Starting /dee2/code/volunteer_pipeline.sh SRR11462697 current disk space = 3050318336000 free memory = 1408148520 SRR11462697 SRAfilesize 1a1c600060bad88462e0b4822f364b85 SRR11462697.sra SRR11462697.sra file validated SRR11462697 is single end SRR11462697 is conventional basespace SRR11462697 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR11462697_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 fail #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 22.8525 32.0 2.0 32.0 2.0 32.0 2 31.77125 32.0 32.0 32.0 32.0 32.0 3 34.55 37.0 32.0 37.0 32.0 37.0 4 36.2025 37.0 37.0 37.0 32.0 37.0 5 36.40125 37.0 37.0 37.0 37.0 37.0 6 39.8845 41.0 41.0 41.0 37.0 41.0 7 40.1535 41.0 41.0 41.0 37.0 41.0 8 40.283 41.0 41.0 41.0 37.0 41.0 9 40.23175 41.0 41.0 41.0 37.0 41.0 10-14 40.302749999999996 41.0 41.0 41.0 38.6 41.0 15-19 40.2416 41.0 41.0 41.0 37.8 41.0 20-24 40.18455 41.0 41.0 41.0 37.8 41.0 25-29 40.173500000000004 41.0 41.0 41.0 38.6 41.0 30-34 40.087849999999996 41.0 41.0 41.0 37.0 41.0 35-39 40.02875 41.0 41.0 41.0 37.0 41.0 40-44 40.09325 41.0 41.0 41.0 37.8 41.0 45-49 40.076100000000004 41.0 41.0 41.0 37.8 41.0 50-54 40.06705 41.0 41.0 41.0 38.6 41.0 55-59 40.01435 41.0 41.0 41.0 37.0 41.0 60-64 39.97095 41.0 41.0 41.0 37.0 41.0 65-69 39.9565 41.0 41.0 41.0 37.0 41.0 70-74 39.75404999999999 41.0 41.0 41.0 37.0 41.0 75-79 39.71055 41.0 40.2 41.0 37.0 41.0 80-84 40.1724 41.0 41.0 41.0 39.4 41.0 85-89 40.0403 41.0 41.0 41.0 37.8 41.0 90-94 40.076649999999994 41.0 41.0 41.0 37.8 41.0 95-99 39.9748 41.0 41.0 41.0 37.0 41.0 100-104 39.772850000000005 41.0 41.0 41.0 37.0 41.0 105-109 39.7129 41.0 41.0 41.0 37.0 41.0 110-114 39.759499999999996 41.0 41.0 41.0 37.0 41.0 115-119 39.66335 41.0 41.0 41.0 37.0 41.0 120-124 39.625 41.0 41.0 41.0 37.0 41.0 125-129 39.3198 41.0 41.0 41.0 37.0 41.0 130-134 39.23435 41.0 41.0 41.0 37.0 41.0 135-139 38.9971 41.0 41.0 41.0 35.0 41.0 140-144 38.927499999999995 41.0 41.0 41.0 33.0 41.0 145-149 38.66585 41.0 41.0 41.0 32.0 41.0 150-151 37.70025 41.0 39.0 41.0 29.5 41.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 19 1.0 20 0.0 21 0.0 22 0.0 23 0.0 24 3.0 25 3.0 26 5.0 27 10.0 28 8.0 29 18.0 30 29.0 31 37.0 32 42.0 33 48.0 34 61.0 35 84.0 36 89.0 37 132.0 38 162.0 39 293.0 40 2975.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 5.6939501779359425 36.04982206405694 43.87900355871886 14.377224199288255 2 24.7 44.85 20.1 10.35 3 22.1 29.75 37.525 10.625 4 32.80780780780781 23.998998998999 28.353353353353356 14.839839839839838 5 26.950000000000003 25.825 29.875 17.349999999999998 6 28.449999999999996 24.725 26.950000000000003 19.875 7 23.175 26.450000000000003 28.175 22.2 8 23.925 26.35 30.7 19.025 9 21.6 26.8 30.55 21.05 10-14 25.0 25.605 28.749999999999996 20.645 15-19 