Starting /dee2/code/volunteer_pipeline.sh SRR6127941 current disk space = 1526226915328 free memory = 1559187052 SRR6127941 SRAfilesize 03d95568a42cd6909749a70e67c3e6be SRR6127941.sra SRR6127941.sra file validated SRR6127941 is paired end SRR6127941 is conventional basespace SRR6127941 read1 length is 100 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR6127941_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 100 %GC 49 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 32.381 33.0 33.0 33.0 33.0 33.0 2 32.5295 33.0 33.0 33.0 33.0 33.0 3 32.73875 33.0 33.0 33.0 33.0 33.0 4 36.6875 37.0 37.0 37.0 37.0 37.0 5 36.71525 37.0 37.0 37.0 37.0 37.0 6 36.661 37.0 37.0 37.0 37.0 37.0 7 36.635 37.0 37.0 37.0 37.0 37.0 8 36.657 37.0 37.0 37.0 37.0 37.0 9 36.63825 37.0 37.0 37.0 37.0 37.0 10-11 36.658375 37.0 37.0 37.0 37.0 37.0 12-13 36.62625 37.0 37.0 37.0 37.0 37.0 14-15 38.91175 40.0 40.0 40.0 37.0 40.0 16-17 38.92725 40.0 40.0 40.0 37.0 40.0 18-19 38.94525 40.0 40.0 40.0 37.0 40.0 20-21 38.920125 40.0 40.0 40.0 37.0 40.0 22-23 38.733625 40.0 40.0 40.0 37.0 40.0 24-25 38.70725 40.0 38.5 40.0 37.0 40.0 26-27 38.628625 40.0 37.0 40.0 37.0 40.0 28-29 38.62375 40.0 37.0 40.0 37.0 40.0 30-31 38.576375 40.0 37.0 40.0 37.0 40.0 32-33 38.454125000000005 40.0 37.0 40.0 37.0 40.0 34-35 38.4 40.0 37.0 40.0 37.0 40.0 36-37 38.306625 40.0 37.0 40.0 37.0 40.0 38-39 38.141375 40.0 37.0 40.0 37.0 40.0 40-41 38.010374999999996 40.0 37.0 40.0 35.0 40.0 42-43 37.706375 40.0 37.0 40.0 33.0 40.0 44-45 37.648125 40.0 37.0 40.0 33.0 40.0 46-47 37.393249999999995 40.0 37.0 40.0 33.0 40.0 48-49 37.316375 40.0 37.0 40.0 33.0 40.0 50-51 37.1785 40.0 37.0 40.0 33.0 40.0 52-53 36.884625 38.5 37.0 40.0 33.0 40.0 54-55 36.463875 37.0 37.0 40.0 33.0 40.0 56-57 36.346000000000004 37.0 37.0 40.0 33.0 40.0 58-59 36.1235 37.0 37.0 40.0 33.0 40.0 60-61 35.881625 37.0 37.0 40.0 33.0 40.0 62-63 35.66275 37.0 37.0 40.0 33.0 40.0 64-65 35.454499999999996 37.0 37.0 38.5 33.0 40.0 66-67 35.036874999999995 37.0 33.0 37.0 30.0 40.0 68-69 34.8795 37.0 33.0 37.0 30.0 40.0 70-71 34.599625 37.0 33.0 37.0 27.0 40.0 72-73 34.287875 37.0 33.0 37.0 27.0 38.5 74-75 33.869375000000005 37.0 33.0 37.0 27.0 37.0 76-77 31.2125 33.0 30.0 35.0 24.5 37.0 78-79 33.00725 37.0 33.0 37.0 27.0 37.0 80-81 33.14825 37.0 33.0 37.0 27.0 37.0 82-83 33.321875000000006 37.0 33.0 37.0 27.0 37.0 84-85 33.26525 37.0 33.0 37.0 27.0 37.0 86-87 33.24225 37.0 33.0 37.0 27.0 37.0 88-89 33.028499999999994 37.0 33.0 37.0 27.0 37.0 90-91 32.92825 37.0 33.0 37.0 27.0 37.0 92-93 32.772875 37.0 33.0 37.0 27.0 37.0 94-95 32.6725 37.0 33.0 37.0 27.0 37.0 96-97 32.358000000000004 37.0 33.0 37.0 22.0 37.0 98-99 31.961750000000002 37.0 33.0 37.0 22.0 37.0 100 28.27425 33.0 27.0 33.0 2.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 6 1.0 7 0.0 8 2.0 9 3.0 10 4.0 11 4.0 12 5.0 13 5.0 14 4.0 15 7.0 16 10.0 17 10.0 18 8.0 19 10.0 20 14.0 21 15.0 22 13.0 23 11.0 24 16.0 25 16.0 26 29.0 27 31.0 28 26.0 29 49.0 30 60.0 31 61.0 32 96.0 33 136.0 34 179.0 35 258.0 36 634.0 37 1306.0 38 975.0 39 2.