Starting /dee2/code/volunteer_pipeline.sh SRR6793145 current disk space = 3089584783360 free memory = 1433127272 SRR6793145 SRAfilesize a74ab7d1a18891f4054911ca0636346e SRR6793145.sra SRR6793145.sra file validated SRR6793145 is single end SRR6793145 is conventional basespace SRR6793145 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR6793145_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 47 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 31.4955 32.0 32.0 32.0 32.0 32.0 2 31.5905 32.0 32.0 32.0 32.0 32.0 3 31.716 32.0 32.0 32.0 32.0 32.0 4 31.659 32.0 32.0 32.0 32.0 32.0 5 31.682 32.0 32.0 32.0 32.0 32.0 6 35.01425 36.0 36.0 36.0 36.0 36.0 7 35.361 36.0 36.0 36.0 36.0 36.0 8 35.36725 36.0 36.0 36.0 36.0 36.0 9 35.3495 36.0 36.0 36.0 36.0 36.0 10-14 35.3125 36.0 36.0 36.0 36.0 36.0 15-19 35.29915 36.0 36.0 36.0 36.0 36.0 20-24 35.215999999999994 36.0 36.0 36.0 36.0 36.0 25-29 35.13705 36.0 36.0 36.0 36.0 36.0 30-34 35.1948 36.0 36.0 36.0 36.0 36.0 35-39 35.09885 36.0 36.0 36.0 36.0 36.0 40-44 35.07705 36.0 36.0 36.0 36.0 36.0 45-49 35.044 36.0 36.0 36.0 36.0 36.0 50-54 35.030950000000004 36.0 36.0 36.0 36.0 36.0 55-59 34.94475 36.0 36.0 36.0 36.0 36.0 60-64 34.820750000000004 36.0 36.0 36.0 34.4 36.0 65-69 34.757600000000004 36.0 36.0 36.0 32.0 36.0 70-74 34.589299999999994 36.0 36.0 36.0 32.0 36.0 75-79 34.6202 36.0 36.0 36.0 32.0 36.0 80-84 34.42985 36.0 36.0 36.0 32.0 36.0 85-89 34.5812 36.0 36.0 36.0 32.0 36.0 90-94 34.41074999999999 36.0 36.0 36.0 32.0 36.0 95-99 34.33489999999999 36.0 36.0 36.0 32.0 36.0 100-104 34.37515 36.0 36.0 36.0 32.0 36.0 105-109 34.157650000000004 36.0 36.0 36.0 32.0 36.0 110-114 34.108799999999995 36.0 36.0 36.0 31.0 36.0 115-119 34.0726 36.0 36.0 36.0 32.0 36.0 120-124 34.0334 36.0 36.0 36.0 30.0 36.0 125-129 33.819700000000005 36.0 34.4 36.0 28.0 36.0 130-134 33.78365000000001 36.0 34.4 36.0 27.0 36.0 135-139 33.235850000000006 36.0 32.0 36.0 27.0 36.0 140-144 33.310449999999996 36.0 32.0 36.0 27.0 36.0 145-149 32.488150000000005 36.0 32.0 36.0 27.0 36.0 150-151 30.427625 34.0 29.5 36.0 20.5 36.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 18 1.0 19 4.0 20 1.0 21 4.0 22 6.0 23 7.0 24 12.0 25 15.0 26 24.0 27 34.0 28 60.0 29 68.0 30 101.0 31 130.0 32 153.0 33 270.0 34 706.0 35 2404.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 24.075 12.85 12.8 50.275000000000006 2 22.95 19.8 31.75 25.5 3 21.2 23.325000000000003 22.15 33.324999999999996 4 27.025 28.65 18.275 26.05 5 26.5 30.0 22.05 21.45 6 20.684448917966783 32.51132360342224 22.44589833920483 24.35832913940614 7 18.0 16.075 42.725 23.200000000000003 8 20.95 19.35 31.624999999999996 28.075 9 22.900000000000002 20.724999999999998 32.125 24.25 10-14 22.16 26.805 26.805 24.23 15-19 23.185 26.965 28.249999999999996 21.6 20-24 23.765 26.810000000000002 26.855 22.57 25-29 23.855 27.295 25.319999999999997 23.53 30-34 22.55 25.88 26.905 24.665 35-39 22.95 26.484999999999996 25.85 24.715 