Starting /dee2/code/volunteer_pipeline.sh ERR6133484 current disk space = 1544846954496 free memory = 1600780804 ERR6133484 SRAfilesize 317bd47e95a51d3309027def91f0eb45 ERR6133484.sra ERR6133484.sra file validated ERR6133484 is single end ERR6133484 is conventional basespace ERR6133484 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133484_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 70-93 %GC 45 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 35.40075 37.0 33.0 37.0 33.0 37.0 2 36.2875 37.0 37.0 37.0 33.0 37.0 3 35.756 37.0 37.0 37.0 33.0 37.0 4 35.30825 37.0 37.0 37.0 33.0 37.0 5 35.20975 37.0 37.0 37.0 33.0 37.0 6 35.4515 37.0 37.0 37.0 33.0 37.0 7 37.16325 37.0 37.0 40.0 33.0 40.0 8 37.2765 37.0 37.0 40.0 33.0 40.0 9 37.38875 37.0 37.0 40.0 33.0 40.0 10-11 37.362875 37.0 37.0 40.0 33.0 40.0 12-13 37.205 37.0 37.0 40.0 33.0 40.0 14-15 37.215875 37.0 37.0 40.0 33.0 40.0 16-17 37.105875 37.0 37.0 40.0 33.0 40.0 18-19 36.900375 37.0 37.0 40.0 33.0 40.0 20-21 36.56725 37.0 37.0 40.0 33.0 40.0 22-23 36.573625 37.0 37.0 40.0 33.0 40.0 24-25 36.5135 37.0 37.0 40.0 33.0 40.0 26-27 36.665875 37.0 37.0 40.0 33.0 40.0 28-29 36.75475 37.0 37.0 40.0 33.0 40.0 30-31 36.614000000000004 37.0 37.0 40.0 33.0 40.0 32-33 36.509 37.0 37.0 40.0 33.0 40.0 34-35 36.5105 37.0 37.0 40.0 33.0 40.0 36-37 36.398624999999996 37.0 37.0 40.0 33.0 40.0 38-39 36.32875 37.0 37.0 40.0 33.0 40.0 40-41 36.1105 37.0 37.0 40.0 33.0 40.0 42-43 36.037 37.0 37.0 40.0 33.0 40.0 44-45 35.95375 37.0 35.0 40.0 33.0 40.0 46-47 35.99325 37.0 35.0 40.0 33.0 40.0 48-49 35.98975 37.0 35.0 38.5 33.0 40.0 50-51 35.813500000000005 37.0 33.0 37.0 33.0 40.0 52-53 35.465875 37.0 33.0 37.0 33.0 40.0 54-55 35.363625 37.0 33.0 37.0 33.0 40.0 56-57 35.260374999999996 37.0 33.0 37.0 33.0 40.0 58-59 34.124875 37.0 33.0 37.0 27.0 37.0 60-61 34.553 37.0 33.0 37.0 27.0 37.0 62-63 34.675875000000005 37.0 33.0 37.0 30.0 37.0 64-65 34.502875 37.0 33.0 37.0 27.0 37.0 66-67 34.4585 37.0 33.0 37.0 30.0 37.0 68-69 33.736125 35.0 33.0 37.0 30.0 37.0 70-71 33.887990146538655 35.0 33.0 37.0 27.0 37.0 72-73 34.18225042593693 37.0 33.0 37.0 27.0 37.0 74-75 34.09892295226885 37.0 33.0 37.0 27.0 37.0 76-77 34.02567909834886 37.0 33.0 37.0 27.0 37.0 78-79 33.787772724554415 37.0 33.0 37.0 27.0 37.0 80-81 33.73793226748337 37.0 33.0 37.0 27.0 37.0 82-83 33.64753054434384 37.0 33.0 37.0 27.0 37.0 84-85 33.35956708003155 35.0 33.0 37.0 27.0 37.0 86-87 33.266103635843116 33.0 33.0 37.0 27.0 37.0 88-89 33.41425708559977 35.0 33.0 37.0 27.0 37.0 90-91 33.248067563698825 33.0 33.0 37.0 27.0 37.0 92-93 33.265531062124246 33.0 33.0 37.0 27.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 12.0 21 6.0 22 19.0 23 20.0 24 22.0 25 28.0 26 26.0 27 44.0 28 59.0 29 71.0 30 104.0 31 100.0 32 169.0 33 200.0 34 278.0 35 429.0 36 886.0 37 856.0 38 629.0 39 42.