Starting /dee2/code/volunteer_pipeline.sh SRR6793147 current disk space = 3089623457792 free memory = 1581064024 SRR6793147 SRAfilesize a6707d2e69197eb20515fdd50a79d7e6 SRR6793147.sra SRR6793147.sra file validated SRR6793147 is single end SRR6793147 is conventional basespace SRR6793147 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR6793147_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 48 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 31.52 32.0 32.0 32.0 32.0 32.0 2 31.63225 32.0 32.0 32.0 32.0 32.0 3 31.64375 32.0 32.0 32.0 32.0 32.0 4 31.70175 32.0 32.0 32.0 32.0 32.0 5 31.69275 32.0 32.0 32.0 32.0 32.0 6 35.218 36.0 36.0 36.0 36.0 36.0 7 35.3785 36.0 36.0 36.0 36.0 36.0 8 35.36025 36.0 36.0 36.0 36.0 36.0 9 35.351 36.0 36.0 36.0 36.0 36.0 10-14 35.3447 36.0 36.0 36.0 36.0 36.0 15-19 35.36405 36.0 36.0 36.0 36.0 36.0 20-24 35.292350000000006 36.0 36.0 36.0 36.0 36.0 25-29 35.285849999999996 36.0 36.0 36.0 36.0 36.0 30-34 35.24745 36.0 36.0 36.0 36.0 36.0 35-39 35.14335 36.0 36.0 36.0 36.0 36.0 40-44 35.18495 36.0 36.0 36.0 36.0 36.0 45-49 35.1447 36.0 36.0 36.0 36.0 36.0 50-54 35.098150000000004 36.0 36.0 36.0 36.0 36.0 55-59 35.00150000000001 36.0 36.0 36.0 36.0 36.0 60-64 34.9137 36.0 36.0 36.0 34.4 36.0 65-69 34.78495 36.0 36.0 36.0 32.0 36.0 70-74 34.759249999999994 36.0 36.0 36.0 32.0 36.0 75-79 34.69584999999999 36.0 36.0 36.0 32.0 36.0 80-84 34.5271 36.0 36.0 36.0 32.0 36.0 85-89 34.63075 36.0 36.0 36.0 32.0 36.0 90-94 34.508950000000006 36.0 36.0 36.0 32.0 36.0 95-99 34.4073 36.0 36.0 36.0 32.0 36.0 100-104 34.44805 36.0 36.0 36.0 32.0 36.0 105-109 34.1831 36.0 36.0 36.0 32.0 36.0 110-114 34.219800000000006 36.0 36.0 36.0 31.0 36.0 115-119 34.14855 36.0 36.0 36.0 32.0 36.0 120-124 34.15555 36.0 36.0 36.0 32.0 36.0 125-129 33.899350000000005 36.0 36.0 36.0 29.0 36.0 130-134 33.8789 36.0 34.4 36.0 29.0 36.0 135-139 33.31545 36.0 32.0 36.0 27.0 36.0 140-144 33.31865 36.0 32.0 36.0 27.0 36.0 145-149 32.665049999999994 36.0 32.0 36.0 27.0 36.0 150-151 30.603 34.0 29.5 36.0 20.5 36.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 17 1.0 18 2.0 19 0.0 20 2.0 21 1.0 22 0.0 23 7.0 24 11.0 25 15.0 26 23.0 27 39.0 28 43.0 29 68.0 30 77.0 31 117.0 32 169.0 33 260.0 34 746.0 35 2419.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 24.625 11.875 14.025000000000002 49.475 2 22.45 19.2 33.7 24.65 3 22.8 24.325 22.325 30.55 4 29.049999999999997 27.800000000000004 17.2 25.95 5 26.974999999999998 31.424999999999997 21.5 20.1 6 21.951831409934773 33.14099347717009 22.17762167586553 22.729553437029605 7 19.55 16.7 40.35 23.400000000000002 8 23.825 18.15 29.325000000000003 28.7 9 23.150000000000002 20.525 31.1 25.224999999999998 10-14 23.535 26.91 25.165 24.39 15-19 24.385 25.81 27.575 22.23 20-24 24.0 26.200000000000003 26.75 23.05 25-29 24.065 26.1 24.395 25.44 30-34 23.095 24.98 26.115 25.81 35-39 23.955000000000002 25.965 25.224999999999998 24.855 40-44 23.419999999999998 25.55 26.595000000000002 24.435000000000002 45-49 23.93 26.229999999999997 26.090000000000003 23.75 50-54 23.64 26.935 26.465 22.96 55-59 23.119999999999997 26.419999999999998 27.084999999999997 23.375 60-64 23.375 25.169999999999998 27.295 24.16 65-69 23.880000000000003 26.029999999999998 27.12 22.97 70-74 23.635 26.029999999999998 25.96 24.375 75-79 24.01740174017402 