Starting /dee2/code/volunteer_pipeline.sh SRR6941538 current disk space = 1551545425920 free memory = 1607239636 SRR6941538 SRAfilesize 17b53adae5eec905a28e3252a9e15075 SRR6941538.sra SRR6941538.sra file validated SRR6941538 is single end SRR6941538 is conventional basespace SRR6941538 read1 length is 101 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR6941538_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 32.975 34.0 33.0 34.0 32.0 34.0 2 33.17525 34.0 33.0 34.0 32.0 34.0 3 32.351 34.0 33.0 34.0 28.0 34.0 4 32.85725 34.0 33.0 34.0 32.0 34.0 5 32.994 34.0 33.0 34.0 31.0 34.0 6 36.884 38.0 37.0 38.0 36.0 38.0 7 37.20525 38.0 38.0 38.0 36.0 38.0 8 37.309 38.0 38.0 38.0 37.0 38.0 9 37.47225 38.0 38.0 38.0 37.0 38.0 10-11 37.405625 38.0 38.0 38.0 37.0 38.0 12-13 37.296875 38.0 38.0 38.0 37.0 38.0 14-15 37.349500000000006 38.0 38.0 38.0 37.0 38.0 16-17 36.253 38.0 37.5 38.0 31.5 38.0 18-19 36.84425 38.0 38.0 38.0 34.5 38.0 20-21 35.66974999999999 38.0 37.0 38.0 30.5 38.0 22-23 36.856375 38.0 37.5 38.0 33.5 38.0 24-25 37.341499999999996 38.0 38.0 38.0 37.0 38.0 26-27 37.269625000000005 38.0 38.0 38.0 37.0 38.0 28-29 37.363375000000005 38.0 38.0 38.0 37.0 38.0 30-31 37.318875 38.0 38.0 38.0 37.0 38.0 32-33 37.23425 38.0 38.0 38.0 37.0 38.0 34-35 37.159625 38.0 38.0 38.0 37.0 38.0 36-37 37.057625 38.0 38.0 38.0 36.5 38.0 38-39 37.163 38.0 38.0 38.0 37.0 38.0 40-41 37.01775 38.0 38.0 38.0 36.5 38.0 42-43 36.949875000000006 38.0 38.0 38.0 36.0 38.0 44-45 36.9845 38.0 38.0 38.0 36.0 38.0 46-47 36.9075 38.0 38.0 38.0 36.0 38.0 48-49 36.989875 38.0 38.0 38.0 36.5 38.0 50-51 36.76375 38.0 38.0 38.0 35.5 38.0 52-53 36.719375 38.0 38.0 38.0 35.5 38.0 54-55 36.885000000000005 38.0 38.0 38.0 36.0 38.0 56-57 36.855625 38.0 38.0 38.0 35.5 38.0 58-59 37.03725 38.0 38.0 38.0 36.0 38.0 60-61 37.054500000000004 38.0 38.0 38.0 36.0 38.0 62-63 36.645125 38.0 38.0 38.0 34.5 38.0 64-65 36.4745 38.0 37.5 38.0 34.0 38.0 66-67 36.151624999999996 38.0 37.0 38.0 31.5 38.0 68-69 36.688125 38.0 38.0 38.0 35.0 38.0 70-71 36.210875 38.0 37.0 38.0 32.0 38.0 72-73 36.182 38.0 37.0 38.0 33.0 38.0 74-75 35.972875 38.0 37.0 38.0 31.5 38.0 76-77 35.849999999999994 38.0 37.0 38.0 32.0 38.0 78-79 35.738 38.0 37.0 38.0 30.0 38.0 80-81 36.164500000000004 38.0 38.0 38.0 34.0 38.0 82-83 36.2415 38.0 38.0 38.0 34.0 38.0 84-85 36.295125 38.0 38.0 38.0 34.0 38.0 86-87 36.053250000000006 38.0 38.0 38.0 34.0 38.0 88-89 36.0475 38.0 38.0 38.0 34.0 38.0 90-91 35.9705 38.0 38.0 38.0 34.0 38.0 92-93 35.757374999999996 38.0 38.0 38.0 33.5 38.0 94-95 35.306125 38.0 38.0 38.0 32.5 38.0 96-97 32.54425 38.0 35.0 38.0 8.5 38.0 98-99 29.30725 38.0 24.5 38.0 2.0 38.0 100-101 25.665125 38.0 2.0 38.0 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 1.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 1.0 9 0.0 10 0.0 11 0.0 12 0.0 13 1.0 14 0.0 15 0.0 16 0.0 17 1.0 18 0.0 19 5.0 20 3.0 21 3.0 22 3.0 23 5.0 24 6.0 25 13.0 26 17.0 27 31.0 28 54.0 29 38.0 30 42.0 31 52.0 32 76.0 33 109.0 34 216.0 35 532.0 36 824.0 37 1967.