Starting /dee2/code/volunteer_pipeline.sh SRR11462743 current disk space = 3051269443584 free memory = 1582696056 SRR11462743 SRAfilesize 915946dce5f53ff312a5f8b450028852 SRR11462743.sra SRR11462743.sra file validated SRR11462743 is single end SRR11462743 is conventional basespace SRR11462743 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR11462743_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 22.27375 32.0 2.0 32.0 2.0 32.0 2 31.69625 32.0 32.0 32.0 32.0 32.0 3 34.53125 37.0 32.0 37.0 32.0 37.0 4 36.19 37.0 37.0 37.0 32.0 37.0 5 36.4975 37.0 37.0 37.0 37.0 37.0 6 39.916 41.0 41.0 41.0 37.0 41.0 7 40.24125 41.0 41.0 41.0 37.0 41.0 8 40.19475 41.0 41.0 41.0 37.0 41.0 9 40.2435 41.0 41.0 41.0 37.0 41.0 10-14 40.308350000000004 41.0 41.0 41.0 39.4 41.0 15-19 40.30705 41.0 41.0 41.0 40.2 41.0 20-24 40.255199999999995 41.0 41.0 41.0 38.6 41.0 25-29 40.2038 41.0 41.0 41.0 38.6 41.0 30-34 40.261799999999994 41.0 41.0 41.0 40.2 41.0 35-39 40.25429999999999 41.0 41.0 41.0 40.2 41.0 40-44 40.22445 41.0 41.0 41.0 40.2 41.0 45-49 40.2115 41.0 41.0 41.0 40.2 41.0 50-54 40.182649999999995 41.0 41.0 41.0 39.4 41.0 55-59 40.226099999999995 41.0 41.0 41.0 38.6 41.0 60-64 40.09785 41.0 41.0 41.0 37.0 41.0 65-69 40.023250000000004 41.0 41.0 41.0 37.0 41.0 70-74 39.9613 41.0 41.0 41.0 37.0 41.0 75-79 39.643100000000004 41.0 40.2 41.0 37.0 41.0 80-84 40.21575000000001 41.0 41.0 41.0 38.6 41.0 85-89 40.22725 41.0 41.0 41.0 40.2 41.0 90-94 40.12765 41.0 41.0 41.0 39.4 41.0 95-99 39.9951 41.0 41.0 41.0 37.8 41.0 100-104 40.04390000000001 41.0 41.0 41.0 37.0 41.0 105-109 39.87845 41.0 41.0 41.0 37.0 41.0 110-114 39.9077 41.0 41.0 41.0 37.0 41.0 115-119 39.919349999999994 41.0 41.0 41.0 37.0 41.0 120-124 39.673500000000004 41.0 41.0 41.0 37.0 41.0 125-129 39.4623 41.0 41.0 41.0 37.0 41.0 130-134 39.4457 41.0 41.0 41.0 37.0 41.0 135-139 39.2538 41.0 41.0 41.0 37.0 41.0 140-144 38.87985 41.0 41.0 41.0 35.0 41.0 145-149 38.74165 41.0 41.0 41.0 34.0 41.0 150-151 37.854625 41.0 39.0 41.0 29.5 41.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 24 1.0 25 1.0 26 5.0 27 6.0 28 6.0 29 19.0 30 13.0 31 26.0 32 28.0 33 36.0 34 56.0 35 85.0 36 85.0 37 141.0 38 186.0 39 365.0 40 2941.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 5.461876832844575 36.10703812316716 42.558651026392965 15.872434017595308 2 27.775 40.375 18.975 12.875 3 22.45 28.4 38.975 10.174999999999999 4 33.875 25.05 27.0 14.075 5 29.375 25.95 27.075 17.599999999999998 6 24.45 26.650000000000002 30.75 18.15 7 22.85 26.375 29.225 21.55 8 25.974999999999998 25.5 30.55 17.974999999999998 9 22.650000000000002 21.775 34.1 21.475 10-14 25.745 24.945 30.17 19.139999999999997 15-19 24.89 26.695 29.365000000000002 19.05 20-24 23.805 27.815 28.884999999999998 19.495 25-29 24.625 26.484999999999996 29.270000000000003 19.62 30-34 24.295 25.945 29.565 20.195 35-39 24.23 26.615 28.955 20.200000000000003 