Starting /dee2/code/volunteer_pipeline.sh SRR11462699 current disk space = 3050254381056 free memory = 1579635136 SRR11462699 SRAfilesize 04867e4bc8db9bc46d2567941e4e38c0 SRR11462699.sra SRR11462699.sra file validated SRR11462699 is single end SRR11462699 is conventional basespace SRR11462699 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR11462699_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 44 >>END_MODULE >>Per base sequence quality fail #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 21.785 32.0 2.0 32.0 2.0 32.0 2 31.71875 32.0 32.0 32.0 32.0 32.0 3 34.3775 37.0 32.0 37.0 32.0 37.0 4 36.18 37.0 37.0 37.0 32.0 37.0 5 36.35875 37.0 37.0 37.0 37.0 37.0 6 39.9265 41.0 41.0 41.0 37.0 41.0 7 40.20325 41.0 41.0 41.0 37.0 41.0 8 40.233 41.0 41.0 41.0 37.0 41.0 9 40.268 41.0 41.0 41.0 37.0 41.0 10-14 40.29895 41.0 41.0 41.0 38.6 41.0 15-19 40.25765 41.0 41.0 41.0 38.6 41.0 20-24 40.211850000000005 41.0 41.0 41.0 38.6 41.0 25-29 40.1677 41.0 41.0 41.0 38.6 41.0 30-34 40.09609999999999 41.0 41.0 41.0 37.8 41.0 35-39 40.09125 41.0 41.0 41.0 37.8 41.0 40-44 40.13565 41.0 41.0 41.0 37.0 41.0 45-49 40.1015 41.0 41.0 41.0 38.6 41.0 50-54 40.0911 41.0 41.0 41.0 37.8 41.0 55-59 40.03585 41.0 41.0 41.0 37.0 41.0 60-64 39.9304 41.0 41.0 41.0 37.0 41.0 65-69 40.0005 41.0 41.0 41.0 37.0 41.0 70-74 39.7488 41.0 41.0 41.0 37.0 41.0 75-79 39.70385 41.0 40.2 41.0 37.0 41.0 80-84 40.124700000000004 41.0 41.0 41.0 39.4 41.0 85-89 40.06175 41.0 41.0 41.0 37.0 41.0 90-94 39.99955 41.0 41.0 41.0 37.8 41.0 95-99 39.979150000000004 41.0 41.0 41.0 37.0 41.0 100-104 39.81025 41.0 41.0 41.0 37.0 41.0 105-109 39.776450000000004 41.0 41.0 41.0 37.0 41.0 110-114 39.781600000000005 41.0 41.0 41.0 37.0 41.0 115-119 39.7349 41.0 41.0 41.0 37.0 41.0 120-124 39.6711 41.0 41.0 41.0 37.0 41.0 125-129 39.36215 41.0 41.0 41.0 37.0 41.0 130-134 39.263749999999995 41.0 41.0 41.0 37.0 41.0 135-139 39.08025 41.0 41.0 41.0 36.0 41.0 140-144 39.0857 41.0 41.0 41.0 37.0 41.0 145-149 38.88705 41.0 41.0 41.0 35.0 41.0 150-151 37.99 41.0 39.0 41.0 29.5 41.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 22 2.0 23 1.0 24 2.0 25 4.0 26 6.0 27 7.0 28 8.0 29 12.0 30 21.0 31 24.0 32 44.0 33 60.0 34 70.0 35 79.0 36 92.0 37 136.0 38 154.0 39 311.0 40 2967.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 6.529080675422138 37.4484052532833 40.90056285178236 15.121951219512194 2 26.6 42.3 19.35 11.75 3 21.575 30.925000000000004 37.85 9.65 4 34.35076307230423 24.44333249937453 26.82011508631474 14.385789342006506 5 27.700000000000003 27.675 26.625 18.0 6 25.3 26.474999999999998 29.549999999999997 18.675 7 23.275000000000002 26.025 30.225 20.474999999999998 8 24.45 25.724999999999998 30.975 18.85 9 21.725 24.525 32.074999999999996 21.675 10-14 24.94 25.6 30.06 19.400000000000002 15-19 24.92 27.07 28.21 19.8 20-24 24.6 27.034999999999997 28.675 19.689999999999998 25-29 24.425 26.669999999999998 29.24 19.665 30-34 24.365000000000002 26.545 29.095 19.994999999999997 