40-44 22.59 25.655 27.560000000000002 24.195 45-49 22.445 27.165 26.375 24.015 50-54 23.36 27.084999999999997 27.265 22.29 55-59 22.75 26.845000000000002 27.455000000000002 22.95 60-64 22.755 26.029999999999998 27.944999999999997 23.27 65-69 23.16 26.61 27.355 22.875 70-74 23.044999999999998 26.700000000000003 26.415 23.84 75-79 23.14615730786539 27.301365068253414 26.061303065153258 23.491174558727938 80-84 23.139255702280913 25.78531412565026 26.51060424169668 24.56482593037215 85-89 23.97959183673469 26.5906362545018 26.880752300920367 22.54901960784314 90-94 24.148451958185365 26.86440254088931 26.729355274346023 22.257790226579303 95-99 23.127720246135375 27.244984741607887 26.87478112962129 22.75251388263545 100-104 23.23 26.985 27.12 22.665 105-109 22.85557001301171 26.934240816735063 27.129416474827345 23.080772695425882 110-114 23.35134594215951 27.67437206044231 25.60792554788352 23.36635644951466 115-119 23.598879103282627 27.17674139311449 26.4111289031225 22.813250600480384 120-124 24.528679301895284 27.799169875481322 25.25378806821023 22.418362754413163 125-129 24.733390076603413 28.308216091723825 23.661943623892252 23.296450207780502 130-134 24.21468587434974 27.926170468187273 24.614845938375353 23.244297719087633 135-139 25.42551061273528 27.968562274729674 23.363035642771326 23.242891469763716 140-144 25.629347880486463 28.36194384665432 22.546419098143236 23.46228917471598 145-149 25.177553265979796 28.173452035610687 22.451735520656197 24.197259177753324 150-151 23.923923923923923 30.643143143143142 20.995995995995994 24.436936936936938 >>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 0.5 14 0.5 15 0.5 16 0.5 17 0.0 18 0.0 19 0.0 20 1.5 21 2.0 22 0.5 23 0.0 24 1.5 25 2.0 26 1.0 27 2.5 28 6.5 29 12.5 30 15.0 31 15.0 32 17.0 33 20.5 34 31.0 35 58.5 36 96.5 37 107.0 38 111.0 39 126.5 40 121.0 41 129.0 42 154.0 43 172.0 44 211.5 45 234.0 46 221.0 47 218.0 48 206.0 49 195.0 50 180.0 51 152.5 52 152.0 53 158.0 54 135.5 55 123.0 56 117.5 57 117.0 58 100.5 59 68.5 60 62.5 61 40.0 62 20.5 63 13.5 64 5.5 65 5.0 66 6.0 67 10.0 68 11.5 69 10.0 70 6.0 71 1.5 72 1.5 73 2.0 74 1.5 75 1.0 76 1.5 77 1.5 78 1.0 79 0.0 80 0.0 81 0.5 82 0.5 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 0.5 100 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 0.65 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 0.005 80-84 0.04 85-89 0.04 90-94 0.034999999999999996 95-99 0.055 100-104 0.0 105-109 0.09 110-114 0.06999999999999999 115-119 0.08 120-124 0.015 125-129 0.135 130-134 0.04 135-139 0.12 140-144 0.095 145-149 0.03 150-151 0.1 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 79.85 #Duplication Level Percentage of deduplicated Percentage of total 1 90.67000626174077 72.39999999999999 2 4.69630557294928 7.5 3 1.878522229179712 4.5 4 0.8766437069505322 2.8000000000000003 5 0.469630557294928 1.875 6 0.4383218534752661 2.1 7 0.18785222291797118 1.05 8 0.25046963055729493 