Starting /dee2/code/volunteer_pipeline.sh SRR9668908 current disk space = 3051692154880 free memory = 1415656104 SRR9668908 SRAfilesize c48f9787c304fe7d689616bc3f09456e SRR9668908.sra SRR9668908.sra file validated SRR9668908 is paired end SRR9668908 is conventional basespace SRR9668908 read1 length is 40-76 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR9668908_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 40-76 %GC 49 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 31.66225 32.0 32.0 32.0 32.0 32.0 2 31.58325 32.0 32.0 32.0 32.0 32.0 3 31.71825 32.0 32.0 32.0 32.0 32.0 4 31.75 32.0 32.0 32.0 32.0 32.0 5 31.75275 32.0 32.0 32.0 32.0 32.0 6 35.4215 36.0 36.0 36.0 36.0 36.0 7 35.45125 36.0 36.0 36.0 36.0 36.0 8 35.371 36.0 36.0 36.0 36.0 36.0 9 35.3425 36.0 36.0 36.0 36.0 36.0 10-11 35.31 36.0 36.0 36.0 36.0 36.0 12-13 35.3815 36.0 36.0 36.0 36.0 36.0 14-15 35.305375 36.0 36.0 36.0 36.0 36.0 16-17 35.365875 36.0 36.0 36.0 36.0 36.0 18-19 35.40575 36.0 36.0 36.0 36.0 36.0 20-21 35.311375 36.0 36.0 36.0 36.0 36.0 22-23 35.366375 36.0 36.0 36.0 36.0 36.0 24-25 35.23375 36.0 36.0 36.0 36.0 36.0 26-27 35.23375 36.0 36.0 36.0 36.0 36.0 28-29 35.247375 36.0 36.0 36.0 36.0 36.0 30-31 35.2325 36.0 36.0 36.0 36.0 36.0 32-33 35.15975 36.0 36.0 36.0 36.0 36.0 34-35 35.210875 36.0 36.0 36.0 36.0 36.0 36-37 35.103375 36.0 36.0 36.0 36.0 36.0 38-39 35.13475 36.0 36.0 36.0 36.0 36.0 40-41 35.152771161540386 36.0 36.0 36.0 36.0 36.0 42-43 35.17429357339335 36.0 36.0 36.0 36.0 36.0 44-45 35.126406601650416 36.0 36.0 36.0 36.0 36.0 46-47 35.05263815953988 36.0 36.0 36.0 36.0 36.0 48-49 35.05413853463366 36.0 36.0 36.0 36.0 36.0 50-51 34.990997749437355 36.0 36.0 36.0 36.0 36.0 52-53 34.841835458864715 36.0 36.0 36.0 34.0 36.0 54-55 34.84796199049762 36.0 36.0 36.0 34.0 36.0 56-57 34.848337084271066 36.0 36.0 36.0 32.0 36.0 58-59 34.776582436827624 36.0 36.0 36.0 32.0 36.0 60-61 34.688822752276096 36.0 36.0 36.0 32.0 36.0 62-63 34.72934401602404 36.0 36.0 36.0 32.0 36.0 64-65 34.689542590063674 36.0 36.0 36.0 32.0 36.0 66-67 34.74652419698708 36.0 36.0 36.0 32.0 36.0 68-69 34.569064928553516 36.0 36.0 36.0 32.0 36.0 70-71 34.44322817889049 36.0 36.0 36.0 32.0 36.0 72-73 34.463790477317694 36.0 36.0 36.0 32.0 36.0 74-75 34.45401147226943 36.0 36.0 36.0 32.0 36.0 76 33.59861465548669 36.0 32.0 36.0 27.0 36.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 17 1.0 18 0.0 19 0.0 20 0.0 21 1.0 22 2.0 23 5.0 24 4.0 25 6.0 26 17.0 27 21.0 28 37.0 29 49.0 30 65.0 31 98.0 32 113.0 33 170.0 34 459.0 35 2952.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 49.85 12.25 6.7 31.2 2 23.225 14.975 34.849999999999994 26.950000000000003 3 19.15 20.05 27.250000000000004 33.550000000000004 4 24.9 28.549999999999997 21.75 24.8 5 23.525 31.874999999999996 22.05 22.55 6 22.05 31.525 24.5 21.925 7 16.85 20.65 41.85 20.65 8 19.1 20.075000000000003 30.875000000000004 29.95 9 19.625 20.974999999999998 31.874999999999996 27.525 10-11 22.7625 29.349999999999998 22.375 25.5125 12-13 22.3 22.8625 27.3375 27.500000000000004 14-15 22.6375 24.2625 27.3625 25.7375 16-17 23.265408176022003 24.415551943992998 26.515814476809602 25.803225403175396 18-19 23.150000000000002 24.7 26.375 25.775 20-21 22.8375 25.587500000000002 26.2625 25.3125 22-23 22.5625 25.25 25.5625 26.625 24-25 22.875 24.0 25.7875 27.3375 26-27 22.237499999999997 24.9875 25.674999999999997 27.1 28-29 22.4375 23.8125 25.900000000000002 27.85 30-31 22.640330041255158 24.278034754344294 26.453306663332913 26.62832854106763 32-33 23.0875 24.0625 25.637500000000003 27.212500000000002 34-35 22.6 25.474999999999998 26.2875 