35-39 24.474999999999998 26.35 29.29 19.885 40-44 23.7 27.725 28.675 19.900000000000002 45-49 24.165 26.35 28.435 21.05 50-54 24.275 27.3 28.305000000000003 20.119999999999997 55-59 24.465 27.24 28.32 19.975 60-64 24.185000000000002 26.825 29.315 19.675 65-69 25.5 27.134999999999998 27.365000000000002 20.0 70-74 25.240000000000002 26.88 28.365000000000002 19.515 75-79 24.065 27.560000000000002 28.310000000000002 20.064999999999998 80-84 24.595 27.465 28.42 19.52 85-89 24.25 27.884999999999998 28.51 19.355 90-94 25.2 26.035000000000004 28.555000000000003 20.21 95-99 24.065 27.18 28.515 20.24 100-104 24.36 26.965 28.634999999999998 20.04 105-109 23.645 26.765 28.299999999999997 21.29 110-114 24.27 27.089999999999996 28.4 20.24 115-119 23.935000000000002 27.250000000000004 28.939999999999998 19.875 120-124 24.635 27.125 28.98 19.259999999999998 125-129 24.065 27.79 28.075 20.07 130-134 24.255 28.110000000000003 27.755000000000003 19.88 135-139 24.4 27.605 27.07 20.925 140-144 24.965 28.134999999999998 26.775 20.125 145-149 24.47 27.834999999999997 27.01 20.685000000000002 150-151 23.5 28.3625 26.2875 21.85 >>END_MODULE >>Per sequence GC content pass #GC Content Count 0 2.0 1 1.0 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 0.0 18 0.0 19 0.0 20 0.5 21 1.0 22 0.5 23 0.5 24 1.0 25 2.5 26 5.5 27 8.0 28 10.5 29 16.0 30 19.5 31 19.5 32 32.0 33 41.5 34 52.0 35 75.5 36 113.0 37 135.5 38 143.5 39 171.5 40 203.5 41 220.0 42 240.0 43 260.0 44 276.0 45 280.5 46 264.5 47 247.0 48 218.5 49 176.0 50 128.5 51 104.5 52 98.5 53 90.0 54 69.5 55 59.0 56 46.0 57 37.0 58 38.5 59 23.5 60 15.5 61 12.0 62 6.5 63 8.0 64 6.5 65 1.5 66 2.0 67 2.0 68 2.0 69 2.0 70 4.5 71 4.0 72 0.0 73 0.0 74 0.0 75 0.0 76 0.5 77 0.5 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 fail #Base N-Count 1 33.375 2 0.0 3 0.0 4 0.075 5 0.0 6 0.0 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 0.0 80-84 0.0 85-89 0.0 90-94 0.0 95-99 0.0 100-104 0.0 105-109 0.0 110-114 0.0 115-119 0.0 120-124 0.0 125-129 0.0 130-134 0.0 135-139 0.0 140-144 0.0 145-149 0.0 150-151 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 91.3 #Duplication Level Percentage of deduplicated Percentage of total 1 94.24972617743703 86.05000000000001 2 4.490690032858708 8.200000000000001 3 0.6571741511500547 1.7999999999999998 4 0.19167579408543264 0.7000000000000001 5 0.16429353778751368 0.75 6 0.027382256297918947 0.15 7 0.0 0.0 8 0.054764512595837894 0.4 9 0.054764512595837894 0.44999999999999996 >10 0.10952902519167579 1.5 >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 TATTTGCTACTCGGATAACCGTAGTAATTCTAGAGCTAATACGTGCAACA 20 0.5 No Hit TGGCATCGTCGAGACTGAGAAGAACTATGTCTCCTCCGTAGTCATGGAGG 16 0.4 No Hit ATGCGCTCCTGGCCTTAACTGGCCGGGTCGTGCCTCCGGTGCTGTTACTT 13 0.325 No Hit AACTATCATGTTTGATGTGGGATTGGGAGTGGATTAATAATGTAATTTCT 11 0.27499999999999997 No Hit TGTGGGATTGGGAGTGGATTAATAATGTAATTTCTGATAAATAATCTGTG 9 0.22499999999999998 No Hit NATTTGCTACTCGGATAACCGTAGTAATTCTAGAGCTAATACGTGCAACA 9 