1.6 9 0.06261740763932373 0.44999999999999996 >10 0.469630557294928 5.7250000000000005 >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 CCCGACTGTCCCTGTTAATCATTACTCCGATCCCGAAGGCCAACACAATA 35 0.8750000000000001 No Hit CGCGCCTGCTGCCTTCCTTGGATGTGGTAGCCGTTTCTCAGGCTCCCTCT 26 0.65 No Hit CCCAACTTTCGTTCTTGATTAATGAAAACATCCTTGGCAAATGCTTTCGC 21 0.525 No Hit CAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGG 18 0.44999999999999996 No Hit CGCCTGCTGCCTTCCTTGGATGTGGTAGCCGTTTCTCAGGCTCCCTCTCC 15 0.375 No Hit CGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCT 15 0.375 No Hit CCAACTTTCGTTCTTGATTAATGAAAACATCCTTGGCAAATGCTTTCGCA 14 0.35000000000000003 No Hit CTGCCAGTAGTCATATGCTTGTCTCAAAGATTAAGCCATGCATGTGTAAG 13 0.325 No Hit CAACTTTCGTTCTTGATTAATGAAAACATCCTTGGCAAATGCTTTCGCAG 11 0.27499999999999997 No Hit CTGCTGCCTTCCTTGGATGTGGTAGCCGTTTCTCAGGCTCCCTCTCCGGA 11 0.27499999999999997 No Hit CTTCCGTCAATTCCTTTAAGTTTCAGCCTTGCGACCATACTCCCCCCAGA 10 0.25 No Hit CCCCAACTTTCGTTCTTGATTAATGAAAACATCCTTGGCAAATGCTTTCG 10 0.25 No Hit CGCGGCTGCTGGCACCAGACTTGCCCTCCAATGGATCCTCGTTAAGGGAT 10 0.25 No Hit ACCAGGTCCAGACATAGTAAGGATTGACAGACTGAGAGCTCTTTCTTGAT 10 0.25 No Hit CCAGGTCCAGACATAGTAAGGATTGACAGACTGAGAGCTCTTTCTTGATT 10 0.25 No Hit CAAATTTCTGCCCTATCAACTTTCGATGGTAGGATAGAGGCCTACCATGG 9 0.22499999999999998 No Hit AGAAATTTGAATGATGCGTCGCCAGCACGAAGGCCGTGCGATCCGTCGAG 9 0.22499999999999998 No Hit GCCGTTCTTAGTTGGTGGAGCGATTTGTCTGGTTAATTCCGTTAACGAAC 8 0.2 No Hit CAAACCCCGACTTCTGGAAGGGACGCATTTATTAGATAAAAGGTCGACGC 8 0.2 No Hit CCCCGACTGTCCCTGTTAATCATTACTCCGATCCCGAAGGCCAACACAAT 8 0.2 No Hit CGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCA 8 0.2 No Hit CTCCAATGGATCCTCGTTAAGGGATTTAGATTGTACTCATTCCAATTACC 8 0.2 No Hit CAGGTCCAGACATAGTAAGGATTGACAGACTGAGAGCTCTTTCTTGATTC 8 0.2 No Hit GCGCCTGCTGCCTTCCTTGGATGTGGTAGCCGTTTCTCAGGCTCCCTCTC 8 0.2 No Hit GTTAATCATTACTCCGATCCCGAAGGCCAACACAATAGGATCGAAATCCT 8 0.2 No Hit GTCGCCTCGTCCCTTCTACCGGCGATGCGCTCCTGGCCTTAACTGGCCGG 7 0.17500000000000002 No Hit GCCTGCTGCCTTCCTTGGATGTGGTAGCCGTTTCTCAGGCTCCCTCTCCG 7 0.17500000000000002 No Hit CGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACT 7 0.17500000000000002 No Hit GTCTGTGATGCCCTTAGATGTTCTGGGCCGCACGCGCGCTACACTGATGT 7 0.17500000000000002 No Hit TGCTGCCTTCCTTGGATGTGGTAGCCGTTTCTCAGGCTCCCTCTCCGGAA 7 0.17500000000000002 No Hit GGAAGTTTGAGGCAATAACAGGTCTGTGATGCCCTTAGATGTTCTGGGCC 7 0.17500000000000002 No Hit CTTACCAGGTCCAGACATAGTAAGGATTGACAGACTGAGAGCTCTTTCTT 6 0.15 No Hit CGGCCTTCGTGCTGGCGACGCATCATTCAAATTTCTGCCCTATCAACTTT 6 0.15 No Hit CACGGCCTTCGTGCTGGCGACGCATCATTCAAATTTCTGCCCTATCAACT 6 0.15 No Hit GTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTA 6 0.15 No Hit TGAAATTTCAAAGATTACCCGGGCCTGTCGGCCAAGGCTATAGACTCGTT 6 0.15 No Hit GCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTC 6 0.15 No Hit CCCCCATCACGATGAAATTTCAAAGATTACCCGGGCCTGTCGGCCAAGGC 6 0.15 No Hit CTCAAAGATTAAGCCATGCATGTGTAAGTATGAACTAATTCAGACTGTGA 6 0.15 No Hit