Starting /dee2/code/volunteer_pipeline.sh SRR11462693 current disk space = 3050295848960 free memory = 1373659320 SRR11462693 SRAfilesize 3d2f78ae429145c3be1564a4aaf4749f SRR11462693.sra SRR11462693.sra file validated SRR11462693 is single end SRR11462693 is conventional basespace SRR11462693 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR11462693_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 23.8775 32.0 2.0 32.0 2.0 32.0 2 31.7975 32.0 32.0 32.0 32.0 32.0 3 34.61 37.0 32.0 37.0 32.0 37.0 4 36.26625 37.0 37.0 37.0 32.0 37.0 5 36.48125 37.0 37.0 37.0 37.0 37.0 6 39.86475 41.0 41.0 41.0 37.0 41.0 7 40.218 41.0 41.0 41.0 37.0 41.0 8 40.16925 41.0 41.0 41.0 37.0 41.0 9 40.2065 41.0 41.0 41.0 37.0 41.0 10-14 40.251650000000005 41.0 41.0 41.0 37.0 41.0 15-19 40.29625 41.0 41.0 41.0 38.6 41.0 20-24 40.224199999999996 41.0 41.0 41.0 37.8 41.0 25-29 40.09765 41.0 41.0 41.0 37.0 41.0 30-34 40.2525 41.0 41.0 41.0 40.2 41.0 35-39 40.2118 41.0 41.0 41.0 40.2 41.0 40-44 40.15514999999999 41.0 41.0 41.0 38.6 41.0 45-49 40.1496 41.0 41.0 41.0 37.8 41.0 50-54 40.130250000000004 41.0 41.0 41.0 38.6 41.0 55-59 40.0867 41.0 41.0 41.0 37.8 41.0 60-64 40.00905 41.0 41.0 41.0 37.0 41.0 65-69 39.926100000000005 41.0 41.0 41.0 37.0 41.0 70-74 39.88175 41.0 41.0 41.0 37.0 41.0 75-79 39.5559 41.0 40.2 41.0 37.0 41.0 80-84 40.1356 41.0 41.0 41.0 38.6 41.0 85-89 40.0712 41.0 41.0 41.0 37.8 41.0 90-94 40.037 41.0 41.0 41.0 37.0 41.0 95-99 39.898700000000005 41.0 41.0 41.0 37.0 41.0 100-104 39.887 41.0 41.0 41.0 37.0 41.0 105-109 39.8143 41.0 41.0 41.0 37.0 41.0 110-114 39.82015 41.0 41.0 41.0 37.0 41.0 115-119 39.73405 41.0 41.0 41.0 37.0 41.0 120-124 39.5182 41.0 41.0 41.0 37.0 41.0 125-129 39.39725 41.0 41.0 41.0 37.0 41.0 130-134 39.43055 41.0 41.0 41.0 37.0 41.0 135-139 39.18835 41.0 41.0 41.0 37.0 41.0 140-144 38.86085 41.0 41.0 41.0 34.0 41.0 145-149 38.67905 41.0 41.0 41.0 32.0 41.0 150-151 37.694874999999996 41.0 39.0 41.0 29.5 41.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 23 2.0 24 1.0 25 6.0 26 5.0 27 3.0 28 12.0 29 12.0 30 17.0 31 35.0 32 34.0 33 47.0 34 61.0 35 64.0 36 103.0 37 147.0 38 181.0 39 378.0 40 2892.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 6.666666666666667 38.51099830795262 38.578680203045685 16.243654822335024 2 26.450000000000003 42.775 19.025 11.75 3 24.224999999999998 29.775000000000002 36.15 9.85 4 36.15 24.925 25.424999999999997 13.5 5 26.75 28.175 27.474999999999998 17.599999999999998 6 25.674999999999997 26.85 29.825000000000003 17.65 7 23.599999999999998 26.974999999999998 29.5 19.925 8 25.0 26.450000000000003 30.275000000000002 18.275 9 24.099999999999998 22.400000000000002 31.974999999999998 21.525 10-14 25.055 25.555 29.799999999999997 19.59 15-19 24.57 26.57 28.935 19.925 20-24 25.074999999999996 27.175 28.275 19.475 25-29 25.025 26.82 28.194999999999997 19.96 30-34 24.44 26.77 28.854999999999997 19.935 35-39 24.6 