Starting /dee2/code/volunteer_pipeline.sh SRR11462712 current disk space = 3049266962432 free memory = 1582680728 SRR11462712 SRAfilesize ef7745ea8cd5d4851f6ae82db1e57dd9 SRR11462712.sra SRR11462712.sra file validated SRR11462712 is single end SRR11462712 is conventional basespace SRR11462712 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR11462712_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 46 >>END_MODULE >>Per base sequence quality fail #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 24.0775 32.0 2.0 32.0 2.0 32.0 2 31.75 32.0 32.0 32.0 32.0 32.0 3 34.72125 37.0 32.0 37.0 32.0 37.0 4 36.14625 37.0 37.0 37.0 32.0 37.0 5 36.47125 37.0 37.0 37.0 37.0 37.0 6 40.0575 41.0 41.0 41.0 37.0 41.0 7 40.09325 41.0 41.0 41.0 37.0 41.0 8 40.08875 41.0 41.0 41.0 37.0 41.0 9 40.323 41.0 41.0 41.0 41.0 41.0 10-14 40.29655 41.0 41.0 41.0 40.2 41.0 15-19 40.24785 41.0 41.0 41.0 38.6 41.0 20-24 40.213049999999996 41.0 41.0 41.0 38.6 41.0 25-29 40.210049999999995 41.0 41.0 41.0 39.4 41.0 30-34 40.04765 41.0 41.0 41.0 37.0 41.0 35-39 40.070949999999996 41.0 41.0 41.0 39.4 41.0 40-44 40.08055 41.0 41.0 41.0 37.8 41.0 45-49 40.06145 41.0 41.0 41.0 37.0 41.0 50-54 40.01145 41.0 41.0 41.0 38.6 41.0 55-59 39.9671 41.0 41.0 41.0 37.0 41.0 60-64 39.9895 41.0 41.0 41.0 37.0 41.0 65-69 39.986999999999995 41.0 41.0 41.0 37.0 41.0 70-74 39.87205 41.0 41.0 41.0 37.0 41.0 75-79 39.70655 41.0 41.0 41.0 37.0 41.0 80-84 40.16395 41.0 41.0 41.0 38.6 41.0 85-89 40.180949999999996 41.0 41.0 41.0 40.2 41.0 90-94 40.02915 41.0 41.0 41.0 37.8 41.0 95-99 39.94235 41.0 41.0 41.0 37.0 41.0 100-104 39.9166 41.0 41.0 41.0 37.0 41.0 105-109 39.70975 41.0 41.0 41.0 37.0 41.0 110-114 39.7313 41.0 41.0 41.0 37.0 41.0 115-119 39.75359999999999 41.0 41.0 41.0 37.0 41.0 120-124 39.53135 41.0 41.0 41.0 37.0 41.0 125-129 39.54815 41.0 41.0 41.0 37.0 41.0 130-134 39.46385 41.0 41.0 41.0 37.0 41.0 135-139 39.08595 41.0 41.0 41.0 36.0 41.0 140-144 39.062549999999995 41.0 41.0 41.0 36.0 41.0 145-149 38.63755 41.0 41.0 41.0 32.0 41.0 150-151 37.7665 41.0 39.0 41.0 29.5 41.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 23 3.0 24 1.0 25 1.0 26 4.0 27 6.0 28 10.0 29 18.0 30 27.0 31 43.0 32 57.0 33 49.0 34 43.0 35 69.0 36 93.0 37 136.0 38 148.0 39 286.0 40 3006.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 6.351351351351352 36.891891891891895 39.96621621621622 16.79054054054054 2 25.974999999999998 43.5 18.825 11.700000000000001 3 23.25 29.375 36.625 10.75 4 36.05 23.65 24.575 15.725 5 29.849999999999998 25.025 27.625 17.5 6 26.950000000000003 27.3 24.95 20.8 7 24.0 27.175 27.474999999999998 21.349999999999998 8 27.55 24.349999999999998 29.275000000000002 18.825 9 23.125 25.074999999999996 28.375 23.425 10-14 26.085 24.535 28.24 21.14 15-19 25.624999999999996 27.075 26.700000000000003 20.599999999999998 20-24 26.229999999999997 25.314999999999998 