Starting /dee2/code/volunteer_pipeline.sh SRR11462701 current disk space = 3049989300224 free memory = 1580661568 SRR11462701 SRAfilesize 83d248e453ff3c73f0c3e3e12c08c3f9 SRR11462701.sra SRR11462701.sra file validated SRR11462701 is single end SRR11462701 is conventional basespace SRR11462701 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR11462701_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 20.90875 32.0 2.0 32.0 2.0 32.0 2 31.73625 32.0 32.0 32.0 32.0 32.0 3 34.225 37.0 32.0 37.0 32.0 37.0 4 36.2225 37.0 37.0 37.0 32.0 37.0 5 36.3575 37.0 37.0 37.0 37.0 37.0 6 39.92675 41.0 41.0 41.0 37.0 41.0 7 40.151 41.0 41.0 41.0 37.0 41.0 8 40.2465 41.0 41.0 41.0 37.0 41.0 9 40.23675 41.0 41.0 41.0 37.0 41.0 10-14 40.30645 41.0 41.0 41.0 39.4 41.0 15-19 40.283100000000005 41.0 41.0 41.0 39.4 41.0 20-24 40.195449999999994 41.0 41.0 41.0 38.6 41.0 25-29 40.24775 41.0 41.0 41.0 40.2 41.0 30-34 40.07555 41.0 41.0 41.0 37.8 41.0 35-39 40.0724 41.0 41.0 41.0 37.0 41.0 40-44 40.09445 41.0 41.0 41.0 38.6 41.0 45-49 40.10690000000001 41.0 41.0 41.0 38.6 41.0 50-54 40.0628 41.0 41.0 41.0 38.6 41.0 55-59 40.027499999999996 41.0 41.0 41.0 37.0 41.0 60-64 39.910900000000005 41.0 41.0 41.0 37.0 41.0 65-69 39.96295 41.0 41.0 41.0 37.0 41.0 70-74 39.822199999999995 41.0 41.0 41.0 37.0 41.0 75-79 39.6807 41.0 40.2 41.0 37.0 41.0 80-84 40.1677 41.0 41.0 41.0 39.4 41.0 85-89 40.1512 41.0 41.0 41.0 38.6 41.0 90-94 40.033300000000004 41.0 41.0 41.0 37.8 41.0 95-99 39.9796 41.0 41.0 41.0 37.0 41.0 100-104 39.82190000000001 41.0 41.0 41.0 37.0 41.0 105-109 39.79835 41.0 41.0 41.0 37.0 41.0 110-114 39.7789 41.0 41.0 41.0 37.0 41.0 115-119 39.7142 41.0 41.0 41.0 37.0 41.0 120-124 39.649550000000005 41.0 41.0 41.0 37.0 41.0 125-129 39.367200000000004 41.0 41.0 41.0 37.0 41.0 130-134 39.21319999999999 41.0 41.0 41.0 37.0 41.0 135-139 39.04109999999999 41.0 41.0 41.0 36.0 41.0 140-144 39.02785 41.0 41.0 41.0 37.0 41.0 145-149 38.8179 41.0 41.0 41.0 34.0 41.0 150-151 37.855875 41.0 39.0 41.0 29.5 41.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 21 1.0 22 1.0 23 2.0 24 3.0 25 3.0 26 3.0 27 2.0 28 15.0 29 24.0 30 18.0 31 27.0 32 45.0 33 49.0 34 63.0 35 88.0 36 83.0 37 135.0 38 173.0 39 307.0 40 2958.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 5.612244897959184 38.0690737833595 41.915227629513346 14.403453689167975 2 26.55 41.825 19.675 11.95 3 22.725 28.975 38.324999999999996 9.975000000000001 4 33.558389597399355 24.33108277069267 27.481870467616904 14.628657164291074 5 28.599999999999998 26.174999999999997 26.924999999999997 18.3 6 25.525 26.974999999999998 28.299999999999997 19.2 7 22.650000000000002 27.675 30.575000000000003 19.1 8 24.8 26.150000000000002 30.3 18.75 9 23.025000000000002 23.25 31.225 