27.150000000000002 27.88 20.369999999999997 40-44 24.365000000000002 27.125 28.549999999999997 19.96 45-49 24.43 26.99 29.015 19.564999999999998 50-54 24.834999999999997 27.125 27.85 20.19 55-59 24.88 27.12 28.465 19.535 60-64 24.325 27.325 28.73 19.62 65-69 24.740000000000002 26.44 28.835 19.985 70-74 24.86 26.555 28.87 19.715 75-79 24.095 27.015 28.715000000000003 20.175 80-84 24.349999999999998 27.305 28.465 19.88 85-89 24.595 27.060000000000002 27.91 20.435 90-94 24.79 26.765 28.660000000000004 19.785 95-99 23.810000000000002 27.224999999999998 28.465 20.5 100-104 24.44 27.250000000000004 28.18 20.13 105-109 23.405 27.950000000000003 28.345 20.3 110-114 24.64 27.49 27.205000000000002 20.665 115-119 23.87 27.485 28.29 20.355 120-124 23.895 27.67 27.589999999999996 20.845 125-129 23.525 28.175 27.04 21.26 130-134 23.565 28.744999999999997 27.029999999999998 20.66 135-139 24.035 28.415000000000003 25.885 21.665 140-144 24.18 28.7 26.075 21.044999999999998 145-149 24.07 28.67 25.775 21.485000000000003 150-151 24.0625 27.950000000000003 26.0 21.987499999999997 >>END_MODULE >>Per sequence GC content pass #GC Content Count 0 2.0 1 1.5 2 0.5 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 0.5 20 1.0 21 0.5 22 0.5 23 1.0 24 1.0 25 1.0 26 3.0 27 7.0 28 10.5 29 10.5 30 16.0 31 20.0 32 24.5 33 37.5 34 54.5 35 78.5 36 104.5 37 130.0 38 139.0 39 149.0 40 180.0 41 211.5 42 246.0 43 271.5 44 278.0 45 285.5 46 279.5 47 253.0 48 220.5 49 184.0 50 157.0 51 128.5 52 100.0 53 96.5 54 78.0 55 55.0 56 47.5 57 41.5 58 34.5 59 16.0 60 6.0 61 4.0 62 3.0 63 7.5 64 6.0 65 0.5 66 0.0 67 2.0 68 4.5 69 2.5 70 0.0 71 2.0 72 2.5 73 1.0 74 0.5 75 0.0 76 0.0 77 0.5 78 0.5 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 26.125 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10-14 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 93.575 #Duplication Level Percentage of deduplicated Percentage of total 1 94.81699171787336 88.725 2 4.167779855730697 7.8 3 0.6679134384183809 1.875 4 0.18701576275714668 0.7000000000000001 5 0.10686615014694097 0.5 6 0.02671653753673524 0.15 7 0.0 0.0 8 0.0 0.0 9 0.0 0.0 >10 0.02671653753673524 0.25 >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 TGTGGGATTGGGAGTGGATTAATAATGTAATTTCTGATAAATAATCTGTG 10 0.25 No Hit AATGTGATTTCTGCCCAGTGCTCTGAATGTCAAAGTGAAGAAATTCAACC 6 0.15 No Hit TGGCATCGTCGAGACTGAGAAGAACTATGTCTCCTCCGTAGTCATGGAGG 5 0.125 No Hit AATGACGTGCCTGACACACCTGGTAAAGCAGACGACGCAGAGTTTGCCGG 5 0.125 No Hit TATTTGCTACTCGGATAACCGTAGTAATTCTAGAGCTAATACGTGCAACA 5 0.125 No Hit AGCTGAGAACGATGGCAAGTGCAACTGCGGTACTGGCTGCACTTGCACTA 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 0.025 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 0.037500000000000006 0.0 0.0 0.0 0.0 20-21 0.05 0.0 0.0 0.0 0.0 22-23 0.075 0.0 0.0 0.0 0.0 24-25 0.1 0.0 0.0 0.0 0.0 26-27 0.1375 0.0 0.0 0.0 0.0 28-29 0.15 0.0 0.0 0.0 0.0 30-31 0.2 0.0 0.0 0.0 0.0 32-33 0.275 