Starting /dee2/code/volunteer_pipeline.sh SRR11462730 current disk space = 3051113529344 free memory = 1581440656 SRR11462730 SRAfilesize 39e40ad502977e15941a30a474d7ee03 SRR11462730.sra SRR11462730.sra file validated SRR11462730 is single end SRR11462730 is conventional basespace SRR11462730 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR11462730_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 43 >>END_MODULE >>Per base sequence quality fail #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 23.23125 32.0 2.0 32.0 2.0 32.0 2 31.79375 32.0 32.0 32.0 32.0 32.0 3 34.6375 37.0 32.0 37.0 32.0 37.0 4 36.22625 37.0 37.0 37.0 32.0 37.0 5 36.57625 37.0 37.0 37.0 37.0 37.0 6 40.076 41.0 41.0 41.0 37.0 41.0 7 40.162 41.0 41.0 41.0 37.0 41.0 8 40.18925 41.0 41.0 41.0 37.0 41.0 9 40.269 41.0 41.0 41.0 37.0 41.0 10-14 40.29075 41.0 41.0 41.0 38.6 41.0 15-19 40.2351 41.0 41.0 41.0 37.8 41.0 20-24 40.202299999999994 41.0 41.0 41.0 37.8 41.0 25-29 40.09415 41.0 41.0 41.0 37.0 41.0 30-34 39.99575 41.0 41.0 41.0 37.0 41.0 35-39 39.9914 41.0 41.0 41.0 37.0 41.0 40-44 40.044349999999994 41.0 41.0 41.0 37.0 41.0 45-49 39.996500000000005 41.0 41.0 41.0 37.0 41.0 50-54 39.9849 41.0 41.0 41.0 37.0 41.0 55-59 39.8586 41.0 41.0 41.0 37.0 41.0 60-64 39.81185 41.0 41.0 41.0 37.0 41.0 65-69 39.83305 41.0 41.0 41.0 37.0 41.0 70-74 39.71355 41.0 41.0 41.0 37.0 41.0 75-79 39.6303 41.0 40.2 41.0 37.0 41.0 80-84 40.061350000000004 41.0 41.0 41.0 37.0 41.0 85-89 39.91725 41.0 41.0 41.0 37.0 41.0 90-94 39.965349999999994 41.0 41.0 41.0 37.0 41.0 95-99 39.85225 41.0 41.0 41.0 37.0 41.0 100-104 39.784800000000004 41.0 41.0 41.0 37.0 41.0 105-109 39.783350000000006 41.0 41.0 41.0 37.0 41.0 110-114 39.681200000000004 41.0 41.0 41.0 37.0 41.0 115-119 39.722449999999995 41.0 41.0 41.0 37.0 41.0 120-124 39.4928 41.0 41.0 41.0 37.0 41.0 125-129 39.341249999999995 41.0 41.0 41.0 37.0 41.0 130-134 39.15795 41.0 41.0 41.0 36.0 41.0 135-139 39.0151 41.0 41.0 41.0 35.0 41.0 140-144 38.8467 41.0 41.0 41.0 34.0 41.0 145-149 38.556799999999996 41.0 41.0 41.0 32.0 41.0 150-151 37.817375 41.0 39.0 41.0 29.5 41.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 22 2.0 23 1.0 24 1.0 25 4.0 26 3.0 27 7.0 28 12.0 29 20.0 30 28.0 31 37.0 32 44.0 33 58.0 34 79.0 35 83.0 36 106.0 37 124.0 38 140.0 39 301.0 40 2950.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 5.528341497550734 38.1035689293212 41.322603219034285 15.04548635409377 2 25.650000000000002 41.675000000000004 20.925 11.75 3 22.3 29.275000000000002 38.5 9.925 4 35.675000000000004 25.324999999999996 25.05 13.950000000000001 5 28.349999999999998 26.474999999999998 26.900000000000002 18.275 6 25.3 25.275 30.425 19.0 7 22.1 25.424999999999997 31.45 21.025 8 24.4 24.375 32.300000000000004 18.925 9 22.125 23.799999999999997 33.925 20.150000000000002 10-14 24.89 25.405 30.18 19.525000000000002 15-19 24.011200560028 26.77133856692835 29.961498074903748 19.255962798139905 