27.029999999999998 21.425 25-29 26.229999999999997 26.305 27.145000000000003 20.32 30-34 25.795 25.55 26.96 21.695 35-39 25.71 24.34 27.625 22.325 40-44 25.009999999999998 25.985000000000003 27.265 21.740000000000002 45-49 24.661233061653082 26.056302815140757 27.391369568478424 21.891094554727736 50-54 25.430000000000003 26.490000000000002 27.04 21.04 55-59 26.13 26.1 26.540000000000003 21.23 60-64 26.57 25.669999999999998 27.894999999999996 19.865 65-69 26.642664266426642 25.577557755775576 26.007600760076006 21.772177217721772 70-74 25.58255825582558 26.067606760676064 26.172617261726174 22.177217721772177 75-79 24.695 26.26 28.075 20.97 80-84 25.896294814740738 26.26131306565328 27.031351567578376 20.811040552027603 85-89 25.424999999999997 27.400000000000002 25.814999999999998 21.36 90-94 26.964044606691 25.568835325298796 26.453968095214282 21.013151972795917 95-99 25.169999999999998 26.085 27.235 21.51 100-104 26.415 25.245 26.575 21.765 105-109 25.655 25.635 26.085 22.625 110-114 25.874999999999996 25.71 27.150000000000002 21.265 115-119 25.629999999999995 25.795 27.589999999999996 20.985 120-124 25.7 26.19 26.884999999999998 21.224999999999998 125-129 24.565 27.839999999999996 26.19 21.404999999999998 130-134 24.995 28.050000000000004 26.07 20.885 135-139 24.395 27.97 25.77 21.865000000000002 140-144 25.28 27.42 24.85 22.45 145-149 24.79 27.425 24.45 23.335 150-151 23.400000000000002 27.037499999999998 23.7875 25.775 >>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 0.0 17 0.0 18 0.0 19 0.0 20 0.0 21 0.0 22 0.0 23 1.0 24 1.0 25 1.0 26 3.0 27 4.5 28 5.5 29 4.5 30 7.0 31 13.5 32 17.5 33 26.5 34 42.0 35 69.5 36 94.0 37 99.5 38 105.0 39 116.0 40 137.0 41 157.0 42 185.5 43 209.5 44 242.5 45 259.5 46 223.5 47 212.0 48 210.0 49 179.5 50 154.0 51 144.5 52 148.0 53 142.5 54 129.5 55 129.5 56 105.5 57 81.5 58 68.0 59 41.5 60 36.5 61 35.0 62 30.0 63 35.5 64 23.0 65 5.0 66 4.0 67 7.5 68 8.0 69 9.0 70 8.5 71 12.5 72 10.0 73 2.0 74 1.5 75 0.5 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 26.0 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10-14 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 0.005 50-54 0.0 55-59 0.0 60-64 0.0 65-69 0.01 70-74 0.01 75-79 0.0 80-84 0.005 85-89 0.0 90-94 0.015 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 82.425 #Duplication Level Percentage of deduplicated Percentage of total 1 91.50743099787687 75.425 2 5.520169851380043 9.1 3 1.0919017288444042 2.7 4 0.5156202608431908 1.7000000000000002 5 0.3033060357901122 1.25 6 0.27297543221110104 1.35 7 0.21231422505307856 1.225 8 0.030330603579011222 0.2 9 0.060661207158022444 0.44999999999999996 >10 0.4549590536851683 5.2749999999999995 >50 0.030330603579011222 1.325 >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 53 1.325 No Hit ATGCGCTCCTGGCCTTAACTGGCCGGGTCGTGCCTCCGGTGCTGTTACTT 27 0.675 No Hit