Starting /dee2/code/volunteer_pipeline.sh ERR6133503 current disk space = 1544402767872 free memory = 1597930648 ERR6133503 SRAfilesize 51369c30d0a165e863c9bf2c48cd0ad4 ERR6133503.sra ERR6133503.sra file validated ERR6133503 is single end ERR6133503 is conventional basespace ERR6133503 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133503_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 35.49775 37.0 33.0 37.0 33.0 37.0 2 36.46225 37.0 37.0 37.0 37.0 37.0 3 35.77575 37.0 37.0 37.0 33.0 37.0 4 35.2475 37.0 37.0 37.0 33.0 37.0 5 35.2575 37.0 37.0 37.0 33.0 37.0 6 35.5655 37.0 37.0 37.0 33.0 37.0 7 37.30725 37.0 37.0 40.0 33.0 40.0 8 37.4025 37.0 37.0 40.0 33.0 40.0 9 37.34325 37.0 37.0 40.0 33.0 40.0 10-11 37.3155 37.0 37.0 40.0 33.0 40.0 12-13 37.260999999999996 37.0 37.0 40.0 33.0 40.0 14-15 37.20525 37.0 37.0 40.0 33.0 40.0 16-17 37.148375 37.0 37.0 40.0 33.0 40.0 18-19 36.99375 37.0 37.0 40.0 33.0 40.0 20-21 36.723875 37.0 37.0 40.0 33.0 40.0 22-23 36.656625 37.0 37.0 40.0 33.0 40.0 24-25 36.53375 37.0 37.0 40.0 33.0 40.0 26-27 36.753625 37.0 37.0 40.0 33.0 40.0 28-29 36.755250000000004 37.0 37.0 40.0 33.0 40.0 30-31 36.660124999999994 37.0 37.0 40.0 33.0 40.0 32-33 36.591875 37.0 37.0 40.0 33.0 40.0 34-35 36.50375 37.0 37.0 40.0 33.0 40.0 36-37 36.332 37.0 37.0 40.0 33.0 40.0 38-39 36.288624999999996 37.0 37.0 40.0 33.0 40.0 40-41 36.057500000000005 37.0 37.0 40.0 33.0 40.0 42-43 36.11775 37.0 37.0 40.0 33.0 40.0 44-45 36.057 37.0 37.0 40.0 33.0 40.0 46-47 35.804 37.0 35.0 37.0 33.0 40.0 48-49 35.74875 37.0 33.0 37.0 33.0 40.0 50-51 35.6135 37.0 33.0 37.0 33.0 40.0 52-53 35.295500000000004 37.0 33.0 37.0 33.0 40.0 54-55 35.264250000000004 37.0 33.0 37.0 33.0 40.0 56-57 35.102000000000004 37.0 33.0 37.0 33.0 37.0 58-59 34.082625 37.0 33.0 37.0 27.0 37.0 60-61 34.561375 37.0 33.0 37.0 30.0 37.0 62-63 34.451750000000004 37.0 33.0 37.0 27.0 37.0 64-65 34.394 37.0 33.0 37.0 27.0 37.0 66-67 34.324625 37.0 33.0 37.0 27.0 37.0 68-69 33.585499999999996 35.0 33.0 37.0 27.0 37.0 70-71 33.71053455845459 35.0 33.0 37.0 27.0 37.0 72-73 34.09911690120542 37.0 33.0 37.0 27.0 37.0 74-75 34.03360614750236 37.0 33.0 37.0 27.0 37.0 76-77 33.98915394402036 37.0 33.0 37.0 27.0 37.0 78-79 33.87518176570083 37.0 33.0 37.0 27.0 37.0 80-81 33.70229411653267 37.0 33.0 37.0 27.0 37.0 82-83 33.601195078143675 37.0 33.0 37.0 27.0 37.0 84-85 33.3127427337849 35.0 33.0 37.0 27.0 37.0 86-87 33.33825816485225 35.0 33.0 37.0 27.0 37.0 88-89 33.43532918610679 37.0 33.0 37.0 27.0 37.0 90-91 33.17664593053395 33.0 33.0 37.0 27.0 37.0 92-93 33.26270088128564 35.0 33.0 37.0 27.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 9.0 21 10.0 22 14.0 23 22.0 24 30.0 25 27.0 26 33.0 27 46.0 28 44.0 29 67.0 30 93.0 31 115.0 32 155.0 33 193.0 34 283.0 35 501.0 36 902.0 37 956.0 38 491.0 39 9.