26.292629262926294 25.472547254725477 24.217421742174217 80-84 23.747124137241173 25.437631289386815 26.09782934880464 24.71741522456737 85-89 23.727118135440634 26.79803941182355 26.257877363208966 23.21696508952686 90-94 24.972497249724974 26.072607260726073 25.70757075707571 23.24732473247325 95-99 23.373180613214625 26.159155704496573 27.35957585154804 23.108087830740757 100-104 24.275 26.634999999999998 26.245 22.845 105-109 23.566496547583306 25.682978084659265 27.549284499149408 23.201240868608025 110-114 23.951975987993997 26.718359179589797 25.812906453226613 23.516758379189596 115-119 23.70566755039768 26.626982141963886 26.006703016357363 23.660647291281077 120-124 24.387438743874387 26.2976297629763 25.587558755875587 23.72737273727373 125-129 23.655106840814693 27.603462943501977 24.425761897612972 24.31566831807036 130-134 24.14603650912728 26.571642910727682 25.276319079769944 24.006001500375092 135-139 24.34826119589692 27.805854390793094 24.49337002752064 23.35251438578934 140-144 25.60792554788352 26.928850195136594 23.716601621134796 23.746622635845092 145-149 25.377537753775375 27.442744274427444 22.542254225422543 24.63746374637464 150-151 23.705278959219413 29.246935201401055 22.42932199149362 24.618463847885916 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 2.0 1 1.0 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 0.5 17 0.5 18 0.0 19 0.0 20 0.5 21 0.5 22 0.0 23 0.0 24 1.0 25 1.0 26 3.0 27 4.5 28 2.0 29 2.5 30 4.0 31 7.0 32 9.0 33 8.5 34 20.5 35 46.5 36 75.5 37 92.0 38 96.5 39 104.5 40 104.5 41 109.5 42 138.5 43 155.5 44 187.0 45 217.5 46 217.0 47 232.0 48 222.5 49 195.0 50 192.5 51 193.0 52 174.0 53 166.5 54 153.0 55 133.0 56 136.5 57 147.0 58 119.0 59 68.5 60 53.0 61 44.0 62 30.0 63 21.0 64 13.0 65 8.0 66 9.0 67 11.0 68 15.5 69 17.5 70 12.5 71 6.5 72 4.0 73 3.5 74 3.0 75 1.0 76 0.5 77 0.0 78 1.0 79 1.0 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 0.5 >>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 0.35000000000000003 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 0.01 80-84 0.03 85-89 0.03 90-94 0.01 95-99 0.034999999999999996 100-104 0.0 105-109 0.06999999999999999 110-114 0.05 115-119 0.045 120-124 0.01 125-129 0.08499999999999999 130-134 0.025 135-139 0.075 140-144 0.06999999999999999 145-149 0.01 150-151 0.075 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 75.02499999999999 #Duplication Level Percentage of deduplicated Percentage of total 1 87.30423192269244 65.5 2 6.2979006997667435 9.45 3 2.3658780406531155 5.325 4 1.266244585138287 3.8 5 1.13295568143952 4.25 6 0.46651116294568473 2.1 7 0.33322225924691773 1.7500000000000002 8 0.16661112962345886 1.0 9 0.19993335554815062 1.35 >10 0.46651116294568473 5.475 >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 CCCGACTGTCCCTGTTAATCATTACTCCGATCCCGAAGGCCAACACAATA 47 1.175 No Hit CAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGG 23 0.575 No Hit CGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCT 18 0.44999999999999996 No Hit CGCGGCTGCTGGCACCAGACTTGCCCTCCAATGGATCCTCGTTAAGGGAT 15 0.375 No Hit CTCAAACTTCCTTGGCCTGGAAGGCCATAGTCCCTCTAAGAAGCTGGCCG 14 0.35000000000000003 No Hit CCAGAACCCAAAAACTTTGATTTCTCATAAGGTGCTGGCGGAGTCCTAAA 13 0.325 No Hit CCAGGTCCAGACATAGTAAGGATTGACAGACTGAGAGCTCTTTCTTGATT 13 0.325 No Hit