Starting /dee2/code/volunteer_pipeline.sh SRR6941539 current disk space = 1551750811648 free memory = 1603998468 SRR6941539 SRAfilesize 2a5a5b879478b1c66d4dddab81310a54 SRR6941539.sra SRR6941539.sra file validated SRR6941539 is single end SRR6941539 is conventional basespace SRR6941539 read1 length is 101 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR6941539_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 45 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 33.15725 34.0 33.0 34.0 32.0 34.0 2 33.25625 34.0 33.0 34.0 32.0 34.0 3 32.8285 34.0 33.0 34.0 31.0 34.0 4 33.13325 34.0 33.0 34.0 32.0 34.0 5 33.1815 34.0 33.0 34.0 33.0 34.0 6 37.06 38.0 37.0 38.0 36.0 38.0 7 37.3855 38.0 38.0 38.0 37.0 38.0 8 37.50275 38.0 38.0 38.0 37.0 38.0 9 37.534 38.0 38.0 38.0 38.0 38.0 10-11 37.49075 38.0 38.0 38.0 38.0 38.0 12-13 37.4035 38.0 38.0 38.0 37.0 38.0 14-15 37.47125 38.0 38.0 38.0 37.5 38.0 16-17 36.287000000000006 38.0 37.5 38.0 32.0 38.0 18-19 36.96325 38.0 38.0 38.0 34.5 38.0 20-21 35.9765 38.0 37.5 38.0 30.5 38.0 22-23 37.216750000000005 38.0 38.0 38.0 36.5 38.0 24-25 37.460625 38.0 38.0 38.0 37.0 38.0 26-27 37.382625000000004 38.0 38.0 38.0 37.0 38.0 28-29 37.456 38.0 38.0 38.0 37.5 38.0 30-31 37.376999999999995 38.0 38.0 38.0 37.0 38.0 32-33 37.231625 38.0 38.0 38.0 37.0 38.0 34-35 37.20375 38.0 38.0 38.0 37.0 38.0 36-37 37.124 38.0 38.0 38.0 36.5 38.0 38-39 37.081875 38.0 38.0 38.0 37.0 38.0 40-41 37.054874999999996 38.0 38.0 38.0 36.5 38.0 42-43 37.106 38.0 38.0 38.0 36.0 38.0 44-45 37.115625 38.0 38.0 38.0 36.0 38.0 46-47 36.93575 38.0 38.0 38.0 36.0 38.0 48-49 37.051125 38.0 38.0 38.0 36.5 38.0 50-51 36.933 38.0 38.0 38.0 36.0 38.0 52-53 36.94475 38.0 38.0 38.0 36.0 38.0 54-55 37.041375 38.0 38.0 38.0 36.0 38.0 56-57 36.970625 38.0 38.0 38.0 36.0 38.0 58-59 37.139375 38.0 38.0 38.0 37.0 38.0 60-61 37.116125 38.0 38.0 38.0 37.0 38.0 62-63 36.783625 38.0 38.0 38.0 35.5 38.0 64-65 36.56075 38.0 37.5 38.0 34.0 38.0 66-67 36.1325 38.0 37.5 38.0 31.5 38.0 68-69 36.74275 38.0 38.0 38.0 35.0 38.0 70-71 36.368625 38.0 37.5 38.0 33.5 38.0 72-73 35.956125 38.0 37.0 38.0 31.0 38.0 74-75 35.772625000000005 38.0 37.0 38.0 29.0 38.0 76-77 35.780125 38.0 37.0 38.0 30.0 38.0 78-79 36.253375 38.0 37.5 38.0 33.5 38.0 80-81 36.59825 38.0 38.0 38.0 35.0 38.0 82-83 36.6845 38.0 38.0 38.0 35.5 38.0 84-85 36.602000000000004 38.0 38.0 38.0 35.0 38.0 86-87 36.412375 38.0 38.0 38.0 34.5 38.0 88-89 36.5165 38.0 38.0 38.0 34.5 38.0 90-91 36.525875 38.0 38.0 38.0 35.0 38.0 92-93 36.32575 38.0 38.0 38.0 34.0 38.0 94-95 35.864125 38.0 38.0 38.0 34.0 38.0 96-97 33.84825 38.0 36.5 38.0 20.5 38.0 98-99 31.042375 38.0 32.5 38.0 2.0 38.0 100-101 27.674500000000002 38.0 19.5 38.0 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 5 1.0 6 0.0 7 0.0 8 0.0 9 0.0 10 0.0 11 0.0 12 0.0 13 1.0 14 1.0 15 0.0 16 0.0 17 0.0 18 0.0 19 0.0 20 1.0 21 1.0 22 2.0 23 5.0 24 5.0 25 14.0 26 10.0 27 29.0 28 23.0 29 31.0 30 38.0 31 45.0 32 73.0 33 95.0 34 200.0 35 441.0 36 801.0 37 2183.