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 87.9 3.1 3.55 5.45 2 72.925 16.125 6.4750000000000005 4.475 3 34.925 40.375 13.850000000000001 10.85 4 33.25 29.25 19.225 18.275 5 24.75 31.175000000000004 27.224999999999998 16.85 6 20.9 38.1 24.275 16.725 7 37.925 27.675 18.95 15.45 8 30.475 30.85 21.725 16.950000000000003 9 25.8 28.625 26.400000000000002 19.175 10-11 26.387500000000003 27.6625 27.925 18.025 12-13 28.675 27.275 26.5875 17.4625 14-15 21.725 31.587500000000002 27.6875 19.0 16-17 23.7125 31.6 25.4 19.287499999999998 18-19 23.44043005375672 27.84098012251531 27.790973871733964 20.927615951994 20-21 24.55569461827284 25.957446808510635 28.52315394242804 20.963704630788484 22-23 26.6 23.6125 28.325 21.462500000000002 24-25 26.125 25.650000000000002 27.9375 20.2875 26-27 25.15 24.725 31.337500000000002 18.787499999999998 28-29 24.9875 26.737499999999997 27.212500000000002 21.0625 30-31 27.05 25.25 27.1375 20.5625 32-33 23.925 27.3625 27.487499999999997 21.224999999999998 34-35 24.175 27.487499999999997 26.875 21.462500000000002 36-37 25.362681340670335 25.07503751875938 27.43871935967984 22.123561780890444 38-39 27.625 25.35 28.962500000000002 18.0625 40-41 26.972614730523947 24.409153432537202 27.24771789421033 21.370513942728522 42-43 25.2 27.3125 27.3875 20.1 44-45 23.8625 26.3625 29.4125 20.3625 46-47 25.112499999999997 25.374999999999996 26.700000000000003 22.8125 48-49 24.95 25.825 28.6375 20.5875 50-51 24.1625 27.400000000000002 28.012500000000003 20.424999999999997 52-53 24.53350031308704 26.574827802128993 26.236693800876644 22.654978083907327 54-55 24.375 26.224999999999998 30.5375 18.862499999999997 56-57 25.778222277784725 25.14064258032254 29.11613951743968 19.964995624453056 58-59 24.3625 25.874999999999996 28.6875 21.075 60-61 24.0125 25.724999999999998 29.9625 20.3 62-63 21.912499999999998 27.037499999999998 32.6875 18.3625 64-65 23.849999999999998 27.525 29.3375 19.287499999999998 66-67 23.799999999999997 26.6625 29.4875 20.05 68-69 21.6 26.487500000000004 29.425 22.4875 70-71 22.752316553969447 26.145755071374904 29.326321061858252 21.775607312797398 72-73 25.856423173803528 24.55919395465995 28.09823677581864 21.486146095717885 74-75 22.559817698442842 26.82618052918091 30.143056083048485 20.470945689327763 76-77 22.590897533689297 26.27765064836003 28.426137808288836 22.705314009661837 78-79 22.36556392898199 26.51679652573764 30.19542725763188 20.922212287648488 80-81 22.300589894844833 29.776865863041806 29.481918440625805 18.440625801487563 82-83 23.5430335777692 25.910201981217035 29.846905956516146 20.69985848449762 84-85 22.846054333764553 23.712807244501942 33.16946959896507 20.271668822768437 86-87 21.30637636080871 27.46241575946086 30.961638154484188 20.269569725246242 88-89 20.74909279419388 28.525142560912393 30.404354587869364 20.321410057024362 90-91 24.313115603939867 26.788491446345258 29.86003110419907 19.038361845515812 92-93 22.213582166925868 27.6049766718507 30.84499740798341 19.336443753240022 >>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 1.0 15 1.0 16 0.5 17 18.0 18 22.5 19 4.5 20 0.0 21 0.5 22 3.0 23 3.5 24 4.5 25 7.0 26 9.0 27 9.0 28 13.0 29 19.0 30 24.0 31 36.0 32 47.0 33 69.0 34 79.5 35 83.5 36 105.0 37 132.0 38 178.5 39 187.0 40 193.5 41 207.5 42 203.5 43 209.5 44 185.5 45 183.0 46 219.5 47 208.5 48 168.5 49 174.0 50 192.5 51 163.5 52 115.0 53 109.5 54 127.0 55 100.5 56 65.0 57 62.0 58 56.5 59 47.5 60 37.0 61 34.0 62 30.0 63 21.5 64 26.5 65 29.0 66 20.0 67 17.5 68 17.5 69 10.0 70 7.5 71 9.0 72 7.5 73 4.5 74 1.5 75 1.5 76 2.5 77 3.0 78 2.5 79 1.0 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 10-11 0.0 12-13 0.0 14-15 0.0 16-17 0.0 18-19 0.0125 20-21 0.125 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 0.05 38-39 0.0 40-41 0.0375 42-43 0.0 44-45 0.0 46-47 0.0 48-49 0.0 50-51 0.0 52-53 0.1875 54-55 0.0 56-57 0.0125 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 14.0 71 10.0 72 12.0 73 10.0 74 9.0 75 9.0 76 6.0 77 12.0 78 7.0 79 9.0 80 6.0 81 6.0 82 7.0 83 11.0 84 14.0 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 3858.