Starting /dee2/code/volunteer_pipeline.sh SRR11462703 current disk space = 3050070994944 free memory = 1430503696 SRR11462703 SRAfilesize 5aacdef85aec71ee569011105c3353b9 SRR11462703.sra SRR11462703.sra file validated SRR11462703 is single end SRR11462703 is conventional basespace SRR11462703 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR11462703_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 23.1625 32.0 2.0 32.0 2.0 32.0 2 31.795 32.0 32.0 32.0 32.0 32.0 3 34.62125 37.0 32.0 37.0 32.0 37.0 4 36.3025 37.0 37.0 37.0 32.0 37.0 5 36.4275 37.0 37.0 37.0 37.0 37.0 6 40.002 41.0 41.0 41.0 37.0 41.0 7 40.196 41.0 41.0 41.0 37.0 41.0 8 40.30025 41.0 41.0 41.0 37.0 41.0 9 40.28625 41.0 41.0 41.0 37.0 41.0 10-14 40.3229 41.0 41.0 41.0 41.0 41.0 15-19 40.27285 41.0 41.0 41.0 38.6 41.0 20-24 40.2325 41.0 41.0 41.0 39.4 41.0 25-29 40.20395 41.0 41.0 41.0 39.4 41.0 30-34 40.0887 41.0 41.0 41.0 37.0 41.0 35-39 40.10979999999999 41.0 41.0 41.0 38.6 41.0 40-44 40.0961 41.0 41.0 41.0 38.6 41.0 45-49 40.078700000000005 41.0 41.0 41.0 37.0 41.0 50-54 40.1225 41.0 41.0 41.0 38.6 41.0 55-59 40.07435 41.0 41.0 41.0 37.0 41.0 60-64 39.96225 41.0 41.0 41.0 37.0 41.0 65-69 40.00335 41.0 41.0 41.0 37.0 41.0 70-74 39.84015 41.0 41.0 41.0 37.0 41.0 75-79 39.79845 41.0 40.2 41.0 37.0 41.0 80-84 40.225249999999996 41.0 41.0 41.0 40.2 41.0 85-89 40.1214 41.0 41.0 41.0 37.8 41.0 90-94 40.11855 41.0 41.0 41.0 39.4 41.0 95-99 40.03385 41.0 41.0 41.0 37.8 41.0 100-104 39.88155 41.0 41.0 41.0 37.0 41.0 105-109 39.75165 41.0 41.0 41.0 37.0 41.0 110-114 39.711400000000005 41.0 41.0 41.0 37.0 41.0 115-119 39.7034 41.0 41.0 41.0 37.0 41.0 120-124 39.588849999999994 41.0 41.0 41.0 37.0 41.0 125-129 39.36295 41.0 41.0 41.0 37.0 41.0 130-134 39.17265 41.0 41.0 41.0 36.0 41.0 135-139 38.9268 41.0 41.0 41.0 34.0 41.0 140-144 38.8738 41.0 41.0 41.0 34.0 41.0 145-149 38.481100000000005 41.0 41.0 41.0 32.0 41.0 150-151 37.5505 41.0 39.0 41.0 29.5 41.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 23 1.0 24 3.0 25 2.0 26 7.0 27 4.0 28 14.0 29 21.0 30 21.0 31 37.0 32 43.0 33 57.0 34 65.0 35 83.0 36 80.0 37 109.0 38 179.0 39 258.0 40 3016.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 6.357569371268001 38.46153846153847 40.53389532841587 14.64699683877766 2 25.974999999999998 41.675000000000004 20.3 12.049999999999999 3 21.375 30.375000000000004 38.65 9.6 4 35.38538538538539 23.823823823823822 26.626626626626624 14.164164164164164 5 28.475 27.200000000000003 26.55 17.775 6 24.85 27.150000000000002 28.275 19.725 7 22.425 27.275 31.175000000000004 19.125 8 24.2 24.95 32.550000000000004 18.3 9 23.400000000000002 22.075 33.35 21.175 10-14 25.224999999999998 25.22 30.54 19.015 15-19 24.025 27.310000000000002 29.244999999999997 19.42 20-24 24.26 27.389999999999997 28.999999999999996 19.35 25-29 24.525 26.235000000000003 29.54 19.7 30-34 