deletion average length | 1.30 Insertion rate per base | 0.00% Insertion average length | 1.03 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 7592492 % of reads mapped to multiple loci | 41.28% Number of reads mapped to too many loci | 7416698 % of reads mapped to too many loci | 40.32% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 5.74% % of reads unmapped: other | 0.44% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 8553367 8553367 8553367 N_multimapping 7592492 7592492 7592492 N_noFeature 1181560 1419877 1994744 N_ambiguous 53329 39745 335 UnstrandedReadsAssigned:1011592 PositiveStrandReadsAssigned:786859 NegativeStrandReadsAssigned:251402 Dataset is classified unstranded MeadianReadLen=33 20thPercentileLength=27 echo kmer=23 SRR8846552 Starting Kallisto single end mapping to ensembl reference transcriptome. kmer=23 [quant] fragment length distribution is truncated gaussian with mean = 100, sd = 20 [index] k-mer length: 23 [index] number of targets: 52,972 [index] number of k-mers: 66,237,239 [index] number of equivalence classes: 154,277 [quant] running in single-end mode [quant] will process file 1: SRR8846552-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 18,392,340 reads, 4,656,220 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 905 rounds 52973 SRR8846552.ke.tsv 35125 SRR8846552.se.tsv 88098 total ==> SRR8846552.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 837 0 0 PNS24247 1044 945 0.333333 0.0520574 PNS24249 1928 1829 0 0 PNS24246 1044 945 0.333333 0.0520574 PNS24248 1044 945 0.333333 0.0520574 PNS24244 1471 1372 5 0.537838 PNS24243 293 194 0 0 KQK14069 1603 1504 267.905 26.2887 KQK14071 474 375 21.6634 8.5257 ==> SRR8846552.se.tsv <== BRADI_1g14170v3 379 BRADI_1g53295v3 0 BRADI_1g59795v3 8 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 13 BRADI_1g74790v3 18 BRADI_1g09890v3 0 BRADI_1g77505v3 1 BRADI_1g48960v3 0 SRR8846552 completed mapping pipeline successfully