Starting /dee2/code/volunteer_pipeline.sh SRR11462736 current disk space = 3051115823104 free memory = 1432629812 SRR11462736 SRAfilesize 19e14060055149a6df3112a8ed8a82fe SRR11462736.sra SRR11462736.sra file validated SRR11462736 is single end SRR11462736 is conventional basespace SRR11462736 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR11462736_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 23.19125 32.0 2.0 32.0 2.0 32.0 2 31.76875 32.0 32.0 32.0 32.0 32.0 3 34.6875 37.0 32.0 37.0 32.0 37.0 4 36.34625 37.0 37.0 37.0 32.0 37.0 5 36.3925 37.0 37.0 37.0 37.0 37.0 6 40.00625 41.0 41.0 41.0 37.0 41.0 7 40.18025 41.0 41.0 41.0 37.0 41.0 8 40.30525 41.0 41.0 41.0 37.0 41.0 9 40.26175 41.0 41.0 41.0 37.0 41.0 10-14 40.3464 41.0 41.0 41.0 40.2 41.0 15-19 40.30335 41.0 41.0 41.0 40.2 41.0 20-24 40.25295 41.0 41.0 41.0 38.6 41.0 25-29 40.2203 41.0 41.0 41.0 40.2 41.0 30-34 40.142199999999995 41.0 41.0 41.0 38.6 41.0 35-39 40.05495 41.0 41.0 41.0 37.0 41.0 40-44 40.083450000000006 41.0 41.0 41.0 37.0 41.0 45-49 40.108050000000006 41.0 41.0 41.0 39.4 41.0 50-54 40.116299999999995 41.0 41.0 41.0 39.4 41.0 55-59 40.05505000000001 41.0 41.0 41.0 37.0 41.0 60-64 40.0097 41.0 41.0 41.0 37.0 41.0 65-69 40.0105 41.0 41.0 41.0 37.0 41.0 70-74 39.7799 41.0 41.0 41.0 37.0 41.0 75-79 39.7633 41.0 40.2 41.0 37.0 41.0 80-84 40.224900000000005 41.0 41.0 41.0 40.2 41.0 85-89 40.151599999999995 41.0 41.0 41.0 37.8 41.0 90-94 40.087 41.0 41.0 41.0 37.8 41.0 95-99 40.033849999999994 41.0 41.0 41.0 37.0 41.0 100-104 39.8815 41.0 41.0 41.0 37.0 41.0 105-109 39.81595 41.0 41.0 41.0 37.0 41.0 110-114 39.7846 41.0 41.0 41.0 37.0 41.0 115-119 39.74075 41.0 41.0 41.0 37.0 41.0 120-124 39.57985 41.0 41.0 41.0 37.0 41.0 125-129 39.43455 41.0 41.0 41.0 37.0 41.0 130-134 39.29815 41.0 41.0 41.0 37.0 41.0 135-139 38.92125 41.0 41.0 41.0 34.0 41.0 140-144 38.9893 41.0 41.0 41.0 36.0 41.0 145-149 38.66845000000001 41.0 41.0 41.0 33.0 41.0 150-151 37.64575 41.0 39.0 41.0 29.5 41.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 18 1.0 19 0.0 20 0.0 21 0.0 22 0.0 23 0.0 24 0.0 25 4.0 26 5.0 27 6.0 28 12.0 29 21.0 30 18.0 31 30.0 32 36.0 33 36.0 34 75.0 35 81.0 36 103.0 37 150.0 38 162.0 39 296.0 40 2964.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 4.683677036001399 37.36455784690668 42.18804613771409 15.763718979377838 2 25.650000000000002 41.525 21.5 11.325000000000001 3 23.225 28.175 38.6 10.0 4 33.033258314578646 25.18129532383096 26.331582895723933 15.453863465866466 5 26.05 28.925 27.750000000000004 17.275 6 24.95 27.0 30.575000000000003 17.474999999999998 7 21.65 28.025 30.5 19.825 8 25.5 26.575 30.75 17.175 9 22.25 23.125 33.1 21.525 10-14 24.474999999999998 26.655 29.880000000000003 18.990000000000002 15-19 24.104999999999997 27.195000000000004 29.18 19.52 20-24 24.085 27.92 28.73 19.265 25-29 24.19 26.900000000000002 29.49 19.42 30-34 23.525 26.58 29.2 20.695 35-39 23.835 26.810000000000002 29.325000000000003 20.03 40-44 23.515 