25.637500000000003 36-37 21.762500000000003 25.362499999999997 26.325 26.55 38-39 22.9875 23.724999999999998 24.837500000000002 28.449999999999996 40-41 22.96537067133392 24.978122265283158 25.390673834229275 26.665833229153645 42-43 22.968242060515127 24.60615153788447 26.44411102775694 25.98149537384346 44-45 22.218054513628406 24.50612653163291 26.831707926981746 26.44411102775694 46-47 22.680670167541887 24.293573393348336 27.169292323080768 25.85646411602901 48-49 22.18054513628407 24.93123280820205 26.36909227306827 26.51912978244561 50-51 21.642910727681922 25.28132033008252 26.51912978244561 26.556639159789945 52-53 22.143035758939735 24.76869217304326 26.93173293323331 26.156539134783696 54-55 21.767941985496375 24.956239059764943 25.6064016004001 27.66941735433858 56-57 20.86771692923231 24.493623405851466 26.994248562140534 27.644411102775695 58-59 22.12909682261696 24.843632724543408 26.1195896922692 26.90768076057043 60-61 23.03166854424834 25.222180498185004 25.585179621980224 26.16097133558643 62-63 21.84526790185278 23.748122183274912 26.214321482223333 28.192288432648972 64-65 21.69067000626174 24.571070757670633 26.80025046963056 26.938008766437072 66-67 21.037463976945244 24.82145094599674 27.26475379025185 26.876331286806167 68-69 21.44647781398847 24.85585359739283 26.77362747555778 26.92404111306092 70-71 21.485011915213846 24.457544211714534 26.9660102847109 27.09143358836072 72-73 21.683255638150435 25.311830666498675 25.81579942043593 27.189114274914957 74-75 21.87044641674394 22.810968340177507 26.55980924625778 28.758775996820773 76 24.352898286547575 0.0 37.91469194312796 37.73240977032446 >>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 0.5 15 0.5 16 0.0 17 0.0 18 1.5 19 2.0 20 0.5 21 0.0 22 1.0 23 2.5 24 4.0 25 4.5 26 4.0 27 8.0 28 11.5 29 12.0 30 16.0 31 25.5 32 32.5 33 29.5 34 41.5 35 61.0 36 68.5 37 74.0 38 87.5 39 103.0 40 110.0 41 138.0 42 165.5 43 184.0 44 193.5 45 215.0 46 246.0 47 277.0 48 292.0 49 266.5 50 244.0 51 234.0 52 235.0 53 222.0 54 206.0 55 212.5 56 215.0 57 188.0 58 172.5 59 173.5 60 153.5 61 94.5 62 49.0 63 44.5 64 29.0 65 22.0 66 20.0 67 12.0 68 12.0 69 11.0 70 7.0 71 5.0 72 10.5 73 13.0 74 6.5 75 2.0 76 1.5 77 1.0 78 0.5 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 0.5 91 0.5 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 0.0125 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 0.0125 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 0.0 >>END_MODULE >>Sequence Length Distribution warn #Length Count 40 1.0 41 0.0 42 0.0 43 0.0 44 0.0 45 0.0 46 0.0 47 0.0 48 0.0 49 0.0 50 0.0 51 0.0 52 0.0 53 0.0 54 0.0 55 0.0 56 0.0 57 2.0 58 0.0 59 2.0 60 1.0 61 0.0 62 0.0 63 1.0 64 1.0 65 1.0 66 1.0 67 1.0 68 0.0 69 1.0 70 3.0 71 6.0 72 21.0 73 67.0 74 233.0 75 915.0 76 2743.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 84.425 #Duplication Level Percentage of deduplicated Percentage of total 1 89.78383180337578 75.8 2 6.42582173526799 10.85 3 2.0432336393248445 5.175 4 0.7403020432336394 2.5 5 0.3553449807521469 1.5 6 0.26650873556411014 1.35 7 0.11844832691738229 0.7000000000000001 8 0.08883624518803672 0.6 9 0.059224163458691144 0.44999999999999996 >10 0.11844832691738229 1.075 >50 0.0 0.0 >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 warn #Sequence Count Percentage Possible Source CGGCAATCGGACGGCGGGCGCACGCGTCGCATCTAGCCCGGATTCTGACT 13 0.325 No Hit GTCGGCATCGTTTATGGTTGAGACTAGGACGGTATCTGATCGTCTTCGAG 10 0.25 No Hit GTTCGATTAGTCTTTCGCCCCTATACCCAAGTCAGACGAACGATTTGCACGTCAGTATCGCTGCGGGCCTCCACC 10 0.25 No Hit GATAGAACTCGCACCGAGCTCCAGCTATCCTGAGGGAAACTTCGGAGGGA 10 0.25 No Hit