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 34.55 24.275 16.3 24.875 2 31.48148148148148 32.63263263263263 17.842842842842842 18.043043043043046 3 30.925000000000004 20.175 25.900000000000002 23.0 4 29.232308077019255 28.532133033258315 14.978744686171543 27.25681420355089 5 40.849999999999994 18.95 22.925 17.275 6 21.05 36.125 23.974999999999998 18.85 7 41.55 20.775 22.95 14.725 8 23.175 16.6 42.25 17.974999999999998 9 18.6 41.575 21.925 17.9 10-11 36.275 27.712500000000002 19.7375 16.275000000000002 12-13 18.6875 15.6125 23.2875 42.412499999999994 14-15 20.6375 38.75 25.35 15.262500000000001 16-17 28.225 17.65 39.137499999999996 14.9875 18-19 39.550000000000004 21.4375 24.462500000000002 14.549999999999999 20-21 14.4375 26.737499999999997 37.4375 21.3875 22-23 31.324999999999996 28.3875 23.8125 16.475 24-25 31.112499999999997 30.049999999999997 23.549999999999997 15.287500000000001 26-27 38.074999999999996 24.474999999999998 21.175 16.275000000000002 28-29 17.1125 37.574999999999996 22.8125 22.5 30-31 20.8875 11.125 45.087500000000006 22.900000000000002 32-33 30.525000000000002 12.8875 29.599999999999998 26.987499999999997 34-35 36.2375 21.1125 26.3125 16.3375 36-37 41.5875 18.6625 28.125 11.625 38-39 24.65 19.3875 34.4 21.5625 40-41 22.537499999999998 16.025 24.2875 37.15 42-43 35.225 25.55 18.7 20.525 44-45 51.737500000000004 14.5375 15.262500000000001 18.462500000000002 46-47 30.4 27.8875 14.8625 26.85 48-49 21.6125 25.3125 18.175 34.9 50-51 27.1125 26.637499999999996 8.1875 38.0625 52-53 27.950000000000003 43.8 7.35 20.9 54-55 17.875 30.4875 20.2625 31.374999999999996 56-57 11.4 33.475 16.075 39.050000000000004 58-59 13.525 28.95 27.35 30.175 60-61 18.2875 24.087500000000002 27.1125 30.5125 62-63 11.275 33.637499999999996 19.8875 35.199999999999996 64-65 9.65 32.237500000000004 32.45 25.662499999999998 66-67 14.5875 20.7125 33.975 30.725 68-69 20.125 25.424999999999997 27.1375 27.3125 70-71 14.325 28.825 36.449999999999996 20.4 72-73 17.1375 19.6375 34.699999999999996 28.525 74-75 15.075 13.7125 29.275000000000002 41.9375 76-77 20.225 11.774999999999999 43.65 24.349999999999998 78-79 19.35 9.3625 41.975 29.312500000000004 80-81 20.8875 9.5125 35.0625 34.5375 82-83 27.950000000000003 6.950000000000001 38.25 26.85 84-85 19.650000000000002 7.5625 38.15 34.637499999999996 86-87 19.375 15.275 40.7375 24.6125 88-89 12.962499999999999 34.675 33.3125 19.05 90-91 10.424999999999999 39.2125 31.724999999999998 18.637500000000003 92-93 16.150000000000002 45.5125 24.9375 13.4 94-95 11.799999999999999 61.95 18.775 7.475 96-97 8.512500000000001 76.97500000000001 11.6875 2.825 98-99 4.7625 89.4125 3.95 1.875 100-101 1.55 93.30000000000001 3.35 1.7999999999999998 >>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 3.0 34 3.0 35 3.0 36 2.0 37 3.5 38 10.5 39 20.0 40 46.0 41 108.5 42 207.5 43 471.5 44 583.0 45 404.0 46 367.0 47 342.0 48 215.5 49 238.5 50 309.5 51 287.0 52 173.0 53 61.5 54 55.5 55 39.0 56 11.5 57 17.0 58 13.5 59 1.5 60 1.0 61 0.0 62 0.0 63 0.0 64 0.0 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 pass #Base N-Count 1 0.0 2 0.1 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 fail #Total Deduplicated Percentage 49.375 #Duplication Level Percentage of deduplicated Percentage of total 1 88.15189873417721 43.525000000000006 2 4.10126582278481 4.05 3 2.0759493670886076 3.075 4 1.3164556962025316 2.6 5 0.6582278481012658 1.625 6 0.5569620253164557 1.6500000000000001 7 0.5063291139240507 1.7500000000000002 8 0.3037974683544304 