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 35.25 27.725 16.6 20.424999999999997 2 34.150000000000006 25.825 17.5 22.525000000000002 3 29.5 18.2 24.375 27.925 4 32.225 24.6 18.425 24.75 5 41.05 21.85 20.175 16.925 6 22.925 32.25 22.875 21.95 7 35.475 20.724999999999998 28.225 15.575 8 27.6 17.4 37.6 17.4 9 22.6 35.425000000000004 27.325 14.649999999999999 10-11 36.6125 25.587500000000002 16.85 20.95 12-13 19.675 15.425 25.3 39.6 14-15 21.637500000000003 37.762499999999996 23.5375 17.0625 16-17 28.712500000000002 15.950000000000001 38.15 17.1875 18-19 38.7 21.8125 22.5 16.9875 20-21 16.925 26.625 34.825 21.625 22-23 28.9 29.7875 23.7125 17.599999999999998 24-25 30.775000000000002 29.25 23.599999999999998 16.375 26-27 40.362500000000004 22.037499999999998 20.5625 17.0375 28-29 18.575 38.9625 22.325 20.1375 30-31 21.3625 10.7375 46.6625 21.2375 32-33 30.2625 14.85 29.912499999999998 24.975 34-35 36.7375 19.787499999999998 26.687499999999996 16.7875 36-37 42.2875 16.025 26.700000000000003 14.9875 38-39 24.05 18.4375 33.7375 23.775 40-41 26.887499999999996 16.0875 21.4875 35.5375 42-43 34.0375 29.062500000000004 18.862499999999997 18.0375 44-45 51.0125 14.9875 12.75 21.25 46-47 25.6 32.4 15.262500000000001 26.737499999999997 48-49 22.325 24.9125 18.725 34.0375 50-51 26.3625 25.662499999999998 9.7875 38.1875 52-53 27.175 42.1 7.9750000000000005 22.75 54-55 16.025 27.537499999999998 21.7375 34.699999999999996 56-57 13.625000000000002 33.6625 14.95 37.762499999999996 58-59 22.575 25.7125 23.1125 28.599999999999998 60-61 10.237499999999999 21.525 33.324999999999996 34.9125 62-63 10.1875 23.4125 19.3875 47.0125 64-65 13.525 28.012500000000003 31.4625 27.0 66-67 13.65 16.9625 35.8875 33.5 68-69 18.925 20.95 26.3 33.825 70-71 12.075 21.75 37.5375 28.6375 72-73 18.862499999999997 11.6125 34.637499999999996 34.887499999999996 74-75 15.675 9.7125 29.925 44.6875 76-77 20.0375 12.687499999999998 44.824999999999996 22.45 78-79 18.5 8.975 39.2 33.324999999999996 80-81 21.5625 9.0875 33.575 35.775 82-83 25.5625 6.6000000000000005 41.4 26.437500000000004 84-85 18.0375 9.625 40.862500000000004 31.474999999999998 86-87 19.925 17.837500000000002 39.65 22.5875 88-89 14.0375 38.8875 27.287499999999998 19.787499999999998 90-91 9.8375 42.8625 31.387500000000003 15.9125 92-93 15.975 50.9875 21.925 11.1125 94-95 9.725 65.9875 16.775000000000002 7.512499999999999 96-97 7.75 77.6625 10.7875 3.8 98-99 4.075 87.7875 5.0874999999999995 3.05 100-101 2.1875 90.2375 4.237500000000001 3.3375000000000004 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 0.0 1 0.0 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10 0.0 11 0.0 12 0.0 13 0.0 14 0.0 15 0.0 16 0.0 17 0.0 18 0.0 19 0.0 20 0.0 21 0.0 22 0.0 23 0.0 24 0.0 25 0.0 26 0.0 27 0.0 28 0.0 29 0.0 30 0.0 31 0.0 32 0.0 33 2.5 34 4.5 35 5.0 36 10.0 37 10.0 38 7.0 39 10.5 40 19.0 41 35.0 42 83.0 43 179.0 44 446.0 45 573.5 46 442.0 47 362.0 48 286.5 49 233.5 50 362.0 51 353.5 52 195.0 53 131.0 54 67.5 55 49.0 56 32.5 57 20.5 58 39.5 59 31.5 60 3.5 61 2.5 62 1.5 63 1.0 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 pass #Base N-Count 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 10-11 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 53.15 #Duplication Level Percentage of deduplicated Percentage of total 1 88.00564440263405 46.775 2 4.985888993414863 5.3 3 2.257761053621825 3.5999999999999996 4 0.8466603951081844 1.7999999999999998 5 0.6114769520225777 1.625 6 0.7996237064910631 2.55 7 0.23518344308560676 