CCCGACTGTCCCTGTTAATCATTACTCCGATCCCGAAGGCCAACACAATA 9 0.22499999999999998 No Hit GTCGAGTTATCATGAATCATCAGAGCAACGGGCAGAGCCCGCGTCGACCTTTTATCTAATAAATGCGTCCCTTCC 9 0.22499999999999998 No Hit GTCAGGATTGGGTAATTTGCGCGCCTGCTGCCTTCCTTGGATGTGGTAGC 8 0.2 No Hit GTCAATTCCTTTAAGTTTCAGCCTTGCGACCATACTCCCCCCAGAACCCA 8 0.2 No Hit CCAGAACCCAAAAACTTTGATTTCTCATAAGGTGCTGGCGGAGTCCTAAA 8 0.2 No Hit CTTTTATCTAATAAATGCGTCCCTTCCAGAAGTCGGGGTTTGTTGCACGT 7 0.17500000000000002 No Hit CCGACATCGAAGGATCAAAAAGCAACGTCGCTATGAACGCTTGGCTGCCA 7 0.17500000000000002 No Hit GTGGTTTCGCTGGATAGTAGACAGGGACAGTGGGAATCTCGTTAATCCAT 7 0.17500000000000002 No Hit GTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCAT 7 0.17500000000000002 No Hit CCTAGATGTCCAGTCAACTGCTGCGCCTCAACGCATTTCGGGGAGAACCA 6 0.15 No Hit CCTATACCCAAGTCAGACGAACGATTTGCACGTCAGTATCGCTGCGGGCC 6 0.15 No Hit GTCAGTATCGCTGCGGGCCTCCACCAGAGTTTCCTCTGGCTTCGCCCCGC 6 0.15 No Hit GTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCAAAGATTACCCGGGCCTGTCGGCCA 6 0.15 No Hit ATCACGATGAAATTTCAAAGATTACCCGGGCCTGTCGGCCAAGGCTATAG 6 0.15 No Hit GTCAATTCCTTTGAGTTTCATTCTTGCGAACGTACTCCCCAGGCGGGATACTTAACGCGTTAGCTACAGCACTGC 6 0.15 No Hit GCCCGTTCCCTTGGCTGTGGTTTCGCTGGATAGTAGACAGGGACAGTGGG 6 0.15 No Hit GGGCTTACTACTTAGATGCTTTCAGCAGTTATCCGCTCCGCACTTGGCTACCCAGCGTTTACCGTGGGCACAATA 6 0.15 No Hit GTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGAATTCCTCGTTGAAGACCAACA 6 0.15 No Hit AGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCAAACTTCCTTGGCCTGGAAGGCCATAGTCCCTCTAAGA 5 0.125 No Hit CCCATCACGATGAAATTTCAAAGATTACCCGGGCCTGTCGGCCAAGGCTATAGACTCGTTGAATACATCAGTGT 5 0.125 No Hit CTTGGCTGTGGTTTCGCTGGATAGTAGACAGGGACAGTGGGAATCTCGTTAATCCATTCATGCGCGTCACTAATT 5 0.125 No Hit GCGCCTGCTGCCTTCCTTGGATGTGGTAGCCGTTTCTCAGGCTCCCTCTCCGGAATCGAACCCTAATTCTCCGTC 5 0.125 No Hit GCCGCAGGCTCCACTCCTGGTGGTGCCCTTCCGTCAATTCCTTTAAGTTTCAGCCTTGCGACCATACTCCCCCC 5 0.125 No Hit GTGAATTCTGCTTCACAATGATAGGAAGAGCCGACATCGAAGGATCAAAA 5 0.125 No Hit CTTTTGTTCCACACGAGATTTCTGTTCTCGTTGAGCTCATCTTAGGACAC 5 0.125 No Hit GTTCTAGGTTAGCGCGCAGTTGGGCACCGTAACCCGGCTTCCGGTTCATCCCGCATCGCCAGTTCTGCTTACCAA 5 0.125 No Hit CCGGAATCGAACCCTAATTCTCCGTCACCCGTCACCACCATGGTAGGCCT 5 0.125 No Hit GGCACGTGCCTCCGGGGCCAAGAGGCCCCTACTGCAGGTCGGCAATCGGA 5 0.125 No Hit GTCTTTCTGTCCAGGTGCAGGTAGTCCGCATCTTCACAGACATGTCTATT 5 0.125 No Hit GTCGGCAATCGGACGGCGGGCGCACGCGTCGCATCTAGCCCGGATTCTGACTTAGAGGCGTTCAGTCATAATCCA 5 0.125 No Hit >>END_MODULE >>Adapter Content pass #Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence SOLID Small RNA Adapter 1 0.0 0.0 0.0 0.0 0.0 2 0.0 0.0 0.0 0.0 0.0 3 0.0 0.0 0.0 0.0 0.0 4 0.0 0.0 0.0 0.0 0.0 5 0.0 0.0 0.0 0.0 0.0 6 0.0 0.0 0.0 0.0 0.0 7 0.0 0.0 0.0 0.0 0.0 8 0.0 0.0 0.0 0.0 0.0 9 0.0 0.0 0.0 0.0 0.0 10 0.0 0.0 0.0 0.0 0.0 11 0.0 0.0 0.0 0.0 0.0 12 0.0 0.0 0.0 0.0 0.0 13 0.0 0.0 0.0 0.0 0.0 14 0.0 0.0 0.0 0.0 0.0 15 0.0 0.0 0.0 0.0 0.0 16 0.0 0.0 0.0 0.0 0.0 17 0.0 0.0 0.0 0.0 0.0 18 0.0 0.0 0.0 0.0 0.0 19 0.0 0.0 0.0 0.0 0.0 20 0.0 0.0 0.0 0.0 0.0 21 0.0 0.0 0.0 0.0 0.0 22 0.0 0.0 0.0 0.0 0.0 23 0.0 0.0 0.0 0.0 0.0 24 0.0 0.0 0.0 0.0 0.0 25 0.0 0.0 0.0 0.0 0.0 26 0.0 0.0 0.0 0.0 0.0 27 0.0 0.0 0.0 0.0 0.0 28 0.0 0.0 0.0 0.0 0.0 29 0.0 0.0 0.0 0.0 0.0 30 0.0 0.0 0.0 0.0 0.0 31 0.0 0.0 0.0 0.0 0.0 32 0.0 0.0 0.0 0.0 0.0 33 0.0 0.0 0.0 0.0 0.0 34 0.0 0.0 0.0 0.0 0.0 35 0.0 0.0 0.0 0.0 0.0 36 0.0 0.0 0.0 0.0 0.0 37 0.0 0.0 0.0 0.0 0.0 38 0.0 0.0 0.0 0.0 0.0 39 0.0 0.0 0.0 0.0 0.0 40 0.0 0.0 0.0 0.0 0.0 41 0.0 0.0 0.0 0.0 0.0 42 0.0 0.0 0.0 0.0 0.0 43 0.0 0.0 0.0 0.0 0.0 44 0.0 0.0 0.0 0.0 0.0 45 0.0 0.0 0.0 0.0 0.0 46 0.0 0.0 0.0 0.0 0.0 47 0.0 0.0 0.0 0.0 0.0 48 0.0 0.0 0.0 0.0 0.0 49 0.0 0.0 0.0 0.0 0.0 50 0.0 0.0 0.0 0.0 0.0 51 0.0 0.0 0.0 0.0 0.0 52 0.0 0.0 0.0 0.0 0.0 53 0.0 0.0 0.0 0.0 0.0 54 0.0 0.0 0.0 0.0 0.0 55 0.0 0.0 0.0 0.0 0.0 56 0.0 0.0 0.0 0.0 0.0 57 0.0 0.0 0.0 0.0 0.0 58 0.0 0.0 0.0 0.0 0.0 59 0.0 0.0 0.0 0.0 0.0 60 0.0 0.0 0.0 0.0 0.0 61 0.0 0.0 0.0 0.0 0.0 62 0.0 0.0 0.0 0.0 0.0 63 0.0 0.0 0.0 0.0 0.0 64 0.0 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE SRR9668908 read2 length is 40-76 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR9668908_2.