Starting /dee2/code/volunteer_pipeline.sh SRR11462714 current disk space = 3049436119040 free memory = 1431738140 SRR11462714 SRAfilesize 56a3b608495b7b2a6169327aa495ff92 SRR11462714.sra SRR11462714.sra file validated SRR11462714 is single end SRR11462714 is conventional basespace SRR11462714 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR11462714_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 45 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 24.44875 32.0 12.0 32.0 2.0 32.0 2 31.76375 32.0 32.0 32.0 32.0 32.0 3 34.80625 37.0 32.0 37.0 32.0 37.0 4 36.1575 37.0 37.0 37.0 32.0 37.0 5 36.50875 37.0 37.0 37.0 37.0 37.0 6 40.0925 41.0 41.0 41.0 37.0 41.0 7 40.1415 41.0 41.0 41.0 37.0 41.0 8 40.0975 41.0 41.0 41.0 37.0 41.0 9 40.3295 41.0 41.0 41.0 41.0 41.0 10-14 40.32695 41.0 41.0 41.0 41.0 41.0 15-19 40.294050000000006 41.0 41.0 41.0 39.4 41.0 20-24 40.24525 41.0 41.0 41.0 40.2 41.0 25-29 40.18835 41.0 41.0 41.0 38.6 41.0 30-34 40.0843 41.0 41.0 41.0 37.8 41.0 35-39 40.0587 41.0 41.0 41.0 38.6 41.0 40-44 40.1585 41.0 41.0 41.0 39.4 41.0 45-49 40.02665 41.0 41.0 41.0 37.0 41.0 50-54 40.0156 41.0 41.0 41.0 37.0 41.0 55-59 39.9578 41.0 41.0 41.0 37.0 41.0 60-64 40.00925 41.0 41.0 41.0 37.0 41.0 65-69 39.9885 41.0 41.0 41.0 37.0 41.0 70-74 39.8846 41.0 41.0 41.0 37.0 41.0 75-79 39.7106 41.0 41.0 41.0 37.0 41.0 80-84 40.133 41.0 41.0 41.0 37.8 41.0 85-89 40.1719 41.0 41.0 41.0 40.2 41.0 90-94 40.015950000000004 41.0 41.0 41.0 37.0 41.0 95-99 40.03415 41.0 41.0 41.0 37.8 41.0 100-104 39.9169 41.0 41.0 41.0 37.0 41.0 105-109 39.79019999999999 41.0 41.0 41.0 37.0 41.0 110-114 39.798500000000004 41.0 41.0 41.0 37.0 41.0 115-119 39.7282 41.0 41.0 41.0 37.0 41.0 120-124 39.528499999999994 41.0 41.0 41.0 37.0 41.0 125-129 39.491949999999996 41.0 41.0 41.0 37.0 41.0 130-134 39.2952 41.0 41.0 41.0 37.0 41.0 135-139 39.087599999999995 41.0 41.0 41.0 37.0 41.0 140-144 38.9665 41.0 41.0 41.0 35.0 41.0 145-149 38.54585 41.0 41.0 41.0 32.0 41.0 150-151 37.617875 41.0 39.0 41.0 27.0 41.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 23 1.0 24 1.0 25 4.0 26 5.0 27 8.0 28 23.0 29 26.0 30 25.0 31 22.0 32 35.0 33 44.0 34 60.0 35 93.0 36 89.0 37 107.0 38 152.0 39 289.0 40 3016.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 6.965174129353234 38.37479270315091 38.73963515754561 15.92039800995025 2 27.900000000000002 40.8 19.375 11.924999999999999 3 24.025 29.15 36.55 10.274999999999999 4 36.175000000000004 24.025 25.0 14.799999999999999 5 29.075 27.175 26.625 17.125 6 26.6 25.85 27.250000000000004 20.3 7 22.400000000000002 26.625 29.075 21.9 8 26.150000000000002 26.55 29.575000000000003 17.724999999999998 9 21.925 25.124999999999996 31.5 21.45 10-14 26.279999999999998 25.045 28.28 20.395 15-19 26.325 25.995 27.544999999999998 20.135 20-24 26.32 26.340000000000003 27.525 19.814999999999998 25-29 25.324999999999996 26.325 27.639999999999997 20.71 30-34 25.705 25.900000000000002 27.22 21.175 35-39 24.68 26.19 27.555000000000003 21.575 40-44 24.32 26.474999999999998 28.285 20.919999999999998 45-49 24.727472747274728 