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 82.075 5.35 4.475 8.1 2 65.125 19.475 10.0 5.4 3 35.65 35.575 17.05 11.725 4 31.900000000000002 28.95 19.0 20.150000000000002 5 27.800000000000004 28.499999999999996 25.374999999999996 18.325 6 19.2 38.75 24.15 17.9 7 36.875 28.749999999999996 20.200000000000003 14.174999999999999 8 28.375 29.175 23.724999999999998 18.725 9 25.724999999999998 29.975 27.625 16.675 10-11 24.075 30.0875 28.3875 17.45 12-13 25.3 28.925 27.0 18.775 14-15 21.987499999999997 31.137500000000003 29.1875 17.6875 16-17 25.85 30.5 24.125 19.525000000000002 18-19 25.35 25.887500000000003 28.425 20.3375 20-21 26.728341042630326 26.403300412551566 28.141017627203404 18.7273409176147 22-23 29.175 23.4375 26.900000000000002 20.4875 24-25 25.275 25.2 28.749999999999996 20.775 26-27 26.3 25.3 29.012500000000003 19.3875 28-29 24.1875 29.075 27.8625 18.875 30-31 30.0375 25.275 26.650000000000002 18.0375 32-33 25.3 26.5375 27.1625 21.0 34-35 23.974999999999998 30.349999999999998 26.737499999999997 18.9375 36-37 25.724999999999998 25.95 25.45 22.875 38-39 29.425 25.1875 27.375 18.0125 40-41 24.2375 25.825 30.525000000000002 19.412499999999998 42-43 25.85 31.724999999999998 25.3125 17.1125 44-45 24.224999999999998 27.675 29.625 18.475 46-47 26.0 24.8125 26.8375 22.35 48-49 25.3125 25.3125 28.287499999999998 21.087500000000002 50-51 22.425 29.2875 27.425 20.8625 52-53 24.06156156156156 27.815315315315313 25.175175175175173 22.94794794794795 54-55 22.925 28.3875 28.599999999999998 20.0875 56-57 26.8 28.525 25.9625 18.712500000000002 58-59 23.0875 27.450000000000003 29.5375 19.925 60-61 28.0875 26.0375 27.212500000000002 18.6625 62-63 21.175 29.95 30.062499999999996 18.8125 64-65 22.162499999999998 31.9625 26.937499999999996 18.9375 66-67 25.7625 30.912499999999998 25.5375 17.7875 68-69 22.412499999999998 26.650000000000002 28.925 22.0125 70-71 23.950741392309627 28.23573762251822 25.458657954259866 22.354863030912288 72-73 26.57351621586976 25.74028970644789 28.791180617869504 18.895013459812844 74-75 25.602605863192185 29.680781758957654 26.20195439739414 18.514657980456025 76-77 22.122373463724067 26.840227302761992 27.0516717325228 23.985727500991146 78-79 26.090457656690376 27.580190578445844 27.217823110991812 19.111528653871964 80-81 22.678864008738394 33.547241944292736 25.914800655379572 17.859093391589294 82-83 25.331472435450102 26.699232379623165 26.643405443126312 21.32588974180042 84-85 22.85225815643254 26.62772474711497 30.930331956119105 19.589685140333383 86-87 22.044088176352705 29.330088748926425 27.712567993129117 20.913255081591757 88-89 20.125966218150587 30.747208703120528 29.30146006298311 19.825365015745778 90-91 25.694245634125394 30.460921843687377 26.00916117950186 17.835671342685373 92-93 21.142284569138276 32.07844259948469 26.939593472659606 19.839679358717436 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 0.0 1 0.0 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10 0.0 11 0.0 12 0.0 13 0.0 14 0.0 15 0.5 16 0.5 17 4.5 18 5.0 19 1.5 20 1.5 21 1.0 22 1.5 23 3.5 24 7.5 25 11.0 26 10.5 27 17.5 28 25.5 29 27.0 30 36.0 31 44.5 32 53.0 33 71.0 34 94.5 35 112.0 36 129.5 37 154.5 38 185.0 39 185.5 40 188.0 41 210.5 42 204.0 43 196.5 44 187.0 45 187.5 46 183.0 47 181.0 48 170.5 49 167.5 50 169.0 51 146.0 52 119.5 53 131.0 54 207.0 55 155.5 56 56.0 57 47.0 58 44.0 59 40.5 60 33.5 61 27.5 62 24.0 63 23.5 64 20.0 65 12.5 66 8.5 67 8.0 68 9.5 69 10.0 70 9.5 71 9.0 72 8.0 73 5.0 74 3.0 75 1.5 76 1.5 77 1.5 78 0.0 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 0.0 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10-11 0.0 12-13 0.0 14-15 0.0 16-17 0.0 18-19 0.0 20-21 0.0125 22-23 0.0 24-25 0.0 26-27 0.0 28-29 0.0 30-31 0.0 