0.22499999999999998 No Hit AAAGACGAACAACTGCGAAAGCATTTGCCAAGGATGTTTTCATTAATCAA 8 0.2 No Hit NGGCATCGTCGAGACTGAGAAGAACTATGTCTCCTCCGTAGTCATGGAGG 8 0.2 No Hit NAAGACGAACAACTGCGAAAGCATTTGCCAAGGATGTTTTCATTAATCAA 6 0.15 No Hit NACCTGGTTGATCCTGCCAGTAGTCATATGCTTGTCTCAAAGATTAAGCC 5 0.125 No Hit CTACTCGGATAACCGTAGTAATTCTAGAGCTAATACGTGCAACAAACCCC 5 0.125 No Hit NAAGGATATTGTAGCTCTCTCTGGGGGCCACACCCTGGGAAGGTGCCACA 5 0.125 No Hit TAAGGATATTGTAGCTCTCTCTGGGGGCCACACCCTGGGAAGGTGCCACA 5 0.125 No Hit CAGCCAAGCGTTCATAGCGACGTTGCTTTTTGATCCTTCGATGTCGGCTC 5 0.125 No Hit NGTGGGATTGGGAGTGGATTAATAATGTAATTTCTGATAAATAATCTGTG 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 0.025 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 0.05 0.0 0.0 0.0 0.0 28-29 0.0625 0.0 0.0 0.0 0.0 30-31 0.15 0.0 0.0 0.0 0.0 32-33 0.175 0.0 0.0 0.0 0.0 34-35 0.175 0.0 0.0 0.0 0.0 36-37 0.21250000000000002 0.0 0.0 0.0 0.0 38-39 0.275 0.0 0.0 0.0 0.0 40-41 0.2875 0.0 0.0 0.0 0.0 42-43 0.325 0.0 0.0 0.0 0.0 44-45 0.36250000000000004 0.0 0.0 0.0 0.0 46-47 0.425 0.0 0.0 0.0 0.0 48-49 0.475 0.0 0.0 0.0 0.0 50-51 0.5875 0.0 0.0 0.0 0.0 52-53 0.6625000000000001 0.0 0.0 0.0 0.0 54-55 0.7124999999999999 0.0 0.0 0.0 0.0 56-57 0.775 0.0 0.0 0.0 0.0 58-59 0.8 0.0 0.0 0.0 0.0 60-61 0.825 0.0 0.0 0.0 0.0 62-63 0.9750000000000001 0.0 0.0 0.0 0.0 64-65 1.125 0.0 0.0 0.0 0.0 66-67 1.25 0.0 0.0 0.0 0.0 68-69 1.325 0.0 0.0 0.0 0.0 70-71 1.35 0.0 0.0 0.0 0.0 72-73 1.4 0.0 0.0 0.0 0.0 74-75 1.525 0.0 0.0 0.0 0.0 76-77 1.625 0.0 0.0 0.0 0.0 78-79 1.7000000000000002 0.0 0.0 0.0 0.0 80-81 1.9125 0.0 0.0 0.0 0.0 82-83 2.0125 0.0 0.0 0.0 0.0 84-85 2.275 0.0 0.0 0.0 0.0 86-87 2.4625000000000004 0.0 0.0 0.0 0.0 88-89 2.6375 0.0 0.0 0.0 0.0 90-91 3.0 0.0 0.0 0.0 0.0 92-93 3.2125 0.0 0.0 0.0 0.0 94-95 3.4000000000000004 0.0 0.0 0.0 0.0 96-97 3.5125 0.0 0.0 0.0 0.0 98-99 3.6125 0.0 0.0 0.0 0.0 100-101 3.8875 0.0 0.0 0.0 0.0 102-103 4.1875 0.0 0.0 0.0 0.0 104-105 4.5125 0.0 0.0 0.0 0.0 106-107 4.775 0.0 0.0 0.0 0.0 108-109 5.275 0.0 0.0 0.0 0.0 110-111 5.9 0.0 0.0 0.0 0.0 112-113 6.6625 0.0 0.0 0.0 0.0 114-115 7.275 0.0 0.0 0.0 0.0 116-117 7.8375 0.0 0.0 0.0 0.0 118-119 8.575 0.0 0.0 0.0 0.0 120-121 9.0875 0.0 0.0 0.0 0.0 122-123 9.8375 0.0 0.0 0.0 0.0 124-125 10.6875 0.0 0.0 0.0 0.0 126-127 11.6125 0.0 0.0 0.0 0.0 128-129 12.6125 0.0 0.0 0.0 0.0 130-131 13.6 0.0 0.0 0.0 0.0 132-133 14.725 0.0 0.0 0.0 0.0 134-135 15.675 0.0 0.0 0.0 0.0 136-137 16.8375 0.0 0.0 0.0 0.0 138-139 18.0625 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Rejected 1993650 READS because READLEN < 1 Read 1993650 spots for SRR11462699.sra Written 1993650 spots for SRR11462699.sra Rejected 1993650 READS because READLEN < 1 Read 1993650 spots for SRR11462699.sra Written 1993650 spots for SRR11462699.sra Rejected 1993650 READS because READLEN < 1 Read 1993650 spots for SRR11462699.sra Written 1993650 spots for SRR11462699.sra Rejected 1993650 READS because READLEN < 1 Read 1993650 spots for SRR11462699.sra Written 1993650 spots for SRR11462699.sra