0.8750000000000001 8 0.18814675446848542 0.8 9 0.28222013170272814 1.35 >10 1.5051740357478833 20.4 >50 0.18814675446848542 6.275 >100 0.09407337723424271 8.649999999999999 >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 GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGAATTCTCGGGTGCCAAGG 232 5.800000000000001 Illumina Small RNA Adapter 2 (100% over 21bp) TCGGACCAGGCTTCATTCCCCTGGAATTCTCGGGTGCCAAGGAACTCCAG 114 2.85 RNA PCR Primer, Index 1 (100% over 29bp) CATCGAGTAGACCTTGTTATTGTGAGAATTTGGAATTCTCGGGTGCCAAG 91 2.275 No Hit GGAGAGATGGCTGAGTGGACTAAAGCGGCGGATTTGGAATTCTCGGGTGC 56 1.4000000000000001 No Hit GTCAGGATAGCTCAGTTGGTAGAGCAGAGGACTTGGAATTCTCGGGTGCC 53 1.325 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTCTGGAATTCTCGGGTGCCAA 51 1.275 No Hit CGGTCGAGGGCACGCCTGCCTGGGCGTCACGCTGGAATTCTCGGGTGCCA 50 1.25 No Hit GAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAG 47 1.175 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGGAATTCTCGGGTGCC 44 1.0999999999999999 No Hit TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAGTTCCATCTCGTATGC 40 1.0 RNA PCR Primer, Index 14 (100% over 50bp) GCGAGCGTAGTTCAATGGTAAAACATCTCCTTTGGAATTCTCGGGTGCCA 40 1.0 No Hit ACTTTGTATCGCGCGCATGACTTGGAATTCTCGGGTGCCAAGGAACTCCA 37 0.9249999999999999 RNA PCR Primer, Index 1 (100% over 28bp) CATCGAGTAGACCTTGTTATTGTGAGAATTCTTGGAATTCTCGGGTGCCA 37 0.9249999999999999 No Hit ATATTGGGTAGGTTGTGGTATTTCATTGCTTGGAATTCTCGGGTGCCAAG 34 0.8500000000000001 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTGGAATTCTCGGGTGCCAAGG 34 0.8500000000000001 Illumina Small RNA Adapter 2 (100% over 21bp) CTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCA 32 0.8 RNA PCR Primer, Index 1 (100% over 28bp) GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTTGGAATTCTCGGGTGC 32 0.8 No Hit GAACTTTGTATCGCGCGCATGACTTGGAATTCTCGGGTGCCAAGGAACTC 30 0.75 RNA PCR Primer, Index 1 (100% over 26bp) AACTTTGTATCGCGCGCATGACTTGGAATTCTCGGGTGCCAAGGAACTCC 30 0.75 RNA PCR Primer, Index 1 (100% over 27bp) GGTGGCTGTAGTTTAGTGGTGAGAATTCCACGTTTGGAATTCTCGGGTGC 30 0.75 No Hit ATATTGGGTAGGTTGTGGTATTTCATTGCTGGAATTCTCGGGTGCCAAGG 29 0.7250000000000001 Illumina Small RNA Adapter 2 (100% over 21bp) ACCTGCTCTGATACCATGTTGTGATGGAATTCTCGGGTGCCAAGGAACTC 27 0.675 RNA PCR Primer, Index 1 (100% over 26bp) TCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACTC 25 0.625 RNA PCR Primer, Index 1 (100% over 26bp) GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGATTTGGAATTCTCGGGTG 24 0.6 No Hit TGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAA 23 0.575 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCCTGGAATTCTCGGGTGC 22 0.5499999999999999 No Hit GCGGATGTAGCCAAGTGGATCAAGGCAGTGGAATTCTCGGGTGCCAAGGA 19 0.475 RNA PCR Primer, Index 1 (100% over 22bp) GGGATTGTAGTTCAATTGGTCAGAGCACCGCCTGGAATTCTCGGGTGCCA 15 0.375 No Hit GGGTGTTTGGTCTAGTGGTATGATTCTCGCTTGGAATTCTCGGGTGCCAA 14 0.35000000000000003 No Hit AGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGG 14 0.35000000000000003 Illumina Small RNA Adapter 2 (100% over 21bp) GTCAGGATAGCTCAGTTGGTAGAGCAGAGGACTGATGGAATTCTCGGGTG 12 0.3 No Hit TTGACAGAAGAGAGTGAGCACTGGAATTCTCGGGTGCCAAGGAACTCCAG 12 0.3 RNA PCR Primer, Index 1 (100% over 29bp) GTCAGGATAGCTCAGTTGGTAGAGCAGAGGACTGGAATTCTCGGGTGCCA 11 0.27499999999999997 No