Starting /dee2/code/volunteer_pipeline.sh ERR6133380 current disk space = 1547648311296 free memory = 1598189168 ERR6133380 SRAfilesize 2808430f387f71e0e754ee105c078819 ERR6133380.sra ERR6133380.sra file validated ERR6133380 is single end ERR6133380 is conventional basespace ERR6133380 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133380_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 36.89025 37.0 37.0 37.0 37.0 37.0 2 36.80175 37.0 37.0 37.0 37.0 37.0 3 36.6095 37.0 37.0 37.0 37.0 37.0 4 36.1025 37.0 37.0 37.0 33.0 37.0 5 36.11175 37.0 37.0 37.0 33.0 37.0 6 36.22975 37.0 37.0 37.0 33.0 37.0 7 38.17625 40.0 37.0 40.0 37.0 40.0 8 38.1135 40.0 37.0 40.0 37.0 40.0 9 38.13775 40.0 37.0 40.0 37.0 40.0 10-11 38.119625 40.0 37.0 40.0 37.0 40.0 12-13 38.115750000000006 40.0 37.0 40.0 37.0 40.0 14-15 38.078500000000005 40.0 37.0 40.0 37.0 40.0 16-17 37.9865 40.0 37.0 40.0 33.0 40.0 18-19 37.91825 40.0 37.0 40.0 33.0 40.0 20-21 37.754625 40.0 37.0 40.0 33.0 40.0 22-23 37.76175 40.0 37.0 40.0 33.0 40.0 24-25 37.60725 40.0 37.0 40.0 33.0 40.0 26-27 37.436125000000004 37.0 37.0 40.0 33.0 40.0 28-29 37.35725 37.0 37.0 40.0 33.0 40.0 30-31 37.291125 37.0 37.0 40.0 33.0 40.0 32-33 37.02975 37.0 37.0 40.0 33.0 40.0 34-35 36.87875 37.0 37.0 40.0 33.0 40.0 36-37 36.8645 37.0 37.0 40.0 33.0 40.0 38-39 36.972125 37.0 37.0 40.0 33.0 40.0 40-41 37.189875 37.0 37.0 40.0 33.0 40.0 42-43 37.11925 37.0 37.0 40.0 33.0 40.0 44-45 37.045625 37.0 37.0 40.0 33.0 40.0 46-47 36.773624999999996 37.0 37.0 40.0 33.0 40.0 48-49 36.686875 37.0 37.0 40.0 33.0 40.0 50-51 36.592124999999996 37.0 37.0 38.5 33.0 40.0 52-53 36.473375 37.0 37.0 37.0 33.0 40.0 54-55 36.259375000000006 37.0 37.0 37.0 33.0 40.0 56-57 35.9985 37.0 37.0 37.0 33.0 40.0 58-59 35.873000000000005 37.0 37.0 37.0 33.0 40.0 60-61 35.761875 37.0 37.0 37.0 33.0 37.0 62-63 35.464124999999996 37.0 33.0 37.0 33.0 37.0 64-65 35.283500000000004 37.0 33.0 37.0 33.0 37.0 66-67 35.34175 37.0 33.0 37.0 33.0 37.0 68-69 34.306 35.0 33.0 37.0 30.0 37.0 70-71 34.54121965897693 37.0 33.0 37.0 33.0 37.0 72-73 34.995023555672034 37.0 33.0 37.0 33.0 37.0 74-75 34.98161966971708 37.0 33.0 37.0 33.0 37.0 76-77 34.8614814696349 37.0 33.0 37.0 33.0 37.0 78-79 34.93305132641395 37.0 33.0 37.0 33.0 37.0 80-81 34.79986286480824 37.0 33.0 37.0 33.0 37.0 82-83 34.504546277305295 37.0 33.0 37.0 33.0 37.0 84-85 34.551907461422296 37.0 33.0 37.0 33.0 37.0 86-87 34.45860883364189 37.0 33.0 37.0 33.0 37.0 88-89 34.38296746892357 37.0 33.0 37.0 33.0 37.0 90-91 34.01785241999471 37.0 33.0 37.0 27.0 37.0 92-93 33.667944988098384 37.0 33.0 37.0 27.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 1.0 21 7.0 22 4.0 23 11.0 24 12.0 25 18.0 26 18.0 27 25.0 28 33.0 29 46.0 30 55.0 31 84.0 32 89.0 33 106.0 34 218.0 35 351.0 36 883.0 37 1081.0 38 918.0 39 40.