NATTTGCTACTCGGATAACCGTAGTAATTCTAGAGCTAATACGTGCAACA 21 0.525 No Hit CTACTCGGATAACCGTAGTAATTCTAGAGCTAATACGTGCAACAAACCCC 18 0.44999999999999996 No Hit TACCTGGTTGATCCTGCCAGTAGTCATATGCTTGTCTCAAAGATTAAGCC 16 0.4 No Hit ACCTGGGGCTGTAGTATGTTCCAAGGGTTGGGCTGTTCGCCCATTAAAGC 15 0.375 No Hit TATTTTACTTATTCCGTGAATCGGAGGCGGGGCGCTGCCCCTCTTTTTGG 14 0.35000000000000003 No Hit AGACTGTGAAACTGCGAATGGCTCATTAAATCAGTTATAGTTTGTTTGAT 12 0.3 No Hit TATGGACCCGAACCTGGGTGATCTATCCATGACCAGGATGAAGCTTGGGT 12 0.3 No Hit TTAATCAAGAACGAAAGTTGGGGGCTCGAAGACGATCAGATACCGTCCTA 12 0.3 No Hit TAAAAAGCTCGTAGTTGGACTTTGGGTTGGGTCGGCCGGTCCGCCTCAGG 12 0.3 No Hit CACCGAGCGGCGGGTAGAATCCTTTGCAGACGACTTAAATACGCGACGGG 11 0.27499999999999997 No Hit CAGCCAAGCGTTCATAGCGACGTTGCTTTTTGATCCTTCGATGTCGGCTC 11 0.27499999999999997 No Hit CGGTGAAAGAGCCGCGCGGGCCGCCTTGAAGTACAATTCCCACCGAGCGG 10 0.25 No Hit AAAGACGAACAACTGCGAAAGCATTTGCCAAGGATGTTTTCATTAATCAA 10 0.25 No Hit NTGCGCTCCTGGCCTTAACTGGCCGGGTCGTGCCTCCGGTGCTGTTACTT 10 0.25 No Hit CGTTGACTACGTCCCTGCCCTTTGTACACACCGCCCGTCGCTCCTACCGA 9 0.22499999999999998 No Hit TTAGATAAAAGGTCGACGCGGGCTCTGCCCGTTGCTCTGATGATTCATGA 9 0.22499999999999998 No Hit NAAGACGAACAACTGCGAAAGCATTTGCCAAGGATGTTTTCATTAATCAA 8 0.2 No Hit AATGTGATTTCTGCCCAGTGCTCTGAATGTCAAAGTGAAGAAATTCAACC 7 0.17500000000000002 No Hit TATTAGATAAAAGGTCGACGCGGGCTCTGCCCGTTGCTCTGATGATTCAT 7 0.17500000000000002 No Hit AATAGCGTATATTTAAGTTGTTGCAGTTAAAAAGCTCGTAGTTGGACTTT 7 0.17500000000000002 No Hit CGGGCCGCCTTGAAGTACAATTCCCACCGAGCGGCGGGTAGAATCCTTTG 7 0.17500000000000002 No Hit AACTATCATGTTTGATGTGGGATTGGGAGTGGATTAATAATGTAATTTCT 7 0.17500000000000002 No Hit NGGGCCGCCTTGAAGTACAATTCCCACCGAGCGGCGGGTAGAATCCTTTG 7 0.17500000000000002 No Hit TACTCGGATAACCGTAGTAATTCTAGAGCTAATACGTGCAACAAACCCCG 7 0.17500000000000002 No Hit AATCCGGGCTAGATGCGACGCGTGCGCCCGCCGTCCGATTGCCGACCTGC 6 0.15 No Hit ACTTATTCCGTGAATCGGAGGCGGGGCGCTGCCCCTCTTTTTGGACCCAA 6 0.15 No Hit TGGCATCGTCGAGACTGAGAAGAACTATGTCTCCTCCGTAGTCATGGAGG 6 0.15 No Hit AGGGCAAGTCTGGTGCCAGCAGCCGCGGTAATTCCAGCTCCAATAGCGTA 6 0.15 No Hit TGTGGGATTGGGAGTGGATTAATAATGTAATTTCTGATAAATAATCTGTG 6 0.15 No Hit TGCAACAAACCCCGACTTCTGGAAGGGACGCATTTATTAGATAAAAGGTC 6 0.15 No Hit GGGATAACTGGCTTGTGGCAGCCAAGCGTTCATAGCGACGTTGCTTTTTG 6 0.15 No Hit NAGGGACGCATTTATTAGATAAAAGGTCGACGCGGGCTCTGCCCGTTGCT 6 0.15 No Hit TGGAACAAAAGGGTAAAAGCTCGTTTGATTCTGATTTCCAGTACGAATAC 6 0.15 No Hit NAAAAAGCTCGTAGTTGGACTTTGGGTTGGGTCGGCCGGTCCGCCTCAGG 5 0.125 No Hit CAATAACAGGTCTGTGATGCCCTTAGATGTTCTGGGCCGCACGCGCGCTA 5 0.125 No Hit ACTACTTTTAACGTTATTTTACTTATTCCGTGAATCGGAGGCGGGGCGCT 5 0.125 No Hit TAAGCGCGAGTCATCAGCTCGCGTTGACTACGTCCCTGCCCTTTGTACAC 5 0.125 No Hit NAGCCAAGCGTTCATAGCGACGTTGCTTTTTGATCCTTCGATGTCGGCTC 5 0.125 No Hit NGACTGTGAAACTGCGAATGGCTCATTAAATCAGTTATAGTTTGTTTGAT 5 0.125 No Hit GATGTCGGCTCTTCGCCACCTGGGGCTGTAGTATGTTCCAAGGGTTGGGC 5 0.125 No Hit NGCTGATTGAGCTCGAGGAGGCGAAGAAAGCTTACCCTAACTCCTTTATC 5 0.125 No Hit