1.2 9 0.1518987341772152 0.675 >10 1.6708860759493671 18.95 >50 0.35443037974683544 11.675 >100 0.1518987341772152 9.225 >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 143 3.5749999999999997 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTTGGAATTCTCGGGTGCCAAG 115 2.875 No Hit GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGATTTGGAATTCTCGGGTG 111 2.775 No Hit GAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAG 92 2.3 No Hit CTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCA 78 1.95 RNA PCR Primer, Index 1 (100% over 28bp) CATCGAGTAGACCTTGTTATTGTGAGAATTGGAATTCTCGGGTGCCAAGG 71 1.775 Illumina Small RNA Adapter 2 (100% over 21bp) CATCGAGTAGACCTTGTTATTGTGAGAATTCTGGAATTCTCGGGTGCCAA 59 1.4749999999999999 No Hit TGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAA 58 1.4500000000000002 No Hit TCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACTC 56 1.4000000000000001 RNA PCR Primer, Index 1 (100% over 26bp) CATCGAGTAGACCTTGTTATTGTGAGAATTCTTGGAATTCTCGGGTGCCA 53 1.325 No Hit TCGGACCAGGCTTCATTCCCCTGGAATTCTCGGGTGCCAAGGAACTCCAG 47 1.175 RNA PCR Primer, Index 1 (100% over 29bp) GGGATTGTAGTTCAATTGGTCAGAGCACCGCCTGGAATTCTCGGGTGCCA 44 1.0999999999999999 No Hit GTCAGGATAGCTCAGTTGGTAGAGCAGAGGACTTGGAATTCTCGGGTGCC 42 1.05 No Hit ATATTGGGTAGGTTGTGGTATTTCATTGCTTGGAATTCTCGGGTGCCAAG 40 1.0 No Hit GCGAGCGTAGTTCAATGGTAAAACATCTCCTTTGGAATTCTCGGGTGCCA 40 1.0 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTTGGAATTCTCGGGTGC 38 0.95 No Hit GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGAATTCTCGGGTGCCAAGG 37 0.9249999999999999 Illumina Small RNA Adapter 2 (100% over 21bp) ATATTGGGTAGGTTGTGGTATTTCATTGCTGGAATTCTCGGGTGCCAAGG 34 0.8500000000000001 Illumina Small RNA Adapter 2 (100% over 21bp) TCCGTCGTAGTCTAGGTGGTTAGGATACTCTGGAATTCTCGGGTGCCAAG 33 0.8250000000000001 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCCTGGAATTCTCGGGTGC 29 0.7250000000000001 No Hit GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGATTGGAATTCTCGGGTGC 27 0.675 No Hit GAAGATACGGGTTCGATTCCCGCCGCTCGCCCCATGGAATTCTCGGGTGC 24 0.6 No Hit GGGTGTTTGGTCTAGTGGTATGATTCTCGCTTGGAATTCTCGGGTGCCAA 24 0.6 No Hit GAACTTTGTATCGCGCGCATGACTTGGAATTCTCGGGTGCCAAGGAACTC 21 0.525 RNA PCR Primer, Index 1 (100% over 26bp) AGAAGATACGGGTTCGATTCCCGCCGCTCGCCCCATGGAATTCTCGGGTG 20 0.5 No Hit CGGTCGAGGGCACGCCTGCCTGGGCGTCACGCTGGAATTCTCGGGTGCCA 20 0.5 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATGGAATTCTCGGGTGCCAAGGA 19 0.475 RNA PCR Primer, Index 1 (100% over 22bp) GTCAGGATAGCTCAGTTGGTAGAGCAGAGGACTGGAATTCTCGGGTGCCA 19 0.475 No Hit ACTTTGTATCGCGCGCATGACTTGGAATTCTCGGGTGCCAAGGAACTCCA 19 0.475 RNA PCR Primer, Index 1 (100% over 28bp) GGAGAGATGGCTGAGTGGACTAAAGCGGCGGATTTGGAATTCTCGGGTGC 17 0.42500000000000004 No Hit TAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCAG 16 0.4 RNA PCR Primer, Index 1 (100% over 29bp) GGTGGCTGTAGTTTAGTGGTGAGAATTCCACGTTTGGAATTCTCGGGTGC 14 0.35000000000000003 No Hit GAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC 14 0.35000000000000003 RNA PCR Primer, Index 1 (100% over 33bp) CATCGAGTAGACCTTGTTATTGTGAGAATTATGGAATTCTCGGGTGCCAA 14 0.35000000000000003 No Hit CATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAAC 13 0.325 RNA PCR Primer, Index 1 (100% over 