Starting /dee2/code/volunteer_pipeline.sh SRR11462708 current disk space = 3049705979904 free memory = 1576013744 SRR11462708 SRAfilesize 72fefe0d5097f6213482ec7567bea93d SRR11462708.sra SRR11462708.sra file validated SRR11462708 is single end SRR11462708 is conventional basespace SRR11462708 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR11462708_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 pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 25.23375 32.0 32.0 32.0 2.0 32.0 2 31.75 32.0 32.0 32.0 32.0 32.0 3 34.8325 37.0 32.0 37.0 32.0 37.0 4 36.2225 37.0 37.0 37.0 32.0 37.0 5 36.495 37.0 37.0 37.0 37.0 37.0 6 39.99375 41.0 41.0 41.0 37.0 41.0 7 40.1485 41.0 41.0 41.0 37.0 41.0 8 40.11225 41.0 41.0 41.0 37.0 41.0 9 40.315 41.0 41.0 41.0 37.0 41.0 10-14 40.3104 41.0 41.0 41.0 40.2 41.0 15-19 40.285000000000004 41.0 41.0 41.0 37.8 41.0 20-24 40.2116 41.0 41.0 41.0 37.8 41.0 25-29 40.1743 41.0 41.0 41.0 37.8 41.0 30-34 40.03975 41.0 41.0 41.0 37.0 41.0 35-39 40.05235 41.0 41.0 41.0 37.8 41.0 40-44 40.095299999999995 41.0 41.0 41.0 37.8 41.0 45-49 40.04485 41.0 41.0 41.0 37.0 41.0 50-54 40.0452 41.0 41.0 41.0 37.0 41.0 55-59 39.992200000000004 41.0 41.0 41.0 37.0 41.0 60-64 40.03235 41.0 41.0 41.0 37.0 41.0 65-69 39.9771 41.0 41.0 41.0 37.0 41.0 70-74 39.8882 41.0 41.0 41.0 37.0 41.0 75-79 39.69465 41.0 40.2 41.0 37.0 41.0 80-84 40.168899999999994 41.0 41.0 41.0 38.6 41.0 85-89 40.18135 41.0 41.0 41.0 41.0 41.0 90-94 39.9974 41.0 41.0 41.0 37.8 41.0 95-99 39.9504 41.0 41.0 41.0 37.0 41.0 100-104 39.91005 41.0 41.0 41.0 37.0 41.0 105-109 39.77045 41.0 41.0 41.0 37.0 41.0 110-114 39.7783 41.0 41.0 41.0 37.0 41.0 115-119 39.68715 41.0 41.0 41.0 37.0 41.0 120-124 39.49335 41.0 41.0 41.0 37.0 41.0 125-129 39.43875 41.0 41.0 41.0 37.0 41.0 130-134 39.27570000000001 41.0 41.0 41.0 37.0 41.0 135-139 39.032 41.0 41.0 41.0 36.0 41.0 140-144 38.935500000000005 41.0 41.0 41.0 35.0 41.0 145-149 38.564800000000005 41.0 41.0 41.0 32.0 41.0 150-151 37.67125 41.0 39.0 41.0 27.0 41.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 1.0 21 0.0 22 0.0 23 2.0 24 1.0 25 2.0 26 3.0 27 4.0 28 18.0 29 21.0 30 28.0 31 30.0 32 35.0 33 68.0 34 60.0 35 84.0 36 81.0 37 146.0 38 147.0 39 243.0 40 3026.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 5.933290570878769 37.139191789608724 42.04618345093009 14.881334188582423 2 27.250000000000004 39.900000000000006 20.674999999999997 12.174999999999999 3 21.15 30.049999999999997 38.224999999999994 10.575 4 35.675000000000004 24.6 26.200000000000003 13.525 5 28.425 26.974999999999998 26.075 18.525 6 25.650000000000002 27.200000000000003 29.599999999999998 17.549999999999997 7 23.724999999999998 26.85 29.175 20.25 8 24.775 25.8 30.85 18.575 9 23.35 22.675 31.624999999999996 22.35 10-14 25.115 25.235000000000003 30.044999999999998 19.605 15-19 24.905 26.99 28.685 19.42 20-24 24.834999999999997 26.825 28.24 