32-33 0.0 34-35 0.0 36-37 0.0 38-39 0.0 40-41 0.0 42-43 0.0 44-45 0.0 46-47 0.0 48-49 0.0 50-51 0.0 52-53 0.1 54-55 0.0 56-57 0.0 58-59 0.0 60-61 0.0 62-63 0.0 64-65 0.0 66-67 0.0 68-69 0.0 70-71 0.0 72-73 0.0 74-75 0.0 76-77 0.0 78-79 0.0 80-81 0.0 82-83 0.0 84-85 0.0 86-87 0.0 88-89 0.0 90-91 0.0 92-93 0.0 >>END_MODULE >>Sequence Length Distribution warn #Length Count 70 42.0 71 38.0 72 39.0 73 32.0 74 23.0 75 30.0 76 25.0 77 25.0 78 41.0 79 26.0 80 34.0 81 40.0 82 45.0 83 34.0 84 33.0 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 3493.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 78.625 #Duplication Level Percentage of deduplicated Percentage of total 1 93.8314785373609 73.775 2 3.4340222575516695 5.4 3 0.890302066772655 2.1 4 0.6677265500794912 2.1 5 0.19077901430842606 0.75 6 0.09538950715421303 0.44999999999999996 7 0.03179650238473768 0.17500000000000002 8 0.06359300476947535 0.4 9 0.1271860095389507 0.8999999999999999 >10 0.6359300476947536 9.45 >50 0.0 0.0 >100 0.03179650238473768 4.5 >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 GGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGC 180 4.5 No Hit GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 40 1.0 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 33 0.8250000000000001 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 29 0.7250000000000001 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 26 0.65 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 22 0.5499999999999999 No Hit GGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAAGGCGATCAAATTC 20 0.5 No Hit GAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGC 19 0.475 No Hit GGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAA 19 0.475 No Hit GGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGC 18 0.44999999999999996 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 18 0.44999999999999996 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 17 0.42500000000000004 No Hit GGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTT 16 0.4 No Hit GGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGG 16 0.4 No Hit GGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTT 15 0.375 No Hit GGGGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCT 13 0.325 No Hit GGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGGG 13 0.325 No Hit GGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAAA 12 0.3 No Hit CAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCT 11 0.27499999999999997 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 11 0.27499999999999997 No Hit GGAGTATCCTTGATATATAAATATATAGATAAATAGATTTAAATGGAAAA 10 0.25 No Hit GGGGATGGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACG 9 0.22499999999999998 No Hit GCAGCTTGCAAATGGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAA 9 0.22499999999999998 No Hit GGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTCCT 9 0.22499999999999998 No Hit GGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAA 9 0.22499999999999998 No Hit GTATGGAAGGCGATCAAATTCGAGTTCGCGCCGGTAGATACTATCGATTA 8 0.2 No Hit GGGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTG 8 0.2 No Hit GAAGTATGGAAGGCGATCAAATTCGAGTTCGCGCCGGTAGATACTATCGA 7 0.17500000000000002 No Hit CGAGGAAGGGCGTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAG 6 0.15 No Hit GGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCG 6 0.15 No Hit CAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTG 6 0.15 No Hit GTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAA 5 0.125 No Hit GGGAGTATTATGAAAGGAGATTAATCATAGATTATCAAAAACCCTAGAAA 5 0.125 No Hit GGGCCTGTTATCTCTATCAATATGATTCTAATTCGTCAGATATTATTTAT 5 0.125 No Hit GGGAGGGTGAGAGCCCCGTCCGGCCCGGACCCTGTCGCCCCACGAGGCGC 5 0.125 No Hit GTACAAGCTCGTAACGAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAAT 5 0.125 No Hit GGGGAAGTACACCAGCGACGGCGAGGCCGCCGCCGCCAAGGAAGGCATGT 5 0.125 No Hit >>END_MODULE >>Adapter Content pass #Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence SOLID Small RNA Adapter 1 0.0 0.0 0.0 0.0 0.0 2 0.0 0.0 0.0 0.0 0.0 3 0.0 0.0 0.0 0.0 0.0 4 0.0 0.0 0.0 0.0 0.0 5 0.0 0.0 0.0 0.0 0.0 6 0.0 0.0 0.0 0.0 0.0 7 0.0 0.0 0.0 0.0 0.0 8 0.0 0.0 0.0 0.0 0.0 9 0.0 0.0 0.0 0.0 0.0 10-11 0.0 0.0 0.0 0.0 0.0 12-13 0.0 0.0 0.0 0.0 0.0 14-15 0.0 0.0 0.0 0.0 0.0 16-17 0.0 0.0 0.0 0.0 0.0 18-19 0.0 0.0 0.0 0.0 0.0 20-21 0.0 0.0 0.0 0.0 0.0 22-23 0.0125 0.0 0.0 0.0 0.0 24-25 0.025 0.0 0.0 0.0 0.0 26-27 0.025 0.0 0.0 0.0 0.0 28-29 0.025 0.0 0.0 0.0 0.0 30-31 0.05 0.0 0.0 0.0 0.0 32-33 0.05 0.0 0.0 0.0 0.0 34-35 0.05 0.0 0.0 0.0 0.0 36-37 0.07500000000000001 0.0 0.0 0.0 0.0 38-39 0.1 0.0 0.0 0.0 0.0 40-41 0.125 0.0 0.0 0.0 0.0 42-43 0.125 0.0 0.0 0.0 0.0 44-45 0.125 0.0 0.0 0.0 0.0 46-47 0.15 0.0 0.0 0.0 0.0 48-49 0.16249999999999998 0.0 0.0 0.0 0.0 50-51 0.175 0.0 0.0 0.0 0.0 52-53 0.21250000000000002 0.0 0.0 0.0 0.0 54-55 0.225 0.0 0.0 0.0 0.0 56-57 0.225 0.0 0.0 0.0 0.0 58-59 0.225 0.0 0.0 0.0 0.0 60-61 0.225 0.0 0.0 0.0 0.0 62-63 0.225 0.0 0.0 0.0 0.0 64-65 0.225 0.0 0.0 0.0 0.0 66-67 0.225 0.0 0.0 0.0 0.0 68-69 0.225 0.0 0.0 0.0 0.0 70-71 0.2375 0.0 0.0 0.0 0.0 72-73 0.25 0.0 0.0 0.0 0.0 74-75 0.25 0.0 0.0 0.0 0.0 76-77 0.275 0.0 0.0 0.0 0.0 78-79 0.275 0.0 0.0 0.0 0.0 80-81 0.275 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content fail #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GGGAGAG 40 1.6370905E-11 84.487495 1 CAATACA 40 1.6370905E-11 84.487495 8 GGAGAGC 45 4.5474735E-11 75.1 2 GCAATAC 45 4.5474735E-11 75.1 7 GAGCAAT 45 4.5474735E-11 75.1 5 GAGAGCA 45 4.5474735E-11 75.1 3 AATACAA 45 4.5474735E-11 75.1 9 AGCAATA 45 4.5474735E-11 75.1 6 AGAGCAA 50 1.1823431E-10 67.59 4 CATCACT 40 2.1846063E-9 49.698532 82-83 ATCACTA 40 2.1846063E-9 49.698532 84-85 AGCATCA 40 2.1846063E-9 49.698532 80-81 TCACTAG 40 2.1846063E-9 49.698532 84-85 ACTAGCT 40 2.1846063E-9 49.698532 86-87 AAAGCAT 40 2.1846063E-9 49.698532 78-79 GCATCAC 40 2.1846063E-9 49.698532 82-83 AAGCATC 40 2.1846063E-9 49.698532 80-81 CGAAAGC 40 2.4956535E-9 48.978264 76-77 CCGAAAG 40 2.4956535E-9 48.978264 76-77 AGCCGAA 40 3.6779966E-9 46.9375 74-75 >>END_MODULE Rejected 46548 READS because READLEN < 1 Read 46548 spots for ERR6133484.sra Written 46548 spots for ERR6133484.sra Rejected 46548 READS because READLEN < 1 Read 46548 spots for ERR6133484.sra Written 46548 spots for ERR6133484.sra Rejected 46548 READS because READLEN < 1 Read 46548 spots for ERR6133484.sra Written 46548 spots for ERR6133484.sra Rejected 46548 READS because READLEN < 1 Read 46548 spots for ERR6133484.sra Written 46548 spots for ERR6133484.sra Rejected 46548 