Starting /dee2/code/volunteer_pipeline.sh SRR11462706 current disk space = 3049944023040 free memory = 1581759960 SRR11462706 SRAfilesize 2a0e9e6573ee337bc05118b27fbf6103 SRR11462706.sra SRR11462706.sra file validated SRR11462706 is single end SRR11462706 is conventional basespace SRR11462706 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR11462706_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 pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 24.65875 32.0 27.0 32.0 2.0 32.0 2 31.74 32.0 32.0 32.0 32.0 32.0 3 34.90125 37.0 32.0 37.0 32.0 37.0 4 36.21125 37.0 37.0 37.0 32.0 37.0 5 36.43 37.0 37.0 37.0 37.0 37.0 6 40.055 41.0 41.0 41.0 37.0 41.0 7 40.08425 41.0 41.0 41.0 37.0 41.0 8 40.09325 41.0 41.0 41.0 37.0 41.0 9 40.2495 41.0 41.0 41.0 37.0 41.0 10-14 40.3348 41.0 41.0 41.0 41.0 41.0 15-19 40.28875 41.0 41.0 41.0 39.4 41.0 20-24 40.2109 41.0 41.0 41.0 37.8 41.0 25-29 40.202600000000004 41.0 41.0 41.0 40.2 41.0 30-34 40.080549999999995 41.0 41.0 41.0 37.0 41.0 35-39 40.07084999999999 41.0 41.0 41.0 37.0 41.0 40-44 40.09985 41.0 41.0 41.0 37.0 41.0 45-49 40.017849999999996 41.0 41.0 41.0 38.6 41.0 50-54 40.0292 41.0 41.0 41.0 37.0 41.0 55-59 39.95625 41.0 41.0 41.0 37.0 41.0 60-64 39.952 41.0 41.0 41.0 37.0 41.0 65-69 39.91915 41.0 41.0 41.0 37.0 41.0 70-74 39.84065 41.0 41.0 41.0 37.0 41.0 75-79 39.684999999999995 41.0 41.0 41.0 37.0 41.0 80-84 40.14065000000001 41.0 41.0 41.0 37.8 41.0 85-89 40.1793 41.0 41.0 41.0 40.2 41.0 90-94 40.0326 41.0 41.0 41.0 37.0 41.0 95-99 40.01075 41.0 41.0 41.0 37.8 41.0 100-104 39.972750000000005 41.0 41.0 41.0 37.0 41.0 105-109 39.7965 41.0 41.0 41.0 37.0 41.0 110-114 39.76815 41.0 41.0 41.0 37.0 41.0 115-119 39.7351 41.0 41.0 41.0 37.0 41.0 120-124 39.6216 41.0 41.0 41.0 37.0 41.0 125-129 39.5018 41.0 41.0 41.0 37.0 41.0 130-134 39.34715 41.0 41.0 41.0 37.0 41.0 135-139 39.05925 41.0 41.0 41.0 36.0 41.0 140-144 39.061 41.0 41.0 41.0 36.0 41.0 145-149 38.6272 41.0 41.0 41.0 32.0 41.0 150-151 37.880375 41.0 39.0 41.0 29.5 41.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 22 1.0 23 1.0 24 1.0 25 4.0 26 3.0 27 7.0 28 11.0 29 22.0 30 29.0 31 35.0 32 41.0 33 51.0 34 53.0 35 75.0 36 92.0 37 133.0 38 142.0 39 283.0 40 3016.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 6.241787122207622 38.469119579500656 40.04599211563732 15.243101182654403 2 24.9 43.575 20.200000000000003 11.325000000000001 3 22.525000000000002 30.0 37.6 9.875 4 33.85 24.5 26.724999999999998 14.924999999999999 5 28.125 27.500000000000004 25.924999999999997 18.45 6 26.05 26.875 28.725 18.35 7 23.375 25.974999999999998 30.375000000000004 20.275000000000002 8 25.15 25.324999999999996 31.025000000000002 18.5 9 22.625 23.9 31.974999999999998 21.5 10-14 25.15 25.540000000000003 29.755 19.555 15-19 24.395 26.845000000000002 28.754999999999995 20.005 20-24 24.665 26.790000000000003 28.549999999999997 19.994999999999997 25-29 24.37 26.805 28.999999999999996 19.825 30-34 24.015 26.46 29.15 20.375 35-39 23.97 26.61 28.78 20.64 40-44 