26.66 29.915000000000003 19.91 45-49 23.635 26.740000000000002 29.74 19.885 50-54 23.735 27.315 28.720000000000002 20.23 55-59 24.755 27.474999999999998 27.950000000000003 19.82 60-64 24.33 26.96 29.01 19.7 65-69 24.41 27.195000000000004 28.549999999999997 19.845 70-74 24.695 27.405 28.075 19.825 75-79 23.755000000000003 26.5 29.520000000000003 20.225 80-84 23.810000000000002 27.42 28.565 20.205000000000002 85-89 23.474999999999998 27.944999999999997 28.665000000000003 19.915 90-94 24.635 26.584999999999997 28.560000000000002 20.22 95-99 23.865 27.015 28.470000000000002 20.65 100-104 24.02 27.345000000000002 28.49 20.145 105-109 22.89 27.55 28.405 21.154999999999998 110-114 23.315 27.785 28.99 19.91 115-119 24.165 27.175 28.465 20.195 120-124 23.335 28.4 27.63 20.635 125-129 23.599999999999998 28.549999999999997 26.855 20.995 130-134 23.945 29.354999999999997 26.395000000000003 20.305 135-139 23.685000000000002 28.425 26.479999999999997 21.41 140-144 24.265 29.080000000000002 25.430000000000003 21.224999999999998 145-149 23.419999999999998 29.665000000000003 25.074999999999996 21.84 150-151 22.2 29.5 26.3 22.0 >>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 0.5 13 0.5 14 0.0 15 0.0 16 0.0 17 0.0 18 0.0 19 0.0 20 0.0 21 1.0 22 2.0 23 1.5 24 1.0 25 2.5 26 6.0 27 8.0 28 15.0 29 18.0 30 15.5 31 26.5 32 43.0 33 59.0 34 74.5 35 105.0 36 130.5 37 143.0 38 156.5 39 172.5 40 203.0 41 225.5 42 251.5 43 258.0 44 266.0 45 269.0 46 236.5 47 214.5 48 185.0 49 154.0 50 135.0 51 106.0 52 95.5 53 94.0 54 79.5 55 78.0 56 50.0 57 23.5 58 22.5 59 14.5 60 11.5 61 7.5 62 7.0 63 9.0 64 4.0 65 0.5 66 1.5 67 3.5 68 2.0 69 0.5 70 2.5 71 3.0 72 1.0 73 0.0 74 0.0 75 1.5 76 1.5 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 28.475 2 0.0 3 0.0 4 0.025 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 92.2 #Duplication Level Percentage of deduplicated Percentage of total 1 95.52603036876356 88.075 2 3.606290672451193 6.65 3 0.32537960954446854 0.8999999999999999 4 0.16268980477223427 0.6 5 0.08134490238611713 0.375 6 0.08134490238611713 0.44999999999999996 7 0.0 0.0 8 0.027114967462039046 0.2 9 0.05422993492407809 0.44999999999999996 >10 0.13557483731019523 2.3 >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 36 0.8999999999999999 No Hit TATTTGCTACTCGGATAACCGTAGTAATTCTAGAGCTAATACGTGCAACA 17 0.42500000000000004 No Hit NGGCATCGTCGAGACTGAGAAGAACTATGTCTCCTCCGTAGTCATGGAGG 16 0.4 No Hit NATTTGCTACTCGGATAACCGTAGTAATTCTAGAGCTAATACGTGCAACA 12 0.3 No Hit ATGCGCTCCTGGCCTTAACTGGCCGGGTCGTGCCTCCGGTGCTGTTACTT 11 0.27499999999999997 No Hit GAGACTGAGAAGAACTATGTCTCCTCCGTAGTCATGGAGGTGCCAGCAGC 9 0.22499999999999998 No Hit TACCTGGTTGATCCTGCCAGTAGTCATATGCTTGTCTCAAAGATTAAGCC 9 0.22499999999999998 No Hit NTGCGCTCCTGGCCTTAACTGGCCGGGTCGTGCCTCCGGTGCTGTTACTT 8 0.2 No Hit TATTAGATAAAAGGTCGACGCGGGCTCTGCCCGTTGCTCTGATGATTCAT 6 0.15 No Hit TCTTGGCAAGATTGTGAAGGGGACTGTGGATCAGTCTGATGCTAGCTTCC 6 0.15 No Hit AACTATCATGTTTGATGTGGGATTGGGAGTGGATTAATAATGTAATTTCT 6 