26.312631263126313 28.007800780078007 20.95209520952095 50-54 25.53 26.424999999999997 27.005000000000003 21.04 55-59 25.72 26.834999999999997 26.900000000000002 20.544999999999998 60-64 26.135 25.074999999999996 28.134999999999998 20.655 65-69 25.975195039007804 25.61012202440488 27.855571114222844 20.55911182236447 70-74 25.51510302060412 26.285257051410284 27.340468093618725 20.859171834366876 75-79 24.795 26.590000000000003 28.249999999999996 20.365 80-84 25.437543754375437 26.812681268126816 27.762776277627765 19.986998699869986 85-89 25.474999999999998 26.479999999999997 27.32 20.724999999999998 90-94 25.922776833049916 25.95778733620086 27.848354506351907 20.27108132439732 95-99 24.695 26.924999999999997 27.334999999999997 21.044999999999998 100-104 25.005 26.3 27.845 20.849999999999998 105-109 23.89 26.924999999999997 27.55 21.634999999999998 110-114 24.87 26.93 27.325 20.875 115-119 24.805 27.015 27.295 20.885 120-124 24.165 27.68 27.169999999999998 20.985 125-129 24.695 27.515 26.845000000000002 20.945 130-134 24.42 28.395 26.825 20.36 135-139 24.23 28.17 26.26 21.34 140-144 24.925 27.339999999999996 26.35 21.385 145-149 24.955 27.994999999999997 25.355 21.695 150-151 23.425 28.1625 25.0125 23.400000000000002 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 0.0 1 0.0 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.5 9 0.5 10 0.0 11 0.0 12 0.0 13 0.0 14 0.0 15 0.0 16 0.0 17 0.0 18 0.0 19 0.0 20 0.0 21 0.0 22 0.0 23 1.5 24 3.0 25 2.0 26 2.0 27 3.5 28 4.5 29 8.0 30 15.0 31 19.5 32 26.0 33 33.0 34 44.5 35 68.0 36 85.5 37 97.5 38 121.5 39 137.5 40 150.0 41 178.0 42 209.5 43 218.5 44 248.0 45 274.0 46 245.0 47 232.5 48 221.0 49 186.0 50 158.0 51 145.5 52 147.0 53 134.5 54 105.0 55 92.0 56 79.0 57 59.0 58 51.0 59 40.0 60 28.0 61 18.0 62 17.0 63 21.5 64 13.0 65 4.5 66 2.5 67 6.0 68 9.5 69 9.5 70 9.0 71 9.0 72 5.0 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 24.625 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 0.01 50-54 0.0 55-59 0.0 60-64 0.0 65-69 0.02 70-74 0.02 75-79 0.0 80-84 0.01 85-89 0.0 90-94 0.03 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 88.05 #Duplication Level Percentage of deduplicated Percentage of total 1 92.39068710959683 81.35 2 5.42305508233958 9.55 3 1.1073253833049403 2.9250000000000003 4 0.34071550255536626 1.2 5 0.17035775127768313 0.75 6 0.19875070982396364 1.05 7 0.08517887563884156 0.525 8 0.08517887563884156 0.6 9 0.08517887563884156 0.675 >10 0.1135718341851221 1.375 >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 AAAGACGAACAACTGCGAAAGCATTTGCCAAGGATGTTTTCATTAATCAA 15 0.375 No Hit ATGCGCTCCTGGCCTTAACTGGCCGGGTCGTGCCTCCGGTGCTGTTACTT 12 0.3 No Hit AACTATCATGTTTGATGTGGGATTGGGAGTGGATTAATAATGTAATTTCT 10 0.25 No Hit TAAGCGCGAGTCATCAGCTCGCGTTGACTACGTCCCTGCCCTTTGTACAC 9 0.22499999999999998 No Hit NACTATCATGTTTGATGTGGGATTGGGAGTGGATTAATAATGTAATTTCT 9 0.22499999999999998 No Hit NATTTGCTACTCGGATAACCGTAGTAATTCTAGAGCTAATACGTGCAACA 9 0.22499999999999998 No Hit CGGTGAAAGAGCCGCGCGGGCCGCCTTGAAGTACAATTCCCACCGAGCGG 8 0.2 No Hit TGTGGGATTGGGAGTGGATTAATAATGTAATTTCTGATAAATAATCTGTG 