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 40-76 %GC 50 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 31.24375 32.0 32.0 32.0 32.0 32.0 2 31.10425 32.0 32.0 32.0 32.0 32.0 3 31.24975 32.0 32.0 32.0 32.0 32.0 4 31.16225 32.0 32.0 32.0 32.0 32.0 5 31.2305 32.0 32.0 32.0 32.0 32.0 6 34.681 36.0 36.0 36.0 32.0 36.0 7 34.6675 36.0 36.0 36.0 32.0 36.0 8 34.686 36.0 36.0 36.0 32.0 36.0 9 34.758 36.0 36.0 36.0 36.0 36.0 10-11 34.57725000000001 36.0 36.0 36.0 32.0 36.0 12-13 34.620125 36.0 36.0 36.0 32.0 36.0 14-15 34.584875 36.0 36.0 36.0 32.0 36.0 16-17 34.439125000000004 36.0 36.0 36.0 32.0 36.0 18-19 34.527625 36.0 36.0 36.0 32.0 36.0 20-21 34.3365 36.0 36.0 36.0 32.0 36.0 22-23 34.24225 36.0 36.0 36.0 32.0 36.0 24-25 34.278000000000006 36.0 36.0 36.0 32.0 36.0 26-27 34.13875 36.0 36.0 36.0 32.0 36.0 28-29 34.161375 36.0 36.0 36.0 32.0 36.0 30-31 34.12825 36.0 36.0 36.0 32.0 36.0 32-33 34.16675 36.0 36.0 36.0 32.0 36.0 34-35 34.167 36.0 36.0 36.0 32.0 36.0 36-37 34.023624999999996 36.0 36.0 36.0 32.0 36.0 38-39 34.013374999999996 36.0 36.0 36.0 32.0 36.0 40-41 34.112016316579144 36.0 36.0 36.0 32.0 36.0 42-43 34.00650162540635 36.0 36.0 36.0 32.0 36.0 44-45 33.888847211802954 36.0 36.0 36.0 29.5 36.0 46-47 33.88222055513879 36.0 36.0 36.0 32.0 36.0 48-49 33.82895723930983 36.0 36.0 36.0 29.5 36.0 50-51 33.76619154788697 36.0 36.0 36.0 27.0 36.0 52-53 33.77731932983246 36.0 36.0 36.0 27.0 36.0 54-55 33.648412103025755 36.0 36.0 36.0 27.0 36.0 56-57 33.8485871467867 36.0 36.0 36.0 27.0 36.0 58-59 33.721916437328 36.0 36.0 36.0 29.5 36.0 60-61 33.64425787617597 36.0 36.0 36.0 27.0 36.0 62-63 33.666249374061096 36.0 36.0 36.0 27.0 36.0 64-65 33.61540373509353 36.0 36.0 36.0 27.0 36.0 66-67 33.55395171717819 36.0 36.0 36.0 24.0 36.0 68-69 33.46382173405364 36.0 36.0 36.0 24.0 36.0 70-71 33.606490468085056 36.0 36.0 36.0 27.0 36.0 72-73 33.51664525222024 36.0 36.0 36.0 27.0 36.0 74-75 33.634622309371565 36.0 36.0 36.0 27.0 36.0 76 32.82144191258872 36.0 32.0 36.0 21.0 36.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 14 4.0 15 25.0 16 40.0 17 35.0 18 20.0 19 27.0 20 21.0 21 12.0 22 18.0 23 20.0 24 14.0 25 17.0 26 23.0 27 37.0 28 42.0 29 42.0 30 62.0 31 86.0 32 111.0 33 166.0 34 461.0 35 2717.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 51.71636181408168 19.41869205712854 7.466800300676522 21.398145828113254 2 33.708708708708706 22.372372372372375 27.7027027027027 16.216216216216218 3 27.0 24.8 26.6 21.6 4 30.325000000000003 31.05 19.325 19.3 5 32.725 33.300000000000004 16.975 17.0 6 28.775000000000002 33.675 18.95 18.6 7 26.5 18.975 31.8 22.725 8 27.1 22.525000000000002 23.175 27.200000000000003 9 27.800000000000004 22.275 25.15 24.775 10-11 30.6375 27.675 19.275000000000002 22.412499999999998 12-13 28.6875 23.1125 23.974999999999998 24.224999999999998 14-15 28.675 25.424999999999997 24.4375 21.462500000000002 16-17 29.7375 25.374999999999996 22.95 21.9375 18-19 29.575000000000003 25.412499999999998 23.799999999999997 21.212500000000002 20-21 29.1125 24.762500000000003 24.0375 22.0875 22-23 28.812500000000004 25.575 23.525 22.0875 24-25 29.362500000000004 25.25 