GCCAGTAGTCATATGCTTGTCTCAAAGATTAAGCCATGCATGTGTAAGTA 13 0.325 No Hit CTGCTGCCTTCCTTGGATGTGGTAGCCGTTTCTCAGGCTCCCTCTCCGGA 12 0.3 No Hit CCCAACTTTCGTTCTTGATTAATGAAAACATCCTTGGCAAATGCTTTCGC 11 0.27499999999999997 No Hit GCCGTTCTTAGTTGGTGGAGCGATTTGTCTGGTTAATTCCGTTAACGAAC 10 0.25 No Hit GTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCAT 10 0.25 No Hit CCAACTTTCGTTCTTGATTAATGAAAACATCCTTGGCAAATGCTTTCGCA 10 0.25 No Hit CTGCCAGTAGTCATATGCTTGTCTCAAAGATTAAGCCATGCATGTGTAAG 10 0.25 No Hit CCGACTGTCCCTGTTAATCATTACTCCGATCCCGAAGGCCAACACAATAG 9 0.22499999999999998 No Hit CCCGTGTCAGGATTGGGTAATTTGCGCGCCTGCTGCCTTCCTTGGATGTG 9 0.22499999999999998 No Hit CGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCA 9 0.22499999999999998 No Hit CAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGAATTCCT 9 0.22499999999999998 No Hit ACCAGGTCCAGACATAGTAAGGATTGACAGACTGAGAGCTCTTTCTTGAT 9 0.22499999999999998 No Hit CTTAGATGTTCTGGGCCGCACGCGCGCTACACTGATGTATTCAACGAGTC 9 0.22499999999999998 No Hit CAACTTTCGTTCTTGATTAATGAAAACATCCTTGGCAAATGCTTTCGCAG 8 0.2 No Hit CAGGTCCAGACATAGTAAGGATTGACAGACTGAGAGCTCTTTCTTGATTC 8 0.2 No Hit CCCCGACTGTCCCTGTTAATCATTACTCCGATCCCGAAGGCCAACACAAT 8 0.2 No Hit CAACTTTCGATGGTAGGATAGAGGCCTACCATGGTGGTGACGGGTGACGG 8 0.2 No Hit CGCGCCTGCTGCCTTCCTTGGATGTGGTAGCCGTTTCTCAGGCTCCCTCT 8 0.2 No Hit CTTACCAGGTCCAGACATAGTAAGGATTGACAGACTGAGAGCTCTTTCTT 7 0.17500000000000002 No Hit CCGGAATCGAACCCTAATTCTCCGTCACCCGTCACCACCATGGTAGGCCT 7 0.17500000000000002 No Hit CGTCGAGTTATCATGAATCATCAGAGCAACGGGCAGAGCCCGCGTCGACC 7 0.17500000000000002 No Hit CGAGACCTCAGCCTGCTAACTAGCTATGCGGAGGTGACCCTCCGCGGCCA 7 0.17500000000000002 No Hit TAAGGATTGACAGACTGAGAGCTCTTTCTTGATTCTATGGGTGGTGGTGC 7 0.17500000000000002 No Hit GTCGGCATCGTTTATGGTTGAGACTAGGACGGTATCTGATCGTCTTCGAG 7 0.17500000000000002 No Hit CTGTGATGCCCTTAGATGTTCTGGGCCGCACGCGCGCTACACTGATGTAT 7 0.17500000000000002 No Hit TGAGAAACGGCTACCACATCCAAGGAAGGCAGCAGGCGCGCAAATTACCC 7 0.17500000000000002 No Hit GTCAGGATTGGGTAATTTGCGCGCCTGCTGCCTTCCTTGGATGTGGTAGC 7 0.17500000000000002 No Hit CTTCCGTCAATTCCTTTAAGTTTCAGCCTTGCGACCATACTCCCCCCAGA 7 0.17500000000000002 No Hit CTCTGACTATGAAATACGAATGCCCCCGACTGTCCCTGTTAATCATTACT 6 0.15 No Hit CCCCAACTTTCGTTCTTGATTAATGAAAACATCCTTGGCAAATGCTTTCG 6 0.15 No Hit CTCCGTCACCCGTCACCACCATGGTAGGCCTCTATCCTACCATCGAAAGT 6 0.15 No Hit GGCCGTTCTTAGTTGGTGGAGCGATTTGTCTGGTTAATTCCGTTAACGAA 6 0.15 No Hit GTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACT 6 0.15 No Hit CGTCAATTCCTTTAAGTTTCAGCCTTGCGACCATACTCCCCCCAGAACCC 6 0.15 No Hit CCTGCCAGTAGTCATATGCTTGTCTCAAAGATTAAGCCATGCATGTGTAA 6 0.15 No Hit CTGGAAGGGACGCATTTATTAGATAAAAGGTCGACGCGGGCTCTGCCCGT 6 0.15 No Hit CGGCGATGCGCTCCTGGCCTTAACTGGCCGGGTCGTGCCTCCGGTGCTGT 6 0.15 No Hit GTCCGCCTCAGGTGTGCACCGGTCGCCTCGTCCCTTCTACCGGCGATGCG 6 0.15 No Hit TAAAAAGCTCGTAGTTGGACTTTGGGTTGGGTCGGCCGGTCCGCCTCAGG 6 0.15 No Hit CGACTGTCCCTGTTAATCATTACTCCGATCCCGAAGGCCAACACAATAGG 6 0.15 No Hit CTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATT 6 0.15 No Hit CGGCATCGTTTATGGTTGAGACTAGGACGGTATCTGATCGTCTTCGAGCC 6 0.15 No Hit CTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAAC 5 0.125 No Hit CTTGATTCTATGGGTGGTGGTGCATGGCCGTTCTTAGTTGGTGGAGCGAT 5 0.125 No Hit GTTGGACTTTGGGTTGGGTCGGCCGGTCCGCCTCAGGTGTGCACCGGTCG 5 0.125 No Hit GAAATTTCAAAGATTACCCGGGCCTGTCGGCCAAGGCTATAGACTCGTTG 5 0.125 No Hit CGAACAACTGCGAAAGCATTTGCCAAGGATGTTTTCATTAATCAAGAACG 