Starting /dee2/code/volunteer_pipeline.sh SRR6257530 current disk space = 1544405929984 free memory = 1605875976 SRR6257530 SRAfilesize b7319ee13b11d1d5b12370bb2d116672 SRR6257530.sra SRR6257530.sra file validated SRR6257530 is paired end SRR6257530 is conventional basespace SRR6257530 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR6257530_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 151 %GC 52 >>END_MODULE >>Per base sequence quality fail #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 22.18675 18.0 18.0 27.0 18.0 32.0 2 23.002 18.0 18.0 29.0 18.0 31.0 3 25.9755 27.0 18.0 30.0 18.0 33.0 4 28.53075 32.0 27.0 32.0 15.0 33.0 5 31.446 32.0 32.0 33.0 27.0 33.0 6 35.917 37.0 36.0 38.0 33.0 38.0 7 36.72425 38.0 37.0 38.0 35.0 38.0 8 37.07975 38.0 38.0 38.0 36.0 38.0 9 36.25775 38.0 38.0 38.0 34.0 38.0 10-14 36.6456 38.0 37.8 38.0 34.0 38.0 15-19 37.02685 38.0 38.0 38.0 36.2 38.0 20-24 36.520050000000005 38.0 37.6 38.0 33.6 38.0 25-29 35.862100000000005 38.0 36.8 38.0 30.2 38.0 30-34 36.21895 38.0 37.0 38.0 32.2 38.0 35-39 36.807300000000005 38.0 37.6 38.0 34.4 38.0 40-44 37.12939999999999 38.0 38.0 38.0 36.8 38.0 45-49 34.934749999999994 37.8 34.2 38.0 27.6 38.0 50-54 34.7724 37.8 34.2 38.0 24.6 38.0 55-59 36.69225 38.0 37.8 38.0 34.8 38.0 60-64 36.8938 38.0 38.0 38.0 35.8 38.0 65-69 36.809650000000005 38.0 38.0 38.0 35.0 38.0 70-74 35.779599999999995 38.0 36.8 38.0 30.4 38.0 75-79 34.6965 37.4 34.2 38.0 28.0 38.0 80-84 36.15755 38.0 37.4 38.0 33.0 38.0 85-89 36.17315 38.0 37.4 38.0 33.6 38.0 90-94 36.14485 38.0 37.2 38.0 33.2 38.0 95-99 35.9947 38.0 37.2 38.0 32.6 38.0 100-104 35.7546 38.0 36.6 38.0 32.0 38.0 105-109 35.5997 38.0 36.0 38.0 31.4 38.0 110-114 34.078799999999994 37.8 34.0 38.0 23.2 38.0 115-119 33.450399999999995 37.0 32.4 38.0 22.4 38.0 120-124 34.689 38.0 35.0 38.0 27.0 38.0 125-129 34.1702 38.0 34.8 38.0 24.8 38.0 130-134 29.750999999999998 34.4 23.8 37.6 15.4 38.0 135-139 29.303449999999998 34.4 21.6 38.0 13.4 38.0 140-144 28.60625 33.6 22.6 37.6 11.0 38.0 145-149 28.11995 34.8 21.8 38.0 2.0 38.0 150-151 21.215249999999997 28.0 2.0 36.5 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 16.0 3 1.0 4 1.0 5 1.0 6 1.0 7 0.0 8 0.0 9 0.0 10 1.0 11 0.0 12 0.0 13 0.0 14 0.0 15 3.0 16 4.0 17 4.0 18 6.0 19 5.0 20 7.0 21 10.0 22 8.0 23 12.0 24 11.0 25 19.0 26 30.0 27 52.0 28 50.0 29 73.0 30 85.0 31 146.0 32 191.0 33 308.0 34 541.0 35 1011.0 36 1138.0 37 265.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 38.2738248137683 9.632674030310815 4.495247880811713 47.59825327510917 2 18.584292146073036 10.33016508254127 41.59579789894948 29.48974487243622 3 17.1 14.149999999999999 29.175 39.574999999999996 4 24.5 22.525000000000002 22.900000000000002 30.075000000000003 5 24.355444305381727 26.48310387984981 24.55569461827284 24.60575719649562 6 22.475 28.525 25.074999999999996 23.925 7 17.474999999999998 20.9 41.525 20.1 8 17.549999999999997 16.900000000000002 35.699999999999996 29.849999999999998 9 21.425 18.425 34.475 25.674999999999997 10-14 23.544999999999998 22.57 25.7 28.185 15-19 24.215 21.085 25.275 29.425 20-24 24.09 22.98 25.645 27.284999999999997 25-29 24.351217560878045 20.136006800340017 26.50132506625331 29.011450572528624 30-34 24.75 20.974999999999998 24.365000000000002 29.909999999999997 35-39 23.525 21.705 25.345000000000002 29.425 40-44 24.77 22.305 23.810000000000002 29.115000000000002 45-49 24.32 20.285 25.55 29.845 50-54 24.349999999999998 21.095 26.11 28.444999999999997 55-59 23.825 22.215 26.435 27.525 60-64 25.230000000000004 20.375 26.05 28.345 65-69 24.02 23.31 24.47 28.199999999999996 70-74 24.64 22.275 24.455 28.63 75-79 24.759999999999998 23.47 23.53 28.24 80-84 23.745 24.465 24.175 27.615000000000002 85-89 24.936246812340617 22.80614030701535 23.736186809340467 28.521426071303562 90-94 26.3863193159658 22.72613630681534 22.95114755737787 27.936396819840994 95-99 24.8 22.73 23.97 28.499999999999996 100-104 24.46 22.535 25.395 27.61 105-109 24.19 23.1 24.4 28.310000000000002 110-114 23.435 24.075 24.709999999999997 27.779999999999998 115-119 23.555 24.18 24.245 28.02 120-124 24.265 25.735000000000003 21.584999999999997 28.415000000000003 125-129 23.72 24.295 22.24 29.744999999999997 130-134 23.986199309965496 22.916145807290363 22.011100555027753 31.086554327716385 135-139 24.011200560028 24.226211310565528 22.49612480624031 29.266463323166157 140-144 24.2110527631908 24.561140285071268 22.75068767191798 28.477119279819956 145-149 22.509999999999998 25.355 23.24 28.895 150-151 22.620689655172413 25.642633228840122 22.695924764890282 29.040752351097176 >>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 0.5 25 0.5 26 1.5 27 1.5 28 1.0 29 2.0 30 2.0 31 4.5 32 6.5 33 5.5 34 7.0 35 15.5 36 28.0 37 31.5 38 32.5 39 39.0 40 42.0 41 42.5 