ATCACGATGAAATTTCAAAGATTACCCGGGCCTGTCGGCCAAGGCTATAG 6 0.15 No Hit GTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACT 6 0.15 No Hit GCTGCCTTCCTTGGATGTGGTAGCCGTTTCTCAGGCTCCCTCTCCGGAAT 6 0.15 No Hit GTCAATTCCTTTAAGTTTCAGCCTTGCGACCATACTCCCCCCAGAACCCA 6 0.15 No Hit CTCCGATCCCGAAGGCCAACACAATAGGATCGAAATCCTATGATGTTATC 6 0.15 No Hit CGGCATCGTTTATGGTTGAGACTAGGACGGTATCTGATCGTCTTCGAGCC 6 0.15 No Hit CCTGCCAGTAGTCATATGCTTGTCTCAAAGATTAAGCCATGCATGTGTAA 5 0.125 No Hit ATTTGCTACTCGGATAACCGTAGTAATTCTAGAGCTAATACGTGCAACAA 5 0.125 No Hit CTTGGATTTATGAAAGACGAACAACTGCGAAAGCATTTGCCAAGGATGTT 5 0.125 No Hit CTTAGATGTTCTGGGCCGCACGCGCGCTACACTGATGTATTCAACGAGTC 5 0.125 No Hit AGACGATCAGATACCGTCCTAGTCTCAACCATAAACGATGCCGACCAGGG 5 0.125 No Hit CCTTCCGTCAATTCCTTTAAGTTTCAGCCTTGCGACCATACTCCCCCCAG 5 0.125 No Hit CTCAAAGCAAGCCTACGCTCTGGATACATTAGCATGGGATAACATCATAG 5 0.125 No Hit CGTCGAGTTATCATGAATCATCAGAGCAACGGGCAGAGCCCGCGTCGACC 5 0.125 No Hit CGTAGTTGGACTTTGGGTTGGGTCGGCCGGTCCGCCTCAGGTGTGCACCG 5 0.125 No Hit CAACTTTCGATGGTAGGATAGAGGCCTACCATGGTGGTGACGGGTGACGG 5 0.125 No Hit CAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGAATTCCT 5 0.125 No Hit GACGGATCGCACGGCCTTCGTGCTGGCGACGCATCATTCAAATTTCTGCC 5 0.125 No Hit CTGAGAGCTCTTTCTTGATTCTATGGGTGGTGGTGCATGGCCGTTCTTAG 5 0.125 No Hit CTCAGGTGTGCACCGGTCGCCTCGTCCCTTCTACCGGCGATGCGCTCCTG 5 0.125 No Hit CAGAAATTTGAATGATGCGTCGCCAGCACGAAGGCCGTGCGATCCGTCGA 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 0.0 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 0.025 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 0.037500000000000006 0.0 0.0 0.0 0.0 62-63 0.075 0.0 0.0 0.0 0.0 64-65 0.075 0.0 0.0 0.0 0.0 66-67 0.075 0.0 0.0 0.0 0.0 68-69 0.075 0.0 0.0 0.0 0.0 70-71 0.0875 0.0 0.0 0.0 0.0 72-73 0.1 0.0 0.0 0.0 0.0 74-75 0.1 0.0 0.0 0.0 0.0 76-77 0.1 0.0 0.0 0.0 0.0 78-79 0.1 0.0 0.0 0.0 0.0 80-81 0.1 0.0 0.0 0.0 0.0 82-83 0.1125 0.0 0.0 0.0 0.0 84-85 0.1375 0.0 0.0 0.0 0.0 86-87 0.21250000000000002 0.0 0.0 0.0 0.0 88-89 0.2375 0.0 0.0 0.0 0.0 90-91 0.30000000000000004 0.0 0.0 0.0 0.0 92-93 0.3375 0.0 0.0 0.0 0.0 94-95 0.5125 0.0 0.0 0.0 0.0 96-97 0.6875 0.0 0.0 0.0 0.0 98-99 0.8999999999999999 0.0 0.0 0.0 0.0 100-101 1.1875 0.0 0.0 0.0 0.0 102-103 1.5499999999999998 0.0 0.0 0.0 0.0 104-105 2.0875 0.0 0.0 0.0 0.0 106-107 2.5125 0.0 0.0 0.0 0.0 108-109 2.9 0.0 0.0 0.0 0.0 110-111 3.375 0.0 0.0 0.0 0.0 112-113 4.275 0.0 0.0 0.0 0.0 114-115 5.0875 0.0 0.0 0.0 0.0 116-117 6.050000000000001 0.0 0.0 0.0 0.0 118-119 6.95 0.0 0.0 0.0 0.0 120-121 7.975 0.0 0.0 0.0 0.0 122-123 8.8125 0.0 0.0 0.0 0.0 124-125 9.850000000000001 0.0 0.0 0.0 0.0 126-127 11.1 0.0 0.0 0.0 0.0 128-129 12.5125 0.0 0.0 0.0 0.0 130-131 13.8125 0.0 0.0 0.0 0.0 132-133 15.05 0.0 0.0 0.0 0.0 134-135 17.012500000000003 0.0 0.0 0.0 0.0 136-137 18.6375 0.0 0.0 0.0 0.0 138-139 20.450000000000003 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Rejected 2060249 READS because READLEN < 1 Read 2060249 spots for SRR6793145.sra Written 