0.0 0.0 0.0 0.0 34-35 0.275 0.0 0.0 0.0 0.0 36-37 0.32499999999999996 0.0 0.0 0.0 0.0 38-39 0.4125 0.0 0.0 0.0 0.0 40-41 0.425 0.0 0.0 0.0 0.0 42-43 0.475 0.0 0.0 0.0 0.0 44-45 0.5 0.0 0.0 0.0 0.0 46-47 0.5 0.0 0.0 0.0 0.0 48-49 0.5625 0.0 0.0 0.0 0.0 50-51 0.6375 0.0 0.0 0.0 0.0 52-53 0.7124999999999999 0.0 0.0 0.0 0.0 54-55 0.7875000000000001 0.0 0.0 0.0 0.0 56-57 0.9 0.0 0.0 0.0 0.0 58-59 0.9625 0.0 0.0 0.0 0.0 60-61 1.05 0.0 0.0 0.0 0.0 62-63 1.2 0.0 0.0 0.0 0.0 64-65 1.2875 0.0 0.0 0.0 0.0 66-67 1.35 0.0 0.0 0.0 0.0 68-69 1.5375 0.0 0.0 0.0 0.0 70-71 1.7125 0.0 0.0 0.0 0.0 72-73 1.8875000000000002 0.0 0.0 0.0 0.0 74-75 2.025 0.0 0.0 0.0 0.0 76-77 2.2 0.0 0.0 0.0 0.0 78-79 2.3625 0.0 0.0 0.0 0.0 80-81 2.5999999999999996 0.0 0.0 0.0 0.0 82-83 2.8 0.0 0.0 0.0 0.0 84-85 3.1 0.0 0.0 0.0 0.0 86-87 3.4875 0.0 0.0 0.0 0.0 88-89 3.7249999999999996 0.0 0.0 0.0 0.0 90-91 4.1 0.0 0.0 0.0 0.0 92-93 4.4125 0.0 0.0 0.0 0.0 94-95 4.7875 0.0 0.0 0.0 0.0 96-97 5.35 0.0 0.0 0.0 0.0 98-99 5.8625 0.0 0.0 0.0 0.0 100-101 6.262499999999999 0.0 0.0 0.0 0.0 102-103 6.7625 0.0 0.0 0.0 0.0 104-105 7.325 0.0 0.0 0.0 0.0 106-107 7.925 0.0 0.0 0.0 0.0 108-109 8.399999999999999 0.0 0.0 0.0 0.0 110-111 9.0625 0.0 0.0 0.0 0.0 112-113 9.8625 0.0 0.0 0.0 0.0 114-115 10.725000000000001 0.0 0.0 0.0 0.0 116-117 11.524999999999999 0.0 0.0 0.0 0.0 118-119 12.225000000000001 0.0 0.0 0.0 0.0 120-121 13.225000000000001 0.0 0.0 0.0 0.0 122-123 14.225 0.0 0.0 0.0 0.0 124-125 15.625 0.0 0.0 0.0 0.0 126-127 16.65 0.0 0.0 0.0 0.0 128-129 17.75 0.0 0.0 0.0 0.0 130-131 19.0 0.0 0.0 0.0 0.0 132-133 20.225 0.0 0.0 0.0 0.0 134-135 21.424999999999997 0.0 0.0 0.0 0.0 136-137 22.8125 0.0 0.0 0.0 0.0 138-139 24.362499999999997 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content fail #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position AAAAAAA 90 1.1037282E-6 16.081945 140-144 >>END_MODULE Rejected 1845292 READS because READLEN < 1 Read 1845292 spots for SRR11462693.sra Written 1845292 spots for SRR11462693.sra Rejected 1845292 READS because READLEN < 1 Read 1845292 spots for SRR11462693.sra Written 1845292 spots for SRR11462693.sra Rejected 1845292 READS because READLEN < 1 Read 1845292 spots for SRR11462693.sra Written 1845292 spots for SRR11462693.sra Rejected 1845292 READS because READLEN < 1 Read 1845292 spots for SRR11462693.sra Written 1845292 spots for SRR11462693.sra Rejected 1845292 READS because READLEN < 1 Read 1845292 spots for SRR11462693.sra Written 1845292 spots for SRR11462693.sra Rejected 1845292 READS because READLEN < 1 Read 1845292 spots for SRR11462693.sra Written 1845292 spots for SRR11462693.sra Rejected 1845292 READS because READLEN < 1 Read 1845292 spots for SRR11462693.sra Written 1845292 spots for SRR11462693.sra Rejected 1845292 READS because READLEN < 1 Read 1845292 spots for SRR11462693.sra Written 1845292 spots for SRR11462693.sra Rejected 1845297 READS because