NATCCGGGCTAGATGCGACGCGTGCGCCCGCCGTCCGATTGCCGACCTGC 5 0.125 No Hit GGGCGGTTCGCCGCCGGCGACGTCGCGAGAAGTCCACTGAACCTTATCAT 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 0.025 0.0 0.0 0.0 0.0 2 0.025 0.0 0.0 0.0 0.0 3 0.025 0.0 0.0 0.0 0.0 4 0.025 0.0 0.0 0.0 0.0 5 0.025 0.0 0.0 0.0 0.0 6 0.025 0.0 0.0 0.0 0.0 7 0.025 0.0 0.0 0.0 0.0 8 0.025 0.0 0.0 0.0 0.0 9 0.025 0.0 0.0 0.0 0.0 10-11 0.025 0.0 0.0 0.0 0.0 12-13 0.025 0.0 0.0 0.0 0.0 14-15 0.025 0.0 0.0 0.0 0.0 16-17 0.025 0.0 0.0 0.0 0.0 18-19 0.037500000000000006 0.0 0.0 0.0 0.0 20-21 0.0875 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 0.1 0.0 0.0 0.0 0.0 28-29 0.1375 0.0 0.0 0.0 0.0 30-31 0.15 0.0 0.0 0.0 0.0 32-33 0.1875 0.0 0.0 0.0 0.0 34-35 0.225 0.0 0.0 0.0 0.0 36-37 0.275 0.0 0.0 0.0 0.0 38-39 0.3 0.0 0.0 0.0 0.0 40-41 0.325 0.0 0.0 0.0 0.0 42-43 0.4125 0.0 0.0 0.0 0.0 44-45 0.45 0.0 0.0 0.0 0.0 46-47 0.4625 0.0 0.0 0.0 0.0 48-49 0.4875 0.0 0.0 0.0 0.0 50-51 0.525 0.0 0.0 0.0 0.0 52-53 0.55 0.0 0.0 0.0 0.0 54-55 0.625 0.0 0.0 0.0 0.0 56-57 0.7 0.0 0.0 0.0 0.0 58-59 0.7625 0.0 0.0 0.0 0.0 60-61 0.9 0.0 0.0 0.0 0.0 62-63 1.0375 0.0 0.0 0.0 0.0 64-65 1.1625 0.0 0.0 0.0 0.0 66-67 1.2625 0.0 0.0 0.0 0.0 68-69 1.4625 0.0 0.0 0.0 0.0 70-71 1.6125 0.0 0.0 0.0 0.0 72-73 1.75 0.0 0.0 0.0 0.0 74-75 1.9625 0.0 0.0 0.0 0.0 76-77 2.1875 0.0 0.0 0.0 0.0 78-79 2.3875 0.0 0.0 0.0 0.0 80-81 2.5250000000000004 0.0 0.0 0.0 0.0 82-83 2.7125 0.0 0.0 0.0 0.0 84-85 3.0625 0.0 0.0 0.0 0.0 86-87 3.3125 0.0 0.0 0.0 0.0 88-89 3.7125000000000004 0.0 0.0 0.0 0.0 90-91 4.125 0.0 0.0 0.0 0.0 92-93 4.525 0.0 0.0 0.0 0.0 94-95 4.8625 0.0 0.0 0.0 0.0 96-97 5.324999999999999 0.0 0.0 0.0 0.0 98-99 5.95 0.0 0.0 0.0 0.0 100-101 6.3625 0.0 0.0 0.0 0.0 102-103 6.875 0.0 0.0 0.0 0.0 104-105 7.5625 0.0 0.0 0.0 0.0 106-107 8.2625 0.0 0.0 0.0 0.0 108-109 9.025 0.0 0.0 0.0 0.0 110-111 9.6 0.0 0.0 0.0 0.0 112-113 10.587499999999999 0.0 0.0 0.0 0.0 114-115 11.55 0.0 0.0 0.0 0.0 116-117 12.525 0.0 0.0 0.0 0.0 118-119 13.875 0.0 0.0 0.0 0.0 120-121 14.8625 0.0 0.0 0.0 0.0 122-123 16.2 0.0 0.0 0.0 0.0 124-125 18.1625 0.0 0.0 0.0 0.0 126-127 19.862499999999997 0.0 0.0 0.0 0.0 128-129 21.0875 0.0 0.0 0.0 0.0 130-131 22.2 0.0 0.0 0.0 0.0 132-133 23.6625 0.0 0.0 0.0 0.0 134-135 25.2375 0.0 0.0 0.0 0.0 136-137 26.8375 0.0 0.0 0.0 0.0 138-139 28.425 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TGCGCTC 10 0.0068661636 144.75 2 CTGGCCT 10 0.0068661636 144.75 9 TCCTGGC 10 0.0068661636 144.75 7 CCTGGCC 10 0.0068661636 144.75 8 >>END_MODULE Rejected 2093239 READS because READLEN < 1 Read 2093239 spots for SRR11462712.sra Written 2093239 spots for SRR11462712.sra Rejected 2093239 READS because READLEN < 1 Read 2093239 spots for SRR11462712.sra Written 2093239 spots for SRR11462712.sra Rejected 2093239 READS because READLEN < 1 Read 2093239 spots for SRR11462712.sra Written 2093239 spots for SRR11462712.sra Rejected 