2060249 spots for SRR6793145.sra Rejected 2060249 READS because READLEN < 1 Read 2060249 spots for SRR6793145.sra Written 2060249 spots for SRR6793145.sra Rejected 2060249 READS because READLEN < 1 Read 2060249 spots for SRR6793145.sra Written 2060249 spots for SRR6793145.sra Rejected 2060249 READS because READLEN < 1 Read 2060249 spots for SRR6793145.sra Written 2060249 spots for SRR6793145.sra Rejected 2060249 READS because READLEN < 1 Read 2060249 spots for SRR6793145.sra Written 2060249 spots for SRR6793145.sra Rejected 2060249 READS because READLEN < 1 Read 2060249 spots for SRR6793145.sra Written 2060249 spots for SRR6793145.sra Rejected 2060249 READS because READLEN < 1 Read 2060249 spots for SRR6793145.sra Written 2060249 spots for SRR6793145.sra Rejected 2060249 READS because READLEN < 1 Read 2060249 spots for SRR6793145.sra Written 2060249 spots for SRR6793145.sra Rejected 2060249 READS because READLEN < 1 Read 2060249 spots for SRR6793145.sra Written 2060249 spots for SRR6793145.sra Rejected 2060249 READS because READLEN < 1 Read 2060249 spots for SRR6793145.sra Written 2060249 spots for SRR6793145.sra Rejected 2060249 READS because READLEN < 1 Read 2060249 spots for SRR6793145.sra Written 2060249 spots for SRR6793145.sra Rejected 2060249 READS because READLEN < 1 Read 2060249 spots for SRR6793145.sra Written 2060249 spots for SRR6793145.sra Rejected 2060249 READS because READLEN < 1 Read 2060249 spots for SRR6793145.sra Written 2060249 spots for SRR6793145.sra Rejected 2060249 READS because READLEN < 1 Read 2060249 spots for SRR6793145.sra Written 2060249 spots for SRR6793145.sra Rejected 2060249 READS because READLEN < 1 Read 2060249 spots for SRR6793145.sra Written 2060249 spots for SRR6793145.sra Rejected 2060249 READS because READLEN < 1 Read 2060249 spots for SRR6793145.sra Written 2060249 spots for SRR6793145.sra Rejected 2060249 READS because READLEN < 1 Read 2060249 spots for SRR6793145.sra Written 2060249 spots for SRR6793145.sra Rejected 2060249 READS because READLEN < 1 Read 2060249 spots for SRR6793145.sra Written 2060249 spots for SRR6793145.sra Rejected 2060249 READS because READLEN < 1 Read 2060249 spots for SRR6793145.sra Written 2060249 spots for SRR6793145.sra Rejected 2060249 READS because READLEN < 1 Read 2060249 spots for SRR6793145.sra Written 2060249 spots for SRR6793145.sra SRR ids: ['SRR6793145.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_y6pe5j5k SRR6793145.sra spots: 41204980 blocks: [[1, 2060249], [2060250, 4120498], [4120499, 6180747], [6180748, 8240996], [8240997, 10301245], [10301246, 12361494], [12361495, 14421743], [14421744, 16481992], [16481993, 18542241], [18542242, 20602490], [20602491, 22662739], [22662740, 24722988], [24722989, 26783237], [26783238, 28843486], [28843487, 30903735], [30903736, 32963984], [32963985, 35024233], [35024234, 37084482], [37084483, 39144731], [39144732, 41204980]] SRR6793145 file size 13941315 SRR6793145 