Starting /dee2/code/volunteer_pipeline.sh ERR6133448 current disk space = 1545596993536 free memory = 1600336856 ERR6133448 SRAfilesize 6347df2a2c71ab58e2b33bcad80a5830 ERR6133448.sra ERR6133448.sra file validated ERR6133448 is single end ERR6133448 is conventional basespace ERR6133448 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133448_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 47 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 35.1525 37.0 33.0 37.0 33.0 37.0 2 36.301 37.0 37.0 37.0 33.0 37.0 3 35.7215 37.0 37.0 37.0 33.0 37.0 4 35.48375 37.0 37.0 37.0 33.0 37.0 5 35.30425 37.0 37.0 37.0 33.0 37.0 6 35.58525 37.0 37.0 37.0 33.0 37.0 7 37.2115 37.0 37.0 40.0 33.0 40.0 8 37.3255 37.0 37.0 40.0 33.0 40.0 9 37.33975 37.0 37.0 40.0 33.0 40.0 10-11 37.304375 37.0 37.0 40.0 33.0 40.0 12-13 37.162375 37.0 37.0 40.0 33.0 40.0 14-15 37.18675 37.0 37.0 40.0 33.0 40.0 16-17 36.979 37.0 37.0 40.0 33.0 40.0 18-19 37.1065 37.0 37.0 40.0 33.0 40.0 20-21 37.253625 37.0 37.0 40.0 33.0 40.0 22-23 36.93225 37.0 37.0 40.0 33.0 40.0 24-25 37.072375 37.0 37.0 40.0 33.0 40.0 26-27 36.897875 37.0 37.0 40.0 33.0 40.0 28-29 37.055625 37.0 37.0 40.0 33.0 40.0 30-31 37.073125 37.0 37.0 40.0 33.0 40.0 32-33 36.876875 37.0 37.0 40.0 33.0 40.0 34-35 36.729625 37.0 37.0 40.0 33.0 40.0 36-37 36.772625000000005 37.0 37.0 40.0 33.0 40.0 38-39 36.476749999999996 37.0 37.0 40.0 33.0 40.0 40-41 36.380624999999995 37.0 37.0 40.0 33.0 40.0 42-43 36.320125000000004 37.0 37.0 40.0 33.0 40.0 44-45 36.04275 37.0 35.0 38.5 33.0 40.0 46-47 35.89375 37.0 37.0 37.0 33.0 40.0 48-49 35.738625 37.0 33.0 37.0 33.0 40.0 50-51 35.609750000000005 37.0 33.0 37.0 33.0 40.0 52-53 35.553875000000005 37.0 33.0 37.0 33.0 40.0 54-55 35.299 37.0 33.0 37.0 33.0 40.0 56-57 35.240875 37.0 33.0 37.0 33.0 37.0 58-59 34.696375 37.0 33.0 37.0 30.0 37.0 60-61 34.577125 37.0 33.0 37.0 30.0 37.0 62-63 34.6535 37.0 33.0 37.0 33.0 37.0 64-65 34.245625 37.0 33.0 37.0 27.0 37.0 66-67 34.302125000000004 37.0 33.0 37.0 27.0 37.0 68-69 32.961 35.0 33.0 35.0 27.0 37.0 70-71 33.23879346462619 33.0 33.0 37.0 27.0 37.0 72-73 33.976074436507616 37.0 33.0 37.0 27.0 37.0 74-75 34.2345914292383 37.0 33.0 37.0 27.0 37.0 76-77 34.23847969391298 37.0 33.0 37.0 30.0 37.0 78-79 34.192810560451335 37.0 33.0 37.0 30.0 37.0 80-81 34.13394324525857 37.0 33.0 37.0 30.0 37.0 82-83 33.92493603455647 37.0 33.0 37.0 27.0 37.0 84-85 33.882474606488 37.0 33.0 37.0 27.0 37.0 86-87 33.68680321493389 37.0 33.0 37.0 27.0 37.0 88-89 33.64065335753176 37.0 33.0 37.0 27.0 37.0 90-91 33.55768732175266 33.0 33.0 37.0 27.0 37.0 92-93 33.17461757842884 33.0 33.0 37.0 27.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 8.0 21 8.0 22 14.0 23 16.0 24 19.0 25 24.0 26 33.0 27 40.0 28 41.0 29 61.0 30 75.0 31 103.0 32 155.0 33 174.0 34 234.0 35 550.0 36 1038.0 37 983.0 38 419.0 39 5.