Starting /dee2/code/volunteer_pipeline.sh SRR11462698 current disk space = 3050250309632 free memory = 1578632188 SRR11462698 SRAfilesize 2ff7575f92652f3ae86b63b99c06271f SRR11462698.sra SRR11462698.sra file validated SRR11462698 is single end SRR11462698 is conventional basespace SRR11462698 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR11462698_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 45 >>END_MODULE >>Per base sequence quality fail #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 19.43625 32.0 2.0 32.0 2.0 32.0 2 31.8275 32.0 32.0 32.0 32.0 32.0 3 34.1575 32.0 32.0 37.0 32.0 37.0 4 36.19625 37.0 37.0 37.0 32.0 37.0 5 36.35 37.0 37.0 37.0 37.0 37.0 6 40.05075 41.0 41.0 41.0 37.0 41.0 7 40.318 41.0 41.0 41.0 37.0 41.0 8 40.3575 41.0 41.0 41.0 41.0 41.0 9 40.34575 41.0 41.0 41.0 41.0 41.0 10-14 40.39905 41.0 41.0 41.0 41.0 41.0 15-19 40.36725 41.0 41.0 41.0 41.0 41.0 20-24 40.322250000000004 41.0 41.0 41.0 40.2 41.0 25-29 40.2735 41.0 41.0 41.0 41.0 41.0 30-34 40.19455 41.0 41.0 41.0 40.2 41.0 35-39 40.151349999999994 41.0 41.0 41.0 39.4 41.0 40-44 40.1751 41.0 41.0 41.0 40.2 41.0 45-49 40.16605 41.0 41.0 41.0 39.4 41.0 50-54 40.1755 41.0 41.0 41.0 39.4 41.0 55-59 40.1322 41.0 41.0 41.0 37.8 41.0 60-64 40.012550000000005 41.0 41.0 41.0 37.0 41.0 65-69 40.0777 41.0 41.0 41.0 37.0 41.0 70-74 39.8715 41.0 41.0 41.0 37.0 41.0 75-79 39.8076 41.0 40.2 41.0 37.0 41.0 80-84 40.27265 41.0 41.0 41.0 40.2 41.0 85-89 40.141 41.0 41.0 41.0 39.4 41.0 90-94 40.132349999999995 41.0 41.0 41.0 40.2 41.0 95-99 40.1237 41.0 41.0 41.0 37.8 41.0 100-104 39.9727 41.0 41.0 41.0 37.0 41.0 105-109 39.822950000000006 41.0 41.0 41.0 37.0 41.0 110-114 39.908049999999996 41.0 41.0 41.0 37.0 41.0 115-119 39.8116 41.0 41.0 41.0 37.0 41.0 120-124 39.7658 41.0 41.0 41.0 37.0 41.0 125-129 39.562 41.0 41.0 41.0 37.0 41.0 130-134 39.44175 41.0 41.0 41.0 37.0 41.0 135-139 39.225649999999995 41.0 41.0 41.0 37.0 41.0 140-144 39.2161 41.0 41.0 41.0 37.0 41.0 145-149 38.9416 41.0 41.0 41.0 36.0 41.0 150-151 38.034625 41.0 39.0 41.0 29.5 41.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 24 1.0 25 4.0 26 2.0 27 2.0 28 15.0 29 12.0 30 25.0 31 34.0 32 35.0 33 41.0 34 56.0 35 71.0 36 87.0 37 115.0 38 154.0 39 340.0 40 3006.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 5.967604433077579 39.34356351236147 40.451832907075875 14.23699914748508 2 25.55 42.0 20.674999999999997 11.774999999999999 3 21.75 29.975 38.35 9.925 4 33.88347086771693 22.73068267066767 27.206801700425103 16.179044761190298 5 26.950000000000003 26.8 27.375 18.875 6 25.974999999999998 26.325 29.7 18.0 7 23.275000000000002 27.35 29.975 19.400000000000002 8 23.825 25.924999999999997 31.05 19.2 9 21.45 25.074999999999996 30.599999999999998 22.875 10-14 25.11 25.775 29.43 19.685 15-19 24.22 27.46 28.7 19.62 20-24 25.080000000000002 26.450000000000003 28.405 20.064999999999998 25-29 24.625 26.415 28.83 20.13 30-34 24.8 26.265 28.34 20.595 35-39 