20-24 24.044999999999998 27.700000000000003 29.025000000000002 19.23 25-29 23.93 26.810000000000002 30.005 19.255 30-34 24.041202060103007 27.02135106755338 28.891444572228615 20.046002300115006 35-39 24.45 26.305 29.615000000000002 19.63 40-44 23.674999999999997 26.755000000000003 29.549999999999997 20.02 45-49 23.84619230961548 27.346367318365917 28.72643632181609 20.081004050202512 50-54 24.226211310565528 26.416320816040802 29.186459322966147 20.171008550427523 55-59 24.34621731086554 27.366368318415923 28.821441072053606 19.46597329866493 60-64 23.941197059852993 26.836341817090855 30.211510575528777 19.01095054752738 65-69 23.915 26.995 29.244999999999997 19.845 70-74 24.961248062403122 26.936346817340866 28.7714385719286 19.330966548327417 75-79 23.49 27.27 29.134999999999998 20.105 80-84 23.93 27.735 28.794999999999998 19.54 85-89 23.666183309165458 27.74138706935347 29.106455322766138 19.485974298714936 90-94 24.441222061103055 26.651332566628334 29.066453322666135 19.84099204960248 95-99 23.794999999999998 27.38 28.715000000000003 20.11 100-104 24.23 27.315 28.749999999999996 19.705000000000002 105-109 23.97 27.700000000000003 28.255000000000003 20.075000000000003 110-114 24.47 27.26 27.93 20.34 115-119 23.974999999999998 27.325 28.29 20.41 120-124 23.965 27.805000000000003 27.639999999999997 20.59 125-129 23.78 27.35 27.644999999999996 21.224999999999998 130-134 23.925 28.555000000000003 26.729999999999997 20.79 135-139 24.445 28.050000000000004 26.240000000000002 21.265 140-144 24.13 28.444999999999997 26.005 21.42 145-149 24.08 27.85 26.11 21.959999999999997 150-151 23.4125 28.512500000000003 26.474999999999998 21.6 >>END_MODULE >>Per sequence GC content pass #GC Content Count 0 1.0 1 0.5 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 1.0 21 1.0 22 0.0 23 2.0 24 2.5 25 1.0 26 1.0 27 2.5 28 10.0 29 17.5 30 22.0 31 35.0 32 48.0 33 49.0 34 61.0 35 90.5 36 114.5 37 139.0 38 172.5 39 198.0 40 217.5 41 236.0 42 255.0 43 272.0 44 275.0 45 249.0 46 238.5 47 228.0 48 191.0 49 166.0 50 141.0 51 113.5 52 89.0 53 73.5 54 58.5 55 61.0 56 54.0 57 34.0 58 25.0 59 14.0 60 12.0 61 8.5 62 5.0 63 5.0 64 3.5 65 2.5 66 1.0 67 0.0 68 0.0 69 1.0 70 1.0 71 0.0 72 0.0 73 0.0 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 28.549999999999997 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 0.005 20-24 0.0 25-29 0.0 30-34 0.005 35-39 0.0 40-44 0.0 45-49 0.005 50-54 0.005 55-59 0.005 60-64 0.005 65-69 0.0 70-74 0.005 75-79 0.0 80-84 0.0 85-89 0.005 90-94 0.005 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 92.2 #Duplication Level Percentage of deduplicated Percentage of total 1 94.46854663774403 87.1 2 4.528199566160521 8.35 3 0.46095444685466375 1.275 4 0.2440347071583514 0.8999999999999999 5 0.10845986984815618 0.5 6 0.027114967462039046 0.15 7 0.05422993492407809 0.35000000000000003 8 0.0 0.0 9 0.027114967462039046 0.22499999999999998 >10 0.08134490238611713 1.15 >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 TGGCATCGTCGAGACTGAGAAGAACTATGTCTCCTCCGTAGTCATGGAGG 21 0.525 No Hit AGCTGAGAACGATGGCAAGTGCAACTGCGGTACTGGCTGCACTTGCACTA 13 0.325 No Hit TATTTGCTACTCGGATAACCGTAGTAATTCTAGAGCTAATACGTGCAACA 12 0.3 No Hit NGGCATCGTCGAGACTGAGAAGAACTATGTCTCCTCCGTAGTCATGGAGG 9 0.22499999999999998 No Hit TGTGGGATTGGGAGTGGATTAATAATGTAATTTCTGATAAATAATCTGTG 7 0.17500000000000002 No Hit TACCTGGTTGATCCTGCCAGTAGTCATATGCTTGTCTCAAAGATTAAGCC 7 0.17500000000000002 No Hit NATTTGCTACTCGGATAACCGTAGTAATTCTAGAGCTAATACGTGCAACA 6 0.15 No Hit ATGCGCTCCTGGCCTTAACTGGCCGGGTCGTGCCTCCGGTGCTGTTACTT 5 0.125 No Hit AAAGACGAACAACTGCGAAAGCATTTGCCAAGGATGTTTTCATTAATCAA 5 0.125 No Hit CATACTCCAAGTCTTTTAGTTCATCCATTTAAGCTTAATCAATCAATCAT 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 0.0 0.0 0.0 0.0 0.0 20-21 0.037500000000000006 0.0 0.0 0.0 0.0 22-23 0.05 0.0 0.0 0.0 0.0 24-25 0.05 0.0 0.0 0.0 0.0 26-27 0.05 0.0 0.0 0.0 0.0 28-29 0.0625 0.0 0.0 0.0 0.0 30-31 0.075 0.0 0.0 0.0 0.0 32-33 0.0875 0.0 0.0 0.0 0.0 34-35 0.1 0.0 0.0 0.0 0.0 36-37 0.1 0.0 0.0 0.0 0.0 38-39 0.1 0.0 0.0 0.0 0.0 40-41 0.175 0.0 0.0 0.0 0.0 42-43 0.2 0.0 0.0 0.0 0.0 44-45 0.2 0.0 0.0 0.0 0.0 46-47 0.23750000000000002 0.0 0.0 0.0 0.0 48-49 0.325 0.0 0.0 0.0 0.0 50-51 0.325 0.0 0.0 0.0 0.0 52-53 0.325 0.0 0.0 0.0 0.0 54-55 0.36250000000000004 0.0 0.0 0.0 0.0 56-57 0.4 0.0 0.0 0.0 0.0 58-59 0.4 0.0 0.0 0.0 0.0 60-61 0.4125 0.0 0.0 0.0 0.0 62-63 0.5249999999999999 0.0 0.0 0.0 0.0 64-65 0.7375 0.0 0.0 0.0 0.0 66-67 0.875 0.0 0.0 0.0 0.0 68-69 1.0375 0.0 0.0 0.0 0.0 70-71 1.1375 0.0 0.0 0.0 0.0 72-73 1.225 0.0 0.0 0.0 0.0 74-75 1.325 0.0 0.0 0.0 0.0 76-77 1.4249999999999998 0.0 0.0 0.0 0.0 78-79 1.55 0.0 0.0 0.0 0.0 80-81 1.7125 0.0 0.0 0.0 0.0 82-83 1.9125 0.0 0.0 0.0 0.0 84-85 2.2375 0.0 0.0 0.0 0.0 86-87 2.5999999999999996 0.0 0.0 0.0 0.0 88-89 2.8625 0.0 0.0 0.0 0.0 90-91 3.25 0.0 0.0 0.0 0.0 92-93 3.675 0.0 0.0 0.0 0.0 94-95 4.1875 0.0 0.0 0.0 0.0 96-97 4.512499999999999 0.0 0.0 0.0 0.0 98-99 4.9 0.0 0.0 0.0 0.0 100-101 5.512499999999999 0.0 0.0 0.0 0.0 102-103 6.387499999999999 0.0 0.0 0.0 0.0 104-105 7.0125 0.0 0.0 0.0 0.0 106-107 7.7375 0.0 0.0 0.0 0.0 108-109 8.65 0.0 0.0 0.0 0.0 110-111 9.6375 0.0 0.0 0.0 0.0 112-113 10.537500000000001 0.0 0.0 0.0 0.0 114-115 11.5 0.0 0.0 0.0 0.0 116-117 12.3875 0.0 0.0 0.0 0.0 118-119 13.5 0.0 0.0 0.0 0.0 120-121 14.6875 0.0 0.0 0.0 0.0 122-123 16.0375 0.0 0.0 0.0 0.0 124-125 17.4375 0.0 0.0 0.0 0.0 126-127 18.85 0.0 0.0 0.0 0.0 128-129 20.1125 0.0 0.0 0.0 0.0 130-131 21.262500000000003 0.0 0.0 0.0 0.0 132-133 22.5 0.0 0.0 0.0 0.0 134-135 24.1375 0.0 0.0 0.0 0.0 136-137 25.65 0.0 0.0 0.0 0.0 138-139 27.275 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position CGGTAGC 35 0.0033374364 62.024994 145 ACGGTAG 35 0.0035757453 20.675 140-144 >>END_MODULE Rejected 1664680 READS because READLEN < 1 Read 1664680 spots for SRR11462730.sra Written 1664680 spots for SRR11462730.sra