0.15 No Hit TGTGGGATTGGGAGTGGATTAATAATGTAATTTCTGATAAATAATCTGTG 5 0.125 No Hit CTACTCGGATAACCGTAGTAATTCTAGAGCTAATACGTGCAACAAACCCC 5 0.125 No Hit AACTGCGGTACTGGCTGCACTTGCACTACCTGCACATGCGGTCATTAAGC 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 0.0125 0.0 0.0 0.0 0.0 12-13 0.037500000000000006 0.0 0.0 0.0 0.0 14-15 0.05 0.0 0.0 0.0 0.0 16-17 0.0625 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 0.15 0.0 0.0 0.0 0.0 28-29 0.16249999999999998 0.0 0.0 0.0 0.0 30-31 0.21250000000000002 0.0 0.0 0.0 0.0 32-33 0.275 0.0 0.0 0.0 0.0 34-35 0.35 0.0 0.0 0.0 0.0 36-37 0.4 0.0 0.0 0.0 0.0 38-39 0.475 0.0 0.0 0.0 0.0 40-41 0.525 0.0 0.0 0.0 0.0 42-43 0.55 0.0 0.0 0.0 0.0 44-45 0.6125 0.0 0.0 0.0 0.0 46-47 0.75 0.0 0.0 0.0 0.0 48-49 0.8125 0.0 0.0 0.0 0.0 50-51 0.8374999999999999 0.0 0.0 0.0 0.0 52-53 0.8875 0.0 0.0 0.0 0.0 54-55 0.925 0.0 0.0 0.0 0.0 56-57 1.025 0.0 0.0 0.0 0.0 58-59 1.15 0.0 0.0 0.0 0.0 60-61 1.375 0.0 0.0 0.0 0.0 62-63 1.475 0.0 0.0 0.0 0.0 64-65 1.65 0.0 0.0 0.0 0.0 66-67 1.775 0.0 0.0 0.0 0.0 68-69 1.9249999999999998 0.0 0.0 0.0 0.0 70-71 2.1875 0.0 0.0 0.0 0.0 72-73 2.35 0.0 0.0 0.0 0.0 74-75 2.625 0.0 0.0 0.0 0.0 76-77 2.8125 0.0 0.0 0.0 0.0 78-79 3.0250000000000004 0.0 0.0 0.0 0.0 80-81 3.375 0.0 0.0 0.0 0.0 82-83 3.75 0.0 0.0 0.0 0.0 84-85 3.9625 0.0 0.0 0.0 0.0 86-87 4.2375 0.0 0.0 0.0 0.0 88-89 4.4625 0.0 0.0 0.0 0.0 90-91 4.7 0.0 0.0 0.0 0.0 92-93 5.35 0.0 0.0 0.0 0.0 94-95 6.0375 0.0 0.0 0.0 0.0 96-97 6.575 0.0 0.0 0.0 0.0 98-99 7.125 0.0 0.0 0.0 0.0 100-101 7.6 0.0 0.0 0.0 0.0 102-103 8.225000000000001 0.0 0.0 0.0 0.0 104-105 8.8375 0.0 0.0 0.0 0.0 106-107 9.6 0.0 0.0 0.0 0.0 108-109 10.399999999999999 0.0 0.0 0.0 0.0 110-111 11.45 0.0 0.0 0.0 0.0 112-113 12.8625 0.0 0.0 0.0 0.0 114-115 14.100000000000001 0.0 0.0 0.0 0.0 116-117 15.0125 0.0 0.0 0.0 0.0 118-119 15.975 0.0 0.0 0.0 0.0 120-121 17.3 0.0 0.0 0.0 0.0 122-123 18.625 0.0 0.0 0.0 0.0 124-125 20.1625 0.0 0.0 0.0 0.0 126-127 21.275 0.0 0.0 0.0 0.0 128-129 22.7375 0.0 0.0 0.0 0.0 130-131 24.5875 0.0 0.0 0.0 0.0 132-133 26.475 0.0 0.0 0.0 0.0 134-135 28.325 0.0 0.0 0.0 0.0 136-137 30.1 0.0 0.0 0.0 0.0 138-139 31.8875 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position CACGGCC 15 1.1497979E-4 144.725 145 TGATTGT 10 0.00686971 144.72499 7 TTGGAGA 10 0.00686971 144.72499 145 ACTCGGA 20 3.6149065E-4 108.54375 9 TACTCGG 20 3.6149065E-4 108.54375 8 GCTACTC 25 8.7792624E-4 86.835 6 TTTGCTA 25 8.7792624E-4 86.835 3 CTACTCG 25 8.7792624E-4 86.835 7 TGCTACT 30 0.0018109404 72.3625 5 TTGCTAC 30 0.0018109404 72.3625 4 ATTTGCT 40 0.005663731 54.271873 2 AAAAAAA 245 0.0035383475 6.497857 135-139 >>END_MODULE Rejected 1739115 READS because READLEN < 1 Read 1739115 spots for SRR11462736.sra Written 1739115 spots for SRR11462736.sra Rejected 1739115 READS because READLEN < 1 Read 1739115 spots for SRR11462736.sra Written 1739115 spots for SRR11462736.sra Rejected 1739115 READS because READLEN < 1 Read 1739115 spots for SRR11462736.sra Written 