23.69 26.6 28.99 20.72 45-49 24.351217560878045 26.236311815590778 29.231461573078654 20.181009050452523 50-54 24.695 26.334999999999997 28.96 20.01 55-59 24.13 26.765 28.825 20.28 60-64 24.044999999999998 26.724999999999998 29.115000000000002 20.115 65-69 24.252425242524254 26.832683268326836 28.297829782978294 20.617061706170617 70-74 25.06750675067507 26.432643264326433 28.392839283928396 20.10701070107011 75-79 24.015 27.165 28.675 20.145 80-84 24.40622031101555 26.911345567278367 28.34141707085354 20.341017050852543 85-89 24.6 27.295 28.24 19.865 90-94 24.493674051107668 25.85887883182477 29.55943391508726 20.0880132019803 95-99 23.98 27.165 28.28 20.575 100-104 24.654999999999998 27.295 28.050000000000004 20.0 105-109 23.085 26.915 29.360000000000003 20.64 110-114 23.935000000000002 26.985 28.494999999999997 20.585 115-119 24.665 27.295 27.88 20.16 120-124 22.919999999999998 26.795 29.29 20.995 125-129 23.74 27.339999999999996 28.134999999999998 20.785 130-134 24.065 28.01 27.79 20.135 135-139 23.515 28.29 27.11 21.085 140-144 23.76 28.04 27.485 20.715 145-149 24.085 28.22 26.415 21.279999999999998 150-151 23.599999999999998 28.075 27.3375 20.9875 >>END_MODULE >>Per sequence GC content pass #GC Content Count 0 1.0 1 0.5 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.5 9 0.5 10 0.0 11 0.0 12 0.0 13 0.0 14 0.0 15 0.0 16 0.5 17 0.5 18 0.0 19 0.0 20 0.0 21 2.0 22 2.0 23 1.0 24 1.5 25 1.0 26 3.5 27 6.0 28 6.5 29 10.5 30 15.0 31 19.5 32 31.0 33 47.0 34 73.5 35 94.0 36 101.5 37 122.5 38 150.5 39 167.5 40 184.0 41 216.0 42 236.0 43 247.0 44 268.0 45 266.5 46 254.0 47 243.0 48 213.5 49 182.5 50 164.0 51 132.5 52 96.0 53 83.5 54 70.5 55 63.0 56 50.5 57 36.0 58 35.0 59 23.5 60 18.0 61 16.0 62 8.5 63 7.0 64 6.0 65 2.0 66 0.5 67 0.5 68 2.5 69 4.0 70 4.0 71 4.0 72 2.5 73 0.5 74 0.0 75 0.0 76 0.0 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 fail #Base N-Count 1 23.9 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 0.005 50-54 0.0 55-59 0.0 60-64 0.0 65-69 0.01 70-74 0.01 75-79 0.0 80-84 0.005 85-89 0.0 90-94 0.015 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 91.60000000000001 #Duplication Level Percentage of deduplicated Percentage of total 1 94.05021834061135 86.15 2 4.612445414847162 8.450000000000001 3 0.7368995633187773 2.025 4 0.19104803493449782 0.7000000000000001 5 0.13646288209606985 0.625 6 0.10917030567685589 0.6 7 0.02729257641921397 0.17500000000000002 8 0.02729257641921397 0.2 9 0.05458515283842794 0.44999999999999996 >10 0.05458515283842794 0.625 >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 TGGCATCGTCGAGACTGAGAAGAACTATGTCTCCTCCGTAGTCATGGAGG 14 0.35000000000000003 No Hit TGTGGGATTGGGAGTGGATTAATAATGTAATTTCTGATAAATAATCTGTG 11 0.27499999999999997 No Hit TATTTGCTACTCGGATAACCGTAGTAATTCTAGAGCTAATACGTGCAACA 9 0.22499999999999998 No Hit AACTATCATGTTTGATGTGGGATTGGGAGTGGATTAATAATGTAATTTCT 9 0.22499999999999998 No Hit NACTATCATGTTTGATGTGGGATTGGGAGTGGATTAATAATGTAATTTCT 8 0.2 No Hit TATTTTACTTATTCCGTGAATCGGAGGCGGGGCGCTGCCCCTCTTTTTGG 