23.68 27.815 28.99 19.515 20-24 26.224999999999998 25.81 28.24 19.725 25-29 24.654999999999998 26.305 29.43 19.61 30-34 24.654999999999998 27.055 28.09 20.200000000000003 35-39 24.485 26.305 28.46 20.75 40-44 24.295 26.68 28.875 20.150000000000002 45-49 23.385 26.77 28.735 21.11 50-54 24.099999999999998 28.055000000000003 27.38 20.465 55-59 25.040000000000003 26.86 26.950000000000003 21.15 60-64 25.35 25.465 29.849999999999998 19.335 65-69 25.945 26.3 27.279999999999998 20.474999999999998 70-74 24.715 26.865 27.255000000000003 21.165 75-79 23.89 27.05 28.860000000000003 20.200000000000003 80-84 25.275 27.325 28.32 19.08 85-89 24.29 28.410000000000004 27.125 20.175 90-94 25.635 25.929999999999996 27.785 20.65 95-99 24.490000000000002 25.979999999999997 27.944999999999997 21.584999999999997 100-104 25.240000000000002 26.305 27.025 21.43 105-109 24.055 26.66 26.775 22.509999999999998 110-114 24.82 27.08 27.205000000000002 20.895 115-119 25.224999999999998 26.61 27.48 20.685000000000002 120-124 24.955 27.58 27.46 20.005 125-129 23.995 28.560000000000002 26.090000000000003 21.355 130-134 24.2 28.470000000000002 27.155 20.175 135-139 24.81 28.055000000000003 25.64 21.495 140-144 25.729999999999997 28.360000000000003 24.275 21.634999999999998 145-149 25.005 28.115000000000002 24.26 22.62 150-151 24.087500000000002 28.7375 23.45 23.724999999999998 >>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 0.0 9 0.0 10 0.0 11 0.0 12 0.0 13 0.0 14 0.0 15 0.0 16 0.5 17 1.0 18 0.5 19 1.0 20 1.0 21 0.0 22 0.0 23 1.5 24 2.5 25 3.5 26 6.0 27 7.0 28 8.5 29 12.5 30 19.5 31 33.5 32 38.0 33 44.5 34 64.5 35 91.5 36 103.0 37 109.5 38 133.0 39 159.0 40 181.0 41 195.0 42 221.0 43 235.0 44 298.0 45 301.0 46 220.0 47 204.5 48 204.0 49 159.5 50 117.5 51 111.0 52 119.0 53 114.5 54 95.5 55 82.0 56 50.0 57 36.0 58 36.5 59 26.5 60 25.5 61 22.5 62 19.5 63 26.0 64 17.5 65 4.5 66 1.0 67 3.0 68 6.5 69 5.5 70 4.0 71 6.5 72 4.5 73 2.0 74 1.5 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 29.75 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 85.3 #Duplication Level Percentage of deduplicated Percentage of total 1 93.6400937866354 79.875 2 4.5134818288393905 7.7 3 0.5568581477139508 1.425 4 0.3516998827667058 1.2 5 0.23446658851113714 1.0 6 0.08792497069167644 0.44999999999999996 7 0.11723329425556857 0.7000000000000001 8 0.058616647127784284 0.4 9 0.029308323563892142 0.22499999999999998 >10 0.3810082063305979 5.0 >50 0.029308323563892142 2.025 >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 fail #Sequence Count Percentage Possible Source TATTTGCTACTCGGATAACCGTAGTAATTCTAGAGCTAATACGTGCAACA 81 2.025 No Hit NATTTGCTACTCGGATAACCGTAGTAATTCTAGAGCTAATACGTGCAACA 31 0.775 No Hit ATGCGCTCCTGGCCTTAACTGGCCGGGTCGTGCCTCCGGTGCTGTTACTT 30 0.75 No Hit