8 0.2 No Hit NTGCGCTCCTGGCCTTAACTGGCCGGGTCGTGCCTCCGGTGCTGTTACTT 8 0.2 No Hit TTAATCAAGAACGAAAGTTGGGGGCTCGAAGACGATCAGATACCGTCCTA 7 0.17500000000000002 No Hit NGGCATCGTCGAGACTGAGAAGAACTATGTCTCCTCCGTAGTCATGGAGG 7 0.17500000000000002 No Hit TATTTTACTTATTCCGTGAATCGGAGGCGGGGCGCTGCCCCTCTTTTTGG 7 0.17500000000000002 No Hit CGTTGACTACGTCCCTGCCCTTTGTACACACCGCCCGTCGCTCCTACCGA 6 0.15 No Hit TTTGATGATCTGGAGGGCTTGCAGGAGTATCTTGATTCTTCGGTTGTTGC 6 0.15 No Hit TGGCATCGTCGAGACTGAGAAGAACTATGTCTCCTCCGTAGTCATGGAGG 6 0.15 No Hit TGTTTGTGTCGTCGGTGGTGTTCCGGCAGGGGGGGTGGATTTTATGATTG 6 0.15 No Hit TATTAGATAAAAGGTCGACGCGGGCTCTGCCCGTTGCTCTGATGATTCAT 6 0.15 No Hit TGCAACAAACCCCGACTTCTGGAAGGGACGCATTTATTAGATAAAAGGTC 6 0.15 No Hit CGGGCCGCCTTGAAGTACAATTCCCACCGAGCGGCGGGTAGAATCCTTTG 6 0.15 No Hit NGGTGGTGACGGGTGACGGAGAATTAGGGTTCGATTCCGGAGAGGGAGCC 5 0.125 No Hit GAGACTGAGAAGAACTATGTCTCCTCCGTAGTCATGGAGGTGCCAGCAGC 5 0.125 No Hit ACAACACTCGTCAAGTGCAGTGCATCAGTTTTATCGCCTCCAAGCCGAAG 5 0.125 No Hit AATGTAATTTCTGATAAATAATCTGTGTTCTTCTGTACTTGTGGGTGTGG 5 0.125 No Hit TTAGATAAAAGGTCGACGCGGGCTCTGCCCGTTGCTCTGATGATTCATGA 5 0.125 No Hit CAGCCAAGCGTTCATAGCGACGTTGCTTTTTGATCCTTCGATGTCGGCTC 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 0.037500000000000006 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 0.125 0.0 0.0 0.0 0.0 22-23 0.16249999999999998 0.0 0.0 0.0 0.0 24-25 0.2 0.0 0.0 0.0 0.0 26-27 0.2375 0.0 0.0 0.0 0.0 28-29 0.25 0.0 0.0 0.0 0.0 30-31 0.2625 0.0 0.0 0.0 0.0 32-33 0.30000000000000004 0.0 0.0 0.0 0.0 34-35 0.35 0.0 0.0 0.0 0.0 36-37 0.3875 0.0 0.0 0.0 0.0 38-39 0.4125 0.0 0.0 0.0 0.0 40-41 0.4875 0.0 0.0 0.0 0.0 42-43 0.525 0.0 0.0 0.0 0.0 44-45 0.575 0.0 0.0 0.0 0.0 46-47 0.6375 0.0 0.0 0.0 0.0 48-49 0.7625 0.0 0.0 0.0 0.0 50-51 0.7875000000000001 0.0 0.0 0.0 0.0 52-53 0.9 0.0 0.0 0.0 0.0 54-55 1.0 0.0 0.0 0.0 0.0 56-57 1.0875 0.0 0.0 0.0 0.0 58-59 1.175 0.0 0.0 0.0 0.0 60-61 1.175 0.0 0.0 0.0 0.0 62-63 1.3 0.0 0.0 0.0 0.0 64-65 1.5625 0.0 0.0 0.0 0.0 66-67 1.7 0.0 0.0 0.0 0.0 68-69 1.775 0.0 0.0 0.0 0.0 70-71 1.9625 0.0 0.0 0.0 0.0 72-73 2.1375 0.0 0.0 0.0 0.0 74-75 2.3125 0.0 0.0 0.0 0.0 76-77 2.4625000000000004 0.0 0.0 0.0 0.0 78-79 2.5875 0.0 0.0 0.0 0.0 80-81 2.8625 0.0 0.0 0.0 0.0 82-83 3.075 0.0 0.0 0.0 0.0 84-85 3.45 0.0 0.0 0.0 0.0 86-87 3.6125 0.0 0.0 0.0 0.0 88-89 3.8625 0.0 0.0 0.0 0.0 90-91 4.2125 0.0 0.0 0.0 0.0 92-93 4.5625 0.0 0.0 0.0 0.0 94-95 4.9375 0.0 0.0 0.0 0.0 96-97 5.4625 0.0 0.0 0.0 0.0 98-99 5.975 0.0 0.0 0.0 0.0 100-101 6.637499999999999 0.0 0.0 0.0 0.0 102-103 7.125 0.0 0.0 0.0 0.0 104-105 7.6875 0.0 0.0 0.0 0.0 106-107 8.4125 0.0 0.0 0.0 0.0 108-109 9.0125 0.0 0.0 0.0 0.0 110-111 9.875 0.0 0.0 0.0 0.0 112-113 10.712499999999999 0.0 0.0 0.0 0.0 114-115 11.55 0.0 0.0 0.0 0.0 116-117 12.175 0.0 0.0 0.0 0.0 118-119 12.9875 0.0 0.0 0.0 0.0 120-121 13.925 0.0 0.0 0.0 0.0 122-123 14.837499999999999 0.0 0.0 0.0 0.0 124-125 16.525 0.0 0.0 0.0 0.0 126-127 17.3875 0.0 0.0 0.0 0.0 128-129 18.8125 0.0 0.0 0.0 0.0 130-131 19.825 0.0 0.0 0.0 0.0 132-133 20.8375 0.0 0.0 0.0 0.0 134-135 22.3 0.0 0.0 0.0 0.0 