Starting /dee2/code/volunteer_pipeline.sh SRR11462692 current disk space = 3050323259392 free memory = 1582318204 SRR11462692 SRAfilesize a5c7693d99a09d136e0ca43a880badfd SRR11462692.sra SRR11462692.sra file validated SRR11462692 is single end SRR11462692 is conventional basespace SRR11462692 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR11462692_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 22.88625 32.0 2.0 32.0 2.0 32.0 2 31.7425 32.0 32.0 32.0 32.0 32.0 3 34.555 37.0 32.0 37.0 32.0 37.0 4 36.285 37.0 37.0 37.0 32.0 37.0 5 36.38125 37.0 37.0 37.0 37.0 37.0 6 39.80775 41.0 41.0 41.0 37.0 41.0 7 40.19225 41.0 41.0 41.0 37.0 41.0 8 40.17875 41.0 41.0 41.0 37.0 41.0 9 40.2775 41.0 41.0 41.0 37.0 41.0 10-14 40.279399999999995 41.0 41.0 41.0 38.6 41.0 15-19 40.2457 41.0 41.0 41.0 38.6 41.0 20-24 40.1483 41.0 41.0 41.0 37.8 41.0 25-29 40.155449999999995 41.0 41.0 41.0 37.0 41.0 30-34 40.19805 41.0 41.0 41.0 40.2 41.0 35-39 40.2108 41.0 41.0 41.0 40.2 41.0 40-44 40.129949999999994 41.0 41.0 41.0 38.6 41.0 45-49 40.14485 41.0 41.0 41.0 38.6 41.0 50-54 40.070800000000006 41.0 41.0 41.0 37.8 41.0 55-59 40.0791 41.0 41.0 41.0 37.0 41.0 60-64 39.9871 41.0 41.0 41.0 37.0 41.0 65-69 39.97765 41.0 41.0 41.0 37.0 41.0 70-74 39.91565 41.0 41.0 41.0 37.0 41.0 75-79 39.5742 41.0 40.2 41.0 37.0 41.0 80-84 40.133300000000006 41.0 41.0 41.0 38.6 41.0 85-89 40.084050000000005 41.0 41.0 41.0 37.8 41.0 90-94 40.0225 41.0 41.0 41.0 37.0 41.0 95-99 39.8378 41.0 41.0 41.0 37.0 41.0 100-104 39.867599999999996 41.0 41.0 41.0 37.0 41.0 105-109 39.75150000000001 41.0 41.0 41.0 37.0 41.0 110-114 39.73025 41.0 41.0 41.0 37.0 41.0 115-119 39.62405 41.0 41.0 41.0 37.0 41.0 120-124 39.451800000000006 41.0 41.0 41.0 37.0 41.0 125-129 39.29805 41.0 41.0 41.0 37.0 41.0 130-134 39.1163 41.0 41.0 41.0 36.0 41.0 135-139 38.8585 41.0 41.0 41.0 35.0 41.0 140-144 38.5027 41.0 41.0 41.0 32.0 41.0 145-149 38.2008 41.0 41.0 41.0 32.0 41.0 150-151 37.164625 41.0 39.0 41.0 27.0 41.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 22 1.0 23 1.0 24 3.0 25 1.0 26 8.0 27 7.0 28 11.0 29 14.0 30 18.0 31 31.0 32 39.0 33 48.0 34 74.0 35 94.0 36 105.0 37 141.0 38 181.0 39 385.0 40 2838.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 5.999290024849131 39.829605963791266 39.758608448704294 14.412495562655305 2 27.1 41.9 18.675 12.325 3 22.575 30.375000000000004 36.199999999999996 10.85 4 32.675 25.7 27.224999999999998 14.399999999999999 5 27.875 27.450000000000003 26.275 18.4 6 24.55 27.3 29.125 19.025 7 22.35 27.55 29.925 20.175 8 26.625 26.424999999999997 29.425 17.525 9 21.0 23.75 32.5 22.75 10-14 25.11 25.430000000000003 29.854999999999997 19.605 15-19 25.395 26.795 28.305000000000003 19.505 20-24 24.905 27.439999999999998 27.46 20.195 25-29 24.66 27.0 28.63 19.71 30-34 24.395 26.8 28.13 20.674999999999997 35-39 24.154999999999998 27.189999999999998 28.335 20.32 40-44 24.610000000000003 