23.555 26.57 30.049999999999997 19.825 35-39 24.425 26.595000000000002 29.220000000000002 19.759999999999998 40-44 24.0 26.200000000000003 30.03 19.77 45-49 24.075 26.52 29.865000000000002 19.54 50-54 24.385 26.87 29.395 19.35 55-59 24.88 26.87 29.099999999999998 19.15 60-64 24.385 26.465 29.42 19.73 65-69 24.67 26.845000000000002 29.154999999999998 19.33 70-74 24.535 27.089999999999996 29.04 19.335 75-79 24.12 26.935 28.775000000000002 20.169999999999998 80-84 23.97 27.145000000000003 28.985 19.900000000000002 85-89 24.29 26.529999999999998 29.080000000000002 20.1 90-94 23.935000000000002 27.04 28.849999999999998 20.175 95-99 24.64 27.034999999999997 28.345 19.98 100-104 24.485 27.325 27.91 20.28 105-109 24.115000000000002 27.54 27.37 20.974999999999998 110-114 24.085 27.96 27.48 20.474999999999998 115-119 24.175 27.694999999999997 27.08 21.05 120-124 23.445 28.03 26.845000000000002 21.68 125-129 23.405 27.48 27.265 21.85 130-134 23.125 28.18 26.935 21.759999999999998 135-139 22.23 28.33 26.365 23.075000000000003 140-144 23.09 27.49 26.634999999999998 22.785 145-149 22.445 27.700000000000003 26.72 23.135 150-151 21.2 28.000000000000004 27.400000000000002 23.400000000000002 >>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 0.0 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 0.5 24 1.5 25 1.0 26 0.5 27 3.5 28 9.5 29 15.0 30 17.5 31 21.5 32 29.5 33 48.0 34 75.0 35 97.0 36 123.0 37 140.0 38 161.0 39 176.0 40 190.0 41 230.5 42 259.0 43 268.0 44 285.5 45 275.0 46 246.5 47 240.5 48 207.5 49 170.0 50 138.5 51 114.0 52 110.5 53 89.0 54 61.0 55 49.5 56 36.0 57 26.0 58 22.5 59 13.0 60 9.5 61 6.5 62 6.5 63 7.5 64 4.0 65 3.0 66 2.5 67 2.5 68 1.0 69 1.0 70 0.5 71 0.5 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 28.825 2 0.0 3 0.0 4 0.1 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 93.125 #Duplication Level Percentage of deduplicated Percentage of total 1 95.35570469798658 88.8 2 3.4093959731543624 6.35 3 0.7248322147651006 2.025 4 0.24161073825503354 0.8999999999999999 5 0.10738255033557045 0.5 6 0.026845637583892613 0.15 7 0.026845637583892613 0.17500000000000002 8 0.0 0.0 9 0.05369127516778523 0.44999999999999996 >10 0.05369127516778523 0.65 >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 ATGCGCTCCTGGCCTTAACTGGCCGGGTCGTGCCTCCGGTGCTGTTACTT 13 0.325 No Hit TATTTGCTACTCGGATAACCGTAGTAATTCTAGAGCTAATACGTGCAACA 13 0.325 No Hit TGTTGGCCTTCGGGATCGGAGTAATGATTAACAGGGACAGTCGGGGGCAT 9 0.22499999999999998 No Hit TGGCATCGTCGAGACTGAGAAGAACTATGTCTCCTCCGTAGTCATGGAGG 9 0.22499999999999998 No Hit NGTGGGATTGGGAGTGGATTAATAATGTAATTTCTGATAAATAATCTGTG 7 0.17500000000000002 No Hit TAAGGATATTGTAGCTCTCTCTGGGGGCCACACCCTGGGAAGGTGCCACA 6 0.15 No Hit NAAGACGAACAACTGCGAAAGCATTTGCCAAGGATGTTTTCATTAATCAA 5 0.125 No Hit NGGCATCGTCGAGACTGAGAAGAACTATGTCTCCTCCGTAGTCATGGAGG 5 0.125 No Hit AACTATCATGTTTGATGTGGGATTGGGAGTGGATTAATAATGTAATTTCT 