22.5 10-14 24.54 26.075 29.615000000000002 19.77 15-19 24.545 27.295 28.535 19.625 20-24 25.080000000000002 27.215 27.85 19.855 25-29 24.27 27.065 29.235 19.43 30-34 24.605 26.69 28.360000000000003 20.345 35-39 24.224999999999998 26.22 29.01 20.544999999999998 40-44 24.285 26.6 28.945 20.169999999999998 45-49 23.72237223722372 26.467646764676466 29.532953295329534 20.27702770277028 50-54 24.805 26.25 28.63 20.315 55-59 24.696234811740585 26.806340317015852 28.8114405720286 19.68598429921496 60-64 24.792479247924792 26.37263726372637 28.852885288528853 19.98199819981998 65-69 25.02125106255313 25.871293564678233 28.42642132106605 20.681034051702586 70-74 25.25378806821023 26.829024353653047 27.539130869630448 20.378056708506275 75-79 23.84619230961548 27.061353067653382 29.011450572528624 20.081004050202512 80-84 24.7 26.695 28.994999999999997 19.61 85-89 24.47244724472447 27.382738273827385 28.357835783578356 19.786978697869788 90-94 25.30753075307531 26.6026602660266 28.102810281028102 19.986998699869986 95-99 24.227422742274225 26.647664766476648 28.762876287628764 20.362036203620363 100-104 24.945 26.384999999999998 28.505000000000003 20.165 105-109 24.226211310565528 27.02135106755338 28.526426321316066 20.226011300565027 110-114 23.96 27.384999999999998 28.58 20.075000000000003 115-119 24.39 27.815 27.925 19.869999999999997 120-124 23.705000000000002 27.889999999999997 27.744999999999997 20.66 125-129 23.785 28.665000000000003 26.91 20.64 130-134 24.02 28.765 26.700000000000003 20.515 135-139 23.94 28.915000000000003 26.674999999999997 20.47 140-144 24.535 28.599999999999998 25.645 21.22 145-149 23.86 28.804999999999996 25.415 21.92 150-151 22.900000000000002 28.799999999999997 25.662499999999998 22.6375 >>END_MODULE >>Per sequence GC content pass #GC Content Count 0 1.0 1 0.5 2 0.5 3 0.5 4 0.0 5 0.5 6 0.5 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 0.5 23 0.5 24 1.5 25 1.5 26 2.0 27 4.5 28 6.0 29 11.0 30 15.5 31 21.5 32 34.0 33 43.5 34 60.5 35 89.5 36 113.0 37 133.5 38 149.0 39 165.5 40 195.5 41 223.0 42 229.0 43 220.0 44 277.5 45 300.5 46 248.5 47 227.0 48 214.5 49 181.0 50 140.0 51 117.5 52 106.0 53 96.5 54 79.0 55 65.0 56 44.0 57 33.5 58 35.5 59 24.5 60 19.0 61 14.0 62 7.5 63 11.0 64 8.5 65 3.0 66 2.0 67 3.5 68 4.0 69 5.0 70 4.0 71 1.0 72 0.5 73 1.0 74 1.0 75 0.0 76 0.5 77 0.5 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 36.3 2 0.0 3 0.0 4 0.025 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 0.01 50-54 0.0 55-59 0.005 60-64 0.01 65-69 0.005 70-74 0.015 75-79 0.005 80-84 0.0 85-89 0.01 90-94 0.01 95-99 0.01 100-104 0.0 105-109 0.005 110-114 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 92.325 #Duplication Level Percentage of deduplicated Percentage of total 