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 35.96757852077001 13.753799392097266 7.37082066869301 42.90780141843972 2 23.325000000000003 16.85 38.6 21.224999999999998 3 22.05 22.75 24.75 30.45 4 26.525 29.075 21.75 22.650000000000002 5 26.075 31.8 23.849999999999998 18.275 6 20.825 32.9 23.7 22.575 7 17.175 20.75 42.199999999999996 19.875 8 20.5 20.05 30.025000000000002 29.425 9 20.200000000000003 19.425 33.375 27.0 10-11 25.074999999999996 28.537499999999998 21.0 25.387500000000003 12-13 23.45 22.2125 26.150000000000002 28.1875 14-15 23.724999999999998 24.775 26.8125 24.6875 16-17 24.1375 24.55 25.6125 25.7 18-19 24.7375 24.212500000000002 26.0625 24.9875 20-21 24.0625 24.925 25.9875 25.025 22-23 23.549999999999997 25.174999999999997 25.7875 25.4875 24-25 23.8875 24.5125 26.35 25.25 26-27 23.375 25.374999999999996 26.737499999999997 24.5125 28-29 23.825 24.2625 26.0 25.912499999999998 30-31 23.150000000000002 25.85 25.75 25.25 32-33 23.95 25.362499999999997 25.55 25.137500000000003 34-35 24.337500000000002 24.2875 25.45 25.924999999999997 36-37 23.275000000000002 25.825 25.074999999999996 25.825 38-39 23.1875 25.8625 25.324999999999996 25.624999999999996 40-41 24.837500000000002 25.25 24.8 25.112499999999997 42-43 24.462500000000002 24.6625 24.675 26.200000000000003 44-45 24.4125 25.025 25.9625 24.6 46-47 25.55 25.124999999999996 24.887500000000003 24.4375 48-49 25.674999999999997 24.45 24.675 25.2 50-51 24.4 25.0375 25.1 25.4625 52-53 24.6625 23.7375 25.7875 25.8125 54-55 24.6 23.825 26.337500000000002 25.2375 56-57 24.0 24.7375 25.924999999999997 25.337500000000002 58-59 24.25 25.525 24.5625 25.662499999999998 60-61 24.962500000000002 24.025 25.525 25.4875 62-63 24.0625 25.587500000000002 26.1 24.25 64-65 23.5125 24.9125 25.674999999999997 25.900000000000002 66-67 24.9875 23.625 25.937500000000004 25.45 68-69 24.75 24.8 25.687500000000004 24.762500000000003 70-71 25.912499999999998 25.087500000000002 24.337500000000002 24.6625 72-73 25.25 23.95 25.112499999999997 25.687500000000004 74-75 24.5125 23.7375 25.7 26.05 76-77 24.7 24.7 26.025 24.575 78-79 23.150000000000002 24.9 25.924999999999997 26.025 80-81 24.224999999999998 25.650000000000002 25.887500000000003 24.2375 82-83 24.8125 23.625 26.025 25.5375 84-85 24.0 24.075 25.4375 26.487500000000004 86-87 24.5125 24.712500000000002 25.75 25.025 88-89 24.075 24.75 24.825 26.35 90-91 25.15 24.525 24.0625 26.2625 92-93 24.05 24.6875 25.662499999999998 25.6 94-95 24.6625 25.1 25.05 25.1875 96-97 26.0125 23.95 25.2375 24.8 98-99 24.625 25.775 24.55 25.05 100 27.474999999999998 23.724999999999998 22.425 26.375 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 0.0 1 0.0 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10 0.0 11 0.0 12 0.0 13 0.0 14 0.0 15 0.0 16 0.0 17 0.0 18 0.0 19 0.0 20 0.5 21 0.5 22 0.0 23 0.0 24 0.0 25 1.0 26 1.5 27 1.5 28 2.0 29 7.5 30 14.0 31 15.5 32 18.0 33 30.0 34 42.0 35 46.5 36 59.5 37 65.0 38 78.0 39 96.5 40 101.5 41 114.5 42 120.0 43 123.5 44 137.5 45 146.0 46 178.5 47 213.5 48 213.0 49 197.0 50 157.5 51 141.5 52 160.0 53 156.5 54 135.0 55 126.0 56 126.5 57 116.0 58 97.5 59 87.0 60 86.5 61 80.5 62 71.0 63 62.5 64 57.0 65 54.0 66 47.5 67 39.5 68 39.0 69 36.5 70 25.5 71 17.0 72 10.5 73 10.0 74 9.5 75 7.0 76 5.5 77 3.0 78 2.5 79 2.0 80 1.0 81 0.5 82 0.5 83 0.5 84 0.5 85 0.5 86 0.0 87 0.0 88 0.0 89 0.0 90 0.5 91 0.5 92 0.0 93 0.5 94 0.5 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 1.3 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 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 100 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 88.225 #Duplication Level Percentage of deduplicated Percentage of total 1 92.32077075658826 81.45 2 4.618872201756872 8.15 3 1.7568716350240863 4.65 4 0.6517427033153868 2.3 5 0.3967129498441485 1.7500000000000002 6 0.0850099178237461 0.44999999999999996 7 0.05667327854916407 0.35000000000000003 8 0.05667327854916407 0.4 9 0.028336639274582034 0.22499999999999998 >10 0.028336639274582034 