5 0.125 No Hit AAGCACATCAACTATCATGTTTGATGTGGGATTGGGAGTGGATTAATAAT 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 0.0125 0.0 0.0 0.0 0.0 14-15 0.025 0.0 0.0 0.0 0.0 16-17 0.05 0.0 0.0 0.0 0.0 18-19 0.05 0.0 0.0 0.0 0.0 20-21 0.07500000000000001 0.0 0.0 0.0 0.0 22-23 0.1375 0.0 0.0 0.0 0.0 24-25 0.15 0.0 0.0 0.0 0.0 26-27 0.2 0.0 0.0 0.0 0.0 28-29 0.225 0.0 0.0 0.0 0.0 30-31 0.25 0.0 0.0 0.0 0.0 32-33 0.32499999999999996 0.0 0.0 0.0 0.0 34-35 0.3875 0.0 0.0 0.0 0.0 36-37 0.4875 0.0 0.0 0.0 0.0 38-39 0.55 0.0 0.0 0.0 0.0 40-41 0.5874999999999999 0.0 0.0 0.0 0.0 42-43 0.6125 0.0 0.0 0.0 0.0 44-45 0.675 0.0 0.0 0.0 0.0 46-47 0.8125 0.0 0.0 0.0 0.0 48-49 0.9 0.0 0.0 0.0 0.0 50-51 0.9375 0.0 0.0 0.0 0.0 52-53 0.975 0.0 0.0 0.0 0.0 54-55 0.9875 0.0 0.0 0.0 0.0 56-57 1.0375 0.0 0.0 0.0 0.0 58-59 1.15 0.0 0.0 0.0 0.0 60-61 1.3 0.0 0.0 0.0 0.0 62-63 1.4874999999999998 0.0 0.0 0.0 0.0 64-65 1.725 0.0 0.0 0.0 0.0 66-67 2.0 0.0 0.0 0.0 0.0 68-69 2.2625 0.0 0.0 0.0 0.0 70-71 2.4625 0.0 0.0 0.0 0.0 72-73 2.775 0.0 0.0 0.0 0.0 74-75 3.175 0.0 0.0 0.0 0.0 76-77 3.4625 0.0 0.0 0.0 0.0 78-79 3.875 0.0 0.0 0.0 0.0 80-81 4.425 0.0 0.0 0.0 0.0 82-83 4.9625 0.0 0.0 0.0 0.0 84-85 5.574999999999999 0.0 0.0 0.0 0.0 86-87 6.15 0.0 0.0 0.0 0.0 88-89 7.0 0.0 0.0 0.0 0.0 90-91 8.075 0.0 0.0 0.0 0.0 92-93 9.1625 0.0 0.0 0.0 0.0 94-95 10.025 0.0 0.0 0.0 0.0 96-97 11.024999999999999 0.0 0.0 0.0 0.0 98-99 12.325 0.0 0.0 0.0 0.0 100-101 13.3125 0.0 0.0 0.0 0.0 102-103 14.75 0.0 0.0 0.0 0.0 104-105 16.125 0.0 0.0 0.0 0.0 106-107 17.512500000000003 0.0 0.0 0.0 0.0 108-109 19.0125 0.0 0.0 0.0 0.0 110-111 20.4 0.0 0.0 0.0 0.0 112-113 22.0875 0.0 0.0 0.0 0.0 114-115 23.5625 0.0 0.0 0.0 0.0 116-117 24.887500000000003 0.0 0.0 0.0 0.0 118-119 26.225 0.0 0.0 0.0 0.0 120-121 27.8125 0.0 0.0 0.0 0.0 122-123 29.387500000000003 0.0 0.0 0.0 0.0 124-125 31.25 0.0 0.0 0.0 0.0 126-127 32.825 0.0 0.0 0.0 0.0 128-129 34.325 0.0 0.0 0.0 0.0 130-131 35.7125 0.0 0.0 0.0 0.0 132-133 37.3125 0.0 0.0 0.0 0.0 134-135 39.1375 0.0 0.0 0.0 0.0 136-137 40.900000000000006 0.0 0.0 0.0 0.0 138-139 42.4875 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position ATTAAAG 10 0.006871484 144.71251 7 AAAAAAA 75 1.63187E-7 19.295 140-144 >>END_MODULE Rejected 1792652 READS because READLEN < 1 Read 1792652 spots for SRR11462703.sra Written 1792652 spots for SRR11462703.sra Rejected 1792652 READS because READLEN < 1 Read 1792652 spots for SRR11462703.sra Written 1792652 spots for SRR11462703.sra Rejected 1792652 READS because READLEN < 1 Read 1792652 spots for SRR11462703.sra Written 1792652 spots for SRR11462703.sra Rejected 1792652 READS because READLEN < 1 Read 1792652 spots for SRR11462703.sra Written 1792652 spots for SRR11462703.sra Rejected 1792652 READS because READLEN < 1 Read 1792652 spots for SRR11462703.sra Written 1792652 spots for SRR11462703.sra Rejected 