26.82 28.76 19.81 45-49 24.195 26.724999999999998 29.160000000000004 19.919999999999998 50-54 24.75 26.479999999999997 28.415000000000003 20.355 55-59 24.9 26.985 28.16 19.955000000000002 60-64 24.610000000000003 26.71 28.660000000000004 20.02 65-69 24.425 27.224999999999998 28.22 20.13 70-74 25.495 27.229999999999997 27.975 19.3 75-79 24.73 27.250000000000004 27.68 20.34 80-84 24.310000000000002 27.955000000000002 27.27 20.465 85-89 24.26 27.74 27.634999999999998 20.365 90-94 24.4 26.865 28.425 20.31 95-99 24.279999999999998 27.229999999999997 28.165000000000003 20.325 100-104 24.585 27.365000000000002 27.71 20.34 105-109 23.810000000000002 27.48 28.18 20.53 110-114 23.275000000000002 27.560000000000002 28.065 21.099999999999998 115-119 23.974999999999998 27.735 27.43 20.86 120-124 23.419999999999998 27.98 27.675 20.925 125-129 23.28 28.23 27.200000000000003 21.29 130-134 23.315 28.555000000000003 26.755000000000003 21.375 135-139 22.545 29.165000000000003 26.740000000000002 21.55 140-144 22.585 29.145 26.419999999999998 21.85 145-149 21.725 30.049999999999997 25.795 22.43 150-151 21.325 29.625 27.05 22.0 >>END_MODULE >>Per sequence GC content pass #GC Content Count 0 0.0 1 0.0 2 0.5 3 0.5 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 0.0 21 0.0 22 0.0 23 2.0 24 3.0 25 2.5 26 2.0 27 5.5 28 9.0 29 12.5 30 16.0 31 22.0 32 32.0 33 41.5 34 53.5 35 88.0 36 108.5 37 107.5 38 136.0 39 163.5 40 188.0 41 216.5 42 237.5 43 253.0 44 252.5 45 259.5 46 268.0 47 252.5 48 226.5 49 191.0 50 164.0 51 139.0 52 109.5 53 89.0 54 75.5 55 69.0 56 52.5 57 34.5 58 26.0 59 17.0 60 19.5 61 17.0 62 6.5 63 8.0 64 6.5 65 2.5 66 1.0 67 1.5 68 2.5 69 2.0 70 2.5 71 2.0 72 1.0 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 29.575000000000003 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 94.325 #Duplication Level Percentage of deduplicated Percentage of total 1 95.46779750861384 90.05 2 3.7900874635568513 7.1499999999999995 3 0.47707394646170154 1.35 4 0.05300821627352239 0.2 5 0.0795123244102836 0.375 6 0.10601643254704478 0.6 7 0.0 0.0 8 0.0 0.0 9 0.0 0.0 >10 0.026504108136761195 0.27499999999999997 >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 11 0.27499999999999997 No Hit TGTGGGATTGGGAGTGGATTAATAATGTAATTTCTGATAAATAATCTGTG 6 0.15 No Hit NACTATCATGTTTGATGTGGGATTGGGAGTGGATTAATAATGTAATTTCT 6 0.15 No Hit AACTATCATGTTTGATGTGGGATTGGGAGTGGATTAATAATGTAATTTCT 6 0.15 No Hit TATTTTACTTATTCCGTGAATCGGAGGCGGGGCGCTGCCCCTCTTTTTGG 6 0.15 No Hit ATGCGCTCCTGGCCTTAACTGGCCGGGTCGTGCCTCCGGTGCTGTTACTT 5 0.125 No Hit NGGCATCGTCGAGACTGAGAAGAACTATGTCTCCTCCGTAGTCATGGAGG 5 0.125 No Hit TATTTGCTACTCGGATAACCGTAGTAATTCTAGAGCTAATACGTGCAACA 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 0.075 0.0 0.0 0.0 0.0 2 0.075 0.0 0.0 0.0 0.0 3 0.075 0.0 0.0 0.0 0.0 4 0.075 0.0 0.0 0.0 0.0 5 0.075 0.0 0.0 0.0 0.0 6 0.075 0.0 0.0 0.0 0.0 7 0.075 0.0 0.0 0.0 0.0 8 0.075 0.0 0.0 0.0 0.0 9 0.075 0.0 