42 43.0 43 43.0 44 58.5 45 88.0 46 108.0 47 93.5 48 69.5 49 97.0 50 153.0 51 180.0 52 206.0 53 263.5 54 304.0 55 383.5 56 404.0 57 299.5 58 241.0 59 208.5 60 136.5 61 82.5 62 62.5 63 54.5 64 39.5 65 14.0 66 9.5 67 11.5 68 9.5 69 9.5 70 11.5 71 11.5 72 11.0 73 10.0 74 8.5 75 5.5 76 3.0 77 2.0 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 0.0 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 2.675 2 0.05 3 0.0 4 0.0 5 0.125 6 0.0 7 0.0 8 0.0 9 0.0 10-14 0.0 15-19 0.0 20-24 0.0 25-29 0.005 30-34 0.0 35-39 0.0 40-44 0.0 45-49 0.0 50-54 0.0 55-59 0.0 60-64 0.0 65-69 0.0 70-74 0.0 75-79 0.0 80-84 0.0 85-89 0.005 90-94 0.005 95-99 0.0 100-104 0.0 105-109 0.0 110-114 0.0 115-119 0.0 120-124 0.0 125-129 0.0 130-134 0.005 135-139 0.005 140-144 0.025 145-149 0.0 150-151 0.3125 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 72.675 #Duplication Level Percentage of deduplicated Percentage of total 1 85.27691778465773 61.975 2 7.739938080495357 11.25 3 3.0615755073959408 6.675000000000001 4 1.1351909184726523 3.3000000000000003 5 1.1007911936704506 4.0 6 0.41279669762641896 1.7999999999999998 7 0.3783969728242174 1.925 8 0.10319917440660474 0.6 9 0.13759889920880633 0.8999999999999999 >10 0.6191950464396285 6.25 >50 0.03439972480220158 1.325 >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 GGCATGATGACTTGGCCTCATCCTCTCCTTCCTCCGGCTTAACACCGGCG 53 1.325 No Hit GTCCAGTCAACTGCTGCGCCTCAACGCATTTCGGGGAGAACCAGCTAGCT 20 0.5 No Hit CCCACTGCTGCCTCCCGTAGGAGTCTGGGCCGTGTCTCAGTCCCAGTGTG 19 0.475 No Hit GTTCTATTTCACTACCCACTGGGGGTTCTTTTCACCTTTCCCTCACGGTA 18 0.44999999999999996 No Hit CCCCACTGCTGCCTCCCGTAGGAGTCTGGGCCGTGTCTCAGTCCCAGTGT 17 0.42500000000000004 No Hit CCCGTCAATTCCTTTGAGTTTCATTCTTGCGAACGTACTCCCCAGGCGGG 16 0.4 No Hit CTCCACGCGGCATTGCTCCGTCAGGCTTTCGCCCATTGCGGAAAATTCCC 16 0.4 No Hit GTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACT 15 0.375 No Hit GCTTTCTTTTCCTCTGGCTACTAAGATGTTTCAGTTCGCCAGGTTGTCTC 14 0.35000000000000003 No Hit GTCAATTCCTTTGAGTTTCATTCTTGCGAACGTACTCCCCAGGCGGGATA 13 0.325 No Hit GTCCCTATTAATCATTACTCCGATCCCGAAGGCCAACACAATAGGACCGG 13 0.325 No Hit CGTCAATTCCTTTGAGTTTCATTCTTGCGAACGTACTCCCCAGGCGGGAT 12 0.3 No Hit CCTAGCTTTCGTCTCTCAGTGTCAGTGTCGGCCCAGCAGAGTGCTTTCGC 12 0.3 No Hit GTCGGTTTCGGGTACAGGTACCCTTTTGTTGAAGGTCGTTCGAGCTTTTC 11 0.27499999999999997 No Hit CTCAGATACCGTCATTGTTTCTTCTCCGAGAAAAGAAGTTGACGACCCGT 11 0.27499999999999997 No Hit ATCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCTATA 11 0.27499999999999997 No Hit CCGGAACCCAAAGACTTTGATTTCTCATAAGGTGCCGGCGGAGTCCTATA 11 0.27499999999999997 No Hit CCGGGAACGGATTCACCGCCGTATGGCTGACCGGCGATTACTAGCGATTC 11 0.27499999999999997 No Hit CCTCAGCCTACGGGGTATTAGCAACCGTTTCCAGTTGTTGTTCCCCTCCC 10 0.25 No Hit GTTCGAGCTTTTCCTGGGAGTATGGCATCGGTTACATACTTCAGTGCCGT 9 0.22499999999999998 No Hit GCATGATGACTTGGCCTCATCCTCTCCTTCCTCCGGCTTAACACCGGCGG 9 0.22499999999999998 No Hit GTTTCTTCTCCGAGAAAAGAAGTTGACGACCCGTAGGCCTTCCACCTCCA 9 0.22499999999999998 No Hit GTTTACGGCTAGGACTACTGGGGTCTCTAATCCCATTTGCTCCCCTAGCT 9 0.22499999999999998 No Hit CCTAGATGTCCAGTCAACTGCTGCGCCTCAACGCATTTCGGGGAGAACCA 8 0.2 No Hit CCCGGAACCCAAAGACTTTGATTTCTCATAAGGTGCCGGCGGAGTCCTAT 8 0.2 No Hit GTTCGATCCTGGCTCAGGATGAACGCTGGCGGCATGCTTAACACATGCAA 8 0.2 No Hit GTGGCAACTAAACACGAGGGTTGCGCTCGTTGCGAGACTTAACCCAACAC 7 0.17500000000000002 No Hit GATGACTTGGCCTCATCCTCTCCTTCCTCCGGCTTAACACCGGCGGTCTG 7 0.17500000000000002 No Hit CTTAAACCTATAACCATCTTTCGGCTAACCTAGCCTCCTCCGTCCCTCCG 7 0.17500000000000002 No Hit CTAGAATTACTACGGTTATCCGAGTAGCACGTACCATCAAACAAACTATA 7 0.17500000000000002 No Hit GTCCTCTCAATGCTCTAACGCCCACACCGGATATGGACCGAACTGTCTCA 7 0.17500000000000002 No Hit ATTTGGGAATCTCCGGATCTATGCTTATTTTCAACTCCCCGAAGCATTTC 7 0.17500000000000002 No Hit CCCATCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCT 7 0.17500000000000002 No Hit AGCACGTGTGTCGCCCAGGGCATAAGGGGCATGATGACTTGGCCTCATCC 7 0.17500000000000002 No Hit CCTGTGTCGGTTTCGGGTACAGGTACCCTTTTGTTGAAGGTCGTTCGAGC 7 0.17500000000000002 No Hit GTCCTTAAACCTATAACCATCTTTCGGCTAACCTAGCCTCCTCCGTCCCT 7 0.17500000000000002 No Hit CTCTGCCCCTACCGTACTCCAGCTTGGTAGTTTCCACCGCCTGTCCAGGG 7 0.17500000000000002 No Hit CTCTGTCTTACCGCGGCTGCTGGCACAGAGTTAGCCGATGCTTATTCCTC 6 0.15 No Hit CTTTTGTTCCACACGAGATTTCTGTTCTCGTTGAGCTCATCTTAGGACAC 6 0.15 No Hit CCACTGCTGCCTCCCGTAGGAGTCTGGGCCGTGTCTCAGTCCCAGTGTGG 6 0.15 No Hit CTTCCCTCTAAGGCGGAACGCTCCCCTACCGATGCATTTTGACATCCCAC 6 0.15 No Hit CAATCATTCCGGATAACGCTTGCATCCTCTGTCTTACCGCGGCTGCTGGC 6 0.15 No Hit GCCCAATCATTCCGGATAACGCTTGCATCCTCTGTCTTACCGCGGCTGCT 6 0.15 No Hit CTAGCTTTCGTCTCTCAGTGTCAGTGTCGGCCCAGCAGAGTGCTTTCGCC 6 0.15 No Hit CAGGGTTCCAAACTCATAGTGGCAACTAAACACGAGGGTTGCGCTCGTTG 6 0.15 No Hit GGTCGTTCGAGCTTTTCCTGGGAGTATGGCATCGGTTACATACTTCAGTG 6 0.15 No Hit CCGCATTAATGGGCGAACAGCCCAACCCTTGGAACCACCTACAGCTCCAG 6 0.15 No Hit