40-44 23.494999999999997 27.575 29.28 19.650000000000002 45-49 24.03 26.36 29.580000000000002 20.03 50-54 24.755 26.045 29.4 19.8 55-59 24.51 27.400000000000002 28.945 19.145 60-64 24.27 26.779999999999998 29.435 19.515 65-69 24.68 26.215 29.525000000000002 19.580000000000002 70-74 24.985 27.045 28.415000000000003 19.555 75-79 23.91 27.12 29.18 19.79 80-84 24.085 27.334999999999997 28.875 19.705000000000002 85-89 24.575 27.134999999999998 28.465 19.825 90-94 24.595 26.72 28.794999999999998 19.89 95-99 24.485 27.85 27.52 20.145 100-104 24.275 26.875 28.71 20.14 105-109 23.35 27.55 28.915000000000003 20.185 110-114 24.245 27.715 28.015 20.025000000000002 115-119 23.755000000000003 27.855 27.560000000000002 20.830000000000002 120-124 23.525 28.1 27.395000000000003 20.979999999999997 125-129 23.615 28.000000000000004 27.005000000000003 21.38 130-134 23.990000000000002 28.585 26.35 21.075 135-139 23.875 28.689999999999998 25.805 21.63 140-144 23.705000000000002 28.335 25.669999999999998 22.29 145-149 23.494999999999997 27.994999999999997 26.025 22.485 150-151 23.1375 28.225 25.825 22.8125 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 0.0 1 0.0 2 1.0 3 1.0 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 0.5 17 0.5 18 0.0 19 0.0 20 0.5 21 0.5 22 0.5 23 0.5 24 0.5 25 1.5 26 2.5 27 6.0 28 10.0 29 12.5 30 18.5 31 26.0 32 34.0 33 40.0 34 55.5 35 80.0 36 117.0 37 139.5 38 163.0 39 198.0 40 192.5 41 201.0 42 234.0 43 251.5 44 271.5 45 281.5 46 265.0 47 258.0 48 221.5 49 182.5 50 151.0 51 111.5 52 108.0 53 83.0 54 52.5 55 62.0 56 55.0 57 30.5 58 25.0 59 15.5 60 8.0 61 9.0 62 5.5 63 4.0 64 3.0 65 0.0 66 1.5 67 1.5 68 1.5 69 1.5 70 0.5 71 1.0 72 0.5 73 0.0 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 31.8 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 91.64999999999999 #Duplication Level Percentage of deduplicated Percentage of total 1 94.59901800327333 86.7 2 4.118930714675396 7.55 3 0.6001091107474086 1.6500000000000001 4 0.27277686852154936 1.0 5 0.10911074740861974 0.5 6 0.027277686852154936 0.15 7 0.10911074740861974 0.7000000000000001 8 0.05455537370430987 0.4 9 0.027277686852154936 0.22499999999999998 >10 0.08183306055646482 1.125 >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 22 0.5499999999999999 No Hit ATGCGCTCCTGGCCTTAACTGGCCGGGTCGTGCCTCCGGTGCTGTTACTT 13 0.325 No Hit TGTGGGATTGGGAGTGGATTAATAATGTAATTTCTGATAAATAATCTGTG 10 0.25 No Hit NGTGGGATTGGGAGTGGATTAATAATGTAATTTCTGATAAATAATCTGTG 9 0.22499999999999998 No Hit NGGCATCGTCGAGACTGAGAAGAACTATGTCTCCTCCGTAGTCATGGAGG 8 0.2 No Hit AACTATCATGTTTGATGTGGGATTGGGAGTGGATTAATAATGTAATTTCT 8 0.2 No Hit TGGGATTGGGAGTGGATTAATAATGTAATTTCTGATAAATAATCTGTGTT 7 0.17500000000000002 No Hit NACTATCATGTTTGATGTGGGATTGGGAGTGGATTAATAATGTAATTTCT 7 0.17500000000000002 No Hit TATTTGCTACTCGGATAACCGTAGTAATTCTAGAGCTAATACGTGCAACA 7 0.17500000000000002 No Hit AAGCACATCAACTATCATGTTTGATGTGGGATTGGGAGTGGATTAATAAT 