Hit GGTGGCTGTAGTTTAGTGGTGAGAATTCCACGTTGTTGGAATTCTCGGGT 11 0.27499999999999997 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTATGGAATTCTCGGGTGCCAA 11 0.27499999999999997 No Hit TTCGGACCAGGCTTCATTCCCTGGAATTCTCGGGTGCCAAGGAACTCCAG 10 0.25 RNA PCR Primer, Index 1 (100% over 29bp) GTCCTGCGGCAAAATAGCTCGATGCCAGAATTGGAATTCTCGGGTGCCAA 10 0.25 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATATGGAATTCTCGGGTGCCAAG 10 0.25 No Hit TCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCCAAGGAAC 9 0.22499999999999998 RNA PCR Primer, Index 1 (100% over 24bp) AGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCCAAGGAACTCC 9 0.22499999999999998 RNA PCR Primer, Index 1 (100% over 27bp) GGCGGATGTAGCCAAGAGGATCAAGGCAGTGGAATTCTCGGGTGCCAAGG 9 0.22499999999999998 Illumina Small RNA Adapter 2 (100% over 21bp) GTCGTTGTAGTATAGTGGTAAGTATTCCCGCCTTGGAATTCTCGGGTGCC 9 0.22499999999999998 No Hit GCGAGCGTAGTTCAATGGTAAAACATCTCCTTGCCAAGGATGGAATTCTC 9 0.22499999999999998 No Hit TGTCGTGCCAATTCAACATAAACCCCTGGAATTCTCGGGTGCCAAGGAAC 9 0.22499999999999998 RNA PCR Primer, Index 1 (100% over 24bp) TCCGTCGTAGTCTAGGTGGTTAGGATACTCTGGAATTCTCGGGTGCCAAG 8 0.2 No Hit TGTCGTGCCAATTCAACATAAACCCCTTGGAATTCTCGGGTGCCAAGGAA 8 0.2 RNA PCR Primer, Index 1 (100% over 23bp) TGCCACGATCCACTGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAAT 8 0.2 No Hit GCGAGCGTAGTTCAATGGTAAAACATCTCCTTGTGGAATTCTCGGGTGCC 8 0.2 No Hit AGGGATGTAGCGCAGCTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACA 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 34bp) AATATTGGGTAGGTTGTGGTATTTCATTGCTTGGAATTCTCGGGTGCCAA 7 0.17500000000000002 No Hit GGCGGATGTAGCCAAGTGGACCAAGGCAGTGGAATTCTCGGGTGCCAAGG 7 0.17500000000000002 Illumina Small RNA Adapter 2 (100% over 21bp) GTCAGGATAGCTCAGTTGGTAGAGCAGAGGACCTGGAATTCTCGGGTGCC 7 0.17500000000000002 No Hit CTGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCCA 7 0.17500000000000002 No Hit ATATTGGGTAGGTTGTGGTATTTCATTGTGGAATTCTCGGGTGCCAAGGA 6 0.15 RNA PCR Primer, Index 1 (100% over 22bp) GGAGAGATGGCTGAGTGGACTAAAGCGGCGGATTGCTGGAATTCTCGGGT 6 0.15 No Hit GAAGATACGGGTTCGATTCCCGCCGCTCGCCCCATGGAATTCTCGGGTGC 6 0.15 No Hit TAGAACTCCACATCCTTGGCCTGGAATTCTCGGGTGCCAAGGAACTCCAG 6 0.15 RNA PCR Primer, Index 1 (100% over 29bp) TCGGACCAGGCTTCATTCCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG 6 0.15 RNA PCR Primer, Index 1 (100% over 29bp) GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTGGAATTCTCGGGTG 6 0.15 No Hit TAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCAG 6 0.15 RNA PCR Primer, Index 1 (100% over 29bp) CCTGTGCCTGCCTCTTCCATTTGGAATTCTCGGGTGCCAAGGAACTCCAG 6 0.15 RNA PCR Primer, Index 1 (100% over 29bp) CTCTGATGATGATCAAACTAATACTTTCGTTCTTCTGGAATTCTCGGGTG 6 0.15 No Hit TCCCGTGCTGTAAAATAACTGATTTGCCTATCTGATCTGGAATTCTCGGG 6 0.15 No Hit GCGTCTGTAGTCCAACGGTTAGGATAATTGCCTTCTGGAATTCTCGGGTG 6 0.15 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTCAATGGAATTCTCGGGTGCC 6 0.15 No Hit GGTGGCTGTAGTTTAGTGGTGAGAATTCCACGTTGGAATTCTCGGGTGCC 6 0.15 No Hit CACGACTCTCGGCAACGGATATCTCGGCTTGGAATTCTCGGGTGCCAAGG 6 0.15 Illumina Small RNA Adapter 2 (100% over 21bp) CTTTGTATCGCGCGCATGACTTGGAATTCTCGGGTGCCAAGGAACTCCAG 6 0.15 RNA PCR Primer, Index 1 (100% over 29bp) CAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCCAAGGAACTC 6 0.15 RNA PCR