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 SRR6793145 SRR6793145_1.fastq Input file: SRR6793145_1.fastq trimmed: SRR6793145-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 14:36:48 2025 >> started Thu Feb 13 14:37:23 2025 >> done (35.013s) 41204980 reads processed; of these: 2687 ( 0.01%) short reads filtered out after trimming by size control 2050 ( 0.00%) empty reads filtered out after trimming by size control 41200243 (99.99%) reads available; of these: 3301368 ( 8.01%) trimmed reads available after processing 37898875 (91.99%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 113 0.00% 19 100 0.00% 20 115 0.00% 21 146 0.00% 22 162 0.00% 23 204 0.00% 24 232 0.00% 25 249 0.00% 26 259 0.00% 27 302 0.00% 28 322 0.00% 29 333 0.00% 30 378 0.00% 31 393 0.00% 32 433 0.00% 33 461 0.00% 34 462 0.00% 35 565 0.00% 36 555 0.00% 37 631 0.00% 38 669 0.00% 39 679 0.00% 40 696 0.00% 41 773 0.00% 42 703 0.00% 43 774 0.00% 44 804 0.00% 45 799 0.00% 46 903 0.00% 47 873 0.00% 48 871 0.00% 49 909 0.00% 50 896 0.00% 51 922 0.00% 52 866 0.00% 53 928 0.00% 54 931 0.00% 55 1095 0.00% 56 1072 0.00% 57 1210 0.00% 58 1178 0.00% 59 1551 0.00% 60 1458 0.00% 61 1417 0.00% 62 1539 0.00% 63 1402 0.00% 64 1362 0.00% 65 1328 0.00% 66 1374 0.00% 67 1513 0.00% 68 1685 0.00% 69 1725 0.00% 70 1851 0.00% 71 2302 0.01% 72 2450 0.01% 73 2851 0.01% 74 3060 0.01% 75 3503 0.01% 76 3786 0.01% 77 3829 0.01% 78 4431 0.01% 79 4743 0.01% 80 5763 0.01% 81 6460 0.02% 82 7712 0.02% 83 8788 0.02% 84 10505 0.03% 85 10762 0.03% 86 11915 0.03% 87 13048 0.03% 88 14775 0.04% 89 17178 0.04% 90 19618 0.05% 91 22720 0.06% 92 27607 0.07% 93 31083 0.08% 94 34356 0.08% 95 37837 0.09% 96 41819 0.10% 97 45760 0.11% 98 51305 0.12% 99 60108 0.15% 100 59923 0.15% 101 69477 0.17% 102 77625 0.19% 103 87028 0.21% 104 92785 0.23% 105 94884 0.23% 106 103005 0.25% 107 112593 0.27% 108 119499 0.29% 109 130039 0.32% 110 134899 0.33% 111 160582 0.39% 112 167504 0.41% 113 165491 0.40% 114 178912 0.43% 115 185863 0.45% 116 200333 0.49% 117 191262 0.46% 118 194715 0.47% 119 215075 0.52% 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 53 0.00% 131 205 0.00% 132 85 0.00% 133 135 0.00% 134 163 0.00% 135 173 0.00% 136 115 0.00% 137 22 0.00% 138 63 0.00% 139 16 0.00% 140 0 0.00% 141 20 0.00% 142 9 0.00% 143 488 0.00% 144 307 0.00% 145 25 0.00% 146 40 0.00% 147 218 0.00% 148 1052 0.00% 149 651 0.00% 150 2789 0.01% 151 37898875 91.99% 41200243 reads passed initial QC criterion=sequence-density sequence-density=12.45 sequence-density-rank=1 fanout-score=43.31 fanout-score-rank=2 prefix-density=14.69 prefix-fanout=36.7 sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACGTGAAACGAT criterion=fanout-score sequence-density=0.01 sequence-density-rank=8 fanout-score=62.84 fanout-score-rank=1 prefix-density=0.63 prefix-fanout=1.4 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 AGATCGGAAGAGCACACGTCTGAACTCCAGTCACGTGAAACGAT -o SRR6793145 - Input file: STDIN