0.0 0.0 0.0 10-11 0.0875 0.0 0.0 0.0 0.0 12-13 0.1 0.0 0.0 0.0 0.0 14-15 0.1 0.0 0.0 0.0 0.0 16-17 0.1125 0.0 0.0 0.0 0.0 18-19 0.1875 0.0 0.0 0.0 0.0 20-21 0.225 0.0 0.0 0.0 0.0 22-23 0.2375 0.0 0.0 0.0 0.0 24-25 0.25 0.0 0.0 0.0 0.0 26-27 0.25 0.0 0.0 0.0 0.0 28-29 0.2875 0.0 0.0 0.0 0.0 30-31 0.3625 0.0 0.0 0.0 0.0 32-33 0.4 0.0 0.0 0.0 0.0 34-35 0.425 0.0 0.0 0.0 0.0 36-37 0.45 0.0 0.0 0.0 0.0 38-39 0.575 0.0 0.0 0.0 0.0 40-41 0.6 0.0 0.0 0.0 0.0 42-43 0.65 0.0 0.0 0.0 0.0 44-45 0.725 0.0 0.0 0.0 0.0 46-47 0.8 0.0 0.0 0.0 0.0 48-49 0.875 0.0 0.0 0.0 0.0 50-51 1.0 0.0 0.0 0.0 0.0 52-53 1.1125 0.0 0.0 0.0 0.0 54-55 1.225 0.0 0.0 0.0 0.0 56-57 1.5125 0.0 0.0 0.0 0.0 58-59 1.6875 0.0 0.0 0.0 0.0 60-61 1.8875000000000002 0.0 0.0 0.0 0.0 62-63 2.125 0.0 0.0 0.0 0.0 64-65 2.325 0.0 0.0 0.0 0.0 66-67 2.625 0.0 0.0 0.0 0.0 68-69 2.8499999999999996 0.0 0.0 0.0 0.0 70-71 3.2875 0.0 0.0 0.0 0.0 72-73 3.675 0.0 0.0 0.0 0.0 74-75 4.199999999999999 0.0 0.0 0.0 0.0 76-77 4.675 0.0 0.0 0.0 0.0 78-79 5.0625 0.0 0.0 0.0 0.0 80-81 5.7125 0.0 0.0 0.0 0.0 82-83 6.075 0.0 0.0 0.0 0.0 84-85 6.425 0.0 0.0 0.0 0.0 86-87 6.9125 0.0 0.0 0.0 0.0 88-89 7.4375 0.0 0.0 0.0 0.0 90-91 8.1875 0.0 0.0 0.0 0.0 92-93 8.7 0.0 0.0 0.0 0.0 94-95 9.3125 0.0 0.0 0.0 0.0 96-97 10.4375 0.0 0.0 0.0 0.0 98-99 11.3 0.0 0.0 0.0 0.0 100-101 12.05 0.0 0.0 0.0 0.0 102-103 12.7875 0.0 0.0 0.0 0.0 104-105 13.6875 0.0 0.0 0.0 0.0 106-107 14.4875 0.0 0.0 0.0 0.0 108-109 15.425 0.0 0.0 0.0 0.0 110-111 16.475 0.0 0.0 0.0 0.0 112-113 17.5375 0.0 0.0 0.0 0.0 114-115 18.7375 0.0 0.0 0.0 0.0 116-117 19.799999999999997 0.0 0.0 0.0 0.0 118-119 21.2875 0.0 0.0 0.0 0.0 120-121 22.737499999999997 0.0 0.0 0.0 0.0 122-123 24.0375 0.0 0.0 0.0 0.0 124-125 25.7875 0.0 0.0 0.0 0.0 126-127 27.1 0.0 0.0 0.0 0.0 128-129 28.5875 0.0 0.0 0.0 0.0 130-131 30.1875 0.0 0.0 0.0 0.0 132-133 31.3 0.0 0.0 0.0 0.0 134-135 32.925 0.0 0.0 0.0 0.0 136-137 34.425 0.0 0.0 0.0 0.0 138-139 36.212500000000006 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position CAAGCAA 15 0.007823993 137.80952 1 AAAAAAA 110 1.3262128E-4 19.73182 145 >>END_MODULE Rejected 2017394 READS because READLEN < 1 Read 2017394 spots for SRR11462692.sra Written 2017394 spots for SRR11462692.sra Rejected 2017394 READS because READLEN < 1 Read 2017394 spots for SRR11462692.sra Written 2017394 spots for SRR11462692.sra Rejected 2017394 READS because READLEN < 1 Read 2017394 spots for SRR11462692.sra Written 2017394 spots for SRR11462692.sra Rejected 2017394 READS because READLEN < 1 Read 2017394 spots for SRR11462692.sra Written 2017394 spots for SRR11462692.sra Rejected 2017394 READS because READLEN < 1 Read 2017394 spots for SRR11462692.sra Written 2017394 spots for SRR11462692.sra Rejected 2017394 READS because READLEN < 1 Read 2017394 spots for SRR11462692.sra Written 2017394 spots for SRR11462692.sra Rejected 2017394 READS because READLEN < 1 Read 2017394 spots