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 76.7 #Duplication Level Percentage of deduplicated Percentage of total 1 91.19947848761409 69.95 2 5.019556714471968 7.7 3 1.4993481095176011 3.45 4 0.6192959582790091 1.9 5 0.1955671447196871 0.75 6 0.22816166883963493 1.05 7 0.22816166883963493 1.225 8 0.0651890482398957 0.4 9 0.16297262059973924 1.125 >10 0.7496740547588006 11.0 >50 0.03259452411994785 1.4500000000000002 >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 GGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGC 58 1.4500000000000002 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 50 1.25 No Hit GGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGG 37 0.9249999999999999 No Hit GGAGTATCCTTGATATATAAATATATAGATAAATAGATTTAAATGGAAAA 36 0.8999999999999999 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 32 0.8 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 29 0.7250000000000001 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 25 0.625 No Hit GGGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTG 21 0.525 No Hit GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 19 0.475 No Hit GGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGGG 18 0.44999999999999996 No Hit GGTTTTGAAAAGGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAA 15 0.375 No Hit GGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAACCCTCTTAACT 14 0.35000000000000003 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 13 0.325 No Hit GGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTT 13 0.325 No Hit GGAGTCCCATATATATATGTATAAGATGCCAGCCCGGTTTCGTCAACCAT 13 0.325 No Hit GGAAGAGCCCGAGCTGCTGCAGCAGGTTTTGAAAAGGGAATCGATCGTGA 13 0.325 No Hit GGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGC 13 0.325 No Hit GGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAA 12 0.3 No Hit GGATATCGTGTGTGTACATTTGAATGTACCGACATGGGCTCGAGGAGCAT 12 0.3 No Hit GGAAATGGTGAAGATGATACGAATATGCCGGCCGGGTGCTGATATTGTGA 12 0.3 No Hit GGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTT 11 0.27499999999999997 No Hit GGGAGTATTATGAAAGGAGATTAATCATAGATTATCAAAAACCCTAGAAA 11 0.27499999999999997 No Hit GGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAA 11 0.27499999999999997 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 10 0.25 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 9 0.22499999999999998 No Hit GGAGTGGGGGTGCCATACGCAAAAAGGAAGCGACTCATAGAATGGCAGAG 9 0.22499999999999998 No Hit GGCCTGTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCG 9 0.22499999999999998 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 9 0.22499999999999998 No Hit GAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGC 9 0.22499999999999998 No Hit GGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAAGGCGATCAAATTC 8 0.2 No Hit GGGCCGGGTATCTCTCTGCATGTACGTATGCCTGTAATGTACGTAGCTAC 