7 0.17500000000000002 No Hit AGTGGATTAATAATGTAATTTCTGATAAATAATCTGTGTTCTTCTGTACT 6 0.15 No Hit AAAGACGAACAACTGCGAAAGCATTTGCCAAGGATGTTTTCATTAATCAA 6 0.15 No Hit AAGCCTAAGATTGTGTTTGGAACTAACGGCTCTAGTTCTGATTCTTACAT 6 0.15 No Hit GAGACTGAGAAGAACTATGTCTCCTCCGTAGTCATGGAGGTGCCAGCAGC 6 0.15 No Hit ATGCGCTCCTGGCCTTAACTGGCCGGGTCGTGCCTCCGGTGCTGTTACTT 5 0.125 No Hit AGGATGCCTGTGAGAACTGGGGCTTCTTTGAGCTATTGAACCATGGCATA 5 0.125 No Hit TTTGATGATCTGGAGGGCTTGCAGGAGTATCTTGATTCTTCGGTTGTTGC 5 0.125 No Hit AATGTAATTTCTGATAAATAATCTGTGTTCTTCTGTACTTGTGGGTGTGG 5 0.125 No Hit NGGCATCGTCGAGACTGAGAAGAACTATGTCTCCTCCGTAGTCATGGAGG 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 0.025 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 0.025 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 0.0625 0.0 0.0 0.0 0.0 30-31 0.1375 0.0 0.0 0.0 0.0 32-33 0.15 0.0 0.0 0.0 0.0 34-35 0.15 0.0 0.0 0.0 0.0 36-37 0.2 0.0 0.0 0.0 0.0 38-39 0.30000000000000004 0.0 0.0 0.0 0.0 40-41 0.325 0.0 0.0 0.0 0.0 42-43 0.35 0.0 0.0 0.0 0.0 44-45 0.375 0.0 0.0 0.0 0.0 46-47 0.45 0.0 0.0 0.0 0.0 48-49 0.48750000000000004 0.0 0.0 0.0 0.0 50-51 0.6 0.0 0.0 0.0 0.0 52-53 0.7124999999999999 0.0 0.0 0.0 0.0 54-55 0.8 0.0 0.0 0.0 0.0 56-57 0.85 0.0 0.0 0.0 0.0 58-59 0.925 0.0 0.0 0.0 0.0 60-61 1.0625 0.0 0.0 0.0 0.0 62-63 1.15 0.0 0.0 0.0 0.0 64-65 1.3125 0.0 0.0 0.0 0.0 66-67 1.4375 0.0 0.0 0.0 0.0 68-69 1.65 0.0 0.0 0.0 0.0 70-71 1.725 0.0 0.0 0.0 0.0 72-73 1.7625000000000002 0.0 0.0 0.0 0.0 74-75 1.9500000000000002 0.0 0.0 0.0 0.0 76-77 2.1500000000000004 0.0 0.0 0.0 0.0 78-79 2.375 0.0 0.0 0.0 0.0 80-81 2.5625 0.0 0.0 0.0 0.0 82-83 2.7625 0.0 0.0 0.0 0.0 84-85 2.9625 0.0 0.0 0.0 0.0 86-87 3.2375 0.0 0.0 0.0 0.0 88-89 3.6 0.0 0.0 0.0 0.0 90-91 3.9124999999999996 0.0 0.0 0.0 0.0 92-93 4.0625 0.0 0.0 0.0 0.0 94-95 4.3875 0.0 0.0 0.0 0.0 96-97 4.9625 0.0 0.0 0.0 0.0 98-99 5.3125 0.0 0.0 0.0 0.0 100-101 5.612500000000001 0.0 0.0 0.0 0.0 102-103 6.1125 0.0 0.0 0.0 0.0 104-105 6.5375 0.0 0.0 0.0 0.0 106-107 6.737500000000001 0.0 0.0 0.0 0.0 108-109 7.0625 0.0 0.0 0.0 0.0 110-111 7.625 0.0 0.0 0.0 0.0 112-113 8.1375 0.0 0.0 0.0 0.0 114-115 8.75 0.0 0.0 0.0 0.0 116-117 9.3125 0.0 0.0 0.0 0.0 118-119 10.0125 0.0 0.0 0.0 0.0 120-121 10.725000000000001 0.0 0.0 0.0 0.0 122-123 11.475 0.0 0.0 0.0 0.0 124-125 12.4 0.0 0.0 0.0 0.0 126-127 13.225000000000001 0.0 0.0 0.0 0.0 128-129 14.1 0.0 0.0 0.0 0.0 130-131 15.225 0.0 0.0 0.0 0.0 132-133 16.05 0.0 0.0 0.0 0.0 134-135 17.075 0.0 0.0 0.0 0.0 136-137 18.1375 0.0 0.0 0.0 0.0 138-139 19.387500000000003 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position AAGAGCC 10 0.006864391 144.7625 7 AGAGCCG 10 0.006864391 144.7625 8 ATGTCGC 10 0.006864391 144.7625 145 AAAGAGC 10 0.006864391 144.7625 6 >>END_MODULE Rejected 1943653 READS because READLEN < 1 Read 1943653 spots for SRR11462706.sra Written 1943653 spots for SRR11462706.sra Rejected 1943653 READS because READLEN < 1 Read 1943653 spots for SRR11462706.sra Written 1943653 spots for SRR11462706.sra Rejected 