2093239 READS because READLEN < 1 Read 2093239 spots for SRR11462712.sra Written 2093239 spots for SRR11462712.sra Rejected 2093239 READS because READLEN < 1 Read 2093239 spots for SRR11462712.sra Written 2093239 spots for SRR11462712.sra Rejected 2093239 READS because READLEN < 1 Read 2093239 spots for SRR11462712.sra Written 2093239 spots for SRR11462712.sra Rejected 2093239 READS because READLEN < 1 Read 2093239 spots for SRR11462712.sra Written 2093239 spots for SRR11462712.sra Rejected 2093241 READS because READLEN < 1 Read 2093241 spots for SRR11462712.sra Written 2093241 spots for SRR11462712.sra Rejected 2093239 READS because READLEN < 1 Read 2093239 spots for SRR11462712.sra Written 2093239 spots for SRR11462712.sra Rejected 2093239 READS because READLEN < 1 Read 2093239 spots for SRR11462712.sra Written 2093239 spots for SRR11462712.sra Rejected 2093239 READS because READLEN < 1 Read 2093239 spots for SRR11462712.sra Written 2093239 spots for SRR11462712.sra Rejected 2093239 READS because READLEN < 1 Read 2093239 spots for SRR11462712.sra Written 2093239 spots for SRR11462712.sra Rejected 2093239 READS because READLEN < 1 Read 2093239 spots for SRR11462712.sra Written 2093239 spots for SRR11462712.sra Rejected 2093239 READS because READLEN < 1 Read 2093239 spots for SRR11462712.sra Written 2093239 spots for SRR11462712.sra Rejected 2093239 READS because READLEN < 1 Read 2093239 spots for SRR11462712.sra Written 2093239 spots for SRR11462712.sra Rejected 2093239 READS because READLEN < 1 Read 2093239 spots for SRR11462712.sra Written 2093239 spots for SRR11462712.sra Rejected 2093239 READS because READLEN < 1 Read 2093239 spots for SRR11462712.sra Written 2093239 spots for SRR11462712.sra Rejected 2093239 READS because READLEN < 1 Read 2093239 spots for SRR11462712.sra Written 2093239 spots for SRR11462712.sra Rejected 2093239 READS because READLEN < 1 Read 2093239 spots for SRR11462712.sra Written 2093239 spots for SRR11462712.sra Rejected 2093239 READS because READLEN < 1 Read 2093239 spots for SRR11462712.sra Written 2093239 spots for SRR11462712.sra SRR ids: ['SRR11462712.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_ej5g2rt_ SRR11462712.sra spots: 41864782 blocks: [[1, 2093239], [2093240, 4186478], [4186479, 6279717], [6279718, 8372956], [8372957, 10466195], [10466196, 12559434], [12559435, 14652673], [14652674, 16745912], [16745913, 18839151], [18839152, 20932390], [20932391, 23025629], [23025630, 25118868], [25118869, 27212107], [27212108, 29305346], [29305347, 31398585], [31398586, 33491824], [33491825, 35585063], [35585064, 37678302], [37678303, 39771541], [39771542, 41864782]] SRR11462712 file size 14205784 SRR11462712 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 SRR11462712 SRR11462712_1.fastq Input file: SRR11462712_1.fastq trimmed: SRR11462712-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 