READLEN < 1 Read 1845297 spots for SRR11462693.sra Written 1845297 spots for SRR11462693.sra Rejected 1845292 READS because READLEN < 1 Read 1845292 spots for SRR11462693.sra Written 1845292 spots for SRR11462693.sra Rejected 1845292 READS because READLEN < 1 Read 1845292 spots for SRR11462693.sra Written 1845292 spots for SRR11462693.sra Rejected 1845292 READS because READLEN < 1 Read 1845292 spots for SRR11462693.sra Written 1845292 spots for SRR11462693.sra Rejected 1845292 READS because READLEN < 1 Read 1845292 spots for SRR11462693.sra Written 1845292 spots for SRR11462693.sra Rejected 1845292 READS because READLEN < 1 Read 1845292 spots for SRR11462693.sra Written 1845292 spots for SRR11462693.sra Rejected 1845292 READS because READLEN < 1 Read 1845292 spots for SRR11462693.sra Written 1845292 spots for SRR11462693.sra Rejected 1845292 READS because READLEN < 1 Read 1845292 spots for SRR11462693.sra Written 1845292 spots for SRR11462693.sra Rejected 1845292 READS because READLEN < 1 Read 1845292 spots for SRR11462693.sra Written 1845292 spots for SRR11462693.sra Rejected 1845292 READS because READLEN < 1 Read 1845292 spots for SRR11462693.sra Written 1845292 spots for SRR11462693.sra Rejected 1845292 READS because READLEN < 1 Read 1845292 spots for SRR11462693.sra Written 1845292 spots for SRR11462693.sra Rejected 1845292 READS because READLEN < 1 Read 1845292 spots for SRR11462693.sra Written 1845292 spots for SRR11462693.sra SRR ids: ['SRR11462693.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_imca8miu SRR11462693.sra spots: 36905845 blocks: [[1, 1845292], [1845293, 3690584], [3690585, 5535876], [5535877, 7381168], [7381169, 9226460], [9226461, 11071752], [11071753, 12917044], [12917045, 14762336], [14762337, 16607628], [16607629, 18452920], [18452921, 20298212], [20298213, 22143504], [22143505, 23988796], [23988797, 25834088], [25834089, 27679380], [27679381, 29524672], [29524673, 31369964], [31369965, 33215256], [33215257, 35060548], [35060549, 36905845]] SRR11462693 file size 12520520 SRR11462693 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 SRR11462693 SRR11462693_1.fastq Input file: SRR11462693_1.fastq trimmed: SRR11462693-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 06:14:39 2025 >> started Wed Feb 12 06:15:08 2025 >> done (28.723s) 36905845 reads processed; of these: 14497 ( 0.04%) short reads filtered out after trimming by size control 1415 ( 0.00%) empty reads filtered out after trimming by size control 36889933 (99.96%) reads available; of these: 4750960 (12.88%) trimmed reads available after processing 32138973 (87.12%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 2660 0.01% 19 2779 0.01% 20 3142 0.01% 21 3257 0.01% 22 3724 0.01% 23 3825 0.01% 24 4669 0.01% 25 4240 0.01% 26 5126 0.01% 27 4861 0.01% 28 5226 0.01% 29 5308 0.01% 30 5419 0.01% 31 5914 0.02% 32 5708 0.02% 33 6368 0.02% 34 6470 0.02% 35 6855 0.02% 