Starting /dee2/code/volunteer_pipeline.sh SRR6941536 current disk space = 1551870435328 free memory = 1600791596 SRR6941536 SRAfilesize 8c02ac432c3acc2210b9309227bf6fdd SRR6941536.sra SRR6941536.sra file validated SRR6941536 is single end SRR6941536 is conventional basespace SRR6941536 read1 length is 101 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR6941536_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 33.2135 34.0 33.0 34.0 32.0 34.0 2 33.338 34.0 33.0 34.0 33.0 34.0 3 33.0615 34.0 33.0 34.0 31.0 34.0 4 33.21525 34.0 33.0 34.0 32.0 34.0 5 33.17475 34.0 33.0 34.0 33.0 34.0 6 37.0135 38.0 37.0 38.0 36.0 38.0 7 37.363 38.0 38.0 38.0 37.0 38.0 8 37.502 38.0 38.0 38.0 37.0 38.0 9 37.55225 38.0 38.0 38.0 38.0 38.0 10-11 37.52425 38.0 38.0 38.0 37.5 38.0 12-13 37.489125 38.0 38.0 38.0 38.0 38.0 14-15 37.49375 38.0 38.0 38.0 37.5 38.0 16-17 36.094125 38.0 37.0 38.0 27.0 38.0 18-19 36.826875 38.0 37.5 38.0 33.5 38.0 20-21 36.086625 38.0 38.0 38.0 30.0 38.0 22-23 37.221374999999995 38.0 38.0 38.0 36.5 38.0 24-25 37.45825000000001 38.0 38.0 38.0 37.0 38.0 26-27 37.3905 38.0 38.0 38.0 37.0 38.0 28-29 37.364000000000004 38.0 38.0 38.0 37.0 38.0 30-31 37.291624999999996 38.0 38.0 38.0 37.0 38.0 32-33 37.188375 38.0 38.0 38.0 36.5 38.0 34-35 37.198125000000005 38.0 38.0 38.0 37.0 38.0 36-37 37.183 38.0 38.0 38.0 37.0 38.0 38-39 37.21725 38.0 38.0 38.0 37.0 38.0 40-41 37.11425 38.0 38.0 38.0 37.0 38.0 42-43 37.14125 38.0 38.0 38.0 37.0 38.0 44-45 37.096000000000004 38.0 38.0 38.0 37.0 38.0 46-47 36.923 38.0 38.0 38.0 36.0 38.0 48-49 37.016125 38.0 38.0 38.0 36.0 38.0 50-51 36.89725 38.0 38.0 38.0 36.0 38.0 52-53 36.91975 38.0 38.0 38.0 36.0 38.0 54-55 37.09775 38.0 38.0 38.0 36.0 38.0 56-57 36.960875 38.0 38.0 38.0 36.0 38.0 58-59 37.163875000000004 38.0 38.0 38.0 36.5 38.0 60-61 37.15925 38.0 38.0 38.0 37.0 38.0 62-63 36.93575 38.0 38.0 38.0 36.0 38.0 64-65 36.615125 38.0 38.0 38.0 34.5 38.0 66-67 36.415875 38.0 37.5 38.0 33.5 38.0 68-69 36.7375 38.0 38.0 38.0 35.0 38.0 70-71 36.314125000000004 38.0 37.5 38.0 33.0 38.0 72-73 35.85425 38.0 37.0 38.0 29.5 38.0 74-75 35.609125 38.0 37.0 38.0 29.0 38.0 76-77 35.78 38.0 37.0 38.0 29.0 38.0 78-79 36.19525 38.0 37.5 38.0 33.0 38.0 80-81 36.579 38.0 38.0 38.0 34.5 38.0 82-83 36.49275 38.0 38.0 38.0 34.0 38.0 84-85 36.525625 38.0 38.0 38.0 35.0 38.0 86-87 36.457375 38.0 38.0 38.0 35.0 38.0 88-89 36.5195 38.0 38.0 38.0 34.5 38.0 90-91 36.47925 38.0 38.0 38.0 34.5 38.0 92-93 36.420375 38.0 38.0 38.0 34.0 38.0 94-95 36.283125 38.0 38.0 38.0 34.5 38.0 96-97 35.179125 38.0 37.5 38.0 31.5 38.0 98-99 33.389250000000004 38.0 36.0 38.0 13.5 38.0 100-101 31.429125 38.0 32.0 38.0 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 4 1.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10 1.0 11 0.0 12 1.0 13 0.0 14 1.0 15 0.0 16 0.0 17 2.0 18 0.0 19 1.0 20 2.0 21 1.0 22 3.0 23 3.0 24 1.0 25 7.0 26 4.0 27 25.0 28 36.0 29 34.0 30 26.0 31 42.0 32 70.0 33 96.0 34 141.0 35 325.0 36 715.0 37 2462.