GGCAACTAAACACGAGGGTTGCGCTCGTTGCGAGACTTAACCCAACACCT 6 0.15 No Hit CTTTCTTTTCCTCTGGCTACTAAGATGTTTCAGTTCGCCAGGTTGTCTCT 6 0.15 No Hit CCCAATCATTCCGGATAACGCTTGCATCCTCTGTCTTACCGCGGCTGCTG 5 0.125 No Hit CAGTCAACTGCTGCGCCTCAACGCATTTCGGGGAGAACCAGCTAGCTCTG 5 0.125 No Hit GTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCT 5 0.125 No Hit CGGGATTCCACGTGCCCCATGCTACTCGGGTCAGAGCGTAAGCTAGTGAT 5 0.125 No Hit GTCATTGTTTCTTCTCCGAGAAAAGAAGTTGACGACCCGTAGGCCTTCCA 5 0.125 No Hit CTCCTTTATCACTGAGCGGTCATTTAGGGGCCTTAGCTGGTGATCCGGGC 5 0.125 No Hit GTCAGTGTCGGCCCAGCAGAGTGCTTTCGCCGTTGGTGTTCTTTCCGATC 5 0.125 No Hit CCTACCGTACTCCAGCTTGGTAGTTTCCACCGCCTGTCCAGGGTTGAGCC 5 0.125 No Hit GTACCGCATTAATGGGCGAACAGCCCAACCCTTGGAACCACCTACAGCTC 5 0.125 No Hit GTCAATTCCTTTAAGTTTCAGCCTTGCGACCATACTCCCCCCGGAACCCA 5 0.125 No Hit CTCCCATTTCGCTCGCCGCTACTACGGGAATCGCTTTTGCTTTCTTTTCC 5 0.125 No Hit CGGGAACGGATTCACCGCCGTATGGCTGACCGGCGATTACTAGCGATTCC 5 0.125 No Hit CCCTACCGTACTCCAGCTTGGTAGTTTCCACCGCCTGTCCAGGGTTGAGC 5 0.125 No Hit GTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGC 5 0.125 No Hit ATCGTTTACGGCTAGGACTACTGGGGTCTCTAATCCCATTTGCTCCCCTA 5 0.125 No Hit GTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATT 5 0.125 No Hit GGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAG 5 0.125 No Hit GTACAAGGCCCGGGAACGGATTCACCGCCGTATGGCTGACCGGCGATTAC 5 0.125 No Hit CGCATTAATGGGCGAACAGCCCAACCCTTGGAACCACCTACAGCTCCAGG 5 0.125 No Hit GTCAGGATTGGGTAATTTGCGCGCCTGCTGCCTTCCTTGGATGTGGTAGC 5 0.125 No Hit CATCGTTTACGGCTAGGACTACTGGGGTCTCTAATCCCATTTGCTCCCCT 5 0.125 No Hit TATTAATCATTACTCCGATCCCGAAGGCCAACACAATAGGACCGGAATCC 5 0.125 No Hit GTTCCGTTCCCTTAACCAAGCCACTGCCTATGAGTCGCCGGCTCATTCTT 5 0.125 No Hit CTCAGTGTCAGTGTCGGCCCAGCAGAGTGCTTTCGCCGTTGGTGTTCTTT 5 0.125 No Hit CTTGCCTACATTGTTCCATTGGCCAGAGGCTGTTCACCTTGGAGACCTGA 5 0.125 No Hit GTCGGTTCGGACCTCTGCTTAGTTTCATCCAAGCTTCATCCTGGTCATGG 5 0.125 No Hit GTTCCAAACTCATAGTGGCAACTAAACACGAGGGTTGCGCTCGTTGCGAG 5 0.125 No Hit GCTCCTCAGCCTACGGGGTATTAGCAACCGTTTCCAGTTGTTGTTCCCCT 5 0.125 No Hit GCTTGCTTTGAGCACTCTAATTTCTTCAAAGTAACGATGCCGGAGGCACG 5 0.125 No Hit ATTAATCATTACTCCGATCCCGAAGGCCAACACAATAGGACCGGAATCCT 5 0.125 No Hit CTTTGAGTTTCATTCTTGCGAACGTACTCCCCAGGCGGGATACTTAACGC 5 0.125 No Hit CTCAGCCTACGGGGTATTAGCAACCGTTTCCAGTTGTTGTTCCCCTCCCA 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 0.0 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 0.025 0.0 0.0 0.0 0.0 12-13 0.025 0.0 0.0 0.0 0.0 14-15 0.025 0.0 0.0 0.0 0.0 16-17 0.025 0.0 0.0 0.0 0.0 18-19 0.025 0.0 0.0 0.0 0.0 20-21 0.025 0.0 0.0 0.0 0.0 22-23 0.025 0.0 0.0 0.0 0.0 24-25 0.025 0.0 0.0 0.0 0.0 26-27 0.037500000000000006 0.0 0.0 0.0 0.0 28-29 0.05 0.0 0.0 0.0 0.0 30-31 0.05 0.0 0.0 0.0 0.0 32-33 0.1 0.0 0.0 0.0 0.0 34-35 0.1375 0.0 0.0 0.0 0.0 36-37 0.175 0.0 0.0 0.0 0.0 38-39 0.2 0.0 0.0 0.0 0.0 40-41 0.21250000000000002 0.0 0.0 0.0 0.0 42-43 0.2375 0.0 0.0 0.0 0.0 44-45 0.2625 0.0 0.0 0.0 0.0 46-47 0.2875 0.0 0.0 0.0 0.0 48-49 0.32499999999999996 0.0 0.0 0.0 0.0 50-51 0.375 0.0 0.0 0.0 0.0 52-53 0.3875 0.0 0.0 0.0 0.0 54-55 0.5375000000000001 0.0 0.0 0.0 0.0 56-57 0.6125 0.0 0.0 0.0 0.0 58-59 0.675 0.0 0.0 0.0 0.0 60-61 0.7375 0.0 0.0 0.0 0.0 62-63 0.7625 0.0 0.0 0.0 0.0 64-65 0.8374999999999999 0.0 0.0 0.0 0.0 66-67 0.975 0.0 0.0 0.0 0.0 68-69 1.15 0.0 0.0 0.0 0.0 70-71 1.3125 0.0 0.0 0.0 0.0 72-73 1.4625 0.0 0.0 0.0 0.0 74-75 1.75 0.0 0.0 0.0 0.0 76-77 2.0375 0.0 0.0 0.0 0.0 78-79 2.2625 0.0 0.0 0.0 0.0 80-81 2.5375 0.0 0.0 0.0 0.0 82-83 2.9625 0.0 0.0 0.0 0.0 84-85 3.4 0.0 0.0 0.0 0.0 86-87 3.9375 0.0 0.0 0.0 0.0 88-89 4.4125 0.0 0.0 0.0 0.0 90-91 4.7875 0.0 0.0 0.0 0.0 92-93 5.1875 0.0 0.0 0.0 0.0 94-95 5.8625 0.0 0.0 0.0 0.0 96-97 6.4375 0.0 0.0 0.0 0.0 98-99 7.3125 0.0 0.0 0.0 0.0 100-101 8.3 0.0 0.0 0.0 0.0 102-103 9.0625 0.0 0.0 0.0 0.0 104-105 10.0 0.0 0.0 0.0 0.0 106-107 10.925 0.0 0.0 0.0 0.0 108-109 11.837499999999999 0.0 0.0 0.0 0.0 110-111 13.0625 0.0 0.0 0.0 0.0 112-113 13.925 0.0 0.0 0.0 0.0 114-115 14.975 0.0 0.0 0.0 0.0 116-117 16.025 0.0 0.0 0.0 0.0 118-119 17.1 0.0 0.0 0.0 0.0 120-121 18.025 0.0 0.0 0.0 0.0 122-123 19.05 0.0 0.0 0.0 0.0 124-125 19.95 0.0 0.0 0.0 0.0 126-127 20.875 0.0 0.0 0.0 0.0 128-129 21.7625 0.0 0.0 0.0 0.0 130-131 22.5 0.0 0.0 0.0 0.0 132-133 22.950000000000003 0.0 0.0 0.0 0.0 134-135 23.5375 0.0 0.0 0.0 0.0 136-137 24.275 0.0 0.0 0.0 0.0 138-139 24.9 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE SRR6257530 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR6257530_2.