1 95.20714865962631 87.9 2 3.628486325480639 6.7 3 0.487408610885459 1.35 4 0.27078256160303277 1.0 5 0.05415651232060655 0.25 6 0.08123476848090982 0.44999999999999996 7 0.1083130246412131 0.7000000000000001 8 0.05415651232060655 0.4 9 0.027078256160303276 0.22499999999999998 >10 0.08123476848090982 1.0250000000000001 >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 TATTTGCTACTCGGATAACCGTAGTAATTCTAGAGCTAATACGTGCAACA 18 0.44999999999999996 No Hit NATTTGCTACTCGGATAACCGTAGTAATTCTAGAGCTAATACGTGCAACA 13 0.325 No Hit ATGCGCTCCTGGCCTTAACTGGCCGGGTCGTGCCTCCGGTGCTGTTACTT 10 0.25 No Hit AAAGACGAACAACTGCGAAAGCATTTGCCAAGGATGTTTTCATTAATCAA 9 0.22499999999999998 No Hit TGGCATCGTCGAGACTGAGAAGAACTATGTCTCCTCCGTAGTCATGGAGG 8 0.2 No Hit NTGCGCTCCTGGCCTTAACTGGCCGGGTCGTGCCTCCGGTGCTGTTACTT 8 0.2 No Hit TGTGGGATTGGGAGTGGATTAATAATGTAATTTCTGATAAATAATCTGTG 7 0.17500000000000002 No Hit CTACTCGGATAACCGTAGTAATTCTAGAGCTAATACGTGCAACAAACCCC 7 0.17500000000000002 No Hit TACCTGGTTGATCCTGCCAGTAGTCATATGCTTGTCTCAAAGATTAAGCC 7 0.17500000000000002 No Hit AACTATCATGTTTGATGTGGGATTGGGAGTGGATTAATAATGTAATTTCT 7 0.17500000000000002 No Hit TATGGACCCGAACCTGGGTGATCTATCCATGACCAGGATGAAGCTTGGGT 6 0.15 No Hit TTAATCAAGAACGAAAGTTGGGGGCTCGAAGACGATCAGATACCGTCCTA 6 0.15 No Hit NGCAACAAACCCCGACTTCTGGAAGGGACGCATTTATTAGATAAAAGGTC 6 0.15 No Hit TGTTGGCCTTCGGGATCGGAGTAATGATTAACAGGGACAGTCGGGGGCAT 5 0.125 No Hit GAGACTGAGAAGAACTATGTCTCCTCCGTAGTCATGGAGGTGCCAGCAGC 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 0.05 0.0 0.0 0.0 0.0 2 0.05 0.0 0.0 0.0 0.0 3 0.05 0.0 0.0 0.0 0.0 4 0.05 0.0 0.0 0.0 0.0 5 0.05 0.0 0.0 0.0 0.0 6 0.05 0.0 0.0 0.0 0.0 7 0.05 0.0 0.0 0.0 0.0 8 0.05 0.0 0.0 0.0 0.0 9 0.05 0.0 0.0 0.0 0.0 10-11 0.05 0.0 0.0 0.0 0.0 12-13 0.05 0.0 0.0 0.0 0.0 14-15 0.05 0.0 0.0 0.0 0.0 16-17 0.05 0.0 0.0 0.0 0.0 18-19 0.0625 0.0 0.0 0.0 0.0 20-21 0.15 0.0 0.0 0.0 0.0 22-23 0.175 0.0 0.0 0.0 0.0 24-25 0.21250000000000002 0.0 0.0 0.0 0.0 26-27 0.2375 0.0 0.0 0.0 0.0 28-29 0.2625 0.0 0.0 0.0 0.0 30-31 0.275 0.0 0.0 0.0 0.0 32-33 0.275 0.0 0.0 0.0 0.0 34-35 0.3125 0.0 0.0 0.0 0.0 36-37 0.325 0.0 0.0 0.0 0.0 38-39 0.4 0.0 0.0 0.0 0.0 40-41 0.4125 0.0 0.0 0.0 0.0 42-43 0.5249999999999999 0.0 0.0 0.0 0.0 44-45 0.6375 0.0 0.0 0.0 0.0 46-47 0.65 0.0 0.0 0.0 0.0 48-49 0.7375 0.0 0.0 0.0 0.0 50-51 0.85 0.0 0.0 0.0 0.0 52-53 0.9 0.0 0.0 0.0 0.0 54-55 0.9375 0.0 0.0 0.0 0.0 56-57 1.025 0.0 0.0 0.0 0.0 58-59 1.075 0.0 0.0 0.0 0.0 60-61 1.1625 0.0 0.0 0.0 0.0 62-63 1.2625000000000002 0.0 0.0 0.0 0.0 64-65 1.35 0.0 0.0 0.0 0.0 66-67 1.4625 0.0 0.0 0.0 0.0 68-69 1.4875 0.0 0.0 0.0 0.0 70-71 1.5499999999999998 0.0 0.0 0.0 0.0 72-73 1.6749999999999998 0.0 0.0 0.0 0.0 74-75 1.775 0.0 0.0 0.0 0.0 76-77 1.9 0.0 0.0 0.0 0.0 78-79 2.0374999999999996 0.0 0.0 0.0 0.0 