1739115 spots for SRR11462736.sra Rejected 1739115 READS because READLEN < 1 Read 1739115 spots for SRR11462736.sra Written 1739115 spots for SRR11462736.sra Rejected 1739115 READS because READLEN < 1 Read 1739115 spots for SRR11462736.sra Written 1739115 spots for SRR11462736.sra Rejected 1739115 READS because READLEN < 1 Read 1739115 spots for SRR11462736.sra Written 1739115 spots for SRR11462736.sra Rejected 1739115 READS because READLEN < 1 Read 1739115 spots for SRR11462736.sra Written 1739115 spots for SRR11462736.sra Rejected 1739115 READS because READLEN < 1 Read 1739115 spots for SRR11462736.sra Written 1739115 spots for SRR11462736.sra Rejected 1739115 READS because READLEN < 1 Read 1739115 spots for SRR11462736.sra Written 1739115 spots for SRR11462736.sra Rejected 1739115 READS because READLEN < 1 Read 1739115 spots for SRR11462736.sra Written 1739115 spots for SRR11462736.sra Rejected 1739115 READS because READLEN < 1 Read 1739115 spots for SRR11462736.sra Written 1739115 spots for SRR11462736.sra Rejected 1739115 READS because READLEN < 1 Read 1739115 spots for SRR11462736.sra Written 1739115 spots for SRR11462736.sra Rejected 1739115 READS because READLEN < 1 Read 1739115 spots for SRR11462736.sra Written 1739115 spots for SRR11462736.sra Rejected 1739123 READS because READLEN < 1 Read 1739123 spots for SRR11462736.sra Written 1739123 spots for SRR11462736.sra Rejected 1739115 READS because READLEN < 1 Read 1739115 spots for SRR11462736.sra Written 1739115 spots for SRR11462736.sra Rejected 1739115 READS because READLEN < 1 Read 1739115 spots for SRR11462736.sra Written 1739115 spots for SRR11462736.sra Rejected 1739115 READS because READLEN < 1 Read 1739115 spots for SRR11462736.sra Written 1739115 spots for SRR11462736.sra Rejected 1739115 READS because READLEN < 1 Read 1739115 spots for SRR11462736.sra Written 1739115 spots for SRR11462736.sra Rejected 1739115 READS because READLEN < 1 Read 1739115 spots for SRR11462736.sra Written 1739115 spots for SRR11462736.sra Rejected 1739115 READS because READLEN < 1 Read 1739115 spots for SRR11462736.sra Written 1739115 spots for SRR11462736.sra SRR ids: ['SRR11462736.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_3217_25t SRR11462736.sra spots: 34782308 blocks: [[1, 1739115], [1739116, 3478230], [3478231, 5217345], [5217346, 6956460], [6956461, 8695575], [8695576, 10434690], [10434691, 12173805], [12173806, 13912920], [13912921, 15652035], [15652036, 17391150], [17391151, 19130265], [19130266, 20869380], [20869381, 22608495], [22608496, 24347610], [24347611, 26086725], [26086726, 27825840], [27825841, 29564955], [29564956, 31304070], [31304071, 33043185], [33043186, 34782308]] SRR11462736 file size 11798849 SRR11462736 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 SRR11462736 SRR11462736_1.fastq Input file: SRR11462736_1.fastq trimmed: SRR11462736-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 10:49:21 2025 >> started Wed Feb 12 10:49:42 