23.962500000000002 21.425 26-27 29.4375 26.150000000000002 22.900000000000002 21.512500000000003 28-29 29.4 26.5875 22.275 21.7375 30-31 29.775000000000002 25.2 23.7125 21.3125 32-33 27.825 26.8 23.7375 21.637500000000003 34-35 28.762500000000003 27.787499999999998 21.987499999999997 21.462500000000002 36-37 28.962500000000002 27.4125 22.3375 21.2875 38-39 28.425 27.1375 23.0875 21.349999999999998 40-41 29.216152019002372 26.665833229153645 23.215401925240656 20.902612826603324 42-43 28.419604901225306 26.6816704176044 23.78094523630908 21.117779444861213 44-45 28.032008002000502 25.681420355088775 24.306076519129782 21.980495123780948 46-47 28.507126781695426 25.93148287071768 23.330832708177045 22.230557639409852 48-49 28.28207051762941 26.431607901975497 23.53088272068017 21.75543885971493 50-51 28.28207051762941 26.85671417854464 23.918479619904975 20.94273568392098 52-53 29.369842460615153 26.744186046511626 22.705676419104776 21.180295073768445 54-55 28.032008002000502 27.11927981995499 23.618404601150285 21.230307576894223 56-57 27.906976744186046 26.156539134783696 24.193548387096776 21.742935733933482 58-59 27.795846885163872 26.169627220415308 24.25569176882662 21.778834125594194 60-61 28.86468894730254 25.272249342846415 24.308424083114282 21.554637626736763 62-63 27.979469203805706 25.951427140711065 24.3114672008012 21.75763645468202 64-65 29.96869129618034 26.17407639323732 23.180964308077645 20.676268002504695 66-67 27.16451572484651 26.901390803157497 24.207492795389047 21.726600676606942 68-69 27.42319749216301 26.557993730407524 24.288401253918497 21.730407523510973 70-71 28.54273879753985 25.81900338897954 23.948788753608635 21.68946905987197 72-73 28.00604991177212 27.224602974539952 22.346861608268213 22.42248550541971 74-75 28.025221357660318 23.598068151328146 24.926214113227797 23.450496377783743 76 30.55659320134479 0.0 36.38401195367949 33.05939484497572 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 0.0 1 0.5 2 0.5 3 0.0 4 0.0 5 0.0 6 0.0 7 0.5 8 1.0 9 1.5 10 1.0 11 0.0 12 0.0 13 0.0 14 0.0 15 0.0 16 0.5 17 2.0 18 2.5 19 2.0 20 2.5 21 2.5 22 1.0 23 1.0 24 2.0 25 1.5 26 3.0 27 6.5 28 8.5 29 9.0 30 9.0 31 10.5 32 18.5 33 26.0 34 32.5 35 48.0 36 60.5 37 66.0 38 90.0 39 117.0 40 132.5 41 148.5 42 163.0 43 188.5 44 213.5 45 228.5 46 237.5 47 246.5 48 269.5 49 261.5 50 234.5 51 226.0 52 211.0 53 189.0 54 178.0 55 192.5 56 192.0 57 173.5 58 165.5 59 145.5 60 128.0 61 113.0 62 97.0 63 66.5 64 34.0 65 30.0 66 25.0 67 19.5 68 25.5 69 27.0 70 20.5 71 16.5 72 13.5 73 12.5 74 9.5 75 5.0 76 4.0 77 5.0 78 5.0 79 4.5 80 5.0 81 6.0 82 4.0 83 2.0 84 1.5 85 1.5 86 3.0 87 4.5 88 4.5 89 3.5 90 4.0 91 5.0 92 5.0 93 4.0 94 3.5 95 5.0 96 6.0 97 4.5 98 4.5 99 21.0 100 36.0 >>END_MODULE >>Per base N content pass #Base N-Count 1 0.22499999999999998 2 0.1 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 0.0 >>END_MODULE >>Sequence Length Distribution warn #Length Count 40 1.0 41 0.0 42 0.0 43 0.0 44 0.0 45 0.0 46 0.0 47 0.0 48 0.0 49 0.0 50 0.0 51 0.0 52 0.0 53 0.0 54 0.0 55 0.0 56 0.0 57 2.0 58 0.0 59 2.0 60 1.0 61 0.0 62 0.0 63 1.0 64 1.0 65 1.0 66 1.0 67 1.0 68 3.0 69 1.0 70 3.0 71 8.0 72 14.0 73 68.0 74 330.0 75 885.0 76 2677.