0.27499999999999997 >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 CTTCACTTCAATTGCTGTTGCCAATGACTTCAGCTGACTTGGCGACAGTT 11 0.27499999999999997 No Hit CTTTGATATTCTCTGCATCCTATTTAGGGCTATTGATATTTAACAAATAT 9 0.22499999999999998 No Hit CAATCATCTTCACTTCAATTGCTGTTGCCAATGACTTCAGCTGACTTGGC 8 0.2 No Hit AATGACTTCAGCTGACTTGGCGACAGTTCATCATTAAAGATGAGGAGATC 8 0.2 No Hit GTGATAGATGCCTCTTTAAAATATCTAAGTGCTGGGGTTATGAGTAGGGA 7 0.17500000000000002 No Hit GCAGCAATCAATGTCGTCGGAAGATCCTGAATAAATCCTACTGTATCTGA 7 0.17500000000000002 No Hit CAATGACTTCAGCTGACTTGGCGACAGTTCATCATTAAAGATGAGGAGAT 6 0.15 No Hit GTTGATACCGTCTGCGATAGGCTAGTTCATAAACGAGGGGCGATGCCCGG 6 0.15 No Hit GTCAGCATCGGGATATCATCTGCTTCAAGCTCCTCAAGCAGCCGAAGCAC 6 0.15 No Hit ATCGGGTCCAGCGTGGCAAACAGGAGGTCTTCTTCATAGCTGTCAGCACT 5 0.125 No Hit CGACGAACAACGAAGAGCGACGATGCCCGTTTCAGGTGGTCCTCAGCGTA 5 0.125 No Hit CTTATGTGATAGATGCCTCTTTAAAATATCTAAGTGCTGGGGTTATGAGT 5 0.125 No Hit GTCGGAAGATCCTGAATAAATCCTACTGTATCTGAAAGAAGAACACTGTA 5 0.125 No Hit GGAAGATCCTGAATAAATCCTACTGTATCTGAAAGAAGAACACTGTAGCC 5 0.125 No Hit GCATAATCCTCATTTGAAGAATCAATTAAATGCAGAATTAAATCCGCTTC 5 0.125 No Hit CGCCAATCTATATTACTCACAATATCCTAAAAACGATCAGCCGGCAGGTT 5 0.125 No Hit GTTATGAGTAGGGATGAGCATAAACCAACAACTCTCAAAGAAGATGGGAA 5 0.125 No Hit GTTGAACCATGTTGATTTCCCTGCGTTTGTATAGCCGACAAGCGCAATTT 5 0.125 No Hit GTCAGCACTCGTCAGGCGGTTGAACCATGTTGATTTCCCTGCGTTTGTAT 5 0.125 No Hit GTCAGACGCGGCAGTGCATATTGCAGCTGAGCCAGCTCAATTTGAAGTTT 5 0.125 No Hit GGATAATTGGGATATTCTTTGGTATAGTTGGGATTTTAATATCATTAATA 5 0.125 No Hit GGAAGCTATACTATATAGGTGGCTATCTATCCCTACCAAGGCTTATATTG 5 0.125 No Hit CCGGGATCGGGCAAAGGGGCAACTCGAGCTAATCTCCCCAGCGGCTAGCA 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 10-11 0.0 0.0 0.0 0.0 0.0 12-13 0.0 0.0 0.0 0.0 0.0 14-15 0.0 0.0 0.0 0.0 0.0 16-17 0.0 0.0 0.0 0.0 0.0 18-19 0.0 0.0 0.0 0.0 0.0 20-21 0.0 0.0 0.0 0.0 0.0 22-23 0.0 0.0 0.0 0.0 0.0 24-25 0.0 0.0 0.0 0.0 0.0 26-27 0.0 0.0 0.0 0.0 0.0 28-29 0.0 0.0 0.0 0.0 0.0 30-31 0.0 0.0 0.0 0.0 0.0 32-33 0.0 0.0 0.0 0.0 0.0 34-35 0.0 0.0 0.0 0.0 0.0 36-37 0.0 0.0 0.0 0.0 0.0 38-39 0.0 0.0 0.0 0.0 0.0 40-41 0.0 0.0 0.0 0.0 0.0 42-43 0.025 0.0 0.0 0.0 0.0 44-45 0.05 0.0 0.0 0.0 0.0 46-47 0.05 0.0 0.0 0.0 0.0 48-49 0.05 0.0 0.0 0.0 0.0 50-51 0.05 0.0 0.0 0.0 0.0 52-53 0.05 0.0 0.0 0.0 0.0 54-55 0.075 0.0 0.0 0.0 0.0 56-57 0.075 0.0 0.0 0.0 0.0 58-59 0.075 0.0 0.0 0.0 0.0 60-61 0.075 0.0 0.0 0.0 0.0 62-63 0.1375 0.0 0.0 0.0 0.0 64-65 0.1875 0.0 0.0 0.0 0.0 66-67 0.25 0.0 0.0 0.0 0.0 68-69 0.30000000000000004 0.0 0.0 0.0 0.0 70-71 0.35 0.0 0.0 0.0 0.0 72-73 0.425 0.0 0.0 0.0 0.0 74-75 0.475 0.0 0.0 0.0 0.0 76-77 0.5875 0.0 0.0 0.0 0.0 78-79 0.725 0.0 0.0 0.0 0.0 80-81 0.8374999999999999 0.0 0.0 0.0 0.0 82-83 0.9375 0.0 0.0 0.0 0.0 84-85 1.125 0.0 0.0 0.0 0.0 86-87 1.3625 0.0 0.0 0.0 0.0 88 1.65 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE SRR6127941 read2 length is 101 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR6127941_2.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 101 %GC 50 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 31.78475 33.0 33.0 33.0 33.0 33.0 2 31.86625 33.0 33.0 33.0 33.0 33.0 3 31.95075 33.0 33.0 33.0 33.0 33.0 4 35.494 37.0 37.0 37.0 33.0 37.0 5 35.49775 37.0 37.0 37.0 33.0 37.0 6 35.41975 37.0 37.0 37.0 33.0 37.0 7 35.45325 37.0 37.0 37.0 33.0 37.0 8 35.57625 37.0 37.0 37.0 33.0 37.0 9 35.75025 37.0 37.0 37.0 37.0 37.0 10-11 35.81075 37.0 37.0 37.0 37.0 37.0 12-13 35.80475 37.0 37.0 37.0 37.0 37.0 14-15 38.013625000000005 40.0 37.0 40.0 37.0 40.0 16-17 37.995374999999996 40.0 38.5 40.0 