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 81.15 4.55 4.5249999999999995 9.775 2 59.85 23.724999999999998 10.625 5.800000000000001 3 34.75 36.5 15.9 12.85 4 33.675 25.0 19.425 21.9 5 22.85 32.574999999999996 25.974999999999998 18.6 6 20.150000000000002 37.925 25.5 16.425 7 35.025 28.375 20.275000000000002 16.325 8 29.7 27.975 24.875 17.45 9 25.775 25.825 28.075 20.325 10-11 25.2875 28.462500000000002 26.7625 19.4875 12-13 28.050000000000004 24.9 28.5625 18.4875 14-15 22.4875 25.6 32.2 19.7125 16-17 24.8125 30.7875 26.75 17.65 18-19 23.825 26.937499999999996 27.075 22.162499999999998 20-21 25.45 27.3125 26.887499999999996 20.349999999999998 22-23 27.250000000000004 25.5625 25.6125 21.575 24-25 25.912499999999998 23.4625 28.5625 22.0625 26-27 24.6 25.8 29.95 19.650000000000002 28-29 25.9625 25.3 28.075 20.6625 30-31 25.900000000000002 25.8125 26.900000000000002 21.3875 32-33 23.5125 27.3625 28.65 20.474999999999998 34-35 26.375 24.099999999999998 28.1375 21.3875 36-37 24.637500000000003 24.625 28.6875 22.05 38-39 24.962500000000002 25.874999999999996 30.6375 18.525 40-41 25.9875 25.55 26.85 21.6125 42-43 24.5375 28.8625 26.900000000000002 19.7 44-45 23.6125 26.400000000000002 28.762500000000003 21.224999999999998 46-47 24.3625 24.6 28.212500000000002 22.825 48-49 23.7125 25.5 30.75 20.0375 50-51 24.15 27.212500000000002 28.6625 19.975 52-53 24.837500000000002 26.875 27.950000000000003 20.3375 54-55 24.9875 28.4125 26.974999999999998 19.625 56-57 24.712500000000002 26.174999999999997 28.237499999999997 20.875 58-59 22.1 25.4375 30.099999999999998 22.3625 60-61 24.775 25.650000000000002 28.9875 20.5875 62-63 21.45 28.3875 31.225 18.9375 64-65 23.75 26.900000000000002 29.362500000000004 19.9875 66-67 24.55 27.287499999999998 28.975 19.1875 68-69 23.5 26.437500000000004 28.15 21.912499999999998 70-71 25.31296945418127 24.749624436654983 28.24236354531798 21.695042563845767 72-73 26.46873820606366 25.474902503459557 27.500314504969182 20.55604478550761 74-75 23.425022182786158 26.974267968056786 29.319305361896316 20.281404487260744 76-77 22.994379151762903 26.379662749105776 29.522227899846705 21.10373019928462 78-79 23.42864502833591 24.74240082431736 31.182380216383308 20.64657393096342 80-81 24.113290892555543 27.803040145511236 29.634922697154735 18.448746264778485 82-83 23.739221322184477 24.183433498824144 31.7742356937549 20.30310948523648 84-85 23.23525531072701 24.67343976777939 30.62409288824383 21.46721203324977 86-87 22.25601692673896 27.09600634752711 30.838402539010843 19.80957418672309 88-89 22.44115313409151 29.463104998677597 29.754033324517327 18.341708542713565 90-91 25.83972494049193 26.61994181433483 28.550647976725735 18.989685268447502 92-93 22.732081459931237 28.60354403596932 29.330864850568634 19.33350965353081 >>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 3.0 18 5.0 19 3.0 20 2.5 21 4.0 22 3.5 23 2.5 24 5.5 25 6.5 26 12.5 27 17.5 28 18.5 29 23.0 30 27.5 31 32.5 32 44.5 33 66.5 34 88.5 35 107.0 36 124.5 37 148.5 38 162.5 39 173.5 40 188.0 41 187.0 42 195.5 43 211.0 44 201.5 45 178.5 46 183.5 47 196.0 48 185.0 49 172.5 50 168.5 51 166.5 52 151.0 53 156.5 54 137.5 55 87.0 56 69.5 57 65.5 58 55.5 59 50.0 60 42.0 61 31.0 