1943653 READS because READLEN < 1 Read 1943653 spots for SRR11462706.sra Written 1943653 spots for SRR11462706.sra Rejected 1943653 READS because READLEN < 1 Read 1943653 spots for SRR11462706.sra Written 1943653 spots for SRR11462706.sra Rejected 1943653 READS because READLEN < 1 Read 1943653 spots for SRR11462706.sra Written 1943653 spots for SRR11462706.sra Rejected 1943653 READS because READLEN < 1 Read 1943653 spots for SRR11462706.sra Written 1943653 spots for SRR11462706.sra Rejected 1943653 READS because READLEN < 1 Read 1943653 spots for SRR11462706.sra Written 1943653 spots for SRR11462706.sra Rejected 1943663 READS because READLEN < 1 Read 1943663 spots for SRR11462706.sra Written 1943663 spots for SRR11462706.sra Rejected 1943653 READS because READLEN < 1 Read 1943653 spots for SRR11462706.sra Written 1943653 spots for SRR11462706.sra Rejected 1943653 READS because READLEN < 1 Read 1943653 spots for SRR11462706.sra Written 1943653 spots for SRR11462706.sra Rejected 1943653 READS because READLEN < 1 Read 1943653 spots for SRR11462706.sra Written 1943653 spots for SRR11462706.sra Rejected 1943653 READS because READLEN < 1 Read 1943653 spots for SRR11462706.sra Written 1943653 spots for SRR11462706.sra Rejected 1943653 READS because READLEN < 1 Read 1943653 spots for SRR11462706.sra Written 1943653 spots for SRR11462706.sra Rejected 1943653 READS because READLEN < 1 Read 1943653 spots for SRR11462706.sra Written 1943653 spots for SRR11462706.sra Rejected 1943653 READS because READLEN < 1 Read 1943653 spots for SRR11462706.sra Written 1943653 spots for SRR11462706.sra Rejected 1943653 READS because READLEN < 1 Read 1943653 spots for SRR11462706.sra Written 1943653 spots for SRR11462706.sra Rejected 1943653 READS because READLEN < 1 Read 1943653 spots for SRR11462706.sra Written 1943653 spots for SRR11462706.sra Rejected 1943653 READS because READLEN < 1 Read 1943653 spots for SRR11462706.sra Written 1943653 spots for SRR11462706.sra Rejected 1943653 READS because READLEN < 1 Read 1943653 spots for SRR11462706.sra Written 1943653 spots for SRR11462706.sra Rejected 1943653 READS because READLEN < 1 Read 1943653 spots for SRR11462706.sra Written 1943653 spots for SRR11462706.sra SRR ids: ['SRR11462706.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_q_wcjrg8 SRR11462706.sra spots: 38873070 blocks: [[1, 1943653], [1943654, 3887306], [3887307, 5830959], [5830960, 7774612], [7774613, 9718265], [9718266, 11661918], [11661919, 13605571], [13605572, 15549224], [15549225, 17492877], [17492878, 19436530], [19436531, 21380183], [21380184, 23323836], [23323837, 25267489], [25267490, 27211142], [27211143, 29154795], [29154796, 31098448], [31098449, 33042101], [33042102, 34985754], [34985755, 36929407], [36929408, 38873070]] SRR11462706 file size 13189069 SRR11462706 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 SRR11462706 SRR11462706_1.fastq Input file: SRR11462706_1.fastq trimmed: SRR11462706-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 