for SRR11462692.sra Written 2017394 spots for SRR11462692.sra Rejected 2017394 READS because READLEN < 1 Read 2017394 spots for SRR11462692.sra Written 2017394 spots for SRR11462692.sra Rejected 2017394 READS because READLEN < 1 Read 2017394 spots for SRR11462692.sra Written 2017394 spots for SRR11462692.sra Rejected 2017394 READS because READLEN < 1 Read 2017394 spots for SRR11462692.sra Written 2017394 spots for SRR11462692.sra Rejected 2017395 READS because READLEN < 1 Read 2017395 spots for SRR11462692.sra Written 2017395 spots for SRR11462692.sra Rejected 2017394 READS because READLEN < 1 Read 2017394 spots for SRR11462692.sra Written 2017394 spots for SRR11462692.sra Rejected 2017394 READS because READLEN < 1 Read 2017394 spots for SRR11462692.sra Written 2017394 spots for SRR11462692.sra Rejected 2017394 READS because READLEN < 1 Read 2017394 spots for SRR11462692.sra Written 2017394 spots for SRR11462692.sra Rejected 2017394 READS because READLEN < 1 Read 2017394 spots for SRR11462692.sra Written 2017394 spots for SRR11462692.sra Rejected 2017394 READS because READLEN < 1 Read 2017394 spots for SRR11462692.sra Written 2017394 spots for SRR11462692.sra Rejected 2017394 READS because READLEN < 1 Read 2017394 spots for SRR11462692.sra Written 2017394 spots for SRR11462692.sra Rejected 2017394 READS because READLEN < 1 Read 2017394 spots for SRR11462692.sra Written 2017394 spots for SRR11462692.sra Rejected 2017394 READS because READLEN < 1 Read 2017394 spots for SRR11462692.sra Written 2017394 spots for SRR11462692.sra Rejected 2017394 READS because READLEN < 1 Read 2017394 spots for SRR11462692.sra Written 2017394 spots for SRR11462692.sra SRR ids: ['SRR11462692.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_f4zov461 SRR11462692.sra spots: 40347881 blocks: [[1, 2017394], [2017395, 4034788], [4034789, 6052182], [6052183, 8069576], [8069577, 10086970], [10086971, 12104364], [12104365, 14121758], [14121759, 16139152], [16139153, 18156546], [18156547, 20173940], [20173941, 22191334], [22191335, 24208728], [24208729, 26226122], [26226123, 28243516], [28243517, 30260910], [30260911, 32278304], [32278305, 34295698], [34295699, 36313092], [36313093, 38330486], [38330487, 40347881]] SRR11462692 file size 13690274 SRR11462692 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 SRR11462692 SRR11462692_1.fastq Input file: SRR11462692_1.fastq trimmed: SRR11462692-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 06:26:49 2025 >> started Wed Feb 12 06:27:11 2025 >> done (21.828s) 40347881 reads processed; of these: 28728 ( 0.07%) short reads filtered out after trimming by size control 58220 ( 0.14%) empty reads filtered out after trimming by size control 40260933 (99.78%) reads available; of these: 9243406 (22.96%) trimmed reads available after processing 31017527 (77.04%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 6405 0.02% 19 6981 0.02% 20 7766 