36 6948 0.02% 37 9454 0.03% 38 7075 0.02% 39 8555 0.02% 40 7838 0.02% 41 8557 0.02% 42 9133 0.02% 43 9198 0.02% 44 9377 0.03% 45 10465 0.03% 46 11065 0.03% 47 13274 0.04% 48 11851 0.03% 49 13137 0.04% 50 12536 0.03% 51 13474 0.04% 52 14048 0.04% 53 14036 0.04% 54 15580 0.04% 55 16502 0.04% 56 16676 0.05% 57 17312 0.05% 58 18849 0.05% 59 19744 0.05% 60 19760 0.05% 61 20797 0.06% 62 29901 0.08% 63 21786 0.06% 64 23737 0.06% 65 22946 0.06% 66 23459 0.06% 67 27166 0.07% 68 26184 0.07% 69 28325 0.08% 70 28324 0.08% 71 31790 0.09% 72 32486 0.09% 73 34549 0.09% 74 38218 0.10% 75 36005 0.10% 76 34133 0.09% 77 36867 0.10% 78 38867 0.11% 79 45083 0.12% 80 41177 0.11% 81 43900 0.12% 82 44968 0.12% 83 47435 0.13% 84 50204 0.14% 85 52135 0.14% 86 56153 0.15% 87 56895 0.15% 88 56160 0.15% 89 71985 0.20% 90 61664 0.17% 91 63638 0.17% 92 64436 0.17% 93 69288 0.19% 94 74012 0.20% 95 74810 0.20% 96 83002 0.22% 97 81361 0.22% 98 80793 0.22% 99 83589 0.23% 100 87310 0.24% 101 90091 0.24% 102 105588 0.29% 103 97869 0.27% 104 98486 0.27% 105 105047 0.28% 106 109088 0.30% 107 112509 0.30% 108 117091 0.32% 109 133445 0.36% 110 126073 0.34% 111 123463 0.33% 112 156118 0.42% 113 140340 0.38% 114 138124 0.37% 115 142687 0.39% 116 145512 0.39% 117 155731 0.42% 118 163822 0.44% 119 164343 0.45% 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 0 0.00% 151 32138973 87.12% 36889933 reads passed initial QC criterion=sequence-density sequence-density=10.37 sequence-density-rank=1 fanout-score=40.90 fanout-score-rank=2 prefix-density=12.57 prefix-fanout=33.7 sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCATGGCATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAA criterion=fanout-score sequence-density=0.01 sequence-density-rank=10 fanout-score=154.06 fanout-score-rank=1 prefix-density=0.16 prefix-fanout=12.6 sequence=CAGAAGAAGTTTTAGTGATTGAAGGGATTGAGTATCGAATAGATCTATATATAAAGTTTAACGTGCTCATAAATGACGTGCCTGACACACCTGGTAAAGCAGACGACGCAGAGTTTGCCGGAACCTTTGTCAATGTGCCTCATAATCGTAACAAGACAGTAAAGACAAGTTTGAGGTTGGGAATTTCTGAGCTATTGGAGGATTTGGAAGCTGAAGATGATGAAAGTGTGGTGGTGACTTTGGTGCCGGTAACAAATATAGGTGAGGCTACCATTGGCACTCTCAGGATTGAGCTTCTCAAGGATTGATCATCATAAAAGGAAACTTATCCTTTCGTTTTTAATCATGTCAAGTAATTCGGTTAGCAATTTTATTCCTAGCTAGTAACTTGCACCGAAAAATTTACCAGGTCAGAGCTTCTGTTTCAATAAGGTCCATGTTTAACATGAG 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 AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCATGGCATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAA -o SRR11462693 - Input file: STDIN trimmed: SRR11462693-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCATGGCATCTCGTATGCCGTCTTCTGCTTG -- 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 06:16:37 2025 >> started Wed Feb 12 06:17:28 2025 >> done (51.108s) 30182673 reads processed; of these: 419 ( 0.00%) short reads filtered out after trimming by size control 9 ( 0.00%) empty reads filtered out after trimming by size control 30182245 (100.00%) reads