80-81 2.2625 0.0 0.0 0.0 0.0 82-83 2.4625 0.0 0.0 0.0 0.0 84-85 2.6375 0.0 0.0 0.0 0.0 86-87 2.8625 0.0 0.0 0.0 0.0 88-89 3.1625 0.0 0.0 0.0 0.0 90-91 3.6375 0.0 0.0 0.0 0.0 92-93 3.8 0.0 0.0 0.0 0.0 94-95 4.05 0.0 0.0 0.0 0.0 96-97 4.5 0.0 0.0 0.0 0.0 98-99 4.9375 0.0 0.0 0.0 0.0 100-101 5.449999999999999 0.0 0.0 0.0 0.0 102-103 5.9375 0.0 0.0 0.0 0.0 104-105 6.6625 0.0 0.0 0.0 0.0 106-107 7.1 0.0 0.0 0.0 0.0 108-109 7.8500000000000005 0.0 0.0 0.0 0.0 110-111 8.675 0.0 0.0 0.0 0.0 112-113 9.350000000000001 0.0 0.0 0.0 0.0 114-115 10.25 0.0 0.0 0.0 0.0 116-117 11.1625 0.0 0.0 0.0 0.0 118-119 12.0625 0.0 0.0 0.0 0.0 120-121 12.825 0.0 0.0 0.0 0.0 122-123 13.8 0.0 0.0 0.0 0.0 124-125 14.8125 0.0 0.0 0.0 0.0 126-127 16.175 0.0 0.0 0.0 0.0 128-129 17.3375 0.0 0.0 0.0 0.0 130-131 18.5625 0.0 0.0 0.0 0.0 132-133 19.85 0.0 0.0 0.0 0.0 134-135 21.4625 0.0 0.0 0.0 0.0 136-137 23.15 0.0 0.0 0.0 0.0 138-139 24.487499999999997 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TATTTGC 15 0.005891193 151.25491 1 CACGGCC 15 1.1525718E-4 144.63751 145 TGTTGGG 10 0.006882143 144.6375 4 ACTCGGA 20 3.6236155E-4 108.47813 9 GCTACTC 20 3.6236155E-4 108.47813 6 TGCTACT 20 3.6236155E-4 108.47813 5 TACTCGG 20 3.6236155E-4 108.47813 8 TTTGCTA 20 3.6236155E-4 108.47813 3 CTACTCG 20 3.6236155E-4 108.47813 7 TTGCTAC 20 3.6236155E-4 108.47813 4 ATTTGCT 25 8.800385E-4 86.7825 2 TAACCGT 20 0.006008153 28.9275 15-19 >>END_MODULE Rejected 2180927 READS because READLEN < 1 Read 2180927 spots for SRR11462701.sra Written 2180927 spots for SRR11462701.sra Rejected 2180927 READS because READLEN < 1 Read 2180927 spots for SRR11462701.sra Written 2180927 spots for SRR11462701.sra Rejected 2180927 READS because READLEN < 1 Read 2180927 spots for SRR11462701.sra Written 2180927 spots for SRR11462701.sra Rejected 2180946 READS because READLEN < 1 Read 2180946 spots for SRR11462701.sra Written 2180946 spots for SRR11462701.sra Rejected 2180927 READS because READLEN < 1 Read 2180927 spots for SRR11462701.sra Written 2180927 spots for SRR11462701.sra Rejected 2180927 READS because READLEN < 1 Read 2180927 spots for SRR11462701.sra Written 2180927 spots for SRR11462701.sra Rejected 2180927 READS because READLEN < 1 Read 2180927 spots for SRR11462701.sra Written 2180927 spots for SRR11462701.sra Rejected 2180927 READS because READLEN < 1 Read 2180927 spots for SRR11462701.sra Written 2180927 spots for SRR11462701.sra Rejected 2180927 READS because READLEN < 1 Read 2180927 spots for SRR11462701.sra Written 2180927 spots for SRR11462701.sra Rejected 2180927 READS because READLEN < 1 Read 2180927 spots for SRR11462701.sra Written 2180927 spots for SRR11462701.sra Rejected 2180927 READS because READLEN < 1 Read 2180927 spots for SRR11462701.sra