Starting /dee2/code/volunteer_pipeline.sh SRR11462704 current disk space = 3050252816384 free memory = 1062409388 SRR11462704 SRAfilesize cad98a7ff05039ce69e764552714773d SRR11462704.sra SRR11462704.sra file validated SRR11462704 is single end SRR11462704 is conventional basespace SRR11462704 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR11462704_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 fail #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 22.61125 32.0 2.0 32.0 2.0 32.0 2 31.7675 32.0 32.0 32.0 32.0 32.0 3 34.6 37.0 32.0 37.0 32.0 37.0 4 36.29625 37.0 37.0 37.0 32.0 37.0 5 36.39125 37.0 37.0 37.0 37.0 37.0 6 39.94325 41.0 41.0 41.0 37.0 41.0 7 40.19675 41.0 41.0 41.0 37.0 41.0 8 40.2925 41.0 41.0 41.0 37.0 41.0 9 40.3065 41.0 41.0 41.0 41.0 41.0 10-14 40.38185 41.0 41.0 41.0 41.0 41.0 15-19 40.31145 41.0 41.0 41.0 41.0 41.0 20-24 40.28724999999999 41.0 41.0 41.0 40.2 41.0 25-29 40.24065 41.0 41.0 41.0 41.0 41.0 30-34 40.15145 41.0 41.0 41.0 39.4 41.0 35-39 40.10325 41.0 41.0 41.0 38.6 41.0 40-44 40.196450000000006 41.0 41.0 41.0 39.4 41.0 45-49 40.197050000000004 41.0 41.0 41.0 39.4 41.0 50-54 40.13095 41.0 41.0 41.0 39.4 41.0 55-59 40.0974 41.0 41.0 41.0 37.0 41.0 60-64 39.99775 41.0 41.0 41.0 37.0 41.0 65-69 40.050599999999996 41.0 41.0 41.0 37.0 41.0 70-74 39.90115 41.0 41.0 41.0 37.0 41.0 75-79 39.84665 41.0 40.2 41.0 37.0 41.0 80-84 40.23175 41.0 41.0 41.0 40.2 41.0 85-89 40.146899999999995 41.0 41.0 41.0 39.4 41.0 90-94 40.15265 41.0 41.0 41.0 39.4 41.0 95-99 40.04375 41.0 41.0 41.0 37.0 41.0 100-104 39.900999999999996 41.0 41.0 41.0 37.0 41.0 105-109 39.85545 41.0 41.0 41.0 37.0 41.0 110-114 39.89355 41.0 41.0 41.0 37.0 41.0 115-119 39.7891 41.0 41.0 41.0 37.0 41.0 120-124 39.68855 41.0 41.0 41.0 37.0 41.0 125-129 39.3917 41.0 41.0 41.0 37.0 41.0 130-134 39.3312 41.0 41.0 41.0 37.0 41.0 135-139 38.983349999999994 41.0 41.0 41.0 35.0 41.0 140-144 38.93325 41.0 41.0 41.0 35.0 41.0 145-149 38.6801 41.0 41.0 41.0 33.0 41.0 150-151 37.633375 41.0 39.0 41.0 29.5 41.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 24 4.0 25 1.0 26 4.0 27 6.0 28 7.0 29 11.0 30 24.0 31 29.0 32 36.0 33 54.0 34 70.0 35 79.0 36 82.0 37 133.0 38 189.0 39 293.0 40 2978.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 5.225225225225225 38.34234234234234 41.04504504504505 15.387387387387388 2 25.55 42.275 20.325 11.85 3 21.0 31.424999999999997 37.65 9.925 4 33.46673336668334 25.18759379689845 26.338169084542272 15.007503751875939 5 27.325 27.474999999999998 27.1 18.099999999999998 6 24.3 27.450000000000003 29.4 18.85 7 21.825 27.675 30.4 20.1 8 23.974999999999998 26.224999999999998 31.75 18.05 9 23.275000000000002 23.474999999999998 30.925000000000004 22.325 10-14 24.87 26.115 29.87 19.145 15-19 24.365000000000002 26.840000000000003 29.134999999999998 19.66 20-24 24.84 27.169999999999998 28.03 19.96 25-29 24.474999999999998 26.395000000000003 29.115000000000002 20.015 30-34 23.77 26.200000000000003 29.4 20.630000000000003 35-39 24.925 26.355 28.425 20.294999999999998 40-44 24.474999999999998 26.174999999999997 