READS because READLEN < 1 Read 46548 spots for ERR6133484.sra Written 46548 spots for ERR6133484.sra Rejected 46548 READS because READLEN < 1 Read 46548 spots for ERR6133484.sra Written 46548 spots for ERR6133484.sra Rejected 46548 READS because READLEN < 1 Read 46548 spots for ERR6133484.sra Written 46548 spots for ERR6133484.sra Rejected 46548 READS because READLEN < 1 Read 46548 spots for ERR6133484.sra Written 46548 spots for ERR6133484.sra Rejected 46548 READS because READLEN < 1 Read 46548 spots for ERR6133484.sra Written 46548 spots for ERR6133484.sra Rejected 46548 READS because READLEN < 1 Read 46548 spots for ERR6133484.sra Written 46548 spots for ERR6133484.sra Rejected 46548 READS because READLEN < 1 Read 46548 spots for ERR6133484.sra Written 46548 spots for ERR6133484.sra Rejected 46548 READS because READLEN < 1 Read 46548 spots for ERR6133484.sra Written 46548 spots for ERR6133484.sra Rejected 46548 READS because READLEN < 1 Read 46548 spots for ERR6133484.sra Written 46548 spots for ERR6133484.sra Rejected 46548 READS because READLEN < 1 Read 46548 spots for ERR6133484.sra Written 46548 spots for ERR6133484.sra Rejected 46548 READS because READLEN < 1 Read 46548 spots for ERR6133484.sra Written 46548 spots for ERR6133484.sra Rejected 46548 READS because READLEN < 1 Read 46548 spots for ERR6133484.sra Written 46548 spots for ERR6133484.sra Rejected 46548 READS because READLEN < 1 Read 46548 spots for ERR6133484.sra Written 46548 spots for ERR6133484.sra Rejected 46548 READS because READLEN < 1 Read 46548 spots for ERR6133484.sra Written 46548 spots for ERR6133484.sra Rejected 46564 READS because READLEN < 1 Read 46564 spots for ERR6133484.sra Written 46564 spots for ERR6133484.sra Rejected 46548 READS because READLEN < 1 Read 46548 spots for ERR6133484.sra Written 46548 spots for ERR6133484.sra SRR ids: ['ERR6133484.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_f55ibiu9 ERR6133484.sra spots: 930976 blocks: [[1, 46548], [46549, 93096], [93097, 139644], [139645, 186192], [186193, 232740], [232741, 279288], [279289, 325836], [325837, 372384], [372385, 418932], [418933, 465480], [465481, 512028], [512029, 558576], [558577, 605124], [605125, 651672], [651673, 698220], [698221, 744768], [744769, 791316], [791317, 837864], [837865, 884412], [884413, 930976]] ERR6133484 file size 201228 ERR6133484 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 ERR6133484 ERR6133484_1.fastq Input file: ERR6133484_1.fastq trimmed: ERR6133484-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 Sat Dec 7 07:01:21 2024 >> started Sat Dec 7 07:01:21 2024 >> done (0.926s) 930976 reads processed; of these: 318 ( 0.03%) short reads filtered out after trimming by size control 90 ( 0.01%) empty reads filtered out after trimming by size control 930568 (99.96%) reads available; of these: 16977 ( 1.82%) trimmed reads available after processing 913591 (98.18%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 44 0.00% 19 65 0.01% 20 25 0.00% 21 19 0.00% 22 29 0.00% 23 21 0.00% 24 12 0.00% 25 9 0.00% 26 10 0.00% 27 19 0.00% 28 48 0.01% 29 58 0.01% 30 17 0.00% 31 25 0.00% 32 36 0.00% 33 27 0.00% 34 29 0.00% 35 124 0.01% 36 912 0.10% 37 35 0.00% 38 46 0.00% 39 86 0.01% 40 87 0.01% 41 50 0.01% 42 25 0.00% 43 32 0.00% 44 38 0.00% 45 31 