2025 >> done (20.718s) 34782308 reads processed; of these: 11932 ( 0.03%) short reads filtered out after trimming by size control 1810 ( 0.01%) empty reads filtered out after trimming by size control 34768566 (99.96%) reads available; of these: 6133322 (17.64%) trimmed reads available after processing 28635244 (82.36%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 2912 0.01% 19 3057 0.01% 20 3404 0.01% 21 3625 0.01% 22 4446 0.01% 23 4447 0.01% 24 4930 0.01% 25 4961 0.01% 26 5248 0.02% 27 6138 0.02% 28 5961 0.02% 29 6438 0.02% 30 6726 0.02% 31 6914 0.02% 32 6873 0.02% 33 7524 0.02% 34 8269 0.02% 35 8108 0.02% 36 8335 0.02% 37 9989 0.03% 38 8963 0.03% 39 9426 0.03% 40 9655 0.03% 41 9842 0.03% 42 11068 0.03% 43 11189 0.03% 44 11092 0.03% 45 12454 0.04% 46 13288 0.04% 47 18004 0.05% 48 15441 0.04% 49 17109 0.05% 50 14511 0.04% 51 15753 0.05% 52 15537 0.04% 53 16619 0.05% 54 18187 0.05% 55 18055 0.05% 56 19118 0.05% 57 22612 0.07% 58 20218 0.06% 59 21193 0.06% 60 23373 0.07% 61 23584 0.07% 62 41177 0.12% 63 25889 0.07% 64 26854 0.08% 65 25967 0.07% 66 27580 0.08% 67 29716 0.09% 68 29615 0.09% 69 36821 0.11% 70 33346 0.10% 71 36335 0.10% 72 38470 0.11% 73 46956 0.14% 74 46840 0.13% 75 41073 0.12% 76 40700 0.12% 77 47973 0.14% 78 46221 0.13% 79 56234 0.16% 80 49445 0.14% 81 50119 0.14% 82 55132 0.16% 83 57274 0.16% 84 61383 0.18% 85 62417 0.18% 86 65765 0.19% 87 72433 0.21% 88 68157 0.20% 89 91043 0.26% 90 78033 0.22% 91 82509 0.24% 92 80116 0.23% 93 83780 0.24% 94 88267 0.25% 95 91089 0.26% 96 103871 0.30% 97 113121 0.33% 98 103519 0.30% 99 109149 0.31% 100 111730 0.32% 101 120075 0.35% 102 145302 0.42% 103 128018 0.37% 104 130656 0.38% 105 135824 0.39% 106 141458 0.41% 107 146898 0.42% 108 156462 0.45% 109 173394 0.50% 110 164677 0.47% 111 170809 0.49% 112 275165 0.79% 113 182897 0.53% 114 183889 0.53% 115 185277 0.53% 116 193873 0.56% 117 208834 0.60% 118 209286 0.60% 119 229705 0.66% 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% 150 108 0.00% 151 28635244 82.36% 34768566 reads passed initial QC criterion=sequence-density sequence-density=14.47 sequence-density-rank=1 fanout-score=38.21 fanout-score-rank=1 prefix-density=17.18 prefix-fanout=32.2 sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACGTGAAAATCTCGTATGCCGTCTTCTGCTTGAAAA criterion=fanout-score sequence-density=14.47 sequence-density-rank=1 fanout-score=38.21 fanout-score-rank=1 prefix-density=17.18 prefix-fanout=32.2 sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACGTGAAAATCTCGTATGCCGTCTTCTGCTTGAAAA 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 AGATCGGAAGAGCACACGTCTGAACTCCAGTCACGTGAAAATCTCGTATGCCGTCTTCTGCTTGAAAA -o SRR11462736 - Input file: STDIN trimmed: SRR11462736-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): AGATCGGAAGAGCACACGTCTGAACTCCAGTCACGTGAAAATCTCGTATGCCGTCTTCTGCTTG -- 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 10:50:59 2025 >> started Wed Feb 12 10:51:37 2025 >> done (37.941s) 30132757 reads processed; of