5 0.125 No Hit CTCTAAGAAGCTGGCCGCGGAGGGTCACCTCCGCATAGCTAGTTAGCAGG 5 0.125 No Hit CCTCGCGGTACTTGTTTGCTATCGGTCTCTCGCCCGTATTTAGCCTTGGA 5 0.125 No Hit GCGCTCCTGGCCTTAACTGGCCGGGTCGTGCCTCCGGTGCTGTTACTTTG 5 0.125 No Hit CACGATGAAATTTCAAAGATTACCCGGGCCTGTCGGCCAAGGCTATAGAC 5 0.125 No Hit GGATAACATCATAGGATTTCGATCCTATTGTGTTGGCCTTCGGGATCGGA 5 0.125 No Hit TTCTCCGTCACCCGTCACCACCATGGTAGGCCTCTATCCTACCATCGAAA 5 0.125 No Hit CTTGCTTTGAGCACTCTAATTTCTTCAAAGTAACAGCACCGGAGGCACGA 5 0.125 No Hit CCGCGGCTGCTGGCACCAGACTTGCCCTCCAATGGATCCTCGTTAAGGGA 5 0.125 No Hit CCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAAT 5 0.125 No Hit CTTTGGGTTGGGTCGGCCGGTCCGCCTCAGGTGTGCACCGGTCGCCTCGT 5 0.125 No Hit CAAAGATTAAGCCATGCATGTGTAAGTATGAACTAATTCAGACTGTGAAA 5 0.125 No Hit GTCGCCAGCACGAAGGCCGTGCGATCCGTCGAGTTATCATGAATCATCAG 5 0.125 No Hit GTTAATCATTACTCCGATCCCGAAGGCCAACACAATAGGATCGAAATCCT 5 0.125 No Hit CGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACT 5 0.125 No Hit CTGACTATGAAATACGAATGCCCCCGACTGTCCCTGTTAATCATTACTCC 5 0.125 No Hit GTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTA 5 0.125 No Hit CATCATTCAAATTTCTGCCCTATCAACTTTCGATGGTAGGATAGAGGCCT 5 0.125 No Hit TGCTGCCTTCCTTGGATGTGGTAGCCGTTTCTCAGGCTCCCTCTCCGGAA 5 0.125 No Hit CCGGTCGCCTCGTCCCTTCTACCGGCGATGCGCTCCTGGCCTTAACTGGC 5 0.125 No Hit CCCAGAACCCAAAAACTTTGATTTCTCATAAGGTGCTGGCGGAGTCCTAA 5 0.125 No Hit TGCCAGTAGTCATATGCTTGTCTCAAAGATTAAGCCATGCATGTGTAAGT 5 0.125 No Hit GTCATATGCTTGTCTCAAAGATTAAGCCATGCATGTGTAAGTATGAACTA 5 0.125 No Hit CGAGTCTATAGCCTTGGCCGACAGGCCCGGGTAATCTTTGAAATTTCATC 5 0.125 No Hit CTCAGGTGTGCACCGGTCGCCTCGTCCCTTCTACCGGCGATGCGCTCCTG 5 0.125 No Hit CCAGTAGTCATATGCTTGTCTCAAAGATTAAGCCATGCATGTGTAAGTAT 5 0.125 No Hit CTCGTCCCTTCTACCGGCGATGCGCTCCTGGCCTTAACTGGCCGGGTCGT 5 0.125 No Hit GTCCAGACATAGTAAGGATTGACAGACTGAGAGCTCTTTCTTGATTCTAT 5 0.125 No Hit GTCGAGTTATCATGAATCATCAGAGCAACGGGCAGAGCCCGCGTCGACCT 5 0.125 No Hit GTTTATGGTTGAGACTAGGACGGTATCTGATCGTCTTCGAGCCCCCAACT 5 0.125 No Hit >>END_MODULE >>Adapter Content warn #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 0.0125 0.0 0.0 0.0 0.0 42-43 0.025 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 0.025 0.0 0.0 0.0 0.0 56-57 0.025 0.0 0.0 0.0 0.0 58-59 0.025 0.0 0.0 0.0 0.0 60-61 0.025 0.0 0.0 0.0 0.0 62-63 0.025 0.0 0.0 0.0 0.0 64-65 0.025 0.0 0.0 0.0 0.0 66-67 0.025 0.0 0.0 0.0 0.0 68-69 0.025 0.0 0.0 0.0 0.0 70-71 0.025 0.0 0.0 0.0 0.0 72-73 0.05 0.0 0.0 0.0 0.0 74-75 0.075 0.0 0.0 0.0 0.0 76-77 0.1125 0.0 0.0 0.0 0.0 78-79 0.125 0.0 0.0 0.0 0.0 80-81 0.125 0.0 0.0 0.0 0.0 82-83 0.15 0.0 0.0 0.0 0.0 84-85 0.1875 0.0 0.0 0.0 0.0 86-87 0.21250000000000002 0.0 0.0 0.0 0.0 88-89 0.2875 0.0 0.0 0.0 0.0 90-91 0.3125 0.0 0.0 0.0 0.0 92-93 0.35 0.0 0.0 0.0 0.0 94-95 0.375 0.0 0.0 0.0 0.0 96-97 0.4375 0.0 0.0 0.0 0.0 98-99 0.4875 0.0 0.0 0.0 0.0 100-101 0.6125 0.0 0.0 0.0 0.0 102-103 0.6875 0.0 0.0 0.0 0.0 104-105 0.7625 0.0 0.0 0.0 0.0 106-107 0.95 0.0 0.0 0.0 0.0 108-109 1.275 0.0 0.0 0.0 0.0 110-111 1.525 0.0 0.0 0.0 0.0 112-113 1.8 0.0 0.0 0.0 0.0 114-115 2.075 0.0 0.0 0.0 0.0 116-117 2.5125 0.0 0.0 0.0 0.0 118-119 2.9000000000000004 0.0 0.0 0.0 0.0 120-121 3.25 0.0 0.0 0.0 0.0 122-123 3.8625000000000003 0.0 0.0 0.0 0.0 124-125 4.574999999999999 0.0 0.0 0.0 0.0 126-127 5.199999999999999 0.0 0.0 0.0 0.0 128-129 5.75 0.0 0.0 0.0 0.0 130-131 6.3 0.0 0.0 