8 0.2 No Hit GGGATGGAGATGGCCGCGGAGAACGGCGGCTGCGGCTGCAGCACCTGCAA 7 0.17500000000000002 No Hit GGGAGGGGCTTGGCTACAATTCCGAATACGCTATTACATGTTTGCGCTAG 7 0.17500000000000002 No Hit GGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAAA 7 0.17500000000000002 No Hit GTACAAGCTCGTAACGAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAAT 7 0.17500000000000002 No Hit GGGCAAGGAGAAGTACAAGTGCGGATCCAACGTCTTCTGGAAATGGTGAA 7 0.17500000000000002 No Hit GGGACGCATGCAACGACCATCTACATATAGCTACTCGATCTACCGCTACC 7 0.17500000000000002 No Hit GGAAAAGAGGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTTG 7 0.17500000000000002 No Hit GGAGAAGAACACTTCCTCCGTGCATATGCGTGTACGTGGGTTGATCGGTG 6 0.15 No Hit GGGATGGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACGA 6 0.15 No Hit GGAGTGACGACGGCAGCTGCCTTTACACCTTTTAAGCATGCCACTTTAAT 6 0.15 No Hit GTATGGAAGGCGATCAAATTCGAGTTCGCGCCGGTAGATACTATCGATTA 6 0.15 No Hit GGGGATGGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACG 6 0.15 No Hit CCATGAACCGATCCAAGGCTAGCTGCACAAGCTAGGCCCTTATTTCCCTT 6 0.15 No Hit GATATCTATCTGAACTGAGAACTGAGTCAGTATATACCAGTCTGTATCAC 6 0.15 No Hit GGTGGGGCAATGGGCATTCCGTTGAGTTTGTATGGTGGGTGCTGTTTTGC 5 0.125 No Hit GGATCGGTCGATCATCGGAGAAGAACACTTCCTCCGTGCATATGCGTGTA 5 0.125 No Hit CAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCT 5 0.125 No Hit GGGTGGAATGGGAATTGCTATTCTTTCTACTTCTCGAGGGATAATGACAG 5 0.125 No Hit GGGGAAGTACACCAGCGACGGCGAGGCCGCCGCCGCCAAGGAAGGCATGT 5 0.125 No Hit GAATCGATCGTGATTTAGAACCTGTTCTTTACATGAACCCTCTTAACTAA 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 0.025 0.0 0.0 0.0 0.0 8 0.025 0.0 0.0 0.0 0.0 9 0.025 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 0.05 0.0 0.0 0.0 0.0 24-25 0.05 0.0 0.0 0.0 0.0 26-27 0.05 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 0.05 0.0 0.0 0.0 0.0 34-35 0.0625 0.0 0.0 0.0 0.0 36-37 0.65 0.0 0.0 0.0 0.0 38-39 1.1875 0.0 0.0 0.0 0.0 40-41 1.225 0.0 0.0 0.0 0.0 42-43 1.325 0.0 0.0 0.0 0.0 44-45 1.375 0.0 0.0 0.0 0.0 46-47 1.45 0.0 0.0 0.0 0.0 48-49 1.475 0.0 0.0 0.0 0.0 50-51 1.4875 0.0 0.0 0.0 0.0 52-53 1.525 0.0 0.0 0.0 0.0 54-55 1.525 0.0 0.0 0.0 0.0 56-57 1.525 0.0 0.0 0.0 0.0 58-59 1.55 0.0 0.0 0.0 0.0 60-61 1.55 0.0 0.0 0.0 0.0 62-63 1.55 0.0 0.0 0.0 0.0 64-65 1.55 0.0 0.0 0.0 0.0 66-67 1.575 0.0 0.0 0.0 0.0 68-69 1.575 0.0 0.0 0.0 0.0 70-71 1.575 0.0 0.0 0.0 0.0 72-73 1.575 0.0 0.0 0.0 0.0 74-75 1.575 0.0 0.0 0.0 0.0 76-77 1.5875 0.0 0.0 0.0 0.0 78-79 1.6 0.0 0.0 0.0 0.0 80-81 1.6 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GGATTCA 20 0.0027455038 65.15625 1 GATTCAA 20 0.0027455038 65.15625 2 GGTATGG 25 0.0022176977 35.189877 84-85 TCAAGGT 25 0.0023607365 34.75 32-33 TACTTGG 25 0.0023607365 34.75 50-51 >>END_MODULE Rejected 54404 READS because READLEN < 1 Read 54404 spots for ERR6133503.sra Written 54404 spots for ERR6133503.sra Rejected 54404 READS because READLEN < 1 Read 54404 spots for ERR6133503.sra Written 54404 spots for ERR6133503.sra Rejected 54404 READS because READLEN < 1 Read 54404 spots for ERR6133503.sra Written 54404 spots for ERR6133503.sra Rejected 54404 READS because READLEN < 1 Read 54404 spots for ERR6133503.sra Written 54404 spots for ERR6133503.sra Rejected 54404 READS because READLEN < 1 Read 54404 spots for ERR6133503.sra Written 54404 