29.599999999999998 19.75 45-49 24.19 26.855 28.675 20.28 50-54 24.19 27.1 28.485 20.225 55-59 24.325 26.700000000000003 29.21 19.765 60-64 24.525 26.045 29.775000000000002 19.655 65-69 25.045 26.295 28.605000000000004 20.055 70-74 24.44 26.685 28.599999999999998 20.275000000000002 75-79 24.27 26.765 29.225 19.74 80-84 24.73 26.495 28.565 20.21 85-89 24.215 26.479999999999997 29.185 20.119999999999997 90-94 24.560000000000002 26.765 28.475 20.200000000000003 95-99 24.42 26.61 28.655 20.315 100-104 24.615000000000002 26.695 27.865000000000002 20.825 105-109 23.72 27.36 27.57 21.349999999999998 110-114 24.03 28.03 27.584999999999997 20.355 115-119 24.125 27.860000000000003 26.93 21.085 120-124 23.86 28.560000000000002 26.045 21.535 125-129 24.51 28.055000000000003 25.345000000000002 22.09 130-134 23.745 28.655 26.005 21.595 135-139 24.404999999999998 28.525 24.610000000000003 22.46 140-144 23.435 28.88 24.715 22.97 145-149 23.919999999999998 28.435 24.279999999999998 23.365 150-151 22.6375 29.4125 24.4125 23.5375 >>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 0.5 19 0.5 20 0.5 21 1.0 22 0.5 23 0.5 24 1.5 25 2.5 26 4.5 27 5.5 28 9.0 29 13.0 30 20.5 31 28.0 32 45.5 33 57.5 34 59.5 35 92.5 36 117.5 37 115.5 38 142.0 39 181.5 40 197.0 41 219.0 42 251.0 43 261.0 44 260.5 45 259.0 46 243.5 47 225.0 48 200.5 49 169.0 50 137.5 51 109.5 52 102.0 53 96.0 54 72.5 55 54.5 56 46.5 57 37.0 58 26.5 59 18.0 60 17.0 61 14.5 62 15.5 63 19.5 64 11.5 65 5.0 66 3.5 67 2.5 68 2.5 69 4.5 70 5.0 71 5.5 72 3.5 73 1.0 74 1.0 75 0.0 76 0.5 77 1.0 78 0.5 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 30.625000000000004 2 0.0 3 0.0 4 0.05 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 93.65 #Duplication Level Percentage of deduplicated Percentage of total 1 95.48852108916176 89.425 2 3.6572343833422316 6.8500000000000005 3 0.42712226374799783 1.2 4 0.16017084890549918 0.6 5 0.08008542445274959 0.375 6 0.08008542445274959 0.44999999999999996 7 0.026695141484249865 0.17500000000000002 8 0.0 0.0 9 0.0 0.0 >10 0.08008542445274959 0.9249999999999999 >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 ATGCGCTCCTGGCCTTAACTGGCCGGGTCGTGCCTCCGGTGCTGTTACTT 17 0.42500000000000004 No Hit TATTTGCTACTCGGATAACCGTAGTAATTCTAGAGCTAATACGTGCAACA 10 0.25 No Hit TAAAAAGCTCGTAGTTGGACTTTGGGTTGGGTCGGCCGGTCCGCCTCAGG 10 0.25 No Hit TACCTGGTTGATCCTGCCAGTAGTCATATGCTTGTCTCAAAGATTAAGCC 7 0.17500000000000002 No Hit TGGCATCGTCGAGACTGAGAAGAACTATGTCTCCTCCGTAGTCATGGAGG 6 0.15 No Hit NTGCGCTCCTGGCCTTAACTGGCCGGGTCGTGCCTCCGGTGCTGTTACTT 6 0.15 No Hit TATTTTACTTATTCCGTGAATCGGAGGCGGGGCGCTGCCCCTCTTTTTGG 6 0.15 No Hit AATCCGGGCTAGATGCGACGCGTGCGCCCGCCGTCCGATTGCCGACCTGC 5 0.125 No Hit CAAGACAATGGATTGGTCCCAATTGTGGAGCCAGAAATCTTGCTTGATGG 5 0.125 No Hit CGGGCCGCCTTGAAGTACAATTCCCACCGAGCGGCGGGTAGAATCCTTTG 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 0.037500000000000006 0.0 0.0 0.0 0.0 16-17 0.05 0.0 0.0 0.0 0.0 18-19 0.05 0.0 0.0 0.0 0.0 20-21 0.075 0.0 0.0 0.0 0.0 22-23 0.0875 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 0.1125 0.0 0.0 0.0 0.0 30-31 0.2 0.0 0.0 0.0 0.0 