Rejected 1664682 READS because READLEN < 1 Read 1664682 spots for SRR11462730.sra Written 1664682 spots for SRR11462730.sra Rejected 1664680 READS because READLEN < 1 Read 1664680 spots for SRR11462730.sra Written 1664680 spots for SRR11462730.sra Rejected 1664680 READS because READLEN < 1 Read 1664680 spots for SRR11462730.sra Written 1664680 spots for SRR11462730.sra Rejected 1664680 READS because READLEN < 1 Read 1664680 spots for SRR11462730.sra Written 1664680 spots for SRR11462730.sra Rejected 1664680 READS because READLEN < 1 Read 1664680 spots for SRR11462730.sra Written 1664680 spots for SRR11462730.sra Rejected 1664680 READS because READLEN < 1 Read 1664680 spots for SRR11462730.sra Written 1664680 spots for SRR11462730.sra Rejected 1664680 READS because READLEN < 1 Read 1664680 spots for SRR11462730.sra Written 1664680 spots for SRR11462730.sra Rejected 1664680 READS because READLEN < 1 Read 1664680 spots for SRR11462730.sra Written 1664680 spots for SRR11462730.sra Rejected 1664680 READS because READLEN < 1 Read 1664680 spots for SRR11462730.sra Written 1664680 spots for SRR11462730.sra Rejected 1664680 READS because READLEN < 1 Read 1664680 spots for SRR11462730.sra Written 1664680 spots for SRR11462730.sra Rejected 1664680 READS because READLEN < 1 Read 1664680 spots for SRR11462730.sra Written 1664680 spots for SRR11462730.sra Rejected 1664680 READS because READLEN < 1 Read 1664680 spots for SRR11462730.sra Written 1664680 spots for SRR11462730.sra Rejected 1664680 READS because READLEN < 1 Read 1664680 spots for SRR11462730.sra Written 1664680 spots for SRR11462730.sra Rejected 1664680 READS because READLEN < 1 Read 1664680 spots for SRR11462730.sra Written 1664680 spots for SRR11462730.sra Rejected 1664680 READS because READLEN < 1 Read 1664680 spots for SRR11462730.sra Written 1664680 spots for SRR11462730.sra Rejected 1664680 READS because READLEN < 1 Read 1664680 spots for SRR11462730.sra Written 1664680 spots for SRR11462730.sra Rejected 1664680 READS because READLEN < 1 Read 1664680 spots for SRR11462730.sra Written 1664680 spots for SRR11462730.sra Rejected 1664680 READS because READLEN < 1 Read 1664680 spots for SRR11462730.sra Written 1664680 spots for SRR11462730.sra Rejected 1664680 READS because READLEN < 1 Read 1664680 spots for SRR11462730.sra Written 1664680 spots for SRR11462730.sra SRR ids: ['SRR11462730.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_41v7zw66 SRR11462730.sra spots: 33293602 blocks: [[1, 1664680], [1664681, 3329360], [3329361, 4994040], [4994041, 6658720], [6658721, 8323400], [8323401, 9988080], [9988081, 11652760], [11652761, 13317440], [13317441, 14982120], [14982121, 16646800], [16646801, 18311480], [18311481, 19976160], [19976161, 21640840], [21640841, 23305520], [23305521, 24970200], [24970201, 26634880], [26634881, 28299560], [28299561, 29964240], [29964241, 31628920], [31628921, 33293602]] SRR11462730 file size 11292922 