23.74 26.31 28.410000000000004 21.54 40-44 24.315 26.88 28.325 20.48 45-49 23.87 26.56 29.205 20.365 50-54 24.55 27.334999999999997 27.79 20.325 55-59 25.105 26.484999999999996 27.985 20.424999999999997 60-64 24.615000000000002 25.915 29.470000000000002 20.0 65-69 25.77 26.25 27.744999999999997 20.235 70-74 25.319999999999997 26.534999999999997 27.855 20.29 75-79 24.42 26.724999999999998 28.845 20.01 80-84 25.255 26.46 28.405 19.88 85-89 24.505 27.084999999999997 27.634999999999998 20.775 90-94 26.009999999999998 26.26 28.125 19.605 95-99 24.555 26.435 28.205000000000002 20.805 100-104 25.330000000000002 26.064999999999998 28.22 20.385 105-109 23.935000000000002 26.68 27.96 21.425 110-114 23.96 26.295 28.34 21.404999999999998 115-119 24.815 26.605 28.025 20.555 120-124 24.33 26.43 28.095 21.145 125-129 24.044999999999998 27.045 27.045 21.865000000000002 130-134 24.365000000000002 27.58 26.935 21.12 135-139 23.89 27.525 25.88 22.705000000000002 140-144 24.19 27.76 25.52 22.53 145-149 23.575 27.72 24.87 23.835 150-151 22.787499999999998 28.1375 25.112499999999997 23.962500000000002 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 0.0 1 0.0 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10 0.0 11 0.0 12 0.0 13 0.0 14 0.0 15 0.0 16 0.0 17 0.0 18 0.5 19 0.5 20 0.0 21 0.0 22 0.0 23 0.0 24 2.0 25 3.5 26 5.0 27 9.0 28 11.5 29 13.5 30 20.0 31 28.5 32 38.5 33 44.0 34 58.0 35 82.5 36 114.0 37 143.5 38 151.0 39 154.5 40 175.0 41 197.0 42 234.0 43 240.5 44 255.5 45 294.0 46 252.0 47 207.0 48 192.5 49 158.5 50 129.5 51 117.5 52 101.5 53 89.5 54 77.0 55 72.5 56 63.0 57 41.0 58 33.0 59 25.0 60 24.5 61 20.5 62 14.0 63 24.0 64 16.0 65 4.5 66 5.0 67 6.5 68 10.5 69 9.5 70 5.5 71 10.5 72 11.0 73 2.5 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 41.349999999999994 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 89.95 #Duplication Level Percentage of deduplicated Percentage of total 1 94.60811561978876 85.1 2 3.7798777098387992 6.800000000000001 3 0.5558643690939411 1.5 4 0.500277932184547 1.7999999999999998 5 0.13896609227348528 0.625 6 0.055586436909394105 0.3 7 0.027793218454697052 0.17500000000000002 8 0.08337965536409116 0.6 9 0.08337965536409116 0.675 >10 0.16675931072818231 2.4250000000000003 >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 NATTTGCTACTCGGATAACCGTAGTAATTCTAGAGCTAATACGTGCAACA 23 0.575 No Hit TATTTGCTACTCGGATAACCGTAGTAATTCTAGAGCTAATACGTGCAACA 21 0.525 No Hit NTGCGCTCCTGGCCTTAACTGGCCGGGTCGTGCCTCCGGTGCTGTTACTT 17 0.42500000000000004 No Hit ATGCGCTCCTGGCCTTAACTGGCCGGGTCGTGCCTCCGGTGCTGTTACTT 13 0.325 No Hit TACCTGGTTGATCCTGCCAGTAGTCATATGCTTGTCTCAAAGATTAAGCC 13 0.325 No Hit AATCCGGGCTAGATGCGACGCGTGCGCCCGCCGTCCGATTGCCGACCTGC 10 0.25 No Hit NACCTGGTTGATCCTGCCAGTAGTCATATGCTTGTCTCAAAGATTAAGCC 9 0.22499999999999998 No Hit NATTTTACTTATTCCGTGAATCGGAGGCGGGGCGCTGCCCCTCTTTTTGG 9 0.22499999999999998 No Hit TATTTTACTTATTCCGTGAATCGGAGGCGGGGCGCTGCCCCTCTTTTTGG 9 0.22499999999999998 No Hit