32-33 0.2625 0.0 0.0 0.0 0.0 34-35 0.325 0.0 0.0 0.0 0.0 36-37 0.475 0.0 0.0 0.0 0.0 38-39 0.5 0.0 0.0 0.0 0.0 40-41 0.55 0.0 0.0 0.0 0.0 42-43 0.5875 0.0 0.0 0.0 0.0 44-45 0.7625 0.0 0.0 0.0 0.0 46-47 0.825 0.0 0.0 0.0 0.0 48-49 0.85 0.0 0.0 0.0 0.0 50-51 0.9625 0.0 0.0 0.0 0.0 52-53 1.0499999999999998 0.0 0.0 0.0 0.0 54-55 1.1375000000000002 0.0 0.0 0.0 0.0 56-57 1.2374999999999998 0.0 0.0 0.0 0.0 58-59 1.3125 0.0 0.0 0.0 0.0 60-61 1.4625 0.0 0.0 0.0 0.0 62-63 1.625 0.0 0.0 0.0 0.0 64-65 1.7 0.0 0.0 0.0 0.0 66-67 1.85 0.0 0.0 0.0 0.0 68-69 2.1 0.0 0.0 0.0 0.0 70-71 2.3499999999999996 0.0 0.0 0.0 0.0 72-73 2.5625 0.0 0.0 0.0 0.0 74-75 2.8 0.0 0.0 0.0 0.0 76-77 3.125 0.0 0.0 0.0 0.0 78-79 3.3625 0.0 0.0 0.0 0.0 80-81 3.6375 0.0 0.0 0.0 0.0 82-83 4.0 0.0 0.0 0.0 0.0 84-85 4.475 0.0 0.0 0.0 0.0 86-87 5.1625 0.0 0.0 0.0 0.0 88-89 5.612500000000001 0.0 0.0 0.0 0.0 90-91 6.2125 0.0 0.0 0.0 0.0 92-93 6.775 0.0 0.0 0.0 0.0 94-95 7.5875 0.0 0.0 0.0 0.0 96-97 8.225000000000001 0.0 0.0 0.0 0.0 98-99 9.175 0.0 0.0 0.0 0.0 100-101 10.162500000000001 0.0 0.0 0.0 0.0 102-103 11.1125 0.0 0.0 0.0 0.0 104-105 11.975000000000001 0.0 0.0 0.0 0.0 106-107 12.8625 0.0 0.0 0.0 0.0 108-109 14.1375 0.0 0.0 0.0 0.0 110-111 15.325 0.0 0.0 0.0 0.0 112-113 16.7625 0.0 0.0 0.0 0.0 114-115 18.3125 0.0 0.0 0.0 0.0 116-117 19.5375 0.0 0.0 0.0 0.0 118-119 21.15 0.0 0.0 0.0 0.0 120-121 22.7875 0.0 0.0 0.0 0.0 122-123 24.4125 0.0 0.0 0.0 0.0 124-125 26.2125 0.0 0.0 0.0 0.0 126-127 27.875 0.0 0.0 0.0 0.0 128-129 30.05 0.0 0.0 0.0 0.0 130-131 32.0125 0.0 0.0 0.0 0.0 132-133 33.65 0.0 0.0 0.0 0.0 134-135 35.7625 0.0 0.0 0.0 0.0 136-137 37.875 0.0 0.0 0.0 0.0 138-139 39.849999999999994 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TTAGAGT 10 0.0024544715 203.10527 1 CTCGTAT 60 4.4173235E-4 48.237503 145 TCACGGC 105 8.579767E-5 12.403929 140-144 TCCAGTC 115 2.0048018E-4 11.325326 135-139 AAAAAAA 130 4.9395436E-5 11.131731 140-144 GTCACGG 105 0.001215948 11.025714 140-144 CACGGCT 105 0.001215948 11.025714 140-144 TGAACTC 120 2.976217E-4 10.853437 130-134 ACGTCTG 135 8.820317E-4 9.647501 125-129 CCAGTCA 120 0.0036936759 9.6475 135-139 CTCCAGT 120 0.0036936759 9.6475 135-139 CTGAACT 130 0.0071462733 8.905385 130-134 GAACTCC 130 0.0071462733 8.905385 130-134 AGCACAC 150 0.002308761 8.68275 120-124 CACGTCT 135 0.009738217 8.575556 125-129 CGTCTGA 135 0.009738217 8.575556 125-129 GGAAGAG 160 0.0041421573 8.140079 115-119 >>END_MODULE Rejected 1789381 READS because READLEN < 1 Read 1789381 spots for SRR11462704.sra Written 1789381 spots for SRR11462704.sra Rejected 1789381 READS because READLEN < 1 Read 1789381 spots for SRR11462704.sra Written 1789381 spots for SRR11462704.sra Rejected 1789381 READS because READLEN < 1 Read 1789381 spots for SRR11462704.sra Written 1789381 spots for SRR11462704.sra Rejected 1789381 READS because READLEN < 1 Read 1789381 spots for SRR11462704.sra Written 1789381 spots for SRR11462704.sra Rejected 1789381 READS because READLEN < 1 Read 1789381 spots for SRR11462704.sra Written 1789381 spots for SRR11462704.sra Rejected 1789381 READS