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 37.25 21.9 12.8 28.050000000000004 2 32.624468351263445 35.351513635226425 14.786089567175381 17.237928446334752 3 30.599999999999998 18.425 28.95 22.025 4 26.85671417854464 30.83270817704426 13.328332083020754 28.982245561390346 5 43.9 17.175 22.525000000000002 16.400000000000002 6 18.875 39.375 24.474999999999998 17.275 7 47.675 18.85 21.349999999999998 12.125 8 22.7 14.35 47.825 15.125 9 15.325 47.825 20.275000000000002 16.575 10-11 37.487500000000004 27.85 19.55 15.1125 12-13 16.162499999999998 15.225 22.662499999999998 45.95 14-15 19.0 39.475 28.249999999999996 13.275 16-17 29.075 18.0 39.6125 13.3125 18-19 39.425 23.1625 25.2125 12.2 20-21 13.9375 26.200000000000003 39.7 20.1625 22-23 32.1625 29.15 23.4375 15.25 24-25 32.7625 31.474999999999998 20.2375 15.525 26-27 36.4625 26.8125 18.825 17.9 28-29 17.712500000000002 35.6 23.4125 23.275000000000002 30-31 21.775 12.737499999999999 40.949999999999996 24.5375 32-33 30.15 14.274999999999999 30.4375 25.137500000000003 34-35 34.3375 23.325000000000003 28.025 14.3125 36-37 37.5 22.0125 29.725 10.7625 38-39 23.674999999999997 20.6875 35.5625 20.075000000000003 40-41 22.275 14.7 28.675 34.35 42-43 36.625 19.2125 21.349999999999998 22.8125 44-45 51.4 13.325000000000001 17.2125 18.0625 46-47 34.7875 23.075000000000003 16.225 25.912499999999998 48-49 23.9 25.5375 17.2 33.3625 50-51 28.787499999999998 27.5875 8.3375 35.2875 52-53 30.025000000000002 42.975 6.6875 20.3125 54-55 23.150000000000002 30.9625 17.4875 28.4 56-57 15.425 29.849999999999998 15.437500000000002 39.287499999999994 58-59 20.7625 26.7625 20.3125 32.1625 60-61 20.674999999999997 31.775 18.387500000000003 29.1625 62-63 17.25 38.837500000000006 17.1625 26.75 64-65 19.3 28.925 26.6 25.174999999999997 66-67 24.1125 25.674999999999997 23.9875 26.224999999999998 68-69 25.0625 37.35 19.375 18.212500000000002 70-71 16.425 45.3125 26.987499999999997 11.275 72-73 14.5375 34.300000000000004 29.325000000000003 21.837500000000002 74-75 15.662499999999998 18.712500000000002 28.725 36.9 76-77 20.3375 13.900000000000002 40.5 25.2625 78-79 20.7375 13.2875 40.025 25.95 80-81 20.7875 12.612499999999999 34.2125 32.3875 82-83 27.224999999999998 7.324999999999999 36.175000000000004 29.275000000000002 84-85 20.75 5.3125 37.262499999999996 36.675000000000004 86-87 18.825 10.4375 42.6875 28.050000000000004 88-89 14.2375 24.8125 39.387499999999996 21.5625 90-91 13.0125 29.062500000000004 35.1875 22.7375 92-93 18.2 35.212500000000006 29.725 16.8625 94-95 14.249999999999998 52.925 23.1125 9.7125 96-97 10.137500000000001 70.875 14.9875 4.0 98-99 5.9624999999999995 85.7125 5.8500000000000005 2.475 100-101 2.6625 91.9625 3.15 2.225 >>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 1.5 33 1.5 34 2.5 35 4.5 36 3.5 37 5.0 38 8.5 39 12.5 40 33.0 41 86.0 42 173.0 43 411.5 44 576.5 45 410.5 46 333.0 47 324.0 48 206.5 49 230.0 50 350.5 51 351.0 52 202.0 53 90.0 54 74.0 55 51.5 56 20.0 57 15.0 58 11.5 59 5.5 60 3.0 61 1.0 62 0.5 63 0.0 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 pass #Base N-Count 1 0.0 2 0.075 3 0.0 4 0.025 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 50.1 #Duplication Level Percentage of deduplicated Percentage of total 1 