Written 2180927 spots for SRR11462701.sra Rejected 2180927 READS because READLEN < 1 Read 2180927 spots for SRR11462701.sra Written 2180927 spots for SRR11462701.sra Rejected 2180927 READS because READLEN < 1 Read 2180927 spots for SRR11462701.sra Written 2180927 spots for SRR11462701.sra Rejected 2180927 READS because READLEN < 1 Read 2180927 spots for SRR11462701.sra Written 2180927 spots for SRR11462701.sra Rejected 2180927 READS because READLEN < 1 Read 2180927 spots for SRR11462701.sra Written 2180927 spots for SRR11462701.sra Rejected 2180927 READS because READLEN < 1 Read 2180927 spots for SRR11462701.sra Written 2180927 spots for SRR11462701.sra Rejected 2180927 READS because READLEN < 1 Read 2180927 spots for SRR11462701.sra Written 2180927 spots for SRR11462701.sra Rejected 2180927 READS because READLEN < 1 Read 2180927 spots for SRR11462701.sra Written 2180927 spots for SRR11462701.sra Rejected 2180927 READS because READLEN < 1 Read 2180927 spots for SRR11462701.sra Written 2180927 spots for SRR11462701.sra Rejected 2180927 READS because READLEN < 1 Read 2180927 spots for SRR11462701.sra Written 2180927 spots for SRR11462701.sra SRR ids: ['SRR11462701.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd__xd1htq6 SRR11462701.sra spots: 43618559 blocks: [[1, 2180927], [2180928, 4361854], [4361855, 6542781], [6542782, 8723708], [8723709, 10904635], [10904636, 13085562], [13085563, 15266489], [15266490, 17447416], [17447417, 19628343], [19628344, 21809270], [21809271, 23990197], [23990198, 26171124], [26171125, 28352051], [28352052, 30532978], [30532979, 32713905], [32713906, 34894832], [34894833, 37075759], [37075760, 39256686], [39256687, 41437613], [41437614, 43618559]] SRR11462701 file size 14801794 SRR11462701 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 SRR11462701 SRR11462701_1.fastq Input file: SRR11462701_1.fastq trimmed: SRR11462701-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 07:18:07 2025 >> started Wed Feb 12 07:18:30 2025 >> done (23.944s) 43618559 reads processed; of these: 16850 ( 0.04%) short reads filtered out after trimming by size control 9337 ( 0.02%) empty reads filtered out after trimming by size control 43592372 (99.94%) reads available; of these: 5685757 (13.04%) trimmed reads available after processing 37906615 (86.96%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 3824 0.01% 19 3995 0.01% 20 4613 0.01% 21 4813 0.01% 22 5495 0.01% 23 5778 0.01% 24 6228 0.01% 25 6244 0.01% 26 6673 0.02% 27 7351 0.02% 28 7049 0.02% 29 7387 0.02% 30 7577 0.02% 31 7906 0.02% 32 7812 0.02% 33 7946 0.02% 34 8617 0.02% 35 8720 0.02% 36 8708 0.02% 37 12250 0.03% 38 9453 0.02% 39 9895 0.02% 40 9775 0.02% 41 10046 0.02% 42 11248 0.03% 43 11212 0.03% 44 10954 0.03% 45 