NTGCGCTCCTGGCCTTAACTGGCCGGGTCGTGCCTCCGGTGCTGTTACTT 18 0.44999999999999996 No Hit TACTCGGATAACCGTAGTAATTCTAGAGCTAATACGTGCAACAAACCCCG 18 0.44999999999999996 No Hit AAAGACGAACAACTGCGAAAGCATTTGCCAAGGATGTTTTCATTAATCAA 15 0.375 No Hit TATTAGATAAAAGGTCGACGCGGGCTCTGCCCGTTGCTCTGATGATTCAT 14 0.35000000000000003 No Hit AGACTGTGAAACTGCGAATGGCTCATTAAATCAGTTATAGTTTGTTTGAT 12 0.3 No Hit NACCTGGTTGATCCTGCCAGTAGTCATATGCTTGTCTCAAAGATTAAGCC 11 0.27499999999999997 No Hit CTACTCGGATAACCGTAGTAATTCTAGAGCTAATACGTGCAACAAACCCC 11 0.27499999999999997 No Hit TGTTGGCCTTCGGGATCGGAGTAATGATTAACAGGGACAGTCGGGGGCAT 10 0.25 No Hit TTAATCAAGAACGAAAGTTGGGGGCTCGAAGACGATCAGATACCGTCCTA 10 0.25 No Hit TACCTGGTTGATCCTGCCAGTAGTCATATGCTTGTCTCAAAGATTAAGCC 10 0.25 No Hit TATTTTACTTATTCCGTGAATCGGAGGCGGGGCGCTGCCCCTCTTTTTGG 10 0.25 No Hit TAAAAAGCTCGTAGTTGGACTTTGGGTTGGGTCGGCCGGTCCGCCTCAGG 9 0.22499999999999998 No Hit TGCAACAAACCCCGACTTCTGGAAGGGACGCATTTATTAGATAAAAGGTC 8 0.2 No Hit CAGCCAAGCGTTCATAGCGACGTTGCTTTTTGATCCTTCGATGTCGGCTC 8 0.2 No Hit NGTTGGCCTTCGGGATCGGAGTAATGATTAACAGGGACAGTCGGGGGCAT 7 0.17500000000000002 No Hit GAGACTGAGAAGAACTATGTCTCCTCCGTAGTCATGGAGGTGCCAGCAGC 7 0.17500000000000002 No Hit NATTTTACTTATTCCGTGAATCGGAGGCGGGGCGCTGCCCCTCTTTTTGG 7 0.17500000000000002 No Hit NAAGACGAACAACTGCGAAAGCATTTGCCAAGGATGTTTTCATTAATCAA 7 0.17500000000000002 No Hit NGACTGTGAAACTGCGAATGGCTCATTAAATCAGTTATAGTTTGTTTGAT 6 0.15 No Hit AGTTAAAAAGCTCGTAGTTGGACTTTGGGTTGGGTCGGCCGGTCCGCCTC 6 0.15 No Hit NGTGGGATTGGGAGTGGATTAATAATGTAATTTCTGATAAATAATCTGTG 6 0.15 No Hit AATCCGGGCTAGATGCGACGCGTGCGCCCGCCGTCCGATTGCCGACCTGC 5 0.125 No Hit AATGTGATTTCTGCCCAGTGCTCTGAATGTCAAAGTGAAGAAATTCAACC 5 0.125 No Hit CGGTGAAAGAGCCGCGCGGGCCGCCTTGAAGTACAATTCCCACCGAGCGG 5 0.125 No Hit TGGCATCGTCGAGACTGAGAAGAACTATGTCTCCTCCGTAGTCATGGAGG 5 0.125 No Hit NATTAGATAAAAGGTCGACGCGGGCTCTGCCCGTTGCTCTGATGATTCAT 5 0.125 No Hit TGTGGGATTGGGAGTGGATTAATAATGTAATTTCTGATAAATAATCTGTG 5 0.125 No Hit TTAGATAAAAGGTCGACGCGGGCTCTGCCCGTTGCTCTGATGATTCATGA 5 0.125 No Hit AACTATCATGTTTGATGTGGGATTGGGAGTGGATTAATAATGTAATTTCT 5 0.125 No Hit >>END_MODULE >>Adapter Content fail #Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence SOLID Small RNA Adapter 1 0.0 0.0 0.0 0.0 0.0 2 0.0 0.0 0.0 0.0 0.0 3 0.0 0.0 0.0 0.0 0.0 4 0.0 0.0 0.0 0.0 0.0 5 0.0 0.0 0.0 0.0 0.0 6 0.0 0.0 0.0 0.0 0.0 7 0.0 0.0 0.0 0.0 0.0 8 0.0 0.0 0.0 0.0 0.0 9 0.0 0.0 0.0 0.0 0.0 10-11 0.0 0.0 0.0 0.0 0.0 12-13 0.0 0.0 0.0 0.0 0.0 14-15 0.0 0.0 0.0 0.0 0.0 16-17 0.0 0.0 0.0 0.0 0.0 18-19 0.0125 0.0 0.0 0.0 0.0 20-21 0.05 0.0 0.0 0.0 0.0 22-23 0.1 0.0 0.0 0.0 0.0 24-25 0.1 0.0 0.0 0.0 0.0 26-27 0.125 0.0 0.0 0.0 0.0 28-29 0.15 0.0 0.0 0.0 0.0 30-31 0.225 0.0 0.0 0.0 0.0 32-33 0.2375 0.0 0.0 0.0 0.0 34-35 0.2625 0.0 0.0 0.0 0.0 36-37 0.30000000000000004 0.0 0.0 0.0 0.0 38-39 