62 31.0 63 30.0 64 35.5 65 31.0 66 15.0 67 11.5 68 13.0 69 7.5 70 2.5 71 1.0 72 1.5 73 2.0 74 1.5 75 1.0 76 0.5 77 0.0 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 0.0 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 0.0 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 12.0 71 8.0 72 11.0 73 17.0 74 15.0 75 14.0 76 18.0 77 14.0 78 18.0 79 20.0 80 9.0 81 7.0 82 20.0 83 19.0 84 17.0 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 3781.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 82.375 #Duplication Level Percentage of deduplicated Percentage of total 1 93.01972685887708 76.625 2 4.188163884673749 6.9 3 1.1229135053110775 2.775 4 0.3641881638846738 1.2 5 0.3338391502276176 1.375 6 0.2731411229135053 1.35 7 0.09104704097116845 0.525 8 0.12139605462822459 0.8 9 0.030349013657056147 0.22499999999999998 >10 0.42488619119878607 6.550000000000001 >50 0.030349013657056147 1.675 >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 67 1.675 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 34 0.8500000000000001 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 29 0.7250000000000001 No Hit GAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGC 25 0.625 No Hit GGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTT 22 0.5499999999999999 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 21 0.525 No Hit GGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGGG 21 0.525 No Hit GGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAA 18 0.44999999999999996 No Hit GGGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTG 17 0.42500000000000004 No Hit GGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGG 16 0.4 No Hit GTATTTAGCCTTGCAAGGTGGTCCTTGCTGATTCACACGGGATTCCACGT 13 0.325 No Hit GTATGGAAGGCGATCAAATTCGAGTTCGCGCCGGTAGATACTATCGATTA 12 0.3 No Hit GGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAA 12 0.3 No Hit GGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGC 12 0.3 No Hit GCAGCTTGCAAATGGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAA 10 0.25 No Hit GGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAACCCTCTTAACT 9 0.22499999999999998 No Hit GGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGC 8 0.2 No Hit CAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAACGAAGGG 8 0.2 No Hit GGGCTCGAGGAGCATATGTACATTTGAACCCTGACTACACATTTACACAC 8 0.2 No Hit GTACAAGCTCGTAACGAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAAT 8 0.2 No Hit GGATATCGTGTGTGTACATTTGAATGTACCGACATGGGCTCGAGGAGCAT 7 0.17500000000000002 No Hit GGAGTATCCTTGATATATAAATATATAGATAAATAGATTTAAATGGAAAA 7 0.17500000000000002 No Hit GGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTT 7 0.17500000000000002 No Hit GGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCG 6 0.15 No Hit GACGATTTTATTGAAAAAGATCGTGCTCGCGGTATCTTTTTCACTCAGGA 6 0.15 No Hit GGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAAA 6 0.15 No Hit GAAGTATGGAAGGCGATCAAATTCGAGTTCGCGCCGGTAGATACTATCGA 6 0.15 No Hit GGGAGTATTATGAAAGGAGATTAATCATAGATTATCAAAAACCCTAGAAA 