24bp) GCGAGCGTAGTTCAATGGTAAAACATCTCCTTGTGGAATTCTCGGGTGCC 13 0.325 No Hit TTGACAGAAGAGAGTGAGCACTGGAATTCTCGGGTGCCAAGGAACTCCAG 13 0.325 RNA PCR Primer, Index 1 (100% over 29bp) AACTTTGTATCGCGCGCATGACTTGGAATTCTCGGGTGCCAAGGAACTCC 12 0.3 RNA PCR Primer, Index 1 (100% over 27bp) CATCGAGTAGACCTTGTTATTGTGAGAATATGGAATTCTCGGGTGCCAAG 12 0.3 No Hit CAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCCAAGGAACTC 12 0.3 RNA PCR Primer, Index 1 (100% over 26bp) GCGAGCGTAGTTCAATGGTAAAACATCTCCTTGGAATTCTCGGGTGCCAA 11 0.27499999999999997 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCTGGAATTCTCGGGTGCCAAGG 10 0.25 Illumina Small RNA Adapter 2 (100% over 21bp) TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACATGTCAATCTCGTATGC 10 0.25 RNA PCR Primer, Index 15 (100% over 50bp) GGAGAGATGGCTGAGTGGACTAAAGCGGCGGATTGCTGGAATTCTCGGGT 9 0.22499999999999998 No Hit AGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGG 9 0.22499999999999998 Illumina Small RNA Adapter 2 (100% over 21bp) CATCGAGTAGACCTTGTTATTGTGAGAATTCTTAATGGAATTCTCGGGTG 9 0.22499999999999998 No Hit CATCGAGTAGACCTTGTTATTGTGAGATGGAATTCTCGGGTGCCAAGGAA 8 0.2 RNA PCR Primer, Index 1 (100% over 23bp) GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGATTGTGAATCTGGAATTC 8 0.2 No Hit GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGATTGTGGAATTCTCGGGT 8 0.2 No Hit ATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACT 8 0.2 RNA PCR Primer, Index 1 (100% over 25bp) TCGCTTGGTGCAGATCGGGACTGGAATTCTCGGGTGCCAAGGAACTCCAG 8 0.2 RNA PCR Primer, Index 1 (100% over 29bp) CTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCA 8 0.2 No Hit CGAACTTTGTATCGCGCGCATGACTTGGAATTCTCGGGTGCCAAGGAACT 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 25bp) TGTCGTGCCAATTCAACATAAACCCCTTGGAATTCTCGGGTGCCAAGGAA 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 23bp) TCCTCAGTAGCTCAGTGGTAGAGCGGTCGGCTTGGAATTCTCGGGTGCCA 7 0.17500000000000002 No Hit AATATTGGGTAGGTTGTGGTATTTCATTGCTTGGAATTCTCGGGTGCCAA 7 0.17500000000000002 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTCTATGGAATTCTCGGGTGCC 7 0.17500000000000002 No Hit TCCACTGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGT 7 0.17500000000000002 No Hit GGTAGTTCGACCGCGGAATTGGAATTCTCGGGTGCCAAGGAACTCCAGTC 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 31bp) GGGGATGTAGCTCAGATGGTAGATGGAATTCTCGGGTGCCAAGGAACTCC 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 27bp) GGTGGCTGTAGTTTAGTGGTGAGAATTCCACGTTGTTGGAATTCTCGGGT 7 0.17500000000000002 No Hit GCGAGCGTAGTTCAATGGTAAAACATCTCCTTGCCAAGGATGGAATTCTC 7 0.17500000000000002 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATAAATGGAATTCTCGGGTGCCA 6 0.15 No Hit CACCATGCGCGGGTTCAATTCCCGTCGTTCGCCCCATGGAATTCTCGGGT 6 0.15 No Hit GGGATTGTAGTTCAATTGGACAGAGCACCGCCCTGGAATTCTCGGGTGCC 6 0.15 No Hit TTGTATCGCGCGCATGACTTGGAATTCTCGGGTGCCAAGGAACTCCAGTC 6 0.15 RNA PCR Primer, Index 1 (100% over 31bp) CTCTGATGATGATCAAACTAATACTTTCGTTCTTCTGGAATTCTCGGGTG 6 0.15 No Hit GGTGGCTGTAGTTTAGTGGTGAGAATTCCACGTTGTGGAATTCTCGGGTG 6 0.15 No Hit ATATTGGGTAGGTTGTGGTATTTCATTGCTATGGAATTCTCGGGTGCCAA 6 0.15 No Hit ACGAACTTTGTATCGCGCGCATGACTTGGAATTCTCGGGTGCCAAGGAAC 6 0.15 RNA PCR Primer, Index 1 (100% over 24bp) AACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCAGT 6 0.15 RNA PCR Primer, Index 1 (100% over 30bp) TGTCGTGCCAATTCAACATAAACCCCTGGAATTCTCGGGTGCCAAGGAAC 6 0.15 RNA PCR Primer, Index 1 (100% over 24bp) ATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCCAAGGAA 6 0.15 RNA PCR Primer, Index 1 (100% over 23bp) CACGACTCTCGGCAACGGATATCTCGGCTCTTGGAATTCTCGGGTGCCAA 5 0.125 No Hit AGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCCAAGGAACTCC 5 0.125 RNA PCR Primer, Index 1 (100% over 27bp) TGACAGAAGAGAGTGAGCACTGGAATTCTCGGGTGCCAAGGAACTCCAGT 5 0.125 RNA PCR Primer, Index 1 (100% over 30bp) GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTGGAATTCTCGGGTG 5 0.125 No Hit GGGATTGTAGTTCAATAGGTCAGAGCACCGCCCTGGAATTCTCGGGTGCC 5 0.125 No Hit GACACGACTCTCGGCAACGGATATCTCTGGAATTCTCGGGTGCCAAGGAA 5 0.125 RNA PCR Primer, Index 1 (100% over 23bp) GACACGACTCTCGGCAACGGATATCTTGGAATTCTCGGGTGCCAAGGAAC 5 0.125 RNA PCR Primer, Index 1 (100% over 24bp) TCGGACCAGGCTTCGATCCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG 5 0.125 RNA PCR Primer, Index 1 (100% over 29bp) GGGGATATGGCGAAATCGGTAGACGCTACGGACTTTGGAATTCTCGGGTG 5 0.125 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTCAATGGAATTCTCGGGTGCC 5 0.125 No Hit CAGCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTG 5 0.125 No Hit GGGATTGTAGTTCAATTGGACAGAGCACCGCCTGGAATTCTCGGGTGCCA 5 0.125 No Hit CTTTGTATCGCGCGCATGACTTGGAATTCTCGGGTGCCAAGGAACTCCAG 5 0.125 RNA PCR Primer, Index 1 (100% over 29bp) >>END_MODULE >>Adapter Content fail #Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence SOLID Small RNA Adapter 1 0.0 0.375 0.0 0.0 0.0 2 0.0 0.375 0.0 0.0 0.0 3 0.0 0.4 0.0 0.0 0.0 4 0.0 0.4 0.0 0.0 0.0 5 0.0 0.4 0.0 0.0 0.0 6 0.0 0.4 0.0 0.0 0.0 7 0.0 0.4 0.0 0.0 0.0 8 0.0 0.4 0.0 0.0 0.0 9 0.0 0.4 0.0 0.0 0.0 10-11 0.0 0.45 0.0 0.0 0.0 12-13 0.0 0.5125 0.0 0.0 0.0 14-15 0.0 0.6 0.0 0.0 0.0 16-17 0.0 0.7749999999999999 0.0 0.0 0.0 18-19 0.0 1.625 0.0 0.0 0.0 20-21 0.0 3.1 0.0 0.0 0.0 22-23 0.0 10.475 0.0 0.0 0.0 24-25 0.0 23.6625 0.0 0.0 0.0 26-27 0.0 35.8125 0.0 0.0 0.0 28-29 0.0 40.0125 0.0 0.0 0.0 30-31 0.0 51.8 0.0 0.0 0.0 32-33 0.0 67.36250000000001 0.0 0.0 0.0 34-35 0.0 82.5875 0.0 0.0 0.0 36-37 0.0 92.5 0.0 0.0 0.0 38-39 0.0 94.76249999999999 0.0 0.0 0.0 40-41 0.0 95.625 0.0 0.0 0.0 42-43 0.0 96.2625 0.0 0.0 0.0 44-45 0.0 96.5375 0.0 0.0 0.0 46-47 0.0 96.625 0.0 0.0 0.0 48-49 0.0 96.625 0.0 0.0 0.0 50-51 0.0 96.625 0.0 0.0 0.0 52-53 0.0 96.625 0.0 0.0 0.0 54-55 0.0 96.625 0.0 0.0 0.0 56-57 0.0 96.625 0.0 0.0 0.0 58-59 0.0 96.625 0.0 0.0 0.0 60-61 0.0 96.625 0.0 0.0 0.0 62-63 0.0 96.625 0.0 0.0 0.0 64-65 0.0 96.625 0.0 0.0 0.0 66-67 0.0 96.625 0.0 0.0 0.0 68-69 0.0 96.625 0.0 0.0 0.0 70-71 0.0 96.625 0.0 0.0 0.0 72-73 0.0 96.625 0.0 0.0 0.0 74-75 0.0 96.625 0.0 0.0 0.0 76-77 0.0 96.625 0.0 0.0 0.0 78-79 0.0 96.625 0.0 0.0 0.0 80-81 0.0 96.625 0.0 0.0 0.0 82-83 0.0 96.6625 0.0 0.0 0.0 84-85 0.0 96.7 0.0 0.0 0.0 86-87 0.0 96.7 0.0 0.0 0.0 88-89 0.0 96.7 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position AGCTCAG 20 1.5392321E-5 95.00001 9 AGGATAG 20 1.5392321E-5 95.00001 4 GTCGTAG 20 1.5392321E-5 95.00001 4 TAGCTCA 20 1.5392321E-5 95.00001 8 CGTAGTC 20 1.5392321E-5 95.00001 6 CCGTCGT 20 1.5392321E-5 95.00001 2 TAGTCTA 20 1.5392321E-5 95.00001 8 GGATAGC 20 1.5392321E-5 95.00001 5 ATAGCTC 20 1.5392321E-5 95.00001 7 CGTCGTA 20 