08:32:39 2025 >> started Wed Feb 12 08:33:02 2025 >> done (23.107s) 41864782 reads processed; of these: 9761 ( 0.02%) short reads filtered out after trimming by size control 631 ( 0.00%) empty reads filtered out after trimming by size control 41854390 (99.98%) reads available; of these: 6627160 (15.83%) trimmed reads available after processing 35227230 (84.17%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 2116 0.01% 19 2324 0.01% 20 3239 0.01% 21 2731 0.01% 22 3831 0.01% 23 3561 0.01% 24 3894 0.01% 25 3656 0.01% 26 3727 0.01% 27 5253 0.01% 28 4261 0.01% 29 4459 0.01% 30 4643 0.01% 31 4835 0.01% 32 4923 0.01% 33 5021 0.01% 34 5445 0.01% 35 5559 0.01% 36 5660 0.01% 37 8824 0.02% 38 6458 0.02% 39 6648 0.02% 40 6817 0.02% 41 7064 0.02% 42 8566 0.02% 43 8468 0.02% 44 7770 0.02% 45 8420 0.02% 46 9410 0.02% 47 11350 0.03% 48 10381 0.02% 49 12595 0.03% 50 10668 0.03% 51 11931 0.03% 52 13197 0.03% 53 13994 0.03% 54 16920 0.04% 55 14130 0.03% 56 14995 0.04% 57 18612 0.04% 58 19323 0.05% 59 19103 0.05% 60 19557 0.05% 61 21856 0.05% 62 54610 0.13% 63 20099 0.05% 64 25156 0.06% 65 22785 0.05% 66 26719 0.06% 67 30399 0.07% 68 24828 0.06% 69 31754 0.08% 70 27742 0.07% 71 30882 0.07% 72 38734 0.09% 73 39311 0.09% 74 43382 0.10% 75 44241 0.11% 76 37836 0.09% 77 48591 0.12% 78 45730 0.11% 79 58084 0.14% 80 45271 0.11% 81 48408 0.12% 82 74787 0.18% 83 85623 0.20% 84 62933 0.15% 85 64449 0.15% 86 68459 0.16% 87 110974 0.27% 88 98530 0.24% 89 146136 0.35% 90 84031 0.20% 91 102209 0.24% 92 79443 0.19% 93 83839 0.20% 94 99337 0.24% 95 101145 0.24% 96 125129 0.30% 97 122098 0.29% 98 102405 0.24% 99 113960 0.27% 100 111263 0.27% 101 129973 0.31% 102 147620 0.35% 103 156822 0.37% 104 149524 0.36% 105 136362 0.33% 106 144726 0.35% 107 159712 0.38% 108 154871 0.37% 109 185383 0.44% 110 168157 0.40% 111 183653 0.44% 112 442997 1.06% 113 199182 0.48% 114 195997 0.47% 115 191048 0.46% 116 201894 0.48% 117 234099 0.56% 118 239861 0.57% 119 237772 0.57% 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 35227230 84.17% 41854390 reads passed initial QC criterion=sequence-density sequence-density=13.53 sequence-density-rank=1 fanout-score=41.91 fanout-score-rank=1 prefix-density=16.05 prefix-fanout=35.3 sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACTTAGGCATCTCGTATGCCGTCTTCTGCTTGAA criterion=fanout-score sequence-density=13.53 sequence-density-rank=1 fanout-score=41.91 fanout-score-rank=1 prefix-density=16.05 prefix-fanout=35.3 sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACTTAGGCATCTCGTATGCCGTCTTCTGCTTGAA 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 AGATCGGAAGAGCACACGTCTGAACTCCAGTCACTTAGGCATCTCGTATGCCGTCTTCTGCTTGAA -o SRR11462712 - Input file: STDIN trimmed: SRR11462712-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): AGATCGGAAGAGCACACGTCTGAACTCCAGTCACTTAGGCATCTCGTATGCCGTCTTCTGCTTG -- 