86.77644710578842 43.475 2 5.738522954091816 5.75 3 2.345309381237525 3.5249999999999995 4 1.2974051896207583 2.6 5 0.499001996007984 1.25 6 0.5489021956087825 1.6500000000000001 7 0.249500998003992 0.8750000000000001 8 0.14970059880239522 0.6 9 0.34930139720558884 1.575 >10 1.4970059880239521 14.625 >50 0.34930139720558884 10.975 >100 0.19960079840319359 13.100000000000001 >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 GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGGAATTCTCGGGTGCC 174 4.35 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTTGGAATTCTCGGGTGCCAAG 134 3.35 No Hit GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGATTTGGAATTCTCGGGTG 114 2.85 No Hit GAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAG 102 2.55 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTCTGGAATTCTCGGGTGCCAA 97 2.4250000000000003 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTTGGAATTCTCGGGTGC 66 1.6500000000000001 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTCTTGGAATTCTCGGGTGCCA 61 1.525 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCTGGAATTCTCGGGTGCCA 59 1.4749999999999999 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTGGAATTCTCGGGTGCCAAGG 53 1.325 Illumina Small RNA Adapter 2 (100% over 21bp) TGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAA 52 1.3 No Hit CTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCA 51 1.275 RNA PCR Primer, Index 1 (100% over 28bp) GTCAGGATAGCTCAGTTGGTAGAGCAGAGGACTTGGAATTCTCGGGTGCC 44 1.0999999999999999 No Hit TCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACTC 44 1.0999999999999999 RNA PCR Primer, Index 1 (100% over 26bp) GCGAGCGTAGTTCAATGGTAAAACATCTCCTTTGGAATTCTCGGGTGCCA 43 1.075 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCCTGGAATTCTCGGGTGC 25 0.625 No Hit GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGATTGGAATTCTCGGGTGC 25 0.625 No Hit AGAAGATACGGGTTCGATTCCCGCCGCTCGCCCCATGGAATTCTCGGGTG 23 0.575 No Hit GTCAGGATAGCTCAGTTGGTAGAGCAGAGGACTGGAATTCTCGGGTGCCA 23 0.575 No Hit GAAGATACGGGTTCGATTCCCGCCGCTCGCCCCATGGAATTCTCGGGTGC 22 0.5499999999999999 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATATGGAATTCTCGGGTGCCAAG 22 0.5499999999999999 No Hit ATATTGGGTAGGTTGTGGTATTTCATTGCTGGAATTCTCGGGTGCCAAGG 22 0.5499999999999999 Illumina Small RNA Adapter 2 (100% over 21bp) ATATTGGGTAGGTTGTGGTATTTCATTGCTTGGAATTCTCGGGTGCCAAG 21 0.525 No Hit GCGAGCGTAGTTCAATGGTAAAACATCTCCTTGGAATTCTCGGGTGCCAA 21 0.525 No Hit TCGGACCAGGCTTCATTCCCCTGGAATTCTCGGGTGCCAAGGAACTCCAG 19 0.475 RNA PCR Primer, Index 1 (100% over 29bp) GGTGGCTGTAGTTTAGTGGTGAGAATTCCACGTTTGGAATTCTCGGGTGC 18 0.44999999999999996 No Hit GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGATTGTGAATCTGGAATTC 17 0.42500000000000004 No Hit GCGAGCGTAGTTCAATGGTAAAACATCTCCTTGCCAAGGATGGAATTCTC 17 0.42500000000000004 No Hit GCGAGCGTAGTTCAATGGTAAAACATCTCCTTGTGGAATTCTCGGGTGCC 17 0.42500000000000004 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATGGAATTCTCGGGTGCCAAGGA 16 0.4 RNA PCR Primer, Index 1 (100% over 22bp) TCCTCAGTAGCTCAGTGGTAGAGCGGTCGGCTTGGAATTCTCGGGTGCCA 14 0.35000000000000003 No Hit