Rejected 1993650 READS because READLEN < 1 Read 1993650 spots for SRR11462699.sra Written 1993650 spots for SRR11462699.sra Rejected 1993650 READS because READLEN < 1 Read 1993650 spots for SRR11462699.sra Written 1993650 spots for SRR11462699.sra Rejected 1993650 READS because READLEN < 1 Read 1993650 spots for SRR11462699.sra Written 1993650 spots for SRR11462699.sra Rejected 1993662 READS because READLEN < 1 Read 1993662 spots for SRR11462699.sra Written 1993662 spots for SRR11462699.sra Rejected 1993650 READS because READLEN < 1 Read 1993650 spots for SRR11462699.sra Written 1993650 spots for SRR11462699.sra Rejected 1993650 READS because READLEN < 1 Read 1993650 spots for SRR11462699.sra Written 1993650 spots for SRR11462699.sra Rejected 1993650 READS because READLEN < 1 Read 1993650 spots for SRR11462699.sra Written 1993650 spots for SRR11462699.sra Rejected 1993650 READS because READLEN < 1 Read 1993650 spots for SRR11462699.sra Written 1993650 spots for SRR11462699.sra Rejected 1993650 READS because READLEN < 1 Read 1993650 spots for SRR11462699.sra Written 1993650 spots for SRR11462699.sra Rejected 1993650 READS because READLEN < 1 Read 1993650 spots for SRR11462699.sra Written 1993650 spots for SRR11462699.sra Rejected 1993650 READS because READLEN < 1 Read 1993650 spots for SRR11462699.sra Written 1993650 spots for SRR11462699.sra Rejected 1993650 READS because READLEN < 1 Read 1993650 spots for SRR11462699.sra Written 1993650 spots for SRR11462699.sra Rejected 1993650 READS because READLEN < 1 Read 1993650 spots for SRR11462699.sra Written 1993650 spots for SRR11462699.sra Rejected 1993650 READS because READLEN < 1 Read 1993650 spots for SRR11462699.sra Written 1993650 spots for SRR11462699.sra Rejected 1993650 READS because READLEN < 1 Read 1993650 spots for SRR11462699.sra Written 1993650 spots for SRR11462699.sra Rejected 1993650 READS because READLEN < 1 Read 1993650 spots for SRR11462699.sra Written 1993650 spots for SRR11462699.sra SRR ids: ['SRR11462699.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_wumy2t_b SRR11462699.sra spots: 39873012 blocks: [[1, 1993650], [1993651, 3987300], [3987301, 5980950], [5980951, 7974600], [7974601, 9968250], [9968251, 11961900], [11961901, 13955550], [13955551, 15949200], [15949201, 17942850], [17942851, 19936500], [19936501, 21930150], [21930151, 23923800], [23923801, 25917450], [25917451, 27911100], [27911101, 29904750], [29904751, 31898400], [31898401, 33892050], [33892051, 35885700], [35885701, 37879350], [37879351, 39873012]] SRR11462699 file size 13528893 SRR11462699 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 SRR11462699 SRR11462699_1.fastq Input file: SRR11462699_1.fastq trimmed: SRR11462699-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 Wed Feb 12 07:03:08 2025 >> started Wed Feb 12 07:03:30 2025 >> done (22.045s) 39873012 reads processed; of these: 7412 ( 0.02%) short reads filtered out after trimming by size control 918 ( 0.00%) empty reads