AAAGACGAACAACTGCGAAAGCATTTGCCAAGGATGTTTTCATTAATCAA 8 0.2 No Hit NGGCATCGTCGAGACTGAGAAGAACTATGTCTCCTCCGTAGTCATGGAGG 8 0.2 No Hit CGGGCCGCCTTGAAGTACAATTCCCACCGAGCGGCGGGTAGAATCCTTTG 8 0.2 No Hit NGACTGTGAAACTGCGAATGGCTCATTAAATCAGTTATAGTTTGTTTGAT 7 0.17500000000000002 No Hit CGGTGAAAGAGCCGCGCGGGCCGCCTTGAAGTACAATTCCCACCGAGCGG 6 0.15 No Hit AGACTGTGAAACTGCGAATGGCTCATTAAATCAGTTATAGTTTGTTTGAT 6 0.15 No Hit TTAATCAAGAACGAAAGTTGGGGGCTCGAAGACGATCAGATACCGTCCTA 5 0.125 No Hit TAAAAAGCTCGTAGTTGGACTTTGGGTTGGGTCGGCCGGTCCGCCTCAGG 5 0.125 No Hit NATCCGGGCTAGATGCGACGCGTGCGCCCGCCGTCCGATTGCCGACCTGC 5 0.125 No Hit CAGCCAAGCGTTCATAGCGACGTTGCTTTTTGATCCTTCGATGTCGGCTC 5 0.125 No Hit TGGAACAAAAGGGTAAAAGCTCGTTTGATTCTGATTTCCAGTACGAATAC 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 0.0 0.0 0.0 0.0 0.0 22-23 0.0 0.0 0.0 0.0 0.0 24-25 0.025 0.0 0.0 0.0 0.0 26-27 0.0625 0.0 0.0 0.0 0.0 28-29 0.0875 0.0 0.0 0.0 0.0 30-31 0.1 0.0 0.0 0.0 0.0 32-33 0.1 0.0 0.0 0.0 0.0 34-35 0.1125 0.0 0.0 0.0 0.0 36-37 0.15 0.0 0.0 0.0 0.0 38-39 0.175 0.0 0.0 0.0 0.0 40-41 0.21250000000000002 0.0 0.0 0.0 0.0 42-43 0.225 0.0 0.0 0.0 0.0 44-45 0.2625 0.0 0.0 0.0 0.0 46-47 0.325 0.0 0.0 0.0 0.0 48-49 0.4 0.0 0.0 0.0 0.0 50-51 0.4625 0.0 0.0 0.0 0.0 52-53 0.525 0.0 0.0 0.0 0.0 54-55 0.575 0.0 0.0 0.0 0.0 56-57 0.625 0.0 0.0 0.0 0.0 58-59 0.675 0.0 0.0 0.0 0.0 60-61 0.7875000000000001 0.0 0.0 0.0 0.0 62-63 0.8625 0.0 0.0 0.0 0.0 64-65 0.9875 0.0 0.0 0.0 0.0 66-67 1.1 0.0 0.0 0.0 0.0 68-69 1.2875 0.0 0.0 0.0 0.0 70-71 1.375 0.0 0.0 0.0 0.0 72-73 1.4625 0.0 0.0 0.0 0.0 74-75 1.625 0.0 0.0 0.0 0.0 76-77 1.9 0.0 0.0 0.0 0.0 78-79 2.1625 0.0 0.0 0.0 0.0 80-81 2.4375 0.0 0.0 0.0 0.0 82-83 2.6 0.0 0.0 0.0 0.0 84-85 2.7625 0.0 0.0 0.0 0.0 86-87 2.9749999999999996 0.0 0.0 0.0 0.0 88-89 3.2375 0.0 0.0 0.0 0.0 90-91 3.6125 0.0 0.0 0.0 0.0 92-93 3.95 0.0 0.0 0.0 0.0 94-95 4.4125 0.0 0.0 0.0 0.0 96-97 4.725 0.0 0.0 0.0 0.0 98-99 5.1375 0.0 0.0 0.0 0.0 100-101 5.625 0.0 0.0 0.0 0.0 102-103 6.1 0.0 0.0 0.0 0.0 104-105 6.7 0.0 0.0 0.0 0.0 106-107 7.0625 0.0 0.0 0.0 0.0 108-109 7.6125 0.0 0.0 0.0 0.0 110-111 8.1875 0.0 0.0 0.0 0.0 112-113 9.0625 0.0 0.0 0.0 0.0 114-115 9.9875 0.0 0.0 0.0 0.0 116-117 10.825 0.0 0.0 0.0 0.0 118-119 11.7125 0.0 0.0 0.0 0.0 120-121 12.5375 0.0 0.0 0.0 0.0 122-123 13.524999999999999 0.0 0.0 0.0 0.0 124-125 14.475 0.0 0.0 0.0 0.0 126-127 15.662500000000001 0.0 0.0 0.0 0.0 128-129 16.7125 0.0 0.0 0.0 0.0 130-131 18.1875 0.0 0.0 0.0 0.0 132-133 19.725 0.0 0.0 0.0 0.0 134-135 21.3125 0.0 0.0 0.0 0.0 136-137 22.737499999999997 0.0 0.0 0.0 0.0 138-139 24.0125 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TTATTCC 10 0.0068892627 144.5875 9 GTCCTAA 10 0.0068892627 144.5875 145 CTTATTC 10 0.0068892627 144.5875 8 TACTTAT 10 0.0068892627 144.5875 6 AAAAAAA 40 0.0077818553 18.073437 140-144 >>END_MODULE Rejected 2423221 READS because READLEN < 1 Read 2423221 spots for SRR11462698.sra Written 2423221 spots for SRR11462698.sra Rejected 2423221 READS