12394 0.03% 46 12471 0.03% 47 16165 0.04% 48 14440 0.03% 49 16425 0.04% 50 14247 0.03% 51 15113 0.03% 52 15769 0.04% 53 16221 0.04% 54 17731 0.04% 55 17210 0.04% 56 17967 0.04% 57 21250 0.05% 58 19332 0.04% 59 20397 0.05% 60 22063 0.05% 61 22031 0.05% 62 41168 0.09% 63 23291 0.05% 64 25893 0.06% 65 24524 0.06% 66 25471 0.06% 67 28269 0.06% 68 27357 0.06% 69 32978 0.08% 70 30412 0.07% 71 34015 0.08% 72 35846 0.08% 73 40544 0.09% 74 43737 0.10% 75 39045 0.09% 76 36808 0.08% 77 43551 0.10% 78 41754 0.10% 79 51503 0.12% 80 43918 0.10% 81 45734 0.10% 82 51126 0.12% 83 51940 0.12% 84 56823 0.13% 85 57157 0.13% 86 61248 0.14% 87 64887 0.15% 88 63240 0.15% 89 110447 0.25% 90 70241 0.16% 91 75881 0.17% 92 70247 0.16% 93 77043 0.18% 94 84558 0.19% 95 83652 0.19% 96 92360 0.21% 97 97090 0.22% 98 93500 0.21% 99 97096 0.22% 100 98172 0.23% 101 108292 0.25% 102 125323 0.29% 103 116398 0.27% 104 117305 0.27% 105 121902 0.28% 106 126256 0.29% 107 135022 0.31% 108 143882 0.33% 109 164978 0.38% 110 152235 0.35% 111 154180 0.35% 112 243227 0.56% 113 173881 0.40% 114 169714 0.39% 115 172406 0.40% 116 178557 0.41% 117 197969 0.45% 118 200616 0.46% 119 208154 0.48% 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% 150 139 0.00% 151 37906615 86.96% 43592372 reads passed initial QC criterion=sequence-density sequence-density=11.09 sequence-density-rank=1 fanout-score=40.97 fanout-score-rank=1 prefix-density=13.33 prefix-fanout=34.1 sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACAGTCAAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAA criterion=fanout-score sequence-density=11.09 sequence-density-rank=1 fanout-score=40.97 fanout-score-rank=1 prefix-density=13.33 prefix-fanout=34.1 sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACAGTCAAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAA 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 AGATCGGAAGAGCACACGTCTGAACTCCAGTCACAGTCAAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAA -o SRR11462701 - Input file: STDIN trimmed: SRR11462701-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): AGATCGGAAGAGCACACGTCTGAACTCCAGTCACAGTCAAATCTCGTATGCCGTCTTCTGCTTG -- 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 07:20:40 2025 >> started Wed Feb 12 07:21:21 2025 >> done (41.093s) 36326977 reads processed; of these: 515 ( 0.00%) short reads filtered out after trimming by size control 51 ( 0.00%) empty reads filtered out after trimming by size control 36326411 (100.00%) reads available; of these: 8043264 (22.14%) trimmed reads available after processing 28283147 (77.86%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 3307 0.01% 19 3398 0.01% 20 3889 0.01% 21 4065 0.01% 22 4627 0.01% 23 4824 0.01% 24 5206 0.01% 25 5199 0.01% 26 5585 0.02% 27 