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 88.97500000000001 2.5 2.55 5.975 2 73.88582874311467 15.448172258387583 6.71006509764647 3.9559339008512766 3 39.75 38.025 12.325 9.9 4 35.0 28.275 16.45 20.275000000000002 5 26.075 29.875 25.224999999999998 18.825 6 21.325 39.2 22.325 17.150000000000002 7 35.65 29.349999999999998 18.575 16.425 8 30.075000000000003 28.249999999999996 24.4 17.275 9 26.6 28.499999999999996 25.35 19.55 10-11 26.5375 27.0125 26.8 19.650000000000002 12-13 28.000000000000004 24.7375 26.5625 20.7 14-15 23.474999999999998 28.787499999999998 28.762500000000003 18.975 16-17 25.6125 30.0875 24.637500000000003 19.662499999999998 18-19 24.8625 26.5625 25.4625 23.1125 20-21 26.174999999999997 26.5125 26.787499999999998 20.525 22-23 28.425 23.175 25.924999999999997 22.475 24-25 26.974999999999998 23.425 26.700000000000003 22.900000000000002 26-27 25.85 25.724999999999998 28.4125 20.0125 28-29 26.200000000000003 27.150000000000002 25.4625 21.1875 30-31 29.299999999999997 25.4 23.6375 21.6625 32-33 25.112499999999997 27.3125 25.724999999999998 21.85 34-35 26.8125 24.087500000000002 26.375 22.725 36-37 25.75 23.3125 26.974999999999998 23.962500000000002 38-39 26.8375 24.4125 29.125 19.625 40-41 26.924999999999997 25.412499999999998 25.650000000000002 22.0125 42-43 25.7125 29.3375 23.962500000000002 20.9875 44-45 25.137500000000003 24.1375 27.4125 23.3125 46-47 25.724999999999998 22.7625 26.924999999999997 24.587500000000002 48-49 26.1 23.7125 29.3375 20.849999999999998 50-51 26.875 25.5625 27.650000000000002 19.9125 52-53 25.1 28.012500000000003 25.5375 21.349999999999998 54-55 23.525 28.725 25.837500000000002 21.912499999999998 56-57 26.8125 25.137500000000003 26.987499999999997 21.0625 58-59 24.5125 25.0625 27.787499999999998 22.6375 60-61 25.525 23.549999999999997 27.650000000000002 23.275000000000002 62-63 23.0375 28.1125 29.9625 18.8875 64-65 24.349999999999998 27.775 27.212500000000002 20.6625 66-67 24.4875 27.5125 26.125 21.875 68-69 24.887500000000003 25.412499999999998 26.875 22.825 70-71 26.158276984723265 25.406962183821687 26.045579764588027 22.389181066867017 72-73 27.5415198792149 23.905385002516354 26.383995973829894 22.169099144438853 74-75 24.086483752686814 28.01871285876849 28.13250727019851 19.762296118346185 76-77 22.64294790343075 25.527318932655657 28.86912325285896 22.96060991105464 78-79 25.127420998980632 24.24821610601427 28.69520897043833 21.92915392456677 80-81 24.69578583322659 27.29601639554246 28.97399769437684 19.034200076854106 82-83 27.00579523502898 21.957501609787506 28.783000643915003 22.253702511268514 84-85 24.3877154334586 23.24737592328625 28.9361150706233 23.42879357263185 86-87 22.621208192896034 25.628726989888513 31.086336530982628 20.663728286232825 88-89 23.645320197044335 29.10292973813845 28.89551464869069 18.356235416126523 90-91 27.365828364013485 25.74539797770288 26.98988851438942 19.89888514389422 92-93 23.606429867772878 28.688099559242936 27.430645579465907 20.27482499351828 >>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 0.0 16 0.0 17 5.5 18 6.5 19 1.5 20 2.0 21 4.0 22 4.0 23 5.5 24 6.5 25 4.5 26 5.0 27 9.0 28 14.0 29 16.0 30 21.0 31 24.0 32 28.5 33 45.5 34 61.0 35 73.5 36 86.5 37 112.5 38 143.0 39 150.5 40 152.5 41 162.0 42 167.0 43 168.0 44 167.0 45 168.5 46 221.5 47 209.5 48 147.5 49 141.0 50 145.0 51 165.5 52 175.0 53 