ACTTTGTATCGCGCGCATGACTTGGAATTCTCGGGTGCCAAGGAACTCCA 14 0.35000000000000003 RNA PCR Primer, Index 1 (100% over 28bp) CATCGAGTAGACCTTGTTATTGTGAGAATTCTTAATGGAATTCTCGGGTG 14 0.35000000000000003 No Hit GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGAATTCTCGGGTGCCAAGG 13 0.325 Illumina Small RNA Adapter 2 (100% over 21bp) GGAGAGATGGCTGAGTGGACTAAAGCGGCGGATTTGGAATTCTCGGGTGC 13 0.325 No Hit GGGTGTTTGGTCTAGTGGTATGATTCTCGCTTGGAATTCTCGGGTGCCAA 13 0.325 No Hit TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTGAAAATCTCGTATGC 12 0.3 RNA PCR Primer, Index 19 (100% over 50bp) GGAGAGATGGCTGAGTGGACTAAAGCGGCGGATTGCTAATCTGGAATTCT 11 0.27499999999999997 No Hit AGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGG 11 0.27499999999999997 Illumina Small RNA Adapter 2 (100% over 21bp) CATCGAGTAGACCTTGTTATTGTGAGAATTATGGAATTCTCGGGTGCCAA 11 0.27499999999999997 No Hit AATATTGGGTAGGTTGTGGTATTTCATTGCTTGGAATTCTCGGGTGCCAA 10 0.25 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCTGGAATTCTCGGGTGCCAAGG 10 0.25 Illumina Small RNA Adapter 2 (100% over 21bp) CATCGAGTAGACCTTGTTATTGTGAGAATAAATGGAATTCTCGGGTGCCA 9 0.22499999999999998 No Hit TCCGTCGTAGTCTAGGTGGTTAGGATACTCTGGAATTCTCGGGTGCCAAG 9 0.22499999999999998 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTCAATGGAATTCTCGGGTGCC 9 0.22499999999999998 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTCTTTGGAATTCTCGGGTGCC 9 0.22499999999999998 No Hit CATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAAC 9 0.22499999999999998 RNA PCR Primer, Index 1 (100% over 24bp) CATCGAGTAGACCTTGTTATTGTGAGAATTAAATGGAATTCTCGGGTGCC 9 0.22499999999999998 No Hit ATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACT 9 0.22499999999999998 RNA PCR Primer, Index 1 (100% over 25bp) GGAGAGATGGCTGAGTGGACTAAAGCGGCGGATTGCTGGAATTCTCGGGT 8 0.2 No Hit CGGTCGAGGGCACGCCTGCCTGGGCGTCACGCTGGAATTCTCGGGTGCCA 8 0.2 No Hit ATATTGGGTAGGTTGTGGTATTTCATTGCTATGGAATTCTCGGGTGCCAA 8 0.2 No Hit CACCATGCGCGGGTTCAATTCCCGTCGTTCGCCCCATGGAATTCTCGGGT 7 0.17500000000000002 No Hit GACACGACTCTCGGCAACGGATATCTCGGCTTGGAATTCTCGGGTGCCAA 7 0.17500000000000002 No Hit AACTTTGTATCGCGCGCATGACTTGGAATTCTCGGGTGCCAAGGAACTCC 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 27bp) CATCGAGTAGACCTTGTTATTGTGAGAATTCTAATGGAATTCTCGGGTGC 7 0.17500000000000002 No Hit CACGACTCTCGGCAACGGATATCTCGGCTTGGAATTCTCGGGTGCCAAGG 7 0.17500000000000002 Illumina Small RNA Adapter 2 (100% over 21bp) GGCGGATGTAGCCAAGAGGATCAAGGCAGTGGATTTGGAATTCTCGGGTG 6 0.15 No Hit GGGATTGTAGTTCAATTGGACAGAGCACCGCCCTGGAATTCTCGGGTGCC 6 0.15 No Hit GCGAGCGTAGTTCAATGGTAAAACATCTCCTTGCCAAGGAGTGGAATTCT 6 0.15 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTCTTAATTGGAATTCTCGGGT 6 0.15 No Hit CATCGAGTAGACCTTGATATTGTGAGAATTGGAATTCTCGGGTGCCAAGG 6 0.15 Illumina Small RNA Adapter 2 (100% over 21bp) GGGATTGTAGTTCAATTGGACAGAGCACCGCCCTTGGAATTCTCGGGTGC 6 0.15 No Hit GAACTTTGTATCGCGCGCATGACTTGGAATTCTCGGGTGCCAAGGAACTC 6 0.15 RNA PCR Primer, Index 1 (100% over 26bp) TAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCAG 6 0.15 RNA PCR Primer, Index 1 (100% over 29bp) TGTCGTGCCAATTCAACATAAACCCTGGAATTCTCGGGTGCCAAGGAACT 6 0.15 RNA PCR Primer, Index 1 (100% over 