37.0 40.0 18-19 38.029875000000004 40.0 38.5 40.0 37.0 40.0 20-21 37.99 40.0 37.0 40.0 37.0 40.0 22-23 37.269875 40.0 37.0 40.0 33.0 40.0 24-25 37.74925 40.0 37.0 40.0 35.0 40.0 26-27 37.851749999999996 40.0 37.0 40.0 37.0 40.0 28-29 37.8755 40.0 37.0 40.0 37.0 40.0 30-31 37.78075 40.0 37.0 40.0 37.0 40.0 32-33 37.644875 40.0 37.0 40.0 35.0 40.0 34-35 37.598625 40.0 37.0 40.0 35.0 40.0 36-37 37.495375 40.0 37.0 40.0 33.0 40.0 38-39 37.3725 40.0 37.0 40.0 33.0 40.0 40-41 37.288875 40.0 37.0 40.0 33.0 40.0 42-43 37.22125 40.0 37.0 40.0 33.0 40.0 44-45 36.935625 40.0 37.0 40.0 33.0 40.0 46-47 36.825374999999994 40.0 37.0 40.0 33.0 40.0 48-49 36.683499999999995 40.0 37.0 40.0 33.0 40.0 50-51 35.006375 37.0 35.0 38.5 30.0 40.0 52-53 35.271 37.0 35.0 38.5 30.0 40.0 54-55 35.97775 37.0 37.0 40.0 33.0 40.0 56-57 35.917500000000004 37.0 37.0 40.0 33.0 40.0 58-59 35.717749999999995 37.0 37.0 40.0 33.0 40.0 60-61 35.364999999999995 37.0 37.0 40.0 33.0 40.0 62-63 35.201499999999996 37.0 37.0 38.5 33.0 40.0 64-65 35.0325 37.0 37.0 37.0 33.0 40.0 66-67 34.896375 37.0 37.0 37.0 33.0 40.0 68-69 34.556 37.0 33.0 37.0 27.0 40.0 70-71 34.469625 37.0 33.0 37.0 30.0 40.0 72-73 34.234 37.0 33.0 37.0 27.0 38.5 74-75 34.07425 37.0 33.0 37.0 27.0 37.0 76-77 33.757374999999996 37.0 33.0 37.0 27.0 37.0 78-79 33.35825 37.0 33.0 37.0 27.0 37.0 80-81 33.182874999999996 37.0 33.0 37.0 27.0 37.0 82-83 33.239000000000004 37.0 33.0 37.0 27.0 37.0 84-85 33.2475 37.0 33.0 37.0 27.0 37.0 86-87 33.27925 37.0 33.0 37.0 27.0 37.0 88-89 33.09175 37.0 33.0 37.0 27.0 37.0 90-91 33.03475 37.0 33.0 37.0 27.0 37.0 92-93 32.93575 37.0 33.0 37.0 27.0 37.0 94-95 32.807 37.0 33.0 37.0 27.0 37.0 96-97 32.513625000000005 37.0 33.0 37.0 22.0 37.0 98-99 32.475375 37.0 33.0 37.0 22.0 37.0 100-101 30.803375000000003 35.0 30.0 37.0 18.5 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 68.0 3 6.0 4 5.0 5 6.0 6 2.0 7 4.0 8 3.0 9 2.0 10 5.0 11 2.0 12 4.0 13 5.0 14 10.0 15 4.0 16 8.0 17 7.0 18 4.0 19 7.0 20 5.0 21 8.0 22 15.0 23 12.0 24 12.0 25 17.0 26 22.0 27 19.0 28 25.0 29 42.0 30 39.0 31 48.0 32 93.0 33 135.0 34 156.0 35 276.0 36 477.0 37 1488.0 38 957.0 39 2.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 33.875 19.15 9.25 37.724999999999994 2 28.249999999999996 24.9 29.975 16.875 3 21.7 26.724999999999998 27.125 24.45 4 25.25 32.1 19.475 23.175 5 26.474999999999998 34.849999999999994 17.875 20.8 6 22.7 34.300000000000004 19.05 23.95 7 21.099999999999998 18.4 36.55 23.95 8 22.7 20.875 23.724999999999998 32.7 9 24.625 21.375 27.125 26.875 10-11 26.2125 28.050000000000004 19.575 26.1625 12-13 26.3 22.35 24.474999999999998 26.875 14-15 24.6 25.374999999999996 25.0625 24.962500000000002 16-17 26.903362920365048 24.603075384423054 22.7903487935992 25.703212901612705 18-19 25.965745718214777 26.003250406300786 23.140392549068633 24.8906113264158 20-21 24.990623827978496 26.328291036379547 23.202900362545318 25.478184773096636 22-23 26.403300412551566 25.54069258657332 22.890361295161895 25.165645705713214 24-25 24.478059757469683 26.128266033254157 23.952994124265533 25.440680085010626 26-27 25.662499999999998 26.0 22.875 25.4625 28-29 25.662499999999998 25.2 23.674999999999997 25.4625 30-31 25.05 25.687500000000004 23.375 25.887500000000003 32-33 25.412499999999998 25.924999999999997 24.0625 24.6 34-35 26.224999999999998 25.4625 23.3875 24.925 36-37 25.5375 25.75 23.5875 25.124999999999996 38-39 25.674999999999997 25.687500000000004 23.825 24.8125 40-41 26.0375 25.874999999999996 23.1625 24.925 42-43 25.3125 25.775 