6134 0.02% 28 5912 0.02% 29 6140 0.02% 30 6354 0.02% 31 6652 0.02% 32 6583 0.02% 33 6696 0.02% 34 7198 0.02% 35 7331 0.02% 36 7330 0.02% 37 10403 0.03% 38 8028 0.02% 39 8350 0.02% 40 8175 0.02% 41 8330 0.02% 42 9427 0.03% 43 9355 0.03% 44 9266 0.03% 45 10432 0.03% 46 10544 0.03% 47 13546 0.04% 48 12077 0.03% 49 13846 0.04% 50 11990 0.03% 51 12711 0.03% 52 13151 0.04% 53 13638 0.04% 54 14802 0.04% 55 14490 0.04% 56 14957 0.04% 57 17879 0.05% 58 16102 0.04% 59 17170 0.05% 60 18641 0.05% 61 18559 0.05% 62 34569 0.10% 63 19477 0.05% 64 21623 0.06% 65 20571 0.06% 66 21237 0.06% 67 23754 0.07% 68 23157 0.06% 69 27814 0.08% 70 25956 0.07% 71 28368 0.08% 72 30140 0.08% 73 34104 0.09% 74 36684 0.10% 75 32401 0.09% 76 30768 0.08% 77 36428 0.10% 78 35202 0.10% 79 43231 0.12% 80 36958 0.10% 81 39368 0.11% 82 42955 0.12% 83 43407 0.12% 84 46373 0.13% 85 47829 0.13% 86 51517 0.14% 87 54505 0.15% 88 53458 0.15% 89 92373 0.25% 90 60033 0.17% 91 63546 0.17% 92 59453 0.16% 93 64178 0.18% 94 70690 0.19% 95 69737 0.19% 96 77758 0.21% 97 80883 0.22% 98 78544 0.22% 99 82113 0.23% 100 82487 0.23% 101 91552 0.25% 102 104779 0.29% 103 97712 0.27% 104 98430 0.27% 105 102416 0.28% 106 106023 0.29% 107 113010 0.31% 108 121369 0.33% 109 138685 0.38% 110 128018 0.35% 111 129385 0.36% 112 204237 0.56% 113 144760 0.40% 114 142219 0.39% 115 143718 0.40% 116 148993 0.41% 117 159722 0.44% 118 161742 0.45% 119 170984 0.47% 120 183832 0.51% 121 188480 0.52% 122 188289 0.52% 123 243379 0.67% 124 225657 0.62% 125 201694 0.56% 126 208985 0.58% 127 222138 0.61% 128 217425 0.60% 129 217604 0.60% 130 218640 0.60% 131 227986 0.63% 132 262168 0.72% 133 255859 0.70% 134 242138 0.67% 135 266129 0.73% 136 248343 0.68% 137 271033 0.75% 138 294806 0.81% 139 269591 0.74% 140 288213 0.79% 141 262164 0.72% 142 283938 0.78% 143 281856 0.78% 144 273489 0.75% 145 318213 0.88% 146 297463 0.82% 147 417893 1.15% 148 792282 2.18% 149 0 0.00% 150 72 0.00% 151 23702950 65.25% criterion=sequence-density sequence-density=0.62 sequence-density-rank=1 fanout-score=2.09 fanout-score-rank=32 prefix-density=0.62 prefix-fanout=2.1 sequence=CTGCGACTGCGCTGACAAGACCCAGTGTGTCAAGAAGGGAAGCAGCTACACTGCTGGCATCGTCGAGACTGAGAAGAACTATGTCTCCTCCGTAGTCATGGAGGTGCCAGCAGCTGAGAACGATGGCAAGTGCAACTGCGGTACTGGCTGCACTTGCACTACCTGCACATGCGGTCATTAAGCAAGCACATCAACTATCATGTTTGATGTGGGATTGGGAGTGGATTAATAATGTAATTTCTGATAAATAATCTGTGTTCTTCTGTACTTGTGGGTGTGGAGTGAACAAACAAAAGTGTCCGTGAGTGTCTTTATCTTTGTGTCTTCTTCATTGTTATGTATTGGCCATGTCTGTGGCCTCTGGTGTGGTTTTAATGAAGTCTTATAATTAGTGTAGTA criterion=fanout-score sequence-density=0.01 sequence-density-rank=36 fanout-score=449.72 fanout-score-rank=1 prefix-density=0.35 prefix-fanout=16.2 