6 0.15 No Hit GGGCATTCGTATTTCATAGTCAGAGGTGAAATTCTTGGATTTATGAAAGA 6 0.15 No Hit GGGGGTCGCAGTGACCAGGCCCGGGCGACTGTTTACCAAAAACACAGGTC 6 0.15 No Hit GGTTTTGAAAAGGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAA 6 0.15 No Hit GGGGAACGCGAAATCACTTTAGGTTTTGTTGATTTATTGCGCGACGATTT 6 0.15 No Hit GGTGGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGC 5 0.125 No Hit GGAGTCCCATATATATATGTATAAGATGCCAGCCCGGTTTCGTCAACCAT 5 0.125 No Hit GAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAAT 5 0.125 No Hit AGTATGGCATCGGTTACATACTTCAGTGCCGTAGCGCCTGGTATGAGCCT 5 0.125 No Hit GGGCAAGGAGAAGTACAAGTGCGGATCCAACGTCTTCTGGAAATGGTGAA 5 0.125 No Hit TAGTTTCCACCGCCTGTCCAGGGTTGAGCCCTGGGATTTGACGGCGGACT 5 0.125 No Hit GATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGGGG 5 0.125 No Hit GGGCCGGGTATCTCTCTGCATGTACGTATGCCTGTAATGTACGTAGCTAC 5 0.125 No Hit CACTCAGGACTGGGTATCCATGCCAGGTGTTATACCAGTAGCTTCAGGTG 5 0.125 No Hit GGGAACGCGAAATCACTTTAGGTTTTGTTGATTTATTGCGCGACGATTTT 5 0.125 No Hit GGGACGCATGCAACGACCATCTACATATAGCTACTCGATCTACCGCTACC 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 0.0 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 0.0125 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 0.075 0.0 0.0 0.0 0.0 42-43 0.075 0.0 0.0 0.0 0.0 44-45 0.075 0.0 0.0 0.0 0.0 46-47 0.075 0.0 0.0 0.0 0.0 48-49 0.075 0.0 0.0 0.0 0.0 50-51 0.075 0.0 0.0 0.0 0.0 52-53 0.0875 0.0 0.0 0.0 0.0 54-55 0.1 0.0 0.0 0.0 0.0 56-57 0.1 0.0 0.0 0.0 0.0 58-59 0.1 0.0 0.0 0.0 0.0 60-61 0.1 0.0 0.0 0.0 0.0 62-63 0.1 0.0 0.0 0.0 0.0 64-65 0.1 0.0 0.0 0.0 0.0 66-67 0.1 0.0 0.0 0.0 0.0 68-69 0.1 0.0 0.0 0.0 0.0 70-71 0.1 0.0 0.0 0.0 0.0 72-73 0.1 0.0 0.0 0.0 0.0 74-75 0.1125 0.0 0.0 0.0 0.0 76-77 0.125 0.0 0.0 0.0 0.0 78-79 0.125 0.0 0.0 0.0 0.0 80-81 0.1375 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Rejected 135275 READS because READLEN < 1 Read 135275 spots for ERR6133380.sra Written 135275 spots for ERR6133380.sra Rejected 135275 READS because READLEN < 1 Read 135275 spots for ERR6133380.sra Written 135275 spots for ERR6133380.sra Rejected 135275 READS because READLEN < 1 Read 135275 spots for ERR6133380.sra Written 135275 spots for ERR6133380.sra Rejected 135275 READS because READLEN < 1 Read 135275 spots for ERR6133380.sra Written 135275 spots for ERR6133380.sra Rejected 135275 READS because READLEN < 1 Read 135275 spots for ERR6133380.sra Written 135275 spots for ERR6133380.sra Rejected 135275 READS because READLEN < 1 Read 135275 spots for ERR6133380.sra Written 135275 spots for ERR6133380.sra Rejected 135275 READS because READLEN < 1 Read 135275 spots for ERR6133380.sra Written 135275 spots for ERR6133380.sra Rejected 135275 READS because READLEN < 1 Read 135275 spots for ERR6133380.sra Written 135275 spots for ERR6133380.sra Rejected 135275 READS because READLEN < 1 Read 135275 spots for ERR6133380.sra Written 135275 spots for ERR6133380.sra Rejected 135275 READS because READLEN < 1 Read 135275 spots for ERR6133380.sra Written 135275 spots for ERR6133380.sra Rejected 