1792652 READS because READLEN < 1 Read 1792652 spots for SRR11462703.sra Written 1792652 spots for SRR11462703.sra Rejected 1792652 READS because READLEN < 1 Read 1792652 spots for SRR11462703.sra Written 1792652 spots for SRR11462703.sra Rejected 1792652 READS because READLEN < 1 Read 1792652 spots for SRR11462703.sra Written 1792652 spots for SRR11462703.sra Rejected 1792652 READS because READLEN < 1 Read 1792652 spots for SRR11462703.sra Written 1792652 spots for SRR11462703.sra Rejected 1792652 READS because READLEN < 1 Read 1792652 spots for SRR11462703.sra Written 1792652 spots for SRR11462703.sra Rejected 1792652 READS because READLEN < 1 Read 1792652 spots for SRR11462703.sra Written 1792652 spots for SRR11462703.sra Rejected 1792652 READS because READLEN < 1 Read 1792652 spots for SRR11462703.sra Written 1792652 spots for SRR11462703.sra Rejected 1792652 READS because READLEN < 1 Read 1792652 spots for SRR11462703.sra Written 1792652 spots for SRR11462703.sra Rejected 1792654 READS because READLEN < 1 Read 1792654 spots for SRR11462703.sra Written 1792654 spots for SRR11462703.sra Rejected 1792652 READS because READLEN < 1 Read 1792652 spots for SRR11462703.sra Written 1792652 spots for SRR11462703.sra Rejected 1792652 READS because READLEN < 1 Read 1792652 spots for SRR11462703.sra Written 1792652 spots for SRR11462703.sra Rejected 1792652 READS because READLEN < 1 Read 1792652 spots for SRR11462703.sra Written 1792652 spots for SRR11462703.sra Rejected 1792652 READS because READLEN < 1 Read 1792652 spots for SRR11462703.sra Written 1792652 spots for SRR11462703.sra Rejected 1792652 READS because READLEN < 1 Read 1792652 spots for SRR11462703.sra Written 1792652 spots for SRR11462703.sra Rejected 1792652 READS because READLEN < 1 Read 1792652 spots for SRR11462703.sra Written 1792652 spots for SRR11462703.sra SRR ids: ['SRR11462703.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_kwo300mj SRR11462703.sra spots: 35853042 blocks: [[1, 1792652], [1792653, 3585304], [3585305, 5377956], [5377957, 7170608], [7170609, 8963260], [8963261, 10755912], [10755913, 12548564], [12548565, 14341216], [14341217, 16133868], [16133869, 17926520], [17926521, 19719172], [19719173, 21511824], [21511825, 23304476], [23304477, 25097128], [25097129, 26889780], [26889781, 28682432], [28682433, 30475084], [30475085, 32267736], [32267737, 34060388], [34060389, 35853042]] SRR11462703 file size 12162731 SRR11462703 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 SRR11462703 SRR11462703_1.fastq Input file: SRR11462703_1.fastq trimmed: SRR11462703-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 07:13:24 2025 >> started Wed Feb 12 07:13:54 2025 >> done (30.132s) 35853042 reads processed; of these: 8900 ( 0.02%) short reads filtered out after trimming by size control 753 ( 0.00%) empty reads filtered out after trimming