07:25:27 2025 >> started Wed Feb 12 07:25:48 2025 >> done (20.744s) 38873070 reads processed; of these: 13253 ( 0.03%) short reads filtered out after trimming by size control 1445 ( 0.00%) empty reads filtered out after trimming by size control 38858372 (99.96%) reads available; of these: 4351216 (11.20%) trimmed reads available after processing 34507156 (88.80%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 2817 0.01% 19 2953 0.01% 20 3567 0.01% 21 3543 0.01% 22 4140 0.01% 23 4470 0.01% 24 5054 0.01% 25 4661 0.01% 26 5294 0.01% 27 5635 0.01% 28 5477 0.01% 29 5869 0.02% 30 6014 0.02% 31 6208 0.02% 32 6209 0.02% 33 6213 0.02% 34 6811 0.02% 35 6998 0.02% 36 6988 0.02% 37 9914 0.03% 38 7484 0.02% 39 8378 0.02% 40 8181 0.02% 41 8267 0.02% 42 9385 0.02% 43 9034 0.02% 44 8987 0.02% 45 10459 0.03% 46 10862 0.03% 47 14331 0.04% 48 12597 0.03% 49 15058 0.04% 50 12354 0.03% 51 12844 0.03% 52 13694 0.04% 53 13742 0.04% 54 15855 0.04% 55 15153 0.04% 56 16169 0.04% 57 18221 0.05% 58 16478 0.04% 59 18664 0.05% 60 18655 0.05% 61 19378 0.05% 62 30605 0.08% 63 20306 0.05% 64 21990 0.06% 65 21186 0.05% 66 21864 0.06% 67 26555 0.07% 68 24291 0.06% 69 27991 0.07% 70 26391 0.07% 71 28850 0.07% 72 30669 0.08% 73 32784 0.08% 74 36649 0.09% 75 33002 0.08% 76 30499 0.08% 77 34093 0.09% 78 36842 0.09% 79 43443 0.11% 80 37872 0.10% 81 43886 0.11% 82 39876 0.10% 83 42155 0.11% 84 47558 0.12% 85 47561 0.12% 86 52999 0.14% 87 50621 0.13% 88 50970 0.13% 89 78553 0.20% 90 54181 0.14% 91 57595 0.15% 92 56044 0.14% 93 59832 0.15% 94 67502 0.17% 95 66063 0.17% 96 72740 0.19% 97 73902 0.19% 98 70470 0.18% 99 73569 0.19% 100 74392 0.19% 101 80053 0.21% 102 99670 0.26% 103 88123 0.23% 104 85691 0.22% 105 90494 0.23% 106 95108 0.24% 107 100963 0.26% 108 104507 0.27% 109 123132 0.32% 110 110250 0.28% 111 113040 0.29% 112 146457 0.38% 113 121884 0.31% 114 123718 0.32% 115 126653 0.33% 116 130643 0.34% 117 141880 0.37% 118 146273 0.38% 119 153261 0.39% 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 34507156 88.80% 38858372 reads passed initial QC criterion=sequence-density sequence-density=9.19 sequence-density-rank=1 fanout-score=41.36 fanout-score-rank=1 prefix-density=11.15 prefix-fanout=34.1 sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACGATCAGATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAA criterion=fanout-score sequence-density=9.19 sequence-density-rank=1 fanout-score=41.36 fanout-score-rank=1 prefix-density=11.15 prefix-fanout=34.1 sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACGATCAGATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAA 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 AGATCGGAAGAGCACACGTCTGAACTCCAGTCACGATCAGATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAA -o SRR11462706 - Input file: STDIN trimmed: SRR11462706-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): AGATCGGAAGAGCACACGTCTGAACTCCAGTCACGATCAGATCTCGTATGCCGTCTTCTGCTTG -- 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 07:27:37 2025 >> started