spots for ERR6133503.sra Rejected 54404 READS because READLEN < 1 Read 54404 spots for ERR6133503.sra Written 54404 spots for ERR6133503.sra Rejected 54404 READS because READLEN < 1 Read 54404 spots for ERR6133503.sra Written 54404 spots for ERR6133503.sra Rejected 54404 READS because READLEN < 1 Read 54404 spots for ERR6133503.sra Written 54404 spots for ERR6133503.sra Rejected 54404 READS because READLEN < 1 Read 54404 spots for ERR6133503.sra Written 54404 spots for ERR6133503.sra Rejected 54404 READS because READLEN < 1 Read 54404 spots for ERR6133503.sra Written 54404 spots for ERR6133503.sra Rejected 54404 READS because READLEN < 1 Read 54404 spots for ERR6133503.sra Written 54404 spots for ERR6133503.sra Rejected 54404 READS because READLEN < 1 Read 54404 spots for ERR6133503.sra Written 54404 spots for ERR6133503.sra Rejected 54404 READS because READLEN < 1 Read 54404 spots for ERR6133503.sra Written 54404 spots for ERR6133503.sra Rejected 54404 READS because READLEN < 1 Read 54404 spots for ERR6133503.sra Written 54404 spots for ERR6133503.sra Rejected 54417 READS because READLEN < 1 Read 54417 spots for ERR6133503.sra Written 54417 spots for ERR6133503.sra Rejected 54404 READS because READLEN < 1 Read 54404 spots for ERR6133503.sra Written 54404 spots for ERR6133503.sra Rejected 54404 READS because READLEN < 1 Read 54404 spots for ERR6133503.sra Written 54404 spots for ERR6133503.sra Rejected 54404 READS because READLEN < 1 Read 54404 spots for ERR6133503.sra Written 54404 spots for ERR6133503.sra Rejected 54404 READS because READLEN < 1 Read 54404 spots for ERR6133503.sra Written 54404 spots for ERR6133503.sra Rejected 54404 READS because READLEN < 1 Read 54404 spots for ERR6133503.sra Written 54404 spots for ERR6133503.sra SRR ids: ['ERR6133503.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_w5kgoka3 ERR6133503.sra spots: 1088093 blocks: [[1, 54404], [54405, 108808], [108809, 163212], [163213, 217616], [217617, 272020], [272021, 326424], [326425, 380828], [380829, 435232], [435233, 489636], [489637, 544040], [544041, 598444], [598445, 652848], [652849, 707252], [707253, 761656], [761657, 816060], [816061, 870464], [870465, 924868], [924869, 979272], [979273, 1033676], [1033677, 1088093]] ERR6133503 file size 238791 ERR6133503 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 ERR6133503 ERR6133503_1.fastq Input file: ERR6133503_1.fastq trimmed: ERR6133503-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 07:26:03 2024 >> started Sat Dec 7 07:26:04 2024 >> done (0.867s) 1088093 reads processed; of these: 244 ( 0.02%) short reads filtered out after trimming by size control 117 ( 0.01%) empty reads filtered out after trimming by size control 1087732 (99.97%) reads available; of these: 35839 ( 3.29%) trimmed reads available after processing 1051893 (96.71%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 21 0.00% 19 57 0.01% 20 15 0.00% 21 18 0.00% 22 25 0.00% 23 15 0.00% 24 8 0.00% 25 10 0.00% 26 13 0.00% 27 18 0.00% 28 36 0.00% 29 98 0.01% 30 44 0.00% 31 87 0.01% 32 137 0.01% 33 184 0.02% 34 247 0.02% 35 584 0.05% 36 12779 1.17% 37 178 0.02% 38 154 0.01% 39 226 0.02% 40 221 0.02% 41 189 0.02% 42 204 0.02% 43 187 0.02% 44 197 0.02% 45 199 0.02% 46 183 0.02% 47 