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 151 %GC 53 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 31.99325 33.0 32.0 33.0 28.0 34.0 2 32.48775 33.0 33.0 34.0 32.0 34.0 3 29.61275 33.0 28.0 33.0 18.0 34.0 4 30.71775 33.0 31.0 33.0 27.0 34.0 5 32.05175 33.0 32.0 34.0 28.0 34.0 6 36.7005 38.0 38.0 38.0 35.0 38.0 7 36.8635 38.0 38.0 38.0 36.0 38.0 8 32.14625 38.0 29.0 38.0 16.0 38.0 9 35.72225 38.0 36.0 38.0 30.0 38.0 10-14 35.57305 38.0 36.8 38.0 28.0 38.0 15-19 35.893550000000005 38.0 36.0 38.0 30.8 38.0 20-24 36.860099999999996 38.0 38.0 38.0 36.0 38.0 25-29 36.929500000000004 38.0 38.0 38.0 35.8 38.0 30-34 36.6528 38.0 38.0 38.0 34.8 38.0 35-39 36.92815 38.0 38.0 38.0 36.0 38.0 40-44 37.01925 38.0 38.0 38.0 36.8 38.0 45-49 36.871 38.0 38.0 38.0 36.0 38.0 50-54 36.76545 38.0 38.0 38.0 35.8 38.0 55-59 36.71365000000001 38.0 38.0 38.0 35.2 38.0 60-64 36.7824 38.0 38.0 38.0 35.6 38.0 65-69 36.63715 38.0 38.0 38.0 34.8 38.0 70-74 36.6121 38.0 38.0 38.0 34.8 38.0 75-79 36.636300000000006 38.0 38.0 38.0 34.8 38.0 80-84 35.36845 38.0 36.0 38.0 28.8 38.0 85-89 36.3262 38.0 37.8 38.0 33.8 38.0 90-94 35.115950000000005 38.0 35.6 38.0 29.0 38.0 95-99 34.0274 37.8 32.6 38.0 24.6 38.0 100-104 35.5379 38.0 36.2 38.0 30.8 38.0 105-109 35.153650000000006 38.0 35.6 38.0 29.0 38.0 110-114 32.3598 36.4 28.8 38.0 19.8 38.0 115-119 34.75365 38.0 34.8 38.0 26.8 38.0 120-124 34.90035 38.0 35.0 38.0 28.4 38.0 125-129 34.68405 38.0 34.2 38.0 27.6 38.0 130-134 34.101150000000004 38.0 33.0 38.0 25.6 38.0 135-139 33.240899999999996 38.0 33.0 38.0 21.4 38.0 140-144 30.039499999999997 35.0 25.0 38.0 12.6 38.0 145-149 30.3411 36.0 28.6 38.0 5.6 38.0 150-151 24.9675 31.5 15.0 37.0 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 20.0 3 5.0 4 0.0 5 0.0 6 0.0 7 2.0 8 0.0 9 0.0 10 0.0 11 0.0 12 2.0 13 2.0 14 0.0 15 1.0 16 7.0 17 2.0 18 6.0 19 4.0 20 7.0 21 8.0 22 11.0 23 6.0 24 10.0 25 18.0 26 21.0 27 43.0 28 39.0 29 70.0 30 79.0 31 89.0 32 143.0 33 196.0 34 300.0 35 571.0 36 1278.0 37 1060.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 42.3 15.7 4.95 37.05 2 29.25 18.425 31.1 21.224999999999998 3 22.3 21.95 29.65 26.1 4 28.625 30.5 19.75 21.125 5 31.574999999999996 31.5 17.224999999999998 19.7 6 24.525 36.025 16.725 22.725 7 23.175 21.0 32.550000000000004 23.275000000000002 8 25.575 21.625 25.3 27.500000000000004 9 28.975 20.974999999999998 24.099999999999998 25.95 10-14 28.89 25.0 21.605 24.505 15-19 28.939999999999998 26.095000000000002 21.18 23.785 20-24 29.044999999999998 24.654999999999998 21.404999999999998 24.895 25-29 29.195 25.165 21.52 24.12 30-34 28.794999999999998 25.509999999999998 21.6 24.095 35-39 29.054999999999996 27.089999999999996 20.985 22.869999999999997 40-44 30.264999999999997 26.08 20.495 23.16 45-49 29.49 25.619999999999997 20.925 23.965 50-54 29.465000000000003 25.019999999999996 21.525 23.990000000000002 55-59 29.270000000000003 25.85 21.560000000000002 23.32 60-64 29.645 24.82 22.67 22.865 65-69 30.11 25.155 21.16 23.575 70-74 30.305 24.25 21.6 23.845 75-79 29.475 24.84 21.755 23.93 80-84 29.515 25.09 22.25 23.145 85-89 29.69 24.765 21.490000000000002 24.055 90-94 30.020000000000003 25.990000000000002 20.945 23.044999999999998 95-99 30.175 24.834999999999997 21.425 23.565 100-104 29.93 27.295 21.34 21.435000000000002 105-109 30.935000000000002 24.695 22.264999999999997 22.105 110-114 30.035 25.945 22.325 21.695 115-119 30.759999999999998 26.224999999999998 20.765 22.25 120-124 30.380000000000003 26.97 19.37 23.28 125-129 30.580000000000002 26.875 19.84 22.705000000000002 130-134 30.869999999999997 26.784999999999997 20.13 22.215 135-139 30.81 25.7 21.25 22.24 140-144 30.959999999999997 26.305 21.990000000000002 20.745 145-149 30.615 27.67 21.19 20.525 150-151 32.239889820959064 26.993865030674847 19.40653562038312 21.35970952798297 >>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 1.0 27 1.5 28 1.5 29 3.0 30 2.0 31 2.5 32 4.0 33 6.5 34 11.0 35 16.5 36 22.0 37 33.0 38 39.5 39 44.0 40 46.5 41 41.0 42 44.0 43 57.5 44 62.0 45 65.0 46 74.0 47 81.5 48 89.0 49 102.0 50 134.5 51 159.5 52 177.0 53 240.5 54 356.0 55 425.5 56 372.5 57 279.5 58 216.5 59 173.0 60 142.5 61 115.0 62 99.0 63 68.5 64 30.0 65 17.5 66 17.5 67 19.0 68 20.0 69 18.0 70 12.0 71 12.5 72 15.0 73 9.0 74 5.0 75 4.0 76 3.5 77 2.0 78 2.0 79 2.5 80 0.5 81 0.0 82 0.0 83 0.0 84 0.0 85 0.0 86 0.0 87 0.0 88 0.0 89 0.0 90 0.0 91 0.0 92 0.0 93 0.0 94 0.0 95 0.0 96 0.0 97 0.0 98 0.0 99 0.0 100 0.0 >>END_MODULE >>Per base N content pass #Base N-Count 1 0.0 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10-14 0.0 15-19 0.0 20-24 0.0 25-29 0.0 30-34 0.0 35-39 0.0 40-44 0.0 45-49 0.0 50-54 0.0 55-59 0.0 60-64 0.0 65-69 0.0 70-74 0.0 75-79 0.0 80-84 0.0 85-89 0.0 90-94 0.0 95-99 0.0 100-104 0.0 105-109 0.0 110-114 0.0 115-119 0.0 120-124 0.0 125-129 0.0 130-134 0.0 135-139 0.0 140-144 0.0 145-149 0.0 150-151 0.1625 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 77.725 #Duplication Level Percentage of deduplicated Percentage of total 1 86.23351559987135 67.025 2 8.459311675779993 13.15 3 2.6053393374075267 6.075 4 1.4474107430041814 