135275 READS because READLEN < 1 Read 135275 spots for ERR6133380.sra Written 135275 spots for ERR6133380.sra Rejected 135275 READS because READLEN < 1 Read 135275 spots for ERR6133380.sra Written 135275 spots for ERR6133380.sra Rejected 135275 READS because READLEN < 1 Read 135275 spots for ERR6133380.sra Written 135275 spots for ERR6133380.sra Rejected 135275 READS because READLEN < 1 Read 135275 spots for ERR6133380.sra Written 135275 spots for ERR6133380.sra Rejected 135275 READS because READLEN < 1 Read 135275 spots for ERR6133380.sra Written 135275 spots for ERR6133380.sra Rejected 135275 READS because READLEN < 1 Read 135275 spots for ERR6133380.sra Written 135275 spots for ERR6133380.sra Rejected 135275 READS because READLEN < 1 Read 135275 spots for ERR6133380.sra Written 135275 spots for ERR6133380.sra Rejected 135275 READS because READLEN < 1 Read 135275 spots for ERR6133380.sra Written 135275 spots for ERR6133380.sra Rejected 135284 READS because READLEN < 1 Read 135284 spots for ERR6133380.sra Written 135284 spots for ERR6133380.sra Rejected 135275 READS because READLEN < 1 Read 135275 spots for ERR6133380.sra Written 135275 spots for ERR6133380.sra SRR ids: ['ERR6133380.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_9hlelkmn ERR6133380.sra spots: 2705509 blocks: [[1, 135275], [135276, 270550], [270551, 405825], [405826, 541100], [541101, 676375], [676376, 811650], [811651, 946925], [946926, 1082200], [1082201, 1217475], [1217476, 1352750], [1352751, 1488025], [1488026, 1623300], [1623301, 1758575], [1758576, 1893850], [1893851, 2029125], [2029126, 2164400], [2164401, 2299675], [2299676, 2434950], [2434951, 2570225], [2570226, 2705509]] ERR6133380 file size 594898 ERR6133380 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 ERR6133380 ERR6133380_1.fastq Input file: ERR6133380_1.fastq trimmed: ERR6133380-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 02:28:18 2024 >> started Sat Dec 7 02:28:19 2024 >> done (1.424s) 2705509 reads processed; of these: 220 ( 0.01%) short reads filtered out after trimming by size control 5 ( 0.00%) empty reads filtered out after trimming by size control 2705284 (99.99%) reads available; of these: 107342 ( 3.97%) trimmed reads available after processing 2597942 (96.03%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 25 0.00% 19 45 0.00% 20 18 0.00% 21 6 0.00% 22 15 0.00% 23 5 0.00% 24 9 0.00% 25 13 0.00% 26 8 0.00% 27 10 0.00% 28 12 0.00% 29 38 0.00% 30 8 0.00% 31 13 0.00% 32 22 0.00% 33 9 0.00% 34 9 0.00% 35 5 0.00% 36 7 0.00% 37 12 0.00% 38 25 0.00% 39 53 0.00% 40 112 0.00% 41 18 0.00% 42 22 0.00% 43 18 0.00% 44 24 0.00% 45 23 0.00% 46 65 0.00% 47 54 0.00% 48 136 0.01% 49 881 0.03% 50 245 0.01% 51 255 0.01% 52 283 0.01% 53 319 0.01% 54 307 0.01% 55 391 0.01% 56 432 0.02% 57 508 0.02% 58 479 0.02% 59 615 0.02% 60 691 0.03% 61 596 0.02% 62 669 0.02% 63 882 0.03% 64 851 0.03% 65 882 0.03% 66 955 0.04% 67 1072 0.04% 68 1364 0.05% 69 686 0.03% 70 11963 0.44% 71 11573 0.43% 72 13568 0.50% 73 11975 