25bp) TCTCATGGAGAGTTCGATCCTGGCTTGGAATTCTCGGGTGCCAAGGAACT 6 0.15 RNA PCR Primer, Index 1 (100% over 25bp) GCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAA 6 0.15 RNA PCR Primer, Index 1 (100% over 23bp) CATCGAGTAGACCTTGTTATTGTGAGAATTCTTAAATGGAATTCTCGGGT 5 0.125 No Hit TCGGACCAGGCTTCGATCCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG 5 0.125 RNA PCR Primer, Index 1 (100% over 29bp) GGTGGCTGTAGTTTAGTGGTGAGAATTCCACGTTGTGGAATTCTCGGGTG 5 0.125 No Hit AAGATACGGGTTCGATTCCCGCCGCTCGCCCCATGGAATTCTCGGGTGCC 5 0.125 No Hit GGTGGCTGTAGTTTAGTGGTGAGAATTCCACGTTGTTGGAATTCTCGGGT 5 0.125 No Hit TGTCGTGCCAATTCAACATAAACCCCTGGAATTCTCGGGTGCCAAGGAAC 5 0.125 RNA PCR Primer, Index 1 (100% over 24bp) GGGATTGTAGTTCAATTGGACAGAGCACCGCCTGGAATTCTCGGGTGCCA 5 0.125 No Hit CATCGAGTAGACCTTGTTAGTGTGAGAATTTGGAATTCTCGGGTGCCAAG 5 0.125 No Hit TGCAGCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGG 5 0.125 No Hit CTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCA 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 0.35 0.0 0.0 0.0 2 0.0 0.35 0.0 0.0 0.0 3 0.0 0.35 0.0 0.0 0.0 4 0.0 0.35 0.0 0.0 0.0 5 0.0 0.375 0.0 0.0 0.0 6 0.0 0.375 0.0 0.0 0.0 7 0.0 0.375 0.0 0.0 0.0 8 0.0 0.375 0.0 0.0 0.0 9 0.0 0.4 0.0 0.0 0.0 10-11 0.0 0.4125 0.0 0.0 0.0 12-13 0.0 0.425 0.0 0.0 0.0 14-15 0.0 0.48750000000000004 0.0 0.0 0.0 16-17 0.0 0.6375 0.0 0.0 0.0 18-19 0.0 1.0125 0.0 0.0 0.0 20-21 0.0 1.675 0.0 0.0 0.0 22-23 0.0 6.487500000000001 0.0 0.0 0.0 24-25 0.0 16.025 0.0 0.0 0.0 26-27 0.0 25.825 0.0 0.0 0.0 28-29 0.0 30.4625 0.0 0.0 0.0 30-31 0.0 42.225 0.0 0.0 0.0 32-33 0.0 60.025000000000006 0.0 0.0 0.0 34-35 0.0 77.8625 0.0 0.0 0.0 36-37 0.0 89.225 0.0 0.0 0.0 38-39 0.0 92.4875 0.0 0.0 0.0 40-41 0.0 93.9625 0.0 0.0 0.0 42-43 0.0 96.0875 0.0 0.0 0.0 44-45 0.0 96.8375 0.0 0.0 0.0 46-47 0.0 97.0625 0.0 0.0 0.0 48-49 0.0 97.1 0.0 0.0 0.0 50-51 0.0 97.1375 0.0 0.0 0.0 52-53 0.0 97.15 0.0 0.0 0.0 54-55 0.0 97.15 0.0 0.0 0.0 56-57 0.0 97.15 0.0 0.0 0.0 58-59 0.0 97.1625 0.0 0.0 0.0 60-61 0.0 97.175 0.0 0.0 0.0 62-63 0.0 97.175 0.0 0.0 0.0 64-65 0.0 97.175 0.0 0.0 0.0 66-67 0.0 97.175 0.0 0.0 0.0 68-69 0.0 97.175 0.0 0.0 0.0 70-71 0.0 97.175 0.0 0.0 0.0 72-73 0.0 97.175 0.0 0.0 0.0 74-75 0.0 97.175 0.0 0.0 0.0 76-77 0.0 97.175 0.0 0.0 0.0 78-79 0.0 97.2 0.0 0.0 0.0 80-81 0.0 97.225 0.0 0.0 0.0 82-83 0.0 97.25 0.0 0.0 0.0 84-85 0.0 97.275 0.0 0.0 0.0 86-87 0.0 97.275 0.0 0.0 0.0 88-89 0.0 97.275 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GAGCGTA 20 1.5392321E-5 95.00001 3 CGTAGTT 20 1.5392321E-5 95.00001 6 CGAGCGT 20 1.5392321E-5 95.00001 2 GCGTAGT 20 1.5392321E-5 95.00001 5 AGCGTAG 20 1.5392321E-5 95.00001 4 GCGAGCG 20 1.5392321E-5 95.00001 1 GGATGTA 25 3.8289727E-7 95.0 4 GTAGACC 50 0.0 95.0 7 AGCTCAG 15 6.142176E-4 95.0 9 TTGTAGT 65 0.0 95.0 5 AGTAGAC 50 0.0 95.0 6 GATGTAG 25 3.8289727E-7 95.0 5 TAGCTCA 15 6.142176E-4 95.0 8 TAGCCAA 25 3.8289727E-7 95.0 9 GGATTGT 65 0.0 95.0 2 CGGATGT 25 3.8289727E-7 95.0 3 GCGGATG 25 3.8289727E-7 95.0 2 GATTGTA 65 0.0 95.0 3 TAGTTCA 85 0.0 95.0 8 ATAGCTC 15 6.142176E-4 95.0 7 >>END_MODULE Rejected 280129 READS because READLEN < 1 Read 280129 