0.00% 46 31 0.00% 47 43 0.00% 48 29 0.00% 49 27 0.00% 50 24 0.00% 51 66 0.01% 52 31 0.00% 53 25 0.00% 54 16 0.00% 55 16 0.00% 56 15 0.00% 57 34 0.00% 58 22 0.00% 59 17 0.00% 60 24 0.00% 61 22 0.00% 62 0 0.00% 63 0 0.00% 64 2 0.00% 65 4 0.00% 66 4 0.00% 67 11 0.00% 68 21 0.00% 69 79 0.01% 70 9451 1.02% 71 8640 0.93% 72 9019 0.97% 73 8315 0.89% 74 8316 0.89% 75 8750 0.94% 76 7137 0.77% 77 7652 0.82% 78 8453 0.91% 79 8904 0.96% 80 7763 0.83% 81 8580 0.92% 82 9613 1.03% 83 10491 1.13% 84 7719 0.83% 85 29 0.00% 86 58 0.01% 87 85 0.01% 88 152 0.02% 89 312 0.03% 90 605 0.07% 91 1975 0.21% 92 9329 1.00% 93 786698 84.54% 930568 reads passed initial QC criterion=sequence-density sequence-density=1.40 sequence-density-rank=1 fanout-score=1.99 fanout-score-rank=27 prefix-density=1.40 prefix-fanout=2.0 sequence=CAAGGCTAAATAC criterion=fanout-score sequence-density=0.13 sequence-density-rank=17 fanout-score=33.20 fanout-score-rank=1 prefix-density=4.44 prefix-fanout=1.0 sequence=CAGCTTGTGAAATATGGAAAGCGATCAAATT Started job on | Dec 07 07:01:33 Started mapping on | Dec 07 07:01:33 Finished on | Dec 07 07:01:39 Mapping speed, Million of reads per hour | 558.34 Number of input reads | 930568 Average input read length | 90 UNIQUE READS: Uniquely mapped reads number | 529482 Uniquely mapped reads % | 56.90% Average mapped length | 90.46 Number of splices: Total | 19748 Number of splices: Annotated (sjdb) | 16425 Number of splices: GT/AG | 18833 Number of splices: GC/AG | 533 Number of splices: AT/AC | 7 Number of splices: Non-canonical | 375 Mismatch rate per base, % | 0.48% Deletion rate per base | 0.04% Deletion average length | 1.81 Insertion rate per base | 0.02% Insertion average length | 1.86 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 301242 % of reads mapped to multiple loci | 32.37% Number of reads mapped to too many loci | 16434 % of reads mapped to too many loci | 1.77% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 8.82% % of reads unmapped: other | 0.14% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 99844 99844 99844 N_multimapping 301242 301242 301242 N_noFeature 36958 42416 505041 N_ambiguous 21558 2558 96 UnstrandedReadsAssigned:470966 PositiveStrandReadsAssigned:484508 NegativeStrandReadsAssigned:24345 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=93 echo kmer=89 ERR6133484 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: 52,972 [index] number of k-mers: 66,720,672 [index] number of equivalence classes: 111,837 [quant] running in single-end mode [quant] will process file 1: ERR6133484-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 930,568 reads, 655,672 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 907 rounds 52973 ERR6133484.ke.tsv 35125 ERR6133484.se.tsv 88098 total ==> ERR6133484.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 837 0 0 PNS24247 1044 945 0 0 PNS24249 1928 1829 0 0 PNS24246 1044 945 0 0 PNS24248 1044 945 0 0 PNS24244 1471 1372 19 29.3028 PNS24243 293 194 0 0 KQK14069 1603 1504 8 11.2551 KQK14071 474 375 0 0 ==> ERR6133484.se.tsv <== BRADI_1g14170v3 8 BRADI_1g53295v3 2 BRADI_1g59795v3 8 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 4 BRADI_1g74790v3 14 BRADI_1g09890v3 0 BRADI_1g77505v3 6 BRADI_1g48960v3 0 ERR6133484 completed mapping pipeline successfully