Primer, Index 1 (100% over 26bp) TCGCTTGGTGCAGATCGGGACTGGAATTCTCGGGTGCCAAGGAACTCCAG 6 0.15 RNA PCR Primer, Index 1 (100% over 29bp) CATCGAGTAGACCTTGTTATTGTGAGAATAAATGGAATTCTCGGGTGCCA 5 0.125 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATGGAATTCTCGGGTGCCAAGGA 5 0.125 RNA PCR Primer, Index 1 (100% over 22bp) TGAAGCTGCCAGCATGATCTGATGGAATTCTCGGGTGCCAAGGAACTCCA 5 0.125 RNA PCR Primer, Index 1 (100% over 28bp) GCCTTGATGGTGAAATGGTAGACACGCGAGACTCAAAATCTTGGAATTCT 5 0.125 No Hit GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGATTGGAATTCTCGGGTGC 5 0.125 No Hit TCCACTGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGT 5 0.125 No Hit CCCTATAGAACTCCACATCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG 5 0.125 RNA PCR Primer, Index 1 (100% over 29bp) CATCGAGTAGACCTTGTTATTGTGAGATGGAATTCTCGGGTGCCAAGGAA 5 0.125 RNA PCR Primer, Index 1 (100% over 23bp) GGTGGCTGTAGTTTAGTGGTGAGAATTCCACGTTGTGGAATTCTCGGGTG 5 0.125 No Hit ACGAACTTTGTATCGCGCGCATGACTTGGAATTCTCGGGTGCCAAGGAAC 5 0.125 RNA PCR Primer, Index 1 (100% over 24bp) CATCGAGTAGACCTTGTTATTGTGAGAATTAATGGAATTCTCGGGTGCCA 5 0.125 No Hit GCGAGCGTAGTTCAATGGTAAAACATCTCCTTGGAATTCTCGGGTGCCAA 5 0.125 No Hit CCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCCAAGGAACT 5 0.125 RNA PCR Primer, Index 1 (100% over 25bp) >>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 1.3 0.0 0.0 0.0 2 0.0 1.3 0.0 0.0 0.0 3 0.0 1.3 0.0 0.0 0.0 4 0.0 1.3 0.0 0.0 0.0 5 0.0 1.3 0.0 0.0 0.0 6 0.0 1.3 0.0 0.0 0.0 7 0.0 1.3 0.0 0.0 0.0 8 0.0 1.3 0.0 0.0 0.0 9 0.0 1.325 0.0 0.0 0.0 10-11 0.0 1.325 0.0 0.0 0.0 12-13 0.0 1.3625 0.0 0.0 0.0 14-15 0.0 1.5 0.0 0.0 0.0 16-17 0.0 1.9375 0.0 0.0 0.0 18-19 0.0 2.5 0.0 0.0 0.0 20-21 0.0 3.75 0.0 0.0 0.0 22-23 0.0 13.462499999999999 0.0 0.0 0.0 24-25 0.0 27.7 0.0 0.0 0.0 26-27 0.0 40.474999999999994 0.0 0.0 0.0 28-29 0.0 44.45 0.0 0.0 0.0 30-31 0.0 59.224999999999994 0.0 0.0 0.0 32-33 0.0 71.4125 0.0 0.0 0.0 34-35 0.0 83.55 0.0 0.0 0.0 36-37 0.0 91.5125 0.0 0.0 0.0 38-39 0.0 94.4125 0.0 0.0 0.0 40-41 0.0 95.5125 0.0 0.0 0.0 42-43 0.0 96.4375 0.0 0.0 0.0 44-45 0.0 96.9375 0.0 0.0 0.0 46-47 0.0 97.17500000000001 0.0 0.0 0.0 48-49 0.0 97.275 0.0 0.0 0.0 50-51 0.0 97.275 0.0 0.0 0.0 52-53 0.0 97.3 0.0 0.0 0.0 54-55 0.0 97.3 0.0 0.0 0.0 56-57 0.0 97.3 0.0 0.0 0.0 58-59 0.0 97.3 0.0 0.0 0.0 60-61 0.0 97.3 0.0 0.0 0.0 62-63 0.0 97.3 0.0 0.0 0.0 64-65 0.0 97.3 0.0 0.0 0.0 66-67 0.0 97.3 0.0 0.0 0.0 68-69 0.0 97.3 0.0 0.0 0.0 70-71 0.0 97.3 0.0 0.0 0.0 72-73 0.0 97.3 0.0 0.0 0.0 74-75 0.0 97.3 0.0 0.0 0.0 76-77 0.0 97.3 0.0 0.0 0.0 78-79 0.0 97.3 0.0 0.0 0.0 80-81 0.0 97.3 0.0 0.0 0.0 82-83 0.0 97.3 0.0 0.0 0.0 84-85 0.0 97.3 0.0 0.0 0.0 86-87 0.0 97.3 0.0 0.0 0.0 88-89 0.0 97.3 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TTGTAGT 20 1.5392321E-5 95.00001 5 GGATTGT 20 1.5392321E-5 95.00001 2 GATTGTA 20 1.5392321E-5 95.00001 3 ATTGTAG 20 1.5392321E-5 95.00001 4 GGGATTG 20 1.5392321E-5 95.00001 1 GGCGGAT 20 1.5392321E-5 95.00001 1 TGGTCTA 15 6.142176E-4 95.0 8 GTAGACC 15 6.142176E-4 95.0 7 AGTAGAC 15 6.142176E-4 95.0 6 GGACCAG 25 3.8289727E-7 95.0 3 GGTCTAG 15 6.142176E-4 95.0 9 CGGACCA 25 3.8289727E-7 95.0 2 TCGGACC 25 3.8289727E-7 95.0 1 TAGTTCA 30 9.458745E-9 95.0 8 GAGTAGA 15 6.142176E-4 95.0 5 AGGCTTC 25 3.8289727E-7 95.0 8 GGCTTCA 25 