24.45 24.462500000000002 44-45 25.724999999999998 25.362499999999997 24.087500000000002 24.825 46-47 25.974999999999998 25.7375 23.962500000000002 24.325 48-49 25.99074884360545 24.065508188523566 24.40305038129766 25.54069258657332 50-51 25.35 26.2125 24.65 23.7875 52-53 25.687500000000004 25.674999999999997 23.6875 24.95 54-55 25.17814726840855 25.828228528566072 24.01550193774222 24.978122265283158 56-57 25.153144143017876 25.803225403175396 24.815601950243778 24.228028503562946 58-59 26.0125 25.2375 23.8125 24.9375 60-61 25.8125 26.400000000000002 24.2 23.5875 62-63 25.4375 25.662499999999998 25.074999999999996 23.825 64-65 24.640580072509064 26.415801975246904 24.32804100512564 24.615576947118388 66-67 25.95 25.3125 24.2 24.5375 68-69 24.678084760595073 25.340667583447928 25.165645705713214 24.815601950243778 70-71 25.412499999999998 24.925 24.525 25.137500000000003 72-73 25.240655081885237 25.30316289536192 24.01550193774222 25.440680085010626 74-75 24.825 25.25 24.8125 25.112499999999997 76-77 25.7 26.6 23.525 24.175 78-79 25.465683210401302 26.62832854106763 23.590448806100763 24.315539442430303 80-81 25.074999999999996 26.674999999999997 24.587500000000002 23.6625 82-83 26.469117279319832 25.431357839459867 24.031007751937985 24.06851712928232 84-85 25.087543771885944 25.87543771885943 24.6248124062031 24.412206103051524 86-87 25.128141017627204 25.62820352544068 24.36554569321165 24.878109763720467 88-89 26.450000000000003 26.0125 24.2 23.3375 90-91 25.362499999999997 25.912499999999998 23.962500000000002 24.762500000000003 92-93 25.99074884360545 25.90323790473809 24.265533191648956 23.8404800600075 94-95 26.7625 26.85 23.575 22.8125 96-97 26.424999999999997 25.900000000000002 24.325 23.35 98-99 25.25 27.4125 23.9375 23.400000000000002 100-101 26.700000000000003 26.700000000000003 23.3125 23.2875 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 0.0 1 0.0 2 0.0 3 0.5 4 0.5 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10 0.0 11 0.0 12 0.5 13 0.5 14 0.0 15 0.0 16 0.0 17 0.0 18 1.0 19 1.5 20 1.0 21 1.0 22 1.0 23 1.5 24 1.5 25 0.5 26 1.5 27 3.5 28 4.5 29 4.0 30 9.5 31 20.5 32 23.0 33 24.0 34 32.5 35 44.5 36 53.0 37 62.0 38 76.0 39 86.0 40 96.0 41 101.5 42 99.0 43 127.0 44 143.0 45 142.5 46 164.5 47 186.0 48 195.5 49 175.0 50 152.5 51 147.0 52 152.0 53 156.5 54 147.5 55 145.5 56 127.0 57 111.0 58 116.0 59 109.0 60 94.5 61 77.5 62 77.0 63 77.0 64 69.0 65 64.0 66 61.0 67 52.0 68 36.5 69 33.5 70 25.5 71 17.0 72 18.5 73 14.5 74 8.5 75 4.5 76 5.5 77 3.5 78 0.5 79 1.5 80 1.0 81 0.0 82 1.0 83 2.0 84 1.5 85 0.5 86 0.5 87 1.0 88 0.5 89 0.0 90 0.0 91 0.0 92 0.0 93 0.5 94 0.5 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 0.0125 20-21 0.0125 22-23 0.0125 24-25 0.0125 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 0.0125 50-51 0.0 52-53 0.0 54-55 0.0125 56-57 0.0125 58-59 0.0 60-61 0.0 62-63 0.0 64-65 0.0125 66-67 0.0 68-69 0.0125 70-71 0.0 72-73 0.0125 74-75 0.0 76-77 0.0 78-79 0.0125 80-81 0.0 82-83 0.025 84-85 0.05 86-87 0.0125 88-89 0.0 90-91 0.0 92-93 0.0125 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 pass #Total Deduplicated Percentage 89.60000000000001 #Duplication Level Percentage of deduplicated Percentage of total 1 92.52232142857143 82.89999999999999 2 5.078125 9.1 3 1.5345982142857142 4.125 4 0.4185267857142857 1.5 5 0.1953125 0.8750000000000001 6 0.13950892857142858 0.75 7 0.055803571428571425 0.35000000000000003 8 0.055803571428571425 0.4 9 0.0 0.0 >10 0.0 0.0 >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 