7 0.17500000000000002 No Hit TGTTTGTGTCGTCGGTGGTGTTCCGGCAGGGGGGGTGGATTTTATGATTG 6 0.15 No Hit ACAACACTCGTCAAGTGCAGTGCATCAGTTTTATCGCCTCCAAGCCGAAG 5 0.125 No Hit CCTCCAAGCCGAAGGGTGTCTAGGTTCCAAGATTTGATGAGTCCCTAGCT 5 0.125 No Hit TAATGTAATTTCTGATAAATAATCTGTGTTCTTCTGTACTTGTGGGTGTG 5 0.125 No Hit TAAGAGCTGTTGCGATGTAGAATCTGGTTCAGTCCCATGTAAATCTCTCT 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 0.0 0.0 0.0 0.0 0.0 18-19 0.0 0.0 0.0 0.0 0.0 20-21 0.0125 0.0 0.0 0.0 0.0 22-23 0.025 0.0 0.0 0.0 0.0 24-25 0.07500000000000001 0.0 0.0 0.0 0.0 26-27 0.1 0.0 0.0 0.0 0.0 28-29 0.125 0.0 0.0 0.0 0.0 30-31 0.1875 0.0 0.0 0.0 0.0 32-33 0.2 0.0 0.0 0.0 0.0 34-35 0.25 0.0 0.0 0.0 0.0 36-37 0.275 0.0 0.0 0.0 0.0 38-39 0.325 0.0 0.0 0.0 0.0 40-41 0.3375 0.0 0.0 0.0 0.0 42-43 0.35 0.0 0.0 0.0 0.0 44-45 0.3625 0.0 0.0 0.0 0.0 46-47 0.3875 0.0 0.0 0.0 0.0 48-49 0.4 0.0 0.0 0.0 0.0 50-51 0.4625 0.0 0.0 0.0 0.0 52-53 0.6125 0.0 0.0 0.0 0.0 54-55 0.6625000000000001 0.0 0.0 0.0 0.0 56-57 0.7375 0.0 0.0 0.0 0.0 58-59 0.775 0.0 0.0 0.0 0.0 60-61 0.95 0.0 0.0 0.0 0.0 62-63 1.0 0.0 0.0 0.0 0.0 64-65 1.175 0.0 0.0 0.0 0.0 66-67 1.325 0.0 0.0 0.0 0.0 68-69 1.3875 0.0 0.0 0.0 0.0 70-71 1.5625 0.0 0.0 0.0 0.0 72-73 1.8 0.0 0.0 0.0 0.0 74-75 1.9874999999999998 0.0 0.0 0.0 0.0 76-77 2.2125000000000004 0.0 0.0 0.0 0.0 78-79 2.3625 0.0 0.0 0.0 0.0 80-81 2.6375 0.0 0.0 0.0 0.0 82-83 3.075 0.0 0.0 0.0 0.0 84-85 3.6125 0.0 0.0 0.0 0.0 86-87 4.0625 0.0 0.0 0.0 0.0 88-89 4.6 0.0 0.0 0.0 0.0 90-91 5.3 0.0 0.0 0.0 0.0 92-93 5.9375 0.0 0.0 0.0 0.0 94-95 6.449999999999999 0.0 0.0 0.0 0.0 96-97 7.1625 0.0 0.0 0.0 0.0 98-99 7.9625 0.0 0.0 0.0 0.0 100-101 8.787500000000001 0.0 0.0 0.0 0.0 102-103 9.7375 0.0 0.0 0.0 0.0 104-105 10.4875 0.0 0.0 0.0 0.0 106-107 11.4375 0.0 0.0 0.0 0.0 108-109 12.3375 0.0 0.0 0.0 0.0 110-111 13.212499999999999 0.0 0.0 0.0 0.0 112-113 14.274999999999999 0.0 0.0 0.0 0.0 114-115 15.5 0.0 0.0 0.0 0.0 116-117 16.9 0.0 0.0 0.0 0.0 118-119 18.200000000000003 0.0 0.0 0.0 0.0 120-121 19.35 0.0 0.0 0.0 0.0 122-123 20.65 0.0 0.0 0.0 0.0 124-125 22.6125 0.0 0.0 0.0 0.0 126-127 23.9375 0.0 0.0 0.0 0.0 128-129 25.35 0.0 0.0 0.0 0.0 130-131 26.8125 0.0 0.0 0.0 0.0 132-133 28.137500000000003 0.0 0.0 0.0 0.0 134-135 29.6375 0.0 0.0 0.0 0.0 136-137 31.4125 0.0 0.0 0.0 0.0 138-139 33.3 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Rejected 2172841 READS because READLEN < 1 Read 2172841 spots for SRR11462743.sra Written 2172841 spots for SRR11462743.sra Rejected 2172841 READS because READLEN < 1 Read 2172841 spots for SRR11462743.sra Written 2172841 spots for SRR11462743.sra Rejected 2172841 READS because READLEN < 1 Read 2172841 spots for SRR11462743.sra Written 2172841 spots for SRR11462743.sra Rejected 2172841 READS because READLEN < 1 Read 2172841 spots for SRR11462743.sra Written 2172841 spots for SRR11462743.sra Rejected 2172841 READS because READLEN < 1 