filtered out after trimming by size control 39864682 (99.98%) reads available; of these: 3555217 ( 8.92%) trimmed reads available after processing 36309465 (91.08%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 1644 0.00% 19 1915 0.00% 20 2140 0.01% 21 2200 0.01% 22 2483 0.01% 23 2734 0.01% 24 2897 0.01% 25 2875 0.01% 26 2983 0.01% 27 3701 0.01% 28 3195 0.01% 29 3456 0.01% 30 3722 0.01% 31 3568 0.01% 32 3528 0.01% 33 3823 0.01% 34 4155 0.01% 35 4122 0.01% 36 4163 0.01% 37 5960 0.01% 38 4596 0.01% 39 4572 0.01% 40 4680 0.01% 41 4702 0.01% 42 5472 0.01% 43 5338 0.01% 44 5467 0.01% 45 6218 0.02% 46 6381 0.02% 47 8409 0.02% 48 7613 0.02% 49 9469 0.02% 50 7358 0.02% 51 7694 0.02% 52 7915 0.02% 53 8336 0.02% 54 9663 0.02% 55 8784 0.02% 56 9633 0.02% 57 11454 0.03% 58 10117 0.03% 59 10672 0.03% 60 12010 0.03% 61 12210 0.03% 62 25004 0.06% 63 12853 0.03% 64 14325 0.04% 65 13810 0.03% 66 14098 0.04% 67 15902 0.04% 68 15140 0.04% 69 19160 0.05% 70 17388 0.04% 71 18862 0.05% 72 20959 0.05% 73 25230 0.06% 74 25537 0.06% 75 23323 0.06% 76 21188 0.05% 77 25721 0.06% 78 24987 0.06% 79 31626 0.08% 80 26327 0.07% 81 26841 0.07% 82 29969 0.08% 83 30824 0.08% 84 33339 0.08% 85 34757 0.09% 86 39096 0.10% 87 39259 0.10% 88 39255 0.10% 89 84208 0.21% 90 42888 0.11% 91 47943 0.12% 92 43784 0.11% 93 48761 0.12% 94 53382 0.13% 95 50611 0.13% 96 57244 0.14% 97 59627 0.15% 98 57640 0.14% 99 61025 0.15% 100 60553 0.15% 101 66370 0.17% 102 83227 0.21% 103 72852 0.18% 104 73968 0.19% 105 77331 0.19% 106 80224 0.20% 107 86507 0.22% 108 92411 0.23% 109 114520 0.29% 110 101564 0.25% 111 101246 0.25% 112 154195 0.39% 113 122041 0.31% 114 110130 0.28% 115 112354 0.28% 116 116165 0.29% 117 130058 0.33% 118 134590 0.34% 119 138857 0.35% 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 0 0.00% 131 0 0.00% 132 0 0.00% 133 0 0.00% 134 0 0.00% 135 0 0.00% 136 0 0.00% 137 0 0.00% 138 0 0.00% 139 0 0.00% 140 0 0.00% 141 0 0.00% 142 0 0.00% 143 0 0.00% 144 0 0.00% 145 0 0.00% 146 0 0.00% 147 0 0.00% 148 0 0.00% 149 0 0.00% 150 134 0.00% 151 36309465 91.08% 39864682 reads passed initial QC criterion=sequence-density sequence-density=8.35 sequence-density-rank=1 fanout-score=42.13 fanout-score-rank=1 prefix-density=10.23 prefix-fanout=34.4 sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACATGTCAATCTCGTATGCCGTCTTCTGCTTGAAA criterion=fanout-score sequence-density=8.35 sequence-density-rank=1 fanout-score=42.13 fanout-score-rank=1 prefix-density=10.23 prefix-fanout=34.4 sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACATGTCAATCTCGTATGCCGTCTTCTGCTTGAAA 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 AGATCGGAAGAGCACACGTCTGAACTCCAGTCACATGTCAATCTCGTATGCCGTCTTCTGCTTGAAA -o SRR11462699 - Input file: STDIN trimmed: SRR11462699-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): AGATCGGAAGAGCACACGTCTGAACTCCAGTCACATGTCAATCTCGTATGCCGTCTTCTGCTTG -- 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 Wed Feb 12 07:05:10 2025 >> started Wed Feb 12 07:05:45 