136-137 24.0625 0.0 0.0 0.0 0.0 138-139 25.95 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TGCACAT 10 0.006864391 144.7625 8 GGATTGC 10 0.006864391 144.7625 4 >>END_MODULE Rejected 1880937 READS because READLEN < 1 Read 1880937 spots for SRR11462714.sra Written 1880937 spots for SRR11462714.sra Rejected 1880937 READS because READLEN < 1 Read 1880937 spots for SRR11462714.sra Written 1880937 spots for SRR11462714.sra Rejected 1880937 READS because READLEN < 1 Read 1880937 spots for SRR11462714.sra Written 1880937 spots for SRR11462714.sra Rejected 1880937 READS because READLEN < 1 Read 1880937 spots for SRR11462714.sra Written 1880937 spots for SRR11462714.sra Rejected 1880937 READS because READLEN < 1 Read 1880937 spots for SRR11462714.sra Written 1880937 spots for SRR11462714.sra Rejected 1880937 READS because READLEN < 1 Read 1880937 spots for SRR11462714.sra Written 1880937 spots for SRR11462714.sra Rejected 1880937 READS because READLEN < 1 Read 1880937 spots for SRR11462714.sra Written 1880937 spots for SRR11462714.sra Rejected 1880937 READS because READLEN < 1 Read 1880937 spots for SRR11462714.sra Written 1880937 spots for SRR11462714.sra Rejected 1880937 READS because READLEN < 1 Read 1880937 spots for SRR11462714.sra Written 1880937 spots for SRR11462714.sra Rejected 1880937 READS because READLEN < 1 Read 1880937 spots for SRR11462714.sra Written 1880937 spots for SRR11462714.sra Rejected 1880937 READS because READLEN < 1 Read 1880937 spots for SRR11462714.sra Written 1880937 spots for SRR11462714.sra Rejected 1880937 READS because READLEN < 1 Read 1880937 spots for SRR11462714.sra Written 1880937 spots for SRR11462714.sra Rejected 1880945 READS because READLEN < 1 Read 1880945 spots for SRR11462714.sra Written 1880945 spots for SRR11462714.sra Rejected 1880937 READS because READLEN < 1 Read 1880937 spots for SRR11462714.sra Written 1880937 spots for SRR11462714.sra Rejected 1880937 READS because READLEN < 1 Read 1880937 spots for SRR11462714.sra Written 1880937 spots for SRR11462714.sra Rejected 1880937 READS because READLEN < 1 Read 1880937 spots for SRR11462714.sra Written 1880937 spots for SRR11462714.sra Rejected 1880937 READS because READLEN < 1 Read 1880937 spots for SRR11462714.sra Written 1880937 spots for SRR11462714.sra Rejected 1880937 READS because READLEN < 1 Read 1880937 spots for SRR11462714.sra Written 1880937 spots for SRR11462714.sra Rejected 1880937 READS because READLEN < 1 Read 1880937 spots for SRR11462714.sra Written 1880937 spots for SRR11462714.sra Rejected 1880937 READS because READLEN < 1 Read 1880937 spots for SRR11462714.sra Written 1880937 spots for SRR11462714.sra SRR ids: ['SRR11462714.