by size control 35843389 (99.97%) reads available; of these: 10224006 (28.52%) trimmed reads available after processing 25619383 (71.48%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 2265 0.01% 19 2499 0.01% 20 3179 0.01% 21 3076 0.01% 22 3544 0.01% 23 4166 0.01% 24 4439 0.01% 25 4329 0.01% 26 4513 0.01% 27 5373 0.01% 28 5061 0.01% 29 5664 0.02% 30 6091 0.02% 31 6157 0.02% 32 6389 0.02% 33 6665 0.02% 34 7351 0.02% 35 7544 0.02% 36 7789 0.02% 37 10638 0.03% 38 8767 0.02% 39 9658 0.03% 40 9471 0.03% 41 9896 0.03% 42 11980 0.03% 43 11683 0.03% 44 11910 0.03% 45 14374 0.04% 46 14137 0.04% 47 19733 0.06% 48 17200 0.05% 49 21969 0.06% 50 17511 0.05% 51 19303 0.05% 52 19731 0.06% 53 20923 0.06% 54 24153 0.07% 55 23606 0.07% 56 25527 0.07% 57 29906 0.08% 58 27424 0.08% 59 30029 0.08% 60 33631 0.09% 61 33900 0.09% 62 60163 0.17% 63 37721 0.11% 64 42374 0.12% 65 41978 0.12% 66 44463 0.12% 67 49388 0.14% 68 48771 0.14% 69 61758 0.17% 70 55340 0.15% 71 65183 0.18% 72 69937 0.20% 73 81787 0.23% 74 83083 0.23% 75 77464 0.22% 76 75128 0.21% 77 88414 0.25% 78 89964 0.25% 79 109065 0.30% 80 94107 0.26% 81 99224 0.28% 82 107258 0.30% 83 110303 0.31% 84 129122 0.36% 85 127967 0.36% 86 141519 0.39% 87 138583 0.39% 88 139364 0.39% 89 275763 0.77% 90 156481 0.44% 91 167253 0.47% 92 158762 0.44% 93 166995 0.47% 94 189497 0.53% 95 176773 0.49% 96 208465 0.58% 97 207052 0.58% 98 194261 0.54% 99 201311 0.56% 100 201068 0.56% 101 216473 0.60% 102 269436 0.75% 103 227027 0.63% 104 223901 0.62% 105 230561 0.64% 106 237497 0.66% 107 248355 0.69% 108 253101 0.71% 109 302691 0.84% 110 263380 0.73% 111 263967 0.74% 112 395864 1.10% 113 279704 0.78% 114 267372 0.75% 115 268304 0.75% 116 263956 0.74% 117 285498 0.80% 118 288936 0.81% 119 291611 0.81% 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% 150 109 0.00% 151 25619383 71.48% 35843389 reads passed initial QC criterion=sequence-density sequence-density=15.09 sequence-density-rank=1 fanout-score=38.83 fanout-score-rank=1 prefix-density=17.64 prefix-fanout=33.2 sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCTTGTAATCTCGTATGCCGTCTTCTGCTTGAAAAAA criterion=fanout-score sequence-density=15.09 sequence-density-rank=1 fanout-score=38.83 fanout-score-rank=1 prefix-density=17.64 prefix-fanout=33.2 sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCTTGTAATCTCGTATGCCGTCTTCTGCTTGAAAAAA 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 AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCTTGTAATCTCGTATGCCGTCTTCTGCTTGAAAAAA -o SRR11462703 - Input file: STDIN trimmed: SRR11462703-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCTTGTAATCTCGTATGCCGTCTTCTGCTTG -- 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 07:15:18 2025 >> started Wed Feb 12 07:16:01 2025 >> done (43.290s) 31362966 reads processed; of these: 328 ( 0.00%) short reads filtered out after trimming by