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 08:34:35 2025 >> started Wed Feb 12 08:35:16 2025 >> done (40.312s) 35875192 reads processed; of these: 318 ( 0.00%) short reads filtered out after trimming by size control 4 ( 0.00%) empty reads filtered out after trimming by size control 35874870 (100.00%) reads available; of these: 8879412 (24.75%) trimmed reads available after processing 26995458 (75.25%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 1843 0.01% 19 2041 0.01% 20 2834 0.01% 21 2381 0.01% 22 3277 0.01% 23 3132 0.01% 24 3368 0.01% 25 3166 0.01% 26 3261 0.01% 27 4520 0.01% 28 3689 0.01% 29 3896 0.01% 30 4037 0.01% 31 4180 0.01% 32 4243 0.01% 33 4280 0.01% 34 4667 0.01% 35 4862 0.01% 36 4852 0.01% 37 7613 0.02% 38 5556 0.02% 39 5817 0.02% 40 5831 0.02% 41 6081 0.02% 42 7414 0.02% 43 7304 0.02% 44 6719 0.02% 45 7335 0.02% 46 8217 0.02% 47 9790 0.03% 48 8946 0.02% 49 10782 0.03% 50 9261 0.03% 51 10232 0.03% 52 11456 0.03% 53 12408 0.03% 54 14562 0.04% 55 12148 0.03% 56 12688 0.04% 57 16211 0.05% 58 16531 0.05% 59 16536 0.05% 60 16950 0.05% 61 19036 0.05% 62 47117 0.13% 63 17253 0.05% 64 21672 0.06% 65 19647 0.05% 66 23058 0.06% 67 26276 0.07% 68 21437 0.06% 69 27271 0.08% 70 25115 0.07% 71 26630 0.07% 72 33437 0.09% 73 33444 0.09% 74 37408 0.10% 75 37637 0.10% 76 32737 0.09% 77 42153 0.12% 78 40118 0.11% 79 49897 0.14% 80 40372 0.11% 81 43961 0.12% 82 64107 0.18% 83 72462 0.20% 84 52180 0.15% 85 54829 0.15% 86 59196 0.17% 87 95946 0.27% 88 85762 0.24% 89 126013 0.35% 90 81873 0.23% 91 88279 0.25% 92 69803 0.19% 93 72283 0.20% 94 85806 0.24% 95 84647 0.24% 96 108350 0.30% 97 98742 0.28% 98 87854 0.24% 99 98168 0.27% 100 96086 0.27% 101 113378 0.32% 102 127228 0.35% 103 136034 0.38% 104 127893 0.36% 105 118244 0.33% 106 124154 0.35% 107 137411 0.38% 108 137642 0.38% 109 162631 0.45% 110 145875 0.41% 111 158195 0.44% 112 381529 1.06% 113 166558 0.46% 114 166934 0.47% 115 163526 0.46% 116 173491 0.48% 117 195539 0.55% 118 200474 0.56% 119 201308 0.56% 120 240926 0.67% 121 264328 0.74% 122 227562 0.63% 123 299311 0.83% 124 286939 0.80% 125 215703 0.60% 126 256921 0.72% 127 271223 0.76% 128 252093 0.70% 129 230487 0.64% 130 232851 0.65% 131 253357 0.71% 132 336700 0.94% 133 323226 0.90% 134 275590 0.77% 135 304243 0.85% 136 269646 0.75% 137 294438 0.82% 138 314765 0.88% 139 294738 0.82% 140 296308 0.83% 141 276161 0.77% 142 296362 0.83% 143 285992 0.80% 144 279028 0.78% 145 446774 1.25% 146 293127 0.82% 147 385313 1.07% 148 684584 1.91% 149 0 0.00% 150 0 0.00% 151 21485151 59.89% criterion=sequence-density sequence-density=0.59 sequence-density-rank=1 fanout-score=2.04 fanout-score-rank=32 prefix-density=0.58 prefix-fanout=2.0 sequence=CTGCGACTGCGCTGACAAGACCCAGTGTGTCAAGAAGGGAAGCAGCTACACTGCTGGCATCGTCGAGACTGAGAAGAACTATGTCTCCTCCGTAGTCATGGAGGTGCCAGCAG criterion=fanout-score sequence-density=0.02 sequence-density-rank=37 