1.5392321E-5 95.00001 3 TCGTAGT 20 1.5392321E-5 95.00001 5 TCCGTCG 20 1.5392321E-5 95.00001 1 AGTCTAG 20 1.5392321E-5 95.00001 9 GTAGTCT 20 1.5392321E-5 95.00001 7 GATAGCT 20 1.5392321E-5 95.00001 6 GTAGACC 65 0.0 95.0 7 TTGTAGT 30 9.458745E-9 95.0 5 AGTAGAC 65 0.0 95.0 6 TCAGGAT 15 6.142176E-4 95.0 2 GGATTGT 30 9.458745E-9 95.0 2 >>END_MODULE Rejected 261289 READS because READLEN < 1 Read 261289 spots for SRR6941539.sra Written 261289 spots for SRR6941539.sra Rejected 261289 READS because READLEN < 1 Read 261289 spots for SRR6941539.sra Written 261289 spots for SRR6941539.sra Rejected 261289 READS because READLEN < 1 Read 261289 spots for SRR6941539.sra Written 261289 spots for SRR6941539.sra Rejected 261289 READS because READLEN < 1 Read 261289 spots for SRR6941539.sra Written 261289 spots for SRR6941539.sra Rejected 261289 READS because READLEN < 1 Read 261289 spots for SRR6941539.sra Written 261289 spots for SRR6941539.sra Rejected 261289 READS because READLEN < 1 Read 261289 spots for SRR6941539.sra Written 261289 spots for SRR6941539.sra Rejected 261289 READS because READLEN < 1 Read 261289 spots for SRR6941539.sra Written 261289 spots for SRR6941539.sra Rejected 261289 READS because READLEN < 1 Read 261289 spots for SRR6941539.sra Written 261289 spots for SRR6941539.sra Rejected 261289 READS because READLEN < 1 Read 261289 spots for SRR6941539.sra Written 261289 spots for SRR6941539.sra Rejected 261289 READS because READLEN < 1 Read 261289 spots for SRR6941539.sra Written 261289 spots for SRR6941539.sra Rejected 261289 READS because READLEN < 1 Read 261289 spots for SRR6941539.sra Written 261289 spots for SRR6941539.sra Rejected 261289 READS because READLEN < 1 Read 261289 spots for SRR6941539.sra Written 261289 spots for SRR6941539.sra Rejected 261289 READS because READLEN < 1 Read 261289 spots for SRR6941539.sra Written 261289 spots for SRR6941539.sra Rejected 261289 READS because READLEN < 1 Read 261289 spots for SRR6941539.sra Written 261289 spots for SRR6941539.sra Rejected 261289 READS because READLEN < 1 Read 261289 spots for SRR6941539.sra Written 261289 spots for SRR6941539.sra Rejected 261289 READS because READLEN < 1 Read 261289 spots for SRR6941539.sra Written 261289 spots for SRR6941539.sra Rejected 261289 READS because READLEN < 1 Read 261289 spots for SRR6941539.sra Written 261289 spots for SRR6941539.sra Rejected 261289 READS because READLEN < 1 Read 261289 spots for SRR6941539.sra Written 261289 spots for SRR6941539.sra Rejected 261289 READS because READLEN < 1 Read 261289 spots for SRR6941539.sra Written 261289 spots for SRR6941539.sra Rejected 261291 READS because READLEN < 1 Read 261291 spots for SRR6941539.sra Written 261291 spots for SRR6941539.sra SRR ids: ['SRR6941539.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_h8ll4_ds SRR6941539.sra spots: 5225782 blocks: [[1, 261289], [261290, 522578], [522579, 783867], [783868, 1045156], [1045157, 1306445], [1306446, 1567734], [1567735, 1829023], [1829024, 2090312], [2090313, 2351601], [2351602, 2612890], [2612891, 2874179], [2874180, 3135468], [3135469, 3396757], [3396758, 3658046], [3658047, 3919335], [3919336, 4180624], [4180625, 4441913], [4441914, 4703202], [4703203, 4964491], [4964492, 5225782]] SRR6941539 file size 