because READLEN < 1 Read 2423221 spots for SRR11462698.sra Written 2423221 spots for SRR11462698.sra Rejected 2423221 READS because READLEN < 1 Read 2423221 spots for SRR11462698.sra Written 2423221 spots for SRR11462698.sra Rejected 2423221 READS because READLEN < 1 Read 2423221 spots for SRR11462698.sra Written 2423221 spots for SRR11462698.sra Rejected 2423221 READS because READLEN < 1 Read 2423221 spots for SRR11462698.sra Written 2423221 spots for SRR11462698.sra Rejected 2423221 READS because READLEN < 1 Read 2423221 spots for SRR11462698.sra Written 2423221 spots for SRR11462698.sra Rejected 2423221 READS because READLEN < 1 Read 2423221 spots for SRR11462698.sra Written 2423221 spots for SRR11462698.sra Rejected 2423239 READS because READLEN < 1 Read 2423239 spots for SRR11462698.sra Written 2423239 spots for SRR11462698.sra Rejected 2423221 READS because READLEN < 1 Read 2423221 spots for SRR11462698.sra Written 2423221 spots for SRR11462698.sra Rejected 2423221 READS because READLEN < 1 Read 2423221 spots for SRR11462698.sra Written 2423221 spots for SRR11462698.sra Rejected 2423221 READS because READLEN < 1 Read 2423221 spots for SRR11462698.sra Written 2423221 spots for SRR11462698.sra Rejected 2423221 READS because READLEN < 1 Read 2423221 spots for SRR11462698.sra Written 2423221 spots for SRR11462698.sra Rejected 2423221 READS because READLEN < 1 Read 2423221 spots for SRR11462698.sra Written 2423221 spots for SRR11462698.sra Rejected 2423221 READS because READLEN < 1 Read 2423221 spots for SRR11462698.sra Written 2423221 spots for SRR11462698.sra Rejected 2423221 READS because READLEN < 1 Read 2423221 spots for SRR11462698.sra Written 2423221 spots for SRR11462698.sra Rejected 2423221 READS because READLEN < 1 Read 2423221 spots for SRR11462698.sra Written 2423221 spots for SRR11462698.sra Rejected 2423221 READS because READLEN < 1 Read 2423221 spots for SRR11462698.sra Written 2423221 spots for SRR11462698.sra Rejected 2423221 READS because READLEN < 1 Read 2423221 spots for SRR11462698.sra Written 2423221 spots for SRR11462698.sra Rejected 2423221 READS because READLEN < 1 Read 2423221 spots for SRR11462698.sra Written 2423221 spots for SRR11462698.sra Rejected 2423221 READS because READLEN < 1 Read 2423221 spots for SRR11462698.sra Written 2423221 spots for SRR11462698.sra SRR ids: ['SRR11462698.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_y83xo8z2 SRR11462698.sra spots: 48464438 blocks: [[1, 2423221], [2423222, 4846442], [4846443, 7269663], [7269664, 9692884], [9692885, 12116105], [12116106, 14539326], [14539327, 16962547], [16962548, 19385768], [19385769, 21808989], [21808990, 24232210], [24232211, 26655431], [26655432, 29078652], [29078653, 31501873], [31501874, 33925094], [33925095, 36348315], [36348316, 38771536], [38771537, 41194757], [41194758, 43617978], [43617979, 46041199], [46041200, 48464438]] SRR11462698 file size 16448635 SRR11462698 