0.0 0.0 132-133 7.225 0.0 0.0 0.0 0.0 134-135 8.05 0.0 0.0 0.0 0.0 136-137 8.85 0.0 0.0 0.0 0.0 138-139 9.7 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GCTGGCA 10 0.006830828 145.0 8 CTGGCAC 10 0.006830828 145.0 9 GTCCTCA 10 0.006830828 145.0 6 >>END_MODULE Rejected 1815038 READS because READLEN < 1 Read 1815038 spots for SRR6793147.sra Written 1815038 spots for SRR6793147.sra Rejected 1815038 READS because READLEN < 1 Read 1815038 spots for SRR6793147.sra Written 1815038 spots for SRR6793147.sra Rejected 1815038 READS because READLEN < 1 Read 1815038 spots for SRR6793147.sra Written 1815038 spots for SRR6793147.sra Rejected 1815038 READS because READLEN < 1 Read 1815038 spots for SRR6793147.sra Written 1815038 spots for SRR6793147.sra Rejected 1815038 READS because READLEN < 1 Read 1815038 spots for SRR6793147.sra Written 1815038 spots for SRR6793147.sra Rejected 1815038 READS because READLEN < 1 Read 1815038 spots for SRR6793147.sra Written 1815038 spots for SRR6793147.sra Rejected 1815038 READS because READLEN < 1 Read 1815038 spots for SRR6793147.sra Written 1815038 spots for SRR6793147.sra Rejected 1815038 READS because READLEN < 1 Read 1815038 spots for SRR6793147.sra Written 1815038 spots for SRR6793147.sra Rejected 1815038 READS because READLEN < 1 Read 1815038 spots for SRR6793147.sra Written 1815038 spots for SRR6793147.sra Rejected 1815038 READS because READLEN < 1 Read 1815038 spots for SRR6793147.sra Written 1815038 spots for SRR6793147.sra Rejected 1815038 READS because READLEN < 1 Read 1815038 spots for SRR6793147.sra Written 1815038 spots for SRR6793147.sra Rejected 1815042 READS because READLEN < 1 Read 1815042 spots for SRR6793147.sra Written 1815042 spots for SRR6793147.sra Rejected 1815038 READS because READLEN < 1 Read 1815038 spots for SRR6793147.sra Written 1815038 spots for SRR6793147.sra Rejected 1815038 READS because READLEN < 1 Read 1815038 spots for SRR6793147.sra Written 1815038 spots for SRR6793147.sra Rejected 1815038 READS because READLEN < 1 Read 1815038 spots for SRR6793147.sra Written 1815038 spots for SRR6793147.sra Rejected 1815038 READS because READLEN < 1 Read 1815038 spots for SRR6793147.sra Written 1815038 spots for SRR6793147.sra Rejected 1815038 READS because READLEN < 1 Read 1815038 spots for SRR6793147.sra Written 1815038 spots for SRR6793147.sra Rejected 1815038 READS because READLEN < 1 Read 1815038 spots for SRR6793147.sra Written 1815038 spots for SRR6793147.sra Rejected 1815038 READS because READLEN < 1 Read 1815038 spots for SRR6793147.sra Written 1815038 spots for SRR6793147.sra Rejected 1815038 READS because READLEN < 1 Read 1815038 spots for SRR6793147.sra Written 1815038 spots for SRR6793147.sra SRR ids: ['SRR6793147.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_8fb4zgsz SRR6793147.sra spots: 36300764 blocks: [[1, 1815038], [1815039, 3630076], [3630077, 5445114], [5445115, 7260152], [7260153, 9075190], [9075191, 10890228], [10890229, 12705266], [12705267, 14520304], [14520305, 16335342], [16335343, 18150380], [18150381, 19965418], [19965419, 21780456], [21780457, 23595494], [23595495, 25410532], [25410533, 27225570], [27225571, 29040608], [29040609, 30855646], [30855647, 32670684], [32670685, 34485722], [34485723, 36300764]] SRR6793147 file size 12279437 SRR6793147 