these: 420 ( 0.00%) short reads filtered out after trimming by size control 14 ( 0.00%) empty reads filtered out after trimming by size control 30132323 (100.00%) reads available; of these: 8040386 (26.68%) trimmed reads available after processing 22091937 (73.32%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 2566 0.01% 19 2776 0.01% 20 2983 0.01% 21 3183 0.01% 22 3846 0.01% 23 3933 0.01% 24 4343 0.01% 25 4362 0.01% 26 4597 0.02% 27 5342 0.02% 28 5264 0.02% 29 5677 0.02% 30 5917 0.02% 31 6089 0.02% 32 5998 0.02% 33 6635 0.02% 34 7150 0.02% 35 7088 0.02% 36 7309 0.02% 37 8797 0.03% 38 7854 0.03% 39 8234 0.03% 40 8481 0.03% 41 8599 0.03% 42 9565 0.03% 43 9809 0.03% 44 9714 0.03% 45 10915 0.04% 46 11686 0.04% 47 15747 0.05% 48 13385 0.04% 49 14964 0.05% 50 12743 0.04% 51 13838 0.05% 52 13712 0.05% 53 14539 0.05% 54 15773 0.05% 55 15759 0.05% 56 16534 0.05% 57 19824 0.07% 58 17634 0.06% 59 18585 0.06% 60 20515 0.07% 61 20752 0.07% 62 36148 0.12% 63 22662 0.08% 64 23457 0.08% 65 22582 0.07% 66 24123 0.08% 67 25917 0.09% 68 26017 0.09% 69 32226 0.11% 70 29363 0.10% 71 31560 0.10% 72 33577 0.11% 73 40958 0.14% 74 40879 0.14% 75 35848 0.12% 76 35602 0.12% 77 41952 0.14% 78 40416 0.13% 79 48997 0.16% 80 43177 0.14% 81 44561 0.15% 82 48115 0.16% 83 50153 0.17% 84 53029 0.18% 85 54623 0.18% 86 57385 0.19% 87 63304 0.21% 88 59971 0.20% 89 79421 0.26% 90 68700 0.23% 91 72294 0.24% 92 70229 0.23% 93 72974 0.24% 94 76950 0.26% 95 79524 0.26% 96 90701 0.30% 97 98731 0.33% 98 90469 0.30% 99 96112 0.32% 100 97563 0.32% 101 105513 0.35% 102 126849 0.42% 103 112022 0.37% 104 113852 0.38% 105 118314 0.39% 106 123620 0.41% 107 127742 0.42% 108 136815 0.45% 109 151328 0.50% 110 144060 0.48% 111 148759 0.49% 112 240974 0.80% 113 159323 0.53% 114 160625 0.53% 115 160866 0.53% 116 169230 0.56% 117 175285 0.58% 118 175606 0.58% 119 196059 0.65% 120 207247 0.69% 121 203115 0.67% 122 202227 0.67% 123 241711 0.80% 124 244692 0.81% 125 218824 0.73% 126 226524 0.75% 127 228603 0.76% 128 235770 0.78% 129 241738 0.80% 130 230068 0.76% 131 239844 0.80% 132 278381 0.92% 133 292624 0.97% 134 248806 0.83% 135 268918 0.89% 136 249300 0.83% 137 271961 0.90% 138 305431 1.01% 139 266602 0.88% 140 278545 0.92% 141 255676 0.85% 142 279777 0.93% 143 288238 0.96% 144 263627 0.87% 145 294323 0.98% 146 278501 0.92% 147 371119 1.23% 148 628701 2.09% 149 0 0.00% 150 63 0.00% 151 16951239 56.26% criterion=sequence-density sequence-density=1.28 sequence-density-rank=1 fanout-score=2.06 fanout-score-rank=30 prefix-density=1.28 prefix-fanout=2.1 sequence=CTGCGACTGCGCTGACAAGACCCAGTGTGTCAAGAAGGGAAGCAGCTACACTGCTGGCATCGTCGAGACTGAGAAGAACTATGTCTCCTCCGTAGTCATGGAGGTGCCAGCAGCTGAGAACGATGGCAAGTGCAACTGCGGTACTGGCTGCACTTGCACTACCTGCACATGCGGTCATTAAGCAAGCACATCAACTATCATGTTTGATGTGGGATTGGGAGTGGATTAATAATGTAATTTCTGATAAATAATCTGTGTTCTTCTGTACTTGTGGGTGTGGAGTGAACAAACAAAAGTGTCCGTGAGTGTCTTTATCTTTGTGTCTTCTTCATTGTTATGTATTGGCCATGTCTGTGGCCTCTGGTGTGGTTTTAATGAAGTCTTATAATTAGTGTAGTACTCTGCT