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 86.0 #Duplication Level Percentage of deduplicated Percentage of total 1 90.87209302325581 78.14999999999999 2 6.191860465116279 10.65 3 1.9476744186046513 5.025 4 0.4069767441860465 1.4000000000000001 5 0.20348837209302326 0.8750000000000001 6 0.11627906976744186 0.6 7 0.05813953488372093 0.35000000000000003 8 0.05813953488372093 0.4 9 0.029069767441860465 0.22499999999999998 >10 0.0872093023255814 0.975 >50 0.029069767441860465 1.35 >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 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 54 1.35 No Hit GTCTGACATGTGTGCGAGTCAACGGGCGAGTAAACCCGTAAGGCGCAAGGAAGCTGACTGGCGGGATCCCCTCG 16 0.4 No Hit ACCAGGTCCAGACATAGTAAGGATTGACAGACTGAGAGCTCTTTCTTGAT 13 0.325 No Hit GTTAGTTTTACCCTACTGATGACAGTGTCGCAATAGTAATCCAACCTAGTACGAGAGGAACCGTTGATTCGCACA 10 0.25 No Hit GCCAGTAGTCATATGCTTGTCTCAAAGATTAAGCCATGCATGTGTAAGTA 9 0.22499999999999998 No Hit GCCGTTCTTAGTTGGTGGAGCGATTTGTCTGGTTAATTCCGTTAACGAAC 8 0.2 No Hit AGAAAAGTTACCACAGGGATAACTGGCTTGTGGCAGCCAAGCGTTCATAG 8 0.2 No Hit TACCAGGTCCAGACATAGTAAGGATTGACAGACTGAGAGCTCTTTCTTGA 7 0.17500000000000002 No Hit CTGACATGTGTGCGAGTCAACGGGCGAGTAAACCCGTAAGGCGCAAGGAA 7 0.17500000000000002 No Hit GTTACTTTGAAGAAATTAGAGTGCTCAAAGCAAGCCTACGCTCTGGATAC 6 0.15 No Hit GAGCGATTTGTCTGGTTAATTCCGTTAACGAACGAGACCTCAGCCTGCTA 6 0.15 No Hit GTTCTATCGGGTAAAGCCAATGATTAGAGGCATCGGGGGCGCAACGCCCT 6 0.15 No Hit GGCGGGACTACCCGCTGAGTTTAAGCATATCAATAAGCGGAGGAAAAGAA 6 0.15 No Hit CTTACCAGGTCCAGACATAGTAAGGATTGACAGACTGAGAGCTCTTTCTT 5 0.125 No Hit GCGGGACTACCCGCTGAGTTTAAGCATATCAATAAGCGGAGGAAAAGAAA 5 0.125 No Hit GGGGAATCCGACTGTTTAATTAAAACAAAGCATTGCGATGGTCCCTGCGG 5 0.125 No Hit GACAGGTTAGTTTTACCCTACTGATGACAGTGTCGCAATAGTAATCCAAC 5 0.125 No Hit GATTAAGCCATGCATGTGTAAGTATGAACTAATTCAGACTGTGAAACTGC 5 0.125 No Hit GTTGGGTTAAGTCCCGCAACGAGCGCAACCCTCGTGTTTAGTTGCCACCG 5 0.125 No Hit GTTCGATCCTGGCTCAGGATGAACGCTGGCGGCATGCTTAACACATGCAA 5 0.125 No Hit >>END_MODULE >>Adapter Content pass #Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence SOLID Small RNA Adapter 1 0.0 0.0 0.0 0.0 0.0 2 0.0 0.0 0.0 0.0 0.0 3 0.0 0.0 0.0 0.0 0.0 4 0.0 0.0 0.0 0.0 0.0 5 0.0 0.0 0.0 0.0 0.0 6 0.0 0.0 0.0 0.0 0.0 7 0.0 0.0 0.0 0.0 0.0 8 0.0 0.0 0.0 0.0 0.0 9 0.0 0.0 0.0 0.0 0.0 10 0.0 0.0 0.0 0.0 0.0 11 0.0 0.0 0.0 0.0 0.0 12 0.0 0.0 0.0 0.0 0.0 13 0.0 0.0 0.0 0.0 0.0 14 0.0 0.0 0.0 0.0 0.0 15 0.0 0.0 0.0 0.0 0.0 16 0.0 0.0 0.0 0.0 0.0 17 0.0 0.0 0.0 0.0 0.0 18 0.0 0.0 0.0 0.0 0.0 19 0.0 0.0 0.0 0.0 0.0 20 0.0 0.0 0.0 0.0 0.0 21 0.0 0.0 0.0 0.0 0.0 22 0.0 0.0 0.0 0.0 0.0 23 0.0 0.0 0.0 0.0 0.0 24 0.0 0.0 0.0 0.0 0.0 25 0.0 0.0 0.0 0.0 0.0 26 0.0 0.0 0.0 0.0 0.0 27 0.0 0.0 0.0 0.0 0.0 28 0.0 0.0 0.0 0.0 0.0 29 0.0 0.0 0.0 0.0 0.0 30 0.0 0.0 0.0 0.0 0.0 31 0.0 0.0 0.0 0.0 0.0 32 0.0 0.0 0.0 0.0 0.0 33 0.0 0.0 0.0 0.0 0.0 34 0.0 0.0 0.0 0.0 0.0 35 0.0 0.0 0.0 0.0 0.0 36 0.0 0.0 0.0 0.0 0.0 37 0.0 0.0 0.0 0.0 0.0 38 0.0 0.0 0.0 0.0 0.0 39 0.0 0.0 0.0 0.0 0.0 40 0.0 0.0 0.0 0.0 0.0 41 0.0 0.0 0.0 0.0 0.0 42 0.0 0.0 0.0 0.0 0.0 43 0.0 0.0 0.0 0.0 0.0 44 0.0 0.0 0.0 0.0 0.0 45 0.0 0.0 0.0 0.0 0.0 46 0.0 0.0 0.0 0.0 0.0 47 0.0 0.0 0.0 0.0 0.0 48 0.0 0.0 0.0 0.0 0.0 49 0.0 0.0 0.0 0.0 0.0 50 0.0 0.0 0.0 0.0 0.0 51 0.0 0.0 0.0 0.0 0.0 52 0.0 0.0 0.0 0.0 0.0 53 0.0 0.0 0.0 0.0 0.0 54 0.0 0.0 0.0 0.0 0.0 55 0.0 0.0 0.0 0.0 0.0 56 0.0 0.0 0.0 0.0 0.0 57 0.0 0.0 0.0 0.0 0.0 58 0.0 0.0 0.0 0.0 0.0 59 0.0 0.0 0.0 0.0 0.0 60 0.0 0.0 0.0 0.0 0.0 61 0.0 0.0 0.0 0.0 0.0 62 0.0 0.0 0.0 0.0 0.0 63 0.0 0.0 0.0 0.0 0.0 64 0.0 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Read 1492199 spots for SRR9668908.sra Written 1492199 spots for SRR9668908.sra Read 1492199 spots for SRR9668908.sra Written 1492199 spots for SRR9668908.sra Read 1492199 spots for SRR9668908.sra Written 1492199 spots for SRR9668908.sra Read 1492199 spots for SRR9668908.sra Written 1492199 spots for SRR9668908.sra Read 1492199 spots for SRR9668908.sra Written 1492199 spots for SRR9668908.sra Read 1492199 spots for SRR9668908.sra Written 1492199 spots for SRR9668908.sra