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_eevwslr7 SRR11462714.sra spots: 37618748 blocks: [[1, 1880937], [1880938, 3761874], [3761875, 5642811], [5642812, 7523748], [7523749, 9404685], [9404686, 11285622], [11285623, 13166559], [13166560, 15047496], [15047497, 16928433], [16928434, 18809370], [18809371, 20690307], [20690308, 22571244], [22571245, 24452181], [24452182, 26333118], [26333119, 28214055], [28214056, 30094992], [30094993, 31975929], [31975930, 33856866], [33856867, 35737803], [35737804, 37618748]] SRR11462714 file size 12762796 SRR11462714 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 SRR11462714 SRR11462714_1.fastq Input file: SRR11462714_1.fastq trimmed: SRR11462714-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 08:19:20 2025 >> started Wed Feb 12 08:19:54 2025 >> done (34.106s) 37618748 reads processed; of these: 13305 ( 0.04%) short reads filtered out after trimming by size control 1640 ( 0.00%) empty reads filtered out after trimming by size control 37603803 (99.96%) reads available; of these: 5235302 (13.92%) trimmed reads available after processing 32368501 (86.08%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 3084 0.01% 19 3330 0.01% 20 3796 0.01% 21 4047 0.01% 22 4743 0.01% 23 5017 0.01% 24 5107 0.01% 25 5226 0.01% 26 5191 0.01% 27 6472 0.02% 28 5966 0.02% 29 6098 0.02% 30 6127 0.02% 31 6392 0.02% 32 6171 0.02% 33 6573 0.02% 34 7186 0.02% 35 7235 0.02% 36 7297 0.02% 37 10399 0.03% 38 8052 0.02% 39 8405 0.02% 40 8375 0.02% 41 8517 0.02% 42 9922 0.03% 43 9664 0.03% 44 9574 0.03% 45 10129 0.03% 46 11090 0.03% 47 14283 0.04% 48 11900 0.03% 49 13629 0.04% 50 12376 0.03% 51 13055 0.03% 52 14309 0.04% 53 14479 0.04% 54 16928 0.05% 55 15537 0.04% 56 16728 0.04% 57 19363 0.05% 58 17512 0.05% 59 19701 0.05% 60 19928 0.05% 61 20448 0.05% 62 38928 0.10% 63 21751 0.06% 64 24013 0.06% 65 22881 0.06% 66 24399 0.06% 67 27104 0.07% 68 24257 0.06% 69 28854 0.08% 70 27141 0.07% 71 32042 0.09% 72 33448 0.09% 73 34457 0.09% 74 37554 0.10% 75 36439 0.10% 76 33593 0.09% 77 38470 0.10% 78 38702 0.10% 79 46198 0.12% 80 40055 0.11% 81 42657 0.11% 82 52542 0.14% 83 58907 0.16% 84 52675 0.14% 85 53997 0.14% 86 58628 0.16% 87 73536 0.20% 88 69824 0.19% 89 88636 0.24% 90 66416 0.18% 91 69370 0.18% 92 64350 0.17% 93 68539 0.18% 94 79348 0.21% 95 79391 0.21% 96 92460 0.25% 97 91956 0.24% 98 83763 0.22% 99 89683 0.24% 100 90350 0.24% 101 100754 0.27% 102 117246 0.31% 103 117948 0.31% 104 114217 0.30% 105 110334 0.29% 106 115397 0.31% 107 124711 0.33% 108 124128 0.33% 109 145770 0.39% 110 135743 0.36% 111 141606 0.38% 112 217562 0.58% 113 157110 0.42% 114 155481 0.41% 115 157408 0.42% 116 159865 0.43% 117 183770 0.49% 118 189141 0.50% 119 190436 0.51% 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 32368501 86.08% 37603803 reads passed initial QC criterion=sequence-density sequence-density=11.89 sequence-density-rank=1 fanout-score=41.93 fanout-score-rank=1 prefix-density=14.26 prefix-fanout=35.0 sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCGATGTATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAA criterion=fanout-score sequence-density=11.89 sequence-density-rank=1 fanout-score=41.93 fanout-score-rank=1 prefix-density=14.26 prefix-fanout=35.0 sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCGATGTATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAA 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 AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCGATGTATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAA -o SRR11462714 - Input file: STDIN trimmed: SRR11462714-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCGATGTATCTCGTATGCCGTCTTCTGCTTG -- 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 08:21:19 2025 >> started Wed Feb 12 08:22:07 2025 >> done (48.400s) 31336503 reads processed; of these: 441 ( 0.00%) short reads filtered out after trimming by size control 15 ( 0.00%) empty reads filtered out after trimming by size control 31336047 (100.00%) reads available; of these: 7226558 (23.06%) trimmed reads available after processing 24109489 (76.94%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 2652 0.01% 19 2848 0.01% 20 3202 0.01% 21 3417 0.01% 22 4033 0.01% 23 4260 0.01% 24 4279 0.01% 25 4349 0.01% 26 4371 0.01% 27 5430 0.02% 28 5080 0.02% 29 5149 0.02% 30 5144 0.02% 31 5377 0.02% 32 5187 0.02% 33 5514 0.02% 34 6016 0.02% 35 6137 0.02% 36 6120 0.02% 37 8759 0.03% 38 6750 0.02% 39 7029 0.02% 40 6987 0.02% 41 7162 0.02% 42 8319 0.03% 43 8175 0.03% 44 8133 0.03% 45 8541 0.03% 46 9367 0.03% 47 12063 0.04% 48 9965 0.03% 49 11544 0.04% 50 10437 0.03% 51 10954 0.03% 52 11953 0.04% 53 12340 0.04% 54 14189 0.05% 55 13015 0.04% 56 13892 0.04% 57 16299 0.05% 58 14699 0.05% 59 16531 0.05% 60 17066 0.05% 61 17237 0.06% 62 32775 0.10% 63 18161 0.06% 64 20045 0.06% 65 19205 0.06% 66 20547 0.07% 67 22778 0.07% 68 20383 0.07% 69 24247 0.08% 70 23311 0.07% 71 26675 0.09% 72 28019 0.09% 73 28893 0.09% 74 31471 0.10% 75 30338 0.10% 76 28291 0.09% 77 32400 0.10% 78 32703 0.10% 79 38628 0.12% 80 34230 0.11% 81 38076 0.12% 82 43783 0.14% 83 48634 0.16% 84 41981 0.13% 85 45212 0.14% 86 49478 0.16% 87 61715 0.20% 88 59145 0.19% 89 74420 0.24% 90 59871 0.19% 91 58181 0.19% 92 54806 0.17% 93 57390 0.18% 94 66543 0.21% 95 65475 0.21% 96 78034 0.25% 97 74156 0.24% 98 70042 0.22% 99 75391 0.24% 100 76038 0.24% 101 85436 0.27% 102 98460 0.31% 103 99142 0.32% 104 95483 0.30% 105 92698 0.30% 106 96413 0.31% 107 104998 0.34% 108 105799 0.34% 109 123126 0.39% 110 114249 0.36% 111 118658 0.38% 112 182529 0.58% 113 129983 0.41% 114 130299 0.42% 115 131291 0.42% 116 133487 0.43% 117 148209 0.47% 118 153161 0.49% 119 156588 0.50% 120 172002 0.55% 121 182307 0.58% 122 177051 0.57% 123 247380 0.79% 124 216288 0.69% 125 179147 0.57% 126 199199 0.64% 127 210886 0.67% 128 197434 0.63% 129 189884 0.61% 130 191180 0.61% 131 206846 0.66% 132 226104 0.72% 133 235765 0.75% 134 216948 0.69% 135 239961 0.77% 136 220666 0.70% 137 246882 0.79% 138 268242 0.86% 139 245996 0.79% 140 255331 0.81% 141 229810 0.73% 142 249166 0.80% 143 250166 0.80% 144 245578 0.78% 145 299700 0.96% 146 252750 0.81% 147 352107 1.12% 148 659686 2.11% 149 0 0.00% 150 0 0.00% 151 19890134 63.47% criterion=sequence-density sequence-density=0.63 sequence-density-rank=1 fanout-score=2.06 fanout-score-rank=33 prefix-density=0.63 prefix-fanout=2.1 