3.8289727E-7 95.0 9 CGAGTAG 15 6.142176E-4 95.0 4 CAGGCTT 25 3.8289727E-7 95.0 7 AGACCTT 15 6.142176E-4 95.0 9 >>END_MODULE Rejected 230591 READS because READLEN < 1 Read 230591 spots for SRR6941538.sra Written 230591 spots for SRR6941538.sra Rejected 230591 READS because READLEN < 1 Read 230591 spots for SRR6941538.sra Written 230591 spots for SRR6941538.sra Rejected 230591 READS because READLEN < 1 Read 230591 spots for SRR6941538.sra Written 230591 spots for SRR6941538.sra Rejected 230591 READS because READLEN < 1 Read 230591 spots for SRR6941538.sra Written 230591 spots for SRR6941538.sra Rejected 230591 READS because READLEN < 1 Read 230591 spots for SRR6941538.sra Written 230591 spots for SRR6941538.sra Rejected 230591 READS because READLEN < 1 Read 230591 spots for SRR6941538.sra Written 230591 spots for SRR6941538.sra Rejected 230591 READS because READLEN < 1 Read 230591 spots for SRR6941538.sra Written 230591 spots for SRR6941538.sra Rejected 230604 READS because READLEN < 1 Read 230604 spots for SRR6941538.sra Written 230604 spots for SRR6941538.sra Rejected 230591 READS because READLEN < 1 Read 230591 spots for SRR6941538.sra Written 230591 spots for SRR6941538.sra Rejected 230591 READS because READLEN < 1 Read 230591 spots for SRR6941538.sra Written 230591 spots for SRR6941538.sra Rejected 230591 READS because READLEN < 1 Read 230591 spots for SRR6941538.sra Written 230591 spots for SRR6941538.sra Rejected 230591 READS because READLEN < 1 Read 230591 spots for SRR6941538.sra Written 230591 spots for SRR6941538.sra Rejected 230591 READS because READLEN < 1 Read 230591 spots for SRR6941538.sra Written 230591 spots for SRR6941538.sra Rejected 230591 READS because READLEN < 1 Read 230591 spots for SRR6941538.sra Written 230591 spots for SRR6941538.sra Rejected 230591 READS because READLEN < 1 Read 230591 spots for SRR6941538.sra Written 230591 spots for SRR6941538.sra Rejected 230591 READS because READLEN < 1 Read 230591 spots for SRR6941538.sra Written 230591 spots for SRR6941538.sra Rejected 230591 READS because READLEN < 1 Read 230591 spots for SRR6941538.sra Written 230591 spots for SRR6941538.sra Rejected 230591 READS because READLEN < 1 Read 230591 spots for SRR6941538.sra Written 230591 spots for SRR6941538.sra Rejected 230591 READS because READLEN < 1 Read 230591 spots for SRR6941538.sra Written 230591 spots for SRR6941538.sra Rejected 230591 READS because READLEN < 1 Read 230591 spots for SRR6941538.sra Written 230591 spots for SRR6941538.sra SRR ids: ['SRR6941538.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_3_xfuab7 SRR6941538.sra spots: 4611833 blocks: [[1, 230591], [230592, 461182], [461183, 691773], [691774, 922364], [922365, 1152955], [1152956, 1383546], [1383547, 1614137], [1614138, 1844728], [1844729, 2075319], [2075320, 2305910], [2305911, 2536501], [2536502, 2767092], [2767093, 2997683], [2997684, 3228274], [3228275, 3458865], [3458866, 3689456], [3689457, 3920047], [3920048, 4150638], [4150639, 4381229], [4381230, 4611833]] SRR6941538 file size 1101247 SRR6941538 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 SRR6941538 SRR6941538_1.fastq Input file: SRR6941538_1.fastq trimmed: SRR6941538-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 Fri Dec 6 10:31:26 2024 >> started Fri Dec 6 10:31:29 2024 >> done (3.180s) 4611833 reads processed; of these: 81 ( 0.00%) short reads filtered out after trimming by size control 18 ( 0.00%) empty reads filtered out after trimming by size control 4611734 (100.00%) reads available; of these: 1049620 (22.76%) trimmed reads available after processing 3562114 (77.24%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 3 0.00% 19 3 0.00% 20 8 0.00% 21 12 0.00% 22 8 0.00% 23 11 0.00% 24 9 0.00% 25 19 0.00% 26 39 0.00% 27 38 0.00% 28 51 0.00% 29 62 0.00% 30 66 0.00% 31 40 0.00% 32 41 0.00% 33 34 0.00% 34 40 0.00% 35 34 0.00% 36 32 0.00% 37 28 0.00% 38 34 0.00% 39 45 0.00% 40 45 0.00% 41 44 0.00% 42 30 0.00% 43 39 0.00% 44 20 0.00% 45 28 0.00% 46 31 0.00% 47 26 0.00% 48 33 0.00% 49 34 0.00% 50 28 0.00% 51 32 0.00% 52 16 0.00% 53 22 0.00% 54 23 0.00% 55 20 0.00% 56 31 0.00% 57 24 0.00% 58 27 0.00% 59 20 0.00% 60 41 0.00% 61 43 0.00% 62 36 0.00% 63 46 0.00% 64 48 0.00% 65 45 0.00% 66 71 0.00% 67 107 0.00% 68 215 0.00% 69 277 0.01% 70 557 0.01% 71 487 0.01% 72 857 0.02% 73 2206 0.05% 74 15477 0.34% 75 9630 0.21% 76 2852 0.06% 77 733 0.02% 78 872 0.02% 79 860 0.02% 80 1098 0.02% 81 1140 0.02% 82 1402 0.03% 83 1790 0.04% 84 2547 0.06% 85 2831 0.06% 86 2901 0.06% 87 3102 0.07% 88 3859 0.08% 89 5527 0.12% 90 10217 0.22% 91 11909 0.26% 92 12925 0.28% 93 23838 0.52% 94 44400 0.96% 95 137164 2.97% 96 123863 2.69% 97 116638 2.53% 98 207004 4.49% 99 217355 4.71% 100 81420 1.77% 101 3562114 77.24% 4611734 reads passed initial QC criterion=sequence-density sequence-density=97.83 sequence-density-rank=1 fanout-score=28.80 fanout-score-rank=1 prefix-density=97.02 prefix-fanout=28.8 sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAGTTCCATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAA criterion=fanout-score sequence-density=97.83 sequence-density-rank=1 fanout-score=28.80 fanout-score-rank=1 prefix-density=97.02 prefix-fanout=28.8 sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAGTTCCATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAA 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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAGTTCCATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAA -o SRR6941538 - Input file: STDIN trimmed: SRR6941538-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAGTTCCATCTCGTATGCCGTCTTCTGCTTGA -- 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 Fri Dec 6 10:31:38 2024 >> started Fri Dec 6 10:31:44 2024 >> done (5.777s) 4517617 reads processed; of these: 52729 ( 1.17%) short reads filtered out after trimming by size control 57873 ( 1.28%) empty reads filtered out after trimming by size control 4407015 (97.55%) reads available; of these: 4382663 (99.45%) trimmed reads available after processing 24352 ( 0.55%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 12964 0.29% 19 35530 0.81% 20 47821 1.09% 21 343525 7.79% 22 171034 3.88% 23 138824 3.15% 24 886298 20.11% 25 114249 2.59% 26 92965 2.11% 27 77887 1.77% 28 112857 2.56% 29 464881 10.55% 30 310031 7.03% 31 242587 5.50% 32 281172 6.38% 33 305716 6.94% 34 257276 5.84% 35 173334 3.93% 36 108103 2.45% 37 56661 1.29% 38 26961 0.61% 39 18406 0.42% 40 24568 0.56% 41 29340 0.67% 42 18931 0.43% 43 5717 0.13% 44 13881 0.31% 45 5406 0.12% 