1248140 SRR6941539 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 SRR6941539 SRR6941539_1.fastq Input file: SRR6941539_1.fastq trimmed: SRR6941539-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 10:40:44 2024 >> started Fri Dec 6 10:40:48 2024 >> done (3.732s) 5225782 reads processed; of these: 72 ( 0.00%) short reads filtered out after trimming by size control 10 ( 0.00%) empty reads filtered out after trimming by size control 5225700 (100.00%) reads available; of these: 933660 (17.87%) trimmed reads available after processing 4292040 (82.13%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 8 0.00% 19 4 0.00% 20 6 0.00% 21 6 0.00% 22 8 0.00% 23 8 0.00% 24 15 0.00% 25 15 0.00% 26 11 0.00% 27 16 0.00% 28 17 0.00% 29 37 0.00% 30 31 0.00% 31 17 0.00% 32 21 0.00% 33 13 0.00% 34 24 0.00% 35 21 0.00% 36 38 0.00% 37 27 0.00% 38 17 0.00% 39 23 0.00% 40 29 0.00% 41 33 0.00% 42 31 0.00% 43 43 0.00% 44 37 0.00% 45 73 0.00% 46 56 0.00% 47 43 0.00% 48 36 0.00% 49 30 0.00% 50 34 0.00% 51 35 0.00% 52 30 0.00% 53 27 0.00% 54 23 0.00% 55 21 0.00% 56 23 0.00% 57 25 0.00% 58 22 0.00% 59 26 0.00% 60 38 0.00% 61 37 0.00% 62 42 0.00% 63 33 0.00% 64 46 0.00% 65 26 0.00% 66 45 0.00% 67 58 0.00% 68 82 0.00% 69 93 0.00% 70 143 0.00% 71 142 0.00% 72 224 0.00% 73 581 0.01% 74 3571 0.07% 75 2687 0.05% 76 948 0.02% 77 339 0.01% 78 453 0.01% 79 506 0.01% 80 512 0.01% 81 573 0.01% 82 671 0.01% 83 851 0.02% 84 1388 0.03% 85 1723 0.03% 86 1826 0.03% 87 2113 0.04% 88 2680 0.05% 89 4013 0.08% 90 5881 0.11% 91 10008 0.19% 92 13321 0.25% 93 23057 0.44% 94 39448 0.75% 95 102012 1.95% 96 118665 2.27% 97 123054 2.35% 98 181029 3.46% 99 210403 4.03% 100 79278 1.52% 101 4292040 82.13% 5225700 reads passed initial QC criterion=sequence-density sequence-density=97.09 sequence-density-rank=1 fanout-score=24.08 fanout-score-rank=3 prefix-density=97.53 prefix-fanout=24.0 sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACATGTCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAA criterion=fanout-score sequence-density=0.01 sequence-density-rank=9 fanout-score=45.52 fanout-score-rank=1 prefix-density=0.29 prefix-fanout=1.0 sequence=CCATCGAGTAGACCTTGTTATTGTGAGAATT 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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACATGTCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAA -o SRR6941539 - Input file: STDIN trimmed: SRR6941539-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACATGTCAATCTCGTATGCCGTCTTCTGCTTGA -- 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 10:41:51 2024 >> started Fri Dec 6 10:41:57 2024 >> done (5.909s) 5119053 reads processed; of these: 44980 ( 0.88%) short reads filtered out after trimming by size control 14132 ( 0.28%) empty reads filtered out after trimming by size control 5059941 (98.85%) reads available; of these: 5020099 (99.21%) trimmed reads available after processing 39842 ( 0.79%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 16891 0.33% 19 38604 0.76% 20 50406 1.00% 21 259143 5.12% 22 233633 4.62% 23 146527 2.90% 24 927532 18.33% 25 138134 2.73% 26 122825 2.43% 27 100595 1.99% 28 103691 2.05% 29 315864 6.24% 30 510841 10.10% 31 353480 6.99% 32 380638 7.52% 33 440676 8.71% 34 313872 6.20% 35 295934 5.85% 36 101155 2.00% 