Wed Feb 12 07:28:12 2025 >> done (34.672s) 31086698 reads processed; of these: 329 ( 0.00%) short reads filtered out after trimming by size control 10 ( 0.00%) empty reads filtered out after trimming by size control 31086359 (100.00%) reads available; of these: 6006575 (19.32%) trimmed reads available after processing 25079784 (80.68%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 2298 0.01% 19 2447 0.01% 20 2910 0.01% 21 2907 0.01% 22 3400 0.01% 23 3639 0.01% 24 4086 0.01% 25 3771 0.01% 26 4247 0.01% 27 4537 0.01% 28 4466 0.01% 29 4748 0.02% 30 4881 0.02% 31 5036 0.02% 32 5030 0.02% 33 5026 0.02% 34 5428 0.02% 35 5637 0.02% 36 5658 0.02% 37 8056 0.03% 38 6039 0.02% 39 6788 0.02% 40 6558 0.02% 41 6652 0.02% 42 7579 0.02% 43 7268 0.02% 44 7205 0.02% 45 8473 0.03% 46 8761 0.03% 47 11437 0.04% 48 10169 0.03% 49 12175 0.04% 50 10033 0.03% 51 10237 0.03% 52 10939 0.04% 53 11080 0.04% 54 12744 0.04% 55 12150 0.04% 56 12899 0.04% 57 14791 0.05% 58 13227 0.04% 59 15017 0.05% 60 15095 0.05% 61 15655 0.05% 62 24715 0.08% 63 16326 0.05% 64 17539 0.06% 65 17034 0.05% 66 17613 0.06% 67 21464 0.07% 68 19742 0.06% 69 22562 0.07% 70 21398 0.07% 71 22999 0.07% 72 24835 0.08% 73 26178 0.08% 74 29580 0.10% 75 26436 0.09% 76 24895 0.08% 77 27805 0.09% 78 29780 0.10% 79 34813 0.11% 80 30222 0.10% 81 36980 0.12% 82 31954 0.10% 83 33922 0.11% 84 36600 0.12% 85 38062 0.12% 86 42709 0.14% 87 40812 0.13% 88 41301 0.13% 89 63163 0.20% 90 44327 0.14% 91 46732 0.15% 92 45670 0.15% 93 47885 0.15% 94 54173 0.17% 95 52660 0.17% 96 58641 0.19% 97 58915 0.19% 98 56871 0.18% 99 59538 0.19% 100 60092 0.19% 101 64627 0.21% 102 80016 0.26% 103 71346 0.23% 104 69408 0.22% 105 72819 0.23% 106 75760 0.24% 107 80525 0.26% 108 84484 0.27% 109 99074 0.32% 110 88658 0.29% 111 91072 0.29% 112 118944 0.38% 113 97480 0.31% 114 99953 0.32% 115 100613 0.32% 116 104512 0.34% 117 109833 0.35% 118 113175 0.36% 119 121179 0.39% 120 130513 0.42% 121 133558 0.43% 122 131717 0.42% 123 186431 0.60% 124 161614 0.52% 125 140107 0.45% 126 150719 0.48% 127 156413 0.50% 128 151580 0.49% 129 154176 0.50% 130 155558 0.50% 131 166420 0.54% 132 173466 0.56% 133 188645 0.61% 134 176730 0.57% 135 189322 0.61% 136 178994 0.58% 137 197421 0.64% 138 226806 0.73% 139 204106 0.66% 140 220474 0.71% 141 193632 0.62% 142 202046 0.65% 143 213907 0.69% 144 206249 0.66% 145 225043 0.72% 146 227420 0.73% 147 336258 1.08% 148 699298 2.25% 149 0 0.00% 150 0 0.00% 151 21716136 69.86% criterion=sequence-density sequence-density=0.70 sequence-density-rank=1 fanout-score=2.08 fanout-score-rank=26 prefix-density=0.70 prefix-fanout=2.1 sequence=CTGCGACTGCGCTGACAAGACCCAGTGTGTCAAGAAGGGAAGCAGCTACACTGCTGGCATCGTCGAGACTGAGAAGAACTATGTCTCCTCCGTAGTCATGGAGGTGCCAGCAGCTGAGAACGATGGCAAGTGCAACTGCGGTACTGGCTGCACTTGCACTACCTGCACATGCGGTCATTAAGCAAGCACATCAACTATCATGTTTGATGTGGGATTGGGAGTGGATTAATAATGTAATTTCTGATAAATAATCTGTGTTCTTCTGTACTTGTGGGTGTGGAGTGAACAAACAAAAGTGTCCGTGAGTGTCTTTATCTTTGTGTCTTCTTCATTGTTATGTATTGGCCATGTCTGTGGCCTCTGGTGTGGTTTTAATGAAGTCTTATAATTAGTGTA