Read 1492199 spots for SRR9668908.sra Written 1492199 spots for SRR9668908.sra Read 1492199 spots for SRR9668908.sra Written 1492199 spots for SRR9668908.sra Read 1492199 spots for SRR9668908.sra Written 1492199 spots for SRR9668908.sra Read 1492199 spots for SRR9668908.sra Written 1492199 spots for SRR9668908.sra Read 1492199 spots for SRR9668908.sra Written 1492199 spots for SRR9668908.sra Read 1492199 spots for SRR9668908.sra Written 1492199 spots for SRR9668908.sra Read 1492199 spots for SRR9668908.sra Written 1492199 spots for SRR9668908.sra Read 1492199 spots for SRR9668908.sra Written 1492199 spots for SRR9668908.sra Read 1492199 spots for SRR9668908.sra Written 1492199 spots for SRR9668908.sra Read 1492199 spots for SRR9668908.sra Written 1492199 spots for SRR9668908.sra Read 1492215 spots for SRR9668908.sra Written 1492215 spots for SRR9668908.sra Read 1492199 spots for SRR9668908.sra Written 1492199 spots for SRR9668908.sra Read 1492199 spots for SRR9668908.sra Written 1492199 spots for SRR9668908.sra Read 1492199 spots for SRR9668908.sra Written 1492199 spots for SRR9668908.sra SRR ids: ['SRR9668908.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_24i__77j SRR9668908.sra spots: 29843996 blocks: [[1, 1492199], [1492200, 2984398], [2984399, 4476597], [4476598, 5968796], [5968797, 7460995], [7460996, 8953194], [8953195, 10445393], [10445394, 11937592], [11937593, 13429791], [13429792, 14921990], [14921991, 16414189], [16414190, 17906388], [17906389, 19398587], [19398588, 20890786], [20890787, 22382985], [22382986, 23875184], [23875185, 25367383], [25367384, 26859582], [26859583, 28351781], [28351782, 29843996]] SRR9668908 file size 5661537 SRR9668908 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 SRR9668908 SRR9668908_1.fastq SRR9668908_2.fastq Input file: SRR9668908_1.fastq Paired file: SRR9668908_2.fastq trimmed: SRR9668908-trimmed-pair1.fastq, SRR9668908-trimmed-pair2.fastq Parameters used: -- 3' end adapter sequence (-x): AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -- paired 3' end adapter sequence (-y): AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA -- 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 -- number of concurrent threads (-t): 20 Wed Feb 12 15:47:37 2025 >> started Wed Feb 12 15:48:20 2025 >> done (42.967s) 29843996 read pairs processed; of these: 0 ( 0.00%) short read pairs filtered out after trimming by size control 24036 ( 0.08%) empty read pairs filtered out after trimming by size control 29819960 (99.92%) read pairs available; of these: 3436 ( 0.01%) trimmed read pairs available after processing 29816524 (99.99%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 22 3 0.00% 23 4 0.00% 24 6 0.00% 25 7 0.00% 26 9 0.00% 27 9 0.00% 28 9 0.00% 29 9 0.00% 30 15 0.00% 31 18 0.00% 32 10 0.00% 33 28 0.00% 34 14 0.00% 35 161 0.00% 36 205 0.00% 37 208 0.00% 38 269 0.00% 39 342 0.00% 40 417 0.00% 41 542 0.00% 42 571 0.00% 43 617 0.00% 44 707 0.00% 45 815 0.00% 46 855 0.00% 47 970 0.00% 48 1221 0.00% 49 1353 0.00% 50 1634 0.01% 51 1827 0.01% 52 2263 0.01% 53 2384 0.01% 54 2461 0.01% 55 2988 0.01% 56 3257 0.01% 57 3525 0.01% 58 3888 0.01% 59 4307 0.01% 60 4913 0.02% 61 5398 0.02% 62 5854 0.02% 63 6523 0.02% 64 6746 0.02% 65 7012 0.02% 66 7853 0.03% 67 7930 0.03% 68 8495 0.03% 69 9038 0.03% 70 10966 0.04% 71 15420 0.05% 72 29174 0.10% 73 214165 0.72% 74 2179779 7.31% 75 13764290 46.16% 76 13498476 45.27% 29819960 reads passed initial QC criterion=sequence-density sequence-density=1.07 sequence-density-rank=1 fanout-score=1.98 fanout-score-rank=24 prefix-density=1.00 prefix-fanout=2.0 sequence=CCGTCAATTCCTTT