204 0.02% 48 170 0.02% 49 173 0.02% 50 145 0.01% 51 142 0.01% 52 125 0.01% 53 104 0.01% 54 95 0.01% 55 90 0.01% 56 72 0.01% 57 56 0.01% 58 44 0.00% 59 47 0.00% 60 52 0.00% 61 37 0.00% 62 2 0.00% 63 0 0.00% 64 2 0.00% 65 1 0.00% 66 0 0.00% 67 6 0.00% 68 10 0.00% 69 27 0.00% 70 3186 0.29% 71 2696 0.25% 72 2759 0.25% 73 2431 0.22% 74 2695 0.25% 75 2695 0.25% 76 2257 0.21% 77 2549 0.23% 78 2767 0.25% 79 3134 0.29% 80 2707 0.25% 81 2943 0.27% 82 3346 0.31% 83 3489 0.32% 84 2645 0.24% 85 45 0.00% 86 77 0.01% 87 99 0.01% 88 205 0.02% 89 421 0.04% 90 919 0.08% 91 2596 0.24% 92 12873 1.18% 93 1010260 92.88% 1087732 reads passed initial QC criterion=sequence-density sequence-density=0.29 sequence-density-rank=1 fanout-score=3.63 fanout-score-rank=18 prefix-density=0.35 prefix-fanout=3.1 sequence=GTGTTGTGTTGT criterion=fanout-score sequence-density=0.02 sequence-density-rank=30 fanout-score=63.37 fanout-score-rank=1 prefix-density=0.16 prefix-fanout=6.4 sequence=AAAAGAAGGGGTGTTCCATCTCCGGACGACGATCCTGCCTGCGGAGGAAGACATGCCGGCGATCATGTCGAGCTTCAAGAAGTTCAACGACTCATTCATGGAGCAATACCAAGACTACTCCAGGCTGTGATGTGAAGAGGGAAACAACGACGTCATCATCGACATGATATATTGCTGCTATTTTCCACCAGCGATTAAAAGTTAAAAAATTTAGCTGTAAGCTGTAACTATCTTGAAGAAACTAAACTGGTTGCTGTGCTT Started job on | Dec 07 07:26:19 Started mapping on | Dec 07 07:26:19 Finished on | Dec 07 07:26:22 Mapping speed, Million of reads per hour | 1305.28 Number of input reads | 1087732 Average input read length | 91 UNIQUE READS: Uniquely mapped reads number | 773198 Uniquely mapped reads % | 71.08% Average mapped length | 91.93 Number of splices: Total | 33880 Number of splices: Annotated (sjdb) | 28306 Number of splices: GT/AG | 32607 Number of splices: GC/AG | 851 Number of splices: AT/AC | 29 Number of splices: Non-canonical | 393 Mismatch rate per base, % | 0.39% Deletion rate per base | 0.04% Deletion average length | 1.83 Insertion rate per base | 0.02% Insertion average length | 1.99 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 278092 % of reads mapped to multiple loci | 25.57% Number of reads mapped to too many loci | 4708 % of reads mapped to too many loci | 0.43% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 2.88% % of reads unmapped: other | 0.03% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 36442 36442 36442 N_multimapping 278092 278092 278092 N_noFeature 51794 60057 737425 N_ambiguous 30683 3203 99 UnstrandedReadsAssigned:690721 PositiveStrandReadsAssigned:709938 NegativeStrandReadsAssigned:35674 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=93 echo kmer=89 ERR6133503 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: ERR6133503-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 1,087,732 reads, 893,452 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 891 rounds 52973 ERR6133503.ke.tsv 35125 ERR6133503.se.tsv 88098 total ==> ERR6133503.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 20 21.8013 PNS24243 293 194 0 0 KQK14069 1603 1504 23 22.8711 KQK14071 474 375 0 0 ==> ERR6133503.se.tsv <== BRADI_1g14170v3 23 BRADI_1g53295v3 5 BRADI_1g59795v3 1 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 14 BRADI_1g74790v3 11 BRADI_1g09890v3 0 BRADI_1g77505v3 23 BRADI_1g48960v3 0 ERR6133503 completed mapping pipeline successfully