TGAAAATTCTATGGAAGAGCTAGCATCTCTGACGAAAACAGCAGACGGAA 8 0.2 No Hit CTCGTAACCAAACATGCACAGCGGTCAAACAGTATGTCCCAAGGGGACTT 8 0.2 No Hit CAGAAATCGCATTCATGAAATCAACACACAGCTTTCCACTGTCATTCGCC 7 0.17500000000000002 No Hit GAAAATTCTATGGAAGAGCTAGCATCTCTGACGAAAACAGCAGACGGAAA 7 0.17500000000000002 No Hit AAAAAAACGAACCTTTGGGTTCCAGAGCTGTACGGTCGCACTGAACTCGG 6 0.15 No Hit CACATGCTAGCCGCTGGGGAGATTAGCTCGAGTTGCCCCTTTGCCCGATC 6 0.15 No Hit CTATGGAAGAGCTAGCATCTCTGACGAAAACAGCAGACGGAAAAGTACTG 6 0.15 No Hit CTCTCATTGGTTTATACTTCAATATAAGCCTTGGTAGGGATAGATAGCCA 6 0.15 No Hit CTTCAAATTGCGCTTGTCGGCTATACAAACGCAGGGAAATCAACATGGTT 6 0.15 No Hit CAGCAATTGAAGTGAAGATGATTGACCGCACGCAATTGATATTAGATATT 5 0.125 No Hit AAAGAATATCCCAATTATCCATAAAACTGTAACTAAGTGAGGCTCTCTCA 5 0.125 No Hit CGGGCGTCGGCATCCAGACCGTCGGCTGATCGTGGTTTTACTAGGCTAGA 5 0.125 No Hit CCCTAACTTAATGGACGGGAGGTATCCCAATAGGAGGTTTCCTCCTATGG 5 0.125 No Hit CTTAGATATTTTAAAGAGGCATCTATCACATAAGGCATCATTATAACTAA 5 0.125 No Hit AGAAGACCTCCTGTTTGCCACGCTGGACCCGATGACCAGAAAAATGGTCC 5 0.125 No Hit CGAATAGCTCGTAACCAAACATGCACAGCGGTCAAACAGTATGTCCCAAG 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 10-11 0.0 0.0 0.0 0.0 0.0 12-13 0.0 0.0 0.0 0.0 0.0 14-15 0.0 0.0 0.0 0.0 0.0 16-17 0.0 0.0 0.0 0.0 0.0 18-19 0.0 0.0 0.0 0.0 0.0 20-21 0.0 0.0 0.0 0.0 0.0 22-23 0.0 0.0 0.0 0.0 0.0 24-25 0.0 0.0 0.0 0.0 0.0 26-27 0.0 0.0 0.0 0.0 0.0 28-29 0.0 0.0 0.0 0.0 0.0 30-31 0.0 0.0 0.0 0.0 0.0 32-33 0.0 0.0 0.0 0.0 0.0 34-35 0.0 0.0 0.0 0.0 0.0 36-37 0.0 0.0 0.0 0.0 0.0 38-39 0.0 0.0 0.0 0.0 0.0 40-41 0.0 0.0 0.0 0.0 0.0 42-43 0.0125 0.0 0.0 0.0 0.0 44-45 0.025 0.0 0.0 0.0 0.0 46-47 0.025 0.0 0.0 0.0 0.0 48-49 0.025 0.0 0.0 0.0 0.0 50-51 0.025 0.0 0.0 0.0 0.0 52-53 0.025 0.0 0.0 0.0 0.0 54-55 0.05 0.0 0.0 0.0 0.0 56-57 0.05 0.0 0.0 0.0 0.0 58-59 0.05 0.0 0.0 0.0 0.0 60-61 0.05 0.0 0.0 0.0 0.0 62-63 0.1375 0.0 0.0 0.0 0.0 64-65 0.1875 0.0 0.0 0.0 0.0 66-67 0.25 0.0 0.0 0.0 0.0 68-69 0.30000000000000004 0.0 0.0 0.0 0.0 70-71 0.35 0.0 0.0 0.0 0.0 72-73 0.425 0.0 0.0 0.0 0.0 74-75 0.475 0.0 0.0 0.0 0.0 76-77 0.5875 0.0 0.0 0.0 0.0 78-79 0.725 0.0 0.0 0.0 0.0 80-81 0.8374999999999999 0.0 0.0 0.0 0.0 82-83 0.9375 0.0 0.0 0.0 0.0 84-85 1.1124999999999998 0.0 0.0 0.0 0.0 86-87 1.3875 0.0 0.0 0.0 0.0 88-89 1.775 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Read 1443007 spots for SRR6127941.sra Written 1443007 spots for SRR6127941.sra Read 1443007 spots for SRR6127941.sra Written 1443007 spots for SRR6127941.sra Read 1443007 spots for SRR6127941.sra Written 1443007 spots for SRR6127941.sra Read 1443007 spots for SRR6127941.sra Written 1443007 spots for SRR6127941.sra Read 1443007 spots for SRR6127941.sra Written 1443007 spots for SRR6127941.sra Read 1443007 spots for SRR6127941.sra Written 1443007 spots for SRR6127941.sra Read 1443007 spots for SRR6127941.sra Written 1443007 spots for SRR6127941.sra Read 1443007 spots for SRR6127941.sra Written 1443007 spots for SRR6127941.sra Read 1443007 spots for SRR6127941.sra Written 1443007 spots for SRR6127941.sra Read 1443007 spots for SRR6127941.sra Written 1443007 spots for SRR6127941.sra Read 1443007 spots for SRR6127941.sra Written 1443007 spots for SRR6127941.sra Read 1443007 spots for SRR6127941.sra Written 1443007 spots for SRR6127941.sra Read 1443007 spots for SRR6127941.sra Written 1443007 spots for SRR6127941.sra Read 1443007 spots for SRR6127941.sra Written 1443007 spots for SRR6127941.sra Read 1443007 spots for SRR6127941.sra Written 1443007 spots for SRR6127941.sra Read 1443007 spots for SRR6127941.sra Written 1443007 spots for SRR6127941.sra Read 1443007 spots for SRR6127941.sra Written 1443007 spots for SRR6127941.sra Read 1443007 spots for SRR6127941.sra Written 1443007 spots for SRR6127941.sra Read 1443007 spots for SRR6127941.sra Written 1443007 spots for SRR6127941.sra Read 1443023 spots for SRR6127941.sra Written 1443023 spots for SRR6127941.sra SRR ids: ['SRR6127941.