0.02% 21 8669 0.02% 22 9730 0.02% 23 10279 0.03% 24 10983 0.03% 25 11101 0.03% 26 11324 0.03% 27 12484 0.03% 28 12730 0.03% 29 13777 0.03% 30 14231 0.04% 31 14923 0.04% 32 14905 0.04% 33 15346 0.04% 34 16362 0.04% 35 16903 0.04% 36 17392 0.04% 37 20003 0.05% 38 18398 0.05% 39 19894 0.05% 40 19956 0.05% 41 20553 0.05% 42 22837 0.06% 43 23165 0.06% 44 23213 0.06% 45 25527 0.06% 46 26750 0.07% 47 36019 0.09% 48 29301 0.07% 49 31974 0.08% 50 29964 0.07% 51 32814 0.08% 52 33499 0.08% 53 34561 0.09% 54 38004 0.09% 55 38140 0.09% 56 40675 0.10% 57 44208 0.11% 58 41657 0.10% 59 46631 0.12% 60 47108 0.12% 61 48244 0.12% 62 66976 0.17% 63 51827 0.13% 64 55998 0.14% 65 54079 0.13% 66 55986 0.14% 67 60782 0.15% 68 60270 0.15% 69 67445 0.17% 70 65933 0.16% 71 72714 0.18% 72 75615 0.19% 73 79504 0.20% 74 85623 0.21% 75 79750 0.20% 76 77080 0.19% 77 83639 0.21% 78 87151 0.22% 79 96815 0.24% 80 90250 0.22% 81 94328 0.23% 82 97538 0.24% 83 99858 0.25% 84 112705 0.28% 85 111867 0.28% 86 121654 0.30% 87 119652 0.30% 88 118562 0.29% 89 147417 0.37% 90 127465 0.32% 91 131118 0.33% 92 130987 0.33% 93 136414 0.34% 94 146225 0.36% 95 146415 0.36% 96 176155 0.44% 97 166232 0.41% 98 155977 0.39% 99 163652 0.41% 100 162186 0.40% 101 174094 0.43% 102 201070 0.50% 103 181025 0.45% 104 183548 0.46% 105 186734 0.46% 106 193163 0.48% 107 201815 0.50% 108 206678 0.51% 109 235104 0.58% 110 215832 0.54% 111 219104 0.54% 112 289316 0.72% 113 227925 0.57% 114 228539 0.57% 115 232713 0.58% 116 236635 0.59% 117 252177 0.63% 118 259158 0.64% 119 259546 0.64% 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 31017527 77.04% 40260933 reads passed initial QC criterion=sequence-density sequence-density=13.81 sequence-density-rank=1 fanout-score=39.24 fanout-score-rank=1 prefix-density=16.25 prefix-fanout=33.4 sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCATTTTATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAA criterion=fanout-score sequence-density=13.81 sequence-density-rank=1 fanout-score=39.24 fanout-score-rank=1 prefix-density=16.25 prefix-fanout=33.4 sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCATTTTATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAA 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 AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCATTTTATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAA -o SRR11462692 - Input file: STDIN trimmed: SRR11462692-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCATTTTATCTCGTATGCCGTCTTCTGCTTG -- 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 06:28:45 2025 >> started Wed Feb 12 06:29:23 2025 >> done (38.328s) 34509371 reads processed; of these: 976 ( 0.00%) short reads filtered out after trimming by size control 320 ( 0.00%) empty reads filtered out after trimming by size control 34508075 (100.00%) reads available; of these: 8623079 (24.99%) trimmed reads available after processing 25884996 (75.01%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 5623 0.02% 19 6110 0.02% 20 6721 0.02% 21 7591 0.02% 22 8487 0.02% 23 8849 0.03% 24 9502 0.03% 25 9710 0.03% 26 9811 0.03% 27 10815 0.03% 28 11020 0.03% 29 11934 0.03% 30 12129 0.04% 31 12806 0.04% 32 12895 0.04% 33 13315 0.04% 34 14090 0.04% 35 14712 0.04% 36 15107 0.04% 37 17350 0.05% 38 15959 0.05% 39 17138 0.05% 40 17182 0.05% 41 17741 0.05% 42 19746 0.06% 43 20034 0.06% 44 20119 0.06% 45 22143 0.06% 46 23241 0.07% 47 31059 0.09% 48 25441 0.07% 49 27659 0.08% 50 26073 0.08% 51 28342 0.08% 52 28859 0.08% 53 30114 0.09% 54 32875 0.10% 55 32970 0.10% 56 34985 0.10% 57 38059 0.11% 58 36012 0.10% 59 40116 0.12% 60 41129 0.12% 61 41727 0.12% 62 57928 0.17% 63 44836 0.13% 64 48051 0.14% 65 47165 0.14% 66 48694 0.14% 67 52488 0.15% 68 52126 0.15% 69 58236 0.17% 70 56968 0.17% 71 62449 0.18% 72 65343 0.19% 73 68685 0.20% 74 74060 0.21% 75 68442 0.20% 76 67151 0.19% 77 72516 0.21% 78 75228 0.22% 79 83456 0.24% 80 77317 0.22% 81 86534 0.25% 82 84127 0.24% 83 86274 0.25% 84 92642 0.27% 85 96450 0.28% 86 105361 0.31% 87 103462 0.30% 88 103065 0.30% 89 126980 0.37% 90 111028 0.32% 91 113550 0.33% 92 113034 0.33% 93 117341 0.34% 94 126195 0.37% 95 126405 0.37% 96 152479 0.44% 97 143157 0.41% 98 134450 0.39% 99 141486 0.41% 100 139730 0.40% 101 150656 0.44% 102 173606 0.50% 103 156208 0.45% 104 158574 0.46% 105 160390 0.46% 106 167010 0.48% 107 173403 0.50% 108 178702 0.52% 109 202699 0.59% 110 186359 0.54% 111 188667 0.55% 112 250738 0.73% 113 195416 0.57% 114 197004 0.57% 115 199268 0.58% 116 203495 0.59% 117 209501 0.61% 118 215371 0.62% 119 219866 0.64% 120 239397 0.69% 121 235423 0.68% 122 236203 0.68% 123 305090 0.88% 124 281366 0.82% 125 242365 0.70% 126 252227 0.73% 127 257833 0.75% 128 253650 0.74% 129 249060 0.72% 130 248959 0.72% 131 267917 0.78% 132 276190 0.80% 133 298813 0.87% 134 265170 0.77% 135 281120 0.81% 136 267615 0.78% 137 290137 0.84% 138 307023 0.89% 139 280832 0.81% 140 283638 0.82% 141 263048 0.76% 142 281674 0.82% 143 288176 0.84% 144 273829 0.79% 145 282404 0.82% 146 278804 0.81% 147 380584 1.10% 148 657287 1.90% 149 0 0.00% 150 0 0.00% 151 18223119 52.81% criterion=sequence-density sequence-density=0.63 sequence-density-rank=1 fanout-score=2.08 fanout-score-rank=31 prefix-density=0.63 prefix-fanout=2.1 sequence=CTGCGACTGCGCTGACAAGACCCAGTGTGTCAAGAAGGGAAGCAGCTACACTGCTGGCATCGTCGAGACTGAGAAGAACTATGTCTCCTCCGTAGTCATGGAGGTGCCAGCAGCTGAGAACGATGGCAAGTGCAACTGCGGTACTGGCTGCACTTGCACTACCTGCACATGCGGTCATTAAGCAAGCACATCAACTATCATGTTTGATGTGGGATTGGGAGTGGATTAATAATGTAATTTCTGATAAATAATCTGTGTTCTTCTGTACTTGTGGGTGTGGAGTGAACAAACAAAAGTGTCCGTGAGTGTCTTTATCTTTGTGTCTTCTTCATTGTTATGTATTGGCCATGTCTGTGGCCTCTGGTGTGGTTTTAATGAAGTCTTATAATTAGTGTAGTACTCTGCT criterion=fanout-score sequence-density=0.06 sequence-density-rank=28 fanout-score=11.76 fanout-score-rank=1 prefix-density=0.18 prefix-fanout=3.8 