available; of these: 6275518 (20.79%) trimmed reads available after processing 23906727 (79.21%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 2209 0.01% 19 2275 0.01% 20 2593 0.01% 21 2745 0.01% 22 3091 0.01% 23 3204 0.01% 24 3872 0.01% 25 3511 0.01% 26 4261 0.01% 27 4027 0.01% 28 4297 0.01% 29 4428 0.01% 30 4523 0.01% 31 4911 0.02% 32 4735 0.02% 33 5287 0.02% 34 5438 0.02% 35 5729 0.02% 36 5778 0.02% 37 7883 0.03% 38 5755 0.02% 39 6945 0.02% 40 6450 0.02% 41 7107 0.02% 42 7571 0.03% 43 7591 0.03% 44 7728 0.03% 45 8690 0.03% 46 9240 0.03% 47 10926 0.04% 48 9753 0.03% 49 10866 0.04% 50 10501 0.03% 51 11165 0.04% 52 11602 0.04% 53 11717 0.04% 54 12868 0.04% 55 13508 0.04% 56 13711 0.05% 57 14281 0.05% 58 15672 0.05% 59 16359 0.05% 60 16337 0.05% 61 17430 0.06% 62 24612 0.08% 63 18108 0.06% 64 19693 0.07% 65 19023 0.06% 66 19388 0.06% 67 22590 0.07% 68 21844 0.07% 69 23348 0.08% 70 23492 0.08% 71 26087 0.09% 72 26939 0.09% 73 28552 0.09% 74 31622 0.10% 75 29700 0.10% 76 28310 0.09% 77 30520 0.10% 78 31872 0.11% 79 37358 0.12% 80 33936 0.11% 81 37923 0.13% 82 37131 0.12% 83 39066 0.13% 84 39867 0.13% 85 43086 0.14% 86 46500 0.15% 87 46983 0.16% 88 46781 0.15% 89 59789 0.20% 90 51450 0.17% 91 52778 0.17% 92 53119 0.18% 93 57030 0.19% 94 60797 0.20% 95 61388 0.20% 96 68448 0.23% 97 67148 0.22% 98 66946 0.22% 99 69242 0.23% 100 71937 0.24% 101 74336 0.25% 102 87033 0.29% 103 81170 0.27% 104 81927 0.27% 105 87039 0.29% 106 90008 0.30% 107 92059 0.31% 108 96457 0.32% 109 110130 0.36% 110 103853 0.34% 111 101703 0.34% 112 129002 0.43% 113 115609 0.38% 114 114407 0.38% 115 117000 0.39% 116 119393 0.40% 117 123005 0.41% 118 129957 0.43% 119 132824 0.44% 120 140134 0.46% 121 145135 0.48% 122 145485 0.48% 123 186661 0.62% 124 171531 0.57% 125 154901 0.51% 126 160231 0.53% 127 170907 0.57% 128 166399 0.55% 129 172756 0.57% 130 171290 0.57% 131 183043 0.61% 132 183309 0.61% 133 199405 0.66% 134 183337 0.61% 135 199060 0.66% 136 192428 0.64% 137 205564 0.68% 138 227547 0.75% 139 207325 0.69% 140 244945 0.81% 141 203197 0.67% 142 215519 0.71% 143 221124 0.73% 144 218051 0.72% 145 220631 0.73% 146 231504 0.77% 147 336478 1.11% 148 663571 2.20% 149 0 0.00% 150 0 0.00% 151 20150892 66.76% criterion=sequence-density sequence-density=0.37 sequence-density-rank=1 fanout-score=2.45 fanout-score-rank=28 prefix-density=0.40 prefix-fanout=2.3 sequence=CTGCGACTGCGCTGACAAGACCCAGTGTGTCAAGAAGGGAAGCAGCTACACTGCTGGCATCGTCGAGACTGAGAAGAACTATGTCTCCTCCGTAGTCATGGAGGTGCCAGCAGCTGAGAACGATGGCAAGTGCAACTGCGGTACTGGCTGCACTTGCACTACCTGCACATGCGGTCATTAAGCAAGCACATCAACTATCATGTTTGATGTGGGATTGGGAGTGGATTAATAATGTAATTTCTGATAAATAATCTGTGTTCTTCTGTACTTGTGGGTGTGGAGTGAACAAACAAAAGTGTCCGTGAGTGTCTTTATCTTTGTGTCTTCTTCATTGTTATGTATTGGCCATGTCTGTGGCCTCTGGTGTGGT criterion=fanout-score sequence-density=0.01 sequence-density-rank=33 fanout-score=144.73 fanout-score-rank=1 prefix-density=0.16 prefix-fanout=12.5 