Read 2172841 spots for SRR11462743.sra Written 2172841 spots for SRR11462743.sra Rejected 2172841 READS because READLEN < 1 Read 2172841 spots for SRR11462743.sra Written 2172841 spots for SRR11462743.sra Rejected 2172841 READS because READLEN < 1 Read 2172841 spots for SRR11462743.sra Written 2172841 spots for SRR11462743.sra Rejected 2172841 READS because READLEN < 1 Read 2172841 spots for SRR11462743.sra Written 2172841 spots for SRR11462743.sra Rejected 2172841 READS because READLEN < 1 Read 2172841 spots for SRR11462743.sra Written 2172841 spots for SRR11462743.sra Rejected 2172841 READS because READLEN < 1 Read 2172841 spots for SRR11462743.sra Written 2172841 spots for SRR11462743.sra Rejected 2172841 READS because READLEN < 1 Read 2172841 spots for SRR11462743.sra Written 2172841 spots for SRR11462743.sra Rejected 2172841 READS because READLEN < 1 Read 2172841 spots for SRR11462743.sra Written 2172841 spots for SRR11462743.sra Rejected 2172841 READS because READLEN < 1 Read 2172841 spots for SRR11462743.sra Written 2172841 spots for SRR11462743.sra Rejected 2172841 READS because READLEN < 1 Read 2172841 spots for SRR11462743.sra Written 2172841 spots for SRR11462743.sra Rejected 2172841 READS because READLEN < 1 Read 2172841 spots for SRR11462743.sra Written 2172841 spots for SRR11462743.sra Rejected 2172849 READS because READLEN < 1 Read 2172849 spots for SRR11462743.sra Written 2172849 spots for SRR11462743.sra Rejected 2172841 READS because READLEN < 1 Read 2172841 spots for SRR11462743.sra Written 2172841 spots for SRR11462743.sra Rejected 2172841 READS because READLEN < 1 Read 2172841 spots for SRR11462743.sra Written 2172841 spots for SRR11462743.sra Rejected 2172841 READS because READLEN < 1 Read 2172841 spots for SRR11462743.sra Written 2172841 spots for SRR11462743.sra Rejected 2172841 READS because READLEN < 1 Read 2172841 spots for SRR11462743.sra Written 2172841 spots for SRR11462743.sra SRR ids: ['SRR11462743.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_7ggtp5mm SRR11462743.sra spots: 43456828 blocks: [[1, 2172841], [2172842, 4345682], [4345683, 6518523], [6518524, 8691364], [8691365, 10864205], [10864206, 13037046], [13037047, 15209887], [15209888, 17382728], [17382729, 19555569], [19555570, 21728410], [21728411, 23901251], [23901252, 26074092], [26074093, 28246933], [28246934, 30419774], [30419775, 32592615], [32592616, 34765456], [34765457, 36938297], [36938298, 39111138], [39111139, 41283979], [41283980, 43456828]] SRR11462743 file size 14746831 SRR11462743 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 SRR11462743 SRR11462743_1.fastq Input file: SRR11462743_1.fastq trimmed: SRR11462743-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 12:49:57 2025 >> started Wed Feb 12 12:50:33 2025 >> done (36.020s) 43456828 reads processed; of these: 7269 ( 0.02%) short reads filtered out after trimming by size