46 1394 0.03% 47 1562 0.04% 48 629 0.01% 49 316 0.01% 50 187 0.00% 51 178 0.00% 52 105 0.00% 53 68 0.00% 54 44 0.00% 55 30 0.00% 56 21 0.00% 57 33 0.00% 58 18 0.00% 59 18 0.00% 60 18 0.00% 61 22 0.00% 62 5 0.00% 63 10 0.00% 64 13 0.00% 65 13 0.00% 66 15 0.00% 67 15 0.00% 68 24 0.00% 69 28 0.00% 70 45 0.00% 71 26 0.00% 72 36 0.00% 73 40 0.00% 74 49 0.00% 75 67 0.00% 76 59 0.00% 77 167 0.00% 78 49 0.00% 79 89 0.00% 80 204 0.00% 81 99 0.00% 82 144 0.00% 83 177 0.00% 84 82 0.00% 85 74 0.00% 86 134 0.00% 87 176 0.00% 88 87 0.00% 89 92 0.00% 90 96 0.00% 91 166 0.00% 92 187 0.00% 93 212 0.00% 94 259 0.01% 95 305 0.01% 96 311 0.01% 97 326 0.01% 98 616 0.01% 99 432 0.01% 100 463 0.01% 101 20055 0.46% criterion=sequence-density sequence-density=8.65 sequence-density-rank=1 fanout-score=1.00 fanout-score-rank=6 prefix-density=0.05 prefix-fanout=1.0 sequence=GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGATTGTGAATCC criterion=fanout-score sequence-density=0.19 sequence-density-rank=26 fanout-score=58.39 fanout-score-rank=1 prefix-density=6.19 prefix-fanout=1.8 sequence=GTGAGAATTCTAAAAA Started job on | Dec 06 10:31:57 Started mapping on | Dec 06 10:31:57 Finished on | Dec 06 10:32:11 Mapping speed, Million of reads per hour | 1157.43 Number of input reads | 4501132 Average input read length | 30 UNIQUE READS: Uniquely mapped reads number | 1077288 Uniquely mapped reads % | 23.93% Average mapped length | 25.87 Number of splices: Total | 4729 Number of splices: Annotated (sjdb) | 1568 Number of splices: GT/AG | 4517 Number of splices: GC/AG | 138 Number of splices: AT/AC | 2 Number of splices: Non-canonical | 72 Mismatch rate per base, % | 0.13% Deletion rate per base | 0.00% Deletion average length | 1.56 Insertion rate per base | 0.00% Insertion average length | 1.04 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 2576222 % of reads mapped to multiple loci | 57.23% Number of reads mapped to too many loci | 652528 % of reads mapped to too many loci | 14.50% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 3.68% % of reads unmapped: other | 0.65% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 847622 847622 847622 N_multimapping 2576222 2576222 2576222 N_noFeature 735006 888072 920312 N_ambiguous 9789 5709 211 UnstrandedReadsAssigned:332493 PositiveStrandReadsAssigned:183507 NegativeStrandReadsAssigned:156765 Dataset is classified unstranded MeadianReadLen=29 20thPercentileLength=24 echo kmer=19 SRR6941538 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: SRR6941538-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 4,501,132 reads, 2,281,910 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 918 rounds 52973 SRR6941538.ke.tsv 35125 SRR6941538.se.tsv 88098 total ==> SRR6941538.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 837 0 0 PNS24247 1044 945 0 0 PNS24249 1928 1829 3 0.216096 PNS24246 1044 945 0 0 PNS24248 1044 945 0 0 PNS24244 1471 1372 0 0 PNS24243 293 194 0 0 KQK14069 1603 1504 0 0 KQK14071 474 375 1.1038 0.387792 ==> SRR6941538.se.tsv <== BRADI_1g14170v3 60 BRADI_1g53295v3 0 BRADI_1g59795v3 2 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 0 BRADI_1g74790v3 6 BRADI_1g09890v3 0 BRADI_1g77505v3 2 BRADI_1g48960v3 0 SRR6941538 completed mapping pipeline successfully