193.5 54 186.5 55 132.5 56 88.0 57 71.5 58 76.0 59 78.0 60 67.0 61 54.0 62 46.5 63 43.5 64 50.5 65 47.0 66 32.5 67 28.5 68 29.5 69 21.0 70 8.5 71 5.0 72 5.0 73 4.5 74 4.0 75 4.0 76 2.5 77 0.5 78 0.0 79 0.5 80 1.0 81 0.5 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 0.15 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 0.0 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 0.0 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 0.02591009198082653 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 5.0 72 14.0 73 8.0 74 9.0 75 14.0 76 2.0 77 5.0 78 10.0 79 10.0 80 11.0 81 9.0 82 13.0 83 14.0 84 5.0 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 3857.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 78.10000000000001 #Duplication Level Percentage of deduplicated Percentage of total 1 91.86939820742637 71.75 2 4.929577464788732 7.7 3 1.120358514724712 2.625 4 0.7042253521126761 2.1999999999999997 5 0.41613316261203587 1.625 6 0.16005121638924455 0.75 7 0.09603072983354673 0.525 8 0.03201024327784891 0.2 9 0.03201024327784891 0.22499999999999998 >10 0.5441741357234315 7.3 >50 0.09603072983354673 5.1 >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 GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 80 2.0 No Hit GGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGG 65 1.625 No Hit GGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGC 59 1.4749999999999999 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 38 0.95 No Hit GGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGGG 37 0.9249999999999999 No Hit GGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAA 28 0.7000000000000001 No Hit GGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTT 22 0.5499999999999999 No Hit GGGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTG 21 0.525 No Hit GGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCG 16 0.4 No Hit GTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAA 15 0.375 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 13 0.325 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 13 0.325 No Hit GGGGAAGTACACCAGCGACGGCGAGGCCGCCGCCGCCAAGGAAGGCATGT 13 0.325 No Hit GGAAAAGAAAGCAAAAGCGATTCCCGTAGTAGCGGCGAGCGAAATGGGAG 13 0.325 No Hit GGAGTATCCTTGATATATAAATATATAGATAAATAGATTTAAATGGAAAA 12 0.3 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 11 0.27499999999999997 No Hit GGCCTGTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCG 10 0.25 No Hit GGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAA 10 0.25 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 10 0.25 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 10 0.25 No Hit GGGAGTATTATGAAAGGAGATTAATCATAGATTATCAAAAACCCTAGAAA 9 0.22499999999999998 No Hit GGTGGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGC 8 0.2 No Hit GGGCTGCGAGGAATCCGGCAAGGCATAAACAACCAAGGACAGCTCCGTAT 7 0.17500000000000002 No Hit GGAGTCCCATATATATATGTATAAGATGCCAGCCCGGTTTCGTCAACCAT 7 0.17500000000000002 No Hit GGGGAAGAAGACCTCTTTCTGGGAGGCCGAAGCCACTTCGGCACCGGTAC 7 0.17500000000000002 No Hit GGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCTAAA 6 0.15 No Hit TGAGTATGATGAGTCTGGTCCAGCGATTGTTCACAGGAAGTGCTTCTAAG 6 0.15 No Hit GGGCAAGGAGAAGTACAAGTGCGGATCCAACGTCTTCTGGAAATGGTGAA 6 0.15 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 6 0.15 No Hit GCAGCTGGGGAAGTACACCAGCGACGGCGAGGCCGCCGCCGCCAAGGAAG 6 0.15 No Hit GACCACAGCGCATTCCCAATTAGCATCTAAGCTCTCGTTGACATTTCCTT 5 0.125 No Hit GGGATGGAGATGGCCGCGGAGAACGGCGGCTGCGGCTGCAGCACCTGCAA 5 0.125 No Hit CAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATAT 5 0.125 No Hit GGGATGGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACGA 5 0.125 No Hit GGGGATGGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACG 5 0.125 No Hit GAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAAT 5 0.125 No Hit GGATTTGAAGAAAAAAAAGACTTCGATTCATTTTCTATTTATTTCGTTAG 5 0.125 No Hit GGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCTAAATGGATTC 5 0.125 No Hit GGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGC 5 0.125 No Hit GTATTTAGCCTTGCAAGGTGGTCCTTGCTGATTCACACGGGATTCCACGT 5 0.125 No Hit GGCATATGCCAGCTCTGACCGAAATCTTTGGGGATGATTCTGTATTACAA 5 0.125 No Hit GGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAACCCTCTTAACT 5 0.125 No Hit GGATTCTTCTTTTTTGTGGGCCATTTGTGGCATGCAGGAAGAGCCCGAGC 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 0.0125 0.0 0.0 0.0 0.0 14-15 0.025 0.0 0.0 0.0 0.0 16-17 0.025 0.0 0.0 0.0 0.0 18-19 0.025 0.0 0.0 0.0 0.0 20-21 0.025 0.0 0.0 0.0 0.0 22-23 0.025 0.0 0.0 0.0 0.0 24-25 0.025 0.0 0.0 0.0 0.0 26-27 0.025 0.0 0.0 0.0 0.0 28-29 0.025 0.0 0.0 0.0 0.0 30-31 0.025 0.0 0.0 0.0 0.0 32-33 0.025 0.0 0.0 0.0 0.0 34-35 0.025 0.0 0.0 0.0 0.0 36-37 0.025 0.0 0.0 0.0 0.0 38-39 0.025 0.0 0.0 0.0 0.0 40-41 0.025 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 0.025 0.0 0.0 0.0 0.0 74-75 0.025 0.0 0.0 0.0 0.0 76-77 0.025 0.0 0.0 0.0 0.0 78-79 0.025 0.0 0.0 0.0 0.0 80-81 0.025 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Rejected 139571 READS because READLEN < 1 Read 139571 spots for ERR6133448.sra Written 139571 spots for ERR6133448.sra Rejected 139571 READS because READLEN < 1 Read 139571 spots for ERR6133448.sra Written 139571 spots for ERR6133448.sra Rejected 139571 READS because READLEN < 1 Read 139571 spots for ERR6133448.sra Written 139571 spots for ERR6133448.sra Rejected 139571 READS because READLEN < 1 Read 139571 spots for ERR6133448.sra Written 139571 spots for ERR6133448.sra Rejected 139571 READS because READLEN < 1 Read 139571 spots for ERR6133448.sra Written 139571 spots for ERR6133448.sra Rejected 139571 READS because READLEN < 1 Read 139571 spots for ERR6133448.sra Written 139571 spots for ERR6133448.sra Rejected 139571 READS because READLEN < 1 Read 139571 spots for ERR6133448.sra Written 139571 spots for ERR6133448.sra Rejected 139571 READS because READLEN < 1 Read 139571 spots for ERR6133448.sra Written 139571 spots for ERR6133448.sra Rejected 139571 READS because READLEN < 1 Read 139571 spots for ERR6133448.sra Written 139571 spots for ERR6133448.sra Rejected 139571 READS because READLEN < 1 Read 139571 spots for ERR6133448.sra Written 139571 spots for ERR6133448.sra Rejected 139571 READS because READLEN < 1 Read 139571 spots for ERR6133448.sra Written 139571 spots for ERR6133448.sra Rejected 139571 READS because READLEN < 1 Read 139571 spots for ERR6133448.sra Written 139571 spots for ERR6133448.sra Rejected 139571 READS because READLEN < 1 Read 139571 spots for ERR6133448.sra Written 139571 spots for ERR6133448.sra Rejected 139571 READS because READLEN < 1 Read 139571 spots for ERR6133448.sra Written 139571 spots for ERR6133448.sra Rejected 139571 READS because READLEN < 1 Read 139571 spots for ERR6133448.sra Written 139571 spots for ERR6133448.sra Rejected 139571 READS because READLEN < 1 Read 139571 spots for ERR6133448.sra Written 139571 spots for ERR6133448.sra Rejected 139571 READS because READLEN < 1 Read 139571 spots for ERR6133448.sra Written 139571 spots for ERR6133448.sra Rejected 139571 READS because READLEN < 1 Read 139571 spots for ERR6133448.sra Written 139571 spots for ERR6133448.sra Rejected 139571 READS because READLEN < 1 Read 139571 spots for ERR6133448.sra Written 139571 spots for ERR6133448.sra Rejected 139576 READS because READLEN < 1 Read 139576 spots for ERR6133448.sra Written 139576 spots for ERR6133448.sra SRR ids: ['ERR6133448.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_5x9wql3b ERR6133448.sra spots: 2791425 blocks: [[1, 139571], [139572, 279142], [279143, 418713], [418714, 558284], [558285, 697855], [697856, 837426], [837427, 976997], [976998, 1116568], [1116569, 1256139], [1256140, 1395710], [1395711, 1535281], [1535282, 1674852], [1674853, 1814423], [1814424, 1953994], [1953995, 2093565], [2093566, 2233136], [2233137, 2372707], [2372708, 2512278], [2512279, 2651849], [2651850, 2791425]] ERR6133448 file size 615888 ERR6133448 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 ERR6133448 ERR6133448_1.fastq Input file: ERR6133448_1.fastq trimmed: ERR6133448-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 06:15:27 2024 >> started Sat Dec 7 06:15:29 2024 >> done (2.356s) 2791425 reads processed; of these: 1247 ( 0.04%) short reads filtered out after trimming by size control 16 ( 0.00%) empty reads filtered out after trimming by size control 2790162 (99.95%) reads available; of these: 41358 ( 1.48%) trimmed reads available after processing 2748804 (98.52%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 28 0.00% 19 56 0.00% 20 19 0.00% 21 10 0.00% 22 14 0.00% 23 11 0.00% 24 5 0.00% 25 9 0.00% 26 7 0.00% 27 6 0.00% 28 9 0.00% 29 54 0.00% 30 10 0.00% 31 13 0.00% 32 15 0.00% 33 12 0.00% 34 6 0.00% 35 4 0.00% 36 12 0.00% 37 9 0.00% 38 24 0.00% 39 31 0.00% 40 68 0.00% 41 24 0.00% 42 22 0.00% 43 20 0.00% 44 17 0.00% 45 12 0.00% 46 15 0.00% 47 13 0.00% 48 10 0.00% 49 18 0.00% 50 21 0.00% 51 55 0.00% 52 24 0.00% 53 21 0.00% 54 19 0.00% 55 25 0.00% 56 26 0.00% 57 22 0.00% 58 15 0.00% 59 15 0.00% 60 21 0.00% 61 6 0.00% 62 1 0.00% 63 0 0.00% 64 0 0.00% 65 4 0.00% 66 9 0.00% 67 10 0.00% 68 21 0.00% 69 81 0.00% 70 8464 0.30% 71 7048 0.25% 72 7317 0.26% 73 6736 0.24% 74 7210 0.26% 75 7029 0.25% 76 6084 0.22% 77 6264 0.22% 78 7318 0.26% 79 8257 0.30% 80 7195 0.26% 81 7630 0.27% 82 8749 0.31% 83 8828 0.32% 84 7194 