0.35 0.0 0.0 0.0 0.0 40-41 0.375 0.0 0.0 0.0 0.0 42-43 0.4 0.0 0.0 0.0 0.0 44-45 0.425 0.0 0.0 0.0 0.0 46-47 0.4625 0.0 0.0 0.0 0.0 48-49 0.5 0.0 0.0 0.0 0.0 50-51 0.575 0.0 0.0 0.0 0.0 52-53 0.6125 0.0 0.0 0.0 0.0 54-55 0.675 0.0 0.0 0.0 0.0 56-57 0.7375 0.0 0.0 0.0 0.0 58-59 0.8 0.0 0.0 0.0 0.0 60-61 0.925 0.0 0.0 0.0 0.0 62-63 1.1375 0.0 0.0 0.0 0.0 64-65 1.3375 0.0 0.0 0.0 0.0 66-67 1.4375 0.0 0.0 0.0 0.0 68-69 1.5875 0.0 0.0 0.0 0.0 70-71 1.7374999999999998 0.0 0.0 0.0 0.0 72-73 1.9125 0.0 0.0 0.0 0.0 74-75 2.125 0.0 0.0 0.0 0.0 76-77 2.35 0.0 0.0 0.0 0.0 78-79 2.6125 0.0 0.0 0.0 0.0 80-81 2.9375 0.0 0.0 0.0 0.0 82-83 3.1125 0.0 0.0 0.0 0.0 84-85 3.3 0.0 0.0 0.0 0.0 86-87 3.675 0.0 0.0 0.0 0.0 88-89 3.9375 0.0 0.0 0.0 0.0 90-91 4.7375 0.0 0.0 0.0 0.0 92-93 5.175000000000001 0.0 0.0 0.0 0.0 94-95 5.5875 0.0 0.0 0.0 0.0 96-97 5.949999999999999 0.0 0.0 0.0 0.0 98-99 6.5875 0.0 0.0 0.0 0.0 100-101 7.175000000000001 0.0 0.0 0.0 0.0 102-103 7.8875 0.0 0.0 0.0 0.0 104-105 8.45 0.0 0.0 0.0 0.0 106-107 9.125 0.0 0.0 0.0 0.0 108-109 9.9 0.0 0.0 0.0 0.0 110-111 10.7875 0.0 0.0 0.0 0.0 112-113 12.175 0.0 0.0 0.0 0.0 114-115 13.5125 0.0 0.0 0.0 0.0 116-117 14.287500000000001 0.0 0.0 0.0 0.0 118-119 15.175 0.0 0.0 0.0 0.0 120-121 16.15 0.0 0.0 0.0 0.0 122-123 17.325 0.0 0.0 0.0 0.0 124-125 18.575 0.0 0.0 0.0 0.0 126-127 20.0875 0.0 0.0 0.0 0.0 128-129 21.612499999999997 0.0 0.0 0.0 0.0 130-131 22.7875 0.0 0.0 0.0 0.0 132-133 24.1625 0.0 0.0 0.0 0.0 134-135 25.887500000000003 0.0 0.0 0.0 0.0 136-137 27.4 0.0 0.0 0.0 0.0 138-139 28.45 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GAATCAA 10 0.00686971 144.72499 5 GGAGGAG 10 0.00686971 144.72499 9 TATTTGC 30 2.7424285E-6 133.08046 1 GCTACTC 35 1.4788384E-9 124.04999 6 ATTTGCT 35 1.4788384E-9 124.04999 2 CTACTCG 35 1.4788384E-9 124.04999 7 TGCTACT 40 3.745299E-9 108.54375 5 TACTCGG 40 3.745299E-9 108.54375 8 TTTGCTA 40 3.745299E-9 108.54375 3 TTGCTAC 40 3.745299E-9 108.54375 4 CACGGCC 40 3.745299E-9 108.54375 145 ACTCGGA 45 8.4928615E-9 96.48334 9 TCTGAAC 80 0.0018209623 36.181248 145 TAGATAA 50 0.001346856 28.945 7 CTCGACG 35 1.2121896E-4 24.81 130-134 TCGACGG 35 1.2121896E-4 24.81 130-134 TTATTAG 35 1.2121896E-4 24.81 75-79 GACGGAT 35 1.2121896E-4 24.81 135-139 GGATCGC 35 1.2121896E-4 24.81 135-139 CGGATCG 35 1.2121896E-4 24.81 135-139 >>END_MODULE Rejected 1858701 READS because READLEN < 1 Read 1858701 spots for SRR11462697.sra Written 1858701 spots for SRR11462697.sra Rejected 1858701 READS because READLEN < 1 Read 1858701 spots for SRR11462697.sra Written 1858701 spots for SRR11462697.sra Rejected 1858701 READS because READLEN < 1 Read 1858701 spots for SRR11462697.sra Written 1858701 spots for SRR11462697.sra Rejected 1858701 READS because READLEN < 1 Read 1858701 spots