sequence=AAGGCTGGAGCCCAGATCTTCAGCGAGGGTGGACTTGACTACTTGGGCAACCCAAGCTTGATCCACGCACAAAGCATCTTGGCCATCTGGGCTACACAGGTGGTCTTGATGGGTGCCGTTGAGGGTTACAGAATTGCTGGCGGGCCACTCGGTGAGGTAACTGACCCAATCTACCCAGGTGGAAGCTTCGACCCACTGGGCTTGGCTGACGATCCCGAAGCATTCGCTGAGTTGAAGGTGAAGGAACTCAAGAATGGTAGGTTGGCTATGTTCTCAATGTTCGGATTCTTTGTCCAGGCCATTGTGACCGGAAAGGGACCACTGGAGAACCTGGCTGACCACCTTTCTGACCCAGTAAACAACAACGCCTGGGCATATGCCACAAACTTCGTTCCCGGAAAGTGAGCAACAAAAGAGTTTTTTCTGTGCTGGGACTATTGGCTTGTAATGTTAACTTGTGATGTAACGAGCTCATG Started job on | Feb 12 06:29:59 Started mapping on | Feb 12 06:30:00 Finished on | Feb 12 06:31:17 Mapping speed, Million of reads per hour | 1882.27 Number of input reads | 40259637 Average input read length | 134 UNIQUE READS: Uniquely mapped reads number | 35613586 Uniquely mapped reads % | 88.46% Average mapped length | 131.75 Number of splices: Total | 15404476 Number of splices: Annotated (sjdb) | 15111832 Number of splices: GT/AG | 15112358 Number of splices: GC/AG | 227015 Number of splices: AT/AC | 9478 Number of splices: Non-canonical | 55625 Mismatch rate per base, % | 0.40% Deletion rate per base | 0.02% Deletion average length | 2.09 Insertion rate per base | 0.01% Insertion average length | 1.86 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 1065520 % of reads mapped to multiple loci | 2.65% Number of reads mapped to too many loci | 1504670 % of reads mapped to too many loci | 3.74% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 5.07% % of reads unmapped: other | 0.08% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 3580531 3580531 3580531 N_multimapping 1065520 1065520 1065520 N_noFeature 1600934 2189663 34633330 N_ambiguous 538843 147410 818 UnstrandedReadsAssigned:33473809 PositiveStrandReadsAssigned:33276513 NegativeStrandReadsAssigned:979438 Dataset is classified positive stranded MeadianReadLen=151 20thPercentileLength=114 echo kmer=109 SRR11462692 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: SRR11462692-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 40,259,637 reads, 34,255,784 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,321 rounds 52401 SRR11462692.ke.tsv 34699 SRR11462692.se.tsv 87100 total ==> SRR11462692.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1919 2381 39.5563 Potri.005G024800.1.v4.1 1035 936 615 20.9474 Potri.004G059700.1.v4.1 961 862 35 1.29447 Potri.007G009000.2.v4.1 1416 1317 0 0 Potri.003G141000.2.v4.1 2943 2844 3432.24 38.4751 Potri.016G087400.1.v4.1 270 171 2228 415.384 Potri.015G069301.1.v4.1 564 465 0 0 Potri.010G195200.1.v4.1 1773 1674 206 3.92322 Potri.012G127500.1.v4.1 977 878 178 6.46333 ==> SRR11462692.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 112 Potri.001G233950.v4.1 1 Potri.001G122700.v4.1 274 Potri.001G212900.v4.1 32 Potri.001G182400.v4.1 1 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 11 Potri.001G416900.v4.1 2 Potri.001G452600.v4.1 13 SRR11462692 completed mapping pipeline successfully