criterion=fanout-score sequence-density=0.01 sequence-density-rank=33 fanout-score=288.13 fanout-score-rank=1 prefix-density=0.18 prefix-fanout=16.7 sequence=TGGATTTGATTAGATCCACCAATAAAAAGGGCTTGCCTTACACTCTTGGTCTTAATCAATTTGCTGATTGGACATGGCAAGAGTTCCAAAAGTACAGACTGGGAGCTGCCCAAAATTGCTCTGCAACCACAAGGGGCAATCACAAGCTTACGAACGCTCTTCTTCCTGAAACGAAAGACTGGAGGGAAGAAGGCATAGTCAGTCCCGTTAAGAATCAAGGTCACTGTGGATCTTGCTGGACTTTCAGCACCACTGGAGCTCTAGAGGCTGCTTACCACCAGGCTTTTGGGAAAGGAATCTCTCTGTCTGAACAGCAGCTTGTGGACTGTGCTAGAGCATTTAATAACTTTGGCTGCAATG Started job on | Feb 12 10:52:12 Started mapping on | Feb 12 10:52:13 Finished on | Feb 12 10:53:23 Mapping speed, Million of reads per hour | 1788.08 Number of input reads | 34768132 Average input read length | 137 UNIQUE READS: Uniquely mapped reads number | 29871021 Uniquely mapped reads % | 85.91% Average mapped length | 135.23 Number of splices: Total | 13284341 Number of splices: Annotated (sjdb) | 12985411 Number of splices: GT/AG | 13075357 Number of splices: GC/AG | 155616 Number of splices: AT/AC | 7162 Number of splices: Non-canonical | 46206 Mismatch rate per base, % | 0.35% Deletion rate per base | 0.02% Deletion average length | 2.19 Insertion rate per base | 0.01% Insertion average length | 1.77 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 823728 % of reads mapped to multiple loci | 2.37% Number of reads mapped to too many loci | 2070589 % of reads mapped to too many loci | 5.96% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 5.66% % of reads unmapped: other | 0.10% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 4073383 4073383 4073383 N_multimapping 823728 823728 823728 N_noFeature 1769804 2301340 28952903 N_ambiguous 501412 115187 732 UnstrandedReadsAssigned:27599805 PositiveStrandReadsAssigned:27454494 NegativeStrandReadsAssigned:917386 Dataset is classified positive stranded MeadianReadLen=151 20thPercentileLength=123 echo kmer=119 SRR11462736 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: SRR11462736-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 34,768,132 reads, 28,157,392 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,273 rounds 52401 SRR11462736.ke.tsv 34699 SRR11462736.se.tsv 87100 total ==> SRR11462736.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1919 2721 51.0769 Potri.005G024800.1.v4.1 1035 936 711 27.363 Potri.004G059700.1.v4.1 961 862 5 0.208946 Potri.007G009000.2.v4.1 1416 1317 0 0 Potri.003G141000.2.v4.1 2943 2844 3728.63 47.2269 Potri.016G087400.1.v4.1 270 171 1183 249.207 Potri.015G069301.1.v4.1 564 465 0 0 Potri.010G195200.1.v4.1 1773 1674 1005.97 21.6472 Potri.012G127500.1.v4.1 977 878 52 2.13344 ==> SRR11462736.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 7 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 232 Potri.001G212900.v4.1 0 Potri.001G182400.v4.1 1 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 3 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 14 SRR11462736 completed mapping pipeline successfully