4.5 5 0.418140881312319 1.625 6 0.2573174654229656 1.2 7 0.1929880990672242 1.05 8 0.0 0.0 9 0.0964940495336121 0.675 >10 0.2894821486008363 4.7 >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 fail #Sequence Count Percentage Possible Source GTTCGATCCTGGCTCAGGATGAACGCTGGCGGCATGCTTAACACATGCAA 49 1.225 No Hit CCTTACCAGGGCTTGACATGCCGCGAATCCTCTTGAAAGAGAGGGGTGCC 34 0.8500000000000001 No Hit GGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAG 22 0.5499999999999999 No Hit CCTGCCAGTAGTCATATGCTTGTCTCAAAGATTAAGCCATGCATGTGCAA 19 0.475 No Hit CCTGGCTCAGGATGAACGCTGGCGGCATGCTTAACACATGCAAGTCGAAC 17 0.42500000000000004 No Hit CTTACCAGGGCTTGACATGCCGCGAATCCTCTTGAAAGAGAGGGGTGCCC 14 0.35000000000000003 No Hit CAGGGCTTGACATGCCGCGAATCCTCTTGAAAGAGAGGGGTGCCCTCGGG 11 0.27499999999999997 No Hit GAGAAATCCGCCCAAGGAGGGGCTCGCGTCTGATTAGCTAGTTGGTGAGG 11 0.27499999999999997 No Hit CTTACCAGGTCCAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTT 11 0.27499999999999997 No Hit CTTGCGGTGGATACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCG 9 0.22499999999999998 No Hit GTTGGGTTAAGTCTCGCAACGAGCGCAACCCTCGTGTTTAGTTGCCACTA 9 0.22499999999999998 No Hit GGATGATCAGCCACACTGGGACTGAGACACGGCCCAGACTCCTACGGGAG 9 0.22499999999999998 No Hit CTTGAAAGAGAGGGGTGCCCTCGGGAACGCGGACACAGGTGGTGCATGGC 7 0.17500000000000002 No Hit CTCAGGATGAACGCTGGCGGCATGCTTAACACATGCAAGTCGAACGGGAA 7 0.17500000000000002 No Hit CAACAACTGGAAACGGTTGCTAATACCCCGTAGGCTGAGGAGCAAAAGGA 7 0.17500000000000002 No Hit GTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTTTAA 7 0.17500000000000002 No Hit CTGACACTGAGAGACGAAAGCTAGGGGAGCAAATGGGATTAGAGACCCCA 7 0.17500000000000002 No Hit AGAACCTTACCAGGGCTTGACATGCCGCGAATCCTCTTGAAAGAGAGGGG 7 0.17500000000000002 No Hit GGAACAACAACTGGAAACGGTTGCTAATACCCCGTAGGCTGAGGAGCAAA 6 0.15 No Hit TGAACGCTGGCGGCATGCTTAACACATGCAAGTCGAACGGGAAGTGGTGT 6 0.15 No Hit ACCTTACCAGGGCTTGACATGCCGCGAATCCTCTTGAAAGAGAGGGGTGC 6 0.15 No Hit CCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTTCG 6 0.15 No Hit GAACCTTACCAGGGCTTGACATGCCGCGAATCCTCTTGAAAGAGAGGGGT 6 0.15 No Hit ACCAGGTCCAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTTGAT 6 0.15 No Hit ATTATTTCTAGTTAATATGTGTGCTTGGGAGTCCTTGCAATTTGAATAAA 6 0.15 No Hit GTTAGTTTTACCCTACTGATGACCGTGCCGCGATAGTAATTCAACCTAGT 6 0.15 No Hit GTCTGGTGCCAGCAGCCGCGGTAATTCCAGCTCCAATAGCGTATATTTAA 5 0.125 No Hit GCCGCGAATCCTCTTGAAAGAGAGGGGTGCCCTCGGGAACGCGGACACAG 5 0.125 No Hit GGATTAGAGACCCCAGTAGTCCTAGCCGTAAACGATGGATACTAGGTGCT 5 0.125 No Hit GTTTGAGGCAATAACAGGTCTGTGATGCCCTTAGATGTTCTGGGCCGCAC 5 0.125 No Hit GTGGAAGGCCTACGGGTCGTCAACTTCTTTTCTCGGAGAAGAAACAATGA 5 0.125 No Hit GGAAGGGCGTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAGCAT 5 0.125 No Hit GTGAAATTCTTGGATTTATGAAAGACGAACAACTGCGAAAGCATTTGCCA 5 0.125 No Hit GGCAAGTCTGGTGCCAGCAGCCGCGGTAATTCCAGCTCCAATAGCGTATA 5 0.125 No Hit GGGAACGGAACCCACCGGAGCCGTAGCGAAAGCGAGTCTTCATAGGGCGA 5 0.125 No Hit CGGGTGAGTAACGCGTAAGAACCTGCCCTTGGGAGGGGAACAACAACTGG 5 0.125 No Hit GAAACAATGACGGTATCTGAGGAATAAGCATCGGCTAACTCTGTGCCAGC 5 0.125 No Hit GGCAGAAGGGAGCTTGACTGCAAGACTCACCCGTCGAGCAGAGACGAAAG 5 0.125 No Hit GTCAAATCCCAGGGCTCAACCCTGGACAGGCGGTGGAAACTACCAAGCTG 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 0.0 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 0.0125 0.0 0.0 0.0 0.0 28-29 0.025 0.0 0.0 0.0 0.0 30-31 0.025 0.0 0.0 0.0 0.0 32-33 0.07500000000000001 0.0 0.0 0.0 0.0 34-35 0.1125 0.0 0.0 0.0 0.0 36-37 0.15 0.0 0.0 0.0 0.0 38-39 0.175 0.0 0.0 0.0 0.0 40-41 0.2 0.0 0.0 0.0 0.0 42-43 0.2375 0.0 0.0 0.0 0.0 44-45 0.2625 0.0 0.0 0.0 0.0 46-47 0.2875 0.0 0.0 0.0 0.0 48-49 0.32499999999999996 0.0 0.0 0.0 0.0 50-51 0.375 0.0 0.0 0.0 0.0 52-53 0.3875 0.0 0.0 0.0 0.0 54-55 0.5375000000000001 0.0 0.0 0.0 0.0 56-57 0.6125 0.0 0.0 0.0 0.0 58-59 0.675 0.0 0.0 0.0 0.0 60-61 0.75 0.0 0.0 0.0 0.0 62-63 0.8125 0.0 0.0 0.0 0.0 64-65 0.8875 0.0 0.0 0.0 0.0 66-67 1.025 0.0 0.0 0.0 0.0 68-69 1.2 0.0 0.0 0.0 0.0 70-71 1.3624999999999998 0.0 0.0 0.0 0.0 72-73 1.575 0.0 0.0 0.0 0.0 74-75 1.9125 0.0 0.0 0.0 0.0 76-77 2.2125 0.0 0.0 0.0 0.0 78-79 2.4125 0.0 0.0 0.0 0.0 80-81 2.6625 0.0 0.0 0.0 0.0 82-83 3.0375 0.0 0.0 0.0 0.0 84-85 3.4375 0.0 0.0 0.0 0.0 86-87 3.9375 0.0 0.0 0.0 0.0 88-89 4.2375 0.0 0.0 0.0 0.0 90-91 4.5125 0.0 0.0 0.0 0.0 92-93 4.8875 0.0 0.0 0.0 0.0 94-95 5.5375 0.0 0.0 0.0 0.0 96-97 6.137499999999999 0.0 0.0 0.0 0.0 98-99 6.887499999999999 0.0 0.0 0.0 0.0 100-101 7.7 0.0 0.0 0.0 0.0 102-103 8.325 0.0 0.0 0.0 0.0 104-105 9.2 0.0 0.0 0.0 0.0 106-107 10.087499999999999 0.0 0.0 0.0 0.0 108-109 10.9375 0.0 0.0 0.0 0.0 110-111 12.0625 0.0 0.0 0.0 0.0 112-113 13.025 0.0 0.0 0.0 0.0 114-115 14.2 0.0 0.0 0.0 0.0 116-117 15.25 0.0 0.0 0.0 0.0 118-119 16.325000000000003 0.0 0.0 0.0 0.0 120-121 17.299999999999997 0.0 0.0 0.0 0.0 122-123 18.5 0.0 0.0 0.0 0.0 124-125 19.725 