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 SRR6793147 SRR6793147_1.fastq Input file: SRR6793147_1.fastq trimmed: SRR6793147-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -- maximum error ratio allowed (-r): 0.100 -- maximum indel error ratio allowed (-d): 0.030 -- end quality threshold (-q): 10 -- minimum read length allowed after trimming (-l): 18 -- file format (-f): Sanger/Illumina 1.8+ FASTQ -- minimum overlap length for adapter detection (-k): inf -- number of concurrent threads (-t): 20 Thu Feb 13 14:34:38 2025 >> started Thu Feb 13 14:35:02 2025 >> done (23.732s) 36300764 reads processed; of these: 2786 ( 0.01%) short reads filtered out after trimming by size control 424 ( 0.00%) empty reads filtered out after trimming by size control 36297554 (99.99%) reads available; of these: 1374128 ( 3.79%) trimmed reads available after processing 34923426 (96.21%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 161 0.00% 19 200 0.00% 20 213 0.00% 21 215 0.00% 22 259 0.00% 23 273 0.00% 24 308 0.00% 25 378 0.00% 26 424 0.00% 27 467 0.00% 28 480 0.00% 29 525 0.00% 30 606 0.00% 31 616 0.00% 32 654 0.00% 33 645 0.00% 34 708 0.00% 35 895 0.00% 36 918 0.00% 37 838 0.00% 38 980 0.00% 39 845 0.00% 40 974 0.00% 41 1129 0.00% 42 929 0.00% 43 1073 0.00% 44 1094 0.00% 45 1062 0.00% 46 1178 0.00% 47 1151 0.00% 48 1148 0.00% 49 1273 0.00% 50 1182 0.00% 51 1323 0.00% 52 1261 0.00% 53 1335 0.00% 54 1374 0.00% 55 1490 0.00% 56 1500 0.00% 57 1619 0.00% 58 1627 0.00% 59 2100 0.01% 60 1889 0.01% 61 1929 0.01% 62 1934 0.01% 63 1816 0.01% 64 1844 0.01% 65 1699 0.00% 66 1763 0.00% 67 1783 0.00% 68 1798 0.00% 69 1703 0.00% 70 1826 0.01% 71 2284 0.01% 72 2314 0.01% 73 2529 0.01% 74 2505 0.01% 75 2810 0.01% 76 2782 0.01% 77 2849 0.01% 78 3050 0.01% 79 3131 0.01% 80 3532 0.01% 81 3890 0.01% 82 4170 0.01% 83 4504 0.01% 84 4944 0.01% 85 5408 0.01% 86 5385 0.01% 87 5862 0.02% 88 6374 0.02% 89 6990 0.02% 90 7884 0.02% 91 9151 0.03% 92 11067 0.03% 93 12339 0.03% 94 12815 0.04% 95 14115 0.04% 96 15571 0.04% 97 17487 0.05% 98 19071 0.05% 99 21455 0.06% 100 21709 0.06% 101 25195 0.07% 102 28465 0.08% 103 31342 0.09% 104 34774 0.10% 105 35442 0.10% 106 38124 0.11% 107 43014 0.12% 108 46173 0.13% 109 51549 0.14% 110 53342 0.15% 111 66052 0.18% 112 67170 0.19% 113 67333 0.19% 114 72570 0.20% 115 77764 0.21% 116 81906 0.23% 117 79454 0.22% 118 82864 0.23% 119 90317 0.25% 120 0 0.00% 121 0 0.00% 122 0 0.00% 123 0 0.00% 124 0 0.00% 125 0 0.00% 126 0 0.00% 127 0 0.00% 128 0 0.00% 129 0 0.00% 130 44 0.00% 131 168 0.00% 132 73 0.00% 133 111 0.00% 134 160 0.00% 135 168 0.00% 136 91 0.00% 137 18 0.00% 138 56 0.00% 139 8 0.00% 140 0 0.00% 141 16 0.00% 142 10 0.00% 143 422 0.00% 144 275 0.00% 145 24 0.00% 146 22 0.00% 147 170 0.00% 148 888 0.00% 149 610 0.00% 150 2553 0.01% 151 34923426 96.21% 36297554 reads passed initial QC criterion=sequence-density sequence-density=6.85 sequence-density-rank=1 fanout-score=46.88 fanout-score-rank=2 prefix-density=8.25 prefix-fanout=38.9 sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACTGACCAA criterion=fanout-score sequence-density=0.04 sequence-density-rank=9 fanout-score=48.06 fanout-score-rank=1 prefix-density=1.33 prefix-fanout=1.3 sequence=CGCATCGCCGGCCCCCATCCACTTCCCTCCCGACAATTTCAAGCACTCTTTGACTCTCTTTTCAAAGTCCTTTTCATCTTTCCCTCGCGGTACTTGTTTGCTATCGGTCTCTCGCCCGTATTTAGCCTTGGACGGAATTTACCGCCCGATTGGGGCTGCATTCCCAAACAACCCGACTCGCAGACAGCGCCTCGTGGTGCGGCAGGGTCCAGCCACGACGGGGCTCTCACCCTCTCCGGCGCCCCTTTCCAGGGGACTTGGGCCTGGTCCGCCGCTGAGGACGCTTCTCCAGACTACAATTCGGACGCCGCAGGCGCCAGATTCTCAAGCTGGGCATTTCCCGGTTCGCTCGCCGTTACTAGGGGAATCCTTGTAAGTTTCTTTTCCT Potential 3prime adapter identified. Now checking if in reference sequence Warning: gzbuffer added in zlib v1.2.3.5. Unable to change buffer size from default of 8192. 