criterion=fanout-score sequence-density=0.15 sequence-density-rank=24 fanout-score=13.03 fanout-score-rank=1 prefix-density=1.10 prefix-fanout=1.8 sequence=CGCATCGCCGGCCCCCATCCACTTCCCTCCCGACAATTTCAAGCACTCTTTGACTCTCTTTTCAAAGTCCTTTTCATCTTTCCCTCGCGGTACTTGTTTGCTATCGGTCTCTCGCCCGTATTTAGCCT criterion=sequence-density sequence-density=0.58 sequence-density-rank=1 fanout-score=2.03 fanout-score-rank=22 prefix-density=0.61 prefix-fanout=1.9 sequence=ACGTGAGCTGGGTT criterion=fanout-score sequence-density=0.01 sequence-density-rank=28 fanout-score=16.61 fanout-score-rank=1 prefix-density=0.07 prefix-fanout=2.4 sequence=CAAAACCACATATAGAGGGTGTAATAGCTAAGTAGCCTGTAAGAGATGGCTTCCTCTGTGATTTCATCGGCGGCCGTTGCCACAGTTAACCGCACCCC SRR9668908 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 12 15:48:57 Started mapping on | Feb 12 15:48:57 Finished on | Feb 12 15:55:14 Mapping speed, Million of reads per hour | 284.75 Number of input reads | 29819960 Average input read length | 150 UNIQUE READS: Uniquely mapped reads number | 15886767 Uniquely mapped reads % | 53.28% Average mapped length | 149.96 Number of splices: Total | 5486505 Number of splices: Annotated (sjdb) | 5424974 Number of splices: GT/AG | 5379906 Number of splices: GC/AG | 88204 Number of splices: AT/AC | 4577 Number of splices: Non-canonical | 13818 Mismatch rate per base, % | 0.63% Deletion rate per base | 0.02% Deletion average length | 2.19 Insertion rate per base | 0.03% Insertion average length | 2.76 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 1461188 % of reads mapped to multiple loci | 4.90% Number of reads mapped to too many loci | 8190000 % of reads mapped to too many loci | 27.46% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 13.35% % of reads unmapped: other | 1.01% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 12472005 12472005 12472005 N_multimapping 1461188 1461188 1461188 N_noFeature 2816984 15452355 2889550 N_ambiguous 443799 2518 80260 UnstrandedReadsAssigned:12625984 PositiveStrandReadsAssigned:431894 NegativeStrandReadsAssigned:12916957 Dataset is classified negative stranded MeadianReadLen=76 20thPercentileLength=75 echo kmer=71 SRR9668908 Starting Kallisto paired end mapping to ensembl reference transcriptome [quant] fragment length distribution will be estimated from the data [index] k-mer length: 31 [index] number of targets: 52,400 [index] number of k-mers: 62,057,036 [index] number of equivalence classes: 130,681 [quant] running in paired-end mode [quant] will process pair 1: SRR9668908-trimmed-pair1.fastq SRR9668908-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 29,819,960 reads, 19,547,134 reads pseudoaligned [quant] estimated average fragment length: 190.004 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,026 rounds 52401 SRR9668908.ke.tsv 34699 SRR9668908.se.tsv 87100 total ==> SRR9668908.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1829 215 3.76941 Potri.005G024800.1.v4.1 1035 845.996 80 3.03228 Potri.004G059700.1.v4.1 961 771.996 40 1.66147 Potri.007G009000.2.v4.1 1416 1227 0 0 Potri.003G141000.2.v4.1 2943 2754 201 2.34035 Potri.016G087400.1.v4.1 270 95.5719 782.661 262.598 Potri.015G069301.1.v4.1 564 375.156 0 0 Potri.010G195200.1.v4.1 1773 1584 3 0.0607316 Potri.012G127500.1.v4.1 977 787.996 3319 135.061 ==> SRR9668908.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 13 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 210 Potri.001G212900.v4.1 0 Potri.001G182400.v4.1 0 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 53 Potri.001G416900.v4.1 1 Potri.001G452600.v4.1 6 SRR9668908 completed mapping pipeline successfully