sequence=TTGGATTTGATTAGATCCACCAATAAAAAGGGCTTGCCTTACACTCTTGGTCTTAATCAATTTGCTGATTGGACATGGCAAGAGTTCCAAAAGTACAGACTGGGAGCTGCCCAAAATTGCTCTGCAACCACAAGGGGCAATCACAAGCTTACGAACGCTCTTCTTCCTGAAACGAAAGACTGGAGGGAAGAAGGCATAGTCAGTCCCGTTAAGAATCAAGGTCACTGTGGATCTTGCTGGACTTTCAGCACCACTGGAGCTCTAGAGGCTGCTTACCACCAGGCTTTTGGGAAAGGAATCTCTCTGTCTGAACAGCAGCTTGTGGACTGTGCTAGAGCATTTAATAACTTTGGCTGCAATG Started job on | Feb 12 07:21:58 Started mapping on | Feb 12 07:21:58 Finished on | Feb 12 07:23:32 Mapping speed, Million of reads per hour | 1669.47 Number of input reads | 43591806 Average input read length | 141 UNIQUE READS: Uniquely mapped reads number | 36406984 Uniquely mapped reads % | 83.52% Average mapped length | 138.52 Number of splices: Total | 16271821 Number of splices: Annotated (sjdb) | 15856131 Number of splices: GT/AG | 15989224 Number of splices: GC/AG | 212774 Number of splices: AT/AC | 8999 Number of splices: Non-canonical | 60824 Mismatch rate per base, % | 0.37% Deletion rate per base | 0.02% Deletion average length | 2.15 Insertion rate per base | 0.01% Insertion average length | 1.82 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 1049722 % of reads mapped to multiple loci | 2.41% Number of reads mapped to too many loci | 3545140 % of reads mapped to too many loci | 8.13% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 5.83% % of reads unmapped: other | 0.12% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 6135100 6135100 6135100 N_multimapping 1049722 1049722 1049722 N_noFeature 2105953 2735251 35365044 N_ambiguous 555110 142500 823 UnstrandedReadsAssigned:33745921 PositiveStrandReadsAssigned:33529233 NegativeStrandReadsAssigned:1041117 Dataset is classified positive stranded MeadianReadLen=151 20thPercentileLength=131 echo kmer=127 SRR11462701 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: SRR11462701-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 43,591,806 reads, 35,114,340 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,256 rounds 52401 SRR11462701.ke.tsv 34699 SRR11462701.se.tsv 87100 total ==> SRR11462701.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1919 3232 56.7463 Potri.005G024800.1.v4.1 1035 936 1343 48.3439 Potri.004G059700.1.v4.1 961 862 10 0.390872 Potri.007G009000.2.v4.1 1416 1317 0 0 Potri.003G141000.2.v4.1 2943 2844 3481 41.2397 Potri.016G087400.1.v4.1 270 171 2505 493.575 Potri.015G069301.1.v4.1 564 465 0 0 Potri.010G195200.1.v4.1 1773 1674 1987.99 40.0129 Potri.012G127500.1.v4.1 977 878 109 4.18286 ==> SRR11462701.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 15 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 241 Potri.001G212900.v4.1 0 Potri.001G182400.v4.1 2 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 9 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 29 SRR11462701 completed mapping pipeline successfully