20.1 25-29 24.94 26.169999999999998 28.565 20.325 30-34 24.365000000000002 26.265 29.494999999999997 19.875 35-39 24.715 26.119999999999997 28.749999999999996 20.415 40-44 24.08 26.705000000000002 28.71 20.505000000000003 45-49 24.135 26.305 29.354999999999997 20.205000000000002 50-54 25.195 26.655 27.900000000000002 20.25 55-59 24.64 26.71 28.725 19.925 60-64 25.424999999999997 25.755 29.005 19.814999999999998 65-69 25.005 26.565 28.410000000000004 20.02 70-74 24.98 26.795 27.884999999999998 20.34 75-79 24.235 26.255 29.38 20.13 80-84 24.54 26.515 28.17 20.775 85-89 24.18 27.72 28.09 20.01 90-94 25.0 26.674999999999997 28.09 20.235 95-99 24.305 27.205000000000002 28.065 20.424999999999997 100-104 25.130000000000003 26.290000000000003 28.305000000000003 20.275000000000002 105-109 23.965 26.86 28.470000000000002 20.705000000000002 110-114 24.33 27.68 27.6 20.39 115-119 24.32 27.26 27.735 20.685000000000002 120-124 23.7 27.77 27.16 21.37 125-129 24.065 27.49 27.33 21.115000000000002 130-134 23.925 29.044999999999998 26.224999999999998 20.805 135-139 24.015 27.91 26.534999999999997 21.54 140-144 23.505000000000003 28.785 25.72 21.990000000000002 145-149 23.89 28.98 25.169999999999998 21.959999999999997 150-151 23.9875 28.6875 25.525 21.8 >>END_MODULE >>Per sequence GC content pass #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 1.5 23 1.5 24 0.5 25 2.0 26 1.5 27 4.5 28 7.5 29 8.0 30 12.0 31 22.0 32 29.0 33 37.0 34 60.5 35 92.0 36 103.0 37 114.5 38 142.0 39 158.5 40 191.0 41 220.5 42 238.0 43 249.5 44 251.5 45 254.0 46 262.5 47 256.0 48 223.5 49 185.5 50 155.0 51 132.5 52 115.0 53 97.5 54 73.0 55 64.5 56 54.0 57 40.0 58 34.0 59 22.5 60 17.5 61 13.0 62 7.5 63 13.5 64 9.5 65 0.5 66 1.5 67 3.0 68 2.5 69 1.5 70 4.0 71 5.0 72 2.0 73 1.0 74 0.5 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 22.05 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 0.0 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 91.925 #Duplication Level Percentage of deduplicated Percentage of total 1 94.18003807451727 86.575 2 4.405765569757955 8.1 3 0.8158825129181398 2.25 4 0.27196083763937995 1.0 5 0.16317650258362795 0.75 6 0.054392167527875984 0.3 7 0.027196083763937992 0.17500000000000002 8 0.0 0.0 9 0.027196083763937992 0.22499999999999998 >10 0.054392167527875984 0.625 >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 AACTATCATGTTTGATGTGGGATTGGGAGTGGATTAATAATGTAATTTCT 14 0.35000000000000003 No Hit TGTGGGATTGGGAGTGGATTAATAATGTAATTTCTGATAAATAATCTGTG 11 0.27499999999999997 No Hit TATTTGCTACTCGGATAACCGTAGTAATTCTAGAGCTAATACGTGCAACA 9 0.22499999999999998 No Hit CTACTCGGATAACCGTAGTAATTCTAGAGCTAATACGTGCAACAAACCCC 7 0.17500000000000002 No Hit TGGCATCGTCGAGACTGAGAAGAACTATGTCTCCTCCGTAGTCATGGAGG 6 0.15 No Hit AGACTGTGAAACTGCGAATGGCTCATTAAATCAGTTATAGTTTGTTTGAT 6 0.15 No Hit AGTGGATTAATAATGTAATTTCTGATAAATAATCTGTGTTCTTCTGTACT 5 0.125 No Hit