for SRR11462697.sra Written 1858701 spots for SRR11462697.sra Rejected 1858701 READS because READLEN < 1 Read 1858701 spots for SRR11462697.sra Written 1858701 spots for SRR11462697.sra Rejected 1858701 READS because READLEN < 1 Read 1858701 spots for SRR11462697.sra Written 1858701 spots for SRR11462697.sra Rejected 1858701 READS because READLEN < 1 Read 1858701 spots for SRR11462697.sra Written 1858701 spots for SRR11462697.sra Rejected 1858701 READS because READLEN < 1 Read 1858701 spots for SRR11462697.sra Written 1858701 spots for SRR11462697.sra Rejected 1858701 READS because READLEN < 1 Read 1858701 spots for SRR11462697.sra Written 1858701 spots for SRR11462697.sra Rejected 1858701 READS because READLEN < 1 Read 1858701 spots for SRR11462697.sra Written 1858701 spots for SRR11462697.sra Rejected 1858701 READS because READLEN < 1 Read 1858701 spots for SRR11462697.sra Written 1858701 spots for SRR11462697.sra Rejected 1858701 READS because READLEN < 1 Read 1858701 spots for SRR11462697.sra Written 1858701 spots for SRR11462697.sra Rejected 1858701 READS because READLEN < 1 Read 1858701 spots for SRR11462697.sra Written 1858701 spots for SRR11462697.sra Rejected 1858701 READS because READLEN < 1 Read 1858701 spots for SRR11462697.sra Written 1858701 spots for SRR11462697.sra Rejected 1858701 READS because READLEN < 1 Read 1858701 spots for SRR11462697.sra Written 1858701 spots for SRR11462697.sra Rejected 1858701 READS because READLEN < 1 Read 1858701 spots for SRR11462697.sra Written 1858701 spots for SRR11462697.sra Rejected 1858701 READS because READLEN < 1 Read 1858701 spots for SRR11462697.sra Written 1858701 spots for SRR11462697.sra Rejected 1858709 READS because READLEN < 1 Read 1858709 spots for SRR11462697.sra Written 1858709 spots for SRR11462697.sra Rejected 1858701 READS because READLEN < 1 Read 1858701 spots for SRR11462697.sra Written 1858701 spots for SRR11462697.sra Rejected 1858701 READS because READLEN < 1 Read 1858701 spots for SRR11462697.sra Written 1858701 spots for SRR11462697.sra SRR ids: ['SRR11462697.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_9xptpzxp SRR11462697.sra spots: 37174028 blocks: [[1, 1858701], [1858702, 3717402], [3717403, 5576103], [5576104, 7434804], [7434805, 9293505], [9293506, 11152206], [11152207, 13010907], [13010908, 14869608], [14869609, 16728309], [16728310, 18587010], [18587011, 20445711], [20445712, 22304412], [22304413, 24163113], [24163114, 26021814], [26021815, 27880515], [27880516, 29739216], [29739217, 31597917], [31597918, 33456618], [33456619, 35315319], [35315320, 37174028]] SRR11462697 file size 12611660 SRR11462697 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 SRR11462697 SRR11462697_1.fastq Input file: SRR11462697_1.fastq trimmed: SRR11462697-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 06:37:19 2025 >> started Wed Feb 12 06:37:41 2025 >> done (21.747s) 37174028 reads processed; of these: 9982 ( 0.03%) short reads filtered out after trimming by size control 865 ( 0.00%) empty reads filtered out after trimming by size control 37163181 (99.97%) reads available; of these: 5926925 (15.95%) trimmed reads available after processing 31236256 (84.05%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 2279 0.01% 19 2530 0.01% 20 2813 0.01% 21 3002 0.01% 22 3261 0.01% 23 3626 0.01% 24 3852 0.01% 25 3731 0.01% 26 3683 0.01% 27 5668 0.02% 28 4270 0.01% 29 4810 0.01% 30 4998 0.01% 31 4946 0.01% 32 5049 0.01% 33 5152 0.01% 34 5837 0.02% 35 5616 0.02% 36 5806 0.02% 37 8648 0.02% 38 6671 0.02% 39 6684 0.02% 40 6829 0.02% 41 7101 0.02% 42 8824 0.02% 43 9155 0.02% 44 7868 0.02% 45 8874 0.02% 46 9429 0.03% 47 11616 0.03% 48 11273 0.03% 49 15119 0.04% 50 10820 0.03% 51 11872 0.03% 52 12388 0.03% 53 13100 0.04% 54 15040 0.04% 55 14075 0.04% 56 14451 0.04% 57 17442 0.05% 58 17343 0.05% 59 17378 0.05% 60 20147 0.05% 61 19504 0.05% 62 58488 0.16% 63 20064 0.05% 64 23492 0.06% 65 21826 0.06% 66 22891 0.06% 67 25454 0.07% 68 24460 0.07% 69 35562 0.10% 70 27696 0.07% 71 30071 0.08% 72 34231 0.09% 73 48467 0.13% 74 42095 0.11% 75 38779 0.10% 76 34904 0.09% 77 51906 0.14% 78 39970 0.11% 79 57296 0.15% 80 41918 0.11% 81 44602 0.12% 82 50245 0.14% 83 52540 0.14% 84 58112 0.16% 85 56144 0.15% 86 59266 0.16% 87 68923 0.19% 88 65615 0.18% 89 174947 0.47% 90 71953 0.19% 91 87144 0.23% 92 73332 0.20% 93 78460 0.21% 94 88519 0.24% 95 85955 0.23% 96 97548 0.26% 97 107493 0.29% 98 96667 0.26% 99 101588 0.27% 100 101190 0.27% 101 112409 0.30% 102 123929 0.33% 103 118214 0.32% 104 123238 0.33% 105 125423 0.34% 106 129032 0.35% 107 137211 0.37% 108 149013 0.40% 109 182823 0.49% 110 154454 0.42% 111 163191 0.44% 112 418494 1.13% 113 173612 0.47% 114 174968 0.47% 115 172047 0.46% 116 181739 0.49% 117 201087 0.54% 118 197698 0.53% 119 205834 0.55% 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% 150 116 0.00% 151 31236256 84.05% 37163181 reads passed initial QC criterion=sequence-density sequence-density=12.86 sequence-density-rank=1 fanout-score=41.23 fanout-score-rank=1 prefix-density=15.29 prefix-fanout=34.7 sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACGTAGAGATCTCGTATGCCGTCTTCTGCTTGA criterion=fanout-score sequence-density=12.86 sequence-density-rank=1 fanout-score=41.23 fanout-score-rank=1 prefix-density=15.29 prefix-fanout=34.7 sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACGTAGAGATCTCGTATGCCGTCTTCTGCTTGA 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 AGATCGGAAGAGCACACGTCTGAACTCCAGTCACGTAGAGATCTCGTATGCCGTCTTCTGCTTGA -o SRR11462697 - Input