0.0 0.0 0.0 0.0 126-127 20.9625 0.0 0.0 0.0 0.0 128-129 22.1 0.0 0.0 0.0 0.0 130-131 23.025 0.0 0.0 0.0 0.0 132-133 23.875 0.0 0.0 0.0 0.0 134-135 24.7875 0.0 0.0 0.0 0.0 136-137 25.675 0.0 0.0 0.0 0.0 138-139 26.5125 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position AAAAAAA 55 0.0025175211 15.816817 140-144 >>END_MODULE Read 618379 spots for SRR6257530.sra Written 618379 spots for SRR6257530.sra Read 618379 spots for SRR6257530.sra Written 618379 spots for SRR6257530.sra Read 618379 spots for SRR6257530.sra Written 618379 spots for SRR6257530.sra Read 618379 spots for SRR6257530.sra Written 618379 spots for SRR6257530.sra Read 618379 spots for SRR6257530.sra Written 618379 spots for SRR6257530.sra Read 618379 spots for SRR6257530.sra Written 618379 spots for SRR6257530.sra Read 618379 spots for SRR6257530.sra Written 618379 spots for SRR6257530.sra Read 618379 spots for SRR6257530.sra Written 618379 spots for SRR6257530.sra Read 618379 spots for SRR6257530.sra Written 618379 spots for SRR6257530.sra Read 618379 spots for SRR6257530.sra Written 618379 spots for SRR6257530.sra Read 618379 spots for SRR6257530.sra Written 618379 spots for SRR6257530.sra Read 618379 spots for SRR6257530.sra Written 618379 spots for SRR6257530.sra Read 618379 spots for SRR6257530.sra Written 618379 spots for SRR6257530.sra Read 618379 spots for SRR6257530.sra Written 618379 spots for SRR6257530.sra Read 618379 spots for SRR6257530.sra Written 618379 spots for SRR6257530.sra Read 618379 spots for SRR6257530.sra Written 618379 spots for SRR6257530.sra Read 618379 spots for SRR6257530.sra Written 618379 spots for SRR6257530.sra Read 618388 spots for SRR6257530.sra Written 618388 spots for SRR6257530.sra Read 618379 spots for SRR6257530.sra Written 618379 spots for SRR6257530.sra Read 618379 spots for SRR6257530.sra Written 618379 spots for SRR6257530.sra SRR ids: ['SRR6257530.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_5hqvw1gp SRR6257530.sra spots: 12367589 blocks: [[1, 618379], [618380, 1236758], [1236759, 1855137], [1855138, 2473516], [2473517, 3091895], [3091896, 3710274], [3710275, 4328653], [4328654, 4947032], [4947033, 5565411], [5565412, 6183790], [6183791, 6802169], [6802170, 7420548], [7420549, 8038927], [8038928, 8657306], [8657307, 9275685], [9275686, 9894064], [9894065, 10512443], [10512444, 11130822], [11130823, 11749201], [11749202, 12367589]] SRR6257530 file size 4169269 SRR6257530 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 SRR6257530 SRR6257530_1.fastq SRR6257530_2.fastq Input file: SRR6257530_1.fastq Paired file: SRR6257530_2.fastq trimmed: SRR6257530-trimmed-pair1.fastq, SRR6257530-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 Sat Dec 7 09:00:07 2024 >> started Sat Dec 7 09:00:26 2024 >> done (19.461s) 12367589 read pairs processed; of these: 14160 ( 0.11%) short read pairs filtered out after trimming by size control 49972 ( 0.40%) empty read pairs filtered out after trimming by size control 12303457 (99.48%) read pairs available; of these: 8348675 (67.86%) trimmed read pairs available after processing 3954782 (32.14%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 167 0.00% 19 267 0.00% 20 204 0.00% 21 285 0.00% 22 269 0.00% 23 250 0.00% 24 494 0.00% 25 351 0.00% 26 548 0.00% 27 592 0.00% 28 644 0.01% 29 836 0.01% 30 960 0.01% 31 1150 0.01% 32 1493 0.01% 33 1434 0.01% 34 1414 0.01% 35 1600 0.01% 36 1542 0.01% 37 1553 0.01% 38 1758 0.01% 39 1958 0.02% 40 2057 0.02% 41 2303 0.02% 42 2286 0.02% 43 2367 0.02% 44 2591 0.02% 45 2597 0.02% 46 2776 0.02% 47 2826 0.02% 48 2934 0.02% 49 3278 0.03% 50 3390 0.03% 51 3395 0.03% 52 4196 0.03% 53 4072 0.03% 54 4656 0.04% 55 4524 0.04% 56 4526 0.04% 57 5144 0.04% 58 6374 0.05% 59 5978 0.05% 60 6070 0.05% 61 8197 0.07% 62 8562 0.07% 63 7996 0.06% 64 9029 0.07% 65 9594 0.08% 66 9411 0.08% 67 10108 0.08% 68 12045 0.10% 69 11475 0.09% 70 12659 0.10% 71 12310 0.10% 72 14738 0.12% 73 15309 0.12% 74 13807 0.11% 75 16359 0.13% 76 17178 0.14% 77 16536 0.13% 78 17733 0.14% 79 20487 0.17% 80 22394 0.18% 81 21702 0.18% 82 23340 0.19% 83 26940 0.22% 84 25210 0.20% 85 32339 0.26% 86 34638 0.28% 87 33165 0.27% 88 40059 0.33% 89 34079 0.28% 90 35214 0.29% 91 36811 0.30% 92 39397 0.32% 93 43500 0.35% 94 41659 0.34% 95 44173 0.36% 96 43382 0.35% 97 48854 0.40% 98 49397 0.40% 99 51896 0.42% 100 53730 0.44% 101 60066 0.49% 102 65652 0.53% 103 61586 0.50% 104 69750 0.57% 105 59324 0.48% 106 61251 0.50% 107 63283 0.51% 108 66439 0.54% 109 78988 0.64% 110 71852 0.58% 111 71879 0.58% 112 74769 0.61% 113 64862 0.53% 114 65258 0.53% 115 70257 0.57% 116 67786 0.55% 117 68379 0.56% 118 67165 0.55% 119 66493 0.54% 120 75999 0.62% 121 70287 0.57% 122 68222 0.55% 123 83247 0.68% 124 70950 0.58% 125 74999 0.61% 126 71926 0.58% 127 73568 0.60% 