sequence=CAGAAGAAGTTTTAGTGATTGAAGGGATTGAGTATCGAATAGATCTATATATAAAGTTTAACGTGCTCATAAATGACGTGCCTGACACACCTGGTAAAGCAGACGACGCAGAGTTTGCCGGAACCTTTGTCAATGTGCCTCATAATCGTAACAAGACAGTAAAGACAAGTTTGAGGTTGGGAATTTCTGAGCTATTGGAGGATTTGGAAGCTGAAGATGATGAAAGTGTGGTGGTGACTTTGGTGCCGGTAACAAATATAGGTGAGGCTACCATTGGCACTCTCAGGATTGAGCTTCTCAAGGATTGATCATCATAAAAGGAAACTTATCCTTTCGTTTTTAATCATGTCAAGTAATTCGGTTAGCAATTTTATTCCTAGCTAGTAACTTGCACCGAAAAATTTACCAGGTCAGAGCTTCTGTTTCAATAAGGTCCATGTTTAACATGAGTGTT Started job on | Feb 12 06:18:04 Started mapping on | Feb 12 06:18:04 Finished on | Feb 12 06:19:14 Mapping speed, Million of reads per hour | 1897.17 Number of input reads | 36889505 Average input read length | 141 UNIQUE READS: Uniquely mapped reads number | 32787219 Uniquely mapped reads % | 88.88% Average mapped length | 139.39 Number of splices: Total | 14926918 Number of splices: Annotated (sjdb) | 14638250 Number of splices: GT/AG | 14642497 Number of splices: GC/AG | 218610 Number of splices: AT/AC | 8437 Number of splices: Non-canonical | 57374 Mismatch rate per base, % | 0.40% Deletion rate per base | 0.02% Deletion average length | 2.08 Insertion rate per base | 0.01% Insertion average length | 1.93 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 1262129 % of reads mapped to multiple loci | 3.42% Number of reads mapped to too many loci | 1062478 % of reads mapped to too many loci | 2.88% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 4.72% % of reads unmapped: other | 0.09% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 2840157 2840157 2840157 N_multimapping 1262129 1262129 1262129 N_noFeature 1283131 1669917 32092440 N_ambiguous 436802 128762 752 UnstrandedReadsAssigned:31067286 PositiveStrandReadsAssigned:30988540 NegativeStrandReadsAssigned:694027 Dataset is classified positive stranded MeadianReadLen=151 20thPercentileLength=132 echo kmer=127 SRR11462693 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: SRR11462693-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 36,889,505 reads, 32,124,545 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,230 rounds 52401 SRR11462693.ke.tsv 34699 SRR11462693.se.tsv 87100 total ==> SRR11462693.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1919 1245 23.9986 Potri.005G024800.1.v4.1 1035 936 418 16.5193 Potri.004G059700.1.v4.1 961 862 46 1.97397 Potri.007G009000.2.v4.1 1416 1317 0 0 Potri.003G141000.2.v4.1 2943 2844 2402.55 31.2489 Potri.016G087400.1.v4.1 270 171 3572 772.692 Potri.015G069301.1.v4.1 564 465 0 0 Potri.010G195200.1.v4.1 1773 1674 554 12.2418 Potri.012G127500.1.v4.1 977 878 146 6.15105 ==> SRR11462693.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 277 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 149 Potri.001G212900.v4.1 36 Potri.001G182400.v4.1 2 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 9 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 55 SRR11462693 completed mapping pipeline successfully