sequence=CTGCGACTGCGCTGACAAGACCCAGTGTGTCAAGAAGGGAAGCAGCTACACTGCTGGCATCGTCGAGACTGAGAAGAACTATGTCTCCTCCGTAGTCATGGAGGTGCCAGCAGCTGAGAACGATGGCAAGTGCAACTGCGGTACTGGCTGCACTTGCACTACCTGCACATGCGGTCATTAAGCAAGCACATCAACTATCATGTTTGATGTGGGATTGGGAGTGGATTAATAATGTAATTTCTGATAAATAATCTGTGTTCTTCTGTACTTGTGGGTGTGGAGTGAACAAACAAAAGTGTCCGTGAGTGTCTTTATCTTTGTGTCTTCTTCATTGTTATGTATTGGCCATGTCTGTGGCCTCTGGTGTGGTTTTAATGAAGTCTTATAATTAGTGTAGTA criterion=fanout-score sequence-density=0.01 sequence-density-rank=38 fanout-score=36.90 fanout-score-rank=1 prefix-density=0.10 prefix-fanout=5.2 sequence=GAGAAAATCATAAACGACTTCACTCATCTGGTCAATCAAGTTGAACCCTTGAAGAGCTTACACTGGGGCACTAATCTGGGTATTCACGACCTCAATTTCGGATATACTCATGCTTTTGAAACTACCTTTGATGATCTGGAGGGCTTGCAGGAGTATCTTGATTCTTCGGTTGTTGCTAAATTCGCAGAAGGATTCTTGCCAACCATGTCGCA Started job on | Feb 12 08:22:41 Started mapping on | Feb 12 08:22:41 Finished on | Feb 12 08:23:54 Mapping speed, Million of reads per hour | 1854.41 Number of input reads | 37603347 Average input read length | 140 UNIQUE READS: Uniquely mapped reads number | 30905170 Uniquely mapped reads % | 82.19% Average mapped length | 138.41 Number of splices: Total | 13814622 Number of splices: Annotated (sjdb) | 13567072 Number of splices: GT/AG | 13539254 Number of splices: GC/AG | 220206 Number of splices: AT/AC | 8031 Number of splices: Non-canonical | 47131 Mismatch rate per base, % | 0.38% Deletion rate per base | 0.02% Deletion average length | 2.08 Insertion rate per base | 0.01% Insertion average length | 1.96 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 1145537 % of reads mapped to multiple loci | 3.05% Number of reads mapped to too many loci | 4065276 % of reads mapped to too many loci | 10.81% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 3.83% % of reads unmapped: other | 0.13% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 5552640 5552640 5552640 N_multimapping 1145537 1145537 1145537 N_noFeature 1587871 2179701 29921588 N_ambiguous 529463 137792 629 UnstrandedReadsAssigned:28787836 PositiveStrandReadsAssigned:28587677 NegativeStrandReadsAssigned:982953 Dataset is classified positive stranded MeadianReadLen=151 20thPercentileLength=129 echo kmer=125 SRR11462714 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: SRR11462714-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 37,603,347 reads, 30,687,682 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,167 rounds 52401 SRR11462714.ke.tsv 34699 SRR11462714.se.tsv 87100 total ==> SRR11462714.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1919 988 17.671 Potri.005G024800.1.v4.1 1035 936 313 11.4775 Potri.004G059700.1.v4.1 961 862 65 2.58813 Potri.007G009000.2.v4.1 1416 1317 0 0 Potri.003G141000.2.v4.1 2943 2844 2220.61 26.7992 Potri.016G087400.1.v4.1 270 171 2516 505.003 Potri.015G069301.1.v4.1 564 465 0 0 Potri.010G195200.1.v4.1 1773 1674 63 1.29171 Potri.012G127500.1.v4.1 977 878 62 2.42369 ==> SRR11462714.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 366 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 184 Potri.001G212900.v4.1 37 Potri.001G182400.v4.1 0 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 6 Potri.001G416900.v4.1 6 Potri.001G452600.v4.1 26 SRR11462714 completed mapping pipeline successfully