because READLEN < 1 Read 1789381 spots for SRR11462704.sra Written 1789381 spots for SRR11462704.sra Rejected 1789381 READS because READLEN < 1 Read 1789381 spots for SRR11462704.sra Written 1789381 spots for SRR11462704.sra Rejected 1789381 READS because READLEN < 1 Read 1789381 spots for SRR11462704.sra Written 1789381 spots for SRR11462704.sra Rejected 1789381 READS because READLEN < 1 Read 1789381 spots for SRR11462704.sra Written 1789381 spots for SRR11462704.sra Rejected 1789381 READS because READLEN < 1 Read 1789381 spots for SRR11462704.sra Written 1789381 spots for SRR11462704.sra Rejected 1789381 READS because READLEN < 1 Read 1789381 spots for SRR11462704.sra Written 1789381 spots for SRR11462704.sra Rejected 1789381 READS because READLEN < 1 Read 1789381 spots for SRR11462704.sra Written 1789381 spots for SRR11462704.sra Rejected 1789381 READS because READLEN < 1 Read 1789381 spots for SRR11462704.sra Written 1789381 spots for SRR11462704.sra Rejected 1789381 READS because READLEN < 1 Read 1789381 spots for SRR11462704.sra Written 1789381 spots for SRR11462704.sra Rejected 1789396 READS because READLEN < 1 Read 1789396 spots for SRR11462704.sra Written 1789396 spots for SRR11462704.sra Rejected 1789381 READS because READLEN < 1 Read 1789381 spots for SRR11462704.sra Written 1789381 spots for SRR11462704.sra Rejected 1789381 READS because READLEN < 1 Read 1789381 spots for SRR11462704.sra Written 1789381 spots for SRR11462704.sra Rejected 1789381 READS because READLEN < 1 Read 1789381 spots for SRR11462704.sra Written 1789381 spots for SRR11462704.sra Rejected 1789381 READS because READLEN < 1 Read 1789381 spots for SRR11462704.sra Written 1789381 spots for SRR11462704.sra Rejected 1789381 READS because READLEN < 1 Read 1789381 spots for SRR11462704.sra Written 1789381 spots for SRR11462704.sra SRR ids: ['SRR11462704.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_yqo4jnkk SRR11462704.sra spots: 35787635 blocks: [[1, 1789381], [1789382, 3578762], [3578763, 5368143], [5368144, 7157524], [7157525, 8946905], [8946906, 10736286], [10736287, 12525667], [12525668, 14315048], [14315049, 16104429], [16104430, 17893810], [17893811, 19683191], [19683192, 21472572], [21472573, 23261953], [23261954, 25051334], [25051335, 26840715], [26840716, 28630096], [28630097, 30419477], [30419478, 32208858], [32208859, 33998239], [33998240, 35787635]] SRR11462704 file size 12140503 SRR11462704 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 SRR11462704 SRR11462704_1.fastq Input file: SRR11462704_1.fastq trimmed: SRR11462704-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -- maximum error ratio allowed (-r): 0.100 -- maximum indel error ratio allowed (-d): 0.030 -- end quality threshold (-q): 10 -- minimum read length allowed after trimming (-l): 18 -- file format (-f): Sanger/Illumina 1.8+ FASTQ -- minimum overlap length for adapter detection (-k): inf -- number of concurrent threads (-t): 20 Wed Feb 12 06:53:27 2025 >> started Wed Feb 12 06:53:56 2025 >> done (29.026s) 35787635 reads processed; of these: 14666 ( 0.04%) short