control 1680 ( 0.00%) empty reads filtered out after trimming by size control 43447879 (99.98%) reads available; of these: 8454188 (19.46%) trimmed reads available after processing 34993691 (80.54%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 1773 0.00% 19 2015 0.00% 20 2487 0.01% 21 2504 0.01% 22 2917 0.01% 23 3373 0.01% 24 3712 0.01% 25 3416 0.01% 26 3749 0.01% 27 4381 0.01% 28 4335 0.01% 29 4862 0.01% 30 4825 0.01% 31 5168 0.01% 32 4934 0.01% 33 5353 0.01% 34 5944 0.01% 35 6187 0.01% 36 6304 0.01% 37 8264 0.02% 38 6926 0.02% 39 7753 0.02% 40 7557 0.02% 41 7858 0.02% 42 9846 0.02% 43 9097 0.02% 44 9724 0.02% 45 13215 0.03% 46 11330 0.03% 47 18425 0.04% 48 13737 0.03% 49 17254 0.04% 50 13907 0.03% 51 15723 0.04% 52 15787 0.04% 53 16698 0.04% 54 19668 0.05% 55 18487 0.04% 56 21232 0.05% 57 23034 0.05% 58 20697 0.05% 59 25218 0.06% 60 24759 0.06% 61 26238 0.06% 62 48322 0.11% 63 29005 0.07% 64 33140 0.08% 65 30078 0.07% 66 32187 0.07% 67 38073 0.09% 68 36250 0.08% 69 43159 0.10% 70 40951 0.09% 71 47091 0.11% 72 50919 0.12% 73 53014 0.12% 74 59181 0.14% 75 55005 0.13% 76 52669 0.12% 77 57006 0.13% 78 64298 0.15% 79 73730 0.17% 80 68147 0.16% 81 78437 0.18% 82 74725 0.17% 83 78471 0.18% 84 95686 0.22% 85 97085 0.22% 86 114614 0.26% 87 101414 0.23% 88 101195 0.23% 89 155342 0.36% 90 116172 0.27% 91 119265 0.27% 92 121359 0.28% 93 130177 0.30% 94 145681 0.34% 95 138253 0.32% 96 188513 0.43% 97 155849 0.36% 98 152350 0.35% 99 160240 0.37% 100 159851 0.37% 101 176067 0.41% 102 254591 0.59% 103 191964 0.44% 104 188192 0.43% 105 193313 0.44% 106 206953 0.48% 107 222295 0.51% 108 222622 0.51% 109 274788 0.63% 110 239301 0.55% 111 233073 0.54% 112 302455 0.70% 113 252749 0.58% 114 247720 0.57% 115 259636 0.60% 116 257787 0.59% 117 276861 0.64% 118 302723 0.70% 119 293521 0.68% 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 34993691 80.54% 43447879 reads passed initial QC criterion=sequence-density sequence-density=13.91 sequence-density-rank=1 fanout-score=38.57 fanout-score-rank=1 prefix-density=16.28 prefix-fanout=33.0 sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCGGAATATCTCGTATGCCGTCTTCTGCTTGAAAAAA criterion=fanout-score sequence-density=13.91 sequence-density-rank=1 fanout-score=38.57 fanout-score-rank=1 prefix-density=16.28 prefix-fanout=33.0 sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCGGAATATCTCGTATGCCGTCTTCTGCTTGAAAAAA 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 AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCGGAATATCTCGTATGCCGTCTTCTGCTTGAAAAAA -o SRR11462743 - Input file: STDIN trimmed: SRR11462743-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCGGAATATCTCGTATGCCGTCTTCTGCTTG -- 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 12:52:06 2025 >> started Wed Feb 12 12:53:02 2025 >> done (55.972s) 37241039 reads processed; of these: 266 ( 0.00%) short reads filtered out after trimming by size