SRR11462730 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 SRR11462730 SRR11462730_1.fastq Input file: SRR11462730_1.fastq trimmed: SRR11462730-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 10:53:51 2025 >> started Wed Feb 12 10:54:10 2025 >> done (19.739s) 33293602 reads processed; of these: 4484 ( 0.01%) short reads filtered out after trimming by size control 502 ( 0.00%) empty reads filtered out after trimming by size control 33288616 (99.99%) reads available; of these: 5008911 (15.05%) trimmed reads available after processing 28279705 (84.95%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 1086 0.00% 19 1233 0.00% 20 1317 0.00% 21 1422 0.00% 22 1542 0.00% 23 1885 0.01% 24 1922 0.01% 25 2036 0.01% 26 2000 0.01% 27 2667 0.01% 28 2399 0.01% 29 2664 0.01% 30 2741 0.01% 31 2861 0.01% 32 2828 0.01% 33 3108 0.01% 34 3383 0.01% 35 3355 0.01% 36 3604 0.01% 37 4285 0.01% 38 3728 0.01% 39 4059 0.01% 40 4208 0.01% 41 4309 0.01% 42 4999 0.02% 43 4990 0.01% 44 5103 0.02% 45 6920 0.02% 46 6356 0.02% 47 8989 0.03% 48 7721 0.02% 49 12114 0.04% 50 7396 0.02% 51 8320 0.02% 52 8123 0.02% 53 8627 0.03% 54 10017 0.03% 55 9725 0.03% 56 10932 0.03% 57 11999 0.04% 58 11385 0.03% 59 11796 0.04% 60 13680 0.04% 61 13639 0.04% 62 28353 0.09% 63 14868 0.04% 64 16611 0.05% 65 16023 0.05% 66 16889 0.05% 67 19016 0.06% 68 18282 0.05% 69 24804 0.07% 70 20955 0.06% 71 23799 0.07% 72 26437 0.08% 73 30441 0.09% 74 32507 0.10% 75 29323 0.09% 76 27812 0.08% 77 32433 0.10% 78 32192 0.10% 79 39901 0.12% 80 35733 0.11% 81 37201 0.11% 82 40782 0.12% 83 41836 0.13% 84 47135 0.14% 85 50297 0.15% 86 54340 0.16% 87 54927 0.17% 88 54060 0.16% 89 113866 0.34% 90 65705 0.20% 91 69956 0.21% 92 66217 0.20% 93 71778 0.22% 94 79974 0.24% 95 73834 0.22% 96 87703 0.26% 97 88507 0.27% 98 86561 0.26% 99 91873 0.28% 100 93799 0.28% 101 102082 0.31% 102 145787 0.44% 103 110260 0.33% 104 110795 0.33% 105 116834 0.35% 106 121591 0.37% 107 129180 0.39% 108 141607 0.43% 109 164481 0.49% 110 152243 0.46% 111 149368 0.45% 112 243552 0.73% 113 163269 0.49% 114 160593 0.48% 115 166545 0.50% 116 164475 0.49% 117 182417 0.55% 118 188855 0.57% 119 190759 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 15 0.00% 151 28279705 84.95% 33288616 reads passed initial QC criterion=sequence-density sequence-density=12.65 sequence-density-rank=1 fanout-score=39.09 fanout-score-rank=1 prefix-density=15.05 prefix-fanout=32.9 sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACGGTAGCATCTCGTATGCCGTCTTCTGCTTG criterion=fanout-score sequence-density=12.65 sequence-density-rank=1 fanout-score=39.09 fanout-score-rank=1 prefix-density=15.05 prefix-fanout=32.9 sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACGGTAGCATCTCGTATGCCGTCTTCTGCTTG 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 AGATCGGAAGAGCACACGTCTGAACTCCAGTCACGGTAGCATCTCGTATGCCGTCTTCTGCTTG -o SRR11462730 - Input file: STDIN trimmed: SRR11462730-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): AGATCGGAAGAGCACACGTCTGAACTCCAGTCACGGTAGCATCTCGTATGCCGTCTTCTGCTTG -- 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 10:55:23 2025 >> started Wed Feb 12 10:55:55 2025 >> done (31.709s) 28167291 reads processed; of these: 151 ( 0.00%) short reads filtered out after trimming by size control 6 ( 0.00%) empty reads filtered out after trimming by size control 28167134 (100.00%) reads available; of these: 6735536 (23.91%) trimmed reads available after processing 21431598 (76.09%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 916 0.00% 19 1048 0.00% 20 1144 0.00% 21 1225 0.00% 22 1371 0.00% 23 1646 0.01% 24 1650 0.01% 25 1755 0.01% 26 1728 0.01% 27 2294 0.01% 28 2017 0.01% 29 2244 0.01% 30 2289 0.01% 31 2441 0.01% 32 2425 0.01% 33 2642 0.01% 34 2913 0.01% 35 2896 0.01% 36 3072 0.01% 37 3670 0.01% 38 3166 0.01% 39 3449 0.01% 40 3605 0.01% 41 3671 0.01% 42 4331 0.02% 43 4288 0.02% 44 4454 0.02% 45 5959 0.02% 46 5438 0.02% 47 7615 0.03% 48 6523 0.02% 49 10290 0.04% 50 6376 0.02% 51 7101 0.03% 52 6862 0.02% 53 7326 0.03% 54 8542 0.03% 55 8303 0.03% 56 9281 0.03% 57 10305 0.04% 58 9712 0.03% 59 10090 0.04% 60 11771 0.04% 61 11604 0.04% 62 24160 0.09% 63 12763 0.05% 64 14158 0.05% 65 13650 0.05% 66 14465 0.05% 67 16307 0.06% 68 15692 0.06% 69 21139 0.08% 70 18069 0.06% 71 20290 0.07% 72 22548 0.08% 73 26085 0.09% 74 27781 0.10% 75 24942 0.09% 76 23679 0.08% 77 27576 0.10% 78 27543 0.10% 79 34279 0.12% 80 30326 0.11% 81 32387 0.11% 82 34880 0.12% 83 35916 0.13% 84 39411 0.14% 85 42995 0.15% 86 46257 0.16% 87 46960 0.17% 88 46400 0.16% 89 96744 0.34% 90 56507 0.20% 91 60025 0.21% 92 57078 0.20% 93 61076 0.22% 94 67663 0.24% 95 62224 0.22% 96 74721 0.27% 97 75203 0.27% 98 74388 0.26% 99 79047 0.28% 100 79591 0.28% 101 86987 0.31% 102 123872 0.44% 103 94371 0.34% 104 94527 0.34% 105 99323 0.35% 106 103526 0.37% 107 109354 0.39% 108 120636 0.43% 109 139912 0.50% 110 129503 0.46% 111 127065 0.45% 112 208976 0.74% 113 138772 0.49% 114 136789 0.49% 115 140137 0.50% 116 139829 0.50% 117 149312 0.53% 118 154497 0.55% 119 158191 0.56% 120 172504 0.61% 121 177756 0.63% 122 172652 0.61% 123 221220 0.79% 124 198082 0.70% 125 177448 0.63% 126 184607 0.66% 127 213396 0.76% 128 190567 0.68% 129 193445 0.69% 130 194023 0.69% 131 196593 0.70% 132 214624 0.76% 133 250812 0.89% 134 207239 0.74% 135 225754 0.80% 136 209133 0.74% 137 213066 0.76% 138 234217 0.83% 139 217905 0.77% 140 249235 0.88% 141 215388 0.76% 142 222725 0.79% 143 235087 0.83% 144 228677 0.81% 145 226918 0.81% 146 226304 0.80% 147 320019 1.14% 148 591616 2.10% 149 0 0.00% 150 9 0.00% 151 17334161 61.54% criterion=sequence-density sequence-density=0.85 sequence-density-rank=1 fanout-score=2.15 fanout-score-rank=34 prefix-density=0.87 prefix-fanout=2.1 