reads filtered out after trimming by size control 5770 ( 0.02%) empty reads filtered out after trimming by size control 35767199 (99.94%) reads available; of these: 8381472 (23.43%) trimmed reads available after processing 27385727 (76.57%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 3267 0.01% 19 3540 0.01% 20 3793 0.01% 21 4384 0.01% 22 4621 0.01% 23 5154 0.01% 24 5438 0.02% 25 5446 0.02% 26 5366 0.02% 27 6249 0.02% 28 6536 0.02% 29 6673 0.02% 30 6973 0.02% 31 7094 0.02% 32 7369 0.02% 33 7793 0.02% 34 8871 0.02% 35 8522 0.02% 36 8770 0.02% 37 9949 0.03% 38 9307 0.03% 39 9877 0.03% 40 10182 0.03% 41 10384 0.03% 42 12083 0.03% 43 11889 0.03% 44 12159 0.03% 45 12968 0.04% 46 14028 0.04% 47 16393 0.05% 48 15971 0.04% 49 17613 0.05% 50 16321 0.05% 51 17363 0.05% 52 17942 0.05% 53 19485 0.05% 54 20663 0.06% 55 21718 0.06% 56 21823 0.06% 57 25859 0.07% 58 24524 0.07% 59 26354 0.07% 60 28252 0.08% 61 28957 0.08% 62 40189 0.11% 63 31957 0.09% 64 34132 0.10% 65 33231 0.09% 66 35787 0.10% 67 37917 0.11% 68 38623 0.11% 69 46131 0.13% 70 44032 0.12% 71 48645 0.14% 72 51376 0.14% 73 59171 0.17% 74 57207 0.16% 75 56669 0.16% 76 56393 0.16% 77 65537 0.18% 78 63775 0.18% 79 73838 0.21% 80 69359 0.19% 81 72836 0.20% 82 78581 0.22% 83 81783 0.23% 84 89899 0.25% 85 89349 0.25% 86 93586 0.26% 87 102474 0.29% 88 102495 0.29% 89 124046 0.35% 90 111749 0.31% 91 119135 0.33% 92 116533 0.33% 93 122589 0.34% 94 131038 0.37% 95 134963 0.38% 96 151974 0.42% 97 160300 0.45% 98 151595 0.42% 99 161768 0.45% 100 162639 0.45% 101 173826 0.49% 102 194386 0.54% 103 185713 0.52% 104 189889 0.53% 105 196536 0.55% 106 202187 0.57% 107 208100 0.58% 108 222756 0.62% 109 236121 0.66% 110 229078 0.64% 111 239288 0.67% 112 369743 1.03% 113 248747 0.70% 114 254223 0.71% 115 253703 0.71% 116 265683 0.74% 117 281282 0.79% 118 282814 0.79% 119 296049 0.83% 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% 150 124 0.00% 151 27385727 76.57% 35767199 reads passed initial QC criterion=sequence-density sequence-density=17.23 sequence-density-rank=1 fanout-score=39.58 fanout-score-rank=1 prefix-density=20.33 prefix-fanout=33.6 sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACGGCTACATCTCGTATGCCGTCTTCTGCTTGAAA criterion=fanout-score sequence-density=17.23 sequence-density-rank=1 fanout-score=39.58 fanout-score-rank=1 prefix-density=20.33 prefix-fanout=33.6 sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACGGCTACATCTCGTATGCCGTCTTCTGCTTGAAA 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 AGATCGGAAGAGCACACGTCTGAACTCCAGTCACGGCTACATCTCGTATGCCGTCTTCTGCTTGAAA -o SRR11462704 - Input file: STDIN trimmed: SRR11462704-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): AGATCGGAAGAGCACACGTCTGAACTCCAGTCACGGCTACATCTCGTATGCCGTCTTCTGCTTG -- maximum error ratio allowed (-r): 0.100 -- maximum indel error ratio allowed (-d): 0.030 -- minimum read length allowed after trimming (-l): 18 -- file format (-f): Sanger/Illumina 1.8+ FASTQ -- minimum overlap length for adapter detection (-k): 3 -- number of concurrent threads (-t): 20 Wed Feb 12 06:55:24 2025 >> started