spots for SRR6941536.sra Written 280129 spots for SRR6941536.sra Rejected 280129 READS because READLEN < 1 Read 280129 spots for SRR6941536.sra Written 280129 spots for SRR6941536.sra Rejected 280129 READS because READLEN < 1 Read 280129 spots for SRR6941536.sra Written 280129 spots for SRR6941536.sra Rejected 280129 READS because READLEN < 1 Read 280129 spots for SRR6941536.sra Written 280129 spots for SRR6941536.sra Rejected 280129 READS because READLEN < 1 Read 280129 spots for SRR6941536.sra Written 280129 spots for SRR6941536.sra Rejected 280129 READS because READLEN < 1 Read 280129 spots for SRR6941536.sra Written 280129 spots for SRR6941536.sra Rejected 280129 READS because READLEN < 1 Read 280129 spots for SRR6941536.sra Written 280129 spots for SRR6941536.sra Rejected 280129 READS because READLEN < 1 Read 280129 spots for SRR6941536.sra Written 280129 spots for SRR6941536.sra Rejected 280129 READS because READLEN < 1 Read 280129 spots for SRR6941536.sra Written 280129 spots for SRR6941536.sra Rejected 280140 READS because READLEN < 1 Read 280140 spots for SRR6941536.sra Written 280140 spots for SRR6941536.sra Rejected 280129 READS because READLEN < 1 Read 280129 spots for SRR6941536.sra Written 280129 spots for SRR6941536.sra Rejected 280129 READS because READLEN < 1 Read 280129 spots for SRR6941536.sra Written 280129 spots for SRR6941536.sra Rejected 280129 READS because READLEN < 1 Read 280129 spots for SRR6941536.sra Written 280129 spots for SRR6941536.sra Rejected 280129 READS because READLEN < 1 Read 280129 spots for SRR6941536.sra Written 280129 spots for SRR6941536.sra Rejected 280129 READS because READLEN < 1 Read 280129 spots for SRR6941536.sra Written 280129 spots for SRR6941536.sra Rejected 280129 READS because READLEN < 1 Read 280129 spots for SRR6941536.sra Written 280129 spots for SRR6941536.sra Rejected 280129 READS because READLEN < 1 Read 280129 spots for SRR6941536.sra Written 280129 spots for SRR6941536.sra Rejected 280129 READS because READLEN < 1 Read 280129 spots for SRR6941536.sra Written 280129 spots for SRR6941536.sra Rejected 280129 READS because READLEN < 1 Read 280129 spots for SRR6941536.sra Written 280129 spots for SRR6941536.sra Rejected 280129 READS because READLEN < 1 Read 280129 spots for SRR6941536.sra Written 280129 spots for SRR6941536.sra SRR ids: ['SRR6941536.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_06kdno89 SRR6941536.sra spots: 5602591 blocks: [[1, 280129], [280130, 560258], [560259, 840387], [840388, 1120516], [1120517, 1400645], [1400646, 1680774], [1680775, 1960903], [1960904, 2241032], [2241033, 2521161], [2521162, 2801290], [2801291, 3081419], [3081420, 3361548], [3361549, 3641677], [3641678, 3921806], [3921807, 4201935], [4201936, 4482064], [4482065, 4762193], [4762194, 5042322], [5042323, 5322451], [5322452, 5602591]] SRR6941536 file size 1338294 SRR6941536 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 SRR6941536 SRR6941536_1.fastq Input file: SRR6941536_1.fastq trimmed: SRR6941536-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 10:17:29 2024 >> started Fri Dec 6 10:17:35 2024 >> done (6.227s) 5602591 reads processed; of these: 85 ( 0.00%) short reads filtered out after trimming by size control 16 ( 0.00%) empty reads filtered out after trimming by size control 5602490 (100.00%) reads available; of these: 591644 (10.56%) trimmed reads available after processing 5010846 (89.44%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 6 0.00% 19 5 0.00% 20 6 0.00% 21 7 0.00% 22 7 0.00% 23 10 0.00% 24 12 0.00% 25 13 0.00% 26 9 0.00% 27 30 0.00% 28 32 0.00% 29 44 0.00% 30 48 0.00% 31 24 0.00% 32 33 0.00% 33 25 0.00% 34 36 0.00% 35 43 0.00% 36 46 0.00% 37 58 0.00% 38 28 0.00% 39 43 0.00% 40 53 0.00% 41 49 0.00% 42 58 0.00% 43 62 0.00% 44 44 0.00% 45 69 0.00% 46 64 0.00% 47 67 0.00% 48 48 0.00% 49 52 0.00% 50 45 0.00% 51 41 0.00% 52 37 0.00% 53 49 0.00% 54 59 0.00% 55 44 0.00% 56 44 0.00% 57 41 0.00% 58 32 0.00% 59 40 0.00% 60 51 0.00% 61 55 0.00% 62 45 0.00% 63 51 0.00% 64 38 0.00% 65 48 0.00% 66 49 0.00% 67 66 0.00% 68 102 0.00% 69 109 0.00% 70 127 0.00% 71 161 0.00% 72 274 0.00% 73 705 0.01% 74 3961 0.07% 75 3464 0.06% 76 1304 0.02% 77 516 0.01% 78 682 0.01% 79 623 0.01% 80 847 0.02% 81 861 0.02% 82 970 0.02% 83 1099 0.02% 84 1591 0.03% 85 1741 0.03% 86 1821 0.03% 87 1990 0.04% 88 2148 0.04% 89 2834 0.05% 90 4509 0.08% 91 6574 0.12% 92 8956 0.16% 93 15979 0.29% 94 27641 0.49% 95 61029 1.09% 96 76320 1.36% 97 82978 1.48% 98 103728 1.85% 99 120329 2.15% 100 53705 0.96% 101 5010846 89.44% 5602490 reads passed initial QC criterion=sequence-density sequence-density=97.13 sequence-density-rank=1 fanout-score=25.94 fanout-score-rank=3 prefix-density=97.35 prefix-fanout=25.9 sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTGAAAATCTCGTATGCCGTCTTCTGCTTGAAAAA criterion=fanout-score sequence-density=1.55 sequence-density-rank=6 fanout-score=64.20 fanout-score-rank=1 prefix-density=98.01 prefix-fanout=1.0 sequence=CACGTGAAAATATCGTATGCCGT 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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTGAAAATCTCGTATGCCGTCTTCTGCTTGAAAAA -o SRR6941536 - Input file: STDIN trimmed: SRR6941536-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTGAAAATCTCGTATGCCGTCTTCTGCTTGA -- 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 10:18:06 2024 >> started Fri Dec 6 10:18:12 2024 >> done (5.849s) 5488154 reads processed; of these: 32922 ( 0.60%) short reads filtered out after trimming by size control 17307 ( 0.32%) empty reads filtered out after trimming by size control 5437925 (99.08%) reads available; of these: 5386326 (99.05%) trimmed reads available after processing 51599 ( 0.95%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 13279 0.24% 19 28669 0.53% 20 40554 0.75% 21 157016 2.89% 22 175015 3.22% 23 120862 2.22% 24 647775 11.91% 25 141644 2.60% 26 139715 2.57% 27 128775 2.37% 28 132984 2.45% 29 322780 5.94% 30 589397 10.84% 31 425787 7.83% 32 487258 8.96% 33 563164 10.36% 34 394063 7.25% 35 388473 7.14% 36 148340 2.73% 37 82956 1.53% 38 45611 0.84% 39 34857 0.64% 40 48026 0.88% 41 50536 0.93% 42 39263 0.72% 43 9889 0.18% 44 8809 0.16% 45 6964 0.13% 46 2338 0.04% 47 2602 0.05% 48 918 0.02% 49 493 