criterion=fanout-score sequence-density=0.06 sequence-density-rank=31 fanout-score=35.12 fanout-score-rank=1 prefix-density=0.44 prefix-fanout=4.4 sequence=TGATTCTGATGATCAGACAAATACAGGTTTTACACAAACCCGTAAGAGCTGTTGCGATGTAGAATCTGGTTCAGTCCCATGTAAATCTCTCTCCTTCCCATGTAGCAACAGGAGTGACTATGTGTACTGGGATGGAGCCCATTTTACTGAAGCTAAAGCTTGGGCCTTCGGAAAAAGAGCATATAAACGTCAGTCACCAAAGGACGCTTATCCATATGATATCAGCGAACTAGTTAAGCTGAAGCTTGATGATTCTGATGCTTACGATATCAAACATGCCCATCTCTGATGGTGAAGACGATTGTCTAATAAGCAGTCAGAGAATAAGATATTGTGACTGTAAGAACAATTGAAAGACATTTTTAATGTCTTTTCATAGCCTTTCAC Started job on | Feb 12 07:28:48 Started mapping on | Feb 12 07:28:49 Finished on | Feb 12 07:30:01 Mapping speed, Million of reads per hour | 1942.90 Number of input reads | 38858033 Average input read length | 142 UNIQUE READS: Uniquely mapped reads number | 33515286 Uniquely mapped reads % | 86.25% Average mapped length | 140.38 Number of splices: Total | 15399255 Number of splices: Annotated (sjdb) | 15073360 Number of splices: GT/AG | 15114201 Number of splices: GC/AG | 218181 Number of splices: AT/AC | 9616 Number of splices: Non-canonical | 57257 Mismatch rate per base, % | 0.36% Deletion rate per base | 0.02% Deletion average length | 2.08 Insertion rate per base | 0.01% Insertion average length | 1.87 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 1476185 % of reads mapped to multiple loci | 3.80% Number of reads mapped to too many loci | 1929182 % of reads mapped to too many loci | 4.96% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 4.89% % of reads unmapped: other | 0.09% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 3866562 3866562 3866562 N_multimapping 1476185 1476185 1476185 N_noFeature 1742311 2467138 32401869 N_ambiguous 508640 119885 806 UnstrandedReadsAssigned:31264335 PositiveStrandReadsAssigned:30928263 NegativeStrandReadsAssigned:1112611 Dataset is classified positive stranded MeadianReadLen=151 20thPercentileLength=137 echo kmer=133 SRR11462706 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: SRR11462706-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 38,858,033 reads, 32,824,280 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,266 rounds 52401 SRR11462706.ke.tsv 34699 SRR11462706.se.tsv 87100 total ==> SRR11462706.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1919 1661 29.539 Potri.005G024800.1.v4.1 1035 936 403 14.6937 Potri.004G059700.1.v4.1 961 862 38 1.50445 Potri.007G009000.2.v4.1 1416 1317 0 0 Potri.003G141000.2.v4.1 2943 2844 2879 34.5473 Potri.016G087400.1.v4.1 270 171 1854 370.012 Potri.015G069301.1.v4.1 564 465 0 0 Potri.010G195200.1.v4.1 1773 1674 302 6.15677 Potri.012G127500.1.v4.1 977 878 151 5.86927 ==> SRR11462706.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 506 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 121 Potri.001G212900.v4.1 997 Potri.001G182400.v4.1 0 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 14 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 62 SRR11462706 completed mapping pipeline successfully