Wed Feb 12 06:56:12 2025 >> done (47.662s) 31793066 reads processed; of these: 511 ( 0.00%) short reads filtered out after trimming by size control 45 ( 0.00%) empty reads filtered out after trimming by size control 31792510 (100.00%) reads available; of these: 9552305 (30.05%) trimmed reads available after processing 22240205 (69.95%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 2948 0.01% 19 3202 0.01% 20 3489 0.01% 21 3925 0.01% 22 4142 0.01% 23 4654 0.01% 24 4894 0.02% 25 4904 0.02% 26 4817 0.02% 27 5617 0.02% 28 5816 0.02% 29 5933 0.02% 30 6335 0.02% 31 6390 0.02% 32 6583 0.02% 33 6995 0.02% 34 7961 0.03% 35 7697 0.02% 36 7913 0.02% 37 8911 0.03% 38 8331 0.03% 39 8876 0.03% 40 9217 0.03% 41 9378 0.03% 42 10708 0.03% 43 10655 0.03% 44 10931 0.03% 45 11631 0.04% 46 12655 0.04% 47 14757 0.05% 48 14222 0.04% 49 15724 0.05% 50 14713 0.05% 51 15564 0.05% 52 16195 0.05% 53 17575 0.06% 54 18564 0.06% 55 19438 0.06% 56 19518 0.06% 57 23139 0.07% 58 21980 0.07% 59 23587 0.07% 60 25446 0.08% 61 26047 0.08% 62 36010 0.11% 63 28844 0.09% 64 30548 0.10% 65 29803 0.09% 66 32106 0.10% 67 34225 0.11% 68 34870 0.11% 69 41377 0.13% 70 39685 0.12% 71 43245 0.14% 72 46090 0.14% 73 52874 0.17% 74 51292 0.16% 75 50764 0.16% 76 50837 0.16% 77 58777 0.18% 78 57171 0.18% 79 65960 0.21% 80 62195 0.20% 81 66753 0.21% 82 70168 0.22% 83 73030 0.23% 84 79263 0.25% 85 80078 0.25% 86 84148 0.26% 87 91981 0.29% 88 91967 0.29% 89 110894 0.35% 90 100667 0.32% 91 106982 0.34% 92 104626 0.33% 93 109868 0.35% 94 117354 0.37% 95 121178 0.38% 96 136366 0.43% 97 143578 0.45% 98 135742 0.43% 99 145710 0.46% 100 145465 0.46% 101 156664 0.49% 102 173540 0.55% 103 166705 0.52% 104 169365 0.53% 105 175765 0.55% 106 180876 0.57% 107 186144 0.59% 108 200464 0.63% 109 211981 0.67% 110 205471 0.65% 111 214031 0.67% 112 331662 1.04% 113 221797 0.70% 114 227255 0.71% 115 225129 0.71% 116 236170 0.74% 117 242157 0.76% 118 243491 0.77% 119 259148 0.82% 120 281441 0.89% 121 277839 0.87% 122 273583 0.86% 123 306532 0.96% 124 309788 0.97% 125 278742 0.88% 126 296790 0.93% 127 304666 0.96% 128 294190 0.93% 129 296281 0.93% 130 289622 0.91% 131 299208 0.94% 132 351423 1.11% 133 329986 1.04% 134 302199 0.95% 135 321415 1.01% 136 300290 0.94% 137 324937 1.02% 138 329879 1.04% 139 314647 0.99% 140 314761 0.99% 141 299612 0.94% 142 316938 1.00% 143 313793 0.99% 144 294681 0.93% 145 365859 1.15% 146 303329 0.95% 147 379307 1.19% 148 606347 1.91% 149 0 0.00% 150 66 0.00% 151 15032076 47.28% criterion=sequence-density sequence-density=0.79 sequence-density-rank=1 fanout-score=2.04 fanout-score-rank=33 prefix-density=0.77 prefix-fanout=2.0 sequence=CTGCGACTGCGCTGACAAGACCCAGTGTGTCAAGAAGGGAAGCAGCTACACTGCTGGCATCGTCGAGACTGAGAAGAACTATGTCTCCTCCGTAGTCATGGAGGTGCCAGCAGCTGAGAACGATGGCAAGTGCAACTGCGGTACTGGCTGCACTTGCACTACCTGCACATGCGGTCATTAAGCAAGCACATCAACTATCATGTTTGATGTGGGATTGGGAGTGGATTAATAATGTAATTTCTGATAAATAATCTGTGTTCTTCTGTACTTGTGGGTGTGGAGTGAACAAACAAAAGTGTCCGTGAGTGTCTTTATCTTTGTGTCTTCTTCATTGTTATGTATTGGCCATGTCTGTGGCCTCTGGTGTGGTTTTAATGAAGTCTTATAATTAGTGTAGTAC criterion=fanout-score sequence-density=0.02 