128 75125 0.61% 129 75396 0.61% 130 73447 0.60% 131 76826 0.62% 132 76646 0.62% 133 78830 0.64% 134 78685 0.64% 135 79120 0.64% 136 87252 0.71% 137 84691 0.69% 138 88864 0.72% 139 94252 0.77% 140 95124 0.77% 141 100816 0.82% 142 111936 0.91% 143 120828 0.98% 144 135861 1.10% 145 155140 1.26% 146 184542 1.50% 147 234047 1.90% 148 328447 2.67% 149 597910 4.86% 150 2327132 18.91% 151 3954782 32.14% 12303457 reads passed initial QC criterion=sequence-density sequence-density=3.16 sequence-density-rank=1 fanout-score=1.93 fanout-score-rank=30 prefix-density=3.05 prefix-fanout=1.9 sequence=GTATTTAGCCTTG criterion=fanout-score sequence-density=0.02 sequence-density-rank=32 fanout-score=52.71 fanout-score-rank=1 prefix-density=0.89 prefix-fanout=1.0 sequence=GCATCGCCGGCCCCCATCCGCTTCCCTCCCGGCAATTTCAAGCACTCTTTGACTCTCTTTTCAAAGTCCTTTTCATCTTTCCCTCGCGGTACTTGTTCGCTATCGG criterion=sequence-density sequence-density=1.34 sequence-density-rank=1 fanout-score=7.15 fanout-score-rank=9 prefix-density=6.38 prefix-fanout=1.5 sequence=TGGTGCATGGCCGTTCTTAGTTGGTGGAGCGATTTGTCTGGTTAATTCCGTTAACGAACGAGACCTCAGCCTGCTAACTAGCTATGCGGAGCCATCCCTCCGCAGCTAGCTTCTTAGAGGGACTATCGCCGTTTAGGCGACGGAAGTTTGAGGCAATAACAGGTCTGTGATGCCCTTAGATGTTCTGGGCCGCACGCGCGCTACACTGATGTATTCAACGAGTATATAGCCTTGGCCGACAGGCCCGGGTAATCTTGGGAAATTTCATCGTGATGGGGATAGATCATTGCAATTGTTGGTCTTCAACGAGGAATGCCTAGTAAGCGCGAGTCATCAGCTCGCGTTGACTACGTCCCTGCCCTTTGTACACACC criterion=fanout-score sequence-density=0.01 sequence-density-rank=41 fanout-score=33.89 fanout-score-rank=1 prefix-density=0.22 prefix-fanout=1.0 sequence=GCTTTCTTTTCTTCAAAAATTCTTATATGTTAGCGGAAAAACCTTATCCATTAATAGCGGGAACTTCAAGAGCAGCTAGATCTAGAGGGAAGTTGTGAGCATTACGTTCGTGCATTACTTCCATACCAAGATTAGCACGGTTGATGATATCAGCCCAAGTATTAATAACGCGACCTTGACTATCAACTACAGATTGGTTGAAATTGAATCCATTTAGGTTGAACGCCATAGTACTAATACCTAAAGCAGTGAACCAGATTCCTACTACAGGCCAAGCAGCCAAGAAGAAGTGTAAAGAACGAGAGTTGTTGAAACTAGCATATTGGAAGATTAATCGGCCAAAATAACCATGAGCAGCCACAATATTATAAGTCTCTTCCTCTTGACCAAATTTGTAACCCTCATTAGCAGATTCATTTTCAGTAGTTTCCCTGATCAAACTAGAGGTTACCAAGGAACCATGCATAGCACTGAATAGGGAACCGCCGAAAACACCAGCTACACCTAACAT Potential 3prime adapter identified. Now checking if in reference sequence /dee2/code/volunteer_pipeline.sh: line 905: -f: command not found /dee2/code/volunteer_pipeline.sh: line 906: -f: command not found 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 GTATTTAGCCTTG -y TGGTGCATGGCCGTTCTTAGTTGGTGGAGCGATTTGTCTGGTTAATTCCGTTAACGAACGAGACCTCAGCCTGCTAACTAGCTATGCGGAGCCATCCCTCCGCAGCTAGCTTCTTAGAGGGACTATCGCCGTTTAGGCGACGGAAGTTTGAGGCAATAACAGGTCTGTGATGCCCTTAGATGTTCTGGGCCGCACGCGCGCTACACTGATGTATTCAACGAGTATATAGCCTTGGCCGACAGGCCCGGGTAATCTTGGGAAATTTCATCGTGATGGGGATAGATCATTGCAATTGTTGGTCTTCAACGAGGAATGCCTAGTAAGCGCGAGTCATCAGCTCGCGTTGACTACGTCCCTGCCCTTTGTACACACC -o SRR6257530 SRR6257530_1.fastq SRR6257530_2.fastq Input file: SRR6257530_1.fastq Paired file: SRR6257530_2.fastq trimmed: SRR6257530-trimmed-pair1.fastq, SRR6257530-trimmed-pair2.fastq Parameters used: -- 3' end adapter sequence (-x): GTATTTAGCCTTG -- paired 3' end adapter sequence (-y): TGGTGCATGGCCGTTCTTAGTTGGTGGAGCGATTTGTCTGGTTAATTCCGTTAACGAACGAGAC -- 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 -- number of concurrent threads (-t): 20 Sat Dec 7 09:01:21 2024 >> started Sat Dec 7 09:01:28 2024 >> done (6.632s) 4101152 read pairs processed; of these: 231 ( 0.01%) short read pairs filtered out after trimming by size control 480 ( 0.01%) empty read pairs filtered out after trimming by size control 4100441 (99.98%) read pairs available; of these: 1989 ( 0.05%) trimmed read pairs available after processing 4098452 (99.95%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 53 0.00% 19 87 0.00% 20 63 0.00% 21 83 0.00% 22 95 0.00% 23 87 0.00% 24 161 0.00% 25 120 0.00% 26 187 0.00% 27 209 0.01% 28 205 0.00% 29 286 0.01% 30 309 0.01% 31 398 0.01% 32 498 0.01% 33 508 0.01% 34 494 0.01% 35 539 0.01% 36 499 0.01% 37 541 0.01% 38 586 0.01% 39 650 0.02% 40 638 0.02% 41 751 0.02% 42 766 0.02% 43 827 0.02% 44 851 0.02% 45 908 0.02% 46 908 0.02% 47 912 0.02% 48 973 0.02% 49 1086 0.03% 50 1176 0.03% 51 1133 0.03% 52 1402 0.03% 53 1349 0.03% 54 1505 0.04% 55 1461 0.04% 56 1526 0.04% 57 1665 0.04% 58 2079 0.05% 59 1969 0.05% 60 2065 0.05% 61 2671 0.07% 62 2878 0.07% 63 2710 0.07% 64 3004 0.07% 65 3239 0.08% 66 3221 0.08% 67 3343 0.08% 68 4109 0.10% 69 3885 0.09% 70 4202 0.10% 71 4146 0.10% 72 4944 0.12% 73 5215 0.13% 74 4603 0.11% 75 5430 0.13% 76 5671 0.14% 77 5545 0.14% 78 5838 0.14% 79 6753 0.16% 80 7530 0.18% 81 7142 0.17% 82 7760 0.19% 83 8924 0.22% 84 8458 0.21% 85 10753 0.26% 86 11538 0.28% 87 11108 0.27% 88 13420 0.33% 89 11347 0.28% 90 11769 0.29% 91 12257 0.30% 92 13044 0.32% 93 14468 0.35% 94 13707 0.33% 95 14747 0.36% 96 14373 0.35% 97 16272 0.40% 98 16358 0.40% 99 17418 0.42% 100 17986 0.44% 101 19909 0.49% 102 21921 