0.44% 74 12483 0.46% 75 13010 0.48% 76 11020 0.41% 77 11037 0.41% 78 13560 0.50% 79 14556 0.54% 80 12391 0.46% 81 12745 0.47% 82 15656 0.58% 83 19492 0.72% 84 14157 0.52% 85 4209 0.16% 86 4919 0.18% 87 5646 0.21% 88 7248 0.27% 89 7165 0.26% 90 9698 0.36% 91 11741 0.43% 92 11771 0.44% 93 2429499 89.81% 2705284 reads passed initial QC criterion=sequence-density sequence-density=0.30 sequence-density-rank=1 fanout-score=3.25 fanout-score-rank=34 prefix-density=0.33 prefix-fanout=2.9 sequence=GTGTTGTGTTGT criterion=fanout-score sequence-density=0.01 sequence-density-rank=33 fanout-score=269.92 fanout-score-rank=1 prefix-density=0.51 prefix-fanout=5.8 sequence=GAAGAAGAAAAGTTTTCTCAACATGGGGAGGAAGTCCCTCCGAAATTTGATTTGTTATTGTATTGTAAGGGGCTTTTTTAGTATTTATCTAAAGGAAGGAACAAACGAGGATAAGATAAAATTTCTTTAAATTTATTTTGCCCAAGTGGGATATATGGCATACTATTCTTTCCATTTTCATCTTTTTTTCTATTCCACTCCATCTAGATATAAGAAAGAACCCAATGCAATGAAATTCCACTAATATACAATACAAAAAAGAAGAATAGATACAGGGTCTCAAACCTTGCTATAGAGTTTTTGCTTTAAAG Started job on | Dec 07 02:28:31 Started mapping on | Dec 07 02:28:33 Finished on | Dec 07 02:28:40 Mapping speed, Million of reads per hour | 1391.29 Number of input reads | 2705284 Average input read length | 91 UNIQUE READS: Uniquely mapped reads number | 1953210 Uniquely mapped reads % | 72.20% Average mapped length | 91.09 Number of splices: Total | 106466 Number of splices: Annotated (sjdb) | 90036 Number of splices: GT/AG | 101837 Number of splices: GC/AG | 2346 Number of splices: AT/AC | 21 Number of splices: Non-canonical | 2262 Mismatch rate per base, % | 0.57% Deletion rate per base | 0.04% Deletion average length | 1.82 Insertion rate per base | 0.02% Insertion average length | 1.78 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 648529 % of reads mapped to multiple loci | 23.97% Number of reads mapped to too many loci | 22308 % of reads mapped to too many loci | 0.82% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 2.89% % of reads unmapped: other | 0.11% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 103545 103545 103545 N_multimapping 648529 648529 648529 N_noFeature 99107 118403 1861880 N_ambiguous 78979 6947 343 UnstrandedReadsAssigned:1775124 PositiveStrandReadsAssigned:1827860 NegativeStrandReadsAssigned:90987 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=93 echo kmer=89 ERR6133380 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: ERR6133380-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 2,705,284 reads, 2,270,064 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 961 rounds 52973 ERR6133380.ke.tsv 35125 ERR6133380.se.tsv 88098 total ==> ERR6133380.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 60 26.9471 PNS24243 293 194 0 0 KQK14069 1603 1504 168 68.8298 KQK14071 474 375 0 0 ==> ERR6133380.se.tsv <== BRADI_1g14170v3 168 BRADI_1g53295v3 18 BRADI_1g59795v3 28 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 20 BRADI_1g74790v3 21 BRADI_1g09890v3 0 BRADI_1g77505v3 28 BRADI_1g48960v3 0 ERR6133380 completed mapping pipeline successfully