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_9lcknlqi SRR6127941.sra spots: 28860156 blocks: [[1, 1443007], [1443008, 2886014], [2886015, 4329021], [4329022, 5772028], [5772029, 7215035], [7215036, 8658042], [8658043, 10101049], [10101050, 11544056], [11544057, 12987063], [12987064, 14430070], [14430071, 15873077], [15873078, 17316084], [17316085, 18759091], [18759092, 20202098], [20202099, 21645105], [21645106, 23088112], [23088113, 24531119], [24531120, 25974126], [25974127, 27417133], [27417134, 28860156]] SRR6127941 file size 6883317 SRR6127941 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 SRR6127941 SRR6127941_1.fastq SRR6127941_2.fastq Input file: SRR6127941_1.fastq Paired file: SRR6127941_2.fastq trimmed: SRR6127941-trimmed-pair1.fastq, SRR6127941-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 Tue Dec 10 04:30:12 2024 >> started Tue Dec 10 04:30:39 2024 >> done (27.226s) 28860156 read pairs processed; of these: 129554 ( 0.45%) short read pairs filtered out after trimming by size control 474504 ( 1.64%) empty read pairs filtered out after trimming by size control 28256098 (97.91%) read pairs available; of these: 5044624 (17.85%) trimmed read pairs available after processing 23211474 (82.15%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 21 0.00% 19 30 0.00% 20 48 0.00% 21 62 0.00% 22 96 0.00% 23 173 0.00% 24 238 0.00% 25 243 0.00% 26 325 0.00% 27 449 0.00% 28 497 0.00% 29 622 0.00% 30 718 0.00% 31 877 0.00% 32 961 0.00% 33 1138 0.00% 34 1349 0.00% 35 1459 0.01% 36 1656 0.01% 37 1906 0.01% 38 2118 0.01% 39 2372 0.01% 40 2547 0.01% 41 2870 0.01% 42 3103 0.01% 43 3523 0.01% 44 3790 0.01% 45 4241 0.02% 46 4666 0.02% 47 4892 0.02% 48 5420 0.02% 49 5758 0.02% 50 6496 0.02% 51 6793 0.02% 52 7163 0.03% 53 7854 0.03% 54 8596 0.03% 55 9518 0.03% 56 10017 0.04% 57 11064 0.04% 58 12080 0.04% 59 21957 0.08% 60 22821 0.08% 61 24633 0.09% 62 27146 0.10% 63 28793 0.10% 64 31317 0.11% 65 33609 0.12% 66 33301 0.12% 67 34642 0.12% 68 36435 0.13% 69 38550 0.14% 70 40640 0.14% 71 42702 0.15% 72 45224 0.16% 73 46273 0.16% 74 48122 0.17% 75 45727 0.16% 76 45398 0.16% 77 49712 0.18% 78 53795 0.19% 79 56655 0.20% 80 61710 0.22% 81 68235 0.24% 82 71251 0.25% 83 78060 0.28% 84 88332 0.31% 85 96301 0.34% 86 112901 0.40% 87 113503 0.40% 88 110260 0.39% 89 110525 0.39% 90 122857 0.43% 91 135128 0.48% 92 150303 0.53% 93 165134 0.58% 94 192588 0.68% 95 220690 0.78% 96 264032 0.93% 97 330219 1.17% 98 414105 1.47% 99 530734 1.88% 100 23874029 84.49% 28256098 reads passed initial QC criterion=sequence-density sequence-density=0.58 sequence-density-rank=1 fanout-score=2.49 fanout-score-rank=10 prefix-density=0.59 prefix-fanout=2.5 sequence=GGTGTTGTCGAAGCCGATGATGCGGACATAGGCGTC criterion=fanout-score sequence-density=0.04 sequence-density-rank=23 fanout-score=12.80 fanout-score-rank=1 prefix-density=0.20 prefix-fanout=2.8 sequence=GCCGGGAACGATTCCCTGCTCGACAAGGATGTCAACAATCTTCTTGCCATCAACAGTCGATTGGTAGAGGGTCTCCTCGAAGAGGATAGCACCAGAGATGTAATTTCCCAGGCCTGGTGGAGTGACAAGGAGGGTACGGTAAGCCTGGCGGTTAGCCTCAGTGTTCTCAAGGCCAATCGAGTCAAGTCTCTTTCCACAGGTAGCATTGGACTCATCCATGGCTAGGATGCCCCTTCCTGGTGATGCGATGGTTTTCGCGGTCTTGACAAGTTCATCAGCGTATGCGCTGGCACGGACAACCATGGAGACGGTCATCTGCTTGGGAGTGGCAGCCTGGCGGGTGGCGCCCCATTCGGACTTCTTGGGAA