0.26% 85 83 0.00% 86 160 0.01% 87 262 0.01% 88 445 0.02% 89 1022 0.04% 90 2374 0.09% 91 6954 0.25% 92 27719 0.99% 93 2638841 94.58% 2790162 reads passed initial QC criterion=sequence-density sequence-density=0.43 sequence-density-rank=1 fanout-score=5.69 fanout-score-rank=16 prefix-density=0.98 prefix-fanout=2.5 sequence=GCCGCCGCCGCCAAGGAAGGCATGTTCGTCAAGAACTACAGCTACTGATCCTAATCGCATCAAGCTTCAACGCCTGTGAGTGAAAACCAGTGATGAGAGTGCTGCTGCTAGCTAGCGCCGGCATTGATGAGCTTGAGAGGGCACTGTAGCCAGTGTGTCAGTCGTTGTTAAATTACAGGTTGAGATCATCAGCGTACTCCGATGGGAGATGGACATCAGAAAGTATACTGTGTTTTACCACCCTAATTAAGTAAACAACTTTTGGAATGGTGATTATCTTACTGTTTTAAATAAATCTGTTTC criterion=fanout-score sequence-density=0.01 sequence-density-rank=31 fanout-score=193.72 fanout-score-rank=1 prefix-density=0.73 prefix-fanout=2.1 sequence=CAAGTGCGGAGAGGATAACTGCTGAAAGCATATAAGTAGTAAGCCCACCCCAAGATGAGTGCTCTCTCCTCCGACTTCCCTAGAGCCTCCGGTATCACAGCCGAGACAGCGACGGGTTCTCCACCCATACGGGGATGGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACGAGCCGTTTAAATAGGTGTCAAGTGGAAGTGCAGTGATGTATGCAGCTGAGGCATCCTAACGAACGAACGATTTGAACCTTGTTCCTACACGGCCTGATCA Started job on | Dec 07 06:15:42 Started mapping on | Dec 07 06:15:42 Finished on | Dec 07 06:15:46 Mapping speed, Million of reads per hour | 2511.15 Number of input reads | 2790162 Average input read length | 92 UNIQUE READS: Uniquely mapped reads number | 1986404 Uniquely mapped reads % | 71.19% Average mapped length | 92.04 Number of splices: Total | 131522 Number of splices: Annotated (sjdb) | 110811 Number of splices: GT/AG | 128730 Number of splices: GC/AG | 2180 Number of splices: AT/AC | 56 Number of splices: Non-canonical | 556 Mismatch rate per base, % | 0.26% Deletion rate per base | 0.02% Deletion average length | 1.51 Insertion rate per base | 0.00% Insertion average length | 1.54 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 752423 % of reads mapped to multiple loci | 26.97% Number of reads mapped to too many loci | 14597 % of reads mapped to too many loci | 0.52% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.29% % of reads unmapped: other | 0.03% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 51335 51335 51335 N_multimapping 752423 752423 752423 N_noFeature 98457 116137 1901471 N_ambiguous 75222 7959 301 UnstrandedReadsAssigned:1812725 PositiveStrandReadsAssigned:1862308 NegativeStrandReadsAssigned:84632 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=93 echo kmer=89 ERR6133448 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: ERR6133448-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 2,790,162 reads, 2,402,237 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,000 rounds 52973 ERR6133448.ke.tsv 35125 ERR6133448.se.tsv 88098 total ==> ERR6133448.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 45 17.6904 PNS24243 293 194 0 0 KQK14069 1603 1504 3 1.07585 KQK14071 474 375 0 0 ==> ERR6133448.se.tsv <== BRADI_1g14170v3 3 BRADI_1g53295v3 7 BRADI_1g59795v3 7 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 20 BRADI_1g74790v3 12 BRADI_1g09890v3 0 BRADI_1g77505v3 49 BRADI_1g48960v3 0 ERR6133448 completed mapping pipeline successfully