sequence=CTGCGACTGCGCTGACAAGACCCAGTGTGTCAAGAAGGGAAGCAGCTACACTGCTGGCATCGTCGAGACTGAGAAGAACTATGTCTCCTCCGTAGTCATGGAGGTGCCAGCAGCTGAGAACGATGGCAAGTGCAACTGCGGTACTGGCTGCACTTGCACTACCTGCACATGCGGTCATTAAGCAAGCACATCAACTATCATGTTTGATGTGGGATTGGGAGTGGATTAATAATGTAATTTCTGATAAATAATCTGTGTTCTTCTGTACTTGTGGGTGTGGAGTGAACAAACAAAAGTGTCCGTGAGTGTCTTTATCTTTGTGTCTTCTTCATTGTTATGTATTGGCCATGTCTGTGGCCTCTGGTGTGGTTTTAATGAAGTCTTATAATTAGTGTAGTACTCTGCT criterion=fanout-score sequence-density=0.01 sequence-density-rank=39 fanout-score=56.12 fanout-score-rank=1 prefix-density=0.11 prefix-fanout=3.8 sequence=TCTGTTTGTGTCGTCGGTGGTGTTCCGGCAGGGGGGGTGGATTTTATGATTGTTATCTCTACTGTTACTGAGCATGTAATTTAATTTGTCCCAAGTTTTTCTTCCTTCATTTGTAGTCTCAAATGAAACTG Started job on | Feb 12 10:57:09 Started mapping on | Feb 12 10:57:09 Finished on | Feb 12 10:58:19 Mapping speed, Million of reads per hour | 1711.98 Number of input reads | 33288459 Average input read length | 132 UNIQUE READS: Uniquely mapped reads number | 28788098 Uniquely mapped reads % | 86.48% Average mapped length | 130.36 Number of splices: Total | 11628776 Number of splices: Annotated (sjdb) | 11345477 Number of splices: GT/AG | 11434365 Number of splices: GC/AG | 157565 Number of splices: AT/AC | 6863 Number of splices: Non-canonical | 29983 Mismatch rate per base, % | 0.37% Deletion rate per base | 0.02% Deletion average length | 2.11 Insertion rate per base | 0.01% Insertion average length | 1.82 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 817550 % of reads mapped to multiple loci | 2.46% Number of reads mapped to too many loci | 1143009 % of reads mapped to too many loci | 3.43% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 7.58% % of reads unmapped: other | 0.05% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 3682811 3682811 3682811 N_multimapping 817550 817550 817550 N_noFeature 1761355 2213289 27960628 N_ambiguous 485275 109828 695 UnstrandedReadsAssigned:26541468 PositiveStrandReadsAssigned:26464981 NegativeStrandReadsAssigned:826775 Dataset is classified positive stranded MeadianReadLen=143 20thPercentileLength=119 echo kmer=115 SRR11462730 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: SRR11462730-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 33,288,459 reads, 27,042,670 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,215 rounds 52401 SRR11462730.ke.tsv 34699 SRR11462730.se.tsv 87100 total ==> SRR11462730.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1919 2506 53.0703 Potri.005G024800.1.v4.1 1035 936 973 42.2457 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 2599.52 37.1457 Potri.016G087400.1.v4.1 270 171 1314 312.281 Potri.015G069301.1.v4.1 564 465 0 0 Potri.010G195200.1.v4.1 1773 1674 1711.97 41.561 Potri.012G127500.1.v4.1 977 878 16 0.740579 ==> SRR11462730.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 0 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 191 Potri.001G212900.v4.1 0 Potri.001G182400.v4.1 0 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 1 Potri.001G416900.v4.1 2 Potri.001G452600.v4.1 55 SRR11462730 completed mapping pipeline successfully