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 SRR11462698 SRR11462698_1.fastq Input file: SRR11462698_1.fastq trimmed: SRR11462698-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 06:55:23 2025 >> started Wed Feb 12 06:55:51 2025 >> done (27.966s) 48464438 reads processed; of these: 13998 ( 0.03%) short reads filtered out after trimming by size control 788 ( 0.00%) empty reads filtered out after trimming by size control 48449652 (99.97%) reads available; of these: 6410480 (13.23%) trimmed reads available after processing 42039172 (86.77%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 3414 0.01% 19 3604 0.01% 20 3910 0.01% 21 4184 0.01% 22 4749 0.01% 23 5039 0.01% 24 5532 0.01% 25 5370 0.01% 26 5538 0.01% 27 7065 0.01% 28 6057 0.01% 29 6656 0.01% 30 7241 0.01% 31 7104 0.01% 32 6953 0.01% 33 7413 0.02% 34 8115 0.02% 35 8122 0.02% 36 8347 0.02% 37 10602 0.02% 38 8882 0.02% 39 9076 0.02% 40 9720 0.02% 41 9729 0.02% 42 11521 0.02% 43 11702 0.02% 44 11037 0.02% 45 12319 0.03% 46 12858 0.03% 47 15338 0.03% 48 15203 0.03% 49 18330 0.04% 50 14587 0.03% 51 15509 0.03% 52 15764 0.03% 53 16868 0.03% 54 19472 0.04% 55 18183 0.04% 56 18713 0.04% 57 22555 0.05% 58 20826 0.04% 59 21476 0.04% 60 23859 0.05% 61 23642 0.05% 62 48895 0.10% 63 24918 0.05% 64 27080 0.06% 65 26933 0.06% 66 27833 0.06% 67 30157 0.06% 68 29346 0.06% 69 37807 0.08% 70 33207 0.07% 71 35377 0.07% 72 40460 0.08% 73 49948 0.10% 74 45828 0.09% 75 44417 0.09% 76 41330 0.09% 77 51878 0.11% 78 46056 0.10% 79 57637 0.12% 80 48591 0.10% 81 51061 0.11% 82 56760 0.12% 83 57026 0.12% 84 64362 0.13% 85 62801 0.13% 86 65474 0.14% 87 74953 0.15% 88 73449 0.15% 89 123592 0.26% 90 79920 0.16% 91 88157 0.18% 92 79982 0.17% 93 86548 0.18% 94 94460 0.19% 95 94764 0.20% 96 105889 0.22% 97 111460 0.23% 98 105843 0.22% 99 112821 0.23% 100 112842 0.23% 101 122238 0.25% 102 136426 0.28% 103 132255 0.27% 104 133866 0.28% 105 140393 0.29% 106 143471 0.30% 107 149945 0.31% 108 164791 0.34% 109 183066 0.38% 110 172631 0.36% 111 179698 0.37% 112 326161 0.67% 113 194268 0.40% 114 196021 0.40% 115 195197 0.40% 116 205099 0.42% 117 223884 0.46% 118 224372 0.46% 119 234514 0.48% 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% 150 138 0.00% 151 42039172 86.77% 48449652 reads passed initial QC criterion=sequence-density sequence-density=11.48 sequence-density-rank=1 fanout-score=41.39 fanout-score-rank=1 prefix-density=13.80 prefix-fanout=34.4 sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCCGTCCATCTCGTATGCCGTCTTCTGCTTG criterion=fanout-score sequence-density=11.48 sequence-density-rank=1 fanout-score=41.39 fanout-score-rank=1 prefix-density=13.80 prefix-fanout=34.4 sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCCGTCCATCTCGTATGCCGTCTTCTGCTTG 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 AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCCGTCCATCTCGTATGCCGTCTTCTGCTTG -o SRR11462698 - Input file: STDIN trimmed: SRR11462698-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCCGTCCATCTCGTATGCCGTCTTCTGCTTG -- 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 06:57:44 2025 >> started Wed Feb 12 06:58:30 2025 >> done (46.110s) 40374710 reads processed; of these: 451 ( 0.00%) short reads filtered out after trimming by size control 5 ( 0.00%) empty reads filtered out after trimming by size control 40374254 (100.00%) reads available; of these: 9076557 (22.48%) trimmed reads available after processing 31297697 (77.52%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 2876 0.01% 19 3096 0.01% 20 3279 0.01% 21 3586 0.01% 22 3996 0.01% 23 4225 0.01% 24 4657 0.01% 25 4493 0.01% 26 4721 0.01% 27 5846 0.01% 28 5029 0.01% 29 5642 0.01% 30 5963 0.01% 31 5992 0.01% 32 5839 0.01% 33 6263 0.02% 34 6867 0.02% 35 6900 0.02% 36 7096 0.02% 37 8944 0.02% 38 7482 0.02% 39 7593 0.02% 40 8119 0.02% 41 8158 0.02% 42 9713 0.02% 43 9798 0.02% 44 9264 0.02% 45 10400 0.03% 46 10856 0.03% 47 12994 0.03% 48 12739 0.03% 49 15418 0.04% 50 12395 0.03% 51 13112 0.03% 52 13187 0.03% 53 14361 0.04% 54 16474 0.04% 55 15234 0.04% 56 15503 0.04% 57 19057 0.05% 58 17508 0.04% 59 18040 0.04% 60 20005 0.05% 61 19828 0.05% 62 41043 0.10% 63 21072 0.05% 64 22661 0.06% 65 22510 0.06% 66 23343 0.06% 67 25322 0.06% 68 24814 0.06% 69 31759 0.08% 70 28324 0.07% 71 29538 0.07% 72 33884 0.08% 73 41847 0.10% 74 38451 0.10% 75 36926 0.09% 76 34894 0.09% 77 43404 0.11% 78 38863 0.10% 79 48214 0.12% 80 40952 0.10% 81 43175 0.11% 82 47655 0.12% 83 47704 0.12% 84 53608 0.13% 85 52842 0.13% 86 54944 0.14% 87 62789 0.16% 88 61674 0.15% 89 103431 0.26% 90 67836 0.17% 91 73883 0.18% 92 67681 0.17% 93 72652 0.18% 94 79214 0.20% 95 79249 0.20% 96 89184 0.22% 97 93138 0.23% 98 89313 0.22% 99 95268 0.24% 100 94617 0.23% 101 102960 0.26% 102 114183 0.28% 103 111011 0.27% 104 112021 0.28% 105 117752 0.29% 106 120290 0.30% 107 125636 0.31% 108 139374 0.35% 109 154207 0.38% 110 145509 0.36% 111 150627 0.37% 112 274810 0.68% 113 161002 0.40% 114 163856 0.41% 115 161978 0.40% 116 171188 0.42% 117 181069 0.45% 118 181055 0.45% 119 192653 0.48% 120 214304 0.53% 121 228035 0.56% 122 212479 0.53% 123 248103 0.61% 124 250865 0.62% 125 220865 0.55% 126 244628 0.61% 127 254462 0.63% 128 244567 0.61% 129 247017 0.61% 130 245274 0.61% 131 253298 0.63% 132 316518 0.78% 133 301907 0.75% 134 274009 0.68% 135 305079 0.76% 136 284240 0.70% 137 297754 0.74% 138 315409 0.78% 139 303352 0.75% 140 327440 0.81% 141 298536 0.74% 142 321299 0.80% 143 317881 0.79% 144 307090 0.76% 145 416454 1.03% 146 336310 0.83% 147 456476 1.13% 148 838314 2.08% 149 0 0.00% 150 73 0.00% 151 26130809 64.72% criterion=sequence-density sequence-density=0.84 sequence-density-rank=1 fanout-score=1.99 fanout-score-rank=25 prefix-density=0.83 prefix-fanout=2.0 sequence=CGTCGTGAGACAG criterion=fanout-score sequence-density=0.06 sequence-density-rank=22 fanout-score=13.50 fanout-score-rank=1 prefix-density=0.19 prefix-fanout=4.3 