trimmed: SRR6793145-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): AGATCGGAAGAGCACACGTCTGAACTCCAGTCACGTGAAACGAT -- 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 14:39:07 2025 >> started Thu Feb 13 14:40:05 2025 >> done (58.394s) 34861744 reads processed; of these: 31 ( 0.00%) short reads filtered out after trimming by size control 58 ( 0.00%) empty reads filtered out after trimming by size control 34861655 (100.00%) reads available; of these: 7996119 (22.94%) trimmed reads available after processing 26865536 (77.06%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 91 0.00% 19 85 0.00% 20 104 0.00% 21 122 0.00% 22 138 0.00% 23 163 0.00% 24 205 0.00% 25 211 0.00% 26 216 0.00% 27 247 0.00% 28 282 0.00% 29 277 0.00% 30 314 0.00% 31 336 0.00% 32 382 0.00% 33 385 0.00% 34 416 0.00% 35 499 0.00% 36 475 0.00% 37 533 0.00% 38 572 0.00% 39 582 0.00% 40 603 0.00% 41 667 0.00% 42 611 0.00% 43 682 0.00% 44 704 0.00% 45 686 0.00% 46 781 0.00% 47 757 0.00% 48 726 0.00% 49 796 0.00% 50 756 0.00% 51 804 0.00% 52 747 0.00% 53 799 0.00% 54 811 0.00% 55 905 0.00% 56 911 0.00% 57 1023 0.00% 58 948 0.00% 59 1314 0.00% 60 1269 0.00% 61 1217 0.00% 62 1332 0.00% 63 1206 0.00% 64 1161 0.00% 65 1157 0.00% 66 1171 0.00% 67 1284 0.00% 68 1406 0.00% 69 1470 0.00% 70 1582 0.00% 71 1958 0.01% 72 2055 0.01% 73 2416 0.01% 74 2613 0.01% 75 2950 0.01% 76 3246 0.01% 77 3305 0.01% 78 3848 0.01% 79 4093 0.01% 80 4973 0.01% 81 5516 0.02% 82 6537 0.02% 83 7457 0.02% 84 9004 0.03% 85 9105 0.03% 86 10103 0.03% 87 11154 0.03% 88 12658 0.04% 89 14910 0.04% 90 17378 0.05% 91 19431 0.06% 92 23443 0.07% 93 25797 0.07% 94 29109 0.08% 95 32139 0.09% 96 35390 0.10% 97 39005 0.11% 98 43636 0.13% 99 51264 0.15% 100 50882 0.15% 101 59211 0.17% 102 65928 0.19% 103 73691 0.21% 104 78726 0.23% 105 80465 0.23% 106 87388 0.25% 107 96085 0.28% 108 101668 0.29% 109 110784 0.32% 110 114495 0.33% 111 136532 0.39% 112 142300 0.41% 113 140738 0.40% 114 151821 0.44% 115 157142 0.45% 116 169193 0.49% 117 160321 0.46% 118 164626 0.47% 119 184925 0.53% 120 201710 0.58% 121 218924 0.63% 122 207933 0.60% 123 214523 0.62% 124 214102 0.61% 125 226591 0.65% 126 240479 0.69% 127 233443 0.67% 128 253556 0.73% 129 236983 0.68% 130 254208 0.73% 131 242980 0.70% 132 259551 0.74% 133 269540 0.77% 134 293429 0.84% 135 285991 0.82% 136 275809 0.79% 137 278225 0.80% 138 257969 0.74% 139 260206 0.75% 140 259244 0.74% 141 262073 0.75% 142 274022 0.79% 143 288653 0.83% 144 288478 0.83% 145 276398 0.79% 146 305254 0.88% 147 370242 1.06% 148 708074 2.03% 149 422 0.00% 150 1909 0.01% 151 24102399 69.14% criterion=sequence-density sequence-density=0.55 sequence-density-rank=1 fanout-score=6.83 fanout-score-rank=16 prefix-density=1.31 prefix-fanout=2.9 