2025 >> done (35.097s) 31005864 reads processed; of these: 253 ( 0.00%) short reads filtered out after trimming by size control 2 ( 0.00%) empty reads filtered out after trimming by size control 31005609 (100.00%) reads available; of these: 5627621 (18.15%) trimmed reads available after processing 25377988 (81.85%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 1301 0.00% 19 1490 0.00% 20 1670 0.01% 21 1731 0.01% 22 1957 0.01% 23 2154 0.01% 24 2283 0.01% 25 2272 0.01% 26 2342 0.01% 27 2851 0.01% 28 2526 0.01% 29 2636 0.01% 30 2928 0.01% 31 2745 0.01% 32 2733 0.01% 33 2997 0.01% 34 3218 0.01% 35 3272 0.01% 36 3272 0.01% 37 4687 0.02% 38 3583 0.01% 39 3590 0.01% 40 3701 0.01% 41 3664 0.01% 42 4225 0.01% 43 4165 0.01% 44 4272 0.01% 45 4938 0.02% 46 5021 0.02% 47 6616 0.02% 48 5853 0.02% 49 7420 0.02% 50 5834 0.02% 51 6099 0.02% 52 6188 0.02% 53 6554 0.02% 54 7579 0.02% 55 6967 0.02% 56 7515 0.02% 57 8960 0.03% 58 7902 0.03% 59 8411 0.03% 60 9387 0.03% 61 9539 0.03% 62 19557 0.06% 63 10141 0.03% 64 11225 0.04% 65 10787 0.03% 66 11040 0.04% 67 12537 0.04% 68 11836 0.04% 69 15115 0.05% 70 13736 0.04% 71 14890 0.05% 72 16528 0.05% 73 19640 0.06% 74 19838 0.06% 75 18091 0.06% 76 16607 0.05% 77 20188 0.07% 78 19599 0.06% 79 24941 0.08% 80 20729 0.07% 81 21601 0.07% 82 23501 0.08% 83 24073 0.08% 84 25548 0.08% 85 27150 0.09% 86 30674 0.10% 87 30790 0.10% 88 30782 0.10% 89 65755 0.21% 90 34158 0.11% 91 38129 0.12% 92 34716 0.11% 93 37891 0.12% 94 41495 0.13% 95 39185 0.13% 96 44989 0.15% 97 46278 0.15% 98 45388 0.15% 99 48050 0.15% 100 47310 0.15% 101 52157 0.17% 102 65017 0.21% 103 57185 0.18% 104 58262 0.19% 105 60649 0.20% 106 63251 0.20% 107 67853 0.22% 108 72680 0.23% 109 89321 0.29% 110 79521 0.26% 111 79193 0.26% 112 120980 0.39% 113 95289 0.31% 114 86639 0.28% 115 87817 0.28% 116 90531 0.29% 117 97768 0.32% 118 101194 0.33% 119 106459 0.34% 120 113381 0.37% 121 119372 0.39% 122 117403 0.38% 123 166887 0.54% 124 144833 0.47% 125 129173 0.42% 126 133209 0.43% 127 148910 0.48% 128 139721 0.45% 129 139611 0.45% 130 142324 0.46% 131 148620 0.48% 132 165139 0.53% 133 176341 0.57% 134 160857 0.52% 135 178390 0.58% 136 167311 0.54% 137 179171 0.58% 138 206788 0.67% 139 184645 0.60% 140 220033 0.71% 141 181519 0.59% 142 194043 0.63% 143 199158 0.64% 144 197421 0.64% 145 225443 0.73% 146 223122 0.72% 147 330582 1.07% 148 692109 2.23% 149 0 0.00% 150 65 0.00% 151 22704726 73.23% criterion=sequence-density sequence-density=0.64 sequence-density-rank=1 fanout-score=2.12 fanout-score-rank=26 prefix-density=0.65 prefix-fanout=2.1 sequence=CTGCGACTGCGCTGACAAGACCCAGTGTGTCAAGAAGGGAAGCAGCTACACTGCTGGCATCGTCGAGACTGAGAAGAACTATGTCTCCTCCGTAGTCATGGAGGTGCCAGCAGCTGAGAACGATGGCAAGTGCAACTGCGGTACTGGCTGCACTTGCACTACCTGCACATGCGGTCATTAAGCAAGCACATCAACTATCATGTTTGATGTGGGATTGGGAGTGGATTAATAATGTAATTTCTGATAAATAATCTGTGTTCTTCTGTACTTGTGGGTGTGGAGTGAACAAACAAAAGTGTCCGTGAGTGTCTTTATCTTTGTGTCTTCTTCATTGTTATGTATTGGCCATGTCTGTGGCCTCTGGTGTGGTTTTAATGAAGTCTTATAATTAGTGTAGTACTCTGC