sequence=AACTTTGAAGGCCGAAGAGGGGAAAGGTTCCATGTGAACGGCACTTGCACATGGGTTAGTCGATCCTAAGAGACGGGGGAAGCCCGTCCGACAGCGCGTTCGCGCGCGAGCTTCGAAAGGGAATCGGGTTAAAATTCCTGAACCGGGACGTGGCGGCTGACGGCAACGTTAGGGAGTCCGGAGACGTCGGCGGGGGCCTCGGGAAGAGTTATCTTTTCTGTTTAACAGCCCGCCCACCCTGGAAACGACTTAGTCGGAGGTAGGGTCCAGCGGCTGGAAGAGCACCGCACGTCGCGTGGTGTCCGGTGCGCCCCCGGCGGCCCTTGAAAATCCGGAGGACCGAGTGCCTCCCACGCCCGGTCGTACTCATAACCGCATCAGGTCTCCAAGGTGAACAGCCTCTGGTCGATGGAACAATGTAGGCAAGGGAAGTCGGCAAAATGGATCCGTAACCTCGGGAAAAGGATTGGCTCTGAGGGCTGGGCTCGGGGGTCCCAGTCCCGAACCCGTC Started job on | Feb 12 06:59:12 Started mapping on | Feb 12 06:59:12 Finished on | Feb 12 07:01:18 Mapping speed, Million of reads per hour | 1384.26 Number of input reads | 48449196 Average input read length | 140 UNIQUE READS: Uniquely mapped reads number | 36337112 Uniquely mapped reads % | 75.00% Average mapped length | 137.60 Number of splices: Total | 15920774 Number of splices: Annotated (sjdb) | 15530060 Number of splices: GT/AG | 15637534 Number of splices: GC/AG | 222002 Number of splices: AT/AC | 8638 Number of splices: Non-canonical | 52600 Mismatch rate per base, % | 0.37% Deletion rate per base | 0.02% Deletion average length | 2.15 Insertion rate per base | 0.01% Insertion average length | 1.80 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 1198145 % of reads mapped to multiple loci | 2.47% Number of reads mapped to too many loci | 6993198 % of reads mapped to too many loci | 14.43% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 7.90% % of reads unmapped: other | 0.19% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 10913939 10913939 10913939 N_multimapping 1198145 1198145 1198145 N_noFeature 2355687 2848077 35334227 N_ambiguous 645615 135537 787 UnstrandedReadsAssigned:33335810 PositiveStrandReadsAssigned:33353498 NegativeStrandReadsAssigned:1002098 Dataset is classified positive stranded MeadianReadLen=151 20thPercentileLength=131 echo kmer=127 SRR11462698 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: SRR11462698-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 48,449,196 reads, 36,951,861 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,205 rounds 52401 SRR11462698.ke.tsv 34699 SRR11462698.se.tsv 87100 total ==> SRR11462698.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1919 3654 64.1126 Potri.005G024800.1.v4.1 1035 936 1126 40.5054 Potri.004G059700.1.v4.1 961 862 3 0.117183 Potri.007G009000.2.v4.1 1416 1317 0 0 Potri.003G141000.2.v4.1 2943 2844 4896.79 57.9739 Potri.016G087400.1.v4.1 270 171 1407 277.044 Potri.015G069301.1.v4.1 564 465 0 0 Potri.010G195200.1.v4.1 1773 1674 3141.96 63.1967 Potri.012G127500.1.v4.1 977 878 27 1.03543 ==> SRR11462698.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 2 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 303 Potri.001G212900.v4.1 0 Potri.001G182400.v4.1 3 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 2 Potri.001G416900.v4.1 1 Potri.001G452600.v4.1 53 SRR11462698 completed mapping pipeline successfully