control 10 ( 0.00%) empty reads filtered out after trimming by size control 37240763 (100.00%) reads available; of these: 9337394 (25.07%) trimmed reads available after processing 27903369 (74.93%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 1553 0.00% 19 1774 0.00% 20 2159 0.01% 21 2199 0.01% 22 2566 0.01% 23 2887 0.01% 24 3180 0.01% 25 2939 0.01% 26 3272 0.01% 27 3847 0.01% 28 3781 0.01% 29 4238 0.01% 30 4210 0.01% 31 4538 0.01% 32 4320 0.01% 33 4600 0.01% 34 5109 0.01% 35 5382 0.01% 36 5539 0.01% 37 7103 0.02% 38 5960 0.02% 39 6669 0.02% 40 6580 0.02% 41 6864 0.02% 42 8540 0.02% 43 7817 0.02% 44 8382 0.02% 45 11558 0.03% 46 9989 0.03% 47 15913 0.04% 48 11868 0.03% 49 14851 0.04% 50 12328 0.03% 51 13560 0.04% 52 13663 0.04% 53 14458 0.04% 54 16966 0.05% 55 16148 0.04% 56 18208 0.05% 57 19917 0.05% 58 17817 0.05% 59 21637 0.06% 60 21302 0.06% 61 22907 0.06% 62 41892 0.11% 63 25291 0.07% 64 28666 0.08% 65 26333 0.07% 66 27909 0.07% 67 32895 0.09% 68 31732 0.09% 69 37305 0.10% 70 35574 0.10% 71 40241 0.11% 72 44420 0.12% 73 45765 0.12% 74 51074 0.14% 75 47593 0.13% 76 45935 0.12% 77 49724 0.13% 78 55443 0.15% 79 63894 0.17% 80 58802 0.16% 81 74928 0.20% 82 64535 0.17% 83 68066 0.18% 84 75977 0.20% 85 84172 0.23% 86 98834 0.27% 87 87675 0.24% 88 87987 0.24% 89 134255 0.36% 90 101886 0.27% 91 103974 0.28% 92 106241 0.29% 93 111856 0.30% 94 125336 0.34% 95 118286 0.32% 96 163189 0.44% 97 134063 0.36% 98 131798 0.35% 99 139502 0.37% 100 137999 0.37% 101 152079 0.41% 102 218807 0.59% 103 167194 0.45% 104 164123 0.44% 105 166619 0.45% 106 178117 0.48% 107 190633 0.51% 108 192254 0.52% 109 236637 0.64% 110 206403 0.55% 111 201000 0.54% 112 263603 0.71% 113 217724 0.58% 114 213684 0.57% 115 222331 0.60% 116 222954 0.60% 117 230687 0.62% 118 250965 0.67% 119 248274 0.67% 120 262802 0.71% 121 262285 0.70% 122 261008 0.70% 123 428805 1.15% 124 321318 0.86% 125 264451 0.71% 126 272163 0.73% 127 309578 0.83% 128 273946 0.74% 129 265866 0.71% 130 268460 0.72% 131 290573 0.78% 132 277856 0.75% 133 339125 0.91% 134 284495 0.76% 135 302966 0.81% 136 286440 0.77% 137 301700 0.81% 138 350611 0.94% 139 292482 0.79% 140 313886 0.84% 141 270817 0.73% 142 278516 0.75% 143 307424 0.83% 144 285535 0.77% 145 279067 0.75% 146 282791 0.76% 147 396163 1.06% 148 731298 1.96% 149 0 0.00% 150 0 0.00% 151 20894103 56.11% criterion=sequence-density sequence-density=0.79 sequence-density-rank=1 fanout-score=2.10 fanout-score-rank=30 prefix-density=0.80 prefix-fanout=2.1 sequence=CTGCGACTGCGCTGACAAGACCCAGTGTGTCAAGAAGGGAAGCAGCTACACTGCTGGCATCGTCGAGACTGAGAAGAACTATGTCTCCTCCGTAGTCATGGAGGTGCCAGCAGCTGAGAACGATGGCAAGTGCAACTGCGGTACTGGCTGCACTTGCACTACCTGCACATGCGGTCATTAAGCAAGCACATCAACTATCATGTTTGATGTGGGATTGGGAGTGGATTAATAATGTAATTTCTGATAAATAATCTGTGTTCTTCTGTACTTGTGGGTGTGGAGTGAACAAACAAAAGTGTCCGTGAGTGTCTTTATCTTTGTGTCTTCTTCATTGTTATGTATTGGCCATGTCTGTGGCCTCTGGTGTGGTTTTAATGAAGTCTTATAATTAGTGTAGTACTCTGCT