GAGACTGAGAAGAACTATGTCTCCTCCGTAGTCATGGAGGTGCCAGCAGC 5 0.125 No Hit TGTTTGTGTCGTCGGTGGTGTTCCGGCAGGGGGGGTGGATTTTATGATTG 5 0.125 No Hit TAATGTAATTTCTGATAAATAATCTGTGTTCTTCTGTACTTGTGGGTGTG 5 0.125 No Hit TAAGGATATTGTAGCTCTCTCTGGGGGCCACACCCTGGGAAGGTGCCACA 5 0.125 No Hit TATTTTACTTATTCCGTGAATCGGAGGCGGGGCGCTGCCCCTCTTTTTGG 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 0.025 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 0.05 0.0 0.0 0.0 0.0 14-15 0.075 0.0 0.0 0.0 0.0 16-17 0.075 0.0 0.0 0.0 0.0 18-19 0.075 0.0 0.0 0.0 0.0 20-21 0.075 0.0 0.0 0.0 0.0 22-23 0.075 0.0 0.0 0.0 0.0 24-25 0.125 0.0 0.0 0.0 0.0 26-27 0.175 0.0 0.0 0.0 0.0 28-29 0.25 0.0 0.0 0.0 0.0 30-31 0.3125 0.0 0.0 0.0 0.0 32-33 0.3625 0.0 0.0 0.0 0.0 34-35 0.4 0.0 0.0 0.0 0.0 36-37 0.4625 0.0 0.0 0.0 0.0 38-39 0.5625 0.0 0.0 0.0 0.0 40-41 0.6125 0.0 0.0 0.0 0.0 42-43 0.6375 0.0 0.0 0.0 0.0 44-45 0.675 0.0 0.0 0.0 0.0 46-47 0.825 0.0 0.0 0.0 0.0 48-49 0.9 0.0 0.0 0.0 0.0 50-51 0.975 0.0 0.0 0.0 0.0 52-53 1.0375 0.0 0.0 0.0 0.0 54-55 1.0875 0.0 0.0 0.0 0.0 56-57 1.175 0.0 0.0 0.0 0.0 58-59 1.3375 0.0 0.0 0.0 0.0 60-61 1.4500000000000002 0.0 0.0 0.0 0.0 62-63 1.5 0.0 0.0 0.0 0.0 64-65 1.5499999999999998 0.0 0.0 0.0 0.0 66-67 1.6875 0.0 0.0 0.0 0.0 68-69 1.775 0.0 0.0 0.0 0.0 70-71 1.925 0.0 0.0 0.0 0.0 72-73 2.0625 0.0 0.0 0.0 0.0 74-75 2.3125 0.0 0.0 0.0 0.0 76-77 2.5375 0.0 0.0 0.0 0.0 78-79 2.7125 0.0 0.0 0.0 0.0 80-81 2.925 0.0 0.0 0.0 0.0 82-83 3.0875 0.0 0.0 0.0 0.0 84-85 3.425 0.0 0.0 0.0 0.0 86-87 3.8625 0.0 0.0 0.0 0.0 88-89 4.3 0.0 0.0 0.0 0.0 90-91 4.65 0.0 0.0 0.0 0.0 92-93 5.0875 0.0 0.0 0.0 0.0 94-95 5.475 0.0 0.0 0.0 0.0 96-97 5.7875 0.0 0.0 0.0 0.0 98-99 6.199999999999999 0.0 0.0 0.0 0.0 100-101 6.725 0.0 0.0 0.0 0.0 102-103 7.275 0.0 0.0 0.0 0.0 104-105 7.675000000000001 0.0 0.0 0.0 0.0 106-107 8.425 0.0 0.0 0.0 0.0 108-109 9.1375 0.0 0.0 0.0 0.0 110-111 10.075 0.0 0.0 0.0 0.0 112-113 10.8375 0.0 0.0 0.0 0.0 114-115 11.825 0.0 0.0 0.0 0.0 116-117 12.675 0.0 0.0 0.0 0.0 118-119 13.7 0.0 0.0 0.0 0.0 120-121 14.475 0.0 0.0 0.0 0.0 122-123 15.5625 0.0 0.0 0.0 0.0 124-125 16.375 0.0 0.0 0.0 0.0 126-127 17.4375 0.0 0.0 0.0 0.0 128-129 18.7375 0.0 0.0 0.0 0.0 130-131 19.8375 0.0 0.0 0.0 0.0 132-133 21.2 0.0 0.0 0.0 0.0 134-135 22.75 0.0 0.0 0.0 0.0 136-137 24.225 0.0 0.0 0.0 0.0 138-139 25.6 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position AAAAAAA 125 4.3215096E-4 11.583 145 AGATCGG 160 4.0129563E-4 9.049219 140-144 GATCGGA 160 0.004122832 9.049218 145 >>END_MODULE Rejected 1799928 READS because READLEN < 1 Read 1799928 spots for SRR11462708.sra Written 1799928 spots for SRR11462708.sra Rejected 1799928 READS because READLEN < 1 Read 1799928 spots for SRR11462708.sra Written 1799928 spots for SRR11462708.sra Rejected 1799943 READS because READLEN < 1 Read 1799943 spots for SRR11462708.sra Written 1799943 spots for SRR11462708.sra Rejected 1799928 READS because READLEN < 1 Read 