1 reads; of these: 1 (100.00%) were unpaired; of these: 1 (100.00%) aligned 0 times 0 (0.00%) aligned exactly 1 time 0 (0.00%) aligned >1 times 0.00% overall alignment rate Adapter seq not found in reference. Now shuffling file before clipping skewer v0.2.2 [April 4, 2016] COMMAND LINE: skewer -f sanger -l 18 -t 20 -x AGATCGGAAGAGCACACGTCTGAACTCCAGTCACTGACCAA -o SRR6793147 - Input file: STDIN trimmed: SRR6793147-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): AGATCGGAAGAGCACACGTCTGAACTCCAGTCACTGACCAA -- maximum error ratio allowed (-r): 0.100 -- maximum indel error ratio allowed (-d): 0.030 -- minimum read length allowed after trimming (-l): 18 -- file format (-f): Sanger/Illumina 1.8+ FASTQ -- minimum overlap length for adapter detection (-k): 3 -- number of concurrent threads (-t): 20 Thu Feb 13 14:36:25 2025 >> started Thu Feb 13 14:36:57 2025 >> done (31.590s) 25926824 reads processed; of these: 24 ( 0.00%) short reads filtered out after trimming by size control 8 ( 0.00%) empty reads filtered out after trimming by size control 25926792 (100.00%) reads available; of these: 3591449 (13.85%) trimmed reads available after processing 22335343 (86.15%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 119 0.00% 19 126 0.00% 20 155 0.00% 21 149 0.00% 22 182 0.00% 23 191 0.00% 24 223 0.00% 25 282 0.00% 26 302 0.00% 27 354 0.00% 28 342 0.00% 29 404 0.00% 30 452 0.00% 31 457 0.00% 32 471 0.00% 33 462 0.00% 34 533 0.00% 35 637 0.00% 36 649 0.00% 37 599 0.00% 38 710 0.00% 39 618 0.00% 40 691 0.00% 41 824 0.00% 42 680 0.00% 43 802 0.00% 44 801 0.00% 45 745 0.00% 46 832 0.00% 47 838 0.00% 48 820 0.00% 49 907 0.00% 50 866 0.00% 51 949 0.00% 52 937 0.00% 53 937 0.00% 54 999 0.00% 55 1098 0.00% 56 1070 0.00% 57 1146 0.00% 58 1145 0.00% 59 1538 0.01% 60 1334 0.01% 61 1408 0.01% 62 1383 0.01% 63 1297 0.01% 64 1309 0.01% 65 1274 0.00% 66 1270 0.00% 67 1270 0.00% 68 1300 0.01% 69 1195 0.00% 70 1311 0.01% 71 1652 0.01% 72 1702 0.01% 73 1819 0.01% 74 1853 0.01% 75 2048 0.01% 76 1997 0.01% 77 2085 0.01% 78 2152 0.01% 79 2291 0.01% 80 2572 0.01% 81 2724 0.01% 82 3023 0.01% 83 3311 0.01% 84 3574 0.01% 85 3873 0.01% 86 3836 0.01% 87 4227 0.02% 88 4554 0.02% 89 5078 0.02% 90 5877 0.02% 91 6646 0.03% 92 7935 0.03% 93 8738 0.03% 94 9282 0.04% 95 10161 0.04% 96 11212 0.04% 97 12554 0.05% 98 13698 0.05% 99 15468 0.06% 100 15509 0.06% 101 17976 0.07% 102 20322 0.08% 103 22478 0.09% 104 25042 0.10% 105 25530 0.10% 106 27497 0.11% 107 31071 0.12% 108 32855 0.13% 109 37295 0.14% 110 37817 0.15% 111 47226 0.18% 112 48360 0.19% 113 48261 0.19% 114 52097 0.20% 115 55651 0.21% 116 58579 0.23% 117 56101 0.22% 118 59007 0.23% 119 65820 0.25% 120 71079 0.27% 121 78734 0.30% 122 76011 0.29% 123 80093 0.31% 124 79893 0.31% 125 86769 0.33% 126 92706 0.36% 127 92857 0.36% 128 101425 0.39% 129 95681 0.37% 130 102448 0.40% 131 99377 0.38% 132 109091 0.42% 133 111308 