0.53% 103 20552 0.50% 104 23397 0.57% 105 19765 0.48% 106 20382 0.50% 107 21129 0.52% 108 21979 0.54% 109 26331 0.64% 110 23776 0.58% 111 24004 0.59% 112 24968 0.61% 113 21643 0.53% 114 21831 0.53% 115 23350 0.57% 116 22604 0.55% 117 22880 0.56% 118 22420 0.55% 119 22418 0.55% 120 25305 0.62% 121 23579 0.58% 122 22773 0.56% 123 27778 0.68% 124 23548 0.57% 125 25002 0.61% 126 23902 0.58% 127 24351 0.59% 128 24871 0.61% 129 25165 0.61% 130 24372 0.59% 131 25483 0.62% 132 25445 0.62% 133 26315 0.64% 134 26360 0.64% 135 26377 0.64% 136 28836 0.70% 137 28083 0.68% 138 29494 0.72% 139 31173 0.76% 140 31815 0.78% 141 33809 0.82% 142 37407 0.91% 143 40328 0.98% 144 45354 1.11% 145 51708 1.26% 146 61565 1.50% 147 78555 1.92% 148 109626 2.67% 149 199812 4.87% 150 774948 18.90% 151 1317649 32.13% criterion=sequence-density sequence-density=3.16 sequence-density-rank=1 fanout-score=1.93 fanout-score-rank=29 prefix-density=3.06 prefix-fanout=1.9 sequence=GTATTTAGCCTTG criterion=fanout-score sequence-density=0.02 sequence-density-rank=31 fanout-score=51.37 fanout-score-rank=1 prefix-density=0.88 prefix-fanout=1.0 sequence=GCATCGCCGGCCCCCATCCGCTTCCCTCCCGGCAATTTCAAGCACTCTTTGACTCTCTTTTCAAAGTCCTTTTCATCTTTCCCTCGCGGTACTTGTTCGCTATCGG criterion=sequence-density sequence-density=1.32 sequence-density-rank=1 fanout-score=7.18 fanout-score-rank=7 prefix-density=6.34 prefix-fanout=1.5 sequence=TGGTGCATGGCCGTTCTTAGTTGGTGGAGCGATTTGTCTGGTTAATTCCGTTAACGAACGAGACCTCAGCCTGCTAACTAGCTATGCGGAGCCATCCCTCCGCAGCTAGCTTCTTAGAGGGACTATCGCCGTTTAGGCGACGGAAGTTTGAGGCAATAACAGGTCTGTGATGCCCTTAGATGTTCTGGGCCGCACGCGCGCTACACTGATGTATTCAACGAGTATATAGCCTTGGCCGACAGGCCCGGGTAATCTTGGGAAATTTCATCGTGATGGGGATAGATCATTGCAATTGTTGGTCTTCAACGAGGAATGCCTAGTAAGCGCGAGTCATCAGCTCGCGTTGACTACGTCCCTGCCCTTTGTACACACC criterion=fanout-score sequence-density=0.22 sequence-density-rank=18 fanout-score=13.34 fanout-score-rank=1 prefix-density=2.38 prefix-fanout=1.2 sequence=ACGGTATCTGATCGTCTTCGAGCCCCCAACTTTCGTTCTTGATTAATGAAAACATCCTTGGCAAATGCTTTCGCAGTTGTTCGTCTTTCATAAATCCAAGAATTTCACCTCTGACTATGAAATACGAATGCCCCCGACTGTCCCTATTAATCATTACTCCGATCCCGAAGGCCAACACAATAGGACCGGAATCCTATGATGTTATCCCATGCTAATGTATCCAGAGCGATGGCTTGCTTTGAGCACTCTAATTTCTTCAAAGTAACGATGCCGGAGGCACGACCCGGCCAATTAAGGCTAGGAGCGCATCGCCGGCTGAAGGGTCGAGTAGGTCGGTGCTCGCCGTGAGGCGGACCGGCCGACCCGGCCCAAAGTCCAACTACGAGCTTTTTAACTGCAACAACTTAAATATACGCTATTGGAGCTGGAATTACCGCGGCT SRR6257530 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 07 09:02:08 Started mapping on | Dec 07 09:02:09 Finished on | Dec 07 09:03:09 Mapping speed, Million of reads per hour | 738.16 Number of input reads | 12302746 Average input read length | 274 UNIQUE READS: Uniquely mapped reads number | 3163256 Uniquely mapped reads % | 25.71% Average mapped length | 285.27 Number of splices: Total | 330053 Number of splices: Annotated (sjdb) | 239933 Number of splices: GT/AG | 258917 Number of splices: GC/AG | 4799 Number of splices: AT/AC | 1049 Number of splices: Non-canonical | 65288 Mismatch rate per base, % | 0.17% Deletion rate per base | 0.01% Deletion average length | 1.52 Insertion rate per base | 0.00% Insertion average length | 1.87 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 5608629 % of reads mapped to multiple loci | 45.59% Number of reads mapped to too many loci | 689071 % of reads mapped to too many loci | 5.60% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 5.34% % of reads unmapped: other | 17.76% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 3535943 3535943 3535943 N_multimapping 5608629 5608629 5608629 N_noFeature 2540115 3056071 2628287 N_ambiguous 47695 5973 25149 UnstrandedReadsAssigned:575446 PositiveStrandReadsAssigned:101212 NegativeStrandReadsAssigned:509820 Dataset is classified negative stranded MeadianReadLen=150 20thPercentileLength=121 echo kmer=117 SRR6257530 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: SRR6257530-trimmed-pair1.fastq SRR6257530-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 12,302,746 reads, 2,188,674 reads pseudoaligned [quant] estimated average fragment length: 162.182 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 940 rounds 52973 SRR6257530.ke.tsv 35125 SRR6257530.se.tsv 88098 total ==> SRR6257530.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 774.965 0.218669 0.0310799 PNS24247 1044 882.818 0 0 PNS24249 1928 1766.82 1.78133 0.111052 PNS24246 1044 882.818 0 0 PNS24248 1044 882.818 0 0 PNS24244 1471 1309.82 0 0 PNS24243 293 137.835 0 0 KQK14069 1603 1441.82 99.544 7.60463 KQK14071 474 313.689 6.49735 2.28144 ==> SRR6257530.se.tsv <== BRADI_1g14170v3 124 BRADI_1g53295v3 0 BRADI_1g59795v3 1 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 13 BRADI_1g74790v3 1 BRADI_1g09890v3 0 BRADI_1g77505v3 2 BRADI_1g48960v3 0 SRR6257530 completed mapping pipeline successfully