1799928 spots for SRR11462708.sra Written 1799928 spots for SRR11462708.sra Rejected 1799928 READS because READLEN < 1 Read 1799928 spots for SRR11462708.sra Written 1799928 spots for SRR11462708.sra Rejected 1799928 READS because READLEN < 1 Read 1799928 spots for SRR11462708.sra Written 1799928 spots for SRR11462708.sra Rejected 1799928 READS because READLEN < 1 Read 1799928 spots for SRR11462708.sra Written 1799928 spots for SRR11462708.sra Rejected 1799928 READS because READLEN < 1 Read 1799928 spots for SRR11462708.sra Written 1799928 spots for SRR11462708.sra Rejected 1799928 READS because READLEN < 1 Read 1799928 spots for SRR11462708.sra Written 1799928 spots for SRR11462708.sra Rejected 1799928 READS because READLEN < 1 Read 1799928 spots for SRR11462708.sra Written 1799928 spots for SRR11462708.sra Rejected 1799928 READS because READLEN < 1 Read 1799928 spots for SRR11462708.sra Written 1799928 spots for SRR11462708.sra Rejected 1799928 READS because READLEN < 1 Read 1799928 spots for SRR11462708.sra Written 1799928 spots for SRR11462708.sra Rejected 1799928 READS because READLEN < 1 Read 1799928 spots for SRR11462708.sra Written 1799928 spots for SRR11462708.sra Rejected 1799928 READS because READLEN < 1 Read 1799928 spots for SRR11462708.sra Written 1799928 spots for SRR11462708.sra Rejected 1799928 READS because READLEN < 1 Read 1799928 spots for SRR11462708.sra Written 1799928 spots for SRR11462708.sra Rejected 1799928 READS because READLEN < 1 Read 1799928 spots for SRR11462708.sra Written 1799928 spots for SRR11462708.sra Rejected 1799928 READS because READLEN < 1 Read 1799928 spots for SRR11462708.sra Written 1799928 spots for SRR11462708.sra Rejected 1799928 READS because READLEN < 1 Read 1799928 spots for SRR11462708.sra Written 1799928 spots for SRR11462708.sra Rejected 1799928 READS because READLEN < 1 Read 1799928 spots for SRR11462708.sra Written 1799928 spots for SRR11462708.sra Rejected 1799928 READS because READLEN < 1 Read 1799928 spots for SRR11462708.sra Written 1799928 spots for SRR11462708.sra SRR ids: ['SRR11462708.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_jnxye9kc SRR11462708.sra spots: 35998575 blocks: [[1, 1799928], [1799929, 3599856], [3599857, 5399784], [5399785, 7199712], [7199713, 8999640], [8999641, 10799568], [10799569, 12599496], [12599497, 14399424], [14399425, 16199352], [16199353, 17999280], [17999281, 19799208], [19799209, 21599136], [21599137, 23399064], [23399065, 25198992], [25198993, 26998920], [26998921, 28798848], [28798849, 30598776], [30598777, 32398704], [32398705, 34198632], [34198633, 35998575]] SRR11462708 file size 12212190 SRR11462708 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 SRR11462708 SRR11462708_1.fastq Input file: SRR11462708_1.fastq trimmed: SRR11462708-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 07:48:23 2025 >> started Wed Feb 12 07:48:43 2025 >> done (20.192s) 35998575 reads processed; of these: 15722 ( 0.04%) short reads filtered out after trimming by size control 1881 ( 0.01%) empty reads filtered out after trimming by size control 35980972 (99.95%) reads available; of these: 5003731 (13.91%) trimmed reads available after processing 30977241 (86.09%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 3779 0.01% 19 4138 0.01% 20 4692 0.01% 21 4859 0.01% 22 5521 0.02% 23 6020 0.02% 24 6576 0.02% 25 6365 0.02% 26 6454 0.02% 27 7278 0.02% 28 7211 0.02% 29 7862 0.02% 30 7929 0.02% 31 8034 0.02% 32 7776 0.02% 33 8273 0.02% 34 8902 0.02% 35 9235 0.03% 36 9288 0.03% 37 11747 0.03% 38 9828 0.03% 39 10215 0.03% 40 10132 0.03% 41 10468 0.03% 42 11861 0.03% 43 11329 0.03% 44 11362 0.03% 45 12448 0.03% 46 13018 0.04% 47 16985 0.05% 48 14851 0.04% 49 16416 0.05% 50 14346 0.04% 51 15387 0.04% 52 15842 0.04% 53 16179 0.04% 54 17862 0.05% 55 17654 0.05% 56 18531 0.05% 57 21379 0.06% 58 19198 0.05% 59 21420 0.06% 60 21982 0.06% 61 22185 0.06% 62 34353 0.10% 63 23390 0.07% 64 24761 0.07% 65 23888 0.07% 66 25149 0.07% 67 27961 0.08% 68 26633 0.07% 69 30909 0.09% 70 29533 0.08% 71 32946 0.09% 72 34354 0.10% 73 35812 0.10% 74 38743 0.11% 75 36769 0.10% 76 34324 0.10% 77 38118 0.11% 78 39697 0.11% 79 45434 0.13% 80 41930 0.12% 81 44372 0.12% 82 45337 0.13% 83 47246 0.13% 84 52915 0.15% 85 52953 0.15% 86 57569 0.16% 87 57941 0.16% 88 57384 0.16% 89 72052 0.20% 90 61462 0.17% 91 64141 0.18% 92 63444 0.18% 93 67476 0.19% 94 75798 0.21% 95 76142 0.21% 96 82316 0.23% 97 85783 0.24% 98 81427 0.23% 99 85775 0.24% 100 87192 0.24% 101 92875 0.26% 102 110405 0.31% 103 102591 0.29% 104 101913 0.28% 105 106280 0.30% 106 110681 0.31% 107 117681 0.33% 108 121590 0.34% 109 138561 0.39% 110 127908 0.36% 111 132987 0.37% 112 169327 0.47% 113 141562 0.39% 114 146109 0.41% 115 148804 0.41% 116 154185 0.43% 117 169102 0.47% 118 171483 0.48% 119 183441 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 30977241 86.09% 35980972 reads passed initial QC criterion=sequence-density sequence-density=11.37 sequence-density-rank=1 fanout-score=40.42 fanout-score-rank=1 prefix-density=13.67 prefix-fanout=33.6 sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGATCATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAA criterion=fanout-score sequence-density=11.37 sequence-density-rank=1 fanout-score=40.42 fanout-score-rank=1 prefix-density=13.67 prefix-fanout=33.6 sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGATCATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAA 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 AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGATCATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAA -o SRR11462708 - Input file: STDIN trimmed: SRR11462708-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGATCATCTCGTATGCCGTCTTCTGCTTG -- 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 