sequence=CTGCTGGCACCAGACTTGCCCTCCAATGGATCCTCGTTAAGGGATTTAGATTGTACTCATTCCAATTACCAGACTCGAAGAGCCCGGTATTGTTATTTATTGTCACTACCTCCCCGTGTCAGGATTGGGTAATTTGCGCGCCTGCTGCCTTCCTTGGATGTGGTAGCCGTTTCTCAGGCTCCCTCTCCGGAATCGAACCCTAATTCTCCGTCACCCGTCACCACCATGGTAGGCCTCTATCCTACCATCGAAAGTTGATAGGGCAGAAATTTGAATGATGCGTCGCCAGCACGAAGGCCGTGCGATCCGTCGAGTTATCATGAATCATCAGAGCAACGGGCAGAGCCCGCGTCGACCTTTTATCTAATAAATGCGTCCCTTCCAGAAGTCGGGGTTTGTTGCACGTATTAGCTCTAGAATTACTACGGTTATCCGAGTAGCAAATACCATCAAACAAACTATAACTGATTTAATGAGCCATTCGCAGTTTCACAGTCTGAATTAGTTCATA criterion=fanout-score sequence-density=0.06 sequence-density-rank=16 fanout-score=93.98 fanout-score-rank=1 prefix-density=3.99 prefix-fanout=1.5 sequence=CAAAGATTACCTGGGCCTGTCGG Started job on | Feb 13 14:40:47 Started mapping on | Feb 13 14:40:47 Finished on | Feb 13 14:42:59 Mapping speed, Million of reads per hour | 1123.64 Number of input reads | 41200154 Average input read length | 144 UNIQUE READS: Uniquely mapped reads number | 22539414 Uniquely mapped reads % | 54.71% Average mapped length | 143.71 Number of splices: Total | 8516247 Number of splices: Annotated (sjdb) | 8291698 Number of splices: GT/AG | 8334898 Number of splices: GC/AG | 120901 Number of splices: AT/AC | 17015 Number of splices: Non-canonical | 43433 Mismatch rate per base, % | 0.52% Deletion rate per base | 0.03% Deletion average length | 2.74 Insertion rate per base | 0.03% Insertion average length | 2.88 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 2049823 % of reads mapped to multiple loci | 4.98% Number of reads mapped to too many loci | 15849656 % of reads mapped to too many loci | 38.47% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.53% % of reads unmapped: other | 0.32% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 16610917 16610917 16610917 N_multimapping 2049823 2049823 2049823 N_noFeature 2165245 12113193 12335155 N_ambiguous 378478 61073 61556 UnstrandedReadsAssigned:19995691 PositiveStrandReadsAssigned:10365148 NegativeStrandReadsAssigned:10142703 Dataset is classified unstranded MeadianReadLen=151 20thPercentileLength=137 echo kmer=133 SRR6793145 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: SRR6793145-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 41,200,154 reads, 32,867,802 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,189 rounds 52401 SRR6793145.ke.tsv 34699 SRR6793145.se.tsv 87100 total ==> SRR6793145.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1919 9044.61 168.732 Potri.005G024800.1.v4.1 1035 936 473 18.0912 Potri.004G059700.1.v4.1 961 862 13 0.539907 Potri.007G009000.2.v4.1 1416 1317 0 0 Potri.003G141000.2.v4.1 2943 2844 1528.17 19.2364 Potri.016G087400.1.v4.1 270 171 918 192.189 Potri.015G069301.1.v4.1 564 465 0 0 Potri.010G195200.1.v4.1 1773 1674 419 8.96068 Potri.012G127500.1.v4.1 977 878 327 13.3332 ==> SRR6793145.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 564 Potri.001G233950.v4.1 1 Potri.001G122700.v4.1 296 Potri.001G212900.v4.1 2 Potri.001G182400.v4.1 0 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 33 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 8 SRR6793145 completed mapping pipeline successfully