criterion=sequence-density sequence-density=0.53 sequence-density-rank=1 fanout-score=4.53 fanout-score-rank=4 prefix-density=0.83 prefix-fanout=2.9 sequence=ATCCGCTCCAAGTGGGTTCCTTGCCT criterion=fanout-score sequence-density=0.01 sequence-density-rank=28 fanout-score=8.83 fanout-score-rank=1 prefix-density=0.05 prefix-fanout=1.6 sequence=CGAGCTCGCATTTTGAAAATTCTATGGAAGAGCTAGCATCTCTGACGAAAACAGCAGACGGAAAAGTACTGACCAGCGTCACACAAAAACGGAACAGGGCTGACGCCGCTACATATATAGGAAAAGGGAAGGTAGAAGAGCTGAAGGCACTCGTGGAAGAGCTTGAAGCTGATCTCCTCATCTTTAATGATGAACTGTCGCCAAGTCAGCTGAAGTCATTGGCAACAGCAATTGAAGTGAAGATGATTGACCGCACGCAATTGATATTAGATATTTTTGCAAAGCGGGCGAGAACGAGAGAAGGCAAACTTCAAATTGAGCTGGCTCAGCTGCAATATGCACTGCCGCGTCTGACGGGACAAGGGATCAACCTTTCCCGGCAAGGCGGAGGAATTGGGGCAAGAGGTCCCGGGGAAACGAAACTGGAAACCGACCGCCGCCATATCAGAAATCGCATTCATGAAATCAACACACAGCTTTCCACTGTCATTCGCCATAGAAGCCGATACCG SRR6127941 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 10 04:31:39 Started mapping on | Dec 10 04:31:39 Finished on | Dec 10 04:53:21 Mapping speed, Million of reads per hour | 78.13 Number of input reads | 28256098 Average input read length | 196 UNIQUE READS: Uniquely mapped reads number | 16010486 Uniquely mapped reads % | 56.66% Average mapped length | 196.30 Number of splices: Total | 10653823 Number of splices: Annotated (sjdb) | 10116448 Number of splices: GT/AG | 10507504 Number of splices: GC/AG | 126066 Number of splices: AT/AC | 3038 Number of splices: Non-canonical | 17215 Mismatch rate per base, % | 0.37% Deletion rate per base | 0.02% Deletion average length | 2.38 Insertion rate per base | 0.02% Insertion average length | 2.03 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 413520 % of reads mapped to multiple loci | 1.46% Number of reads mapped to too many loci | 68564 % of reads mapped to too many loci | 0.24% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 40.46% % of reads unmapped: other | 1.17% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 11846088 11846088 11846088 N_multimapping 413520 413520 413520 N_noFeature 581309 15571536 689159 N_ambiguous 386095 1539 57310 UnstrandedReadsAssigned:15043082 PositiveStrandReadsAssigned:437411 NegativeStrandReadsAssigned:15264017 Dataset is classified negative stranded MeadianReadLen=100 20thPercentileLength=100 echo kmer=95 SRR6127941 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: 52,972 [index] number of k-mers: 66,720,672 [index] number of equivalence classes: 111,837 [quant] running in paired-end mode [quant] will process pair 1: SRR6127941-trimmed-pair1.fastq SRR6127941-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 28,256,098 reads, 15,401,827 reads pseudoaligned [quant] estimated average fragment length: 164.286 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,136 rounds 52973 SRR6127941.ke.tsv 35125 SRR6127941.se.tsv 88098 total ==> SRR6127941.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 772.855 8.20022 0.953332 PNS24247 1044 880.714 22.7192 2.3178 PNS24249 1928 1764.71 6.14295 0.312766 PNS24246 1044 880.714 22.7192 2.3178 PNS24248 1044 880.714 22.7192 2.3178 PNS24244 1471 1307.71 44.4991 3.05742 PNS24243 293 136.814 0 0 KQK14069 1603 1439.71 2123.1 132.498 KQK14071 474 312.324 119.49 34.3749 ==> SRR6127941.se.tsv <== BRADI_1g14170v3 2628 BRADI_1g53295v3 324 BRADI_1g59795v3 125 BRADI_1g07683v3 0 BRADI_1g00485v3 1 BRADI_1g20270v3 253 BRADI_1g74790v3 84 BRADI_1g09890v3 0 BRADI_1g77505v3 268 BRADI_1g48960v3 0 SRR6127941 completed mapping pipeline successfully