07:50:03 2025 >> started Wed Feb 12 07:50:36 2025 >> done (33.829s) 29984143 reads processed; of these: 550 ( 0.00%) short reads filtered out after trimming by size control 9 ( 0.00%) empty reads filtered out after trimming by size control 29983584 (100.00%) reads available; of these: 6793344 (22.66%) trimmed reads available after processing 23190240 (77.34%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 3252 0.01% 19 3547 0.01% 20 4025 0.01% 21 4127 0.01% 22 4698 0.02% 23 5086 0.02% 24 5463 0.02% 25 5366 0.02% 26 5479 0.02% 27 6107 0.02% 28 5977 0.02% 29 6643 0.02% 30 6701 0.02% 31 6802 0.02% 32 6521 0.02% 33 6917 0.02% 34 7451 0.02% 35 7843 0.03% 36 7839 0.03% 37 9897 0.03% 38 8270 0.03% 39 8579 0.03% 40 8555 0.03% 41 8854 0.03% 42 9915 0.03% 43 9463 0.03% 44 9486 0.03% 45 10541 0.04% 46 11002 0.04% 47 14292 0.05% 48 12390 0.04% 49 13779 0.05% 50 12130 0.04% 51 12860 0.04% 52 13314 0.04% 53 13687 0.05% 54 14976 0.05% 55 14893 0.05% 56 15436 0.05% 57 18007 0.06% 58 16040 0.05% 59 17956 0.06% 60 18536 0.06% 61 18795 0.06% 62 28958 0.10% 63 19629 0.07% 64 20707 0.07% 65 20097 0.07% 66 21193 0.07% 67 23578 0.08% 68 22495 0.08% 69 25969 0.09% 70 24857 0.08% 71 27439 0.09% 72 29002 0.10% 73 30295 0.10% 74 32540 0.11% 75 30772 0.10% 76 29047 0.10% 77 32140 0.11% 78 33291 0.11% 79 37918 0.13% 80 34962 0.12% 81 39123 0.13% 82 37888 0.13% 83 39689 0.13% 84 42453 0.14% 85 44442 0.15% 86 48587 0.16% 87 49206 0.16% 88 48425 0.16% 89 60342 0.20% 90 52308 0.17% 91 53812 0.18% 92 53140 0.18% 93 56005 0.19% 94 63400 0.21% 95 63679 0.21% 96 69395 0.23% 97 71732 0.24% 98 68585 0.23% 99 72140 0.24% 100 73236 0.24% 101 78183 0.26% 102 92531 0.31% 103 86576 0.29% 104 85833 0.29% 105 89582 0.30% 106 92502 0.31% 107 98300 0.33% 108 102475 0.34% 109 116613 0.39% 110 107644 0.36% 111 111096 0.37% 112 142895 0.48% 113 117867 0.39% 114 122952 0.41% 115 123723 0.41% 116 128658 0.43% 117 136049 0.45% 118 138336 0.46% 119 150421 0.50% 120 156718 0.52% 121 159251 0.53% 122 158533 0.53% 123 215619 0.72% 124 197553 0.66% 125 171032 0.57% 126 183012 0.61% 127 186451 0.62% 128 183381 0.61% 129 181757 0.61% 130 183545 0.61% 131 197776 0.66% 132 207598 0.69% 133 215694 0.72% 134 203419 0.68% 135 219592 0.73% 136 206452 0.69% 137 235321 0.78% 138 258466 0.86% 139 230525 0.77% 140 246214 0.82% 141 217888 0.73% 142 234871 0.78% 143 240177 0.80% 144 232818 0.78% 145 257716 0.86% 146 247220 0.82% 147 352151 1.17% 148 653241 2.18% 149 0 0.00% 150 0 0.00% 151 19163384 63.91% criterion=sequence-density sequence-density=0.75 sequence-density-rank=1 fanout-score=2.47 fanout-score-rank=33 prefix-density=0.80 prefix-fanout=2.3 sequence=TGCAAGTGCGGCAG criterion=fanout-score sequence-density=0.03 sequence-density-rank=35 fanout-score=29.49 fanout-score-rank=1 prefix-density=0.30 prefix-fanout=2.8 