size control 6 ( 0.00%) empty reads filtered out after trimming by size control 31362632 (100.00%) reads available; of these: 8267908 (26.36%) trimmed reads available after processing 23094724 (73.64%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 2066 0.01% 19 2238 0.01% 20 2846 0.01% 21 2717 0.01% 22 3163 0.01% 23 3710 0.01% 24 3998 0.01% 25 3847 0.01% 26 4017 0.01% 27 4806 0.02% 28 4516 0.01% 29 4965 0.02% 30 5430 0.02% 31 5527 0.02% 32 5689 0.02% 33 5887 0.02% 34 6490 0.02% 35 6722 0.02% 36 6920 0.02% 37 9315 0.03% 38 7701 0.02% 39 8552 0.03% 40 8382 0.03% 41 8871 0.03% 42 10595 0.03% 43 10313 0.03% 44 10559 0.03% 45 12755 0.04% 46 12496 0.04% 47 17490 0.06% 48 15189 0.05% 49 19570 0.06% 50 15650 0.05% 51 17077 0.05% 52 17517 0.06% 53 18607 0.06% 54 21437 0.07% 55 20869 0.07% 56 22350 0.07% 57 26553 0.08% 58 24118 0.08% 59 26550 0.08% 60 29754 0.09% 61 30280 0.10% 62 53183 0.17% 63 33648 0.11% 64 37231 0.12% 65 37206 0.12% 66 39283 0.13% 67 43915 0.14% 68 43465 0.14% 69 54537 0.17% 70 49393 0.16% 71 57342 0.18% 72 61962 0.20% 73 72220 0.23% 74 73438 0.23% 75 68049 0.22% 76 66425 0.21% 77 78556 0.25% 78 79427 0.25% 79 96446 0.31% 80 82718 0.26% 81 93241 0.30% 82 94399 0.30% 83 97620 0.31% 84 108472 0.35% 85 112778 0.36% 86 125106 0.40% 87 122571 0.39% 88 123741 0.39% 89 243057 0.77% 90 139905 0.45% 91 148066 0.47% 92 140604 0.45% 93 146310 0.47% 94 166596 0.53% 95 155292 0.50% 96 183854 0.59% 97 181745 0.58% 98 171453 0.55% 99 178194 0.57% 100 177266 0.57% 101 191293 0.61% 102 237453 0.76% 103 200421 0.64% 104 197273 0.63% 105 202747 0.65% 106 208745 0.67% 107 218053 0.70% 108 223293 0.71% 109 266098 0.85% 110 231963 0.74% 111 232297 0.74% 112 350724 1.12% 113 245109 0.78% 114 235507 0.75% 115 234126 0.75% 116 231498 0.74% 117 241888 0.77% 118 244258 0.78% 119 251363 0.80% 120 259939 0.83% 121 265232 0.85% 122 254933 0.81% 123 334667 1.07% 124 296238 0.94% 125 256070 0.82% 126 260103 0.83% 127 276033 0.88% 128 258247 0.82% 129 248673 0.79% 130 245737 0.78% 131 255040 0.81% 132 276361 0.88% 133 289612 0.92% 134 251375 0.80% 135 270184 0.86% 136 246375 0.79% 137 261869 0.83% 138 272467 0.87% 139 254691 0.81% 140 281455 0.90% 141 234551 0.75% 142 243947 0.78% 143 251718 0.80% 144 237774 0.76% 145 255837 0.82% 146 236264 0.75% 147 310779 0.99% 148 538161 1.72% 149 0 0.00% 150 60 0.00% 151 14447313 46.07% criterion=sequence-density sequence-density=0.64 sequence-density-rank=1 fanout-score=2.12 fanout-score-rank=34 prefix-density=0.64 prefix-fanout=2.1 sequence=CTGCGACTGCGCTGACAAGACCCAGTGTGTCAAGAAGGGAAGCAGCTACACTGCTGGCATCGTCGAGACTGAGAAGAACTATGTCTCCTCCGTAGTCATGGAGGTGCCAGCAGCTGAGAACGATGGCAAGTGCAACTGCGGTACTGGCTGCACTTGCACTACCTGCACATGCGGTCATTAAGCAAGCACATCAACTATCATGTTTGATGTGGGATTGGGAGTGGATTAATAATGTAATTTCTGATAAATAATCTGTGTTCTTCTGTACTTGTGGGTGTGGAGTGAACAAACAAAAGTGTCCGTGAGTGTCTTTATCTTTGTGTCTTCTTCATTGTTATGTATTGGCCATGTCTGTGGCCTCTGGTGTGGTTTTAATGAAGTCTTATAATTAGTGTAGTACTCTGCT