criterion=fanout-score sequence-density=0.01 sequence-density-rank=32 fanout-score=413.63 fanout-score-rank=1 prefix-density=0.34 prefix-fanout=18.3 sequence=TTGGATTTGATTAGATCCACCAATAAAAAGGGCTTGCCTTACACTCTTGGTCTTAATCAATTTGCTGATTGGACATGGCAAGAGTTCCAAAAGTACAGACTGGGAGCTGCCCAAAATTGCTCTGCAACCACAAGGGGCAATCACAAGCTTACGAACGCTCTTCTTCCTGAAACGAAAGACTGGAGGGAAGAAGGCATAGTCAGTCCCGTTAAGAATCAAGGTCACTGTGGATCTTGCTGGACTTTCAGCACCACTGGAGCTCTAGAGGCTGCTTACCACCAGGCTTTTGGGAAAGGAATCTCTCTGTCTGAACAGCAGCTTGTGGACTGTGCTAGAGCATTTAATAACTTTGGCTGCAATG Started job on | Feb 12 07:06:23 Started mapping on | Feb 12 07:06:23 Finished on | Feb 12 07:07:46 Mapping speed, Million of reads per hour | 1729.06 Number of input reads | 39864427 Average input read length | 144 UNIQUE READS: Uniquely mapped reads number | 33853764 Uniquely mapped reads % | 84.92% Average mapped length | 142.27 Number of splices: Total | 15374937 Number of splices: Annotated (sjdb) | 15007598 Number of splices: GT/AG | 15099906 Number of splices: GC/AG | 208598 Number of splices: AT/AC | 8764 Number of splices: Non-canonical | 57669 Mismatch rate per base, % | 0.37% Deletion rate per base | 0.02% Deletion average length | 2.13 Insertion rate per base | 0.01% Insertion average length | 1.83 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 1150216 % of reads mapped to multiple loci | 2.89% Number of reads mapped to too many loci | 2811283 % of reads mapped to too many loci | 7.05% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 5.03% % of reads unmapped: other | 0.11% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 4860447 4860447 4860447 N_multimapping 1150216 1150216 1150216 N_noFeature 1660606 2339219 32787379 N_ambiguous 520243 132521 668 UnstrandedReadsAssigned:31672915 PositiveStrandReadsAssigned:31382024 NegativeStrandReadsAssigned:1065717 Dataset is classified positive stranded MeadianReadLen=151 20thPercentileLength=141 echo kmer=137 SRR11462699 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: SRR11462699-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 39,864,427 reads, 33,022,576 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,418 rounds 52401 SRR11462699.ke.tsv 34699 SRR11462699.se.tsv 87100 total ==> SRR11462699.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1919 3742 65.7291 Potri.005G024800.1.v4.1 1035 936 886 31.9071 Potri.004G059700.1.v4.1 961 862 1 0.039104 Potri.007G009000.2.v4.1 1416 1317 0 0 Potri.003G141000.2.v4.1 2943 2844 2380.09 28.2094 Potri.016G087400.1.v4.1 270 171 3112 613.441 Potri.015G069301.1.v4.1 564 465 0 0 Potri.010G195200.1.v4.1 1773 1674 4560.97 91.8397 Potri.012G127500.1.v4.1 977 878 19 0.729437 ==> SRR11462699.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 1 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 199 Potri.001G212900.v4.1 2 Potri.001G182400.v4.1 1 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 0 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 51 SRR11462699 completed mapping pipeline successfully