sequence=AACTTTGAAGGCCGAAGAGGGGAAAGGTTCCATGTGAACGGCACTTGCACATGGGTTAGTCGATCCTAAGAGACGGGGGAAGCCCGTCCGACAGCGCGTTCGCGCGCGAGCTTCGAAAGGGAATCGGGTTAAAATTCCTGAACCGGGACGTGGCGGCTGACGGCAACGTTAGGGAGTCCGGAGACGTCGGCGGGGGCCTCGGGAAGAGTTATCTTTTCTGTTTAACAGCCCGCCCACCCTGGAAACGACTTAGTCGGAGGTAGGGTCCAGCGGCTGGAAGAGCACCGCACGTCGCGTGGTGTCCGGTGCGCCCCCGGCGGCCCTTGAAAATCCGGAGGACCGAGTGCCTCCCACGCCCGGTCGTACTCATAACCGCATCAGGTCTCCAAGGTGAACAGCCTCTGGTCGATGGAACAATGTAGGCAAGGGAAGTCGGCAAAATGGATCCGTAACCTCGGGAAAAGGATTGGCTCTGAGGGCTGGGCTCGGGGGTCCCAGTCCCGAACCCGTC Started job on | Feb 12 07:51:11 Started mapping on | Feb 12 07:51:11 Finished on | Feb 12 07:52:17 Mapping speed, Million of reads per hour | 1962.57 Number of input reads | 35980413 Average input read length | 140 UNIQUE READS: Uniquely mapped reads number | 31484092 Uniquely mapped reads % | 87.50% Average mapped length | 137.96 Number of splices: Total | 14778552 Number of splices: Annotated (sjdb) | 14471396 Number of splices: GT/AG | 14500423 Number of splices: GC/AG | 210360 Number of splices: AT/AC | 10007 Number of splices: Non-canonical | 57762 Mismatch rate per base, % | 0.35% Deletion rate per base | 0.02% Deletion average length | 2.13 Insertion rate per base | 0.01% Insertion average length | 1.90 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 967837 % of reads mapped to multiple loci | 2.69% Number of reads mapped to too many loci | 1879805 % of reads mapped to too many loci | 5.22% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 4.51% % of reads unmapped: other | 0.08% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 3528484 3528484 3528484 N_multimapping 967837 967837 967837 N_noFeature 1499152 2167057 30500856 N_ambiguous 435123 119732 782 UnstrandedReadsAssigned:29549817 PositiveStrandReadsAssigned:29197303 NegativeStrandReadsAssigned:982454 Dataset is classified positive stranded MeadianReadLen=151 20thPercentileLength=130 echo kmer=125 SRR11462708 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: SRR11462708-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 35,980,413 reads, 30,415,407 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,211 rounds 52401 SRR11462708.ke.tsv 34699 SRR11462708.se.tsv 87100 total ==> SRR11462708.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1919 1511 28.3623 Potri.005G024800.1.v4.1 1035 936 510 19.6267 Potri.004G059700.1.v4.1 961 862 55 2.2983 Potri.007G009000.2.v4.1 1416 1317 0 0 Potri.003G141000.2.v4.1 2943 2844 2346.62 29.7211 Potri.016G087400.1.v4.1 270 171 2556 538.415 Potri.015G069301.1.v4.1 564 465 0 0 Potri.010G195200.1.v4.1 1773 1674 169 3.6365 Potri.012G127500.1.v4.1 977 878 246 10.0924 ==> SRR11462708.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 403 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 173 Potri.001G212900.v4.1 19 Potri.001G182400.v4.1 1 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 5 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 22 SRR11462708 completed mapping pipeline successfully