file: STDIN trimmed: SRR11462697-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): AGATCGGAAGAGCACACGTCTGAACTCCAGTCACGTAGAGATCTCGTATGCCGTCTTCTGCTTG -- 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 06:39:00 2025 >> started Wed Feb 12 06:39:35 2025 >> done (35.664s) 31445769 reads processed; of these: 307 ( 0.00%) short reads filtered out after trimming by size control 6 ( 0.00%) empty reads filtered out after trimming by size control 31445456 (100.00%) reads available; of these: 7524162 (23.93%) trimmed reads available after processing 23921294 (76.07%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 2002 0.01% 19 2188 0.01% 20 2417 0.01% 21 2567 0.01% 22 2754 0.01% 23 3060 0.01% 24 3326 0.01% 25 3199 0.01% 26 3206 0.01% 27 4865 0.02% 28 3678 0.01% 29 4078 0.01% 30 4237 0.01% 31 4225 0.01% 32 4266 0.01% 33 4395 0.01% 34 4980 0.02% 35 4816 0.02% 36 5006 0.02% 37 7376 0.02% 38 5715 0.02% 39 5704 0.02% 40 5829 0.02% 41 6085 0.02% 42 7463 0.02% 43 7755 0.02% 44 6737 0.02% 45 7697 0.02% 46 8041 0.03% 47 10011 0.03% 48 9497 0.03% 49 12840 0.04% 50 9157 0.03% 51 10131 0.03% 52 10587 0.03% 53 11364 0.04% 54 12849 0.04% 55 12042 0.04% 56 12037 0.04% 57 14867 0.05% 58 14787 0.05% 59 14770 0.05% 60 17119 0.05% 61 16713 0.05% 62 49949 0.16% 63 17208 0.05% 64 20036 0.06% 65 18594 0.06% 66 19539 0.06% 67 21812 0.07% 68 20989 0.07% 69 30392 0.10% 70 24576 0.08% 71 25765 0.08% 72 29326 0.09% 73 41410 0.13% 74 35701 0.11% 75 32320 0.10% 76 29702 0.09% 77 44459 0.14% 78 34171 0.11% 79 48800 0.16% 80 35718 0.11% 81 38245 0.12% 82 42858 0.14% 83 44785 0.14% 84 49187 0.16% 85 47926 0.15% 86 50645 0.16% 87 58835 0.19% 88 56016 0.18% 89 148732 0.47% 90 61890 0.20% 91 74258 0.24% 92 63006 0.20% 93 66779 0.21% 94 75114 0.24% 95 72946 0.23% 96 83363 0.27% 97 91434 0.29% 98 82745 0.26% 99 87094 0.28% 100 86331 0.27% 101 95976 0.31% 102 104940 0.33% 103 101034 0.32% 104 104795 0.33% 105 106773 0.34% 106 109907 0.35% 107 116925 0.37% 108 127806 0.41% 109 155731 0.50% 110 132403 0.42% 111 139145 0.44% 112 357181 1.14% 113 146857 0.47% 114 148590 0.47% 115 144655 0.46% 116 154355 0.49% 117 165266 0.53% 118 162117 0.52% 119 171090 0.54% 120 192606 0.61% 121 202542 0.64% 122 191081 0.61% 123 216822 0.69% 124 228570 0.73% 125 188904 0.60% 126 216299 0.69% 127 225589 0.72% 128 215487 0.69% 129 210708 0.67% 130 207828 0.66% 131 212057 0.67% 132 310525 0.99% 133 260814 0.83% 134 229983 0.73% 135 264452 0.84% 136 234507 0.75% 137 240078 0.76% 138 255942 0.81% 139 247813 0.79% 140 266888 0.85% 141 241478 0.77% 142 263962 0.84% 143 250019 0.80% 144 233829 0.74% 145 351115 1.12% 146 253190 0.81% 147 335594 1.07% 148 604008 1.92% 149 0 0.00% 150 80 0.00% 151 19058046 60.61% criterion=sequence-density sequence-density=1.05 sequence-density-rank=1 