sequence-density-rank=29 fanout-score=38.47 fanout-score-rank=1 prefix-density=0.22 prefix-fanout=3.8 sequence=AACTTTGAAGGCCGAAGAGGGGAAAGGTTCCATGTGAACGGCACTTGCACATGGGTTAGTCGATCCTAAGAGACGGGGGAAGCCCGTCCGACAGCGCGTTCGCGCGCGAGCTTCGAAAGGGAATCGGGTTAAAATTCCTGAACCGGGACGTGGCGGCTGACGGCAACGTTAGGGAGTCCGGAGACGTCGGCGGGGGCCTCGGGAAGAGTTATCTTTTCTGTTTAACAGCCCGCCCACCCTGGAAACGACTTAGTCGGAGGTAGGGTCCAGCGGCTGGAAGAGCACCGCACGTCGCGTGGTGTCCGGTGCGCCCCCGGCGGCCCTTGAAAATCCGGAGGACCGAGTGCCTCCCACGCCCGGTCGTACTCATAACCGCATCAGGTCTCCAAGGTGAACAGCCTCTGGTCGATGGAACAATGTAGGCAAGGGAAGTCGGCAAAATGGATCCGTAACCTCGGGAAAAGGATTGGCTCTGAGGGCTGGGCTCGGGGGTCCCAGTCCCGAACCCGTC Started job on | Feb 12 06:56:46 Started mapping on | Feb 12 06:56:46 Finished on | Feb 12 06:58:00 Mapping speed, Million of reads per hour | 1740.00 Number of input reads | 35766643 Average input read length | 134 UNIQUE READS: Uniquely mapped reads number | 29504293 Uniquely mapped reads % | 82.49% Average mapped length | 130.50 Number of splices: Total | 12348382 Number of splices: Annotated (sjdb) | 12063139 Number of splices: GT/AG | 12142381 Number of splices: GC/AG | 152293 Number of splices: AT/AC | 7230 Number of splices: Non-canonical | 46478 Mismatch rate per base, % | 0.36% Deletion rate per base | 0.02% Deletion average length | 2.09 Insertion rate per base | 0.01% Insertion average length | 1.78 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 846991 % of reads mapped to multiple loci | 2.37% Number of reads mapped to too many loci | 2999604 % of reads mapped to too many loci | 8.39% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 6.66% % of reads unmapped: other | 0.10% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 5415359 5415359 5415359 N_multimapping 846991 846991 846991 N_noFeature 1966178 2359430 28801984 N_ambiguous 421210 112471 757 UnstrandedReadsAssigned:27116905 PositiveStrandReadsAssigned:27032392 NegativeStrandReadsAssigned:701552 Dataset is classified positive stranded MeadianReadLen=147 20thPercentileLength=115 echo kmer=111 SRR11462704 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: SRR11462704-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 35,766,643 reads, 28,264,688 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,218 rounds 52401 SRR11462704.ke.tsv 34699 SRR11462704.se.tsv 87100 total ==> SRR11462704.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1919 2016 42.5065 Potri.005G024800.1.v4.1 1035 936 721 31.1673 Potri.004G059700.1.v4.1 961 862 28 1.31429 Potri.007G009000.2.v4.1 1416 1317 0 0 Potri.003G141000.2.v4.1 2943 2844 3759.23 53.4822 Potri.016G087400.1.v4.1 270 171 1613 381.661 Potri.015G069301.1.v4.1 564 465 0 0 Potri.010G195200.1.v4.1 1773 1674 355 8.5805 Potri.012G127500.1.v4.1 977 878 115 5.2996 ==> SRR11462704.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 90 Potri.001G233950.v4.1 2 Potri.001G122700.v4.1 269 Potri.001G212900.v4.1 0 Potri.001G182400.v4.1 0 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 15 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 10 SRR11462704 completed mapping pipeline successfully