0.43% 134 121679 0.47% 135 121297 0.47% 136 114428 0.44% 137 116184 0.45% 138 111790 0.43% 139 117818 0.45% 140 116877 0.45% 141 121552 0.47% 142 128636 0.50% 143 137534 0.53% 144 139992 0.54% 145 138176 0.53% 146 151250 0.58% 147 211582 0.82% 148 451806 1.74% 149 404 0.00% 150 1449 0.01% 151 21365037 82.41% criterion=sequence-density sequence-density=0.25 sequence-density-rank=1 fanout-score=2.03 fanout-score-rank=29 prefix-density=0.25 prefix-fanout=2.0 sequence=ACCATCTTTCGG criterion=fanout-score sequence-density=0.09 sequence-density-rank=22 fanout-score=113.16 fanout-score-rank=1 prefix-density=6.05 prefix-fanout=1.6 sequence=CAAAGATTACCTGGGCCTGTCGG Started job on | Feb 13 14:37:32 Started mapping on | Feb 13 14:37:32 Finished on | Feb 13 14:39:37 Mapping speed, Million of reads per hour | 1045.37 Number of input reads | 36297522 Average input read length | 147 UNIQUE READS: Uniquely mapped reads number | 15420019 Uniquely mapped reads % | 42.48% Average mapped length | 147.11 Number of splices: Total | 6094947 Number of splices: Annotated (sjdb) | 5925920 Number of splices: GT/AG | 5974518 Number of splices: GC/AG | 89580 Number of splices: AT/AC | 5600 Number of splices: Non-canonical | 25249 Mismatch rate per base, % | 0.56% Deletion rate per base | 0.03% Deletion average length | 2.61 Insertion rate per base | 0.02% Insertion average length | 2.68 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 2113652 % of reads mapped to multiple loci | 5.82% Number of reads mapped to too many loci | 17981756 % of reads mapped to too many loci | 49.54% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.66% % of reads unmapped: other | 0.50% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 18763851 18763851 18763851 N_multimapping 2113652 2113652 2113652 N_noFeature 1409626 8259582 8379664 N_ambiguous 264617 37047 37440 UnstrandedReadsAssigned:13745776 PositiveStrandReadsAssigned:7123390 NegativeStrandReadsAssigned:7002915 Dataset is classified unstranded MeadianReadLen=151 20thPercentileLength=151 echo kmer=147 SRR6793147 Starting Kallisto single end mapping to ensembl reference transcriptome. kmer=31 [quant] fragment length distribution is truncated gaussian with mean = 100, sd = 20 [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 single-end mode [quant] will process file 1: SRR6793147-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 36,297,522 reads, 28,151,741 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,039 rounds 52401 SRR6793147.ke.tsv 34699 SRR6793147.se.tsv 87100 total ==> SRR6793147.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1919 2294.6 59.4342 Potri.005G024800.1.v4.1 1035 936 434 23.0473 Potri.004G059700.1.v4.1 961 862 2 0.115326 Potri.007G009000.2.v4.1 1416 1317 0 0 Potri.003G141000.2.v4.1 2943 2844 948.463 16.5766 Potri.016G087400.1.v4.1 270 171 910 264.515 Potri.015G069301.1.v4.1 564 465 0 0 Potri.010G195200.1.v4.1 1773 1674 3256.98 96.7087 Potri.012G127500.1.v4.1 977 878 180 10.1902 ==> SRR6793147.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 26 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 254 Potri.001G212900.v4.1 4 Potri.001G182400.v4.1 0 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 89 Potri.001G416900.v4.1 3 Potri.001G452600.v4.1 1 SRR6793147 completed mapping pipeline successfully