fanout-score=21.21 fanout-score-rank=1 prefix-density=0.07 prefix-fanout=5.3 sequence=CCATTGCTGTGCAAATCCTCTTGAATAGATTCCGTATTCATGGAATTATTCACTTTGGTAGTGCTGGGAGCCTTGATAAAGAAAGTATAGTGCCAGGTGATGTTTCCGTGCCGCTTGCTGTTGCTTTCACAGGAGCTTGGAATTGGAAGAAATTCGGGTCAGATGAAGGGACGCTGAACTTTGGCGAGTTTAATTATCCAGTGAACGGAGAGAACTTGTTGGCTAGCGTAGACTATGATAAAATAAAATTGTTCTCTAAAGGACAATCACCGCAGGATGTTTTCTGGTTTCCCAGCACCACATCCTGGTATAGTGCTGCCACT Started job on | Feb 12 08:35:51 Started mapping on | Feb 12 08:35:51 Finished on | Feb 12 08:37:35 Mapping speed, Million of reads per hour | 1448.79 Number of input reads | 41854068 Average input read length | 139 UNIQUE READS: Uniquely mapped reads number | 28625419 Uniquely mapped reads % | 68.39% Average mapped length | 137.02 Number of splices: Total | 11978819 Number of splices: Annotated (sjdb) | 11758213 Number of splices: GT/AG | 11748524 Number of splices: GC/AG | 182694 Number of splices: AT/AC | 6572 Number of splices: Non-canonical | 41029 Mismatch rate per base, % | 0.43% Deletion rate per base | 0.01% Deletion average length | 2.08 Insertion rate per base | 0.01% Insertion average length | 1.88 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 1494298 % of reads mapped to multiple loci | 3.57% Number of reads mapped to too many loci | 9648249 % of reads mapped to too many loci | 23.05% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 4.74% % of reads unmapped: other | 0.24% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 11734351 11734351 11734351 N_multimapping 1494298 1494298 1494298 N_noFeature 2413830 2880081 27442991 N_ambiguous 828369 112274 713 UnstrandedReadsAssigned:25383220 PositiveStrandReadsAssigned:25633064 NegativeStrandReadsAssigned:1181715 Dataset is classified positive stranded MeadianReadLen=151 20thPercentileLength=125 echo kmer=121 SRR11462712 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: SRR11462712-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 41,854,068 reads, 30,008,157 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,195 rounds 52401 SRR11462712.ke.tsv 34699 SRR11462712.se.tsv 87100 total ==> SRR11462712.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1919 856 15.7339 Potri.005G024800.1.v4.1 1035 936 304 11.456 Potri.004G059700.1.v4.1 961 862 27 1.10483 Potri.007G009000.2.v4.1 1416 1317 0 0 Potri.003G141000.2.v4.1 2943 2844 2674.66 33.1723 Potri.016G087400.1.v4.1 270 171 1395 287.75 Potri.015G069301.1.v4.1 564 465 0 0 Potri.010G195200.1.v4.1 1773 1674 53 1.11675 Potri.012G127500.1.v4.1 977 878 86 3.45494 ==> SRR11462712.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 456 Potri.001G233950.v4.1 2 Potri.001G122700.v4.1 234 Potri.001G212900.v4.1 22 Potri.001G182400.v4.1 4 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 8 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 36 SRR11462712 completed mapping pipeline successfully