37 48572 0.96% 38 24165 0.48% 39 16373 0.32% 40 22877 0.45% 41 23980 0.47% 42 17195 0.34% 43 3802 0.08% 44 4012 0.08% 45 3081 0.06% 46 928 0.02% 47 1062 0.02% 48 379 0.01% 49 160 0.00% 50 97 0.00% 51 84 0.00% 52 26 0.00% 53 42 0.00% 54 26 0.00% 55 21 0.00% 56 20 0.00% 57 30 0.00% 58 16 0.00% 59 21 0.00% 60 18 0.00% 61 21 0.00% 62 13 0.00% 63 16 0.00% 64 22 0.00% 65 10 0.00% 66 21 0.00% 67 16 0.00% 68 40 0.00% 69 28 0.00% 70 72 0.00% 71 44 0.00% 72 35 0.00% 73 41 0.00% 74 47 0.00% 75 93 0.00% 76 122 0.00% 77 400 0.01% 78 77 0.00% 79 95 0.00% 80 592 0.01% 81 214 0.00% 82 327 0.01% 83 259 0.01% 84 94 0.00% 85 93 0.00% 86 131 0.00% 87 248 0.00% 88 123 0.00% 89 133 0.00% 90 133 0.00% 91 225 0.00% 92 251 0.00% 93 246 0.00% 94 310 0.01% 95 422 0.01% 96 465 0.01% 97 486 0.01% 98 956 0.02% 99 665 0.01% 100 628 0.01% 101 34299 0.68% criterion=sequence-density sequence-density=13.20 sequence-density-rank=1 fanout-score=0.00 fanout-score-rank=10 prefix-density=0.00 prefix-fanout=1.0 sequence=CATCGAGTAGACCTTGTTATTGTGAGAATTCTTAA criterion=fanout-score sequence-density=0.28 sequence-density-rank=14 fanout-score=46.03 fanout-score-rank=1 prefix-density=12.95 prefix-fanout=1.0 sequence=ATTGTGAGAATAAAAA Started job on | Dec 06 10:42:21 Started mapping on | Dec 06 10:42:33 Finished on | Dec 06 10:42:47 Mapping speed, Million of reads per hour | 1328.55 Number of input reads | 5166588 Average input read length | 30 UNIQUE READS: Uniquely mapped reads number | 826564 Uniquely mapped reads % | 16.00% Average mapped length | 25.54 Number of splices: Total | 21386 Number of splices: Annotated (sjdb) | 2016 Number of splices: GT/AG | 20691 Number of splices: GC/AG | 594 Number of splices: AT/AC | 2 Number of splices: Non-canonical | 99 Mismatch rate per base, % | 1.03% Deletion rate per base | 0.01% Deletion average length | 1.29 Insertion rate per base | 0.00% Insertion average length | 1.19 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 3385326 % of reads mapped to multiple loci | 65.52% Number of reads mapped to too many loci | 683295 % of reads mapped to too many loci | 13.23% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 4.56% % of reads unmapped: other | 0.69% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 954698 954698 954698 N_multimapping 3385326 3385326 3385326 N_noFeature 543710 654210 712065 N_ambiguous 8389 3927 567 UnstrandedReadsAssigned:274465 PositiveStrandReadsAssigned:168427 NegativeStrandReadsAssigned:113932 Dataset is classified unstranded MeadianReadLen=30 20thPercentileLength=24 echo kmer=19 SRR6941539 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: SRR6941539-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 5,166,588 reads, 2,292,500 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 938 rounds 52973 SRR6941539.ke.tsv 35125 SRR6941539.se.tsv 88098 total ==> SRR6941539.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 0 0 PNS24243 293 194 3 2.73651 KQK14069 1603 1504 17.4233 2.05003 KQK14071 474 375 0 0 ==> SRR6941539.se.tsv <== BRADI_1g14170v3 15 BRADI_1g53295v3 3 BRADI_1g59795v3 0 BRADI_1g07683v3 0 BRADI_1g00485v3 1 BRADI_1g20270v3 2 BRADI_1g74790v3 10 BRADI_1g09890v3 16 BRADI_1g77505v3 1 BRADI_1g48960v3 0 SRR6941539 completed mapping pipeline successfully