0.01% 50 261 0.00% 51 233 0.00% 52 151 0.00% 53 114 0.00% 54 98 0.00% 55 78 0.00% 56 47 0.00% 57 70 0.00% 58 61 0.00% 59 38 0.00% 60 42 0.00% 61 39 0.00% 62 29 0.00% 63 43 0.00% 64 36 0.00% 65 33 0.00% 66 30 0.00% 67 34 0.00% 68 75 0.00% 69 99 0.00% 70 146 0.00% 71 84 0.00% 72 58 0.00% 73 91 0.00% 74 83 0.00% 75 168 0.00% 76 221 0.00% 77 1035 0.02% 78 138 0.00% 79 212 0.00% 80 1478 0.03% 81 500 0.01% 82 868 0.02% 83 665 0.01% 84 207 0.00% 85 183 0.00% 86 292 0.01% 87 467 0.01% 88 173 0.00% 89 169 0.00% 90 174 0.00% 91 314 0.01% 92 381 0.01% 93 320 0.01% 94 342 0.01% 95 486 0.01% 96 509 0.01% 97 546 0.01% 98 954 0.02% 99 636 0.01% 100 693 0.01% 101 44909 0.83% criterion=sequence-density sequence-density=2.80 sequence-density-rank=1 fanout-score=0.00 fanout-score-rank=13 prefix-density=0.00 prefix-fanout=1.0 sequence=GCGAGCGTAGTTCAATGGTAAAACATCTCCTTGCCAAGGAG criterion=fanout-score sequence-density=0.01 sequence-density-rank=31 fanout-score=59.43 fanout-score-rank=1 prefix-density=0.41 prefix-fanout=1.0 sequence=CCATCGAGTAGACCTTGTTATTGTGAGAATTCTTAA Started job on | Dec 06 10:18:38 Started mapping on | Dec 06 10:19:12 Finished on | Dec 06 10:19:32 Mapping speed, Million of reads per hour | 999.41 Number of input reads | 5552261 Average input read length | 32 UNIQUE READS: Uniquely mapped reads number | 629101 Uniquely mapped reads % | 11.33% Average mapped length | 27.17 Number of splices: Total | 15259 Number of splices: Annotated (sjdb) | 2340 Number of splices: GT/AG | 14678 Number of splices: GC/AG | 458 Number of splices: AT/AC | 5 Number of splices: Non-canonical | 118 Mismatch rate per base, % | 0.93% Deletion rate per base | 0.01% Deletion average length | 1.27 Insertion rate per base | 0.00% Insertion average length | 1.33 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 3786423 % of reads mapped to multiple loci | 68.20% Number of reads mapped to too many loci | 887158 % of reads mapped to too many loci | 15.98% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 4.02% % of reads unmapped: other | 0.48% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 1136737 1136737 1136737 N_multimapping 3786423 3786423 3786423 N_noFeature 383547 490116 518867 N_ambiguous 8642 4671 366 UnstrandedReadsAssigned:236912 PositiveStrandReadsAssigned:134314 NegativeStrandReadsAssigned:109868 Dataset is classified unstranded MeadianReadLen=31 20thPercentileLength=24 echo kmer=19 SRR6941536 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: SRR6941536-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 5,552,261 reads, 2,556,242 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 903 rounds 52973 SRR6941536.ke.tsv 35125 SRR6941536.se.tsv 88098 total ==> SRR6941536.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 1 0.114962 PNS24243 293 194 0 0 KQK14069 1603 1504 0.327852 0.0343826 KQK14071 474 375 0 0 ==> SRR6941536.se.tsv <== BRADI_1g14170v3 18 BRADI_1g53295v3 0 BRADI_1g59795v3 0 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 0 BRADI_1g74790v3 1 BRADI_1g09890v3 12 BRADI_1g77505v3 0 BRADI_1g48960v3 0 SRR6941536 completed mapping pipeline successfully