fanout-score=1.98 fanout-score-rank=29 prefix-density=1.05 prefix-fanout=2.0 sequence=ACGTGAGCTGGGTT criterion=fanout-score sequence-density=0.14 sequence-density-rank=16 fanout-score=16.46 fanout-score-rank=1 prefix-density=1.98 prefix-fanout=1.2 sequence=CGGCGATGCGCCCCGGTCGGATGTGGAACGGTTACAGCCGGTCCGCCGATCGGCTCGGGGCGTGGACC Started job on | Feb 12 06:40:56 Started mapping on | Feb 12 06:40:56 Finished on | Feb 12 06:42:41 Mapping speed, Million of reads per hour | 1274.16 Number of input reads | 37162868 Average input read length | 131 UNIQUE READS: Uniquely mapped reads number | 25699021 Uniquely mapped reads % | 69.15% Average mapped length | 128.36 Number of splices: Total | 10117808 Number of splices: Annotated (sjdb) | 9856630 Number of splices: GT/AG | 9937663 Number of splices: GC/AG | 140874 Number of splices: AT/AC | 6788 Number of splices: Non-canonical | 32483 Mismatch rate per base, % | 0.38% Deletion rate per base | 0.02% Deletion average length | 2.13 Insertion rate per base | 0.01% Insertion average length | 1.80 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 949037 % of reads mapped to multiple loci | 2.55% Number of reads mapped to too many loci | 7546815 % of reads mapped to too many loci | 20.31% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 7.74% % of reads unmapped: other | 0.25% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 10514810 10514810 10514810 N_multimapping 949037 949037 949037 N_noFeature 1764410 2202809 24836877 N_ambiguous 516793 93240 558 UnstrandedReadsAssigned:23417818 PositiveStrandReadsAssigned:23402972 NegativeStrandReadsAssigned:861586 Dataset is classified positive stranded MeadianReadLen=143 20thPercentileLength=118 echo kmer=113 SRR11462697 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: SRR11462697-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 37,162,868 reads, 25,995,601 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,203 rounds 52401 SRR11462697.ke.tsv 34699 SRR11462697.se.tsv 87100 total ==> SRR11462697.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1919 2686 64.2897 Potri.005G024800.1.v4.1 1035 936 862.36 42.3178 Potri.004G059700.1.v4.1 961 862 0 0 Potri.007G009000.2.v4.1 1416 1317 0 0 Potri.003G141000.2.v4.1 2943 2844 3130.5 50.5586 Potri.016G087400.1.v4.1 270 171 995 267.262 Potri.015G069301.1.v4.1 564 465 0 0 Potri.010G195200.1.v4.1 1773 1674 2908.98 79.817 Potri.012G127500.1.v4.1 977 878 12 0.627765 ==> SRR11462697.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 1 Potri.001G233950.v4.1 3 Potri.001G122700.v4.1 236 Potri.001G212900.v4.1 0 Potri.001G182400.v4.1 0 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 3 Potri.001G416900.v4.1 2 Potri.001G452600.v4.1 12 SRR11462697 completed mapping pipeline successfully