criterion=fanout-score sequence-density=0.02 sequence-density-rank=35 fanout-score=383.60 fanout-score-rank=1 prefix-density=0.33 prefix-fanout=17.9 sequence=GCTGCTGCTAGCCATGCCAAGGACAAGAAGAAAGGGTCTGACCCTTTGGAGGAGTATTGCAAGGACAACCCTGAGACAGACGAGTGCCGCACTTATGAAGATTGAAATGGTTTTTACTTTATGAACCTTTTTCAATGATCAAACTTTAGATATGTTTATTAATTTTGGTTTATGTAACGCTGGAGATGCTG Started job on | Feb 12 07:16:34 Started mapping on | Feb 12 07:16:34 Finished on | Feb 12 07:17:36 Mapping speed, Million of reads per hour | 2081.21 Number of input reads | 35843055 Average input read length | 131 UNIQUE READS: Uniquely mapped reads number | 31542905 Uniquely mapped reads % | 88.00% Average mapped length | 129.75 Number of splices: Total | 12948763 Number of splices: Annotated (sjdb) | 12677639 Number of splices: GT/AG | 12730900 Number of splices: GC/AG | 174990 Number of splices: AT/AC | 7832 Number of splices: Non-canonical | 35041 Mismatch rate per base, % | 0.36% Deletion rate per base | 0.02% Deletion average length | 2.04 Insertion rate per base | 0.01% Insertion average length | 1.83 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 932046 % of reads mapped to multiple loci | 2.60% Number of reads mapped to too many loci | 1833332 % of reads mapped to too many loci | 5.11% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 4.23% % of reads unmapped: other | 0.05% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 3368104 3368104 3368104 N_multimapping 932046 932046 932046 N_noFeature 1773114 2368898 30630251 N_ambiguous 436113 119317 649 UnstrandedReadsAssigned:29333678 PositiveStrandReadsAssigned:29054690 NegativeStrandReadsAssigned:912005 Dataset is classified positive stranded MeadianReadLen=145 20thPercentileLength=109 echo kmer=105 SRR11462703 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: SRR11462703-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 35,843,055 reads, 29,963,203 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,259 rounds 52401 SRR11462703.ke.tsv 34699 SRR11462703.se.tsv 87100 total ==> SRR11462703.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1919 2355 46.0136 Potri.005G024800.1.v4.1 1035 936 918 36.7737 Potri.004G059700.1.v4.1 961 862 24 1.04394 Potri.007G009000.2.v4.1 1416 1317 0 0 Potri.003G141000.2.v4.1 2943 2844 2812.91 37.0849 Potri.016G087400.1.v4.1 270 171 2428 532.382 Potri.015G069301.1.v4.1 564 465 0 0 Potri.010G195200.1.v4.1 1773 1674 566 12.6774 Potri.012G127500.1.v4.1 977 878 52 2.22065 ==> SRR11462703.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 41 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 274 Potri.001G212900.v4.1 16 Potri.001G182400.v4.1 0 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 5 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 24 SRR11462703 completed mapping pipeline successfully