criterion=fanout-score sequence-density=0.03 sequence-density-rank=28 fanout-score=206.85 fanout-score-rank=1 prefix-density=0.33 prefix-fanout=18.6 sequence=TTGATGCTGAGAATTCTCCAAGCGTGGTTGCCATCAACGTGAGCCCTATTGAATATGGGCATGTGCTGTTAATCCCACGTGTCCTGGATTGCTTGCCTCAGAGGATTGATCGTGATAGCTTCTTGCTTGCACTTCACATGGCAGCTGAAGCTGGGGATCCATACTTCCGACTGGGTTACAATAGCTTGGGTGCTTTTGCAACCATTAACCATCTTCACTTCCAGGCTTACTACTTGACTGTGCCTTTTCCGATTGAGAAGG Started job on | Feb 12 12:53:41 Started mapping on | Feb 12 12:53:42 Finished on | Feb 12 12:54:56 Mapping speed, Million of reads per hour | 2113.67 Number of input reads | 43447603 Average input read length | 137 UNIQUE READS: Uniquely mapped reads number | 39789727 Uniquely mapped reads % | 91.58% Average mapped length | 135.71 Number of splices: Total | 16981785 Number of splices: Annotated (sjdb) | 16667411 Number of splices: GT/AG | 16662958 Number of splices: GC/AG | 263998 Number of splices: AT/AC | 10171 Number of splices: Non-canonical | 44658 Mismatch rate per base, % | 0.39% Deletion rate per base | 0.02% Deletion average length | 2.04 Insertion rate per base | 0.01% Insertion average length | 1.90 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 1267934 % of reads mapped to multiple loci | 2.92% Number of reads mapped to too many loci | 1127653 % of reads mapped to too many loci | 2.60% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 2.84% % of reads unmapped: other | 0.06% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 2389942 2389942 2389942 N_multimapping 1267934 1267934 1267934 N_noFeature 1856182 2809583 38339956 N_ambiguous 640924 144571 820 UnstrandedReadsAssigned:37292621 PositiveStrandReadsAssigned:36835573 NegativeStrandReadsAssigned:1448951 Dataset is classified positive stranded MeadianReadLen=151 20thPercentileLength=120 echo kmer=115 SRR11462743 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: SRR11462743-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 43,447,603 reads, 37,898,002 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,276 rounds 52401 SRR11462743.ke.tsv 34699 SRR11462743.se.tsv 87100 total ==> SRR11462743.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1919 1911 27.9606 Potri.005G024800.1.v4.1 1035 936 927 27.8077 Potri.004G059700.1.v4.1 961 862 5 0.162864 Potri.007G009000.2.v4.1 1416 1317 0 0 Potri.003G141000.2.v4.1 2943 2844 4533.77 44.7601 Potri.016G087400.1.v4.1 270 171 2114 347.112 Potri.015G069301.1.v4.1 564 465 0 0 Potri.010G195200.1.v4.1 1773 1674 231 3.87452 Potri.012G127500.1.v4.1 977 878 84 2.68625 ==> SRR11462743.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 157 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 277 Potri.001G212900.v4.1 53 Potri.001G182400.v4.1 0 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 7 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 21 SRR11462743 completed mapping pipeline successfully